Mercurial > repos > goeckslab > image_learner
annotate image_learner_cli.py @ 7:801a8b6973fb draft default tip
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
author | goeckslab |
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date | Fri, 08 Aug 2025 13:06:28 +0000 |
parents | 09904b1f61f5 |
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rev | line source |
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54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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changeset
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1 import argparse |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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2 import json |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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3 import logging |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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4 import os |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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5 import shutil |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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6 import sys |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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7 import tempfile |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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8 import zipfile |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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9 from pathlib import Path |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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10 from typing import Any, Dict, Optional, Protocol, Tuple |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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11 |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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12 import numpy as np |
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54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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13 import pandas as pd |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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14 import pandas.api.types as ptypes |
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54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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15 import yaml |
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186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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16 from constants import ( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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17 IMAGE_PATH_COLUMN_NAME, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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18 LABEL_COLUMN_NAME, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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19 METRIC_DISPLAY_NAMES, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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20 MODEL_ENCODER_TEMPLATES, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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21 SPLIT_COLUMN_NAME, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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22 TEMP_CONFIG_FILENAME, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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23 TEMP_CSV_FILENAME, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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24 TEMP_DIR_PREFIX |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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25 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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26 from ludwig.globals import ( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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27 DESCRIPTION_FILE_NAME, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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28 PREDICTIONS_PARQUET_FILE_NAME, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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29 TEST_STATISTICS_FILE_NAME, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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30 TRAIN_SET_METADATA_FILE_NAME, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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31 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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32 from ludwig.utils.data_utils import get_split_path |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
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33 from ludwig.visualize import get_visualizations_registry |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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34 from sklearn.model_selection import train_test_split |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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35 from utils import ( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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36 build_tabbed_html, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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37 encode_image_to_base64, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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38 get_html_closing, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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39 get_html_template, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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40 get_metrics_help_modal |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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41 ) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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42 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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43 # --- Logging Setup --- |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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44 logging.basicConfig( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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45 level=logging.INFO, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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46 format='%(asctime)s %(levelname)s %(name)s: %(message)s', |
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54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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47 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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48 logger = logging.getLogger("ImageLearner") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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49 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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50 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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51 def format_config_table_html( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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52 config: dict, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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53 split_info: Optional[str] = None, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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54 training_progress: dict = None, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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55 ) -> str: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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56 display_keys = [ |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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57 "task_type", |
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54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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58 "model_name", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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59 "epochs", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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60 "batch_size", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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61 "fine_tune", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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62 "use_pretrained", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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63 "learning_rate", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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64 "random_seed", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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65 "early_stop", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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66 ] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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67 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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68 rows = [] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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69 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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70 for key in display_keys: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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71 val = config.get(key, "N/A") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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72 if key == "task_type": |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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73 val = val.title() if isinstance(val, str) else val |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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74 if key == "batch_size": |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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75 if val is not None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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76 val = int(val) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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77 else: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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78 if training_progress: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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79 val = "Auto-selected batch size by Ludwig:<br>" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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80 resolved_val = training_progress.get("batch_size") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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81 val += f"<span style='font-size: 0.85em;'>{resolved_val}</span><br>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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82 else: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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83 val = "auto" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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84 if key == "learning_rate": |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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85 resolved_val = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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86 if val is None or val == "auto": |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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87 if training_progress: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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88 resolved_val = training_progress.get("learning_rate") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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89 val = ( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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90 "Auto-selected learning rate by Ludwig:<br>" |
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91 f"<span style='font-size: 0.85em;'>" |
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92 f"{resolved_val if resolved_val else val}</span><br>" |
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93 "<span style='font-size: 0.85em;'>" |
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94 "Based on model architecture and training setup " |
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95 "(e.g., fine-tuning).<br>" |
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96 "See <a href='https://ludwig.ai/latest/configuration/trainer/" |
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97 "#trainer-parameters' target='_blank'>" |
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98 "Ludwig Trainer Parameters</a> for details." |
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99 "</span>" |
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100 ) |
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101 else: |
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102 val = ( |
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103 "Auto-selected by Ludwig<br>" |
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104 "<span style='font-size: 0.85em;'>" |
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105 "Automatically tuned based on architecture and dataset.<br>" |
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106 "See <a href='https://ludwig.ai/latest/configuration/trainer/" |
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107 "#trainer-parameters' target='_blank'>" |
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108 "Ludwig Trainer Parameters</a> for details." |
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109 "</span>" |
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110 ) |
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111 else: |
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112 val = f"{val:.6f}" |
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113 if key == "epochs": |
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114 if ( |
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115 training_progress |
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116 and "epoch" in training_progress |
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117 and val > training_progress["epoch"] |
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118 ): |
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119 val = ( |
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120 f"Because of early stopping: the training " |
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121 f"stopped at epoch {training_progress['epoch']}" |
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122 ) |
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123 |
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124 if val is None: |
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125 continue |
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126 rows.append( |
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127 f"<tr>" |
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128 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>" |
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129 f"{key.replace('_', ' ').title()}</td>" |
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130 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>" |
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131 f"{val}</td>" |
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132 f"</tr>" |
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133 ) |
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134 |
2
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135 aug_cfg = config.get("augmentation") |
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136 if aug_cfg: |
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137 types = [str(a.get("type", "")) for a in aug_cfg] |
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138 aug_val = ", ".join(types) |
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139 rows.append( |
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140 "<tr>" |
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141 "<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>Augmentation</td>" |
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142 "<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>" |
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143 f"{aug_val}</td>" |
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144 "</tr>" |
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145 ) |
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146 |
0
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147 if split_info: |
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148 rows.append( |
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149 f"<tr>" |
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150 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: left;'>" |
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151 f"Data Split</td>" |
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152 f"<td style='padding: 6px 12px; border: 1px solid #ccc; text-align: center;'>" |
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153 f"{split_info}</td>" |
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154 f"</tr>" |
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155 ) |
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156 |
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157 return ( |
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158 "<h2 style='text-align: center;'>Training Setup</h2>" |
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159 "<div style='display: flex; justify-content: center;'>" |
