def test_get_region_dict(self):
ts = large_image.getTileSource(os.path.join(TEST_DATA_DIR,
'Easy1.png'))
result = cli_utils.get_region_dict([-1, -1, -1, -1], 2000, ts)
expected = {}
assert result == expected, "Expected {}, got {}".format(
expected, result)
result = cli_utils.get_region_dict([100, 110, 250, 240], 500, ts)
expected = dict(region=dict(left=100, top=110, width=250, height=240))
assert result == expected, "Expected {}, got {}".format(
expected, result)
def main(args):
# Read Input Image
print('>> Reading input image')
print(args.inputImageFile)
ts = large_image.getTileSource(args.inputImageFile)
im_input = ts.getRegion(format=large_image.tilesource.TILE_FORMAT_NUMPY,
**utils.get_region_dict(args.region,
args.maxRegionSize, ts))[0]
# Create stain matrix
print('>> Creating stain matrix')
w = utils.get_stain_matrix(args)
print w
# Perform color deconvolution
print('>> Performing color deconvolution')
im_stains = htk_cd.color_deconvolution(im_input, w).Stains
# write stain images to output
print('>> Outputting individual stain images')
print args.outputStainImageFile_1
skimage.io.imsave(args.outputStainImageFile_1, im_stains[:, :, 0])
print args.outputStainImageFile_2
skimage.io.imsave(args.outputStainImageFile_2, im_stains[:, :, 1])
print args.outputStainImageFile_3
skimage.io.imsave(args.outputStainImageFile_3, im_stains[:, :, 2])
def main(args):
utils.create_dask_client(args)
ts = large_image.getTileSource(args.inputImageFile)
make_label_image = args.outputLabelImage is not None
region = utils.get_region_dict(
args.region,
*(args.maxRegionSize, ts) if make_label_image else ()).get('region')
ppc_params = ppc.Parameters(
**{k: getattr(args, k)
for k in ppc.Parameters._fields})
results = ppc.count_slide(
args.inputImageFile,
ppc_params,
region,
args.tile_grouping,
make_label_image,
)
if make_label_image:
stats, label_image = results
# Colorize label image. Colors from the "coolwarm" color map
color_map = np.empty((4, 3), dtype=np.uint8)
color_map[ppc.Labels.NEGATIVE] = 255
color_map[ppc.Labels.WEAK] = 60, 78, 194
color_map[ppc.Labels.PLAIN] = 221, 220, 220
color_map[ppc.Labels.STRONG] = 180, 4, 38
# Cleverly index color_map
label_image = color_map[label_image]
skimage.io.imsave(args.outputLabelImage, label_image)
else:
stats, = results
with open(args.returnParameterFile, 'w') as f:
for k, v in zip(stats._fields, stats):
f.write('{} = {}\n'.format(k, v))
def main(args):
utils.create_dask_client(args)
ts = large_image.getTileSource(args.inputImageFile)
kwargs = dict(format=large_image.tilesource.TILE_FORMAT_NUMPY)
makeLabelImage = args.outputLabelImage is not None
kwargs.update(utils.get_region_dict(
args.region,
*(args.maxRegionSize, ts) if makeLabelImage else ()
))
if makeLabelImage:
tile = ts.getRegion(**kwargs)[0]
results, labelImage = positive_pixel_count_single_tile(
args, tile, makeLabelImage=True)
skimage.io.imsave(args.outputLabelImage, labelImage)
else:
results = []
total_tiles = ts.getSingleTile(**kwargs)['iterator_range']['position']
for position in range(0, total_tiles, args.tile_grouping):
results.append(delayed(positive_pixel_count_tiles)(
args, kwargs, position,
min(args.tile_grouping, total_tiles - position)))
results = delayed(combine)(results).compute()
r = results
total_all_positive = sum(r[k] for k in results_num_keys)
output = (
[(k, r[k]) for k in results_keys] +
[('IntensityAverage',
sum(r[k] for k in results_i_keys) / total_all_positive),
('RatioStrongToTotal',
float(r['NumberStrongPositive']) / total_all_positive),
('IntensityAverageWeakAndPositive',
(r['IntensitySumWeakPositive'] + r['IntensitySumPositive']) /
(r['NumberWeakPositive'] + r['NumberPositive']))]
)
with open(args.returnParameterFile, 'w') as f:
for k, v in output:
f.write('{} = {}\n'.format(k, v))