comparison keras_train_and_eval.py @ 4:9349ed2749c6 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb

3:01111436835d

import argparse
import json
import os
import pickle
import warnings
from itertools import chain

import joblib
import numpy as np
import pandas as pd
from galaxy_ml.externals.selene_sdk.utils import compute_score
from galaxy_ml.keras_galaxy_models import _predict_generator
from galaxy_ml.model_validations import train_test_split
from galaxy_ml.utils import (clean_params, get_main_estimator,
                             get_module, get_scoring, load_model, read_columns,
                             SafeEval, try_get_attr)
from scipy.io import mmread
from sklearn.metrics.scorer import _check_multimetric_scoring
from sklearn.model_selection import _search, _validation
from sklearn.model_selection._validation import _score
from sklearn.pipeline import Pipeline
from sklearn.utils import indexable, safe_indexing

_fit_and_score = try_get_attr("galaxy_ml.model_validations", "_fit_and_score")
setattr(_search, "_fit_and_score", _fit_and_score)
setattr(_validation, "_fit_and_score", _fit_and_score)

N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
CACHE_DIR = os.path.join(os.getcwd(), "cached")
del os
NON_SEARCHABLE = ("n_jobs", "pre_dispatch", "memory", "_path", "nthread", "callbacks")
ALLOWED_CALLBACKS = (
    "EarlyStopping",
    "TerminateOnNaN",
    "ReduceLROnPlateau",
    "CSVLogger",

        index_arr = np.arange(n_samples)
        test = index_arr[np.isin(groups, group_names)]
        train = index_arr[~np.isin(groups, group_names)]
        rval = list(
            chain.from_iterable(
                (safe_indexing(a, train), safe_indexing(a, test)) for a in new_arrays
            )
        )
    else:
        rval = train_test_split(*new_arrays, **kwargs)

        rval[pos * 2: 2] = [None, None]

    return rval


def _evaluate(y_true, pred_probas, scorer, is_multimetric=True):
    """output scores based on input scorer

    Parameters
    ----------
    y_true : array
        True label or target values
    pred_probas : array
        Prediction values, probability for classification problem
    scorer : dict
        dict of `sklearn.metrics.scorer.SCORER`
    is_multimetric : bool, default is True
    """
    if y_true.ndim == 1 or y_true.shape[-1] == 1:
        pred_probas = pred_probas.ravel()
        pred_labels = (pred_probas > 0.5).astype("int32")
        targets = y_true.ravel().astype("int32")
        if not is_multimetric:
            preds = (
                pred_labels
                if scorer.__class__.__name__ == "_PredictScorer"
                else pred_probas
            )
            score = scorer._score_func(targets, preds, **scorer._kwargs)

            return score
        else:
            scores = {}
            for name, one_scorer in scorer.items():
                preds = (
                    pred_labels
                    if one_scorer.__class__.__name__ == "_PredictScorer"
                    else pred_probas
                )
                score = one_scorer._score_func(targets, preds, **one_scorer._kwargs)
                scores[name] = score

    # TODO: multi-class metrics
    # multi-label
    else:
        pred_labels = (pred_probas > 0.5).astype("int32")
        targets = y_true.astype("int32")
        if not is_multimetric:
            preds = (
                pred_labels
                if scorer.__class__.__name__ == "_PredictScorer"
                else pred_probas
            )
            score, _ = compute_score(preds, targets, scorer._score_func)
            return score
        else:
            scores = {}
            for name, one_scorer in scorer.items():
                preds = (
                    pred_labels
                    if one_scorer.__class__.__name__ == "_PredictScorer"
                    else pred_probas
                )
                score, _ = compute_score(preds, targets, one_scorer._score_func)
                scores[name] = score

    return scores


def main(
    inputs,
    infile_estimator,
    infile1,
    infile2,
    outfile_result,
    outfile_object=None,
    outfile_weights=None,
    outfile_y_true=None,
    outfile_y_preds=None,
    groups=None,
    ref_seq=None,
    intervals=None,

