# Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
"""
This module handles the loading of FIT, FITS, TIF, TIFF
"""
from __future__ import annotations
from typing import Tuple, Optional, List, Callable, Union, TYPE_CHECKING
from mantidimaging.core.data import ImageStack
from mantidimaging.core.parallel import utility as pu
from mantidimaging.core.utility.progress_reporting import Progress
if TYPE_CHECKING:
import numpy as np
import numpy.typing as npt
from ...utility.data_containers import Indices
[docs]def execute(load_func: Callable[[str], np.ndarray],
sample_path: List[str],
img_format: str,
dtype: 'npt.DTypeLike',
indices: Union[List[int], Indices, None],
progress: Optional[Progress] = None) -> ImageStack:
"""
Reads a stack of images into memory, assuming dark and flat images
are in separate directories.
Usual type in fits is 16-bit pixel depth, data type is denoted with:
'>i2' - uint16
'>f2' - float16
'>f4' - float32
:returns: ImageStack object
"""
if not sample_path:
raise RuntimeError("No filenames were provided.")
# The following codes assume that all images have the same size and properties as the first.
# This is always true in the case of raw data
first_sample_img = load_func(sample_path[0])
# select the files loaded based on the indices, if any are provided
chosen_input_filenames = sample_path[indices[0]:indices[1]:indices[2]] if indices else sample_path
# get the shape of all images
img_shape = first_sample_img.shape
# forward all arguments to internal class for easy re-usage
il = ImageLoader(load_func, img_format, img_shape, dtype, indices, progress)
sample_data = il.load_sample_data(chosen_input_filenames)
return ImageStack(sample_data, chosen_input_filenames, indices)
[docs]class ImageLoader(object):
def __init__(self,
load_func: Callable[[str], np.ndarray],
img_format: str,
img_shape: Tuple[int, ...],
data_dtype: 'npt.DTypeLike',
indices: Union[List[int], Indices, None],
progress: Optional[Progress] = None):
self.load_func = load_func
self.img_format = img_format
self.img_shape = img_shape
self.data_dtype = data_dtype
self.indices = indices
self.progress = progress
[docs] def load_sample_data(self, input_file_names: List[str]) -> pu.SharedArray:
# determine what the loaded data was
if len(self.img_shape) == 2:
# the loaded file was a single image
return self.load_files(input_file_names)
else:
raise ValueError(f"Data loaded has invalid shape: {self.img_shape}")
def _do_files_load_seq(self, data: pu.SharedArray, files: List[str]) -> pu.SharedArray:
progress = Progress.ensure_instance(self.progress, num_steps=len(files), task_name='Loading')
with progress:
for idx, in_file in enumerate(files):
try:
data.array[idx, :] = self.load_func(in_file)
progress.update(msg='Image')
except ValueError as exc:
raise ValueError("An image has different width and/or height "
"dimensions! All images must have the same "
f"dimensions. Expected dimensions: {self.img_shape} Error "
f"message: {exc}") from exc
except IOError as exc:
raise RuntimeError(f"Could not load file {in_file}. Error details: {exc}") from exc
return data
[docs] def load_files(self, files: List[str]) -> pu.SharedArray:
# Zeroing here to make sure that we can allocate the memory.
# If it's not possible better crash here than later.
num_images = len(files)
shape = (num_images, self.img_shape[0], self.img_shape[1])
data = pu.create_array(shape, self.data_dtype)
return self._do_files_load_seq(data, files)