Mercurial > repos > bgruening > cp_measure_object_size_shape
annotate track_objects.py @ 5:acf3aa487283 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 7d7a519c3a2cc612d38695b335d0f6c75a099de3"
author | bgruening |
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date | Fri, 26 Feb 2021 14:16:44 +0000 |
parents | 79e10d12d90a |
children | d85f11570109 |
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79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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1 #!/usr/bin/env python |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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2 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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3 import argparse |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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4 import json |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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5 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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6 from cp_common_functions import get_json_value |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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7 from cp_common_functions import get_pipeline_lines |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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8 from cp_common_functions import get_total_number_of_modules |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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9 from cp_common_functions import INDENTATION |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
bgruening
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10 from cp_common_functions import update_module_count |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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11 from cp_common_functions import write_pipeline |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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12 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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13 MODULE_NAME = "TrackObjects" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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14 OUTPUT_FILENAME = "output.cppipe" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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15 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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16 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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17 def build_header(module_name, module_number): |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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18 result = "|".join([f"{module_name}:[module_num:{module_number}", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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19 "svn_version:\\'Unknown\\'", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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20 "variable_revision_number:7", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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21 "show_window:True", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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22 "notes:\\x5B\\'Track the embryos across images using the Overlap method\\x3A tracked objects are identified by the amount of frame-to-frame overlap. Save an image of embryos labeled with a unique number across time.\\'\\x5D", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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23 "batch_state:array(\\x5B\\x5D, dtype=uint8)", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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24 "enabled:True", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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25 "wants_pause:False]\n"]) |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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26 return result |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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27 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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28 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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29 def build_main_block(input_params): |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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30 result = INDENTATION.join([f"{INDENTATION}Choose a tracking method:{get_json_value(input_params,'con_tracking_method.tracking_method')}\n", |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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31 f"Select the objects to track:{get_json_value(input_params,'object_to_track')}\n" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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32 ]) |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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33 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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34 tracking_method = get_json_value(input_params, 'con_tracking_method.tracking_method') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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35 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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36 obj_measurement = "None" # default value |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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37 if tracking_method == "Measurements": |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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38 measurement_category = get_json_value(input_params, 'con_tracking_method.con_measurement_category.measurement_category') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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39 measurement = get_json_value(input_params, 'con_tracking_method.con_measurement_category.measurement') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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40 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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41 if measurement_category == "Intensity" or measurement_category == "Location": |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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42 img_measure = get_json_value(input_params, 'con_tracking_method.con_measurement_category.img_measure') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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43 obj_measurement = f"{measurement_category}_{measurement}_{img_measure}" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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44 else: |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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45 obj_measurement = f"{measurement_category}_{measurement}" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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46 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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47 result += INDENTATION.join([f"{INDENTATION}Select object measurement to use for tracking:{obj_measurement}\n"]) |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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48 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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49 if tracking_method == "LAP": # no max distance required, set default for pipeline |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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50 max_distance = 50 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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51 else: |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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52 max_distance = get_json_value(input_params, 'con_tracking_method.max_distance') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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53 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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54 result += INDENTATION.join([f"{INDENTATION}Maximum pixel distance to consider matches:{max_distance}\n"]) |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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55 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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56 display_option = get_json_value(input_params, 'con_tracking_method.display_option') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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57 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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58 output_img_name = "TrackedCells" # default value, required by cppipe regardless of its presence in UI |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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59 save = get_json_value(input_params, 'con_tracking_method.con_save_coded_img.save_coded_img') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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60 if save == "Yes": |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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61 output_img_name = get_json_value(input_params, 'con_tracking_method.con_save_coded_img.name_output_img') |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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62 |
79e10d12d90a
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63 result += INDENTATION.join( |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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64 [f"{INDENTATION}Select display option:{display_option}\n", |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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65 f"Save color-coded image?:{save}\n", |
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66 f"Name the output image:{output_img_name}\n" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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67 ]) |
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68 |
79e10d12d90a
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69 # LAP method default values |
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70 movement_model = "Both" |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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71 no_std = 3.0 |
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72 radius_limit_max = 10.0 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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73 radius_limit_min = 2.0 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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74 radius = "2.0,10.0" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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75 run_second = "Yes" |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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76 gap_closing = 40 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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77 split_alt = 40 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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78 merge_alt = 40 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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79 max_gap_displacement = 5 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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80 max_split = 50 |
79e10d12d90a
