Merge branch 'main' into 2279_Developer_Documentation_on_System_Testing

Author: ashmeigh

docs/release_notes/next/dev-2320-Enhance-System-Tests-for-Spectrum-Viewer

@@ -0,0 +1 @@
+2320: Enhance System Tests for Spectrum Viewer

docs/release_notes/next/dev-2330-PyInstaller-Qt-Bindings

@@ -0,0 +1 @@
+#2330: The PySide6 module is now excluded when building via PyInstaller due to hook clashes

docs/release_notes/next/fix-2281-test-COR-tilit-correlate

@@ -0,0 +1 @@
+#2281 : TestGuiSystemReconstruction test_correlate should check COR and tilt

mantidimaging/core/data/dataset.py

@@ -22,7 +22,7 @@ def remove_nones(image_stacks: list[ImageStack | None]) -> list[ImageStack]:
     return [image_stack for image_stack in image_stacks if image_stack is not None]
 
 
-class BaseDataset:
+class Dataset:
 
     def __init__(
         self,
@@ -185,15 +185,15 @@ def is_processed(self) -> bool:
         return False
 
 
-class MixedDataset(BaseDataset):
+class MixedDataset(Dataset):
     pass
 
 
-class StrictDataset(BaseDataset):
+class StrictDataset(Dataset):
     pass
 
 
-def _get_stack_data_type(stack_id: uuid.UUID, dataset: BaseDataset) -> str:
+def _get_stack_data_type(stack_id: uuid.UUID, dataset: Dataset) -> str:
     """
     Find the data type as a string of a stack.
     :param stack_id: The ID of the stack.

mantidimaging/core/data/test/dataset_test.py

@@ -9,7 +9,7 @@
 import numpy as np
 
 from mantidimaging.core.data import ImageStack
-from mantidimaging.core.data.dataset import BaseDataset, _get_stack_data_type
+from mantidimaging.core.data.dataset import Dataset, _get_stack_data_type
 from mantidimaging.core.utility.data_containers import ProjectionAngles, FILE_TYPES
 from mantidimaging.test_helpers.unit_test_helper import generate_images
 
@@ -19,11 +19,11 @@ def _make_standard_dataset(shape=(2, 5, 5)):
     image_stacks = [generate_images(shape) for _ in range(6)]
     image_stacks[0].name = "samplename"
 
-    ds = BaseDataset(sample=image_stacks[0],
-                     flat_before=image_stacks[1],
-                     flat_after=image_stacks[2],
-                     dark_before=image_stacks[3],
-                     dark_after=image_stacks[4])
+    ds = Dataset(sample=image_stacks[0],
+                 flat_before=image_stacks[1],
+                 flat_after=image_stacks[2],
+                 dark_before=image_stacks[3],
+                 dark_after=image_stacks[4])
     ds.proj180deg = image_stacks[5]
     return ds, image_stacks
 
@@ -41,19 +41,19 @@ def _set_fake_projection_angles(image_stack: ImageStack):
 class DatasetTest(unittest.TestCase):
 
     def test_create_dataset(self):
-        ds = BaseDataset()
+        ds = Dataset()
         self.assertIsInstance(ds.id, uuid.UUID)
         self.assertEqual(ds.name, "")
 
     def test_prevent_positional_parameters(self):
-        self.assertRaises(TypeError, BaseDataset, mock.Mock())
+        self.assertRaises(TypeError, Dataset, mock.Mock())
 
     def test_dataset_name(self):
-        ds = BaseDataset(name="a_dataset")
+        ds = Dataset(name="a_dataset")
         self.assertEqual(ds.name, "a_dataset")
 
     def test_add_recon(self):
-        ds = BaseDataset()
+        ds = Dataset()
         recons = [generate_images() for _ in range(3)]
         [ds.add_recon(r) for r in recons]
 
@@ -62,7 +62,7 @@ def test_add_recon(self):
         self.assertEqual(3, len(ds.recons))
 
     def test_delete_recon(self):
-        ds = BaseDataset()
+        ds = Dataset()
         recons = [generate_images() for _ in range(3)]
         [ds.add_recon(r) for r in recons]
 
