def segment_images(inpDir, outDir, config_data):
""" Workflow for data with similar morphology
as sialyltransferase 1.
Args:
inpDir : path to the input directory
outDir : path to the output directory
config_data : path to the configuration file
"""
logging.basicConfig(format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
datefmt='%d-%b-%y %H:%M:%S')
logger = logging.getLogger("main")
logger.setLevel(logging.INFO)
inpDir_files = os.listdir(inpDir)
for i,f in enumerate(inpDir_files):
logger.info('Segmenting image : {}'.format(f))
# Load image
br = BioReader(os.path.join(inpDir,f))
image = br.read_image()
structure_channel = 0
struct_img0 = image[:,:,:,structure_channel,0]
struct_img0 = struct_img0.transpose(2,0,1).astype(np.float32)
# main algorithm
intensity_scaling_param = config_data['intensity_scaling_param']
struct_img = intensity_normalization(struct_img0, scaling_param=intensity_scaling_param)
gaussian_smoothing_sigma = config_data['gaussian_smoothing_sigma']
structure_img_smooth = image_smoothing_gaussian_3d(struct_img, sigma=gaussian_smoothing_sigma)
global_thresh_method = config_data['global_thresh_method']
object_minArea = config_data['object_minArea']
bw, object_for_debug = MO(structure_img_smooth, global_thresh_method=global_thresh_method, object_minArea=object_minArea, return_object=True)
thin_dist_preserve = config_data['thin_dist_preserve']
thin_dist = config_data['thin_dist']
bw_thin = topology_preserving_thinning(bw>0, thin_dist_preserve, thin_dist)
s3_param = config_data['s3_param']
bw_extra = dot_3d_wrapper(structure_img_smooth, s3_param)
bw_combine = np.logical_or(bw_extra>0, bw_thin)
minArea = config_data['minArea']
seg = remove_small_objects(bw_combine>0, min_size=minArea, connectivity=1, in_place=False)
seg = seg > 0
out_img=seg.astype(np.uint8)
out_img[out_img>0]=255
# create output image
out_img = out_img.transpose(1,2,0)
out_img = out_img.reshape((out_img.shape[0], out_img.shape[1], out_img.shape[2], 1, 1))
# write image using BFIO
bw = BioWriter(os.path.join(outDir,f), metadata=br.read_metadata())
bw.num_x(out_img.shape[1])
bw.num_y(out_img.shape[0])
bw.num_z(out_img.shape[2])
bw.num_c(out_img.shape[3])
bw.num_t(out_img.shape[4])
bw.pixel_type(dtype='uint8')
bw.write_image(out_img)
bw.close_image()
def create_and_write_output(predictions_path, output_path, inpDir):
"""
This script uses the bfio utility to write the output.
Inputs:
predictions_path: The directory in which the neural networks writes its 3 channel output
output_path: The directory in which the user wants the final binary output
inpDir: The input directory consisting of the input collection
"""
filenames = sorted(os.listdir(predictions_path))
for filename in filenames:
# read the 3 channel output image from the neural network
image = cv2.imread(os.path.join(predictions_path, filename))
# create binary image output using the create_binary function
out_image = create_binary(image)
# read and store the metadata from the input image
with BioReader(os.path.join(inpDir, filename)) as br:
metadata = br.metadata
# Write the binary output consisting of the metadata using bfio.
output_image_5channel = np.zeros(
(out_image.shape[0], out_image.shape[1], 1, 1, 1), dtype=np.uint8)
output_image_5channel[:, :, 0, 0, 0] = out_image
with BioWriter(os.path.join(output_path, filename),
metadata=metadata) as bw:
bw.dtype = output_image_5channel.dtype
bw.write(output_image_5channel)
def write_to(self, outfile: Path):
""" Writes a labelled ome.tif to the given path.
This uses the metadata of the input file and sets the dtype depending on the number of labelled objects.
Args:
outfile: Path where the labelled image will be written.
"""
with BioWriter(outfile, metadata=self.metadata, max_workers=cpu_count()) as writer:
writer.dtype = self.dtype()
logger.info(f'writing {outfile.name} with dtype {self.dtype()}...')
tile_size, _, num_cols, num_rows = self._get_iteration_params(writer.Z, writer.Y, writer.X)
tile_count = 0
for z in range(writer.Z):
for y in range(0, writer.Y, tile_size):
y_max = min(writer.Y, y + tile_size)
for x in range(0, writer.X, tile_size):
x_max = min(writer.X, x + tile_size)
tile = extract_tile(self.__polygon_set, (z, z + 1, y, y_max, x, x_max))
writer[y:y_max, x:x_max, z:z + 1, 0, 0] = tile.transpose(1, 2, 0)
tile_count += 1
logger.debug(f'Wrote tile {tile_count}, ({z}, {y}:{y_max}, {x}:{x_max})')
logger.info(f'Writing Progress {100 * tile_count / (num_cols * num_rows * writer.Z):6.3f}%...')
