view 2d_feature_extraction.py @ 4:0a53256b48c6 draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_feature_extraction/ commit 6b687746bdb3d5d1fb11ecffd6dd1bf42dc2c38d

import argparse

import numpy as np
import pandas as pd
import skimage.feature
import skimage.io
import skimage.measure
import skimage.morphology
import skimage.segmentation

# 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:
    perimeter = df['it'].map(lambda ait: regions[ait].perimeter)
    area = df['it'].map(lambda ait: regions[ait].area)
    df['convexity'] = area / (perimeter * perimeter)

del df['it']
df.to_csv(out_file, sep='\t', line_terminator='\n', index=False)