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160 "<table style='border-collapse: collapse; width: 60%; table-layout: auto;'>" |
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161 "<thead><tr>" |
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162 "<th style='padding: 10px; border: 1px solid #ccc; text-align: left;'>" |
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163 "Parameter</th>" |
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164 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center;'>" |
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165 "Value</th>" |
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166 "</tr></thead><tbody>" + "".join(rows) + "</tbody></table></div><br>" |
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167 "<p style='text-align: center; font-size: 0.9em;'>" |
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168 "Model trained using Ludwig.<br>" |
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169 "If want to learn more about Ludwig default settings," |
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170 "please check their <a href='https://ludwig.ai' target='_blank'>" |
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171 "website(ludwig.ai)</a>." |
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172 "</p><hr>" |
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173 ) |
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174 |
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175 |
1
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176 def detect_output_type(test_stats): |
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177 """Detects if the output type is 'binary' or 'category' based on test statistics.""" |
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178 label_stats = test_stats.get("label", {}) |
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179 if "mean_squared_error" in label_stats: |
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180 return "regression" |
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181 per_class = label_stats.get("per_class_stats", {}) |
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182 if len(per_class) == 2: |
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183 return "binary" |
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184 return "category" |
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185 |
1
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186 |
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187 def extract_metrics_from_json( |
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188 train_stats: dict, |
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189 test_stats: dict, |
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190 output_type: str, |
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191 ) -> dict: |
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192 """Extracts relevant metrics from training and test statistics based on the output type.""" |
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193 metrics = {"training": {}, "validation": {}, "test": {}} |
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194 |
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195 def get_last_value(stats, key): |
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196 val = stats.get(key) |
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197 if isinstance(val, list) and val: |
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198 return val[-1] |
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199 elif isinstance(val, (int, float)): |
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200 return val |
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201 return None |
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202 |
1
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203 for split in ["training", "validation"]: |
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204 split_stats = train_stats.get(split, {}) |
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205 if not split_stats: |
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206 logging.warning(f"No statistics found for {split} split") |
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207 continue |
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208 label_stats = split_stats.get("label", {}) |
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209 if not label_stats: |
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210 logging.warning(f"No label statistics found for {split} split") |
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211 continue |
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212 if output_type == "binary": |
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213 metrics[split] = { |
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214 "accuracy": get_last_value(label_stats, "accuracy"), |
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215 "loss": get_last_value(label_stats, "loss"), |
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216 "precision": get_last_value(label_stats, "precision"), |
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217 "recall": get_last_value(label_stats, "recall"), |
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218 "specificity": get_last_value(label_stats, "specificity"), |
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219 "roc_auc": get_last_value(label_stats, "roc_auc"), |
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220 } |
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221 elif output_type == "regression": |
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222 metrics[split] = { |
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223 "loss": get_last_value(label_stats, "loss"), |
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224 "mean_absolute_error": get_last_value( |
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225 label_stats, "mean_absolute_error" |
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226 ), |
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227 "mean_absolute_percentage_error": get_last_value( |
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228 label_stats, "mean_absolute_percentage_error" |
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229 ), |
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230 "mean_squared_error": get_last_value(label_stats, "mean_squared_error"), |
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231 "root_mean_squared_error": get_last_value( |
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232 label_stats, "root_mean_squared_error" |
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233 ), |
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234 "root_mean_squared_percentage_error": get_last_value( |
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235 label_stats, "root_mean_squared_percentage_error" |
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236 ), |
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237 "r2": get_last_value(label_stats, "r2"), |
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238 } |
1
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239 else: |
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240 metrics[split] = { |
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241 "accuracy": get_last_value(label_stats, "accuracy"), |
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242 "accuracy_micro": get_last_value(label_stats, "accuracy_micro"), |
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243 "loss": get_last_value(label_stats, "loss"), |
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244 "roc_auc": get_last_value(label_stats, "roc_auc"), |
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245 "hits_at_k": get_last_value(label_stats, "hits_at_k"), |
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246 } |
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247 |
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248 # Test metrics: dynamic extraction according to exclusions |
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249 test_label_stats = test_stats.get("label", {}) |
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250 if not test_label_stats: |
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251 logging.warning("No label statistics found for test split") |
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252 else: |
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253 combined_stats = test_stats.get("combined", {}) |
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254 overall_stats = test_label_stats.get("overall_stats", {}) |
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255 |
1
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256 # Define exclusions |
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257 if output_type == "binary": |
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258 exclude = {"per_class_stats", "precision_recall_curve", "roc_curve"} |
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259 else: |
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260 exclude = {"per_class_stats", "confusion_matrix"} |
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261 |
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262 # 1. Get all scalar test_label_stats not excluded |
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263 test_metrics = {} |
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264 for k, v in test_label_stats.items(): |
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265 if k in exclude: |
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266 continue |
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267 if k == "overall_stats": |
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268 continue |
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269 if isinstance(v, (int, float, str, bool)): |
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270 test_metrics[k] = v |
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271 |
1
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272 # 2. Add overall_stats (flattened) |
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273 for k, v in overall_stats.items(): |
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274 test_metrics[k] = v |
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275 |
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276 # 3. Optionally include combined/loss if present and not already |
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277 if "loss" in combined_stats and "loss" not in test_metrics: |
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278 test_metrics["loss"] = combined_stats["loss"] |
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279 |
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280 metrics["test"] = test_metrics |
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281 |
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282 return metrics |
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283 |
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284 |
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285 def generate_table_row(cells, styles): |
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286 """Helper function to generate an HTML table row.""" |
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287 return ( |
1
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288 "<tr>" |
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289 + "".join(f"<td style='{styles}'>{cell}</td>" for cell in cells) |
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290 + "</tr>" |
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291 ) |
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292 |
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293 |
1
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294 def format_stats_table_html(train_stats: dict, test_stats: dict) -> str: |
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295 """Formats a combined HTML table for training, validation, and test metrics.""" |
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296 output_type = detect_output_type(test_stats) |
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297 all_metrics = extract_metrics_from_json(train_stats, test_stats, output_type) |
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298 rows = [] |
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299 for metric_key in sorted(all_metrics["training"].keys()): |
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300 if ( |
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301 metric_key in all_metrics["validation"] |
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302 and metric_key in all_metrics["test"] |
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303 ): |
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304 display_name = METRIC_DISPLAY_NAMES.get( |
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305 metric_key, |
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306 metric_key.replace("_", " ").title(), |
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307 ) |
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308 t = all_metrics["training"].get(metric_key) |
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309 v = all_metrics["validation"].get(metric_key) |
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310 te = all_metrics["test"].get(metric_key) |
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311 if all(x is not None for x in [t, v, te]): |
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312 rows.append([display_name, f"{t:.4f}", f"{v:.4f}", f"{te:.4f}"]) |
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313 |
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314 if not rows: |
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315 return "<table><tr><td>No metric values found.</td></tr></table>" |
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316 |
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317 html = ( |
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318 "<h2 style='text-align: center;'>Model Performance Summary</h2>" |
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319 "<div style='display: flex; justify-content: center;'>" |
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320 "<table style='border-collapse: collapse; table-layout: auto;'>" |
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321 "<thead><tr>" |
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322 "<th style='padding: 10px; border: 1px solid #ccc; text-align: left; " |
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323 "white-space: nowrap;'>Metric</th>" |
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324 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
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325 "white-space: nowrap;'>Train</th>" |
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326 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
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327 "white-space: nowrap;'>Validation</th>" |
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328 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
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329 "white-space: nowrap;'>Test</th>" |
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330 "</tr></thead><tbody>" |
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331 ) |
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332 for row in rows: |
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333 html += generate_table_row( |
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334 row, |
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335 "padding: 10px; border: 1px solid #ccc; text-align: center; " |
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336 "white-space: nowrap;", |
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337 ) |
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338 html += "</tbody></table></div><br>" |
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339 return html |
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340 |
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341 |
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342 def format_train_val_stats_table_html(train_stats: dict, test_stats: dict) -> str: |
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343 """Formats an HTML table for training and validation metrics.""" |
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344 output_type = detect_output_type(test_stats) |
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345 all_metrics = extract_metrics_from_json(train_stats, test_stats, output_type) |
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346 rows = [] |
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347 for metric_key in sorted(all_metrics["training"].keys()): |
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348 if metric_key in all_metrics["validation"]: |
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349 display_name = METRIC_DISPLAY_NAMES.get( |
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350 metric_key, |
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351 metric_key.replace("_", " ").title(), |
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352 ) |
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353 t = all_metrics["training"].get(metric_key) |
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354 v = all_metrics["validation"].get(metric_key) |
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355 if t is not None and v is not None: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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356 rows.append([display_name, f"{t:.4f}", f"{v:.4f}"]) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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|