return self
def test_correctness(self):
# calculate the result with the plugin code
with BioReader(self.infile.name) as reader:
with BioWriter(self.outfile.name,
metadata=reader.metadata) as writer:
rolling_ball(
reader=reader,
writer=writer,
ball_radius=self.ball_radius,
light_background=False,
)
# read the image we just wrote into a numpy array
with BioReader(self.outfile.name) as reader:
plugin_result = reader[:]
# calculate the true result
background = restoration.rolling_ball(self.random_image,
radius=self.ball_radius)
true_result = self.random_image - background
# assert correctness
self.assertTrue(numpy.all(numpy.equal(true_result, plugin_result)),
f'The plugin resulted in a different image')
return
def unshade_image(img,
out_dir,
brightfield,
darkfield,
photobleach=None,
offset=None):
with ProcessManager.thread() as active_threads:
with BioReader(img, max_workers=active_threads.count) as br:
with BioWriter(out_dir.joinpath(img.name),
metadata=br.metadata,
max_workers=active_threads.count) as bw:
new_img = br[:, :, :1, 0, 0].squeeze().astype(np.float32)
new_img = new_img - darkfield
new_img = np.divide(new_img, brightfield)
if photobleach != None:
new_img = new_img - np.float32(photobleach)
if offset != None:
new_img = new_img + np.float32(offset)
new_img[new_img < 0] = 0
new_img = new_img.astype(br.dtype)
bw[:] = new_img
def read_file(input_directory, pixelsize, output_directory):
img_pixelsize_x = pixelsize
img_pixelsize_y = pixelsize
modelfile_path = "2d_cell_net_v0-cytoplasm.modeldef.h5"
weightfile_path = "snapshot_cytoplasm_iter_1000.caffemodel.h5"
iofile_path = "output.h5"
out_path = Path(output_directory)
rootdir1 = Path(input_directory)
""" Convert the tif to tiled tiff """
javabridge.start_vm(args=["-Dlog4j.configuration=file:{}".format(LOG4J)],
class_path=JARS,
run_headless=True)
i = 0
try:
for PATH in rootdir1.glob('**/*'):
tile_grid_size = 1
tile_size = tile_grid_size * 1024
# Set up the BioReader
with BioReader(PATH, backend='java',
max_workers=cpu_count()) as br:
# Loop through timepoints
for t in range(br.T):
# Loop through channels
for c in range(br.C):
with BioWriter(out_path.joinpath(f"final{i}.ome.tif"),
metadata=br.metadata,
backend='java') as bw:
# Loop through z-slices
for z in range(br.Z):
# Loop across the length of the image
for y in range(0, br.Y, tile_size):
y_max = min([br.Y, y + tile_size])
# Loop across the depth of the image
for x in range(0, br.X, tile_size):
x_max = min([br.X, x + tile_size])
input_img = np.squeeze(br[y:y_max,
x:x_max,
z:z + 1, c,
t])
img = unet_segmentation(
input_img, img_pixelsize_x,
img_pixelsize_y, modelfile_path,
weightfile_path, iofile_path)
bw[y:y_max, x:x_max, ...] = img
os.remove("output.h5")
i += 1
finally:
# Close the javabridge. Since this is in the finally block, it is always run
javabridge.kill_vm()
def init_zarr_file(path: Path, metadata: Any):
with BioWriter(path, metadata=metadata) as writer:
writer.dtype = numpy.uint32
writer.C = 1
writer.channel_names = ['label']
# noinspection PyProtectedMember
writer._backend._init_writer()
return
def close_thread(dependency: Future,
bw: BioWriter):
""" Close an image once the final tile is written
Args:
dependency (Future): The final tile thread
bw (BioWriter): The BioWriter to clsoe
Returns:
Returns True when completed
"""
dependency.result()
bw.close()
return True
def setUpClass(cls) -> None:
cls.infile = tempfile.NamedTemporaryFile(suffix='.ome.tif')
cls.outfile = tempfile.NamedTemporaryFile(suffix='.ome.tif')
with BioWriter(cls.infile.name) as writer:
writer.X = cls.image_shape[0]
writer.Y = cls.image_shape[1]
writer[:] = cls.random_image[:]
return
def tester(t, ij):
try:
print("Testing {} data type...".format(t))
shape = (2048, 2048)
print("Creating Array...")
array = np.random.randint(0, 255, size=shape, dtype=np.uint16)
print("Converting Array...")
array = NUMPY_TYPES[t][0](array)
dtype0 = ij.py.dtype(array)
print("The initial data type is {}".format(dtype0))
temp_path = Path(__file__).with_name("data-convert-temp")
print("Writing image array to file...")
with BioWriter(temp_path) as writer:
writer.X = shape[0]
writer.Y = shape[1]
writer.dtype = array.dtype
writer[:] = array[:]
print("Reading image from file...")
arr = BioReader(temp_path)
print("Getting data type after reading image...")
dtype1 = ij.py.dtype(arr[:, :, 0:1, 0, 0])
print("Data type after reading image is {}".format(dtype1))
# print('Trying to convert to PlanarImg')
# planarimg = ij.planar(arr)
if dtype0 != dtype1:
print("Manully forcing data type back to {}".format(dtype0))
arr = NUMPY_TYPES[t][0](arr[:, :, 0:1, 0, 0])
print("Converting to Java object...")
arr = ij_converter.to_java(ij, np.squeeze(arr), "ArrayImg")
print("Getting data type after manually forcing...")
dtype2 = ij.py.dtype(arr)
print("Data type after manual forcing is {}".format(dtype2))
val_dtype = dtype2
else:
arr = ij_converter.to_java(ij, np.squeeze(arr[:, :, 0:1, 0,
0]), "ArrayImg")
val_dtype = dtype1
value = 5
print(
"Converting input (value) to Java primitive type {}...".format(
val_dtype))
val = ij_converter.to_java(ij, value, t, val_dtype)
print("Calling ImageJ op...")
out = ij.op().math().add(arr, val)
print("The op was SUCCESSFUL with data type {}".format(t))
except:
print("Testing data type {} was NOT SUCCESSFUL".format(t))
print(traceback.format_exc())
finally:
print("Shutting down JVM...\n\n")
del ij
jpype.shutdownJVM()
def write_cropped_images(
file_paths: list[Path],
output_dir: Path,
bounding_box: helpers.BoundingBox,
):
""" Crops and writes the given group of images using the given bounding box.
Args:
file_paths: A list of Paths for the input images.
output_dir: A Path to the output directory.
bounding_box: The bounding-box to use for cropping the images
"""
z1, z2, y1, y2, x1, x2 = bounding_box
out_depth, out_width, out_height = z2 - z1, y2 - y1, x2 - x1
logger.info(f'Superset bounding {bounding_box = }...')
logger.info(f'Cropping to shape (z, y, x) = {out_depth, out_width, out_height}...')
for file_path in file_paths:
out_path = output_dir.joinpath(helpers.replace_extension(file_path.name))
logger.info(f'Writing {out_path.name}...')
with BioReader(file_path) as reader:
with BioWriter(out_path, metadata=reader.metadata, max_workers=constants.NUM_THREADS) as writer:
writer.Z = out_depth
writer.Y = out_width
writer.X = out_height
for z_out in range(writer.Z):
z_in = z_out + z1
for out_y in range(0, writer.Y, constants.TILE_STRIDE):
out_y_max = min(writer.Y, out_y + constants.TILE_STRIDE)
in_y = out_y + y1
in_y_max = min(y2, in_y + constants.TILE_STRIDE)
for out_x in range(0, writer.X, constants.TILE_STRIDE):
out_x_max = min(writer.X, out_x + constants.TILE_STRIDE)
in_x = out_x + x1
in_x_max = min(x2, in_x + constants.TILE_STRIDE)
try:
tile = reader[in_y:in_y_max, in_x:in_x_max, z_in:z_in + 1, 0, 0]
writer[out_y:out_y_max, out_x:out_x_max, z_out:z_out + 1, 0, 0] = tile[:]
except AssertionError as e:
logger.error(
f'failed to read tile {(in_y, in_y_max, in_x, in_x_max, z_in, z_in + 1) = }\n'
f'and write to {(out_y, out_y_max, out_x, out_x_max, z_out, z_out + 1) = }\n'
f'because {e}'
)
raise e
return
def assemble_image(vector_path: pathlib.Path, out_path: pathlib.Path,
depth: int) -> None:
"""Assemble a 2d or 3d image
This method assembles one image from one stitching vector. It can
assemble both 2d and z-stacked 3d images It is intended to run as
a process to parallelize stitching of multiple images.
