def main(input_dir: pathlib.Path,
output_dir: pathlib.Path,
file_pattern: typing.Optional[str] = None,
group_by: typing.Optional[str] = None,
get_darkfield: typing.Optional[bool] = None,
get_photobleach: typing.Optional[bool] = None,
metadata_dir: pathlib.Path = None) -> None:
if group_by is None:
group_by = 'xyp'
if get_darkfield is None:
get_darkfield = False
if get_photobleach is None:
get_photobleach = False
if file_pattern is None:
filepattern = '.*'
fp = FilePattern(input_dir, file_pattern)
ProcessManager.init_processes("basic")
for files in fp(group_by=group_by):
ProcessManager.submit_process(basic.basic, files, output_dir,
metadata_dir, get_darkfield,
get_photobleach)
ProcessManager.join_processes()
def main(imgPath: pathlib.Path,
stitchPath: pathlib.Path,
outDir: pathlib.Path,
timesliceNaming: typing.Optional[bool]
) -> None:
'''Setup stitching variables/objects'''
# Get a list of stitching vectors
vectors = list(stitchPath.iterdir())
vectors.sort()
# Try to infer a filepattern from the files on disk for faster matching later
global fp # make the filepattern global to share between processes
try:
pattern = filepattern.infer_pattern([f.name for f in imgPath.iterdir()])
logger.info(f'Inferred file pattern: {pattern}')
fp = filepattern.FilePattern(imgPath,pattern)
# Pattern inference didn't work, so just get a list of files
except:
logger.info(f'Unable to infer pattern, defaulting to: .*')
fp = filepattern.FilePattern(imgPath,'.*')
'''Run stitching jobs in separate processes'''
ProcessManager.init_processes('main','asmbl')
for v in vectors:
# Check to see if the file is a valid stitching vector
if 'img-global-positions' not in v.name:
continue
ProcessManager.submit_process(assemble_image,v,outDir)
ProcessManager.join_processes()
def main(inpDir, outDir, projection, method):
# images in the input directory
inpDir_files = os.listdir(inpDir)
inpDir_files = [
filename for filename in inpDir_files if filename.endswith('.ome.tif')
]
# Surround with try/finally for proper error catching
try:
for image_name in inpDir_files:
input_img_path = os.path.join(inpDir, image_name)
output_img_path = os.path.join(outDir, image_name)
ProcessManager.submit_process(process_image, input_img_path,
output_img_path, projection, method)
ProcessManager.join_processes()
except Exception:
traceback.print_exc()
finally:
# Exit the program
logger.info('Exiting the workflow..')
sys.exit()
def main(imgDir: Path,
imgPattern: str,
ffDir: Path,
brightPattern: str,
outDir: Path,
darkPattern: typing.Optional[str] = None,
photoPattern: typing.Optional[str] = None) -> None:
''' Start a process for each set of brightfield/darkfield/photobleach patterns '''
# Create the FilePattern objects to handle file access
ff_files = FilePattern(ffDir, brightPattern)
fp = FilePattern(imgDir, imgPattern)
if darkPattern != None and darkPattern != '':
dark_files = FilePattern(ffDir, darkPattern)
if photoPattern != None and photoPattern != '':
photo_files = FilePattern(
str(Path(ffDir).parents[0].joinpath('metadata').absolute()),
photoPattern)
group_by = [v for v in fp.variables if v not in ff_files.variables]
GROUPED = group_by + ['file']
ProcessManager.init_processes('main', 'unshade')
for files in fp(group_by=group_by):
flat_path = ff_files.get_matching(
**{k.upper(): v
for k, v in files[0].items() if k not in GROUPED})[0]['file']
if flat_path is None:
logger.warning("Could not find a flatfield image, skipping...")
continue
if darkPattern is not None and darkPattern != '':
dark_path = dark_files.get_matching(**{
k.upper(): v
for k, v in files[0].items() if k not in GROUPED
})[0]['file']
if dark_path is None:
logger.warning("Could not find a darkfield image, skipping...")
continue
if photoPattern is not None and photoPattern != '':
photo_path = photo_files.get_matching(**{
k.upper(): v
for k, v in files[0].items() if k not in GROUPED
})[0]['file']
if photo_path is None:
logger.warning(
"Could not find a photobleach file, skipping...")
