Merge pull request #138 from jhlegarreta/AddBundleFeaturePopulationMa…

…thScript

ENH: Add bundle feature population math script

utilities/tests/test_wm_compute_bundle_feature_population_math.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+def test_help_option(script_runner):
+    ret = script_runner.run(
+        ["test_wm_compute_bundle_feature_population_math.py", "--help"])
+    assert ret.success

utilities/wm_compute_bundle_feature_population_math.py

@@ -0,0 +1,231 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""Compute bundle feature population math: computes the
+- difference
+- stats
+- sum
+
+for each bundle feature across participants according to the values contained in
+the provided CSV files.
+
+For the difference case, the first CSV file given is taken as the reference; for
+the sum case, only the streamline count addition is performed.
+"""
+
+import argparse
+import enum
+import os
+from pathlib import Path
+
+import pandas as pd
+
+
+relative_label = "relative"
+sum_label = "sum"
+underscore = "_"
+
+# ToDo
+# Think about the effects of dealing with NANs in the subtractions, stats, etc.
+
+
+class BundlePopulationMathOperation(enum.Enum):
+    DIFFERENCE = "difference"  # for each subject, with respect to a ref
+    STATS = "stats"  # across all subjects
+    SUM = "sum"  # for each subject, only the streamline count
+
+
+class WMABundleFeatureDataMap(enum.Enum):
+    BundleName = ("Name", str)
+    PointCount = ("Num_Points", int)
+    StreamlineCount = ("Num_Fibers", int)
+    MeanLength = ("Mean_Length", float)
+    EstimatedUncertaintyMean = ("EstimatedUncertainty.Mean", float)
+    FA1Mean = ("FA1.Mean", float)
+    FA2Mean = ("FA2.Mean", float)
+    FWMean = ("FreeWater.Mean", float)
+    # ToDo
+    # There is a typo in the HemisphereLocataion (vs. HemisphereLocation)
+    # column: eventually consider both.
+    # HemisphereLocataion.Mean can contain integers, and cannot be cast directly
+    # into integers; would need to do .astype(float).astype("Int64")
+    HemisphereLocationMean = ("HemisphereLocataion.Mean", float)
+    ClusterIdxMean = ("cluster_idx.Mean", float)
+    Trace1Mean = ("trace1.Mean", float)
+    Trace2Mean = ("trace2.Mean", str)
+
+    @staticmethod
+    def get_name(name):
+        return WMABundleFeatureDataMap(name).value[0]
+
+    @staticmethod
+    def get_type(name):
+        return WMABundleFeatureDataMap(name).value[1]
+
+    @staticmethod
+    def get_type_map():
+        type_map = dict(
+            map(
+                lambda x: x.value, WMABundleFeatureDataMap._member_map_.values()
+            )
+        )
+        # Drop the name
+        type_map.pop(
+            WMABundleFeatureDataMap.get_name(WMABundleFeatureDataMap.BundleName)
+        )
+
+        return type_map
+
+
+def compute_bundle_population_feature_diff(df_list):
+    return [df_list[0].subtract(elem, fill_value=0) for elem in df_list[1:]]
+
+
+def compute_bundle_population_feature_diff_relative(df_diff, def_ref):
+    # rel_change = (new_value – ref_value) / ref_value * 100
+    return [df.divide(def_ref).multiply(100) for df in df_diff]
+
+
+def compute_bundle_population_feature_sum(df_list):
+    column_name = WMABundleFeatureDataMap.get_name(WMABundleFeatureDataMap.StreamlineCount)
+    return [pd.DataFrame([df[column_name].sum()], columns=[column_name]) for df in df_list]
+
+
+def compute_bundle_population_feature_stats(df_list):
+    df = pd.concat(df_list)
+    column_name = WMABundleFeatureDataMap.get_name(WMABundleFeatureDataMap.BundleName)
+    return df.groupby(column_name).describe()
+
+
+def perform_bundle_population_operation(operation, df_list):
+
+    if operation == BundlePopulationMathOperation.DIFFERENCE:
+        return compute_bundle_population_feature_diff(df_list)