357 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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358 if not rows: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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359 return "<table><tr><td>No metric values found for Train/Validation.</td></tr></table>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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360 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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361 html = ( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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362 "<h2 style='text-align: center;'>Train/Validation Performance Summary</h2>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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363 "<div style='display: flex; justify-content: center;'>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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364 "<table style='border-collapse: collapse; table-layout: auto;'>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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365 "<thead><tr>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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366 "<th style='padding: 10px; border: 1px solid #ccc; text-align: left; " |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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367 "white-space: nowrap;'>Metric</th>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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368 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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369 "white-space: nowrap;'>Train</th>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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370 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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371 "white-space: nowrap;'>Validation</th>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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372 "</tr></thead><tbody>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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373 ) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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374 for row in rows: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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375 html += generate_table_row( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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376 row, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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377 "padding: 10px; border: 1px solid #ccc; text-align: center; " |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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378 "white-space: nowrap;", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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379 ) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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380 html += "</tbody></table></div><br>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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381 return html |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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382 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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383 |
2
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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384 def format_test_merged_stats_table_html( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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385 test_metrics: Dict[str, Optional[float]], |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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386 ) -> str: |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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387 """Formats an HTML table for test metrics.""" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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388 rows = [] |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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389 for key in sorted(test_metrics.keys()): |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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390 display_name = METRIC_DISPLAY_NAMES.get(key, key.replace("_", " ").title()) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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391 value = test_metrics[key] |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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392 if value is not None: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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393 rows.append([display_name, f"{value:.4f}"]) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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394 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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395 if not rows: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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396 return "<table><tr><td>No test metric values found.</td></tr></table>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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397 |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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398 html = ( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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399 "<h2 style='text-align: center;'>Test Performance Summary</h2>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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400 "<div style='display: flex; justify-content: center;'>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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401 "<table style='border-collapse: collapse; table-layout: auto;'>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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402 "<thead><tr>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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403 "<th style='padding: 10px; border: 1px solid #ccc; text-align: left; " |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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404 "white-space: nowrap;'>Metric</th>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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405 "<th style='padding: 10px; border: 1px solid #ccc; text-align: center; " |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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406 "white-space: nowrap;'>Test</th>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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407 "</tr></thead><tbody>" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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408 ) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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409 for row in rows: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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410 html += generate_table_row( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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411 row, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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412 "padding: 10px; border: 1px solid #ccc; text-align: center; " |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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413 "white-space: nowrap;", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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414 ) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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415 html += "</tbody></table></div><br>" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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416 return html |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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417 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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418 |
0
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419 def split_data_0_2( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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420 df: pd.DataFrame, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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421 split_column: str, |
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422 validation_size: float = 0.1, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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423 random_state: int = 42, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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424 label_column: Optional[str] = None, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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425 ) -> pd.DataFrame: |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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426 """Given a DataFrame whose split_column only contains {0,2}, re-assign a portion of the 0s to become 1s (validation).""" |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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427 out = df.copy() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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428 out[split_column] = pd.to_numeric(out[split_column], errors="coerce").astype(int) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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429 |
54b871dfc51e
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430 idx_train = out.index[out[split_column] == 0].tolist() |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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431 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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432 if not idx_train: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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433 logger.info("No rows with split=0; nothing to do.") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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434 return out |
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|
435 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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436 # Always use stratify if possible |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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437 stratify_arr = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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438 if label_column and label_column in out.columns: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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439 label_counts = out.loc[idx_train, label_column].value_counts() |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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440 if label_counts.size > 1: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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441 # Force stratify even with fewer samples - adjust validation_size if needed |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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442 min_samples_per_class = label_counts.min() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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443 if min_samples_per_class * validation_size < 1: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
444 # Adjust validation_size to ensure at least 1 sample per class, but do not exceed original validation_size |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
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445 adjusted_validation_size = min(validation_size, 1.0 / min_samples_per_class) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
446 if adjusted_validation_size != validation_size: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
447 validation_size = adjusted_validation_size |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
448 logger.info(f"Adjusted validation_size to {validation_size:.3f} to ensure at least one sample per class in validation") |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
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449 stratify_arr = out.loc[idx_train, label_column] |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
450 logger.info("Using stratified split for validation set") |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
451 else: |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
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452 logger.warning("Only one label class found; cannot stratify") |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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changeset
|
453 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
454 if validation_size <= 0: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
455 logger.info("validation_size <= 0; keeping all as train.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
456 return out |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
457 if validation_size >= 1: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
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458 logger.info("validation_size >= 1; moving all train → validation.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
459 out.loc[idx_train, split_column] = 1 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
460 return out |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
461 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
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462 # Always try stratified split first |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
463 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
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464 train_idx, val_idx = train_test_split( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
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465 idx_train, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
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466 test_size=validation_size, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
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467 random_state=random_state, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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diff
changeset
|
468 stratify=stratify_arr, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
469 ) |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
470 logger.info("Successfully applied stratified split") |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
471 except ValueError as e: |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
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472 logger.warning(f"Stratified split failed ({e}); falling back to random split.") |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
473 train_idx, val_idx = train_test_split( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
474 idx_train, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
475 test_size=validation_size, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
476 random_state=random_state, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff
changeset
|
477 stratify=None, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
478 ) |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
479 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
480 out.loc[train_idx, split_column] = 0 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
481 out.loc[val_idx, split_column] = 1 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
482 out[split_column] = out[split_column].astype(int) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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changeset
|
483 return out |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
484 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
485 |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
486 def create_stratified_random_split( |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
487 df: pd.DataFrame, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
488 split_column: str, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
489 split_probabilities: list = [0.7, 0.1, 0.2], |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
490 random_state: int = 42, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
491 label_column: Optional[str] = None, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
492 ) -> pd.DataFrame: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
493 """Create a stratified random split when no split column exists.""" |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
494 out = df.copy() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
495 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
496 # initialize split column |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
497 out[split_column] = 0 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
498 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
499 if not label_column or label_column not in out.columns: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
500 logger.warning("No label column found; using random split without stratification") |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
501 # fall back to simple random assignment |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
502 indices = out.index.tolist() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
503 np.random.seed(random_state) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
504 np.random.shuffle(indices) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
505 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
506 n_total = len(indices) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
507 n_train = int(n_total * split_probabilities[0]) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
508 n_val = int(n_total * split_probabilities[1]) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
509 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
510 out.loc[indices[:n_train], split_column] = 0 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
511 out.loc[indices[n_train:n_train + n_val], split_column] = 1 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
512 out.loc[indices[n_train + n_val:], split_column] = 2 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
513 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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changeset
|
514 return out.astype({split_column: int}) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
515 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
516 # check if stratification is possible |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
517 label_counts = out[label_column].value_counts() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
518 min_samples_per_class = label_counts.min() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
519 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
520 # ensure we have enough samples for stratification: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
521 # Each class must have at least as many samples as the number of splits, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
522 # so that each split can receive at least one sample per class. |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
523 min_samples_required = len(split_probabilities) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
524 if min_samples_per_class < min_samples_required: |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
525 logger.warning( |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
526 f"Insufficient samples per class for stratification (min: {min_samples_per_class}, required: {min_samples_required}); using random split" |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
527 ) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
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diff
changeset
|
528 # fall back to simple random assignment |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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diff
changeset
|
529 indices = out.index.tolist() |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
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parents:
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diff
changeset
|
530 np.random.seed(random_state) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
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diff
changeset
|
531 np.random.shuffle(indices) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
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diff
changeset
|
532 |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
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diff
changeset
|
533 n_total = len(indices) |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
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534 n_train = int(n_total * split_probabilities[0]) |
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535 n_val = int(n_total * split_probabilities[1]) |
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536 |
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537 out.loc[indices[:n_train], split_column] = 0 |
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538 out.loc[indices[n_train:n_train + n_val], split_column] = 1 |
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539 out.loc[indices[n_train + n_val:], split_column] = 2 |
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540 |
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541 return out.astype({split_column: int}) |
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542 |
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543 logger.info("Using stratified random split for train/validation/test sets") |
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544 |
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545 # first split: separate test set |
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546 train_val_idx, test_idx = train_test_split( |
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547 out.index.tolist(), |
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548 test_size=split_probabilities[2], |
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549 random_state=random_state, |
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550 stratify=out[label_column], |
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551 ) |
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552 |
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553 # second split: separate training and validation from remaining data |
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554 val_size_adjusted = split_probabilities[1] / (split_probabilities[0] + split_probabilities[1]) |
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555 train_idx, val_idx = train_test_split( |
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556 train_val_idx, |
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557 test_size=val_size_adjusted, |
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558 random_state=random_state, |
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559 stratify=out.loc[train_val_idx, label_column], |
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560 ) |
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561 |
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562 # assign split values |
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563 out.loc[train_idx, split_column] = 0 |
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564 out.loc[val_idx, split_column] = 1 |
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565 out.loc[test_idx, split_column] = 2 |
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566 |
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567 logger.info("Successfully applied stratified random split") |
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568 logger.info(f"Split counts: Train={len(train_idx)}, Val={len(val_idx)}, Test={len(test_idx)}") |
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569 |
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570 return out.astype({split_column: int}) |
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571 |
801a8b6973fb
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572 |
0
54b871dfc51e
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573 class Backend(Protocol): |
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574 """Interface for a machine learning backend.""" |
1
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575 |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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576 def prepare_config( |
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577 self, |
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578 config_params: Dict[str, Any], |
1
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579 split_config: Dict[str, Any], |
0
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580 ) -> str: |
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581 ... |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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582 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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583 def run_experiment( |
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584 self, |
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585 dataset_path: Path, |
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586 config_path: Path, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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587 output_dir: Path, |
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588 random_seed: int, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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589 ) -> None: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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590 ... |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
591 |
2
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592 def generate_plots(self, output_dir: Path) -> None: |
0
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593 ... |
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594 |
54b871dfc51e
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595 def generate_html_report( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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596 self, |
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597 title: str, |
2
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598 output_dir: str, |
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599 config: Dict[str, Any], |
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600 split_info: str, |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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601 ) -> Path: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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602 ... |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
603 |
54b871dfc51e
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604 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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605 class LudwigDirectBackend: |
1
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606 """Backend for running Ludwig experiments directly via the internal experiment_cli function.""" |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
607 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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608 def prepare_config( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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609 self, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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610 config_params: Dict[str, Any], |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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611 split_config: Dict[str, Any], |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
612 ) -> str: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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613 logger.info("LudwigDirectBackend: Preparing YAML configuration.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
614 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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615 model_name = config_params.get("model_name", "resnet18") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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616 use_pretrained = config_params.get("use_pretrained", False) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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617 fine_tune = config_params.get("fine_tune", False) |
2
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618 if use_pretrained: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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619 trainable = bool(fine_tune) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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620 else: |
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621 trainable = True |
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622 epochs = config_params.get("epochs", 10) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
623 batch_size = config_params.get("batch_size") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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624 num_processes = config_params.get("preprocessing_num_processes", 1) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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625 early_stop = config_params.get("early_stop", None) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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626 learning_rate = config_params.get("learning_rate") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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627 learning_rate = "auto" if learning_rate is None else float(learning_rate) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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628 raw_encoder = MODEL_ENCODER_TEMPLATES.get(model_name, model_name) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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629 if isinstance(raw_encoder, dict): |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
630 encoder_config = { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
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|
631 **raw_encoder, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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632 "use_pretrained": use_pretrained, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
633 "trainable": trainable, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
634 } |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
635 else: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
636 encoder_config = {"type": raw_encoder} |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
637 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
638 batch_size_cfg = batch_size or "auto" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
639 |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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640 label_column_path = config_params.get("label_column_data_path") |
2
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641 label_series = None |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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642 if label_column_path is not None and Path(label_column_path).exists(): |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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643 try: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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644 label_series = pd.read_csv(label_column_path)[LABEL_COLUMN_NAME] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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645 except Exception as e: |
2
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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646 logger.warning(f"Could not read label column for task detection: {e}") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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647 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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648 if ( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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649 label_series is not None |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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650 and ptypes.is_numeric_dtype(label_series.dtype) |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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651 and label_series.nunique() > 10 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
652 ): |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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653 task_type = "regression" |
1
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654 else: |
2
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655 task_type = "classification" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
656 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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657 config_params["task_type"] = task_type |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
658 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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659 image_feat: Dict[str, Any] = { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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660 "name": IMAGE_PATH_COLUMN_NAME, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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661 "type": "image", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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662 "encoder": encoder_config, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
663 } |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
664 if config_params.get("augmentation") is not None: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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665 image_feat["augmentation"] = config_params["augmentation"] |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
666 |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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667 if task_type == "regression": |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
668 output_feat = { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
669 "name": LABEL_COLUMN_NAME, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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670 "type": "number", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
671 "decoder": {"type": "regressor"}, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
672 "loss": {"type": "mean_squared_error"}, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
673 "evaluation": { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
674 "metrics": [ |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
675 "mean_squared_error", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
676 "mean_absolute_error", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
677 "r2", |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
678 ] |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
679 }, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
680 } |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
681 val_metric = config_params.get("validation_metric", "mean_squared_error") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
682 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
683 else: |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
684 num_unique_labels = ( |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
