def test_obsep_deconv_read(self, data_test_dir, tmp_path):
for el in glob(os.path.join(data_test_dir, "obsep", "*")):
shutil.copy(os.path.join(data_test_dir, "obsep", el), tmp_path)
image = GenericImageReader.read_image(tmp_path / "test.obsep")
assert image.channels == 2
assert np.allclose(image.spacing, (500 * 10 ** -9, 64 * 10 ** -9, 64 * 10 ** -9))
assert image.channel_names == ["channel 1", "channel 2"]
shutil.copy(tmp_path / "Cy5.TIF", tmp_path / "Cy5_decon2.TIF")
image = GenericImageReader.read_image(tmp_path / "test.obsep")
assert image.channels == 2
shutil.copy(tmp_path / "Cy5.TIF", tmp_path / "Cy5_deconv.TIF")
image = GenericImageReader.read_image(tmp_path / "test.obsep")
assert image.channels == 3
def load(
cls,
load_locations: typing.List[typing.Union[str, BytesIO, Path]],
range_changed: typing.Callable[[int, int], typing.Any] = None,
step_changed: typing.Callable[[int], typing.Any] = None,
metadata: typing.Optional[dict] = None,
):
if metadata is None:
metadata = {"default_spacing": (10**-6, 10**-6, 10**-6)}
if len(load_locations) == 1:
new_path, ext = os.path.splitext(load_locations[0])
new_path += "_mask" + ext
if not os.path.exists(new_path):
raise ValueError(
"Cannot determine mask file. It need to have '_mask' suffix."
)
load_locations.append(load_locations)
image = GenericImageReader.read_image(
load_locations[0],
load_locations[1],
callback_function=partial(proxy_callback, range_changed,
step_changed),
default_spacing=tuple(metadata["default_spacing"]),
)
return ProjectTuple(load_locations[0], image, mask=image.mask)
def load(
cls,
load_locations: typing.List[typing.Union[str, BytesIO, Path]],
range_changed: typing.Callable[[int, int], typing.Any] = None,
step_changed: typing.Callable[[int], typing.Any] = None,
metadata: typing.Optional[dict] = None,
):
if metadata is None:
metadata = {
"default_spacing":
tuple([1 / UNIT_SCALE[Units.nm.value] for _ in range(3)])
}
if "recursion_limit" not in metadata:
metadata = copy(metadata)
metadata["recursion_limit"] = 3
image = GenericImageReader.read_image(
load_locations[0],
callback_function=partial(proxy_callback, range_changed,
step_changed),
default_spacing=tuple(metadata["default_spacing"]),
)
re_read = True
for el in image.get_ranges():
if el[0] != el[1]:
re_read = False
if re_read and metadata["recursion_limit"] > 0:
metadata["recursion_limit"] -= 1
cls.load(load_locations, range_changed, step_changed, metadata)
return ProjectTuple(load_locations[0], image)
def load(
cls,
load_locations: typing.List[typing.Union[str, BytesIO, Path]],
range_changed: typing.Callable[[int, int], typing.Any] = None,
step_changed: typing.Callable[[int], typing.Any] = None,
metadata: typing.Optional[dict] = None,
) -> MaskProjectTuple:
if metadata is None:
metadata = {"default_spacing": (10**-6, 10**-6, 10**-6)}
image = GenericImageReader.read_image(
load_locations[0],
callback_function=partial(proxy_callback, range_changed,
step_changed),
default_spacing=metadata["default_spacing"],
)
return MaskProjectTuple(image.file_path, image, selected_components=[])
def load(
cls,
load_locations: typing.List[typing.Union[str, BytesIO, Path]],
range_changed: typing.Callable[[int, int], typing.Any] = None,
step_changed: typing.Callable[[int], typing.Any] = None,
metadata: typing.Optional[dict] = None,
) -> SegmentationTuple:
seg = LoadSegmentation.load(load_locations)
if len(load_locations) > 1:
base_file = load_locations[1]
else:
base_file = seg.image
if base_file is None:
raise IOError("base file for segmentation not defined")
if os.path.isabs(base_file):
file_path = base_file
else:
if not isinstance(load_locations[0], str):
raise IOError(
f"Cannot use relative path {base_file} for non path argument"
)
file_path = os.path.join(os.path.dirname(load_locations[0]),
base_file)
if not os.path.exists(file_path):
raise IOError(
f"Base file for segmentation do not exists: {base_file} -> {file_path}"
)
if metadata is None:
metadata = {"default_spacing": (10**-6, 10**-6, 10**-6)}
image = GenericImageReader.read_image(
file_path,
callback_function=partial(proxy_callback, range_changed,
step_changed),
default_spacing=metadata["default_spacing"],
)
