def main(argv):
""""Convert a directory of tifs to an hdf5 stack."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_series2stack(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
series2stack(
args.inputdir,
args.regex,
args.element_size_um,
args.outlayout,
args.datatype,
args.chunksize,
args.dataslices,
args.usempi & ('mpi4py' in sys.modules),
args.outputformats,
args.outputpath,
args.save_steps,
args.protective,
)
def main(argv):
"""Fill holes in labels."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_fill_holes(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
fill_holes(
args.inputfile,
args.methods,
args.selem,
args.labelmask,
args.maskDS,
args.maskMM,
args.maskMX,
args.outputfile,
args.outputholes,
args.outputMA,
args.outputMM,
args.protective,
)
def main(argv):
"""Delete/split/merge/... labels in a labelvolume."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_remap_labels(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
remap_labels(
args.inputfile,
args.delete_labels,
args.delete_files,
args.except_files,
args.merge_labels,
args.merge_files,
args.split_labels,
args.split_files,
args.aux_labelvolume,
args.min_labelsize,
args.min_segmentsize,
args.keep_only_largest,
args.conncomp,
args.nifti_output,
args.nifti_transpose,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Convert/select/downscale/transpose/... an hdf5 dataset."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_stack2stack(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
stack2stack(
args.inputfile,
args.outputfile,
args.dset_name,
args.blockoffset,
args.datatype,
args.uint8conv,
args.inlayout,
args.outlayout,
args.element_size_um,
args.chunksize,
args.additional_outputs,
args.nzfills,
args.dataslices,
args.save_steps,
args.protective,
)
def main(argv):
"""Find labels that do not traverse through the volume."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_nodes_of_ranvier(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
nodes_of_ranvier(
args.inputfile,
args.min_labelsize,
args.remove_small_labels,
args.boundarymask,
args.merge_methods,
args.overlap_threshold,
args.data,
args.maskMM,
args.searchradius,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Merge blocks of data into a single hdf5 dataset."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_mergeblocks(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
mergeblocks(
args.inputfiles,
args.blockoffset,
args.blocksize,
args.margin,
args.fullsize,
args.is_labelimage,
args.relabel,
args.neighbourmerge,
args.save_fwmap,
args.blockreduce,
args.func,
args.datatype,
args.usempi & ('mpi4py' in sys.modules),
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Merge slice-wise overlapping labels."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_merge_slicelabels(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
if args.mode == "MAstitch":
evaluate_overlaps(
args.inputfile,
args.slicedim,
args.offsets,
args.threshold_overlap,
args.do_map_labels,
args.maskMM,
args.min_labelsize,
args.close,
args.relabel_from,
args.usempi & ('mpi4py' in sys.modules),
args.outputfile,
args.save_steps,
args.protective,
)
elif args.mode == "MAfwmap":
map_labels(
args.inputfile,
args.outputfile,
args.save_steps,
args.protective,
)
elif args.mode == "MAfilter":
filter_labels(
args.inputfile,
args.maskMM,
args.min_labelsize,
args.close,
args.relabel_from,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Convert dm3 files to other image formats."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_convert_dm3(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
convert_dm3(
args.inputdir,
args.outputdir,
args.save_steps,
args.protective,
)
def main(argv):
"""Correct attributes of a h5 dataset."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_correct_attributes(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
correct_attributes(
args.inputfile,
args.auxfile,
args.outlayout,
args.element_size_um,
)
def main(argv):
"""Combine volumes by addition."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_combine_vols(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
combine_vols(
args.inputfile,
args.volidxs,
args.outputfile,
args.protective,
)
def main(argv):
"""Filter nodes of ranvier."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_filter_NoR(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
filter_NoR(
args.inputfile,
args.input2D,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Compute segmentation statistics."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_seg_stats(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
seg_stats(
args.h5path_labelMA,
args.h5path_labelMF,
args.h5path_labelUA,
args.stats,
args.outputbasename,
args.protective,
)
def main(argv):
"""Label connected components."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_connected_components_clf(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
if args.mode == 'train':
CC_clf_train(
args.inputfile,
args.outputfile,
args.save_steps,
args.protective,
)
elif args.mode == 'test':
CC_clf_test(
args.classifierpath,
args.scalerpath,
args.basename,
args.map_propnames,
args.max_intensity_mb,
args.max_area,
args.inputfile,
args.outputfile,
args.maskfile,
args.save_steps,
args.protective,
)
if args.mode == 'map':
CC_clf_map(
args.inputfile,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Apply mapping of labelsets to a labelvolume."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_agglo_from_labelmask(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
agglo_from_labelmask(
args.inpufile,
args.labelvolume,
args.ratio_threshold,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Downsample volume by blockwise reduction."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_downsample_blockwise(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
downsample_blockwise(
args.inputfile,
args.blockreduce,
args.func,
args.dataslices,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Downsample a series of 2D images."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_downsample_slices(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
downsample_slices(
args.inputdir,
args.outputdir,
args.regex,
args.downsample_factor,
args.dataslices,
args.usempi & ('mpi4py' in sys.modules),
args.protective,
)
def main(argv):
""""Convert a directory of tifs to an hdf5 stack."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_splitblocks(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
splitblocks(
args.inputfile,
args.dset_name,
args.dataslices,
args.blocksize,
args.margin,
args.blockrange,
args.usempi & ('mpi4py' in sys.modules),
args.outputdir,
args.save_steps,
args.protective,
)
def main(argv):
"""Create thresholded hard segmentations."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_prob2mask(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
if args.step:
for thr in frange(args.step, 1.0, args.step):
prob2mask(
args.inputfile,
args.dataslices,
thr,
args.upper_threshold,
args.size,
args.dilation,
args.inputmask,
args.go2D,
args.outputfile.format(thr),
args.save_steps,
args.protective,
)
else:
prob2mask(
args.inputfile,
args.dataslices,
args.lower_threshold,
args.upper_threshold,
args.size,
args.dilation,
args.inputmask,
args.go2D,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Perform watershed on the intracellular space compartments."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_watershed_ics(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
watershed_ics(
args.inputfile,
args.masks,
args.seedimage,
args.seed_size,
args.lower_threshold,
args.upper_threshold,
args.invert,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Separate the myelin compartment into individual myelin sheaths."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser = parse.parse_separate_sheaths(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
separate_sheaths(
args.inputfile,
args.labelMM,
args.maskWS,
args.maskDS,
args.maskMM,
args.dilation_iterations,
args.distance,
args.sigmoidweighting,
args.margin,
args.outputfile,
args.save_steps,
args.protective,
)
def main(argv):
"""Label connected components."""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
parser = parse.parse_connected_components(parser)
parser = parse.parse_common(parser)
args = parser.parse_args()
if args.mode == '3D':
CC_3D(
args.inputfile,
args.maskDS,
args.min_size_maskMM,
args.min_area,
args.outputfile,
args.protective,
)
elif args.mode == '2D':
CC_2D(
args.inputfile,
args.maskDS,
args.slicedim,
args.usempi & ('mpi4py' in sys.modules),
args.outputfile,
args.protective,
)
elif args.mode == "2Dfilter":
criteria = (
args.min_area,
args.max_area,
args.max_intensity_mb,
args.max_eccentricity,
args.min_solidity,
args.min_euler_number,
args.min_extent
)
CC_2Dfilter(
args.inputfile,
args.map_propnames,
criteria,
args.maskMB,
args.slicedim,
args.usempi & ('mpi4py' in sys.modules),
args.outputfile,
args.protective,
)
elif args.mode == "2Dprops":
CC_2Dprops(
args.inputfile,
args.basename,
args.map_propnames,
args.usempi & ('mpi4py' in sys.modules),
args.outputfile,
args.protective,
)
elif args.mode == "2Dto3D":
CC_2Dto3D(
args.inputfile,
args.outputfile,
args.protective,
)