continue
ProcessManager.submit_process(unshade_batch, files, outDir, flat_path,
dark_path, photo_path)
ProcessManager.join_processes()
def main(
inpDir: Path,
outDir: Path,
) -> None:
ProcessManager.init_processes("main", "zarr")
for file in inpDir.iterdir():
ProcessManager.submit_process(image_to_zarr, file, outDir)
ProcessManager.join_processes()
def main(
inpDir: Path,
filePattern: str,
outDir: Path,
) -> None:
ProcessManager.init_processes("main", "zarr")
fp = FilePattern(inpDir, filePattern)
for files in fp():
for file in files:
ProcessManager.submit_process(image_to_zarr, file["file"], outDir)
ProcessManager.join_processes()
def main(input_dir: Path,
output_dir: Path
) -> None:
logger.info('Extracting tiffs and saving as ome.tif...')
files = [f for f in Path(input_dir).iterdir() if f.suffix=='.czi']
if not files:
logger.error('No CZI files found.')
raise ValueError('No CZI files found.')
ProcessManager.init_processes()
for file in files:
ProcessManager.submit_process(extract_fovs,file,output_dir)
ProcessManager.join_processes()
def main(input_dir: pathlib.Path,
file_pattern: str,
output_dir: pathlib.Path
) -> None:
# create the filepattern object
fp = filepattern.FilePattern(input_dir,file_pattern)
for files in fp(group_by='z'):
output_name = fp.output_name(files)
output_file = output_dir.joinpath(output_name)
ProcessManager.submit_process(_merge_layers,files,output_file)
ProcessManager.join_processes()
def main(input_dir: pathlib.Path, pyramid_type: str, image_type: str,
file_pattern: str, output_dir: pathlib.Path):
# Set ProcessManager config and initialize
ProcessManager.num_processes(multiprocessing.cpu_count())
ProcessManager.num_threads(2 * ProcessManager.num_processes())
ProcessManager.threads_per_request(1)
ProcessManager.init_processes('pyr')
logger.info('max concurrent processes = %s',
ProcessManager.num_processes())
# Parse the input file directory
fp = filepattern.FilePattern(input_dir, file_pattern)
group_by = ''
if 'z' in fp.variables and pyramid_type == 'Neuroglancer':
group_by += 'z'
logger.info(
'Stacking images by z-dimension for Neuroglancer precomputed format.'
)
elif 'c' in fp.variables and pyramid_type == 'Zarr':
group_by += 'c'
logger.info('Stacking channels by c-dimension for Zarr format')
elif 't' in fp.variables and pyramid_type == 'DeepZoom':
group_by += 't'
logger.info('Creating time slices by t-dimension for DeepZoom format.')
else:
logger.info(
f'Creating one pyramid for each image in {pyramid_type} format.')
depth = 0
depth_max = 0
image_dir = ''
processes = []
for files in fp(group_by=group_by):
# Create the output name for Neuroglancer format
if pyramid_type in ['Neuroglancer', 'Zarr']:
try:
image_dir = fp.output_name([file for file in files])
except:
pass
if image_dir in ['', '.*']:
image_dir = files[0]['file'].name
# Reset the depth
depth = 0
depth_max = 0
pyramid_writer = None
for file in files:
with bfio.BioReader(file['file'], max_workers=1) as br:
if pyramid_type == 'Zarr':
d_z = br.c
else:
d_z = br.z
depth_max += d_z
for z in range(d_z):
pyramid_args = {
'base_dir': output_dir.joinpath(image_dir),
'image_path': file['file'],
'image_depth': z,
'output_depth': depth,
'max_output_depth': depth_max,
'image_type': image_type
}
pw = PyramidWriter[pyramid_type](**pyramid_args)
ProcessManager.submit_process(pw.write_slide)
depth += 1
if pyramid_type == 'DeepZoom':
pw.write_info()
if pyramid_type in ['Neuroglancer', 'Zarr']:
if image_type == 'segmentation':
ProcessManager.join_processes()
pw.write_info()
ProcessManager.join_processes()