Spectrum viewer tab for exporting to RITS (#1942)

.github/workflows/conda.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

.github/workflows/cos7_testing.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/docs.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

.github/workflows/license_check.yaml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/u18_testing.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   merge_group:
 
 jobs:

.github/workflows/windows.yml

@@ -6,9 +6,6 @@ on:
     - 'main'
     - 'release-*'
   pull_request:
-    branches:
-      - 'main'
-      - 'release-*'
   release:
   merge_group:
 

docs/release_notes/next/feature-1941-rits-gui

@@ -0,0 +1,2 @@
+#1941 : Spectrum viewer tab for exporting to RITS
+

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -8,6 +8,7 @@
 
 import numpy as np
 
+from logging import getLogger
 from mantidimaging.core.data import ImageStack
 from mantidimaging.core.io.csv_output import CSVOutput
 from mantidimaging.core.io import saver
@@ -16,6 +17,8 @@
 if TYPE_CHECKING:
     from mantidimaging.gui.windows.spectrum_viewer.presenter import SpectrumViewerWindowPresenter
 
+LOG = getLogger(__name__)
+
 
 class SpecType(Enum):
     SAMPLE = 1
@@ -203,6 +206,8 @@ def save_rits(self, path: Path, normalized: bool) -> None:
                 raise RuntimeError("No normalisation stack selected")
             transmission = self.get_spectrum(default_roi, SpecType.SAMPLE_NORMED)
             self.export_spectrum_to_rits(path, tof, transmission, transmission_error)
+        else:
+            LOG.error("Data is not normalised to open beam. This will not export to a valid RITS format")
 
     def get_roi_coords_filename(self, path: Path) -> Path:
         """

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -1,6 +1,8 @@
 # Copyright (C) 2023 ISIS Rutherford Appleton Laboratory UKRI
 # SPDX - License - Identifier: GPL-3.0-or-later
 from __future__ import annotations
+
+from enum import Enum
 from typing import TYPE_CHECKING, Optional
 
 from logging import getLogger
@@ -17,6 +19,12 @@
 LOG = getLogger(__name__)
 
 
+class ExportMode(Enum):
+    # Needs to match GUI tab order
+    ROI_MODE = 0
+    IMAGE_MODE = 1
+
+
 class SpectrumViewerWindowPresenter(BasePresenter):
     """
     The presenter for the spectrum viewer window.
@@ -29,13 +37,15 @@ class SpectrumViewerWindowPresenter(BasePresenter):
     spectrum_mode: SpecType = SpecType.SAMPLE
     current_stack_uuid: Optional['UUID'] = None
     current_norm_stack_uuid: Optional['UUID'] = None
+    export_mode: ExportMode
 
     def __init__(self, view: 'SpectrumViewerWindowView', main_window: 'MainWindowView'):
         super().__init__(view)
 
         self.view = view
         self.main_window = main_window
         self.model = SpectrumViewerWindowModel(self)
+        self.export_mode = ExportMode.ROI_MODE
 
     def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         if uuid == self.current_stack_uuid:
@@ -53,7 +63,6 @@ def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         if uuid is None:
             self.model.set_stack(None)
             self.view.clear()
-            self.handle_button_enabled()
             return
 
         self.model.set_stack(self.main_window.get_stack(uuid))
@@ -68,7 +77,6 @@ def handle_sample_change(self, uuid: Optional['UUID']) -> None:
         self.do_add_roi()
         self.view.set_normalise_error(self.model.normalise_issue())
         self.show_new_sample()
-        self.handle_button_enabled()
 
     def handle_normalise_stack_change(self, normalise_uuid: Optional['UUID']) -> None:
         if normalise_uuid == self.current_norm_stack_uuid:
@@ -147,9 +155,15 @@ def do_set_roi_alpha(self, name: str, alpha: float) -> None:
 
     def handle_button_enabled(self) -> None:
         """
-        Enable the export button if the current stack is not None
+        Enable the export button if the current stack is not None and normalisation is valid
         """
-        self.view.set_export_button_enabled(self.model.has_stack())
+        has_stack = self.model.has_stack()
+        normalisation_on = self.view.normalisation_enabled()
+        normalisation_no_error = (normalisation_on and self.model.normalise_issue() == "") or not normalisation_on
+
+        self.view.exportButton.setEnabled(has_stack and normalisation_no_error)
+        self.view.exportButtonRITS.setEnabled(has_stack and normalisation_on and normalisation_no_error)
+        self.view.addBtn.setEnabled(has_stack)
 
     def handle_export_csv(self) -> None:
         path = self.view.get_csv_filename()
@@ -235,3 +249,7 @@ def do_remove_roi(self, roi_name=None) -> None:
             self.view.spectrum.remove_roi(roi_name)
             self.view.set_spectrum(roi_name, self.model.get_spectrum(roi_name, self.spectrum_mode))
             self.model.remove_roi(roi_name)
+
+    def handle_export_tab_change(self, index: int) -> None:
+        self.export_mode = ExportMode(index)
+        self.view.on_visibility_change()