The basic approach to stitching is:
1. Parse the stitching vector and abstract the image dimensions
2. Generate a thread for each subsection (supertile) of an image.
Args:
vector_path: Path to the stitching vector
out_path: Path to the output directory
depth: depth of the input images
"""
# Grab a free process
with ProcessManager.process():
# Parse the stitching vector
parsed_vector = _parse_stitch(vector_path, timesliceNaming)
# Initialize the output image
with BioReader(parsed_vector['filePos'][0]['file']) as br:
bw = BioWriter(out_path.joinpath(parsed_vector['name']),
metadata=br.metadata,
max_workers=ProcessManager._active_threads)
bw.x = parsed_vector['width']
bw.y = parsed_vector['height']
bw.z = depth
# Assemble the images
ProcessManager.log(f'Begin assembly')
for z in range(depth):
ProcessManager.log(f'Assembling Z position : {z}')
for x in range(0, parsed_vector['width'], chunk_size):
X_range = min(x + chunk_size, parsed_vector['width']
) # max x-pixel index in the assembled image
for y in range(0, parsed_vector['height'], chunk_size):
Y_range = min(y + chunk_size, parsed_vector['height']
) # max y-pixel index in the assembled image
ProcessManager.submit_thread(make_tile, x, X_range, y,
Y_range, z, parsed_vector, bw)
ProcessManager.join_threads()
bw.close()
def setUpClass(cls) -> None:
cls.infile = tempfile.NamedTemporaryFile(suffix='.ome.tif')
cls.outfile = tempfile.NamedTemporaryFile(suffix='.ome.tif')
random_image = numpy.random.randint(
low=0,
high=255,
size=cls.image_shape,
dtype=numpy.uint8,
)
with BioWriter(cls.infile.name) as writer:
writer.X = cls.image_shape[0]
writer.Y = cls.image_shape[1]
writer[:] = random_image[:]
return
def write_corrected_images(
*,
group: list[utils.FPFileDict],
channel_ordering: list[int],
components_dir: Path,
output_dir: Path,
):
logger.info(f'writing corrected images...')
files = [file['file'] for file in group]
if len(channel_ordering) == 0:
channel_ordering = list(range(len(files)))
files = [files[c] for c in channel_ordering]
for image_path in files:
component_path = components_dir.joinpath(image_path.name)
assert component_path.exists()
output_path = output_dir.joinpath(image_path.name)
if output_path.exists():
continue
logger.info(f'writing image {image_path.name}...')
with BioReader(image_path) as image_reader, BioReader(
component_path) as component_reader:
with BioWriter(output_path,
metadata=image_reader.metadata) as writer:
for y_min in range(0, writer.Y, utils.TILE_SIZE_2D):
y_max = min(writer.Y, y_min + utils.TILE_SIZE_2D)
for x_min in range(0, writer.X, utils.TILE_SIZE_2D):
x_max = min(writer.X, x_min + utils.TILE_SIZE_2D)
image_tile = numpy.squeeze(image_reader[y_min:y_max,
x_min:x_max, 0,
0, 0])
component_tile = numpy.squeeze(
component_reader[y_min:y_max, x_min:x_max, 0, 0,
0])
writer[y_min:y_max, x_min:x_max, 0, 0,
0] = image_tile - component_tile
return
def label_cython(input_path: Path, output_path: Path, connectivity: int):
""" Label the input image and writes labels back out.
Args:
input_path: Path to input image.
output_path: Path for output image.
connectivity: Connectivity kind.
"""
with ProcessManager.thread() as active_threads:
with BioReader(
input_path,
max_workers=active_threads.count,
) as reader:
with BioWriter(
output_path,
max_workers=active_threads.count,
metadata=reader.metadata,
) as writer:
# Load an image and convert to binary
image = numpy.squeeze(reader[..., 0, 0])
if not numpy.any(image):
writer.dtype = numpy.uint8
writer[:] = numpy.zeros_like(image, dtype=numpy.uint8)
return
image = (image > 0)
if connectivity > image.ndim:
ProcessManager.log(
f'{input_path.name}: Connectivity is not less than or equal to the number of image dimensions, '
f'skipping this image. connectivity={connectivity}, ndim={image.ndim}'
)
return
# Run the labeling algorithm
labels = ftl.label_nd(image, connectivity)
# Save the image
writer.dtype = labels.dtype
writer[:] = labels
return True
def zarr_to_tif(zarr_path: Path, out_path: Path):
with BioReader(zarr_path, max_workers=utils.NUM_THREADS) as reader:
with BioWriter(out_path,
metadata=reader.metadata,
max_workers=utils.NUM_THREADS) as writer:
writer.dtype = numpy.uint32
for z in range(reader.Z):
for y in range(0, reader.Y, utils.TILE_SIZE):
y_max = min(reader.Y, y + utils.TILE_SIZE)
for x in range(0, reader.X, utils.TILE_SIZE):
x_max = min(reader.X, x + utils.TILE_SIZE)
tile = reader[y:y_max, x:x_max, z:z + 1, 0, 0]
writer[y:y_max, x:x_max, z:z + 1, 0, 0] = tile
shutil.rmtree(zarr_path)
return
def segment_images(inpDir, outDir, config_data):
""" Workflow for data with filamentous structures
such as ZO1, Beta Actin, Titin, Troponin 1.
