def main(
_opName: str,
_in1: Path,
_sigma: str,
_calibration: str,
_out: Path,
) -> None:
"""Initialize ImageJ"""
# Bioformats throws a debug message, disable the loci debugger to mute it
def disable_loci_logs():
DebugTools = scyjava.jimport("loci.common.DebugTools")
DebugTools.setRootLevel("WARN")
scyjava.when_jvm_starts(disable_loci_logs)
# This is the version of ImageJ pre-downloaded into the docker container
logger.info("Starting ImageJ...")
ij = imagej.init("sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4",
headless=True)
# ij_converter.ij = ij
logger.info("Loaded ImageJ version: {}".format(ij.getVersion()))
""" Validate and organize the inputs """
args = []
argument_types = []
arg_len = 0
# Validate opName
opName_values = [
"DefaultTubeness",
]
assert _opName in opName_values, "opName must be one of {}".format(
opName_values)
# Validate in1
in1_types = {
"DefaultTubeness": "RandomAccessibleInterval",
}
# Check that all inputs are specified
if _in1 is None and _opName in list(in1_types.keys()):
raise ValueError("{} must be defined to run {}.".format(
"in1", _opName))
elif _in1 != None:
in1_type = in1_types[_opName]
# switch to images folder if present
if _in1.joinpath("images").is_dir():
_in1 = _in1.joinpath("images").absolute()
args.append([f for f in _in1.iterdir() if f.is_file()])
arg_len = len(args[-1])
else:
argument_types.append(None)
args.append([None])
# Validate sigma
sigma_types = {
"DefaultTubeness": "double",
}
# Check that all inputs are specified
if _sigma is None and _opName in list(sigma_types.keys()):
raise ValueError("{} must be defined to run {}.".format(
"sigma", _opName))
else:
sigma = None
# Validate calibration
calibration_types = {
"DefaultTubeness": "double[]",
}
# Check that all inputs are specified
if _calibration is None and _opName in list(calibration_types.keys()):
raise ValueError("{} must be defined to run {}.".format(
"calibration", _opName))
else:
calibration = None
for i in range(len(args)):
if len(args[i]) == 1:
args[i] = args[i] * arg_len
""" Set up the output """
out_types = {
"DefaultTubeness": "IterableInterval",
}
""" Run the plugin """
try:
for ind, (in1_path, ) in enumerate(zip(*args)):
if in1_path != None:
# Load the first plane of image in in1 collection
logger.info("Processing image: {}".format(in1_path))
in1_br = BioReader(in1_path)
# Convert to appropriate numpy array
in1 = ij_converter.to_java(ij,
np.squeeze(in1_br[:, :, 0:1, 0, 0]),
in1_type)
metadata = in1_br.metadata
fname = in1_path.name
dtype = ij.py.dtype(in1)
if _sigma is not None:
sigma = ij_converter.to_java(ij, _sigma, sigma_types[_opName],
dtype)
if _calibration is not None:
calibration = ij_converter.to_java(ij, _calibration,
calibration_types[_opName],
dtype)
logger.info("Running op...")
if _opName == "DefaultTubeness":
out = ij.op().filter().tubeness(in1, sigma, calibration)
logger.info("Completed op!")
if in1_path != None:
in1_br.close()
# Saving output file to out
logger.info("Saving...")
out_array = ij_converter.from_java(ij, out, out_types[_opName])
bw = BioWriter(_out.joinpath(fname), metadata=metadata)
bw.Z = 1
bw.dtype = out_array.dtype
bw[:] = out_array.astype(bw.dtype)
bw.close()
except:
logger.error("There was an error, shutting down jvm before raising...")
raise
finally:
# Exit the program
logger.info("Shutting down jvm...")
del ij
jpype.shutdownJVM()
logger.info("Complete!")
def main(inpDir: Path, outDir: Path, filePattern: str = None) -> None:
""" Turn labels into flow fields.
Args:
inpDir: Path to the input directory
outDir: Path to the output directory
"""
# Use a gpu if it's available
use_gpu = torch.cuda.is_available()
if use_gpu:
dev = torch.device("cuda")
else:
dev = torch.device("cpu")
logger.info(f'Running on: {dev}')
# Determine the number of threads to run on
num_threads = max([cpu_count() // 2, 1])
logger.info(f'Number of threads: {num_threads}')
# Get all file names in inpDir image collection based on input pattern
if filePattern:
fp = filepattern.FilePattern(inpDir, filePattern)
inpDir_files = [file[0]['file'].name for file in fp()]
logger.info('Processing %d labels based on filepattern ' %
(len(inpDir_files)))
else:
inpDir_files = [f.name for f in Path(inpDir).iterdir() if f.is_file()]
# Loop through files in inpDir image collection and process
processes = []
if use_gpu:
executor = ThreadPoolExecutor(num_threads)
else:
executor = ProcessPoolExecutor(num_threads)
for f in inpDir_files:
br = BioReader(Path(inpDir).joinpath(f).absolute())
out_file = Path(outDir).joinpath(
f.replace('.ome', '_flow.ome').replace('.tif',
'.zarr')).absolute()
bw = BioWriter(out_file, metadata=br.metadata)
bw.C = 4
bw.dtype = np.float32
bw.channel_names = ['cell_probability', 'x', 'y', 'labels']
bw._backend._init_writer()
for z in range(br.Z):
for x in range(0, br.X, TILE_SIZE):
for y in range(0, br.Y, TILE_SIZE):
processes.append(
executor.submit(flow_thread,
Path(inpDir).joinpath(f).absolute(),
out_file, use_gpu, dev, x, y, z))
bw.close()
br.close()
done, not_done = wait(processes, 0)
logger.info(f'Percent complete: {100 * len(done) / len(processes):6.3f}%')
while len(not_done) > 0:
for r in done:
r.result()
done, not_done = wait(processes, 5)
logger.info(
f'Percent complete: {100 * len(done) / len(processes):6.3f}%')
executor.shutdown()