Merge branch 'main' into dask_live_viewer

.github/actions/publish-package/action.yml

@@ -31,7 +31,7 @@ runs:
       conda config --set always_yes yes --set changeps1 no
       # Install build requirements
       # We can't use the makefile target for this because the CONDA_ACTIVATE command is incompatible with GitHub Actions Windows runners
-      conda create -n build-env --yes boa anaconda-client conda-verify
+      conda create -n build-env --yes boa anaconda-client
       conda activate build-env
       # Configure the conda channels
       conda config --env $(cat environment.yml | sed -ne '/channels:/,/dependencies:/{//!p}' | grep '^  -' | sed 's/ - / --append channels /g' | tr -d '\n')

.github/workflows/cos7_testing.yml → .github/workflows/rocky_testing.yml

@@ -1,4 +1,4 @@
-name: Testing with CentOS 7 docker
+name: Testing with Rocky docker
 
 on:
   push:
@@ -16,42 +16,42 @@ concurrency:
 
 jobs:
   test:
-    # It is hosted on Ubuntu but the docker image is built on CentOS 7
+    # It is hosted on Ubuntu but the docker image is built on Rocky
     runs-on: ubuntu-latest
 
     steps:
     - uses: actions/checkout@v4
 
     - name: Pre-load docker image
-      run: docker pull ghcr.io/mantidproject/mantidimaging:centos7
+      run: docker pull ghcr.io/mantidproject/mantidimaging:rocky8
 
     - name: List versions
       uses: ./.github/actions/test
       with:
         command: python --version; conda list ; pip list
-        label: centos7
+        label: rocky8
 
     - name: yapf
       uses: ./.github/actions/test
       with:
         command: yapf --parallel --diff --recursive .
-        label: centos7
+        label: rocky8
 
     - name: ruff
       uses: ./.github/actions/test
       with:
         command: ruff check .
-        label: centos7
+        label: rocky8
 
     - name: mypy
       uses: ./.github/actions/test
       with:
         command: mypy --ignore-missing-imports mantidimaging
-        label: centos7
+        label: rocky8
 
     - name: pytest
       timeout-minutes: 5
       uses: ./.github/actions/test
       with:
         command: xvfb-run pytest -n auto -o log_cli=true --ignore=mantidimaging/eyes_tests --durations=10
-        label: centos7
+        label: rocky8

conda/meta.yaml

@@ -13,7 +13,7 @@ source:
 requirements:
   build:
     - python=3.12.*
-    - setuptools=62.*
+    - setuptools=72.*
   run:
     - python=3.12.*
     - pip

docs/installation.rst

@@ -17,7 +17,7 @@ Requirements
 ------------
 
 Operating system
- - Linux. Tested on Ubuntu 18.04, 20.04, 22.04 and CentOS 7
+ - Linux. Tested on Ubuntu 18.04, 20.04, 22.04 and Rocky 8
  - Windows. Tested on Windows 10
 
 GPU

docs/release_notes/next/feature-2273-live-view-img-timestamp

@@ -0,0 +1 @@
+#2273: Display the modified image timestamp within the live viewer to allow for easier determination of what scan is being displayed within the live viewer. 

docs/release_notes/next/fix-2285-crop-coord-stack-bounds

@@ -0,0 +1 @@
+#2285: Resolve operations windows crop co-ordinates ROI size from being larger than stack bounds. Additionally resolve ROI crop co-ordinate dialog window persistence if parent window closed.

mantidimaging/eyes_tests/live_viewer_window_test.py

@@ -1,21 +1,27 @@
 # Copyright (C) 2024 ISIS Rutherford Appleton Laboratory UKRI
 # SPDX - License - Identifier: GPL-3.0-or-later
-from __future__ import annotations
 
+from __future__ import annotations
+from typing import TYPE_CHECKING
 from unittest import mock
-
 import numpy as np
-
+import os
 from mantidimaging.core.operations.loader import load_filter_packages
 from mantidimaging.gui.windows.live_viewer.model import Image_Data
 from mantidimaging.test_helpers.unit_test_helper import FakeFSTestCase
 from pathlib import Path
-
 from mantidimaging.eyes_tests.base_eyes import BaseEyesTest
 
