# HG changeset patch # User imgteam # Date 1749321496 0 # Node ID 7d80eb2411fb04a013e3716ed51ad0aff6484cd2 # Parent 5224cc463a9765515d93c81fc1830a2e584928e9 planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ commit 01343602708de3cc7fa4986af9000adc36dd0651 diff -r 5224cc463a97 -r 7d80eb2411fb auto_threshold.py --- a/auto_threshold.py Sat Feb 19 15:16:52 2022 +0000 +++ b/auto_threshold.py Sat Jun 07 18:38:16 2025 +0000 @@ -1,47 +1,117 @@ """ -Copyright 2017-2022 Biomedical Computer Vision Group, Heidelberg University. +Copyright 2017-2024 Biomedical Computer Vision Group, Heidelberg University. Distributed under the MIT license. See file LICENSE for detail or copy at https://opensource.org/licenses/MIT - """ import argparse +import numpy as np import skimage.filters -import skimage.io import skimage.util -import tifffile +from giatools.image import Image + + +class DefaultThresholdingMethod: + + def __init__(self, thres, accept: list[str] | None = None, **kwargs): + self.thres = thres + self.accept = accept if accept else [] + self.kwargs = kwargs + + def __call__(self, image, *args, offset=0, **kwargs): + accepted_kwargs = self.kwargs.copy() + for key, val in kwargs.items(): + if key in self.accept: + accepted_kwargs[key] = val + thres = self.thres(image, *args, **accepted_kwargs) + return image > thres + offset + -thOptions = { - 'otsu': lambda img_raw, bz: skimage.filters.threshold_otsu(img_raw), - 'li': lambda img_raw, bz: skimage.filters.threshold_li(img_raw), - 'yen': lambda img_raw, bz: skimage.filters.threshold_yen(img_raw), - 'isodata': lambda img_raw, bz: skimage.filters.threshold_isodata(img_raw), +class ManualThresholding: + + def __call__(self, image, thres1: float, thres2: float | None, **kwargs): + if thres2 is None: + return image > thres1 + else: + thres1, thres2 = sorted((thres1, thres2)) + return skimage.filters.apply_hysteresis_threshold(image, thres1, thres2) + - 'loc_gaussian': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='gaussian'), - 'loc_median': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='median'), - 'loc_mean': lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method='mean') +th_methods = { + 'manual': ManualThresholding(), + + 'otsu': DefaultThresholdingMethod(skimage.filters.threshold_otsu), + 'li': DefaultThresholdingMethod(skimage.filters.threshold_li), + 'yen': DefaultThresholdingMethod(skimage.filters.threshold_yen), + 'isodata': DefaultThresholdingMethod(skimage.filters.threshold_isodata), + + 'loc_gaussian': DefaultThresholdingMethod(skimage.filters.threshold_local, accept=['block_size'], method='gaussian'), + 'loc_median': DefaultThresholdingMethod(skimage.filters.threshold_local, accept=['block_size'], method='median'), + 'loc_mean': DefaultThresholdingMethod(skimage.filters.threshold_local, accept=['block_size'], method='mean'), } -def auto_thresholding(in_fn, out_fn, th_method, block_size=5, dark_bg=True): - img = skimage.io.imread(in_fn) - th = thOptions[th_method](img, block_size) - if dark_bg: - res = img > th - else: - res = img <= th - tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res)) +def do_thresholding( + input_filepath: str, + output_filepath: str, + th_method: str, + block_size: int, + offset: float, + threshold1: float, + threshold2: float | None, + invert_output: bool, +): + assert th_method in th_methods, f'Unknown method "{th_method}"' + + # Load image + img_in = Image.read(input_filepath) + + # Perform thresholding + result = th_methods[th_method]( + image=img_in.data, + block_size=block_size, + offset=offset, + thres1=threshold1, + thres2=threshold2, + ) + if invert_output: + result = np.logical_not(result) + + # Convert to canonical representation for binary images + result = (result * 255).astype(np.uint8) + + # Write result + Image( + data=skimage.util.img_as_ubyte(result), + axes=img_in.axes, + ).normalize_axes_like( + img_in.original_axes, + ).write( + output_filepath, + ) if __name__ == "__main__": - parser = argparse.ArgumentParser(description='Automatic Image Thresholding') - parser.add_argument('im_in', help='Path to the input image') - parser.add_argument('im_out', help='Path to the output image (TIFF)') - parser.add_argument('th_method', choices=thOptions.keys(), help='Thresholding