685 label_series.nunique() if label_series is not None else 2 |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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|
686 ) |
2
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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687 output_type = "binary" if num_unique_labels == 2 else "category" |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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688 output_feat = {"name": LABEL_COLUMN_NAME, "type": output_type} |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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689 val_metric = None |
1
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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|
690 |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
691 conf: Dict[str, Any] = { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
692 "model_type": "ecd", |
2
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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693 "input_features": [image_feat], |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
694 "output_features": [output_feat], |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
695 "combiner": {"type": "concat"}, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
696 "trainer": { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
697 "epochs": epochs, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
698 "early_stop": early_stop, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
699 "batch_size": batch_size_cfg, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
700 "learning_rate": learning_rate, |
2
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|
701 # only set validation_metric for regression |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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|
702 **({"validation_metric": val_metric} if val_metric else {}), |
0
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
703 }, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
704 "preprocessing": { |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
705 "split": split_config, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
706 "num_processes": num_processes, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
707 "in_memory": False, |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
708 }, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
709 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
710 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
711 logger.debug("LudwigDirectBackend: Config dict built.") |
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planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
712 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
713 yaml_str = yaml.dump(conf, sort_keys=False, indent=2) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
714 logger.info("LudwigDirectBackend: YAML config generated.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
715 return yaml_str |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
716 except Exception: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
717 logger.error( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
718 "LudwigDirectBackend: Failed to serialize YAML.", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
719 exc_info=True, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
720 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
721 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
722 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
723 def run_experiment( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
724 self, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
725 dataset_path: Path, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
726 config_path: Path, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
727 output_dir: Path, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
728 random_seed: int = 42, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
729 ) -> None: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
730 """Invoke Ludwig's internal experiment_cli function to run the experiment.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
731 logger.info("LudwigDirectBackend: Starting experiment execution.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
732 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
733 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
734 from ludwig.experiment import experiment_cli |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
735 except ImportError as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
736 logger.error( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
737 "LudwigDirectBackend: Could not import experiment_cli.", |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
738 exc_info=True, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
739 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
740 raise RuntimeError("Ludwig import failed.") from e |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
741 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
742 output_dir.mkdir(parents=True, exist_ok=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
743 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
744 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
745 experiment_cli( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
746 dataset=str(dataset_path), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
747 config=str(config_path), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
748 output_directory=str(output_dir), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
749 random_seed=random_seed, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
750 ) |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
751 logger.info( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
752 f"LudwigDirectBackend: Experiment completed. Results in {output_dir}" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
753 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
754 except TypeError as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
755 logger.error( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
756 "LudwigDirectBackend: Argument mismatch in experiment_cli call.", |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
757 exc_info=True, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
758 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
759 raise RuntimeError("Ludwig argument error.") from e |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
760 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
761 logger.error( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
762 "LudwigDirectBackend: Experiment execution error.", |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
763 exc_info=True, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
764 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
765 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
766 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
767 def get_training_process(self, output_dir) -> Optional[Dict[str, Any]]: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
768 """Retrieve the learning rate used in the most recent Ludwig run.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
769 output_dir = Path(output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
770 exp_dirs = sorted( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
771 output_dir.glob("experiment_run*"), |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
772 key=lambda p: p.stat().st_mtime, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
773 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
774 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
775 if not exp_dirs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
776 logger.warning(f"No experiment run directories found in {output_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
777 return None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
778 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
779 progress_file = exp_dirs[-1] / "model" / "training_progress.json" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
780 if not progress_file.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
781 logger.warning(f"No training_progress.json found in {progress_file}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
782 return None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
783 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
784 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
785 with progress_file.open("r", encoding="utf-8") as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
786 data = json.load(f) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
787 return { |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
788 "learning_rate": data.get("learning_rate"), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
789 "batch_size": data.get("batch_size"), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
790 "epoch": data.get("epoch"), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
791 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
792 except Exception as e: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
793 logger.warning(f"Failed to read training progress info: {e}") |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
794 return {} |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
795 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
796 def convert_parquet_to_csv(self, output_dir: Path): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
797 """Convert the predictions Parquet file to CSV.""" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
798 output_dir = Path(output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
799 exp_dirs = sorted( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
800 output_dir.glob("experiment_run*"), |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
801 key=lambda p: p.stat().st_mtime, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
802 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
803 if not exp_dirs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
804 logger.warning(f"No experiment run dirs found in {output_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
805 return |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
806 exp_dir = exp_dirs[-1] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
807 parquet_path = exp_dir / PREDICTIONS_PARQUET_FILE_NAME |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
808 csv_path = exp_dir / "predictions.csv" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
809 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
810 df = pd.read_parquet(parquet_path) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
811 df.to_csv(csv_path, index=False) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
812 logger.info(f"Converted Parquet to CSV: {csv_path}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
813 except Exception as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
814 logger.error(f"Error converting Parquet to CSV: {e}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
815 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
816 def generate_plots(self, output_dir: Path) -> None: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
817 """Generate all registered Ludwig visualizations for the latest experiment run.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
818 logger.info("Generating all Ludwig visualizations…") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
819 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
820 test_plots = { |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
821 "compare_performance", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
822 "compare_classifiers_performance_from_prob", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
823 "compare_classifiers_performance_from_pred", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
824 "compare_classifiers_performance_changing_k", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
825 "compare_classifiers_multiclass_multimetric", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
826 "compare_classifiers_predictions", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
827 "confidence_thresholding_2thresholds_2d", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
828 "confidence_thresholding_2thresholds_3d", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
829 "confidence_thresholding", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
830 "confidence_thresholding_data_vs_acc", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
831 "binary_threshold_vs_metric", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
832 "roc_curves", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
833 "roc_curves_from_test_statistics", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
834 "calibration_1_vs_all", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
835 "calibration_multiclass", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
836 "confusion_matrix", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
837 "frequency_vs_f1", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
838 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
839 train_plots = { |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
840 "learning_curves", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
841 "compare_classifiers_performance_subset", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
842 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
843 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
844 output_dir = Path(output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
845 exp_dirs = sorted( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
846 output_dir.glob("experiment_run*"), |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
847 key=lambda p: p.stat().st_mtime, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
848 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
849 if not exp_dirs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
850 logger.warning(f"No experiment run dirs found in {output_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
851 return |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
852 exp_dir = exp_dirs[-1] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
853 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
854 viz_dir = exp_dir / "visualizations" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
855 viz_dir.mkdir(exist_ok=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
856 train_viz = viz_dir / "train" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
857 test_viz = viz_dir / "test" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
858 train_viz.mkdir(parents=True, exist_ok=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
859 test_viz.mkdir(parents=True, exist_ok=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
860 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
861 def _check(p: Path) -> Optional[str]: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
862 return str(p) if p.exists() else None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
863 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
864 training_stats = _check(exp_dir / "training_statistics.json") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
865 test_stats = _check(exp_dir / TEST_STATISTICS_FILE_NAME) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
866 probs_path = _check(exp_dir / PREDICTIONS_PARQUET_FILE_NAME) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
867 gt_metadata = _check(exp_dir / "model" / TRAIN_SET_METADATA_FILE_NAME) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
868 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
869 dataset_path = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
870 split_file = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
871 desc = exp_dir / DESCRIPTION_FILE_NAME |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
872 if desc.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
873 with open(desc, "r") as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
874 cfg = json.load(f) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
875 dataset_path = _check(Path(cfg.get("dataset", ""))) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
876 split_file = _check(Path(get_split_path(cfg.get("dataset", "")))) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
877 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
878 output_feature = "" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
879 if desc.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
880 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
881 output_feature = cfg["config"]["output_features"][0]["name"] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
882 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
883 pass |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
884 if not output_feature and test_stats: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
885 with open(test_stats, "r") as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
886 stats = json.load(f) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
887 output_feature = next(iter(stats.keys()), "") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
888 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
889 viz_registry = get_visualizations_registry() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
890 for viz_name, viz_func in viz_registry.items(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
891 if viz_name in train_plots: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
892 viz_dir_plot = train_viz |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
893 elif viz_name in test_plots: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
894 viz_dir_plot = test_viz |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
895 else: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
896 continue |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
897 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
898 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
899 viz_func( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