+if TYPE_CHECKING:
+    import time  # noqa: F401
+
 
 class LiveViewerWindowTest(FakeFSTestCase, BaseEyesTest):
 
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self.initial_time = 4000.0
+
     @classmethod
     def setUpClass(cls) -> None:
         super().setUpClass()
@@ -30,26 +36,30 @@ def setUp(self) -> None:
     def _generate_image(self):
         image = np.zeros((10, 10))
         image[5, :] = np.arange(10)
+        os.utime(self.live_directory, (10, self.initial_time))
+        self.initial_time += 1000
         return image
 
     def _make_simple_dir(self, directory: Path):
         file_list = [directory / f"abc_{i:06d}.tif" for i in range(5)]
-        if not directory.exists():
-            self.fs.create_dir(directory)
-
+        increment = 0
         for file in file_list:
             self.fs.create_file(file)
+            os.utime(file, (10, self.initial_time + increment))
+            increment += 1000
 
         return file_list
 
     @mock.patch('mantidimaging.gui.windows.live_viewer.model.ImageWatcher')
-    def test_live_view_opens_without_data(self, _mock_image_watcher):
+    @mock.patch("time.time", return_value=4000.0)
+    def test_live_view_opens_without_data(self, _mock_time, _mock_image_watcher):
         self.imaging.show_live_viewer(self.live_directory)
         self.check_target(widget=self.imaging.live_viewer)
 
     @mock.patch('mantidimaging.gui.windows.live_viewer.presenter.LiveViewerWindowPresenter.load_image')
     @mock.patch('mantidimaging.gui.windows.live_viewer.model.ImageWatcher')
-    def test_live_view_opens_with_data(self, _mock_image_watcher, mock_load_image):
+    @mock.patch("time.time", return_value=4000.0)
+    def test_live_view_opens_with_data(self, _mock_time, _mock_image_watcher, mock_load_image):
         file_list = self._make_simple_dir(self.live_directory)
         image_list = [Image_Data(path) for path in file_list]
         mock_load_image.return_value = self._generate_image()
@@ -59,7 +69,8 @@ def test_live_view_opens_with_data(self, _mock_image_watcher, mock_load_image):
 
     @mock.patch('mantidimaging.gui.windows.live_viewer.presenter.LiveViewerWindowPresenter.load_image')
     @mock.patch('mantidimaging.gui.windows.live_viewer.model.ImageWatcher')
-    def test_live_view_opens_with_bad_data(self, _mock_image_watcher, mock_load_image):
+    @mock.patch("time.time", return_value=4000.0)
+    def test_live_view_opens_with_bad_data(self, _mock_time, _mock_image_watcher, mock_load_image):
         file_list = self._make_simple_dir(self.live_directory)
         image_list = [Image_Data(path) for path in file_list]
         mock_load_image.side_effect = ValueError
@@ -69,7 +80,8 @@ def test_live_view_opens_with_bad_data(self, _mock_image_watcher, mock_load_imag
 
     @mock.patch('mantidimaging.gui.windows.live_viewer.presenter.LiveViewerWindowPresenter.load_image')
     @mock.patch('mantidimaging.gui.windows.live_viewer.model.ImageWatcher')
-    def test_rotate_operation_rotates_image(self, _mock_image_watcher, mock_load_image):
+    @mock.patch("time.time", return_value=4000.0)
+    def test_rotate_operation_rotates_image(self, _mock_time, _mock_image_watcher, mock_load_image):
         file_list = self._make_simple_dir(self.live_directory)
         image_list = [Image_Data(path) for path in file_list]
         mock_load_image.return_value = self._generate_image()

mantidimaging/gui/test/gui_system_operations_test.py

@@ -49,7 +49,6 @@
 ALLOWED_ERRORS = [
     'Negative values found in result preview for slice 0.',
     'Flat-fielding completed. Slices containing negative values in IMAT_Flower_Tomo_000000: all slices.',
-    'Error applying filter for preview: could not broadcast input array from shape (1,80,80) into shape (1,90,90)'
 ]
 
