Source code for mantidimaging.core.operations.crop_coords.crop_coords

# 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

    from 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 = 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.left:roi.right] return output