def main(args):
args = CLIArgumentParser(xml_file).parse_args(args)
total_start_time = time.time()
print('\n>> CLI Parameters ...\n')
print(args)
if not os.path.isfile(args.inputImageFile):
raise IOError('Input image file does not exist.')
if len(args.reference_mu_lab) != 3:
raise ValueError('Reference Mean LAB should be a 3 element vector.')
if len(args.reference_std_lab) != 3:
raise ValueError('Reference Stddev LAB should be a 3 element vector.')
if len(args.analysis_roi) != 4:
raise ValueError('Analysis ROI must be a vector of 4 elements.')
if np.all(np.array(args.analysis_roi) == -1):
process_whole_image = True
else:
process_whole_image = False
#
# Initiate Dask client
#
print('\n>> Creating Dask client ...\n')
start_time = time.time()
c = cli_utils.create_dask_client(args)
print(c)
dask_setup_time = time.time() - start_time
print('Dask setup time = {}'.format(
cli_utils.disp_time_hms(dask_setup_time)))
#
# Read Input Image
#
print('\n>> Reading input image ... \n')
ts = large_image.getTileSource(args.inputImageFile)
ts_metadata = ts.getMetadata()
print(json.dumps(ts_metadata, indent=2))
is_wsi = ts_metadata['magnification'] is not None
#
# Compute tissue/foreground mask at low-res for whole slide images
#
if is_wsi and process_whole_image:
print('\n>> Computing tissue/foreground mask at low-res ...\n')
start_time = time.time()
im_fgnd_mask_lres, fgnd_seg_scale = \
cli_utils.segment_wsi_foreground_at_low_res(ts)
fgnd_time = time.time() - start_time
print('low-res foreground mask computation time = {}'.format(
cli_utils.disp_time_hms(fgnd_time)))
#
# Compute foreground fraction of tiles in parallel using Dask
#
tile_fgnd_frac_list = [1.0]
it_kwargs = {
'tile_size': {'width': args.analysis_tile_size},
'scale': {'magnification': args.analysis_mag},
}
if not process_whole_image:
it_kwargs['region'] = {
'left': args.analysis_roi[0],
'top': args.analysis_roi[1],
'width': args.analysis_roi[2],
'height': args.analysis_roi[3],
'units': 'base_pixels'
}
if is_wsi:
print('\n>> Computing foreground fraction of all tiles ...\n')
start_time = time.time()
num_tiles = ts.getSingleTile(**it_kwargs)['iterator_range']['position']
print('Number of tiles = {}'.format(num_tiles))
if process_whole_image:
tile_fgnd_frac_list = htk_utils.compute_tile_foreground_fraction(
args.inputImageFile, im_fgnd_mask_lres, fgnd_seg_scale,
**it_kwargs
)
else:
tile_fgnd_frac_list = np.full(num_tiles, 1.0)
num_fgnd_tiles = np.count_nonzero(
tile_fgnd_frac_list >= args.min_fgnd_frac)
percent_fgnd_tiles = 100.0 * num_fgnd_tiles / num_tiles
fgnd_frac_comp_time = time.time() - start_time
print('Number of foreground tiles = {0:d} ({1:2f}%%)'.format(
num_fgnd_tiles, percent_fgnd_tiles))
print('Tile foreground fraction computation time = {}'.format(
cli_utils.disp_time_hms(fgnd_frac_comp_time)))
#
# Compute reinhard stats for color normalization
#
src_mu_lab = None
src_sigma_lab = None
if is_wsi and process_whole_image:
print('\n>> Computing reinhard color normalization stats ...\n')
start_time = time.time()
src_mu_lab, src_sigma_lab = htk_cnorm.reinhard_stats(
args.inputImageFile, 0.01, magnification=args.analysis_mag)
rstats_time = time.time() - start_time
print('Reinhard stats computation time = {}'.format(
cli_utils.disp_time_hms(rstats_time)))
#
# Detect nuclei in parallel using Dask
#
print('\n>> Detecting nuclei ...\n')
start_time = time.time()
tile_nuclei_list = []
for tile in ts.tileIterator(**it_kwargs):
tile_position = tile['tile_position']['position']
if is_wsi and tile_fgnd_frac_list[tile_position] <= args.min_fgnd_frac:
continue
# detect nuclei
cur_nuclei_list = dask.delayed(detect_tile_nuclei)(
args.inputImageFile,
tile_position,
args, it_kwargs,
src_mu_lab, src_sigma_lab
)
# append result to list
tile_nuclei_list.append(cur_nuclei_list)
tile_nuclei_list = dask.delayed(tile_nuclei_list).compute()
nuclei_list = list(itertools.chain.from_iterable(tile_nuclei_list))
nuclei_detection_time = time.time() - start_time
print('Number of nuclei = {}'.format(len(nuclei_list)))
print('Nuclei detection time = {}'.format(
cli_utils.disp_time_hms(nuclei_detection_time)))
#
# Write annotation file
#
print('\n>> Writing annotation file ...\n')
annot_fname = os.path.splitext(
os.path.basename(args.outputNucleiAnnotationFile))[0]
annotation = {
"name": annot_fname + '-nuclei-' + args.nuclei_annotation_format,
"elements": nuclei_list
}
with open(args.outputNucleiAnnotationFile, 'w') as annotation_file:
json.dump(annotation, annotation_file, indent=2, sort_keys=False)
total_time_taken = time.time() - total_start_time
print('Total analysis time = {}'.format(
cli_utils.disp_time_hms(total_time_taken)))
import os
import pprint
from ctk_cli import CLIArgumentParser
import sys
def main(args):
print('>> parsed arguments')
pprint.pprint(vars(args))
if __name__ == '__main__':
if len(sys.argv) == 2:
if sys.argv[1] == '--json':
json_spec_file = os.path.splitext(sys.argv[0])[0] + '.json'
with open(json_spec_file) as f:
print(f.read())
sys.exit(0)
if sys.argv[1] == '--yaml':
yaml_spec_file = os.path.splitext(sys.argv[0])[0] + '.yaml'
with open(yaml_spec_file) as f:
print(f.read())
sys.exit(0)
main(CLIArgumentParser().parse_args())
import histomicstk.preprocessing.color_normalization as htk_cnorm
import histomicstk.preprocessing.color_deconvolution as htk_cdeconv
import histomicstk.utils as htk_utils
import large_image
from ctk_cli import CLIArgumentParser
import logging
logging.basicConfig(level=logging.CRITICAL)
from ..cli_common import utils as cli_utils # noqa
xml_file = os.path.join(os.path.dirname(__file__), 'NucleiDetection.xml')
default_args = CLIArgumentParser(xml_file).parse_args(['a', 'b'])
def detect_nuclei(im_tile, tile_info=None, args=None,
src_mu_lab=None, src_sigma_lab=None):
args = args or default_args
# perform color normalization
im_nmzd = htk_cnorm.reinhard(im_tile,
args.reference_mu_lab,
args.reference_std_lab,
src_mu=src_mu_lab,
src_sigma=src_sigma_lab)
# perform color decovolution
w = cli_utils.get_stain_matrix(args)