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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81 max_merge = 50 |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 35da2dcd86747c9bff138e100dbe08c6106f3780"
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82 max_temporal = 5 |
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83 max_mitosis_dist = 40 |
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84 mitosis_alt = 80 |
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85 |
79e10d12d90a
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86 # LAP method |
79e10d12d90a
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87 if tracking_method == "LAP": |
79e10d12d90a
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88 movement_model = get_json_value(input_params, 'con_tracking_method.movement_method') |
79e10d12d90a
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89 no_std = get_json_value(input_params, 'con_tracking_method.no_std_radius') |
79e10d12d90a
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90 radius_limit_max = get_json_value(input_params, 'con_tracking_method.max_radius') |
79e10d12d90a
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91 radius_limit_min = get_json_value(input_params, 'con_tracking_method.min_radius') |
79e10d12d90a
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92 radius = f"{radius_limit_min},{radius_limit_max}" |
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93 |
79e10d12d90a
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94 run_second = get_json_value(input_params, 'con_tracking_method.con_second_lap.second_lap') |
79e10d12d90a
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95 if run_second == "Yes": |
79e10d12d90a
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96 gap_closing = get_json_value(input_params, 'con_tracking_method.con_second_lap.gap_closing') |
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97 split_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.split_alt') |
79e10d12d90a
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98 merge_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.merge_alt') |
79e10d12d90a
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99 max_gap_displacement = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_gap_displacement') |
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100 max_split = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_split') |
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101 max_merge = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_merge') |
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102 max_temporal = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_temporal') |
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103 max_mitosis_dist = get_json_value(input_params, 'con_tracking_method.con_second_lap.max_mitosis_distance') |
79e10d12d90a
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104 mitosis_alt = get_json_value(input_params, 'con_tracking_method.con_second_lap.mitosis_alt') |
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105 |
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106 result += INDENTATION.join( |
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107 [f"{INDENTATION}Select the movement model:{movement_model}\n", |
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108 f"Number of standard deviations for search radius:{no_std}\n", |
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109 f"Search radius limit, in pixel units (Min,Max):{radius}\n", |
79e10d12d90a
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110 f"Run the second phase of the LAP algorithm?:{run_second}\n", |
79e10d12d90a
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111 f"Gap closing cost:{gap_closing}\n", |
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112 f"Split alternative cost:{split_alt}\n", |
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113 f"Merge alternative cost:{merge_alt}\n", |
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114 f"Maximum gap displacement, in pixel units:{max_gap_displacement}\n", |
79e10d12d90a
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115 f"Maximum split score:{max_split}\n", |
79e10d12d90a
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116 f"Maximum merge score:{max_merge}\n", |
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117 f"Maximum temporal gap, in frames:{max_temporal}\n" |
79e10d12d90a
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118 ]) |
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119 |
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120 # common section |
79e10d12d90a
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121 filter_by_lifetime = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.filter_by_lifetime') |
79e10d12d90a
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122 use_min = "Yes" # default |
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123 min_life = 1 # default |
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124 use_max = "No" # default |
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125 max_life = 100 # default |
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126 |
79e10d12d90a
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127 if filter_by_lifetime == "Yes": |
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128 use_min = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_min.use_min') |
79e10d12d90a
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129 if use_min == "Yes": |
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130 min_life = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_min.min_lifetime') |
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131 |
79e10d12d90a
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132 use_max = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_max.use_max') |
79e10d12d90a
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133 if use_max == "Yes": |
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134 max_life = get_json_value(input_params, 'con_tracking_method.con_filter_by_lifetime.con_use_max.max_lifetime') |
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135 |
79e10d12d90a
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136 result += INDENTATION.join( |
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137 [f"{INDENTATION}Filter objects by lifetime?:{filter_by_lifetime}\n", |
79e10d12d90a
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138 f"Filter using a minimum lifetime?:{use_min}\n", |
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139 f"Minimum lifetime:{min_life}\n", |
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140 f"Filter using a maximum lifetime?:{use_max}\n", |
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141 f"Maximum lifetime:{max_life}\n" |
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142 ]) |
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143 |
79e10d12d90a
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144 # print 2 leftover from LAP |
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145 result += INDENTATION.join( |
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146 [f"{INDENTATION}Mitosis alternative cost:{mitosis_alt}\n", |
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147 f"Maximum mitosis distance, in pixel units:{max_mitosis_dist}\n" |
79e10d12d90a
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148 ]) |
79e10d12d90a
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149 |
79e10d12d90a
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150 # Follow Neighbors |
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151 # defaults |
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152 avg_cell_diameter = 35.0 |
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153 use_adv = "No" |
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154 cost_of_cell = 15.0 |
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155 weight_of_area_diff = 25.0 |
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156 |
79e10d12d90a
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157 if tracking_method == "Follow Neighbors": |
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158 avg_cell_diameter = get_json_value(input_params, 'con_tracking_method.avg_diameter') |
79e10d12d90a
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159 use_adv = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.adv_parameter') |
79e10d12d90a
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160 if use_adv == "Yes": |
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161 cost_of_cell = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.cost') |
79e10d12d90a
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162 weight_of_area_diff = get_json_value(input_params, 'con_tracking_method.con_adv_parameter.weight') |
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163 |
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164 result += INDENTATION.join( |
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165 [f"{INDENTATION}Average cell diameter in pixels:{avg_cell_diameter}\n", |
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166 f"Use advanced configuration parameters:{use_adv}\n", |
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167 f"Cost of cell to empty matching:{cost_of_cell}\n", |
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168 f"Weight of area difference in function matching cost:{weight_of_area_diff}\n" |
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169 ]) |
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170 result = result.rstrip("\n") |
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171 return result |
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172 |
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173 |
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174 if __name__ == "__main__": |
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175 parser = argparse.ArgumentParser() |
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176 parser.add_argument( |
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177 '-p', '--pipeline', |
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178 help='CellProfiler pipeline' |
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179 ) |
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180 parser.add_argument( |
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181 '-i', '--inputs', |
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182 help='JSON inputs from Galaxy' |
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183 ) |
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184 args = parser.parse_args() |
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185 |
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186 pipeline_lines = get_pipeline_lines(args.pipeline) |
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187 inputs_galaxy = json.load(open(args.inputs, "r")) |
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188 |
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189 current_module_num = get_total_number_of_modules(pipeline_lines) |
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190 current_module_num += 1 |
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191 pipeline_lines = update_module_count(pipeline_lines, current_module_num) |
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192 |
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193 header_block = build_header(MODULE_NAME, current_module_num) |
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194 main_block = build_main_block(inputs_galaxy) |
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195 |
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196 module_pipeline = f"\n{header_block}{main_block}\n" |
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197 pipeline_lines.append(module_pipeline) |
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198 |
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199 write_pipeline(OUTPUT_FILENAME, pipeline_lines) |