):
    """
    Parameter
    ---------
    inputs : str
        File path to galaxy tool parameter

    infile_estimator : str
        File path to estimator

    infile1 : str
        File path to dataset containing features

    infile2 : str
        File path to dataset containing target values

    outfile_result : str
        File path to save the results, either cv_results or test result

    outfile_object : str, optional
        File path to save searchCV object

    outfile_weights : str, optional
        File path to save deep learning model weights

    outfile_y_true : str, optional
        File path to target values for prediction

    outfile_y_preds : str, optional
        File path to save deep learning model weights

    groups : str
        File path to dataset containing groups labels

    ref_seq : str
        File path to dataset containing genome sequence file

    intervals : str
        File path to dataset containing interval file

    targets : str
        File path to dataset compressed target bed file

    fasta_path : str
        File path to dataset containing fasta file
    """
    warnings.simplefilter("ignore")

    with open(inputs, "r") as param_handler:
        params = json.load(param_handler)

    #  load estimator
    with open(infile_estimator, "rb") as estimator_handler:
        estimator = load_model(estimator_handler)

    estimator = clean_params(estimator)

    # swap hyperparameter
    swapping = params["experiment_schemes"]["hyperparams_swapping"]

    else:
        infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
        loaded_df[df_key] = infile2

    y = read_columns(
        infile2, c=c, c_option=column_option, sep="\t", header=header, parse_dates=True
    )
    if len(y.shape) == 2 and y.shape[1] == 1:
        y = y.ravel()
    if input_type == "refseq_and_interval":
        estimator.set_params(data_batch_generator__features=y.ravel().tolist())

    if main_est.__class__.__name__ == "IRAPSClassifier":
        main_est.set_params(memory=memory)

    # handle scorer, convert to scorer dict
    scoring = params["experiment_schemes"]["metrics"]["scoring"]
    if scoring is not None:
        # get_scoring() expects secondary_scoring to be a comma separated string (not a list)
        # Check if secondary_scoring is specified
        secondary_scoring = scoring.get("secondary_scoring", None)
        if secondary_scoring is not None:
            # If secondary_scoring is specified, convert the list into comman separated string
            scoring["secondary_scoring"] = ",".join(scoring["secondary_scoring"])

    scorer = get_scoring(scoring)
    scorer, _ = _check_multimetric_scoring(estimator, scoring=scorer)

    # handle test (first) split
    test_split_options = params["experiment_schemes"]["test_split"]["split_algos"]

    if test_split_options["shuffle"] == "group":

        else:
            raise ValueError(
                "Stratified shuffle split is not " "applicable on empty target values!"
            )

    (
        X_train,
        X_test,
        y_train,
        y_test,
        groups_train,
        _groups_test,
    ) = train_test_split_none(X, y, groups, **test_split_options)

    exp_scheme = params["experiment_schemes"]["selected_exp_scheme"]

    # handle validation (second) split
    if exp_scheme == "train_val_test":

            X_train,
            X_val,
            y_train,
            y_val,
            groups_train,
            _groups_val,
        ) = train_test_split_none(X_train, y_train, groups_train, **val_split_options)

    # train and eval
    if hasattr(estimator, "validation_data"):
        if exp_scheme == "train_val_test":
            estimator.fit(X_train, y_train, validation_data=(X_val, y_val))
        else:
            estimator.fit(X_train, y_train, validation_data=(X_test, y_test))
    else:
        estimator.fit(X_train, y_train)

    if hasattr(estimator, "evaluate"):
        steps = estimator.prediction_steps
        batch_size = estimator.batch_size
        generator = estimator.data_generator_.flow(
            X_test, y=y_test, batch_size=batch_size
        )
        predictions, y_true = _predict_generator(
            estimator.model_, generator, steps=steps
        )
        scores = _evaluate(y_true, predictions, scorer, is_multimetric=True)

    else:
        if hasattr(estimator, "predict_proba"):
            predictions = estimator.predict_proba(X_test)
        else:
            predictions = estimator.predict(X_test)

        y_true = y_test
        scores = _score(estimator, X_test, y_test, scorer, is_multimetric=True)
    if outfile_y_true:
        try:
            pd.DataFrame(y_true).to_csv(outfile_y_true, sep="\t", index=False)
            pd.DataFrame(predictions).astype(np.float32).to_csv(
                outfile_y_preds,

                float_format="%g",
                chunksize=10000,
            )
        except Exception as e:
            print("Error in saving predictions: %s" % e)