Args:
inpDir : path to the input directory
outDir : path to the output directory
config_data : path to the configuration file
"""
logging.basicConfig(format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
datefmt='%d-%b-%y %H:%M:%S')
logger = logging.getLogger("main")
logger.setLevel(logging.INFO)
inpDir_files = os.listdir(inpDir)
for i,f in enumerate(inpDir_files):
logger.info('Segmenting image : {}'.format(f))
# Load image
br = BioReader(os.path.join(inpDir,f))
image = br.read_image()
structure_channel = 0
struct_img0 = image[:,:,:,structure_channel,0]
struct_img0 = struct_img0.transpose(2,0,1).astype(np.float32)
# main algorithm
intensity_scaling_param = config_data['intensity_scaling_param']
struct_img = intensity_normalization(struct_img0, scaling_param=intensity_scaling_param)
gaussian_smoothing_sigma = config_data['gaussian_smoothing_sigma']
if config_data['preprocessing_function'] == 'image_smoothing_gaussian_3d':
structure_img_smooth = image_smoothing_gaussian_3d(struct_img, sigma=gaussian_smoothing_sigma)
elif config_data['preprocessing_function'] == 'edge_preserving_smoothing_3d':
structure_img_smooth = edge_preserving_smoothing_3d(struct_img)
f3_param = config_data['f3_param']
bw = filament_3d_wrapper(structure_img_smooth, f3_param)
minArea = config_data['minArea']
seg = remove_small_objects(bw>0, min_size=minArea, connectivity=1, in_place=False)
seg = seg >0
out_img=seg.astype(np.uint8)
out_img[out_img>0]=255
# create output image
out_img = out_img.transpose(1,2,0)
out_img = out_img.reshape((out_img.shape[0], out_img.shape[1], out_img.shape[2], 1, 1))
# write image using BFIO
bw = BioWriter(os.path.join(outDir,f))
bw.num_x(out_img.shape[1])
bw.num_y(out_img.shape[0])
bw.num_z(out_img.shape[2])
bw.num_c(out_img.shape[3])
bw.num_t(out_img.shape[4])
bw.pixel_type(dtype='uint8')
bw.write_image(out_img)
bw.close_image()
# Input and output directory
batch = args.batch.split(',')
output_dir = args.output_directory
# Load Model Architecture and model weights
model = unet()
model.load_weights('unet.h5')
# Iterate over the files to be processed
for filename in batch:
logger.info("Processing image: {}".format(filename))
# Use bfio to read the image
with BioReader(filename) as br:
with BioWriter(str(
Path(output_dir).joinpath(
Path(filename).name).absolute()),
metadata=br.metadata) as bw:
bw.dtype = np.uint8
for x in range(0, br.X, tile_size):
x_max = min([br.X, x + tile_size])
for y in range(0, br.Y, tile_size):
y_max = min([br.Y, y + tile_size])
img = br[y:y_max, x:x_max, 0:1, 0, 0]
# Extract the 2-D grayscale image. Bfio loads an image as a 5-D array.
img = img[:, :, 0, 0, 0]
def segment_images(inpDir, outDir, config_data):
""" Workflow for data with similar morphology
as LAMP-1
Args:
inpDir : path to the input directory
outDir : path to the output directory
config_data : path to the configuration file
"""
logging.basicConfig(
format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
datefmt='%d-%b-%y %H:%M:%S')
logger = logging.getLogger("main")
logger.setLevel(logging.INFO)
inpDir_files = os.listdir(inpDir)
for i, f in enumerate(inpDir_files):
logger.info('Segmenting image : {}'.format(f))
# Load image
br = BioReader(os.path.join(inpDir, f))
image = br.read_image()
structure_channel = 0
struct_img0 = image[:, :, :, structure_channel, 0]
struct_img0 = struct_img0.transpose(2, 0, 1).astype(np.float32)
# main algorithm
intensity_scaling_param = config_data['intensity_scaling_param']
struct_img = intensity_normalization(
struct_img0, scaling_param=intensity_scaling_param)
gaussian_smoothing_sigma = config_data['gaussian_smoothing_sigma']
structure_img_smooth = image_smoothing_gaussian_slice_by_slice(
struct_img, sigma=gaussian_smoothing_sigma)
s2_param = config_data['s2_param']
bw_spot = dot_2d_slice_by_slice_wrapper(structure_img_smooth, s2_param)
f2_param = config_data['f2_param']
bw_filament = filament_2d_wrapper(structure_img_smooth, f2_param)
bw = np.logical_or(bw_spot, bw_filament)
fill_2d = config_data['fill_2d']
if fill_2d == 'True':
fill_2d = True
elif fill_2d == 'False':
fill_2d = False
fill_max_size = config_data['fill_max_size']
minArea = config_data['minArea']
bw_fill = hole_filling(bw, 0, fill_max_size, False)
seg = remove_small_objects(bw_fill > 0,
min_size=minArea,
connectivity=1,
in_place=False)
seg = seg > 0
out_img = seg.astype(np.uint8)
out_img[out_img > 0] = 255
# create output image
out_img = out_img.transpose(1, 2, 0)
out_img = out_img.reshape(
(out_img.shape[0], out_img.shape[1], out_img.shape[2], 1, 1))
# write image using BFIO
bw = BioWriter(os.path.join(outDir, f), metadata=br.read_metadata())
bw.num_x(out_img.shape[1])
bw.num_y(out_img.shape[0])
bw.num_z(out_img.shape[2])
bw.num_c(out_img.shape[3])
bw.num_t(out_img.shape[4])
bw.pixel_type(dtype='uint8')
bw.write_image(out_img)
bw.close_image()
def segment_images(inpDir, outDir, config_data):
""" Workflow for data with shell like shapes
such as lamin B1 (interphase-specific)
Args:
inpDir : path to the input directory
outDir : path to the output directory
config_data : path to the configuration file
"""
logging.basicConfig(
format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
datefmt='%d-%b-%y %H:%M:%S')
logger = logging.getLogger("main")
logger.setLevel(logging.INFO)
inpDir_files = os.listdir(inpDir)
for i, f in enumerate(inpDir_files):
logger.info('Segmenting image : {}'.format(f))
# Load image
br = BioReader(os.path.join(inpDir, f))
image = br.read_image()
structure_channel = 0
struct_img0 = image[:, :, :, structure_channel, 0]
struct_img0 = struct_img0.transpose(2, 0, 1).astype(np.float32)
# main algorithm
intensity_scaling_param = config_data['intensity_scaling_param']
struct_img = intensity_normalization(
struct_img0, scaling_param=intensity_scaling_param)
gaussian_smoothing_sigma = config_data['gaussian_smoothing_sigma']
structure_img_smooth = image_smoothing_gaussian_3d(
struct_img, sigma=gaussian_smoothing_sigma)
middle_frame_method = config_data['middle_frame_method']
mid_z = get_middle_frame(structure_img_smooth,
method=middle_frame_method)
f2_param = config_data['f2_param']
bw_mid_z = filament_2d_wrapper(structure_img_smooth[mid_z, :, :],
f2_param)
hole_max = config_data['hole_max']
hole_min = config_data['hole_min']
bw_fill_mid_z = hole_filling(bw_mid_z, hole_min, hole_max)
seed = get_3dseed_from_mid_frame(
np.logical_xor(bw_fill_mid_z, bw_mid_z), struct_img.shape, mid_z,
hole_min)
bw_filled = watershed(
struct_img, seed.astype(int), watershed_line=True) > 0
seg = np.logical_xor(bw_filled, dilation(bw_filled, selem=ball(1)))
seg = seg > 0
out_img = seg.astype(np.uint8)
out_img[out_img > 0] = 255
# create output image
out_img = out_img.transpose(1, 2, 0)
out_img = out_img.reshape(
(out_img.shape[0], out_img.shape[1], out_img.shape[2], 1, 1))
# write image using BFIO
bw = BioWriter(os.path.join(outDir, f))
bw.num_x(out_img.shape[1])
bw.num_y(out_img.shape[0])
bw.num_z(out_img.shape[2])
bw.num_c(out_img.shape[3])
bw.num_t(out_img.shape[4])
bw.pixel_type(dtype='uint8')
bw.write_image(out_img)
bw.close_image()
def make_tile(x_min: int,
x_max: int,
y_min: int,
y_max: int,
z: int,
parsed_vector: dict,
bw: BioWriter) -> None:
"""Create a supertile from images and save to file
This method builds a supertile, which is a section of the image defined by
the global variable ``chunk_size`` and is composed of multiple smaller tiles
defined by the ``BioReader._TILE_SIZE``. Images are stored on disk as
compressed chunks that are ``_TILE_SIZE`` length and width, and the upper
left pixel of a tile is always a multiple of ``_TILE_SIZE``. To prevent
excessive file loading and to ensure files are properly placed, supertiles
are created from smaller images and saved all at once.
