comparison points2label.py @ 2:30ca5d5d03ec draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/points2labelimage/ commit 2286a6c9da88596349ed9d967c51541409c0a7bf

1:9bd039f46843

import argparse
import sys
import numpy as np
import skimage.io
import pandas as pd 
import warnings

def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
    labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)

    if is_TSV:

        else:
            df = pd.read_csv(labels, header=None)

    for i in range(0, len(df)):
        a_row = df.iloc[i]
        labelimg[a_row[0], a_row[1]] = i+1

    if output_file is not None:
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            skimage.io.imsave(output_file, labelimg, plugin='tifffile')
    else:
        return labelimg

if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
    parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')

2:30ca5d5d03ec

import argparse
import sys
import warnings

import numpy as np
import pandas as pd
import skimage.io


def points2label(labels, shape, output_file=None, has_header=False, is_TSV=True):
    labelimg = np.zeros([shape[0], shape[1]], dtype=np.int32)

    if is_TSV:

        else:
            df = pd.read_csv(labels, header=None)

    for i in range(0, len(df)):
        a_row = df.iloc[i]
        labelimg[a_row[0], a_row[1]] = i + 1

    if output_file is not None:
        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            skimage.io.imsave(output_file, labelimg, plugin='tifffile')
    else:
        return labelimg


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument('label_file', type=argparse.FileType('r'), default=sys.stdin, help='label file')
    parser.add_argument('out_file', type=argparse.FileType('w'), default=sys.stdin, help='out file')