# Copyright (C) 2024 ISIS Rutherford Appleton Laboratory UKRI
# SPDX - License - Identifier: GPL-3.0-or-later
from __future__ import annotations
from functools import partial
from typing import TYPE_CHECKING
from skimage.transform import rotate
from PyQt5.QtWidgets import QComboBox
from mantidimaging import helper as h
from mantidimaging.core.operations.base_filter import BaseFilter
from mantidimaging.core.parallel import shared as ps
from mantidimaging.core.utility.progress_reporting import Progress
from mantidimaging.core.parallel import utility as pu
from mantidimaging.gui.utility.qt_helpers import Type
import numpy as np
if TYPE_CHECKING:
from mantidimaging.core.data import ImageStack
[docs]
class RotateFilter(BaseFilter):
"""Rotates the image data by an arbitrary degree counter-clockwise.
Intended to be used on: Projections
When: 90 or 270 degree rotation for rotation axis to be vertical for some camera types.
Caution: Rotations of images others than multiples of 90 degrees could introduce additional
artifacts in the reconstructed volume. Such rotations are usually not required as
small tilts can be taken into account at the reconstruction stage.
"""
filter_name = "Rotate Stack"
link_histograms = True
[docs]
@staticmethod
def filter_func(data: ImageStack, angle=None, progress=None):
"""
Rotates images by an arbitrary degree.
param data: stack of sample images
param angle: The rotation to be performed, in degrees
return: The rotated images
"""
h.check_data_stack(data)
if angle is None:
raise ValueError('Value must be provided for angle parameter')
progress = Progress.ensure_instance(progress, task_name='Rotate Stack')
_do_rotation(data, round(angle, 3), progress)
return data
[docs]
@staticmethod
def register_gui(form, on_change, view):
from mantidimaging.gui.utility import add_property_to_form
dropdown = QComboBox()
dropdown.addItems(['90', '180', '270', 'Custom'])
_, dropdown = add_property_to_form('Angle presets (degrees)',
Type.CHOICE,
0, ('0', '90', '180', '270', "Custom"),
form=form,
on_change=on_change,
tooltip="How much degrees to rotate counter-clockwise")
_, angle = add_property_to_form('Custom Angle of rotation\ncounter clockwise (degrees)',
Type.FLOAT,
0, (-359, 359),
form=form,
on_change=on_change,
tooltip="How much degrees to rotate counter-clockwise")
angle.setDecimals(3)
angle.setEnabled(False)
dropdown.currentTextChanged.connect(lambda text: RotateFilter._update_angle(angle, dropdown))
return {"angle": angle}
[docs]
@staticmethod
def execute_wrapper(angle=None):
return partial(RotateFilter.filter_func, angle=angle.value())
@staticmethod
def _update_angle(angle, dropdown):
"""
Handle Dropdown change event to set value is angle is not custom
:param angle: angle widget
:param dropdown: dropdown widget
"""
if dropdown.currentText() == 'Custom':
angle.setEnabled(True)
else:
angle.setValue(float(dropdown.currentText()))
angle.setEnabled(False)
def _get_cardinal_angle(general_angle) -> int:
"""
Calculates the cardinal angle based on the general input angle by rounding to
the nearest 90 degree and then mod 360. Ths is used to determine if the angle
is a cardinal angle or not and also return a cardinal angle for in-place rotations.
param: value: general angle of rotation
return: angle: cardinal angle of rotation
"""
return (round(general_angle / 90) * 90) % 360
def _do_rotation(data, angle, progress) -> np.ndarray:
"""
Handle rotation of image slice by angle. This includes rotation of aspect
ratio and in place rotation depending on angle.
param array_index: index of array in array_list
param data: current image data array
param angle: angle of rotation
return: new_data: rotated image data array
"""
angle = angle % 360
if angle == _get_cardinal_angle(angle):
data.shared_array = _cardinal_rotation_per_slice(data, angle, progress)
else:
data.shared_array = _cardinal_rotation_per_slice(data, _get_cardinal_angle(angle), progress)
data.shared_array = _inplace_rotation(data.data.shape[0], data, angle - _get_cardinal_angle(angle), progress)
return data
def _cardinal_rotation_per_slice(data: ImageStack, angle: float, progress) -> pu.SharedArray:
"""
Perform a cardinal rotation of the image stack by angle if angle is cardinal and additionally
in-place rotation if general angle.
param: data: current image data array
param: angle: angle of rotation
param: progress: progress bar
return: new_data: rotated image data array
"""
z_axis, y_axis, x_axis = data.data.shape
rotated_shape: tuple = (z_axis, x_axis, y_axis)
if angle == 0 or angle == 180:
new_data = _inplace_rotation(z_axis, data, angle, progress)
else:
new_data = pu.create_array(rotated_shape, data.data.dtype)
ps.run_compute_func(_compute_cardinal_rotation_per_slice, z_axis, [data.shared_array, new_data],
{"angle": angle}, progress)
return new_data
def _inplace_rotation(number_of_slices: int, data, angle: float, progress) -> pu.SharedArray:
"""
In-place rotation of image slices by angle.
param: number_of_slices: array slices
param: data: current image data array
param: angle: angle of rotation
param: progress: progress bar
return: new_data: rotated image data array
"""
ps.run_compute_func(_compute_rotation_per_slice_inplace, number_of_slices, data.shared_array, {"angle": angle},
progress)
return data.shared_array
def _compute_cardinal_rotation_per_slice(array_index, array_list, angle):
"""
Rotate array in increments of 90 degrees.
param: array_index: index of array in array_list
param: array_list: list of arrays - [old_array, new_array]
param: angle: angle of rotation
"""
cardinal_rotation = {0: 0, 90: 1, 180: 2, 270: 3}
array_list[1][array_index] = np.rot90(array_list[0][array_index], k=cardinal_rotation[angle["angle"]])
def _compute_rotation_per_slice_inplace(array_index, array_list, angle):
"""
Rotate array in-place so that aspect ratio is not changed
param: array_list: list of arrays - [array]
param: angle: angle of rotation
"""
array_list[array_index] = rotate(array_list[array_index], angle["angle"])