Args:
x_min: Minimum x bound of the tile
x_max: Maximum x bound of the tile
y_min: Minimum y bound of the tile
y_max: Maximum y bound of the tile
z: Current z position to assemble
parsed_vector: The result of _parse_vector
local_threads: Used to determine the number of concurrent threads to run
bw: The output file object
"""
with ProcessManager.thread() as active_threads:
# Get the data type
with BioReader(parsed_vector['filePos'][0]['file']) as br:
dtype = br.dtype
# initialize the supertile
template = numpy.zeros((y_max-y_min,x_max-x_min,1,1,1),dtype=dtype)
# get images in bounds of current super tile
for f in parsed_vector['filePos']:
# check that image is within the x-tile bounds
if (f['posX'] >= x_min and f['posX'] <= x_max) \
or (f['posX']+f['width'] >= x_min and f['posX']+f['width'] <= x_max) \
or (f['posX'] <= x_min and f['posX']+f['width'] >= x_max):
# check that image is within the y-tile bounds
if (f['posY'] >= y_min and f['posY'] <= y_max) \
or (f['posY']+f['height'] >= y_min and f['posY']+f['height'] <= y_max) \
or (f['posY'] <= y_min and f['posY']+f['height'] >= y_max):
# get bounds of image within the tile
Xt = [max(0,f['posX']-x_min)]
Xt.append(min(x_max-x_min,f['posX']+f['width']-x_min))
Yt = [max(0,f['posY']-y_min)]
Yt.append(min(y_max-y_min,f['posY']+f['height']-y_min))
# get bounds of image within the image
Xi = [max(0,x_min - f['posX'])]
Xi.append(min(f['width'],x_max - f['posX']))
Yi = [max(0,y_min - f['posY'])]
Yi.append(min(f['height'],y_max - f['posY']))
# Load the image
with BioReader(f['file'],max_workers=active_threads.count) as br:
image = br[Yi[0]:Yi[1],Xi[0]:Xi[1],z:z+1,0,0] # only get the first c,t layer
# Put the image in the buffer
template[Yt[0]:Yt[1],Xt[0]:Xt[1],...] = image
# Save the image
bw.max_workers = ProcessManager._active_threads
bw[y_min:y_max,x_min:x_max,z:z+1,0,0] = template
def _write_components_thread(
self,
output_dir: Path,
image_name: str,
source_index: int,
):
""" Writes the bleed-through components for a single image.
This function can be run in a single thread in a ProcessPoolExecutor.
Args:
output_dir: Path for the directory of the bleed-through components.
image_name: name of the source image.
source_index: index of the source channel.
"""
neighbor_indices = self._get_neighbors(source_index)
neighbor_mins = [self.image_mins[i] for i in neighbor_indices]
neighbor_maxs = [self.image_maxs[i] for i in neighbor_indices]
coefficients = self.__coefficients[source_index]
neighbor_readers = [
BioReader(self.__files[i], max_workers=utils.NUM_THREADS)
for i in neighbor_indices
]
with BioReader(self.__files[source_index],
max_workers=utils.NUM_THREADS) as source_reader:
metadata = source_reader.metadata
num_tiles = utils.count_tiles_2d(source_reader)
tile_indices = list(utils.tile_indices_2d(source_reader))
with BioWriter(
output_dir.joinpath(image_name),
metadata=metadata,
max_workers=utils.NUM_THREADS,
) as writer:
logger.info(f'Writing components for {image_name}...')
for i, (z, y_min, y_max, x_min,
x_max) in enumerate(tile_indices):
tile = numpy.squeeze(source_reader[y_min:y_max,
x_min:x_max, z:z + 1, 0,
0])
original_component = numpy.zeros_like(tile)
if i % 10 == 0:
logger.info(
f'Writing {image_name}: Progress {100 * i / num_tiles:6.2f} %'
)
all_kernel_indices = numpy.asarray(
self._get_kernel_indices(source_index),
dtype=numpy.uint64)
for neighbor_index, (neighbor_reader, min_val,
max_val) in enumerate(
zip(neighbor_readers,
neighbor_mins,
neighbor_maxs)):
neighbor_tile = utils.normalize_tile(
tile=numpy.squeeze(neighbor_reader[y_min:y_max,
x_min:x_max,
z:z + 1, 0, 0]),
min_val=min_val,
max_val=max_val,
)
kernel_size = self.__kernel_size**2
kernel_indices = all_kernel_indices[
kernel_size * neighbor_index:kernel_size *
(1 + neighbor_index)]
kernel = coefficients[kernel_indices]
kernel = numpy.reshape(kernel,
newshape=(self.__kernel_size,
self.__kernel_size))
if numpy.any(kernel > 0):
if self.__kernel_size > 1:
smoothed_tile = scipy.ndimage.gaussian_filter(
neighbor_tile, 2)
smoothed_tile = numpy.min(numpy.dstack(
(smoothed_tile, neighbor_tile)),
axis=-1)
else:
smoothed_tile = neighbor_tile
# apply the coefficient
current_component = scipy.ndimage.correlate(
smoothed_tile, kernel)
