def execute(self, args):
if not args.struct_name == 'skip':
if not args.workflow_name == 'template':
print('only use either workflow_name or struct_name, should use both.')
quit()
args.workflow_name = args.struct_name
try:
if args.wrapper_dir == '_internal_':
module_name = 'aicssegmentation.structure_wrapper.seg_' + args.workflow_name
seg_module = importlib.import_module(module_name)
else:
func_path = args.wrapper_dir
spec = importlib.util.spec_from_file_location('seg_'+ args.workflow_name, func_path + '/seg_'+args.workflow_name+'.py')
seg_module = importlib.util.module_from_spec(spec)
try:
spec.loader.exec_module(seg_module)
except Exception as e:
print('check errors in wrapper script')
print(str(e))
class_name = 'Workflow_'+ args.workflow_name
SegModule = getattr(seg_module, class_name)
except:
print('{} structure not found'.format(args.workflow_name))
sys.exit(1)
output_path = pathlib.Path(args.output_dir)
if not os.path.exists(output_path):
os.mkdir(output_path)
##########################################################################
if args.mode == PER_IMAGE:
fname = os.path.basename(os.path.splitext(args.input_fname)[0])
image_reader = aicsimageio.AICSImage(args.input_fname)
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type, output_path, fname)
elif args.mode == PER_DIR:
filenames = [os.path.basename(os.path.splitext(f)[0])
for f in os.listdir(args.input_dir)
if f.endswith(args.data_type)]
filenames.sort()
for _, fn in enumerate(filenames):
image_reader = aicsimageio.AICSImage(os.path.join(args.input_dir, f'{fn}{args.data_type}'))
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type, output_path, fn)
def execute(self, args):
if not args.workflow_name == 'ignore':
# overwrite struct_name
args.struct_name = args.workflow_name
if args.struct_name not in STRUCTURE_MAPPING.keys():
# this is not a off-the-shelf structure, will interpreted differently
try:
module_name = 'aicssegmentation.structure_wrapper.seg_' + args.struct_name
seg_module = importlib.import_module(module_name)
class_name = 'Workflow_' + args.struct_name
SegModule = getattr(seg_module, class_name)
except:
print('{} structure not found'.format(args.struct_name))
sys.exit(1)
else:
# Pull module info for this structure
seg_module_info = STRUCTURE_MAPPING[args.struct_name]
# Import the module specified for that structure
seg_module = importlib.import_module(seg_module_info['module'])
# Pull out the segmentation class from that module
SegModule = getattr(seg_module, seg_module_info['class'])
output_path = pathlib.Path(args.output_dir)
##########################################################################
if args.mode == PER_IMAGE:
fname = os.path.basename(os.path.splitext(args.input_fname)[0])
image_reader = aicsimageio.AICSImage(args.input_fname)
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type,
output_path, fname)
elif args.mode == PER_DIR:
filenames = [
os.path.basename(os.path.splitext(f)[0])
for f in os.listdir(args.input_dir)
if f.endswith(args.data_type)
]
filenames.sort()
for _, fn in enumerate(filenames):
image_reader = aicsimageio.AICSImage(
os.path.join(args.input_dir, f'{fn}{args.data_type}'))
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type,
output_path, fn)
def execute(self, args):
if args.struct_name not in STRUCTURE_MAPPING.keys():
print('{} structure not found'.format(args.struct_name))
sys.exit(1)
# Pull module info for this structure
seg_module_info = STRUCTURE_MAPPING[args.struct_name]
# Import the module specified for that structure
seg_module = importlib.import_module(seg_module_info['module'])
# Pull out the segmentation class from that module
SegModule = getattr(seg_module, seg_module_info['class'])
output_path = pathlib.Path(args.output_dir)
##########################################################################
if args.mode == PER_IMAGE:
fname = os.path.basename(os.path.splitext(args.input_fname)[0])
image_reader = aicsimageio.AICSImage(args.input_fname)
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type, output_path, fname)
elif args.mode == PER_DIR:
filenames = [os.path.basename(os.path.splitext(f)[0])
for f in os.listdir(args.input_dir)
if f.endswith(args.data_type)]
filenames.sort()
for fi, fn in enumerate(filenames):
image_reader = aicsimageio.AICSImage(os.path.join(args.input_dir, f'{fn}{args.data_type}'))
img = image_reader.data
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