    # handle output
    for name, score in scores.items():
        scores[name] = [score]
    df = pd.DataFrame(scores)
    df = df[sorted(df.columns)]
    df.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)

    memory.clear(warn=False)

    if outfile_object:
        main_est = estimator
        if isinstance(estimator, Pipeline):
            main_est = estimator.steps[-1][-1]

        if hasattr(main_est, "model_") and hasattr(main_est, "save_weights"):
            if outfile_weights:
                main_est.save_weights(outfile_weights)
            del main_est.model_
            del main_est.fit_params
            del main_est.model_class_
            if getattr(main_est, "validation_data", None):
                del main_est.validation_data
            if getattr(main_est, "data_generator_", None):
                del main_est.data_generator_

        with open(outfile_object, "wb") as output_handler:
            pickle.dump(estimator, output_handler, pickle.HIGHEST_PROTOCOL)


if __name__ == "__main__":
    aparser = argparse.ArgumentParser()
    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
    aparser.add_argument("-e", "--estimator", dest="infile_estimator")
    aparser.add_argument("-X", "--infile1", dest="infile1")
    aparser.add_argument("-y", "--infile2", dest="infile2")
    aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
    aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
    aparser.add_argument("-w", "--outfile_weights", dest="outfile_weights")
    aparser.add_argument("-l", "--outfile_y_true", dest="outfile_y_true")
    aparser.add_argument("-p", "--outfile_y_preds", dest="outfile_y_preds")
    aparser.add_argument("-g", "--groups", dest="groups")
    aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
    aparser.add_argument("-b", "--intervals", dest="intervals")

        args.infile_estimator,
        args.infile1,
        args.infile2,
        args.outfile_result,
        outfile_object=args.outfile_object,
        outfile_weights=args.outfile_weights,
        outfile_y_true=args.outfile_y_true,
        outfile_y_preds=args.outfile_y_preds,
        groups=args.groups,
        ref_seq=args.ref_seq,
        intervals=args.intervals,

4:9349ed2749c6

import argparse
import json
import os
import warnings
from itertools import chain

import joblib
import numpy as np
import pandas as pd
from galaxy_ml.keras_galaxy_models import (
    _predict_generator,
    KerasGBatchClassifier,
)
from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
from galaxy_ml.model_validations import train_test_split
from galaxy_ml.utils import (
    clean_params,
    gen_compute_scores,
    get_main_estimator,
    get_module,
    get_scoring,
    read_columns,
    SafeEval
)
from scipy.io import mmread
from sklearn.metrics._scorer import _check_multimetric_scoring
from sklearn.model_selection._validation import _score
from sklearn.utils import _safe_indexing, indexable

N_JOBS = int(os.environ.get("GALAXY_SLOTS", 1))
CACHE_DIR = os.path.join(os.getcwd(), "cached")
NON_SEARCHABLE = (
    "n_jobs",
    "pre_dispatch",
    "memory",
    "_path",
    "_dir",
    "nthread",
    "callbacks",
)
ALLOWED_CALLBACKS = (
    "EarlyStopping",
    "TerminateOnNaN",
    "ReduceLROnPlateau",
    "CSVLogger",

        index_arr = np.arange(n_samples)
        test = index_arr[np.isin(groups, group_names)]
        train = index_arr[~np.isin(groups, group_names)]
        rval = list(
            chain.from_iterable(
                (_safe_indexing(a, train), _safe_indexing(a, test)) for a in new_arrays
            )
        )
    else:
        rval = train_test_split(*new_arrays, **kwargs)

        rval[pos * 2: 2] = [None, None]

    return rval


def _evaluate_keras_and_sklearn_scores(
    estimator,
    data_generator,
    X,
    y=None,
    sk_scoring=None,
    steps=None,
    batch_size=32,
    return_predictions=False,
):
    """output scores for bother keras and sklearn metrics