# Rescale, but do not add in the minimum value offset.
current_component *= (max_val - min_val)
original_component += current_component.astype(
tile.dtype)
# Make sure bleed-through is not higher than the original signal.
original_component = numpy.min(numpy.dstack(
(tile, original_component)),
axis=-1)
writer[y_min:y_max, x_min:x_max, z:z + 1, 0,
0] = original_component
[reader.close() for reader in neighbor_readers]
return
def main(inpDir: Path,
cellprob_threshold: float,
flow_threshold: float,
outDir: Path
) -> None:
# Get the list of files in path
files = [p for p in Path(inpDir).iterdir() if p.name.endswith('_flow.ome.zarr')]
num_threads = max([cpu_count()//2,1])
logger.info(f'Processing tiles with {num_threads} threads using {DEV}')
if len(files) == 0:
logger.critical('No flow files detected.')
quit()
processes = []
with ThreadPoolExecutor(num_threads) as executor:
# Loop through files in inpDir image collection and process
for ind,fpath in enumerate(files):
br = BioReader(fpath)
threads = np.empty((br.shape[:3]),dtype=object)
logger.debug(
'Processing image ({}/{}): {}'.format(ind, len(files),
fpath))
# TODO: Hard coding to ome.tif for now, this should be changed later.
path = Path(outDir).joinpath(fpath.name.replace('_flow.ome.zarr','.ome.tif'))
bw = BioWriter(file_path=Path(path), metadata=br.metadata)
bw.dtype=np.dtype(np.uint32)
bw.C = 1
bw.channel_names = ['label']
for z in range(0, br.Z, 1):
y_ind = None
dependency1 = None
for y in range(0, br.Y, TILE_SIZE):
for x in range(0, br.X, TILE_SIZE):
dependency2 = None if y_ind is None else threads[y_ind,x//TILE_SIZE,z]
processes.append(executor.submit(mask_thread,
(x,y,z),
fpath,bw,
cellprob_threshold,flow_threshold,
dependency1,dependency2))
dependency1 = processes[-1]
threads[y//TILE_SIZE,x//TILE_SIZE,z] = dependency1
y_ind = y//TILE_SIZE
executor.submit(close_thread,dependency1,bw)
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, 15)
logger.info(f'Percent complete: {100 * len(done) / len(processes):6.3f}%')
outvals['width'], outvals['height']))
# Variables for tile building processes
pnum = 0
ptotal = np.ceil(outvals['width'] / 10240) * np.ceil(
outvals['height'] / 10240)
ptotal = 1 / ptotal * 100
# Initialize the output image
logger.info('Initializing output file: {}'.format(outvals['name']))
refImg = str(
Path(imgPath).joinpath(outvals['filePos'][0]['file']).absolute())
outFile = str(Path(outDir).joinpath(outvals['name']).absolute())
br = BioReader(str(Path(refImg).absolute()))
bw = BioWriter(str(Path(outFile).absolute()),
metadata=br.read_metadata(),
max_workers=max([multiprocessing.cpu_count(), 2]))
bw.num_x(outvals['width'])
bw.num_y(outvals['height'])
del br
# Assemble the images
logger.info('Generating tiles...')
threads = []
with ThreadPoolExecutor(max([multiprocessing.cpu_count() // 2,
2])) as executor:
for x in range(0, outvals['width'], 10240):
X_range = min(x + 10240, outvals['width']
) # max x-pixel index in the assembled image
for y in range(0, outvals['height'], 10240):
Y_range = min(y + 10240, outvals['height']
def segment_images(inpDir, outDir, config_data):
""" Workflow for dot like shapes such as
Centrin-2, Desmoplakin, PMP34.
Args:
inpDir : path to the input directory
outDir : path to the output directory
config_data : path to the configuration file
"""
logging.basicConfig(
format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
datefmt='%d-%b-%y %H:%M:%S')
logger = logging.getLogger("main")
logger.setLevel(logging.INFO)
inpDir_files = os.listdir(inpDir)
for i, f in enumerate(inpDir_files):
logger.info('Segmenting image : {}'.format(f))
# Load an image
br = BioReader(os.path.join(inpDir, f))
image = br.read_image()
structure_channel = 0
struct_img0 = image[:, :, :, structure_channel, 0]
struct_img0 = struct_img0.transpose(2, 0, 1).astype(np.float32)
# main algorithm
intensity_scaling_param = config_data['intensity_scaling_param']
struct_img = intensity_normalization(
struct_img0, scaling_param=intensity_scaling_param)
gaussian_smoothing_sigma = config_data['gaussian_smoothing_sigma']
if config_data["gaussian_smoothing"] == "gaussian_slice_by_slice":
structure_img_smooth = image_smoothing_gaussian_slice_by_slice(
struct_img, sigma=gaussian_smoothing_sigma)
else:
structure_img_smooth = image_smoothing_gaussian_3d(
struct_img, sigma=gaussian_smoothing_sigma)
s3_param = config_data['s3_param']
bw = dot_3d_wrapper(structure_img_smooth, s3_param)
minArea = config_data['minArea']
Mask = remove_small_objects(bw > 0,
min_size=minArea,
connectivity=1,
in_place=False)
Seed = dilation(peak_local_max(struct_img,
labels=label(Mask),
min_distance=2,
indices=False),
selem=ball(1))
Watershed_Map = -1 * distance_transform_edt(bw)
seg = watershed(Watershed_Map,
label(Seed),
mask=Mask,
watershed_line=True)
seg = remove_small_objects(seg > 0,
min_size=minArea,
connectivity=1,
in_place=False)
seg = seg > 0
out_img = seg.astype(np.uint8)
out_img[out_img > 0] = 255
# create output image
out_img = out_img.transpose(1, 2, 0)
out_img = out_img.reshape(
(out_img.shape[0], out_img.shape[1], out_img.shape[2], 1, 1))
# write image using BFIO
bw = BioWriter(os.path.join(outDir, f))
bw.num_x(out_img.shape[1])
bw.num_y(out_img.shape[0])
bw.num_z(out_img.shape[2])
bw.num_c(out_img.shape[3])
bw.num_t(out_img.shape[4])
bw.pixel_type(dtype='uint8')
bw.write_image(out_img)
bw.close_image()
unique_levels.update([0])
# Start the javabridge with proper java logging
logger.info('Initializing the javabridge...')