900 training_statistics=[training_stats] if training_stats else [], |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
901 test_statistics=[test_stats] if test_stats else [], |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
902 probabilities=[probs_path] if probs_path else [], |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
903 output_feature_name=output_feature, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
904 ground_truth_split=2, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
905 top_n_classes=[0], |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
906 top_k=3, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
907 ground_truth_metadata=gt_metadata, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
908 ground_truth=dataset_path, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
909 split_file=split_file, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
910 output_directory=str(viz_dir_plot), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
911 normalize=False, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
912 file_format="png", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
913 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
914 logger.info(f"✔ Generated {viz_name}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
915 except Exception as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
916 logger.warning(f"✘ Skipped {viz_name}: {e}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
917 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
918 logger.info(f"All visualizations written to {viz_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
919 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
920 def generate_html_report( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
921 self, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
922 title: str, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
923 output_dir: str, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
924 config: dict, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
925 split_info: str, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
926 ) -> Path: |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
927 """Assemble an HTML report from visualizations under train_val/ and test/ folders.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
928 cwd = Path.cwd() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
929 report_name = title.lower().replace(" ", "_") + "_report.html" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
930 report_path = cwd / report_name |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
931 output_dir = Path(output_dir) |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
932 output_type = None |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
933 |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
934 exp_dirs = sorted( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
935 output_dir.glob("experiment_run*"), |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
936 key=lambda p: p.stat().st_mtime, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
937 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
938 if not exp_dirs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
939 raise RuntimeError(f"No 'experiment*' dirs found in {output_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
940 exp_dir = exp_dirs[-1] |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
941 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
942 base_viz_dir = exp_dir / "visualizations" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
943 train_viz_dir = base_viz_dir / "train" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
944 test_viz_dir = base_viz_dir / "test" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
945 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
946 html = get_html_template() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
947 html += f"<h1>{title}</h1>" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
948 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
949 metrics_html = "" |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
950 train_val_metrics_html = "" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
951 test_metrics_html = "" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
952 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
953 train_stats_path = exp_dir / "training_statistics.json" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
954 test_stats_path = exp_dir / TEST_STATISTICS_FILE_NAME |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
955 if train_stats_path.exists() and test_stats_path.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
956 with open(train_stats_path) as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
957 train_stats = json.load(f) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
958 with open(test_stats_path) as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
959 test_stats = json.load(f) |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
960 output_type = detect_output_type(test_stats) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
961 metrics_html = format_stats_table_html(train_stats, test_stats) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
962 train_val_metrics_html = format_train_val_stats_table_html( |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
963 train_stats, test_stats |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
964 ) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
965 test_metrics_html = format_test_merged_stats_table_html( |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
966 extract_metrics_from_json(train_stats, test_stats, output_type)[ |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
967 "test" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
968 ] |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
969 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
970 except Exception as e: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
971 logger.warning( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
972 f"Could not load stats for HTML report: {type(e).__name__}: {e}" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
973 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
974 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
975 config_html = "" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
976 training_progress = self.get_training_process(output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
977 try: |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
978 config_html = format_config_table_html( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
979 config, split_info, training_progress |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
980 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
981 except Exception as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
982 logger.warning(f"Could not load config for HTML report: {e}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
983 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
984 def render_img_section( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
985 title: str, dir_path: Path, output_type: str = None |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
986 ) -> str: |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
987 if not dir_path.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
988 return f"<h2>{title}</h2><p><em>Directory not found.</em></p>" |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
989 |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
990 imgs = list(dir_path.glob("*.png")) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
991 if not imgs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
992 return f"<h2>{title}</h2><p><em>No plots found.</em></p>" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
993 |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
994 if title == "Test Visualizations" and output_type == "binary": |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
995 order = [ |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
996 "confusion_matrix__label_top2.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
997 "roc_curves_from_prediction_statistics.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
998 "compare_performance_label.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
999 "confusion_matrix_entropy__label_top2.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1000 ] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1001 img_names = {img.name: img for img in imgs} |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1002 ordered_imgs = [ |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1003 img_names[fname] for fname in order if fname in img_names |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1004 ] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1005 remaining = sorted( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1006 [ |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1007 img |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1008 for img in imgs |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1009 if img.name not in order and img.name != "roc_curves.png" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1010 ] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1011 ) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1012 imgs = ordered_imgs + remaining |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1013 |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1014 elif title == "Test Visualizations" and output_type == "category": |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1015 unwanted = { |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1016 "compare_classifiers_multiclass_multimetric__label_best10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1017 "compare_classifiers_multiclass_multimetric__label_top10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1018 "compare_classifiers_multiclass_multimetric__label_worst10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1019 } |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1020 display_order = [ |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1021 "confusion_matrix__label_top10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1022 "roc_curves.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1023 "compare_performance_label.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1024 "compare_classifiers_performance_from_prob.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1025 "compare_classifiers_multiclass_multimetric__label_sorted.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1026 "confusion_matrix_entropy__label_top10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1027 ] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1028 img_names = {img.name: img for img in imgs if img.name not in unwanted} |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1029 ordered_imgs = [ |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1030 img_names[fname] for fname in display_order if fname in img_names |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1031 ] |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1032 remaining = sorted( |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1033 [img for img in img_names.values() if img.name not in display_order] |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1034 ) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1035 imgs = ordered_imgs + remaining |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1036 |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1037 else: |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1038 if output_type == "category": |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1039 unwanted = { |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1040 "compare_classifiers_multiclass_multimetric__label_best10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1041 "compare_classifiers_multiclass_multimetric__label_top10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1042 "compare_classifiers_multiclass_multimetric__label_worst10.png", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1043 } |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1044 imgs = sorted([img for img in imgs if img.name not in unwanted]) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1045 else: |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1046 imgs = sorted(imgs) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1047 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1048 section_html = f"<h2 style='text-align: center;'>{title}</h2><div>" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1049 for img in imgs: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1050 b64 = encode_image_to_base64(str(img)) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1051 section_html += ( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1052 f'<div class="plot" style="margin-bottom:20px;text-align:center;">' |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1053 f"<h3>{img.stem.replace('_', ' ').title()}</h3>" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1054 f'<img src="data:image/png;base64,{b64}" ' |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1055 f'style="max-width:90%;max-height:600px;border:1px solid #ddd;" />' |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1056 f"</div>" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1057 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1058 section_html += "</div>" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1059 return section_html |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1060 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1061 tab1_content = config_html + metrics_html |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1062 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1063 tab2_content = train_val_metrics_html + render_img_section( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1064 "Training & Validation Visualizations", train_viz_dir |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1065 ) |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1066 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1067 # --- Predictions vs Ground Truth table --- |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1068 preds_section = "" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1069 parquet_path = exp_dir / PREDICTIONS_PARQUET_FILE_NAME |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1070 if parquet_path.exists(): |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1071 try: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1072 # 1) load predictions from Parquet |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1073 df_preds = pd.read_parquet(parquet_path).reset_index(drop=True) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1074 # assume the column containing your model's prediction is named "prediction" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1075 # or contains that substring: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1076 pred_col = next( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1077 (c for c in df_preds.columns if "prediction" in c.lower()), |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1078 None, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1079 ) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1080 if pred_col is None: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1081 raise ValueError("No prediction column found in Parquet output") |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1082 df_pred = df_preds[[pred_col]].rename(columns={pred_col: "prediction"}) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1083 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1084 # 2) load ground truth for the test split from prepared CSV |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1085 df_all = pd.read_csv(config["label_column_data_path"]) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1086 df_gt = df_all[df_all[SPLIT_COLUMN_NAME] == 2][ |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1087 LABEL_COLUMN_NAME |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1088 ].reset_index(drop=True) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1089 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1090 # 3) concatenate side‐by‐side |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1091 df_table = pd.concat([df_gt, df_pred], axis=1) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1092 df_table.columns = [LABEL_COLUMN_NAME, "prediction"] |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1093 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1094 # 4) render as HTML |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1095 preds_html = df_table.to_html(index=False, classes="predictions-table") |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1096 preds_section = ( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1097 "<h2 style='text-align: center;'>Predictions vs. Ground Truth</h2>" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1098 "<div style='overflow-x:auto; margin-bottom:20px;'>" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1099 + preds_html |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1100 + "</div>" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1101 ) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1102 except Exception as e: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1103 logger.warning(f"Could not build Predictions vs GT table: {e}") |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1104 # Test tab = Metrics + Preds table + Visualizations |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
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diff
changeset
|
1105 |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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diff
changeset
|