@@ -71,36 +71,36 @@ def test_delete_recon(self):
         self.assertNotIn(recons[-1], ds.all)
 
     def test_delete_failure(self):
-        ds = BaseDataset()
+        ds = Dataset()
         with self.assertRaises(KeyError):
             ds.delete_stack("nonexistent-id")
 
     def test_delete_all_recons(self):
-        ds = BaseDataset()
+        ds = Dataset()
         recons = [generate_images() for _ in range(3)]
         [ds.add_recon(r) for r in recons]
         ds.delete_recons()
         self.assertListEqual(ds.recons.stacks, [])
 
     def test_sinograms(self):
-        ds = BaseDataset()
+        ds = Dataset()
         ds.sinograms = sinograms = generate_images()
         self.assertIs(ds.sinograms, sinograms)
 
     def test_delete_sinograms(self):
-        ds = BaseDataset()
+        ds = Dataset()
         ds.sinograms = sinograms = generate_images()
         ds.delete_stack(sinograms.id)
         self.assertIsNone(ds.sinograms)
 
     def test_stacks_in_all(self):
         image_stacks = [mock.Mock() for _ in range(3)]
-        ds = BaseDataset(stacks=image_stacks)
+        ds = Dataset(stacks=image_stacks)
         self.assertListEqual(ds.all, image_stacks)
 
     def test_sample_in_all(self):
         image_sample = mock.Mock(proj180deg=None)
-        ds = BaseDataset(sample=image_sample)
+        ds = Dataset(sample=image_sample)
         self.assertCountEqual(ds.all, [image_sample])
 
     def test_all_for_full_dataset(self):
@@ -111,27 +111,27 @@ def test_all_for_full_dataset(self):
 
     def test_delete_stack_from_stacks_list(self):
         image_stacks = [mock.Mock() for _ in range(3)]
-        ds = BaseDataset(stacks=image_stacks)
+        ds = Dataset(stacks=image_stacks)
         prev_stacks = image_stacks.copy()
         ds.delete_stack(image_stacks[-1].id)
         self.assertListEqual(ds.all, prev_stacks[:-1])
 
     def test_get_stack_data_type_returns_recon(self):
         recon = generate_images()
         recon_id = recon.id
-        dataset = BaseDataset()
+        dataset = Dataset()
         dataset.recons.append(recon)
         self.assertEqual(_get_stack_data_type(recon_id, dataset), "Recon")
 
     def test_get_stack_data_type_returns_images(self):
         images = generate_images()
         images_id = images.id
-        dataset = BaseDataset(stacks=[images])
+        dataset = Dataset(stacks=[images])
         self.assertEqual(_get_stack_data_type(images_id, dataset), "Images")
 
     def test_attribute_not_set_returns_none(self):
         sample = mock.Mock()
-        dataset = BaseDataset(sample=sample)
+        dataset = Dataset(sample=sample)
 
         self.assertIsNone(dataset.flat_before)
         self.assertIsNone(dataset.flat_after)
@@ -140,7 +140,7 @@ def test_attribute_not_set_returns_none(self):
 
     def test_set_flat_before(self):
         sample = mock.Mock()
-        dataset = BaseDataset(sample=sample)
+        dataset = Dataset(sample=sample)
         flat_before = mock.Mock(id="1234")
         dataset.flat_before = flat_before
         self.assertIs(flat_before, dataset.flat_before)
@@ -258,21 +258,21 @@ def test_delete_dark_after(self):
         self.assertIsNone(ds.dark_after)
 
     def test_set_stack_by_type_sample(self):
-        ds = BaseDataset()
+        ds = Dataset()
         sample = mock.Mock()
         ds.set_stack(FILE_TYPES.SAMPLE, sample)
 
         self.assertEqual(ds.sample, sample)
 
     def test_set_stack_by_type_flat_before(self):
-        ds = BaseDataset()
+        ds = Dataset()
         stack = mock.Mock()
         ds.set_stack(FILE_TYPES.FLAT_BEFORE, stack)
 
         self.assertEqual(ds.flat_before, stack)
 
     def test_set_stack_by_type_180(self):
-        ds = BaseDataset()
+        ds = Dataset()
         sample = mock.Mock()
         stack = mock.Mock()
         ds.set_stack(FILE_TYPES.SAMPLE, sample)
@@ -281,10 +281,10 @@ def test_set_stack_by_type_180(self):
         self.assertEqual(ds.proj180deg, stack)
 
     def test_processed_is_true(self):
-        ds = BaseDataset(sample=generate_images())
+        ds = Dataset(sample=generate_images())
         ds.sample.record_operation("", "")
         self.assertTrue(ds.is_processed)
 
     def test_processed_is_false(self):
-        ds = BaseDataset(sample=generate_images())
+        ds = Dataset(sample=generate_images())
         self.assertFalse(ds.is_processed)

mantidimaging/core/io/saver.py

@@ -22,7 +22,7 @@
 from ..utility.version_check import CheckVersion
 
 if TYPE_CHECKING:
-    from ..data.dataset import StrictDataset
+    from ..data.dataset import Dataset
     from ..data.imagestack import ImageStack
     from ..utility.data_containers import Indices
 
