# Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
from __future__ import annotations
from functools import partial
from typing import Union, Optional, List, TYPE_CHECKING
from mantidimaging import helper as h
from mantidimaging.core.operations.base_filter import BaseFilter, FilterGroup
from mantidimaging.core.parallel import utility as pu
from mantidimaging.core.utility.progress_reporting import Progress
from mantidimaging.core.utility.sensible_roi import SensibleROI
from mantidimaging.gui.utility.qt_helpers import Type
if TYPE_CHECKING:
from mantidimaging.core.data import ImageStack
from PyQt5.QtWidgets import QLineEdit
[docs]class CropCoordinatesFilter(BaseFilter):
"""Crop a region of interest from the image.
Intended to be used on: A stack of projections, or reconstructed slices
When: To select part of the image that is to be processed further; this reduces
memory usage and can greatly improve the speed of reconstruction.
Caution: Make sure the region of cropping does not crop parts of the sample
during the rotation of the sample in the dataset.
"""
filter_name = "Crop Coordinates"
link_histograms = True
[docs] @staticmethod
def filter_func(images: ImageStack,
region_of_interest: Optional[Union[List[int], List[float], SensibleROI]] = None,
progress=None) -> ImageStack:
"""Execute the Crop Coordinates by Region of Interest filter. This does
NOT do any checks if the Region of interest is out of bounds!
If the region of interest is out of bounds, the crop will **FAIL** at
runtime.
If the region of interest is in bounds, but has overlapping coordinates
the crop give back a 0 shape of the coordinates that were wrong.
:param images: Input data as a 3D numpy.ndarray
:param region_of_interest: Crop original images using these coordinates.
The selection is a rectangle and expected order
is - Left Top Right Bottom.
:return: The processed 3D numpy.ndarray
"""
if region_of_interest is None:
region_of_interest = SensibleROI.from_list([0, 0, 50, 50])
if isinstance(region_of_interest, list):
region_of_interest = SensibleROI.from_list(region_of_interest)
assert isinstance(region_of_interest, SensibleROI)
h.check_data_stack(images)
sample = images.data
shape = (sample.shape[0], region_of_interest.height, region_of_interest.width)
if any((s < 0 for s in shape)):
raise ValueError("It seems the Region of Interest is outside of the current image dimensions.\n"
"This can happen on the image preview right after a previous Crop Coordinates.")
output = pu.create_array(shape, images.dtype)
execute_single(sample, region_of_interest, progress, out=output.array)
images.shared_array = output
return images
[docs] @staticmethod
def register_gui(form, on_change, view):
from mantidimaging.gui.utility import add_property_to_form
label, roi_field = add_property_to_form("ROI",
Type.STR,
form=form,
on_change=on_change,
default_value="0, 0, 200, 200")
roi_button, _ = add_property_to_form("Select ROI", Type.BUTTON, form=form, on_change=on_change)
roi_button.clicked.connect(lambda: view.roi_visualiser(roi_field, roi_button))
return {'roi_field': roi_field}
[docs] @staticmethod
def execute_wrapper(roi_field: QLineEdit) -> partial:
try:
roi = SensibleROI.from_list([int(number) for number in roi_field.text().strip("[").strip("]").split(",")])
return partial(CropCoordinatesFilter.filter_func, region_of_interest=roi)
except Exception as e:
raise ValueError(f"The provided ROI string is invalid! Error: {e}")
[docs] @staticmethod
def group_name() -> FilterGroup:
return FilterGroup.Basic
[docs]def execute_single(data, roi, progress=None, out=None):
progress = Progress.ensure_instance(progress, task_name='Crop Coords')
if roi:
progress.add_estimated_steps(1)
with progress:
assert all(isinstance(region, int) for
region in roi), \
"The region of interest coordinates are not integers!"
progress.update(msg="Cropping with coordinates: {0}".format(roi))
output = out[:] if out is not None else data[:]
output[:] = data[:, roi.top:roi.bottom, roi.left:roi.right]
return output