comparison coordinates_of_roi.py @ 1:ee045a6bbdef draft

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tools/coordinates_of_roi/ commit 4efef27bbe105490fc125e3586024ebb51fa929f

0:0d30ffea8874

    data = skimage.io.imread(im)
    if len(data.shape) == 3 and data.shape[-1] > 1:
        data = skimage.color.rgb2grey(data)
    x = []
    y = []
    for i in range(data.shape[0]):
        for j in range(data.shape[1]):
            if white_obj == False:
                if data[i,j] <= threshold:
                    x.append(j + offset[0])
                    y.append(i + offset[1])
            elif data[i,j] >= threshold:
                    x.append(j + offset[0])
                    y.append(i + offset[1])
                    
    df = pd.DataFrame()
    df['x'] = x
    df['y'] = y
    df.to_csv(pixel_table, sep="\t", index = False)

1:ee045a6bbdef

    data = skimage.io.imread(im)
    if len(data.shape) == 3 and data.shape[-1] > 1:
        data = skimage.color.rgb2grey(data)
    x = []
    y = []
    img_height = data.shape[0]
    img_width = data.shape[1]
    for j in range(img_width):
        for i in range(img_height):
            if white_obj == False:
                if data[i,j] <= threshold:
                    x.append(j + offset[0])
                    y.append(img_height-(i+1) + offset[1])
            elif data[i,j] >= threshold:
                    x.append(j + offset[0])
                    y.append(img_height-(i+1) + offset[1])
                    
    df = pd.DataFrame()
    df['x'] = x
    df['y'] = y
    df.to_csv(pixel_table, sep="\t", index = False)