Merge branch 'main' into dask_live_viewer

Author: MikeSullivan7

.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 renamed to .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

docker/Makefile

@@ -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/installation.rst

@@ -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/feature-2273-live-view-img-timestamp

@@ -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.

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

@@ -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/eyes_tests/live_viewer_window_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/test/gui_system_operations_test.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: