ROI support for RITS export (#1958)

docs/release_notes/next/feature-1957-rits-roi

@@ -0,0 +1,2 @@
+#1957 : ROI support for RITS export
+

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -20,6 +20,9 @@
 
 LOG = getLogger(__name__)
 
+ROI_ALL = "all"
+ROI_RITS = "rits_roi"
+
 
 class SpecType(Enum):
     SAMPLE = 1
@@ -44,7 +47,7 @@ def __init__(self, presenter: 'SpectrumViewerWindowPresenter'):
         self.presenter = presenter
         self._roi_id_counter = 0
         self._roi_ranges = {}
-        self.default_roi_list = ["all"]
+        self.special_roi_list = [ROI_ALL]
 
     def roi_name_generator(self) -> str:
         """
@@ -77,7 +80,7 @@ def set_stack(self, stack: Optional[ImageStack]) -> None:
             return
         self._roi_id_counter = 0
         self.tof_range = (0, stack.data.shape[0] - 1)
-        self.set_new_roi(self.default_roi_list[0])
+        self.set_new_roi(ROI_ALL)
 
     def set_new_roi(self, name: str) -> None:
         """
@@ -198,21 +201,18 @@ def save_rits(self, path: Path, normalized: bool) -> None:
         if self._stack is None:
             raise ValueError("No stack selected")
 
-        # Default_roi will likely need updating once UI is implemented
-        default_roi = self.default_roi_list[0]
-
         tof = self.get_stack_time_of_flight()
         if tof is None:
             raise ValueError("No Time of Flights for sample. Make sure spectra log has been loaded")
 
         # RITS expects ToF in μs
         tof *= 1e6
 
-        transmission_error = np.zeros_like(tof)
+        transmission_error = np.full_like(tof, 0.1)
         if normalized:
             if self._normalise_stack is None:
                 raise RuntimeError("No normalisation stack selected")
-            transmission = self.get_spectrum(default_roi, SpecType.SAMPLE_NORMED)
+            transmission = self.get_spectrum(ROI_RITS, 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")
@@ -266,8 +266,8 @@ def remove_roi(self, roi_name) -> None:
         @param roi_name: The name of the ROI to remove
         """
         if roi_name in self._roi_ranges.keys():
-            if roi_name in self.default_roi_list:
-                raise RuntimeError("Cannot remove the 'all' or 'roi' ROIs")
+            if roi_name in self.special_roi_list:
+                raise RuntimeError(f"Cannot remove ROI: {roi_name}")
             del self._roi_ranges[roi_name]
         else:
             raise KeyError(
@@ -283,14 +283,14 @@ def rename_roi(self, old_name: str, new_name: str) -> None:
         @raises RuntimeError: If the ROI is 'all'
         """
         if old_name in self._roi_ranges.keys() and new_name not in self._roi_ranges.keys():
-            if old_name == self.default_roi_list[0]:
-                raise RuntimeError("Cannot rename the 'all' ROI")
+            if old_name in self.special_roi_list:
+                raise RuntimeError(f"Cannot remove ROI: {old_name}")
             self._roi_ranges[new_name] = self._roi_ranges.pop(old_name)
         else:
             raise KeyError(f"Cannot rename {old_name} to {new_name} Available:{self._roi_ranges.keys()}")
 
     def remove_all_roi(self) -> None:
         """
-        Remove all ROIs from the model excluding default ROI 'all'
+        Remove all ROIs from the model
         """
-        self._roi_ranges = {key: value for key, value in self._roi_ranges.items() if key in self.default_roi_list}
+        self._roi_ranges = {}

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -8,7 +8,7 @@
 from logging import getLogger
 from mantidimaging.core.data.dataset import StrictDataset
 from mantidimaging.gui.mvp_base import BasePresenter
-from mantidimaging.gui.windows.spectrum_viewer.model import SpectrumViewerWindowModel, SpecType
+from mantidimaging.gui.windows.spectrum_viewer.model import SpectrumViewerWindowModel, SpecType, ROI_RITS
 
 if TYPE_CHECKING:
     from mantidimaging.gui.windows.spectrum_viewer.view import SpectrumViewerWindowView  # pragma: no cover
@@ -75,6 +75,7 @@ def handle_sample_change(self, uuid: Optional['UUID']) -> None:
             self.model.set_normalise_stack(norm_stack)
 
         self.do_add_roi()
+        self.add_rits_roi()
         self.view.set_normalise_error(self.model.normalise_issue())
         self.show_new_sample()
 
@@ -205,6 +206,13 @@ def do_add_roi(self) -> None:
         self.view.auto_range_image()
         self.do_add_roi_to_table(roi_name)
 
+    def add_rits_roi(self) -> None:
+        roi_name = ROI_RITS
+        self.model.set_new_roi(roi_name)
+        self.view.spectrum.add_roi(self.model.get_roi(roi_name), roi_name)
+        self.view.set_spectrum(roi_name, self.model.get_spectrum(roi_name, self.spectrum_mode))
+        self.view.set_roi_alpha(0, ROI_RITS)
+
     def do_add_roi_to_table(self, roi_name: str) -> None:
         """
         Add a given ROI to the table by ROI name
@@ -224,7 +232,7 @@ def rename_roi(self, old_name: str, new_name: str) -> None:
         self.view.spectrum.rename_roi(old_name, new_name)
         self.model.rename_roi(old_name, new_name)
 