# noinspection PyProtectedMember
# image.file_path = load_locations[0]
return dataclasses.replace(seg,
file_path=image.file_path,
image=image,
segmentation=image.fit_array_to_image(
seg.segmentation))
def load_project(
file: typing.Union[str, Path, tarfile.TarFile, TextIOBase, BufferedIOBase,
RawIOBase, IOBase]
) -> ProjectTuple:
"""Load project from archive"""
tar_file, file_path = open_tar_file(file)
try:
if check_segmentation_type(tar_file) != SegmentationType.analysis:
raise WrongFileTypeException()
image_buffer = BytesIO()
image_tar = tar_file.extractfile(tar_file.getmember("image.tif"))
image_buffer.write(image_tar.read())
image_buffer.seek(0)
reader = GenericImageReader()
image = reader.read(image_buffer, ext=".tif")
image.file_path = file_path
algorithm_str = tar_file.extractfile("algorithm.json").read()
algorithm_dict = load_metadata(algorithm_str)
algorithm_dict = update_algorithm_dict(algorithm_dict)
algorithm_dict.get("project_file_version")
try:
version = parse_version(
json.loads(tar_file.extractfile("metadata.json").read())
["project_version_info"])
except KeyError:
version = Version("1.0")
if version == Version("1.0"):
seg_dict = np.load(tar_to_buff(tar_file, "segmentation.npz"))
mask = seg_dict["mask"] if "mask" in seg_dict else None
segmentation = seg_dict["segmentation"]
else:
segmentation = tifffile.imread(
tar_to_buff(tar_file, "segmentation.tif"))
if "mask.tif" in tar_file.getnames():
mask = tifffile.imread(tar_to_buff(tar_file, "mask.tif"))
if np.max(mask) == 1:
mask = mask.astype(np.bool)
else:
mask = None
history = []
try:
history_buff = tar_file.extractfile(
tar_file.getmember("history/history.json")).read()
history_json = load_metadata(history_buff)
for el in history_json:
history_buffer = BytesIO()
history_buffer.write(
tar_file.extractfile(
f"history/arrays_{el['index']}.npz").read())
history_buffer.seek(0)
el = update_algorithm_dict(el)
segmentation_parameters = {
"algorithm_name": el["algorithm_name"],
"values": el["values"]
}
history.append(
HistoryElement(
segmentation_parameters=segmentation_parameters,
mask_property=el["mask_property"],
arrays=history_buffer,
))
except KeyError:
pass
finally:
if isinstance(file, (str, Path)):
tar_file.close()
image.set_mask(mask)
if version <= project_version_info:
return ProjectTuple(
file_path=file_path,
image=image,
roi=segmentation,
mask=mask,
history=history,
algorithm_parameters=algorithm_dict,
)
print("This project is from new version of PartSeg:",
version,
project_version_info,
file=sys.stderr)
return ProjectTuple(
file_path=file_path,
image=image,
roi=segmentation,
mask=mask,
history=history,
algorithm_parameters=algorithm_dict,
errors=
"This project is from new version of PartSeg. It may load incorrect.",
)
def test_generic_reader(self, data_test_dir):
GenericImageReader.read_image(
os.path.join(data_test_dir, "stack1_components", "stack1_component1.tif"),
os.path.join(data_test_dir, "stack1_components", "stack1_component1_mask.tif"),
)
GenericImageReader.read_image(os.path.join(data_test_dir, "test_czi.czi"))
GenericImageReader.read_image(os.path.join(data_test_dir, "test_lsm2.tif"))
GenericImageReader.read_image(os.path.join(data_test_dir, "test_lsm.tif"))
GenericImageReader.read_image(os.path.join(data_test_dir, "Image0003_01.oif"))
GenericImageReader.read_image(os.path.join(data_test_dir, "N2A_H2BGFP_dapi_falloidin_cycling1.oib"))
from PartSegCore.io_utils import load_metadata_base
from PartSegCore.segmentation.segmentation_algorithm import ThresholdPreview
from PartSegImage import GenericImageReader
file_path = "/home/czaki/Dokumenty/smFish/smFISH_7_001_with_points/test.obsep"
profile_str = '{"__SegmentationProfile__": true, "name": "", "algorithm": "Only Threshold", "values": {"channel": 1, "noise_filtering": {"name": "Gauss", "values": {"dimension_type": {"__Enum__": true, "__subtype__": "PartSegCore.segmentation.noise_filtering.DimensionType", "value": 1}, "radius": 1.0}}, "threshold": 300}}'
profile = load_metadata_base(profile_str)
image = GenericImageReader.read_image(file_path)
algorithm = ThresholdPreview()
algorithm.set_image(image)
algorithm.set_parameters(**profile.values)
res = algorithm.calculation_run(lambda x, y: x)