    Parameters
    -----------
    estimator : object
        Fitted `galaxy_ml.keras_galaxy_models.KerasGBatchClassifier`.
    data_generator : object
        From `galaxy_ml.preprocessors.ImageDataFrameBatchGenerator`.
    X : 2-D array
        Contains indecies of images that need to be evaluated.
    y : None
        Target value.
    sk_scoring : dict
        Galaxy tool input parameters.
    steps : integer or None
        Evaluation/prediction steps before stop.
    batch_size : integer
        Number of samples in a batch
    return_predictions : bool, default is False
        Whether to return predictions and true labels.
    """
    scores = {}

    generator = data_generator.flow(X, y=y, batch_size=batch_size)
    # keras metrics evaluation
    # handle scorer, convert to scorer dict
    generator.reset()
    score_results = estimator.model_.evaluate_generator(generator, steps=steps)
    metrics_names = estimator.model_.metrics_names
    if not isinstance(metrics_names, list):
        scores[metrics_names] = score_results
    else:
        scores = dict(zip(metrics_names, score_results))

    if sk_scoring["primary_scoring"] == "default" and not return_predictions:
        return scores

    generator.reset()
    predictions, y_true = _predict_generator(estimator.model_, generator, steps=steps)

    # for sklearn metrics
    if sk_scoring["primary_scoring"] != "default":
        scorer = get_scoring(sk_scoring)
        if not isinstance(scorer, (dict, list)):
            scorer = [sk_scoring["primary_scoring"]]
        scorer = _check_multimetric_scoring(estimator, scoring=scorer)
        sk_scores = gen_compute_scores(y_true, predictions, scorer)
        scores.update(sk_scores)

    if return_predictions:
        return scores, predictions, y_true
    else:
        return scores, None, None


def main(
    inputs,
    infile_estimator,
    infile1,
    infile2,
    outfile_result,
    outfile_object=None,
    outfile_y_true=None,
    outfile_y_preds=None,
    groups=None,
    ref_seq=None,
    intervals=None,

):
    """
    Parameter
    ---------
    inputs : str
        File path to galaxy tool parameter.

    infile_estimator : str
        File path to estimator.

    infile1 : str
        File path to dataset containing features.

    infile2 : str
        File path to dataset containing target values.

    outfile_result : str
        File path to save the results, either cv_results or test result.

    outfile_object : str, optional
        File path to save searchCV object.

    outfile_y_true : str, optional
        File path to target values for prediction.

    outfile_y_preds : str, optional
        File path to save predictions.

    groups : str
        File path to dataset containing groups labels.

    ref_seq : str
        File path to dataset containing genome sequence file.

    intervals : str
        File path to dataset containing interval file.

    targets : str
        File path to dataset compressed target bed file.

    fasta_path : str
        File path to dataset containing fasta file.
    """
    warnings.simplefilter("ignore")

    with open(inputs, "r") as param_handler:
        params = json.load(param_handler)

    #  load estimator
    estimator = load_model_from_h5(infile_estimator)

    estimator = clean_params(estimator)

    # swap hyperparameter
    swapping = params["experiment_schemes"]["hyperparams_swapping"]

    else:
        infile2 = pd.read_csv(infile2, sep="\t", header=header, parse_dates=True)
        loaded_df[df_key] = infile2

    y = read_columns(
        infile2,
        c=c,
        c_option=column_option,
        sep="\t",
        header=header,
        parse_dates=True,
    )
    if len(y.shape) == 2 and y.shape[1] == 1:
        y = y.ravel()
    if input_type == "refseq_and_interval":
        estimator.set_params(data_batch_generator__features=y.ravel().tolist())

    if main_est.__class__.__name__ == "IRAPSClassifier":
        main_est.set_params(memory=memory)

    # handle scorer, convert to scorer dict
    scoring = params["experiment_schemes"]["metrics"]["scoring"]
    scorer = get_scoring(scoring)
    if not isinstance(scorer, (dict, list)):
        scorer = [scoring["primary_scoring"]]
    scorer = _check_multimetric_scoring(estimator, scoring=scorer)

    # handle test (first) split
    test_split_options = params["experiment_schemes"]["test_split"]["split_algos"]

    if test_split_options["shuffle"] == "group":

        else:
            raise ValueError(
                "Stratified shuffle split is not " "applicable on empty target values!"
            )