log_config = Path(__file__).parent.joinpath("log4j.properties")
jutil.start_vm(args=["-Dlog4j.configuration=file:{}".format(str(log_config.absolute()))],class_path=bioformats.JARS)
# Generate the heatmap images
logger.info('Generating heatmap images...')
for w in widths:
for h in heights:
for l in unique_levels:
out_file = Path(outImages).joinpath(str(w) + '_' + str(h) + '_' + str(l) + '.ome.tif')
if not out_file.exists():
image = np.ones((h,w,1,1,1),dtype=np.uint8)*l
bw = BioWriter(str(Path(outImages).joinpath(str(w) + '_' + str(h) + '_' + str(l) + '.ome.tif').absolute()),X=w,Y=h,Z=1,C=1,T=1)
bw.write_image(image)
bw.close_image()
# Close the javabridge
logger.info('Closing the javabridge...')
jutil.kill_vm()
# Build the output stitching vector
logger.info('Generating the heatmap...')
file_name = '{}_{}_{}.ome.tif'
for num,feat in enumerate(feature_list):
fpath = str(Path(outVectors).joinpath('img-global-positions-' + str(num+1) + '.txt').absolute())
with open(fpath,'w') as fw:
line = 0
while True:
def basic(files: typing.List[Path],
out_dir: Path,
metadata_dir: typing.Optional[Path] = None,
darkfield: bool = False,
photobleach: bool = False):
# Try to infer a filename
try:
pattern = infer_pattern([f['file'].name for f in files])
fp = FilePattern(files[0]['file'].parent,pattern)
base_output = fp.output_name()
# Fallback to the first filename
except:
base_output = files[0]['file'].name
extension = ''.join(files[0]['file'].suffixes)
with ProcessManager.process(base_output):
# Load files and sort
ProcessManager.log('Loading and sorting images...')
img_stk,X,Y = _get_resized_image_stack(files)
img_stk_sort = np.sort(img_stk)
# Initialize options
new_options = _initialize_options(img_stk_sort,darkfield,OPTIONS)
# Initialize flatfield/darkfield matrices
ProcessManager.log('Beginning flatfield estimation')
flatfield_old = np.ones((new_options['size'],new_options['size']),dtype=np.float64)
darkfield_old = np.random.normal(size=(new_options['size'],new_options['size'])).astype(np.float64)
# Optimize until the change in values is below tolerance or a maximum number of iterations is reached
for w in range(new_options['max_reweight_iterations']):
# Optimize using inexact augmented Legrangian multiplier method using L1 loss
A, E1, A_offset = _inexact_alm_l1(copy.deepcopy(img_stk_sort),new_options)
# Calculate the flatfield/darkfield images and update training weights
flatfield, darkfield, new_options = _get_flatfield_and_reweight(A,E1,A_offset,new_options)
# Calculate the change in flatfield and darkfield images between iterations
mad_flat = np.sum(np.abs(flatfield-flatfield_old))/np.sum(np.abs(flatfield_old))
temp_diff = np.sum(np.abs(darkfield - darkfield_old))
if temp_diff < 10**-7:
mad_dark =0
else:
mad_dark = temp_diff/np.max(np.sum(np.abs(darkfield_old)),initial=10**-6)
flatfield_old = flatfield
darkfield_old = darkfield
# Stop optimizing if the change in flatfield/darkfield is below threshold
ProcessManager.log('Iteration {} loss: {}'.format(w+1,mad_flat))
if np.max(mad_flat,initial=mad_dark) < new_options['reweight_tol']:
break
# Calculate photobleaching effects if specified
if photobleach:
pb = _get_photobleach(copy.deepcopy(img_stk),flatfield,darkfield)
# Resize images back to original image size
ProcessManager.log('Saving outputs...')
flatfield = cv2.resize(flatfield,(Y,X),interpolation=cv2.INTER_CUBIC).astype(np.float32)
if new_options['darkfield']:
darkfield = cv2.resize(darkfield,(Y,X),interpolation=cv2.INTER_CUBIC).astype(np.float32)
# Export the flatfield image as a tiled tiff
flatfield_out = base_output.replace(extension,'_flatfield' + extension)
with BioReader(files[0]['file'],max_workers=2) as br:
metadata = br.metadata
with BioWriter(out_dir.joinpath(flatfield_out),metadata=metadata,max_workers=2) as bw:
bw.dtype = np.float32
bw.x = X
bw.y = Y
bw[:] = np.reshape(flatfield,(Y,X,1,1,1))
# Export the darkfield image as a tiled tiff
if new_options['darkfield']:
darkfield_out = base_output.replace(extension,'_darkfield' + extension)
with BioWriter(out_dir.joinpath(darkfield_out),metadata=metadata,max_workers=2) as bw:
bw.dtype = np.float32
bw.x = X
bw.y = Y
bw[:] = np.reshape(darkfield,(Y,X,1,1,1))
# Export the photobleaching components as csv
if photobleach:
offsets_out = base_output.replace(extension,'_offsets.csv')
with open(metadata_dir.joinpath(offsets_out),'w') as fw:
fw.write('file,offset\n')
for f,o in zip(files,pb[0,:].tolist()):
fw.write("{},{}\n".format(f,o))
def main():
logger.info("Parsing arguments...")
parser = argparse.ArgumentParser(
prog='main', description='Image clustering annotation plugin.')
parser.add_argument('--imgdir',
dest='imgdir',
type=str,
help='Input collection- Image data',
required=True)
parser.add_argument('--csvdir',
dest='csvdir',
type=str,
help='Input collection- csv data',
required=True)
parser.add_argument('--borderwidth',
dest='borderwidth',
type=int,
default=2,
help='Border width',
required=False)
parser.add_argument('--outdir',
dest='outdir',
type=str,
help='Output collection',
required=True)
# Parse the arguments
args = parser.parse_args()
#Path to image directory
imgdir = args.imgdir
logger.info('imgdir = {}'.format(imgdir))
#Path to csvfile directory
csvdir = args.csvdir
logger.info('csvdir = {}'.format(csvdir))
#Get the border width
borderwidth = args.borderwidth
logger.info('borderwidth = {}'.format(borderwidth))
#Path to save output image files
outdir = args.outdir
logger.info('outdir = {}'.format(outdir))
#Get list of .ome.tif files in the directory including sub folders
img_ext = '*.ome.tif'
configfiles = list_file(imgdir, img_ext)
config = [os.path.basename(path) for path in configfiles]
#Check whether .ome.tif files are present in the labeled image directory
if not configfiles:
raise ValueError('No .ome.tif files found.')
