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 load_stack(file_path: str, progress: Optional[Progress] = None) -> Images:
image_format = get_file_extension(file_path)
prefix = get_prefix(file_path)
file_names = get_file_names(path=os.path.dirname(file_path),
img_format=image_format,
prefix=prefix) # type: ignore
return load(file_names=file_names, progress=progress).sample
def load_data(
self, file_path: Optional[str]
) -> Tuple[Optional[np.ndarray], Optional[List[str]]]:
if file_path:
file_names = get_file_names(os.path.dirname(file_path),
self.img_format, get_prefix(file_path))
return self.load_files(file_names), file_names
return None, None
def load_data(
self, file_path
) -> Tuple[Optional[np.ndarray], Optional[List[str]], Optional[str]]:
if file_path:
file_names = get_file_names(os.path.dirname(file_path),
self.img_format, get_prefix(file_path))
memory_file_name = pu.create_shared_name(file_names[0])
return self.load_files(
file_names, memory_file_name), file_names, memory_file_name
return None, None, None
def do_update_sample(self):
"""
Updates the memory usage and the indices in the dialog.
"""
selected_file = self.view.select_file("Sample")
if not selected_file:
return False
self.view.sample.path = selected_file
self.view.sample.widget.setExpanded(True)
sample_filename = self.view.sample.file()
self.image_format = get_file_extension(sample_filename)
filename = self.view.sample.path_text()
dirname = self.view.sample.directory()
try:
self.last_file_info = read_in_file_information(dirname,
in_prefix=get_prefix(filename),
in_format=self.image_format)
except Exception as e:
getLogger(__name__).error(f"Failed to read file {sample_filename} {e}")
self.view.show_error("Failed to read this file. See log for details.", traceback.format_exc())
self.last_file_info = None
return
sample_dirname = Path(dirname)
self.view.flat_before.set_images(
self._find_images(sample_dirname, "Flat", suffix="Before", look_without_suffix=True))
self.view.flat_after.set_images(self._find_images(sample_dirname, "Flat", suffix="After"))
self.view.dark_before.set_images(
self._find_images(sample_dirname, "Dark", suffix="Before", look_without_suffix=True))
self.view.dark_after.set_images(self._find_images(sample_dirname, "Dark", suffix="After"))
self.view.proj_180deg.path = self._find_180deg_proj(sample_dirname)
try:
self.set_sample_log(self.view.sample_log, sample_dirname, self.view.sample.directory(),
self.last_file_info.filenames)
except RuntimeError as err:
self.view.show_error(str(err), traceback.format_exc())
self.view.sample_log.use = False
self.view.flat_before_log.path = self._find_log(sample_dirname, self.view.flat_before.directory())
self.view.flat_before_log.use = False
self.view.flat_after_log.path = self._find_log(sample_dirname, self.view.flat_after.directory())
self.view.flat_after_log.use = False
self.view.images_are_sinograms.setChecked(self.last_file_info.sinograms)
self.view.sample.update_indices(self.last_file_info.shape[0])
self.view.sample.update_shape(self.last_file_info.shape[1:])
def do_update_sample(self):
"""
Updates the memory usage and the indices in the dialog.
"""
selected_file = self.view.select_file("Sample")
if not selected_file:
return False
self.view.sample.path = selected_file
self.view.sample.widget.setExpanded(True)
sample_filename = self.view.sample.file()
self.image_format = get_file_extension(sample_filename)
filename = self.view.sample.path_text()
dirname = self.view.sample.directory()
try:
self.last_shape, sinograms = read_in_shape(
dirname,
in_prefix=get_prefix(filename),
in_format=self.image_format)
except Exception as e:
getLogger(__name__).error(
f"Failed to read file {sample_filename} {e}")
self.view.show_error(
"Failed to read this file. See log for details.",
traceback.format_exc())
self.last_shape = (0, 0, 0)
sinograms = False
sample_dirname = Path(dirname)
self.view.flat.set_images(self._find_images(sample_dirname, "Flat"))
self.view.dark.set_images(self._find_images(sample_dirname, "Dark"))
self.view.proj_180deg.path = self._find_180deg_proj(sample_dirname)
self.view.sample_log.path = self._find_log(
sample_dirname, self.view.sample.directory())
self.view.sample_log.use = False
self.view.flat_log.path = self._find_log(sample_dirname,
self.view.flat.directory())
self.view.flat_log.use = False
self.view.images_are_sinograms.setChecked(sinograms)
self.view.sample.update_indices(self.last_shape[0])
self.view.sample.update_shape(self.last_shape[1:])
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