+    elif operation == BundlePopulationMathOperation.STATS:
+        return compute_bundle_population_feature_stats(df_list)
+    elif operation == BundlePopulationMathOperation.SUM:
+        return compute_bundle_population_feature_sum(df_list)
+    else:
+        raise NotImplementedError(
+           f"Unsupported operation:\nFound: {operation}\n"
+           f"Available: {list(BundlePopulationMathOperation.__members__)}"
+        )
+
+
+def cast_feature_data(df):
+
+    # Cast all columns to the appropriate types
+    type_map = WMABundleFeatureDataMap.get_type_map()
+    df = df.astype(type_map)
+
+    return df
+
+
+def clean_up_feature_data(df):
+
+    # Remove whitespaces from column names
+    df.columns = df.columns.str.rstrip(" ")
+    df.columns = df.columns.str.lstrip(" ")
+
+    # Strip the path from the "Name" column
+    column_name = WMABundleFeatureDataMap.get_name(WMABundleFeatureDataMap.BundleName)
+    df[column_name] = pd.Series([str(Path(path)).replace(str(Path(path).parent) + os.sep, "") for path in df[column_name]])
+    df[column_name] = pd.Series([str(Path(path)).replace(str(Path(path).suffix), "") for path in df[column_name]])
+    return df.set_index(column_name)
+
+
+def process_feature_data(df):
+
+    df = clean_up_feature_data(df)
+    return cast_feature_data(df)
+
+
+def _build_arg_parser():
+
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawTextHelpFormatter
+    )
+    parser.add_argument(
+        "operation",
+        help="Population feature math operation.",
+        type=BundlePopulationMathOperation,
+        choices=list(BundlePopulationMathOperation),
+    )
+    parser.add_argument(
+        "bundle_names_fname", help="Bundle names filename (*.txt).", type=Path
+    )
+    parser.add_argument(
+        "--out_fnames",
+        nargs="+",
+        help="Output TSV filenames (*.tsv).",
+        type=Path,
+    )
+    parser.add_argument(
+        "--in_feature_fnames", nargs="+", help="Input feature filenames (*.csv).", type=Path
+    )
+
+    return parser
+
+
+def _parse_args(parser):
+
+    args = parser.parse_args()
+
+    return args
+
+
+def main():
+
+    parser = _build_arg_parser()
+    args = _parse_args(parser)
+
+    with open(args.bundle_names_fname) as file:
+        bndl_names = [line.rstrip() for line in file]
+
+    # for bndl_name in bndl_names:
+
+    df_list = []
+    for fname in args.in_feature_fnames:
+
+        df = pd.read_csv(fname)
+
+        # Prepare the data
+        df = process_feature_data(df)
+
+        # ToDo
+        # Keep only the requested bundles
+
+        df_list.append(df)
+
+    df = perform_bundle_population_operation(args.operation, df_list)
+
+    sep = "\t"
+
+    # Compute the relative difference if applicable
+    if args.operation == BundlePopulationMathOperation.DIFFERENCE:
+        df_rel = compute_bundle_population_feature_diff_relative(df, df_list[0])
+
+        for _df, _df_rel, fname in zip(df, df_rel, args.out_fnames):
+            path = Path(fname).parent
+            stem = Path(fname).stem + underscore + relative_label
+            ext = Path(fname).suffix
+            _fname = Path(path, stem).with_suffix(ext)
+            _df_rel.to_csv(_fname, sep=sep)
+
+            _df.to_csv(fname, sep=sep)
+
+    elif args.operation == BundlePopulationMathOperation.STATS:
+        df.to_csv(args.out_fnames[0], sep=sep)
+    elif args.operation == BundlePopulationMathOperation.SUM:
+        for _df, fname in zip(df, args.out_fnames):
+            _df.to_csv(fname, sep=sep, index=False)
+
+    else:
+        raise NotImplementedError(
+           f"Unsupported operation:\nFound: {args.operation}\n"
+           f"Available: {list(BundlePopulationMathOperation.__members__)}"
+        )
+
+
+if __name__ == "__main__":
+    main()