-    def do_remove_roi(self, roi_name=None) -> None:
+    def do_remove_roi(self, roi_name: str | None = None) -> None:
         """
         Remove a given ROI from the table by ROI name or all ROIs from
         the table if no name is passed as an argument

mantidimaging/gui/windows/spectrum_viewer/roi_table_model.py

@@ -91,6 +91,9 @@ def row_data(self, row: int) -> list:
         """
         return self._data[row]
 
+    def __getitem__(self, item: int) -> list:
+        return self.row_data(item)
+
     def column_data(self, column: int) -> list:
         """
         Return data from selected column

mantidimaging/gui/windows/spectrum_viewer/spectrum_widget.py

@@ -87,7 +87,7 @@ def __init__(self) -> None:
         self.nextRow()
         self.spectrum = self.addPlot()
 
-        self.spectrum_data_dict: dict[str, np.ndarray] = {}
+        self.spectrum_data_dict: dict[str, np.ndarray | None] = {}
         self.nextRow()
         self._tof_range_label = self.addLabel()
 

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

@@ -283,7 +283,7 @@ def test_WHEN_remove_all_rois_called_THEN_all_but_default_rois_removed(self):
         self.model.set_new_roi("new_roi_2")
         self.assertListEqual(self.model.get_list_of_roi_names(), ["all", "new_roi", "new_roi_2"])
         self.model.remove_all_roi()
-        self.assertListEqual(self.model.get_list_of_roi_names(), ["all"])
+        self.assertListEqual(self.model.get_list_of_roi_names(), [])
 
     def test_WHEN_roi_renamed_THEN_roi_name_changed_in_list_of_roi_names(self):
         self.model.set_stack(generate_images())

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

@@ -256,4 +256,4 @@ def test_WHEN_do_remove_roi_called_with_no_arguments_THEN_all_rois_removed(self)
             self.presenter.do_add_roi()
         self.assertEqual(["all", "roi", "roi_1", "roi_2"], self.presenter.model.get_list_of_roi_names())
         self.presenter.do_remove_roi()
-        self.assertEqual(["all"], self.presenter.model.get_list_of_roi_names())
+        self.assertEqual([], self.presenter.model.get_list_of_roi_names())

mantidimaging/gui/windows/spectrum_viewer/view.py

@@ -11,6 +11,7 @@
 from mantidimaging.core.utility import finder
 from mantidimaging.gui.mvp_base import BaseMainWindowView
 from mantidimaging.gui.widgets.dataset_selector import DatasetSelectorWidgetView
+from .model import ROI_RITS
 from .presenter import SpectrumViewerWindowPresenter, ExportMode
 from mantidimaging.gui.widgets import RemovableRowTableView
 from .spectrum_widget import SpectrumWidget
@@ -142,19 +143,22 @@ 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 self.presenter.export_mode == ExportMode.ROI_MODE:
+            for roi_name, _, roi_visible in self.roi_table_model:
                 if roi_visible is False:
                     self.set_roi_alpha(0, roi_name)
                 else:
                     self.set_roi_alpha(255, roi_name)
                     self.presenter.redraw_spectrum(roi_name)
-            else:
-                roi_name, _, _ = self.roi_table_model.row_data(roi_item)
+        else:
+            for roi_name, _, _ in self.roi_table_model:
                 self.set_roi_alpha(0, roi_name)
 
-        return
+        if self.presenter.export_mode == ExportMode.IMAGE_MODE:
+            self.set_roi_alpha(255, ROI_RITS)
+            self.presenter.redraw_spectrum(ROI_RITS)
+        else:
+            self.set_roi_alpha(0, ROI_RITS)
 
     @property
     def roi_table_model(self) -> TableModel:
@@ -209,9 +213,7 @@ def set_spectrum(self, name: str, spectrum_data: 'np.ndarray'):
         self.spectrum.spectrum_data_dict[name] = spectrum_data
         self.spectrum.spectrum.clearPlots()
 
-        for key, value in self.spectrum.spectrum_data_dict.items():
-            if key in self.spectrum.roi_dict:
-                self.spectrum.spectrum.plot(value, name=key, pen=self.spectrum.roi_dict[key].colour)
+        self.show_visible_spectrums()
 
     def clear(self) -> None:
         self.spectrum.spectrum_data_dict = {}
@@ -252,14 +254,15 @@ def set_roi_alpha(self, alpha: float, roi_name: str) -> None:
         """
         self.spectrum.set_roi_alpha(roi_name, alpha)
         if alpha == 0:
-            self.spectrum.spectrum_data_dict[roi_name] = np.zeros(self.spectrum.spectrum_data_dict[roi_name].shape)
-        else:
-            self.spectrum.spectrum_data_dict[roi_name] = self.spectrum.spectrum_data_dict[roi_name]
+            self.spectrum.spectrum_data_dict[roi_name] = None
 
         self.spectrum.spectrum.clearPlots()
         self.spectrum.spectrum.update()
+        self.show_visible_spectrums()
+
+    def show_visible_spectrums(self):
         for key, value in self.spectrum.spectrum_data_dict.items():
-            if key in self.spectrum.roi_dict:
+            if value is not None and key in self.spectrum.roi_dict:
                 self.spectrum.spectrum.plot(value, name=key, pen=self.spectrum.roi_dict[key].colour)
 
     def add_roi_table_row(self, name: str, colour: tuple[int, int, int]):