SegModule(struct_img, self.rescale_ratio, args.output_type, output_path, fn)
def make_one_thumbnail(
infile: str,
outfile: str,
channels: List[int],
colors: List[Tuple[float, float, float]],
size: int,
projection: str = "max",
axis: int = 2,
apply_mask: bool = False,
mask_channel: int = 0,
label: str = "",
):
axistranspose = (1, 0, 2, 3)
if axis == 2: # Z
axistranspose = (1, 0, 2, 3)
elif axis == 0: # X
axistranspose = (2, 0, 1, 3)
elif axis == 1: # Y
axistranspose = (3, 0, 2, 1)
else:
raise ValueError(f"Unknown axis value: {axis}")
with aicsimageio.AICSImage(infile) as image:
imagedata = image.get_image_data("CZYX", T=0)
generator = ThumbnailGenerator(
channel_indices=channels,
size=size,
mask_channel_index=mask_channel,
colors=colors,
projection=projection,
)
# take zeroth time, and transpose projection axis and c
thumbnail = generator.make_thumbnail(imagedata.transpose(axistranspose),
apply_cell_mask=apply_mask)
if label:
# Untested on MacOS
if platform.system() == "Windows":
font_path = "/Windows/Fonts/consola.ttf"
else:
font_path = "/usr/share/fonts/truetype/dejavu/DejaVuSansMono.ttf"
font = ImageFont.truetype(font_path, 12)
img = Image.fromarray(thumbnail.transpose((1, 2, 0)))
draw = ImageDraw.Draw(img)
draw.text((2, 2), label, (255, 255, 255), font=font)
thumbnail = np.array(img)
thumbnail = thumbnail.transpose(2, 0, 1)
with aicsimageio.writers.PngWriter(file_path=outfile,
overwrite_file=True) as writer:
writer.save(thumbnail)
return thumbnail
def test_aicsimageio_no_networking(resources_dir, filename, expected_shape):
# This should test and make sure that distributed isn't imported when aicsimageio is
# Importing distributed on a machine (or container) that doesn't have any
# networking capabilities results in socket errors, _during the import_
# See: https://github.com/AllenCellModeling/aicsimageio/issues/82
if "distributed" in sys.modules:
del sys.modules["distributed"]
# Re import
import aicsimageio # noqa: F401
# Some basic operation to ensure that distributed is not imported
# anywhere down the line
img = aicsimageio.AICSImage(resources_dir / filename)
assert img.data.shape == expected_shape
# Assert not imported
assert "distributed" not in sys.modules
def microscopy_czi(viewer, im_path, im_labels_path):
img = aicsimageio.AICSImage(im_path)
cells = img.data[0]
print("image shape: {}".format(cells.shape))
layer_names = [layer.name for layer in viewer.layers]
ch_nums = [1, 2, 3, 4, 0]
ch_names = ["probe488", "probe561", "probe638", "dapi", "brightfield"]
ch_types = ["fluor", "fluor", "fluor", "fluor", "bf"]
ch_colors = [
[1.0, 0.0, 0.0, 1.0],
[0.0, 1.0, 0.0, 1.0],
[1.0, 1.0, 0.0, 1.0],
[0.0, 0.0, 1.0, 1.0],
[1.0, 1.0, 1.0, 1.0],
]
for ch_num, ch_name, ch_type, ch_color in zip(ch_nums, ch_names, ch_types,
ch_colors):
if ch_num < cells.shape[0]:
channel = cells[ch_num, :, :, :]
else:
channel = np.zeros([1, 1, 1])
if ch_name not in layer_names:
ch = viewer.add_image(channel, name=ch_name)
else:
ch = viewer.layers[ch_name]
ch.image = channel
ch.colormap = Colormap([(0, 0, 0, 1), ch_color])
ch.clim = get_default_range(channel, ch_type)
ch.blending = "additive"
if os.path.exists(im_labels_path):
labels = imread(im_labels_path)
else:
labels = np.zeros(cells[0, 0, :, :].shape, dtype=np.int)
return (viewer, layer_names, labels)
def _run_benchmark(
resources_dir: Path,
extensions: List[str],
non_aicsimageio_reader: List[Callable],
iterations: int = 3,
):
# Collect files matching the extensions provided
files = []
for ext in extensions:
files += list(resources_dir.glob(ext))
# Run reads for each file and store details in results
results = []
for file in files:
info_read = aicsimageio.AICSImage(file)
yx_planes = np.prod(info_read.size("STCZ"))
for reader in [aicsimageio.imread, non_aicsimageio_reader]:
reader_path = f"{reader.__module__}.{reader.__name__}"
for i in tqdm(range(iterations),
desc=f"{reader_path}: {file.name}"):
start = time.perf_counter()
reader(str(file))
results.append({
"file_name":
file.name,
"file_size_gb":
file.stat().st_size / 10e8,
"reader": ("aicsimageio"
if "aicsimageio" in reader_path else "other"),
"yx_planes":
int(yx_planes),
"read_duration":
time.perf_counter() - start,
})
return results
def execute(self, args):
if not args.struct_name == "skip":
if not args.workflow_name == "template":
print(
"only use either workflow_name or struct_name, should use both."