method') - parser.add_argument('block_size', type=int, default=5, help='Odd size of pixel neighborhood for calculating the threshold') - parser.add_argument('dark_bg', default=True, type=bool, help='True if background is dark') + parser = argparse.ArgumentParser(description='Automatic image thresholding') + parser.add_argument('input', type=str, help='Path to the input image') + parser.add_argument('output', type=str, help='Path to the output image (uint8)') + parser.add_argument('th_method', choices=th_methods.keys(), help='Thresholding method') + parser.add_argument('block_size', type=int, help='Odd size of pixel neighborhood for calculating the threshold') + parser.add_argument('offset', type=float, help='Offset of automatically determined threshold value') + parser.add_argument('threshold1', type=float, help='Manual threshold value') + parser.add_argument('--threshold2', type=float, help='Second manual threshold value (for hysteresis thresholding)') + parser.add_argument('--invert_output', default=False, action='store_true', help='Values below/above the threshold are labeled with 0/255 by default, and with 255/0 if this argument is used') args = parser.parse_args() - auto_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.dark_bg) + do_thresholding( + args.input, + args.output, + args.th_method, + args.block_size, + args.offset, + args.threshold1, + args.threshold2, + args.invert_output, + ) diff -r 5224cc463a97 -r 7d80eb2411fb auto_threshold.xml --- a/auto_threshold.xml Sat Feb 19 15:16:52 2022 +0000 +++ b/auto_threshold.xml Sat Jun 07 18:38:16 2025 +0000 @@ -1,54 +1,186 @@ - - applies a standard thresholding algorithm to an image - - scikit-image - tifffile - - - - - + + with scikit-image + + creators.xml + tests.xml + 0.25.0 + 0 + + + + + + + + + operation_3443 + + + scikit-image + scikit-image + + + scikit-image + giatools + + + + + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + + - - - - - + + + + + + + + + + + + + + + + + + + + + + - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - Applies a standard thresholding algorithm to an image. + + **Applies a standard thresholding algorithm to a 2-D single-channel image. Yields a binary image.** + + The thresholding algorithm automatically determines a threshold value (unless manual thresholding is used). + The input image is then thresholded, by assigning white (pixel value 255) to image regions above the determined threshold, + and black (pixel value 0) to image regions below or equal to the determined threshold. + + The assignment of black and white to image regions below and above the threshold is inverted, if the corresponding option is set. + 10.1016/j.jbiotec.2017.07.019 diff -r 5224cc463a97 -r 7d80eb2411fb creators.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/creators.xml Sat Jun 07 18:38:16 2025 +0000 @@ -0,0 +1,33 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out.tif Binary file test-data/out.tif has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out1.tiff Binary file test-data/out1.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out2.tif Binary file test-data/out2.tif has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out2.tiff Binary file test-data/out2.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out3.tiff Binary file test-data/out3.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out4.tiff Binary file test-data/out4.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/out5.tiff Binary file test-data/out5.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/rgb.png Binary file test-data/rgb.png has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/rgb_otsu.tiff Binary file test-data/rgb_otsu.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/sample.tif Binary file test-data/sample.tif has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/sample.tiff Binary file test-data/sample.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/sample2.tiff Binary file test-data/sample2.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb test-data/sample_manual_180_240.tiff Binary file test-data/sample_manual_180_240.tiff has changed diff -r 5224cc463a97 -r 7d80eb2411fb tests.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tests.xml Sat Jun 07 18:38:16 2025 +0000 @@ -0,0 +1,95 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +