annotate keras_train_and_eval.py @ 47:6adef419e041 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5

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,
    KerasGClassifier,
    KerasGRegressor
)
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",
    "None",
)


def _eval_swap_params(params_builder):
    swap_params = {}

    for p in params_builder["param_set"]:
        swap_value = p["sp_value"].strip()
        if swap_value == "":
            continue

        param_name = p["sp_name"]
        if param_name.lower().endswith(NON_SEARCHABLE):
            warnings.warn(
                "Warning: `%s` is not eligible for search and was "
                "omitted!" % param_name
            )
            continue

        if not swap_value.startswith(":"):
            safe_eval = SafeEval(load_scipy=True, load_numpy=True)
            ev = safe_eval(swap_value)
        else:
            # Have `:` before search list, asks for estimator evaluatio
            safe_eval_es = SafeEval(load_estimators=True)
            swap_value = swap_value[1:].strip()
            # TODO maybe add regular express check
            ev = safe_eval_es(swap_value)

        swap_params[param_name] = ev

    return swap_params


def train_test_split_none(*arrays, **kwargs):
    """extend train_test_split to take None arrays
    and support split by group names.
    """
    nones = []
    new_arrays = []
    for idx, arr in enumerate(arrays):
        if arr is None:
            nones.append(idx)
        else:
            new_arrays.append(arr)

    if kwargs["shuffle"] == "None":
        kwargs["shuffle"] = None

    group_names = kwargs.pop("group_names", None)

    if group_names is not None and group_names.strip():
        group_names = [name.strip() for name in group_names.split(",")]
        new_arrays = indexable(*new_arrays)
        groups = kwargs["labels"]
        n_samples = new_arrays[0].shape[0]
        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)

    for pos in nones:
        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_history=None,
    outfile_object=None,
    outfile_y_true=None,
    outfile_y_preds=None,
    groups=None,
    ref_seq=None,
    intervals=None,
    targets=None,
    fasta_path=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_history : str, optional
        File path to save the training history.

    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"]
    swap_params = _eval_swap_params(swapping)
    estimator.set_params(**swap_params)
    estimator_params = estimator.get_params()
    # store read dataframe object
    loaded_df = {}

    input_type = params["input_options"]["selected_input"]
    # tabular input
    if input_type == "tabular":
        header = "infer" if params["input_options"]["header1"] else None
        column_option = params["input_options"]["column_selector_options_1"][
            "selected_column_selector_option"
        ]
        if column_option in [
            "by_index_number",
            "all_but_by_index_number",
            "by_header_name",
            "all_but_by_header_name",
        ]:
            c = params["input_options"]["column_selector_options_1"]["col1"]
        else:
            c = None

        df_key = infile1 + repr(header)
        df = pd.read_csv(infile1, sep="\t", header=header, parse_dates=True)
        loaded_df[df_key] = df

        X = read_columns(df, c=c, c_option=column_option).astype(float)
    # sparse input
    elif input_type == "sparse":
        X = mmread(open(infile1, "r"))

    # fasta_file input
    elif input_type == "seq_fasta":
        pyfaidx = get_module("pyfaidx")
        sequences = pyfaidx.Fasta(fasta_path)
        n_seqs = len(sequences.keys())
        X = np.arange(n_seqs)[:, np.newaxis]
        for param in estimator_params.keys():
            if param.endswith("fasta_path"):
                estimator.set_params(**{param: fasta_path})
                break
        else:
            raise ValueError(
                "The selected estimator doesn't support "
                "fasta file input! Please consider using "
                "KerasGBatchClassifier with "
                "FastaDNABatchGenerator/FastaProteinBatchGenerator "
                "or having GenomeOneHotEncoder/ProteinOneHotEncoder "
                "in pipeline!"
            )

    elif input_type == "refseq_and_interval":
        path_params = {
            "data_batch_generator__ref_genome_path": ref_seq,
            "data_batch_generator__intervals_path": intervals,
            "data_batch_generator__target_path": targets,
        }
        estimator.set_params(**path_params)
        n_intervals = sum(1 for line in open(intervals))
        X = np.arange(n_intervals)[:, np.newaxis]

    # Get target y
    header = "infer" if params["input_options"]["header2"] else None
    column_option = params["input_options"]["column_selector_options_2"][
        "selected_column_selector_option2"
    ]
    if column_option in [
        "by_index_number",
        "all_but_by_index_number",
        "by_header_name",
        "all_but_by_header_name",
    ]:
        c = params["input_options"]["column_selector_options_2"]["col2"]
    else:
        c = None

    df_key = infile2 + repr(header)
    if df_key in loaded_df:
        infile2 = loaded_df[df_key]
    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())
        y = None
    # end y

    # load groups
    if groups:
        groups_selector = (
            params["experiment_schemes"]["test_split"]["split_algos"]
        ).pop("groups_selector")

        header = "infer" if groups_selector["header_g"] else None
        column_option = groups_selector["column_selector_options_g"][
            "selected_column_selector_option_g"
        ]
        if column_option in [
            "by_index_number",
            "all_but_by_index_number",
            "by_header_name",
            "all_but_by_header_name",
        ]:
            c = groups_selector["column_selector_options_g"]["col_g"]
        else:
            c = None

        df_key = groups + repr(header)
        if df_key in loaded_df:
            groups = loaded_df[df_key]

        groups = read_columns(
            groups,
            c=c,
            c_option=column_option,
            sep="\t",
            header=header,
            parse_dates=True,
        )
        groups = groups.ravel()

    # del loaded_df
    del loaded_df

    # cache iraps_core fits could increase search speed significantly
    memory = joblib.Memory(location=CACHE_DIR, verbose=0)
    main_est = get_main_estimator(estimator)
    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)

    # We get 'None' back from the call to 'get_scoring()' if
    # the primary scoring is 'default'. Replace 'default' with
    # the default scoring for classification/regression (accuracy/r2)
    if scorer is None:
        if isinstance(estimator, KerasGClassifier):
            scorer = ['accuracy']
        if isinstance(estimator, KerasGRegressor):
            scorer = ['r2']

    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":
        test_split_options["labels"] = groups
    if test_split_options["shuffle"] == "stratified":
        if y is not None:
            test_split_options["labels"] = y
        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":
        val_split_options = params["experiment_schemes"]["val_split"]["split_algos"]

        if val_split_options["shuffle"] == "group":
            val_split_options["labels"] = groups_train
        if val_split_options["shuffle"] == "stratified":
            if y_train is not None:
                val_split_options["labels"] = y_train
            else:
                raise ValueError(
                    "Stratified shuffle split is not "
                    "applicable on empty target values!"
                )

        (
            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":
            history = estimator.fit(X_train, y_train, validation_data=(X_val, y_val))
        else:
            history = estimator.fit(X_train, y_train, validation_data=(X_test, y_test))
    else:
        history = estimator.fit(X_train, y_train)
    if "callbacks" in estimator_params:
        for cb in estimator_params["callbacks"]:
            if cb["callback_selection"]["callback_type"] == "CSVLogger":
                hist_df = pd.DataFrame(history.history)
                hist_df["epoch"] = np.arange(1, estimator_params["epochs"] + 1)
                epo_col = hist_df.pop('epoch')
                hist_df.insert(0, 'epoch', epo_col)
                hist_df.to_csv(path_or_buf=outfile_history, sep="\t", header=True, index=False)
                break
    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)

        # Un-do OHE of the validation labels
        if len(y_test.shape) == 2:
            rounded_test_labels = np.argmax(y_test, axis=1)
            y_true = rounded_test_labels
            sk_scores = _score(estimator, X_test, rounded_test_labels, scorer)
        else:
            y_true = y_test
            sk_scores = _score(estimator, X_test, y_true, 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,
                sep="\t",
                index=False,
                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("-hi", "--outfile_history", dest="outfile_history")
    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")
    aparser.add_argument("-t", "--targets", dest="targets")
    aparser.add_argument("-f", "--fasta_path", dest="fasta_path")
    args = aparser.parse_args()

    main(
        args.inputs,
        args.infile_estimator,
        args.infile1,
        args.infile2,
        args.outfile_result,
        outfile_history=args.outfile_history,
        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,
        targets=args.targets,
        fasta_path=args.fasta_path,
    )