 

mantidimaging/gui/widgets/mi_image_view/view.py

@@ -7,7 +7,7 @@
 from typing import TYPE_CHECKING
 from collections.abc import Callable
 
-from PyQt5.QtCore import Qt
+from PyQt5.QtCore import Qt, QRectF
 from PyQt5.QtWidgets import QApplication, QHBoxLayout, QLabel, QPushButton, QSizePolicy
 from pyqtgraph import ROI, ImageItem, ImageView, ViewBox
 from pyqtgraph.GraphicsScene.mouseEvents import HoverEvent
@@ -148,6 +148,9 @@ def angles(self, angles: ProjectionAngles | None) -> None:
         self._angles = angles
         self._update_message(self._last_mouse_hover_location)
 
+    def _set_roi_max_bounds(self):
+        self.roi.maxBounds = QRectF(0, 0, self.image_data.shape[2], self.image_data.shape[1])
+
     def setImage(self, image: np.ndarray, *args, **kwargs):
         dimensions_changed = self.image_data is None or self.image_data.shape != image.shape
         if image.ndim == 3:
@@ -195,6 +198,7 @@ def roiChanged(self) -> None:
         roi = self._update_roi_region_avg()
         if self.roi_changed_callback and roi is not None:
             self.roi_changed_callback(roi)
+        self._set_roi_max_bounds()
         self._refresh_message()
 
     def _update_roi_region_avg(self) -> SensibleROI | None:

mantidimaging/gui/widgets/roi_selector/view.py

@@ -69,3 +69,7 @@ def toggle_average_images(self) -> None:
         self.roi_view_averaged = not self.roi_view_averaged
         self.roi_view.roi.show()
         self.roi_view.ui.roiPlot.hide()
+
+    def closeEvent(self, event) -> None:
+        self.roi_view.close()
+        event.accept()

mantidimaging/gui/windows/live_viewer/model.py

@@ -91,12 +91,19 @@ def image_modified_time(self) -> float:
         """Return the image modified time"""
         return self._stat.st_mtime
 
+
     def set_delayed_array(self) -> None:
         if self.image_path.suffix.lower() in [".tif", ".tiff"]:
             self.delayed_array = dask_image.imread.imread(self.image_path)[0]
         elif self.image_path.suffix.lower() == ".fits":
             self.delayed_array = dask.delayed(fits.open)(self.image_path)[0].data
 
+    @property
+    def image_modified_time_stamp(self) -> str:
+        """Return the image modified time as a string"""
+        return time.strftime("%Y-%m-%d %H:%M:%S", time.localtime(self.image_modified_time))
+
+
 
 class SubDirectory:
 

mantidimaging/gui/windows/live_viewer/presenter.py

@@ -76,7 +76,8 @@ def select_image(self, index: int) -> None:
         if not self.model.images:
             return
         self.selected_image = self.model.images[index]
-        self.view.label_active_filename.setText(self.selected_image.image_name)
+        image_timestamp = self.selected_image.image_modified_time_stamp
+        self.view.label_active_filename.setText(f"{self.selected_image.image_name} - {image_timestamp}")
 
         self.display_image(self.selected_image)
 

mantidimaging/gui/windows/operations/presenter.py

@@ -284,14 +284,9 @@ def _post_filter(self, updated_stacks: list[ImageStack], task):
                 if np.any(stack.data < 0):
                     negative_stacks.append(stack)
 
-            if self.view.roi_view is not None:
-                self.view.roi_view.close()
-                self.view.roi_view = None
-
             self.applying_to_all = False
-            self.do_update_previews()
 