    X_train, X_test, y_train, y_test, groups_train, groups_test = train_test_split_none(
        X, y, groups, **test_split_options
    )

    exp_scheme = params["experiment_schemes"]["selected_exp_scheme"]

    # handle validation (second) split
    if exp_scheme == "train_val_test":

            X_train,
            X_val,
            y_train,
            y_val,
            groups_train,
            groups_val,
        ) = train_test_split_none(X_train, y_train, groups_train, **val_split_options)

    # train and eval
    if hasattr(estimator, "config") and hasattr(estimator, "model_type"):
        if exp_scheme == "train_val_test":
            estimator.fit(X_train, y_train, validation_data=(X_val, y_val))
        else:
            estimator.fit(X_train, y_train, validation_data=(X_test, y_test))
    else:
        estimator.fit(X_train, y_train)

    if isinstance(estimator, KerasGBatchClassifier):
        scores = {}
        steps = estimator.prediction_steps
        batch_size = estimator.batch_size
        data_generator = estimator.data_generator_

        scores, predictions, y_true = _evaluate_keras_and_sklearn_scores(
            estimator,
            data_generator,
            X_test,
            y=y_test,
            sk_scoring=scoring,
            steps=steps,
            batch_size=batch_size,
            return_predictions=bool(outfile_y_true),
        )

    else:
        scores = {}
        if hasattr(estimator, "model_") and hasattr(estimator.model_, "metrics_names"):
            batch_size = estimator.batch_size
            score_results = estimator.model_.evaluate(
                X_test, y=y_test, batch_size=batch_size, verbose=0
            )
            metrics_names = estimator.model_.metrics_names
            if not isinstance(metrics_names, list):
                scores[metrics_names] = score_results
            else:
                scores = dict(zip(metrics_names, score_results))

        if hasattr(estimator, "predict_proba"):
            predictions = estimator.predict_proba(X_test)
        else:
            predictions = estimator.predict(X_test)

        y_true = y_test
        sk_scores = _score(estimator, X_test, y_test, scorer)
        scores.update(sk_scores)

    # handle output
    if outfile_y_true:
        try:
            pd.DataFrame(y_true).to_csv(outfile_y_true, sep="\t", index=False)
            pd.DataFrame(predictions).astype(np.float32).to_csv(
                outfile_y_preds,

                float_format="%g",
                chunksize=10000,
            )
        except Exception as e:
            print("Error in saving predictions: %s" % e)
    # handle output
    for name, score in scores.items():
        scores[name] = [score]
    df = pd.DataFrame(scores)
    df = df[sorted(df.columns)]
    df.to_csv(path_or_buf=outfile_result, sep="\t", header=True, index=False)

    memory.clear(warn=False)

    if outfile_object:
        dump_model_to_h5(estimator, outfile_object)


if __name__ == "__main__":
    aparser = argparse.ArgumentParser()
    aparser.add_argument("-i", "--inputs", dest="inputs", required=True)
    aparser.add_argument("-e", "--estimator", dest="infile_estimator")
    aparser.add_argument("-X", "--infile1", dest="infile1")
    aparser.add_argument("-y", "--infile2", dest="infile2")
    aparser.add_argument("-O", "--outfile_result", dest="outfile_result")
    aparser.add_argument("-o", "--outfile_object", dest="outfile_object")
    aparser.add_argument("-l", "--outfile_y_true", dest="outfile_y_true")
    aparser.add_argument("-p", "--outfile_y_preds", dest="outfile_y_preds")
    aparser.add_argument("-g", "--groups", dest="groups")
    aparser.add_argument("-r", "--ref_seq", dest="ref_seq")
    aparser.add_argument("-b", "--intervals", dest="intervals")

        args.infile_estimator,
        args.infile1,
        args.infile2,
        args.outfile_result,
        outfile_object=args.outfile_object,
        outfile_y_true=args.outfile_y_true,
        outfile_y_preds=args.outfile_y_preds,
        groups=args.groups,
        ref_seq=args.ref_seq,
        intervals=args.intervals,