1106 tab3_content = ( |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1107 test_metrics_html |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1108 + preds_section |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1109 + render_img_section("Test Visualizations", test_viz_dir, output_type) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1110 ) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1111 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1112 # assemble the tabs and help modal |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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parents:
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diff
changeset
|
1113 tabbed_html = build_tabbed_html(tab1_content, tab2_content, tab3_content) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1114 modal_html = get_metrics_help_modal() |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
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diff
changeset
|
1115 html += tabbed_html + modal_html + get_html_closing() |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1116 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1117 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1118 with open(report_path, "w") as f: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1119 f.write(html) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
1120 logger.info(f"HTML report generated at: {report_path}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1121 except Exception as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1122 logger.error(f"Failed to write HTML report: {e}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1123 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1124 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1125 return report_path |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1126 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1127 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1128 class WorkflowOrchestrator: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1129 """Manages the image-classification workflow.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1130 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1131 def __init__(self, args: argparse.Namespace, backend: Backend): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1132 self.args = args |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1133 self.backend = backend |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1134 self.temp_dir: Optional[Path] = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1135 self.image_extract_dir: Optional[Path] = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1136 logger.info(f"Orchestrator initialized with backend: {type(backend).__name__}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1137 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1138 def _create_temp_dirs(self) -> None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1139 """Create temporary output and image extraction directories.""" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1140 try: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1141 self.temp_dir = Path( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1142 tempfile.mkdtemp(dir=self.args.output_dir, prefix=TEMP_DIR_PREFIX) |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1143 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1144 self.image_extract_dir = self.temp_dir / "images" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1145 self.image_extract_dir.mkdir() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1146 logger.info(f"Created temp directory: {self.temp_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1147 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1148 logger.error("Failed to create temporary directories", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1149 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1150 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1151 def _extract_images(self) -> None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1152 """Extract images from ZIP into the temp image directory.""" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1153 if self.image_extract_dir is None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1154 raise RuntimeError("Temp image directory not initialized.") |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1155 logger.info( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1156 f"Extracting images from {self.args.image_zip} → {self.image_extract_dir}" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1157 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1158 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1159 with zipfile.ZipFile(self.args.image_zip, "r") as z: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1160 z.extractall(self.image_extract_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1161 logger.info("Image extraction complete.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1162 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1163 logger.error("Error extracting zip file", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1164 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1165 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1166 def _prepare_data(self) -> Tuple[Path, Dict[str, Any], str]: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1167 """Load CSV, update image paths, handle splits, and write prepared CSV.""" |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1168 if not self.temp_dir or not self.image_extract_dir: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1169 raise RuntimeError("Temp dirs not initialized before data prep.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1170 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1171 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1172 df = pd.read_csv(self.args.csv_file) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1173 logger.info(f"Loaded CSV: {self.args.csv_file}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1174 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1175 logger.error("Error loading CSV file", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1176 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1177 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1178 required = {IMAGE_PATH_COLUMN_NAME, LABEL_COLUMN_NAME} |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1179 missing = required - set(df.columns) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1180 if missing: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1181 raise ValueError(f"Missing CSV columns: {', '.join(missing)}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1182 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1183 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1184 df[IMAGE_PATH_COLUMN_NAME] = df[IMAGE_PATH_COLUMN_NAME].apply( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1185 lambda p: str((self.image_extract_dir / p).resolve()) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1186 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1187 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1188 logger.error("Error updating image paths", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1189 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1190 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1191 if SPLIT_COLUMN_NAME in df.columns: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1192 df, split_config, split_info = self._process_fixed_split(df) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1193 else: |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1194 logger.info("No split column; creating stratified random split") |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1195 df = create_stratified_random_split( |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1196 df=df, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1197 split_column=SPLIT_COLUMN_NAME, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1198 split_probabilities=self.args.split_probabilities, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1199 random_state=self.args.random_seed, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1200 label_column=LABEL_COLUMN_NAME, |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1201 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1202 split_config = { |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1203 "type": "fixed", |
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1204 "column": SPLIT_COLUMN_NAME, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1205 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1206 split_info = ( |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1207 f"No split column in CSV. Created stratified random split: " |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1208 f"{[int(p * 100) for p in self.args.split_probabilities]}% " |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1209 f"for train/val/test with balanced label distribution." |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1210 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1211 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1212 final_csv = self.temp_dir / TEMP_CSV_FILENAME |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1213 try: |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1214 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1215 df.to_csv(final_csv, index=False) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1216 logger.info(f"Saved prepared data to {final_csv}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1217 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1218 logger.error("Error saving prepared CSV", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1219 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1220 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1221 return final_csv, split_config, split_info |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1222 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1223 def _process_fixed_split( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1224 self, df: pd.DataFrame |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1225 ) -> Tuple[pd.DataFrame, Dict[str, Any], str]: |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1226 """Process a fixed split column (0=train,1=val,2=test).""" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1227 logger.info(f"Fixed split column '{SPLIT_COLUMN_NAME}' detected.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1228 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1229 col = df[SPLIT_COLUMN_NAME] |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1230 df[SPLIT_COLUMN_NAME] = pd.to_numeric(col, errors="coerce").astype( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1231 pd.Int64Dtype() |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1232 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1233 if df[SPLIT_COLUMN_NAME].isna().any(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1234 logger.warning("Split column contains non-numeric/missing values.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1235 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1236 unique = set(df[SPLIT_COLUMN_NAME].dropna().unique()) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1237 logger.info(f"Unique split values: {unique}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1238 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1239 if unique == {0, 2}: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1240 df = split_data_0_2( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1241 df, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1242 SPLIT_COLUMN_NAME, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1243 validation_size=self.args.validation_size, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1244 label_column=LABEL_COLUMN_NAME, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1245 random_state=self.args.random_seed, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1246 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1247 split_info = ( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1248 "Detected a split column (with values 0 and 2) in the input CSV. " |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1249 f"Used this column as a base and reassigned " |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1250 f"{self.args.validation_size * 100:.1f}% " |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1251 "of the training set (originally labeled 0) to validation (labeled 1) using stratified sampling." |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1252 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1253 logger.info("Applied custom 0/2 split.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1254 elif unique.issubset({0, 1, 2}): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1255 split_info = "Used user-defined split column from CSV." |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1256 logger.info("Using fixed split as-is.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1257 else: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1258 raise ValueError(f"Unexpected split values: {unique}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1259 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1260 return df, {"type": "fixed", "column": SPLIT_COLUMN_NAME}, split_info |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1261 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1262 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1263 logger.error("Error processing fixed split", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1264 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1265 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1266 def _cleanup_temp_dirs(self) -> None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1267 if self.temp_dir and self.temp_dir.exists(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1268 logger.info(f"Cleaning up temp directory: {self.temp_dir}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1269 shutil.rmtree(self.temp_dir, ignore_errors=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1270 self.temp_dir = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1271 self.image_extract_dir = None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1272 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1273 def run(self) -> None: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1274 """Execute the full workflow end-to-end.""" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1275 logger.info("Starting workflow...") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1276 self.args.output_dir.mkdir(parents=True, exist_ok=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1277 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1278 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1279 self._create_temp_dirs() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1280 self._extract_images() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1281 csv_path, split_cfg, split_info = self._prepare_data() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1282 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1283 use_pretrained = self.args.use_pretrained or self.args.fine_tune |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1284 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1285 backend_args = { |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1286 "model_name": self.args.model_name, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1287 "fine_tune": self.args.fine_tune, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1288 "use_pretrained": use_pretrained, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1289 "epochs": self.args.epochs, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1290 "batch_size": self.args.batch_size, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1291 "preprocessing_num_processes": self.args.preprocessing_num_processes, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1292 "split_probabilities": self.args.split_probabilities, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1293 "learning_rate": self.args.learning_rate, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1294 "random_seed": self.args.random_seed, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1295 "early_stop": self.args.early_stop, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1296 "label_column_data_path": csv_path, |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1297 "augmentation": self.args.augmentation, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1298 } |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1299 yaml_str = self.backend.prepare_config(backend_args, split_cfg) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1300 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1301 config_file = self.temp_dir / TEMP_CONFIG_FILENAME |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1302 config_file.write_text(yaml_str) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1303 logger.info(f"Wrote backend config: {config_file}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1304 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1305 self.backend.run_experiment( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1306 csv_path, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1307 config_file, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1308 self.args.output_dir, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1309 self.args.random_seed, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1310 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1311 logger.info("Workflow completed successfully.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1312 self.backend.generate_plots(self.args.output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1313 report_file = self.backend.generate_html_report( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1314 "Image Classification Results", |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1315 self.args.output_dir, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1316 backend_args, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1317 split_info, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1318 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1319 logger.info(f"HTML report generated at: {report_file}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1320 self.backend.convert_parquet_to_csv(self.args.output_dir) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1321 logger.info("Converted Parquet to CSV.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1322 except Exception: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1323 logger.error("Workflow execution failed", exc_info=True) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1324 raise |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1325 finally: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1326 self._cleanup_temp_dirs() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1327 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1328 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1329 def parse_learning_rate(s): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1330 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1331 return float(s) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1332 except (TypeError, ValueError): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1333 return None |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1334 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