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

@@ -6,6 +6,7 @@
 from pathlib import Path
 from unittest import mock
 
+from PyQt5.QtWidgets import QPushButton
 from parameterized import parameterized
 
 from mantidimaging.core.data.dataset import StrictDataset, MixedDataset
@@ -27,6 +28,9 @@ def setUp(self) -> None:
         self.view.current_dataset_id = uuid.uuid4()
         mock_spectrum_roi_dict = mock.create_autospec(dict)
         self.view.spectrum = mock.create_autospec(SpectrumWidget, roi_dict=mock_spectrum_roi_dict)
+        self.view.exportButton = mock.create_autospec(QPushButton)
+        self.view.exportButtonRITS = mock.create_autospec(QPushButton)
+        self.view.addBtn = mock.create_autospec(QPushButton)
         self.presenter = SpectrumViewerWindowPresenter(self.view, self.main_window)
 
     def test_get_dataset_id_for_stack_no_stack_id(self):
@@ -74,7 +78,6 @@ def test_handle_sample_change_no_new_stack(self):
         self.view.try_to_select_relevant_normalise_stack.assert_not_called()
         self.assertIsNone(self.view.current_dataset_id)
         self.presenter.show_new_sample.assert_not_called()
-        self.view.set_export_button_enabled.assert_called_once_with(False)
 
     def test_handle_sample_change_dataset_unchanged(self):
         initial_dataset_id = self.view.current_dataset_id
@@ -86,7 +89,6 @@ def test_handle_sample_change_dataset_unchanged(self):
         self.presenter.handle_sample_change(uuid.uuid4())
         self.presenter.main_window.get_dataset.assert_not_called()
         self.assertEqual(self.view.current_dataset_id, initial_dataset_id)
-        self.view.set_export_button_enabled.assert_called_once_with(True)
 
     def test_handle_sample_change_to_MixedDataset(self):
         self.presenter.get_dataset_id_for_stack = mock.Mock(return_value=uuid.uuid4())
@@ -112,6 +114,45 @@ def test_handle_sample_change_no_flat(self):
         self.presenter.main_window.get_dataset.assert_called_once()
         self.view.try_to_select_relevant_normalise_stack.assert_not_called()
 
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    def test_WHEN_no_stack_THEN_buttons_disabled(self, has_stack):
+        has_stack.return_value = False
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(False)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)
+        self.view.addBtn.setEnabled.assert_called_once_with(False)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    def test_WHEN_has_stack_no_norm_THEN_buttons_set(self, has_stack):
+        has_stack.return_value = True
+        self.view.normalisation_enabled.return_value = False
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(True)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)  # RITS export needs norm
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.normalise_issue")
+    def test_WHEN_has_stack_has_good_norm_THEN_buttons_set(self, normalise_issue, has_stack):
+        has_stack.return_value = True
+        normalise_issue.return_value = ""
+        self.view.normalisation_enabled.return_value = True
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(True)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(True)
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.has_stack")
+    @mock.patch("mantidimaging.gui.windows.spectrum_viewer.model.SpectrumViewerWindowModel.normalise_issue")
+    def test_WHEN_has_stack_has_bad_norm_THEN_buttons_set(self, normalise_issue, has_stack):
+        has_stack.return_value = True
+        normalise_issue.return_value = "Something wrong"
+        self.view.normalisation_enabled.return_value = True
+        self.presenter.handle_button_enabled()
+        self.view.exportButton.setEnabled.assert_called_once_with(False)
+        self.view.exportButtonRITS.setEnabled.assert_called_once_with(False)
+        self.view.addBtn.setEnabled.assert_called_once_with(True)
+
     def test_WHEN_show_sample_call_THEN_add_range_set(self):
         self.presenter.model.tof_range = (0, 9)
         self.presenter.show_new_sample()

mantidimaging/gui/windows/spectrum_viewer/view.py

@@ -5,12 +5,13 @@
 from typing import TYPE_CHECKING, Optional
 
 from PyQt5.QtGui import QPixmap
-from PyQt5.QtWidgets import QCheckBox, QVBoxLayout, QFileDialog, QPushButton, QLabel, QAbstractItemView, QHeaderView
+from PyQt5.QtWidgets import QCheckBox, QVBoxLayout, QFileDialog, QPushButton, QLabel, QAbstractItemView, QHeaderView, \
+    QTabWidget
 
 from mantidimaging.core.utility import finder
 from mantidimaging.gui.mvp_base import BaseMainWindowView
 from mantidimaging.gui.widgets.dataset_selector import DatasetSelectorWidgetView
-from .presenter import SpectrumViewerWindowPresenter
+from .presenter import SpectrumViewerWindowPresenter, ExportMode
 from mantidimaging.gui.widgets import RemovableRowTableView
 from .spectrum_widget import SpectrumWidget
 from mantidimaging.gui.windows.spectrum_viewer.roi_table_model import TableModel
@@ -30,6 +31,7 @@ class SpectrumViewerWindowView(BaseMainWindowView):
     normaliseCheckBox: QCheckBox
     imageLayout: QVBoxLayout
     exportButton: QPushButton
+    exportTabs: QTabWidget
     normaliseErrorIcon: QLabel
     _current_dataset_id: Optional['UUID']
     normalise_error_issue: str = ""
@@ -56,9 +58,14 @@ def __init__(self, main_window: 'MainWindowView'):
 
         self._current_dataset_id = None
         self.sampleStackSelector.stack_selected_uuid.connect(self.presenter.handle_sample_change)
+        self.sampleStackSelector.stack_selected_uuid.connect(self.presenter.handle_button_enabled)
         self.normaliseStackSelector.stack_selected_uuid.connect(self.presenter.handle_normalise_stack_change)
+        self.normaliseStackSelector.stack_selected_uuid.connect(self.presenter.handle_button_enabled)
         self.normaliseCheckBox.stateChanged.connect(self.normaliseStackSelector.setEnabled)
         self.normaliseCheckBox.stateChanged.connect(self.presenter.handle_enable_normalised)
+        self.normaliseCheckBox.stateChanged.connect(self.presenter.handle_button_enabled)
+
+        self.exportTabs.currentChanged.connect(self.presenter.handle_export_tab_change)
 
         # ROI action buttons
         self.addBtn.clicked.connect(self.set_new_roi)
@@ -71,6 +78,7 @@ def __init__(self, main_window: 'MainWindowView'):
         self.try_to_select_relevant_normalise_stack("Flat")
 
         self.exportButton.clicked.connect(self.presenter.handle_export_csv)
+        self.exportButtonRITS.clicked.connect(self.presenter.handle_rits_export)
 
         # Point table
         self.tableView.setSelectionBehavior(QAbstractItemView.SelectRows)
@@ -92,18 +100,6 @@ def on_row_change(item, _) -> None:
 
         self.tableView.selectionModel().currentRowChanged.connect(on_row_change)
 
-        def on_visibility_change() -> None:
-            """
-            When the visibility of an ROI is changed, update the visibility of the ROI in the spectrum widget
-            """
-            for roi_item in range(self.roi_table_model.rowCount()):
-                if self.roi_table_model.row_data(roi_item)[2] is False:
-                    self.set_roi_alpha(0, roi_item)
-                else:
-                    self.set_roi_alpha(255, roi_item)
-                    self.presenter.redraw_spectrum(self.roi_table_model.row_data(roi_item)[0])
-            return
-
         def on_data_in_table_change() -> None:
             """
             Check if an ROI name has changed in the table or if the visibility of an ROI has changed.
@@ -124,7 +120,7 @@ def on_data_in_table_change() -> None:
                 selected_row_data[0] = self.current_roi
 
             selected_row_data[0] = self.current_roi
-            on_visibility_change()
+            self.on_visibility_change()
             return
 
         self.roi_table_model.dataChanged.connect(on_data_in_table_change)
@@ -142,6 +138,23 @@ def cleanup(self):
         self.normaliseStackSelector.unsubscribe_from_main_window()
         self.main_window.spectrum_viewer = None
 
+    def on_visibility_change(self) -> None:
+        """
+        When the visibility of an ROI is changed, update the visibility of the ROI in the spectrum widget
+        """
+        for roi_item in range(self.roi_table_model.rowCount()):
+            if self.presenter.export_mode == ExportMode.ROI_MODE:
+                roi_name, _, roi_visible = self.roi_table_model.row_data(roi_item)
+                if roi_visible is False:
+                    self.set_roi_alpha(0, roi_item)
+                else:
+                    self.set_roi_alpha(255, roi_item)
+                    self.presenter.redraw_spectrum(roi_name)
+            else:
+                self.set_roi_alpha(0, roi_item)
+
+        return
+
     @property
     def roi_table_model(self) -> TableModel:
         if self.tableView.model() is None:
@@ -229,15 +242,6 @@ def set_new_roi(self) -> None:
         """
         self.presenter.do_add_roi()
 
-    def set_export_button_enabled(self, enabled: bool):
-        """
-        Toggle enabled state of the export button
-
-        @param enabled: True to enable the button, False to disable it
-        """
-        self.exportButton.setEnabled(enabled)
-        self.addBtn.setEnabled(enabled)
-
     def set_roi_alpha(self, alpha: float, roi) -> None:
         """
         Set the alpha value for the selected ROI and update the spectrum to reflect the change.