def test_do_load_stack_sample_and_flat(self, load_p_mock: mock.Mock, load_log_mock: mock.Mock):
lp = LoadingParameters()
sample_mock = mock.Mock()
lp.sample = sample_mock
lp.dtype = "dtype_test"
lp.sinograms = False
lp.pixel_size = 101
flat_before_mock = mock.Mock()
lp.flat_before = flat_before_mock
flat_after_mock = mock.Mock()
lp.flat_after = flat_after_mock
progress_mock = mock.Mock()
self.model.do_load_stack(lp, progress_mock)
load_p_mock.assert_has_calls([
mock.call(sample_mock, lp.dtype, progress_mock),
mock.call(flat_before_mock, lp.dtype, progress_mock),
mock.call(flat_after_mock, lp.dtype, progress_mock)
])
load_log_mock.assert_has_calls([
mock.call(sample_mock.log_file),
mock.call(flat_before_mock.log_file),
mock.call(flat_after_mock.log_file)
])
def test_do_load_stack_sample_and_sample_log(self, load_p_mock: mock.Mock, load_log_mock: mock.Mock):
lp = LoadingParameters()
sample_mock = mock.Mock()
lp.sample = sample_mock
lp.dtype = "dtype_test"
lp.sinograms = False
lp.pixel_size = 101
progress_mock = mock.Mock()
self.model.do_load_stack(lp, progress_mock)
load_p_mock.assert_called_once_with(sample_mock, lp.dtype, progress_mock)
load_log_mock.assert_called_once_with(sample_mock.log_file)
def test_do_load_stack_sample_and_flat(self, dataset_mock: mock.Mock,
load_p_mock: mock.Mock,
load_log_mock: mock.Mock):
lp = LoadingParameters()
sample_mock = mock.Mock()
lp.sample = sample_mock
lp.dtype = "dtype_test"
lp.sinograms = False
lp.pixel_size = 101
flat_before_mock = mock.Mock()
lp.flat_before = flat_before_mock
flat_after_mock = mock.Mock()
lp.flat_after = flat_after_mock
progress_mock = mock.Mock()
sample_images_mock = mock.Mock()
flatb_images_mock = mock.Mock()
flata_images_mock = mock.Mock()
load_p_mock.side_effect = [
sample_images_mock, flatb_images_mock, flata_images_mock
]
ds_mock = dataset_mock.return_value
self.model.do_load_dataset(lp, progress_mock)
load_p_mock.assert_has_calls([
mock.call(sample_mock, lp.dtype, progress_mock),
mock.call(flat_before_mock, lp.dtype, progress_mock),
mock.call(flat_after_mock, lp.dtype, progress_mock)
])
load_log_mock.assert_has_calls([
mock.call(sample_mock.log_file),
mock.call(flat_before_mock.log_file),
mock.call(flat_after_mock.log_file)
])
dataset_mock.assert_called_with(sample_images_mock)
assert ds_mock.flat_before == flatb_images_mock
assert ds_mock.flat_after == flata_images_mock
def get_parameters(self) -> LoadingParameters:
lp = LoadingParameters()
sample_log = self.view.sample_log.path_text(
) if self.view.sample_log.use.isChecked() else None
lp.sample = ImageParameters(input_path=self.view.sample.directory(),
format=self.image_format,
prefix=get_prefix(
self.view.sample.path_text()),
indices=self.view.sample.indices,
log_file=sample_log)
lp.name = self.view.sample.file()
lp.pixel_size = self.view.pixelSize.value()
if self.view.flat_before.use.isChecked(
) and self.view.flat_before.path_text() != "":
flat_before_log = self.view.flat_before_log.path_text() if self.view.flat_before_log.use.isChecked() \
else None
lp.flat_before = ImageParameters(
input_path=self.view.flat_before.directory(),
prefix=get_prefix(self.view.flat_before.path_text()),
format=self.image_format,
log_file=flat_before_log)
if self.view.flat_after.use.isChecked(
) and self.view.flat_after.path_text() != "":
flat_after_log = self.view.flat_after_log.path_text() if self.view.flat_after_log.use.isChecked() \
else None
lp.flat_after = ImageParameters(
input_path=self.view.flat_after.directory(),
prefix=get_prefix(self.view.flat_after.path_text()),
format=self.image_format,
log_file=flat_after_log)
if self.view.dark_before.use.isChecked(
) and self.view.dark_before.path_text() != "":
lp.dark_before = ImageParameters(
input_path=self.view.dark_before.directory(),
prefix=get_prefix(self.view.dark_before.path_text()),
format=self.image_format)
if self.view.dark_after.use.isChecked(
) and self.view.dark_after.path_text() != "":
lp.dark_after = ImageParameters(
input_path=self.view.dark_after.directory(),
prefix=get_prefix(self.view.dark_after.path_text()),
format=self.image_format)
if self.view.proj_180deg.use.isChecked(
) and self.view.proj_180deg.path_text() != "":
lp.proj_180deg = ImageParameters(
input_path=self.view.proj_180deg.directory(),
prefix=os.path.splitext(self.view.proj_180deg.path_text())[0],
format=self.image_format)
lp.dtype = self.view.pixel_bit_depth.currentText()
lp.sinograms = self.view.images_are_sinograms.isChecked()