-            if task.error is not None:
+            if task.error:
                 # task failed, show why
                 self.view.show_error_dialog(f"Operation failed: {task.error}")
             elif use_new_data:
@@ -312,6 +307,7 @@ def _post_filter(self, updated_stacks: list[ImageStack], task):
             self.view.filter_applied.emit()
             self._set_apply_buttons_enabled(self.prev_apply_single_state, self.prev_apply_all_state)
             self.filter_is_running = False
+            self.do_update_previews()
 
     def _do_apply_filter(self, apply_to: list[ImageStack]):
         self.filter_is_running = True
@@ -454,11 +450,8 @@ def init_roi_field(self, roi_field: QLineEdit):
         if self.stack is None:
             return
 
-        larger = np.greater(self.stack.data[0].shape, (200, 200))
-        if all(larger):
-            return
-        x = min(self.stack.data[0].shape[0], 200)
-        y = min(self.stack.data[0].shape[1], 200)
+        x = self.stack.data.shape[1] // 2
+        y = self.stack.data.shape[2] // 2
         crop_string = ", ".join(["0", "0", str(y), str(x)])
         roi_field.setText(crop_string)
 

mantidimaging/gui/windows/operations/test/presenter_test.py

@@ -448,14 +448,14 @@ def test_init_roi_field_does_nothing_when_stack_is_none(self):
         self.presenter.init_roi_field(mock_roi_field)
         mock_roi_field.setText.assert_not_called()
 
-    def test_init_roi_field_does_nothing_when_image_is_greater_than_200_by_200(self):
+    def test_init_roi_field_called_with_smaller_values_if_image_is_greater_than_200_by_200(self):
         mock_roi_field = mock.Mock()
         self.presenter.stack = mock.Mock()
         self.presenter.stack.data = np.ones((2, 201, 201))
         self.presenter.init_roi_field(mock_roi_field)
-        mock_roi_field.setText.assert_not_called()
+        mock_roi_field.setText.assert_called_once_with("0, 0, 100, 100")
 
-    @parameterized.expand([(190, 201, "0, 0, 200, 190"), (201, 80, "0, 0, 80, 200"), (200, 200, "0, 0, 200, 200")])
+    @parameterized.expand([(190, 201, "0, 0, 100, 95"), (201, 80, "0, 0, 40, 100"), (200, 200, "0, 0, 100, 100")])
     def test_set_text_called_when_image_not_greater_than_200_by_200(self, shape_x, shape_y, expected):
         mock_roi_field = mock.Mock()
         self.presenter.stack = mock.Mock()

mantidimaging/gui/windows/operations/view.py

@@ -64,6 +64,7 @@ def __init__(self, main_window: MainWindowView):
         self.main_window = main_window
         self.presenter = FiltersWindowPresenter(self, main_window)
         self.roi_view = None
+        self.roi_selector_dialog: ROISelectorView | None = None
         self.roi_view_averaged = False
         self.splitter.setSizes([200, 9999])
         self.splitter.setStretchFactor(0, 1)
@@ -122,8 +123,9 @@ def closeEvent(self, e):
     def cleanup(self):
         self.stackSelector.unsubscribe_from_main_window()
         if self.roi_view is not None:
-            self.roi_view.close()
             self.roi_view = None
+            self.roi_selector_dialog.close()
+
         self.presenter.set_stack(None)
         self.auto_update_triggered.disconnect()
         self.main_window.filters = None
@@ -255,16 +257,17 @@ def roi_changed_callback(callback):
         except ValueError:
             roi_values = None
 
-        window = ROISelectorView(self, self.presenter.stack, self.presenter.model.preview_image_idx, roi_values,
-                                 roi_changed_callback)
+        self.roi_selector_dialog = ROISelectorView(self, self.presenter.stack, self.presenter.model.preview_image_idx,
+                                                   roi_values, roi_changed_callback)
 
         def close_event(event):
             roi_field.setEnabled(True)
             roi_button.setEnabled(True)
             event.accept()
 
-        window.closeEvent = functools.partial(close_event)
-        window.show()
+        self.roi_view = self.roi_selector_dialog.roi_view
+        self.roi_selector_dialog.closeEvent = functools.partial(close_event)
+        self.roi_selector_dialog.show()
 
     def toggle_filters_section(self):
         if self.collapseToggleButton.text() == "<<":