@@ -180,7 +180,7 @@ def image_save(images: ImageStack,
         return names
 
 
-def nexus_save(dataset: StrictDataset, path: str, sample_name: str, save_as_float: bool) -> None:
+def nexus_save(dataset: Dataset, path: str, sample_name: str, save_as_float: bool) -> None:
     """
     Uses information from a StrictDataset to create a NeXus file.
     :param dataset: The dataset to save as a NeXus file.
@@ -202,7 +202,7 @@ def nexus_save(dataset: StrictDataset, path: str, sample_name: str, save_as_floa
     nexus_file.close()
 
 
-def _nexus_save(nexus_file: h5py.File, dataset: StrictDataset, sample_name: str, save_as_float: bool) -> None:
+def _nexus_save(nexus_file: h5py.File, dataset: Dataset, sample_name: str, save_as_float: bool) -> None:
     """
     Takes a NeXus file and writes the StrictDataset information to it.
     :param nexus_file: The NeXus file.
@@ -255,7 +255,7 @@ def _nexus_save(nexus_file: h5py.File, dataset: StrictDataset, sample_name: str,
         _save_recon_to_nexus(nexus_file, recon, dataset.sample.filenames[0])
 
 
-def _save_processed_data_to_nexus(nexus_file: h5py.File, dataset: StrictDataset, rotation_angle: h5py.Dataset,
+def _save_processed_data_to_nexus(nexus_file: h5py.File, dataset: Dataset, rotation_angle: h5py.Dataset,
                                   image_key: h5py.Dataset, save_as_float: bool) -> None:
     data = nexus_file.create_group(NEXUS_PROCESSED_DATA_PATH)
     data["rotation_angle"] = rotation_angle
@@ -270,7 +270,7 @@ def _save_processed_data_to_nexus(nexus_file: h5py.File, dataset: StrictDataset,
     process.create_dataset("version", data=np.bytes_(package_version))
 
 
-def _save_image_stacks_to_nexus(dataset: StrictDataset, data_group: h5py.Group, save_as_float: bool) -> None:
+def _save_image_stacks_to_nexus(dataset: Dataset, data_group: h5py.Group, save_as_float: bool) -> None:
     combined_data_shape = (sum([len(arr) for arr in dataset.nexus_arrays]), ) + dataset.nexus_arrays[0].shape[1:]
 
     index = 0

mantidimaging/eyes_tests/base_eyes.py

@@ -13,7 +13,7 @@
 from PyQt5.QtWidgets import QMainWindow, QMenu, QWidget, QApplication
 
 from mantidimaging.core.data import ImageStack
-from mantidimaging.core.data.dataset import StrictDataset, MixedDataset
+from mantidimaging.core.data.dataset import StrictDataset, Dataset
 from mantidimaging.core.io.loader import loader
 from mantidimaging.core.utility.data_containers import Indices
 from mantidimaging.eyes_tests.eyes_manager import EyesManager
@@ -118,16 +118,15 @@ def _load_strict_data_set(self, set_180: bool = False):
 
         return vis
 
-    def _create_mixed_dataset(self) -> MixedDataset:
-        mixed_dataset = MixedDataset(stacks=[generate_images()], name="a-mixed-dataset")
-
-        self.imaging.presenter.model.add_dataset_to_model(mixed_dataset)
-        self.imaging.presenter.create_mixed_dataset_tree_view_items(mixed_dataset)
-        self.imaging.presenter.create_mixed_dataset_stack_windows(mixed_dataset)
+    def _create_new_dataset(self) -> Dataset:
+        new_dataset = Dataset(sample=generate_images(), name="new")
+        self.imaging.presenter.create_strict_dataset_stack_windows(new_dataset)
+        self.imaging.presenter.create_strict_dataset_tree_view_items(new_dataset)
+        self.imaging.presenter.model.add_dataset_to_model(new_dataset)
 
         QApplication.sendPostedEvents()
 