lp.pixel_size = self.view.pixelSize.value()
return lp
def get_parameters(self) -> LoadingParameters:
lp = LoadingParameters()
lp.sample = ImageParameters(input_path=self.view.sample.directory(),
format=self.image_format,
prefix=get_prefix(
self.view.sample.path_text()),
indices=self.view.sample.indices,
log_file=self.view.sample_log.path_text())
lp.name = self.view.sample.file()
lp.pixel_size = self.view.pixelSize.value()
if self.view.flat.use and self.view.flat.path_text() != "":
lp.flat = ImageParameters(input_path=self.view.flat.directory(),
prefix=get_prefix(
self.view.flat.path_text()),
format=self.image_format)
if self.view.dark.use and self.view.dark.path_text() != "":
lp.dark = ImageParameters(input_path=self.view.dark.directory(),
prefix=get_prefix(
self.view.dark.path_text()),
format=self.image_format)
if self.view.proj_180deg.use and self.view.proj_180deg.path_text(
) != "":
lp.proj_180deg = ImageParameters(
input_path=self.view.proj_180deg.directory(),
prefix=get_prefix(self.view.proj_180deg.path_text()),
format=self.image_format)
lp.dtype = self.view.pixel_bit_depth.currentText()
lp.sinograms = self.view.images_are_sinograms.isChecked()
lp.pixel_size = self.view.pixelSize.value()
return lp
def create_loading_parameters_for_file_path(
file_path: str,
logger: Optional[Logger] = None) -> Optional[LoadingParameters]:
sample_file = find_first_file_that_is_possibly_a_sample(file_path)
if sample_file is None:
return None
loading_parameters = LoadingParameters()
loading_parameters.dtype = DEFAULT_PIXEL_DEPTH
loading_parameters.pixel_size = DEFAULT_PIXEL_SIZE
loading_parameters.sinograms = DEFAULT_IS_SINOGRAM
loading_parameters.name = os.path.basename(sample_file)
_, image_format = os.path.splitext(sample_file)
sample_directory = os.path.dirname(sample_file)
last_file_info = read_in_file_information(
sample_directory,
in_prefix=get_prefix(sample_file),
in_format=image_format)
try:
sample_log: Optional[str] = find_and_verify_sample_log(
sample_directory, last_file_info.filenames)
except FileNotFoundError:
sample_log = None
loading_parameters.sample = ImageParameters(input_path=sample_directory,
format=image_format,
prefix=get_prefix(sample_file),
log_file=sample_log)
# Flat before
flat_before_images = find_images(Path(sample_directory),
"Flat",
suffix="Before",
look_without_suffix=True,
image_format=image_format,
logger=logger)
if len(flat_before_images) > 0:
flat_before_image = flat_before_images[0]
flat_before_directory = os.path.dirname(flat_before_image)
flat_before_log = find_log(Path(sample_directory),
flat_before_directory, logger)
loading_parameters.flat_before = ImageParameters(
input_path=flat_before_directory,
format=image_format,
prefix=get_prefix(flat_before_image),
log_file=flat_before_log)
# Flat after
flat_after_images = find_images(Path(sample_directory),
"Flat",
suffix="After",
image_format=image_format,
logger=logger)
if len(flat_after_images) > 0:
flat_after_image = flat_after_images[0]
flat_after_directory = os.path.dirname(flat_after_image)
flat_after_log = find_log(Path(sample_directory), flat_after_directory,
logger)
loading_parameters.flat_after = ImageParameters(
input_path=flat_after_directory,
format=image_format,
prefix=get_prefix(flat_after_image),
log_file=flat_after_log)
# Dark before
dark_before_images = find_images(Path(sample_directory),
"Dark",
suffix="Before",
look_without_suffix=True,
image_format=image_format,
logger=logger)
if len(dark_before_images) > 0:
dark_before_image = dark_before_images[0]
dark_before_directory = os.path.dirname(dark_before_image)
loading_parameters.dark_before = ImageParameters(
input_path=dark_before_directory,
prefix=get_prefix(dark_before_image),
format=image_format)
# Dark after
dark_after_images = find_images(Path(sample_directory),
"Dark",
suffix="After",
image_format=image_format,
logger=logger)
if len(dark_after_images) > 0:
dark_after_image = dark_after_images[0]
dark_after_directory = os.path.dirname(dark_after_image)
loading_parameters.dark_after = ImageParameters(
input_path=dark_after_directory,
prefix=get_prefix(dark_after_image),
format=image_format)
# 180 Degree projection
proj_180deg = find_180deg_proj(Path(sample_directory), image_format,
logger)
if proj_180deg != "":
loading_parameters.proj_180deg = ImageParameters(
input_path=proj_180deg,
prefix=get_prefix(proj_180deg),
format=image_format)
return loading_parameters