--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/2d_feature_extraction.py	Wed Jan 16 15:32:39 2019 -0500
@@ -0,0 +1,124 @@
+import argparse
+import numpy as np
+import pandas as pd
+import tifffile
+import skimage.io
+import skimage.measure
+import skimage.feature
+import skimage.segmentation
+import skimage.morphology
+
+#TODO make importable by python script
+
+parser = argparse.ArgumentParser(description='Extract Features 2D')
+
+#TODO create factory for boilerplate code
+features = parser.add_argument_group('compute features')
+features.add_argument('--all', dest='all_features', action='store_true')
+features.add_argument('--label', dest='add_label', action='store_true')
+features.add_argument('--patches', dest='add_roi_patches', action='store_true')
+features.add_argument('--max_intensity', dest='max_intensity', action='store_true')
+features.add_argument('--mean_intensity', dest='mean_intensity', action='store_true')
+features.add_argument('--min_intensity', dest='min_intensity', action='store_true')
+features.add_argument('--moments_hu', dest='moments_hu', action='store_true')
+features.add_argument('--centroid', dest='centroid', action='store_true')
+features.add_argument('--bbox', dest='bbox', action='store_true')
+features.add_argument('--area', dest='area', action='store_true')
+features.add_argument('--filled_area', dest='filled_area', action='store_true')
+features.add_argument('--convex_area', dest='convex_area', action='store_true')
+features.add_argument('--perimeter', dest='perimeter', action='store_true')
+features.add_argument('--extent', dest='extent', action='store_true')
+features.add_argument('--eccentricity', dest='eccentricity', action='store_true')
+features.add_argument('--equivalent_diameter', dest='equivalent_diameter', action='store_true')
+features.add_argument('--euler_number', dest='euler_number', action='store_true')
+features.add_argument('--inertia_tensor_eigvals', dest='inertia_tensor_eigvals', action='store_true')
+features.add_argument('--major_axis_length', dest='major_axis_length', action='store_true')
+features.add_argument('--minor_axis_length', dest='minor_axis_length', action='store_true')
+features.add_argument('--orientation', dest='orientation', action='store_true')
+features.add_argument('--solidity', dest='solidity', action='store_true')
+features.add_argument('--moments', dest='moments', action='store_true')
+features.add_argument('--convexity', dest='convexity', action='store_true')
+
+parser.add_argument('--label_file_binary', dest='label_file_binary', action='store_true')
+
+parser.add_argument('--raw', dest='raw_file', type=argparse.FileType('r'),
+                   help='Original input file', required=False)
+parser.add_argument('label_file', type=argparse.FileType('r'),
+                   help='Label input file')
+parser.add_argument('output_file', type=argparse.FileType('w'),
+                   help='Tabular output file')
+args = parser.parse_args()
+
+label_file_binary = args.label_file_binary
+label_file = args.label_file.name
+out_file = args.output_file.name
+add_patch = args.add_roi_patches
+
+raw_image = None
+if args.raw_file is not None:
+    raw_image = skimage.io.imread(args.raw_file.name)
+
+raw_label_image = skimage.io.imread(label_file)
+
+df = pd.DataFrame()
+if label_file_binary:
+    raw_label_image = skimage.measure.label(raw_label_image)
+regions = skimage.measure.regionprops(raw_label_image, intensity_image=raw_image)
+
+df['it'] = np.arange(len(regions))
+
+if add_patch:
+    df['image'] = df['it'].map(lambda ait: regions[ait].image.astype(np.float).tolist())
+    df['intensity_image'] = df['it'].map(lambda ait: regions[ait].intensity_image.astype(np.float).tolist())
+
+#TODO no matrix features, but split in own rows?
+if args.add_label or args.all_features:
+    df['label'] = df['it'].map(lambda ait: regions[ait].label)
+
+if raw_image is not None:
+    if args.max_intensity or args.all_features:
+        df['max_intensity'] = df['it'].map(lambda ait: regions[ait].max_intensity)
+    if args.mean_intensity or args.all_features:
+        df['mean_intensity'] = df['it'].map(lambda ait: regions[ait].mean_intensity)
+    if args.min_intensity or args.all_features:
+        df['min_intensity'] = df['it'].map(lambda ait: regions[ait].min_intensity)
+    if args.moments_hu or args.all_features:
+        df['moments_hu'] = df['it'].map(lambda ait: regions[ait].moments_hu)
+
+if args.centroid or args.all_features:
+    df['centroid'] = df['it'].map(lambda ait: regions[ait].centroid)
+if args.bbox or args.all_features:
+    df['bbox'] = df['it'].map(lambda ait: regions[ait].bbox)
+if args.area or args.all_features:
+    df['area'] = df['it'].map(lambda ait: regions[ait].area)
+if args.filled_area or args.all_features:
+    df['filled_area'] = df['it'].map(lambda ait: regions[ait].filled_area)
+if args.convex_area or args.all_features:
+    df['convex_area'] = df['it'].map(lambda ait: regions[ait].convex_area)
+if args.perimeter or args.all_features:
+    df['perimeter'] = df['it'].map(lambda ait: regions[ait].perimeter)
+if args.extent or args.all_features:
+    df['extent'] = df['it'].map(lambda ait: regions[ait].extent)
+if args.eccentricity or args.all_features:
+    df['eccentricity'] = df['it'].map(lambda ait: regions[ait].eccentricity)
+if args.equivalent_diameter or args.all_features:
+    df['equivalent_diameter'] = df['it'].map(lambda ait: regions[ait].equivalent_diameter)
+if args.euler_number or args.all_features:
+    df['euler_number'] = df['it'].map(lambda ait: regions[ait].euler_number)
+if args.inertia_tensor_eigvals or args.all_features:
+    df['inertia_tensor_eigvals'] = df['it'].map(lambda ait: regions[ait].inertia_tensor_eigvals)
+if args.major_axis_length or args.all_features:
+    df['major_axis_length'] = df['it'].map(lambda ait: regions[ait].major_axis_length)
+if args.minor_axis_length or args.all_features:
+    df['minor_axis_length'] = df['it'].map(lambda ait: regions[ait].minor_axis_length)
+if args.orientation or args.all_features:
+    df['orientation'] = df['it'].map(lambda ait: regions[ait].orientation)
+if args.solidity or args.all_features:
+    df['solidity'] = df['it'].map(lambda ait: regions[ait].solidity)
+if args.moments or args.all_features:
+    df['moments'] = df['it'].map(lambda ait: regions[ait].moments)
+if args.convexity or args.all_features:
+    df['convexity'] = df.area/(df.perimeter*df.perimeter)
+
+del df['it']
+df.to_csv(out_file, sep='\t', line_terminator='\n', index=False)