)
quit()
args.workflow_name = args.struct_name
try:
if args.wrapper_dir == "_internal_":
module_name = ("aicssegmentation.structure_wrapper.seg_" +
args.workflow_name)
seg_module = importlib.import_module(module_name)
else:
func_path = args.wrapper_dir
spec = importlib.util.spec_from_file_location(
"seg_" + args.workflow_name,
func_path + "/seg_" + args.workflow_name + ".py",
)
seg_module = importlib.util.module_from_spec(spec)
try:
spec.loader.exec_module(seg_module)
except Exception as e:
print("check errors in wrapper script")
print(str(e))
class_name = "Workflow_" + args.workflow_name
SegModule = getattr(seg_module, class_name)
except Exception as e:
print(e)
print("{} structure not found".format(args.workflow_name))
sys.exit(1)
output_path = pathlib.Path(args.output_dir)
if not os.path.exists(output_path):
os.mkdir(output_path)
##########################################################################
if args.mode == PER_IMAGE:
fname = os.path.basename(os.path.splitext(args.input_fname)[0])
image_reader = aicsimageio.AICSImage(args.input_fname)
img = image_reader.data
if len(img.shape) == 6:
struct_img = img[0, 0,
args.struct_ch, :, :, :].astype(np.float32)
else:
struct_img = img[0, args.struct_ch, :, :, :].astype(np.float32)
# if args.mitotic_label == 'y':
# mitosis_seg = (args.input_fname).replace("raw", "mito_seg")
# mito_seg_reader = aicsimageio.AICSImage(mitosis_seg)
# mitosis_seg_img = mito_seg_reader.data
# mseg_img = mitosis_seg_img[0,0,:, 0, :, :].astype(np.float32)
# struct_img =struct_img * mseg_img
if args.mitotic_stage is None:
SegModule(struct_img, self.rescale_ratio, args.output_type,
output_path, fname)
else:
SegModule(
struct_img,
args.mitotic_stage,
self.rescale_ratio,
args.output_type,
output_path,
fname,
)
elif args.mode == PER_DIR:
filenames = glob(args.input_dir + "/*" + args.data_type)
# [os.path.basename(os.path.splitext(f)[0])
# for f in os.listdir(args.input_dir)
# if f.endswith(args.data_type)]
filenames.sort()
for _, fn in enumerate(filenames):
if os.path.exists(
str(output_path /
(os.path.splitext(os.path.basename(fn))[0] +
"_struct_segmentation.tiff"))):
print(f"skipping {fn} ....")
continue
image_reader = aicsimageio.AICSImage(fn)
img = image_reader.data
# import pdb; pdb.set_trace()
# fixing the image reading
if len(img.shape) == 6:
# when z and c is not in order
if img.shape[-3] < img.shape[-4]:
img = np.transpose(img, (0, 1, 3, 2, 4, 5))
struct_img = img[0, 0, args.struct_ch, :, :, :].astype(
np.float32)
else:
# when z and c is not in order
if img.shape[-3] < img.shape[-4]:
img = np.transpose(
img,
(
0,
2,
1,
3,
4,
),
)
struct_img = img[0, args.struct_ch, :, :, :].astype(
np.float32)
# Check if the segmenation is mitotic stage specific
if args.mitotic_stage is None:
SegModule(
struct_img,
self.rescale_ratio,
args.output_type,
output_path,
os.path.splitext(os.path.basename(fn))[0],
)
else:
SegModule(
struct_img,
args.mitotic_stage,
self.rescale_ratio,
args.output_type,
output_path,
fn,
)