global VolatileUnsignedByteType
VolatileUnsignedByteType = scyjava.jimport('net.imglib2.type.volatiles.VolatileUnsignedByteType')
global VolatileShortType
VolatileShortType = scyjava.jimport('net.imglib2.type.volatiles.VolatileShortType')
global VolatileUnsignedShortType
VolatileUnsignedShortType = scyjava.jimport('net.imglib2.type.volatiles.VolatileUnsignedShortType')
global VolatileIntType
VolatileIntType = scyjava.jimport('net.imglib2.type.volatiles.VolatileIntType')
global VolatileUnsignedIntType
VolatileUnsignedIntType = scyjava.jimport('net.imglib2.type.volatiles.VolatileUnsignedIntType')
global VolatileLongType
VolatileLongType = scyjava.jimport('net.imglib2.type.volatiles.VolatileLongType')
global VolatileUnsignedLongType
VolatileUnsignedLongType = scyjava.jimport('net.imglib2.type.volatiles.VolatileUnsignedLongType')
scyjava.when_jvm_starts(_java_setup)
def for_np_dtype(dtype, volatile=False):
scyjava.start_jvm()
if dtype == np.uint8:
return VolatileUnsignedByteType() if volatile else UnsignedByteType()
if dtype == np.int8:
return VolatileByteType() if volatile else ByteType()
if dtype == np.uint16:
return VolatileUnsignedShortType() if volatile else UnsignedShortType()
if dtype == np.int16:
return VolatileShortType() if volatile else ShortType()
if dtype == np.uint32:
import imagej
import scyjava
import traceback
import sys
import imglyb
import jpype
import numpy as np
from bfio import BioReader, BioWriter
from pathlib import Path
# 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)
print("Starting JVM...")
# This is the version of ImageJ pre-downloaded into the docker container
ij = imagej.init("sc.fiji:fiji:2.1.1+net.imagej:imagej-legacy:0.37.4",
headless=True)
# ArrayImgs = scyjava.jimport('net.imglib2.img.array.ArrayImgs')
# UnsafeUtil = scyjava.jimport('net.imglib2.img.basictypelongaccess.unsafe.UnsafeUtil')
# Arrays = scyjava.jimport('java.util.Arrays')
# OwningFloatUnsafe = scyjava.jimport('net.imglib2.img.basictypelongaccess.unsafe.owning.OwningFloatUnsafe')
# Fraction = scyjava.jimport('net.imglib2.util.Fraction')
# LongStream = scyjava.jimport('java.util.stream.LongStream')
NUMPY_TYPES = {
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!")