-        return mixed_dataset
+        return new_dataset
 
     def _get_top_level_widget(cls, widget_type):
         for widget in cls.app.topLevelWidgets():

mantidimaging/eyes_tests/main_window_test.py

@@ -87,56 +87,26 @@ def test_show_add_stack_to_existing_dataset_dialog_for_strict_dataset(self):
 
         self.check_target(widget=self.imaging.add_to_dataset_dialog)
 
-    def test_show_add_stack_to_existing_dataset_dialog_for_mixed_dataset(self):
-        self._create_mixed_dataset()
-        self.imaging.show_add_stack_to_existing_dataset_dialog(list(self.imaging.presenter.all_dataset_ids)[0])
-        self.check_target(widget=self.imaging.add_to_dataset_dialog)
-
     def test_clicking_tab_changes_tree_view_selection(self):
         self._load_strict_data_set()
         sample_vis = self._load_strict_data_set()
         sample_vis.raise_()
 
         self.check_target()
 
-    def test_move_stack_dialog_when_both_strict(self):
+    def test_move_within_dataset(self):
         sample_vis = self._load_strict_data_set()
-        self._load_strict_data_set()
-
         self.imaging.presenter._set_tree_view_selection_with_id(sample_vis.id)
-
         self.imaging._move_stack()
-        self.check_target(self.imaging.move_stack_dialog)
-
-    def test_move_stack_dialog_strict_to_mixed(self):
-        sample_vis = self._load_strict_data_set()
-        mixed_ds = self._create_mixed_dataset()
 
-        self.imaging.presenter._set_tree_view_selection_with_id(sample_vis.id)
-
-        self.imaging._move_stack()
-        self.imaging.move_stack_dialog.datasetSelector.setCurrentText(mixed_ds.name)
         self.check_target(self.imaging.move_stack_dialog)
 
-    def test_move_stack_dialog_mixed_to_strict(self):
-        mixed_ds = self._create_mixed_dataset()
+    def test_move_to_another_dataset(self):
         sample_vis = self._load_strict_data_set()
-        strict_ds_id = self.imaging.presenter.model.get_parent_dataset(sample_vis.id)
-        strict_ds = self.imaging.get_dataset(strict_ds_id)
-
-        self.imaging.presenter._set_tree_view_selection_with_id(mixed_ds.all[0].id)
+        new_dataset = self._create_new_dataset()
 
+        self.imaging.presenter._set_tree_view_selection_with_id(sample_vis.id)
         self.imaging._move_stack()
-        self.imaging.move_stack_dialog.datasetSelector.setCurrentText(strict_ds.name)
-        self.check_target(self.imaging.move_stack_dialog)
-
-    def test_move_stack_dialog_both_mixed(self):
-        mixed_ds_1 = self._create_mixed_dataset()
-        mixed_ds_2 = self._create_mixed_dataset()
-        mixed_ds_2.name = "other-mixed-ds-name"
+        self.imaging.move_stack_dialog.datasetSelector.setCurrentText(new_dataset.name)
 
-        self.imaging.presenter._set_tree_view_selection_with_id(mixed_ds_1.all[0].id)
-
-        self.imaging._move_stack()
-        self.imaging.move_stack_dialog.datasetSelector.setCurrentText(mixed_ds_2.name)
         self.check_target(self.imaging.move_stack_dialog)

mantidimaging/eyes_tests/nexus_save_dialog_test.py

@@ -2,21 +2,18 @@
 # SPDX - License - Identifier: GPL-3.0-or-later
 from __future__ import annotations
 
-from typing import NamedTuple
 from unittest import mock
-from uuid import UUID, uuid4
 
+from mantidimaging.core.data.dataset import Dataset
 from mantidimaging.eyes_tests.base_eyes import BaseEyesTest
 
 
 class NexusSaveDialogTest(BaseEyesTest):
 
     def test_save_dialog_opens_with_dataset(self):
-        TestTuple = NamedTuple('TestTuple', [('id', UUID), ('name', str)])
-        dataset_list = [TestTuple(uuid4(), 'Test Dataset')]
-        with mock.patch("mantidimaging.gui.windows.main.MainWindowView.strict_dataset_list",
-                        new_callable=mock.PropertyMock) as mock_dataset_list:
-            mock_dataset_list.return_value = dataset_list
+        with mock.patch("mantidimaging.gui.windows.main.MainWindowPresenter.datasets",
+                        new_callable=mock.PropertyMock) as mock_datasets:
+            mock_datasets.return_value = [Dataset(name='Test Dataset')]
             self.imaging.actionSaveNeXusFile.trigger()
 
         self.check_target(widget=self.imaging.nexus_save_dialog)