1335 |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1336 def aug_parse(aug_string: str): |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1337 """ |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1338 Parse comma-separated augmentation keys into Ludwig augmentation dicts. |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1339 Raises ValueError on unknown key. |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1340 """ |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
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|
1341 mapping = { |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1342 "random_horizontal_flip": {"type": "random_horizontal_flip"}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1343 "random_vertical_flip": {"type": "random_vertical_flip"}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1344 "random_rotate": {"type": "random_rotate", "degree": 10}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1345 "random_blur": {"type": "random_blur", "kernel_size": 3}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1346 "random_brightness": {"type": "random_brightness", "min": 0.5, "max": 2.0}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1347 "random_contrast": {"type": "random_contrast", "min": 0.5, "max": 2.0}, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1348 } |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
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changeset
|
1349 aug_list = [] |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1350 for tok in aug_string.split(","): |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1351 key = tok.strip() |
6
09904b1f61f5
planemo upload for repository https://github.com/goeckslab/gleam.git commit 8499c8d758e3ef28a65a62f59bb403edc4935413
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parents:
2
diff
changeset
|
1352 if not key: |
09904b1f61f5
planemo upload for repository https://github.com/goeckslab/gleam.git commit 8499c8d758e3ef28a65a62f59bb403edc4935413
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parents:
2
diff
changeset
|
1353 continue |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1354 if key not in mapping: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1355 valid = ", ".join(mapping.keys()) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
diff
changeset
|
1356 raise ValueError(f"Unknown augmentation '{key}'. Valid choices: {valid}") |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1357 aug_list.append(mapping[key]) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
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changeset
|
1358 return aug_list |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1359 |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
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parents:
1
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changeset
|
1360 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1361 class SplitProbAction(argparse.Action): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
1362 def __call__(self, parser, namespace, values, option_string=None): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1363 train, val, test = values |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
1364 total = train + val + test |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1365 if abs(total - 1.0) > 1e-6: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1366 parser.error( |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1367 f"--split-probabilities must sum to 1.0; " |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1368 f"got {train:.3f} + {val:.3f} + {test:.3f} = {total:.3f}" |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1369 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1370 setattr(namespace, self.dest, values) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1371 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1372 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1373 def main(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1374 parser = argparse.ArgumentParser( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1375 description="Image Classification Learner with Pluggable Backends", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1376 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1377 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1378 "--csv-file", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1379 required=True, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1380 type=Path, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1381 help="Path to the input CSV", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1382 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1383 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1384 "--image-zip", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1385 required=True, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1386 type=Path, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1387 help="Path to the images ZIP", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1388 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1389 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1390 "--model-name", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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0
diff
changeset
|
1391 required=True, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1392 choices=MODEL_ENCODER_TEMPLATES.keys(), |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1393 help="Which model template to use", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
changeset
|
1394 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1395 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1396 "--use-pretrained", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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0
diff
changeset
|
1397 action="store_true", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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0
diff
changeset
|
1398 help="Use pretrained weights for the model", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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parents:
diff
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|
1399 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1400 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1401 "--fine-tune", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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diff
changeset
|
1402 action="store_true", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1403 help="Enable fine-tuning", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff
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|
1404 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1405 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1406 "--epochs", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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changeset
|
1407 type=int, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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changeset
|
1408 default=10, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff
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|
1409 help="Number of training epochs", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
1410 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1411 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
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changeset
|
1412 "--early-stop", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
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|
1413 type=int, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
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|
1414 default=5, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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diff
changeset
|
1415 help="Early stopping patience", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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changeset
|
1416 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff
changeset
|
1417 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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changeset
|
1418 "--batch-size", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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changeset
|
1419 type=int, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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changeset
|
1420 help="Batch size (None = auto)", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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|
1421 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
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diff
changeset
|
1422 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
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changeset
|
1423 "--output-dir", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
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|
1424 type=Path, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1425 default=Path("learner_output"), |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1426 help="Where to write outputs", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1427 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1428 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1429 "--validation-size", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1430 type=float, |
7
801a8b6973fb
planemo upload for repository https://github.com/goeckslab/gleam.git commit 67df782ea551181e1d240d463764016ba528eba9
goeckslab
parents:
6
diff
changeset
|
1431 default=0.1, |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1432 help="Fraction for validation (0.0–1.0)", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1433 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1434 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1435 "--preprocessing-num-processes", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1436 type=int, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1437 default=max(1, os.cpu_count() // 2), |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1438 help="CPU processes for data prep", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1439 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1440 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1441 "--split-probabilities", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1442 type=float, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1443 nargs=3, |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1444 metavar=("train", "val", "test"), |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1445 action=SplitProbAction, |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1446 default=[0.7, 0.1, 0.2], |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1447 help=( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1448 "Random split proportions (e.g., 0.7 0.1 0.2)." |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1449 "Only used if no split column." |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1450 ), |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1451 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1452 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1453 "--random-seed", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1454 type=int, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1455 default=42, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1456 help="Random seed used for dataset splitting (default: 42)", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1457 ) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1458 parser.add_argument( |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1459 "--learning-rate", |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1460 type=parse_learning_rate, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1461 default=None, |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1462 help="Learning rate. If not provided, Ludwig will auto-select it.", |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1463 ) |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1464 parser.add_argument( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1465 "--augmentation", |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1466 type=str, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1467 default=None, |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1468 help=( |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1469 "Comma-separated list (in order) of any of: " |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1470 "random_horizontal_flip, random_vertical_flip, random_rotate, " |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1471 "random_blur, random_brightness, random_contrast. " |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1472 "E.g. --augmentation random_horizontal_flip,random_rotate" |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1473 ), |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1474 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1475 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1476 args = parser.parse_args() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1477 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1478 if not 0.0 <= args.validation_size <= 1.0: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1479 parser.error("validation-size must be between 0.0 and 1.0") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1480 if not args.csv_file.is_file(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1481 parser.error(f"CSV not found: {args.csv_file}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1482 if not args.image_zip.is_file(): |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1483 parser.error(f"ZIP not found: {args.image_zip}") |
2
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1484 if args.augmentation is not None: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1485 try: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1486 augmentation_setup = aug_parse(args.augmentation) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1487 setattr(args, "augmentation", augmentation_setup) |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1488 except ValueError as e: |
186424a7eca7
planemo upload for repository https://github.com/goeckslab/gleam.git commit 91fa4aba245520fc0680088a07cead66bcfd4ed2
goeckslab
parents:
1
diff
changeset
|
1489 parser.error(str(e)) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1490 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1491 backend_instance = LudwigDirectBackend() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1492 orchestrator = WorkflowOrchestrator(args, backend_instance) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1493 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1494 exit_code = 0 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1495 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1496 orchestrator.run() |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1497 logger.info("Main script finished successfully.") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1498 except Exception as e: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1499 logger.error(f"Main script failed.{e}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1500 exit_code = 1 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1501 finally: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1502 sys.exit(exit_code) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1503 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1504 |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1505 if __name__ == "__main__": |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1506 try: |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1507 import ludwig |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1508 |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1509 logger.debug(f"Found Ludwig version: {ludwig.globals.LUDWIG_VERSION}") |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1510 except ImportError: |
1
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1511 logger.error( |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1512 "Ludwig library not found. Please ensure Ludwig is installed " |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1513 "('pip install ludwig[image]')" |
39202fe5cf97
planemo upload for repository https://github.com/goeckslab/gleam.git commit 06c0da44ac93256dfb616a6b40276b5485a71e8e
goeckslab
parents:
0
diff
changeset
|
1514 ) |
0
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1515 sys.exit(1) |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1516 |
54b871dfc51e
planemo upload for repository https://github.com/goeckslab/gleam.git commit b7411ff35b6228ccdfd36cd4ebd946c03ac7f7e9
goeckslab
parents:
diff
changeset
|
1517 main() |