#Get list of .csv files in the directory including sub folders
csv_ext = '*.csv'
inputcsv = list_file(csvdir, csv_ext)
if not inputcsv:
raise ValueError('No .csv files found.')
for inpfile in inputcsv:
#Get the full path
split_file = os.path.normpath(inpfile)
#split to get only the filename
inpfilename = os.path.split(split_file)
file_name_csv = inpfilename[-1]
file_path = inpfilename[0]
file_name, file_name1 = file_name_csv.split('.', 1)
logger.info('Reading the file ' + file_name)
#Read csv file
cluster_data = pd.read_csv(inpfile)
cluster_data = cluster_data.iloc[:, [0, -1]]
for index, row in cluster_data.iterrows():
filename = row[0]
cluster = row[1]
#get the image file that matches with the filename in csvfile
matches = [match for match in config if filename in match]
if len(matches) == 0:
logger.warning(
f"Could not find image files matching the filename, {filename}. Skipping..."
)
continue
match_getpath = [s for s in configfiles if matches[0] in s]
#Get the full path
full_path = os.path.normpath(match_getpath[0])
#split to get only the filename
file_path = os.path.split(full_path)[0]
#Get the image path and output directory path
imgpath = Path(file_path)
outpath = Path(outdir)
#Read and write(after making changes) the .ome.tif files
with BioReader(imgpath / filename) as br, \
BioWriter(outpath / filename,metadata=br.metadata) as bw:
#Make all pixels zero except the borders of specified thickness and assign the cluster_id to border pixels
mask = np.zeros(br.shape, dtype=np.int16)
mask[:borderwidth, :] = cluster
mask[:, :borderwidth] = cluster
mask[-borderwidth:, :] = cluster
mask[:, -borderwidth:] = cluster
bw.dtype = mask.dtype
bw[:] = mask
logger.info("Finished all processes!")
def binary_operation(image, output, function, extra_arguments, extra_padding,
kernel, Tile_Size):
"""
This function goes through the images and calls the appropriate binary operation
Parameters
----------
image : str
Location of image
function_to_call : str
The binary operation to dispatch on image
extra_arguments : int
Extra argument(s) for the binary operation that is called
extra_padding : int
The extra padding around each tile so that
binary operations do not skewed around the edges.
kernel : cv2 object
The kernel used for most binary operations
output : str
Location for BioWriter
Tile_Size : int
Tile Size for reading images
"""
# Start the javabridge with proper java logging
logger.info('Initializing the javabridge...')
log_config = Path(__file__).parent.joinpath("log4j.properties")
jutil.start_vm(args=[
"-Dlog4j.configuration=file:{}".format(str(log_config.absolute()))
],
class_path=bioformats.JARS)
try:
# Read the image
br = BioReader(image)
# Get the dimensions of the Image
br_x, br_y, br_z, br_c, br_t = br.num_x(), br.num_y(), br.num_z(
), br.num_c(), br.num_t()
br_shape = (br_x, br_y, br_z, br_c, br_t)
datatype = br.pixel_type()
max_datatype_val = np.iinfo(datatype).max
logger.info("Original Datatype {}: ({})".format(
datatype, max_datatype_val))
logger.info("Shape of Input (XYZCT): {}".format(br_shape))
# Initialize Output
bw = BioWriter(file_path=output, metadata=br.read_metadata())
# Initialize the Python Generators to go through each "tile" of the image
tsize = Tile_Size + (2 * extra_padding)
logger.info("Tile Size {}x{}".format(tsize, tsize))
readerator = br.iterate(tile_stride=[Tile_Size, Tile_Size],
tile_size=[tsize, tsize],
batch_size=1)
writerator = bw.writerate(tile_size=[Tile_Size, Tile_Size],
tile_stride=[Tile_Size, Tile_Size],
batch_size=1)
next(writerator)
for images, indices in readerator:
# Extra tiles do not need to be calculated.
# Indices should range from -intkernel < index value < Image_Dimension + intkernel
if (indices[0][0][0]
== br_x - extra_padding) or (indices[1][0][0]
== br_y - extra_padding):
continue
logger.info(indices)
# Images are (1, Tile_Size, Tile_Size, 1)
# Need to convert to (Tile_Size, Tile_Size) to be able to do operation
images = np.squeeze(images)
images[images == max_datatype_val] = 1
# Initialize which function we are dispatching
if callable(function):
trans_image = function(images,
kernel=kernel,
n=extra_arguments)
trans_image = trans_image.astype(datatype)
trans_image[trans_image == 1] = max_datatype_val
# The image needs to be converted back to (1, Tile_Size_Tile_Size, 1) to write it
reshape_img = np.reshape(
trans_image[extra_padding:-extra_padding,
extra_padding:-extra_padding],
(1, Tile_Size, Tile_Size, 1))
# Send it to the Writerator
writerator.send(reshape_img)
# Close the image
bw.close_image()
except:
traceback.print_exc()
# Always close the JavaBridge
finally:
jutil.kill_vm()
# Start the javabridge with proper java logging
logger.info('Initializing the javabridge...')
log_config = Path(__file__).parent.joinpath("log4j.properties")
jutil.start_vm(args=[
"-Dlog4j.configuration=file:{}".format(str(log_config.absolute()))
],
class_path=bioformats.JARS)
inpDir_files = str(images).split(',')
# Loop through files in inpDir image collection and process
try:
for f in inpDir_files:
# Initialize the reader/writer objects
logger.info('Segmenting image: {}'.format(f))
br = BioReader(str(Path(inpDir).joinpath(f)))
bw = BioWriter(str(Path(outDir).joinpath(f)),
metadata=br.read_metadata())
# Initialize the generators
batch_size = min([
20,
br.maximum_batch_size(tile_size=tile_size,
tile_stride=tile_stride)
])
readerator = br.iterate(tile_size=tile_size,
tile_stride=tile_stride,
batch_size=batch_size)
writerator = bw.writerate(tile_size=tile_size,
tile_stride=tile_stride,
batch_size=batch_size)
next(writerator)