Merge 1c42a4e into 4d2ef3e

docs/release_notes/next/feature-2216-export_tof_wavelength_and_energy_to_csv

@@ -0,0 +1 @@
+#2216: Add Wavelength, ToF and Energy unit conversions to Spectrum Viewer CSV Output

mantidimaging/core/io/csv_output.py

@@ -11,6 +11,7 @@ class CSVOutput:
     def __init__(self) -> None:
         self.columns: dict[str, np.ndarray] = {}
         self.num_rows: int | None = None
+        self.units: dict[str, str] = {}
 
     def add_column(self, name: str, values: np.ndarray) -> None:
         as_column = values.reshape((-1, 1))
@@ -24,5 +25,8 @@ def add_column(self, name: str, values: np.ndarray) -> None:
 
     def write(self, outstream: IO[str]) -> None:
         header = ",".join(self.columns.keys())
+        if self.units:
+            units = ",".join(self.units.values()) + ",Counts" * (len(self.columns) - len(self.units))
+        outstream.write("# " + header + "\n" + units + "\n" if self.units else "# " + header + "\n")
         data = np.hstack(list(self.columns.values()))
-        np.savetxt(outstream, data, header=header, fmt="%s", delimiter=",")
+        np.savetxt(outstream, data, fmt="%s", delimiter=",")

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -283,6 +283,18 @@ def save_csv(self, path: Path, normalized: bool) -> None:
 
         csv_output = CSVOutput()
         csv_output.add_column("tof_index", np.arange(self._stack.data.shape[0]))
+        self.tof_data = self.get_stack_time_of_flight()
+        if self.tof_data is not None:
+            self.units.set_data_to_convert(self.tof_data)
+            csv_output.units = {
+                "ToF_index": "#",
+                "Wavelength": "Angstrom",
+                "ToF": "Microseconds",
+                "Energy": "MeV",
+            }
+            csv_output.add_column("Wavelength", self.units.tof_seconds_to_wavelength_in_angstroms())
+            csv_output.add_column("ToF", self.units.tof_seconds_to_us())
+            csv_output.add_column("Energy", self.units.tof_seconds_to_energy())
 
         for roi_name in self.get_list_of_roi_names():
             csv_output.add_column(roi_name, self.get_spectrum(roi_name, SpecType.SAMPLE))
@@ -506,9 +518,9 @@ def set_tof_unit_mode_for_stack(self) -> None:
             self.tof_mode = ToFUnitMode.IMAGE_NUMBER
             self.presenter.change_selected_menu_option("Image Index")
         elif self.tof_mode == ToFUnitMode.ENERGY:
-            self.presenter.change_selected_menu_option("Energy")
+            self.presenter.change_selected_menu_option("Energy MEV")
         elif self.tof_mode == ToFUnitMode.TOF_US:
-            self.presenter.change_selected_menu_option("Time of Flight (\u03BCs)")
+            self.presenter.change_selected_menu_option("Time of Flight")
         else:
             self.tof_mode = ToFUnitMode.WAVELENGTH
             self.presenter.change_selected_menu_option("Wavelength")

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

@@ -39,12 +39,13 @@ def setUp(self) -> None:
     def _set_sample_stack(self, with_tof=False):
         spectrum = np.arange(0, 10)
         stack = ImageStack(np.ones([10, 11, 12]) * spectrum.reshape((10, 1, 1)))
-        self.model.set_stack(stack)
-        self.model.set_new_roi("roi")
         if with_tof:
             mock_inst_log = mock.create_autospec(InstrumentLog, source_file="")
             mock_inst_log.get_column.return_value = np.arange(0, 10) * 0.1
             stack.log_file = mock_inst_log
+        self.model.set_stack(stack)
+        self.model.set_new_roi("roi")
+        stack.tof = np.arange(0, 10) * 0.1
         return stack, spectrum
 
     def _make_mock_path_stream(self):
@@ -182,7 +183,7 @@ def test_save_csv(self):
             self.model.save_csv(mock_path, False)
 
         mock_path.open.assert_called_once_with("w")
-        self.assertIn("# tof_index,all,roi", mock_stream.captured[0])
+        self.assertIn("tof_index,all,roi", mock_stream.captured[0])
         self.assertIn("0.0,0.0,0.0", mock_stream.captured[1])
         self.assertIn("1.0,2.0,2.0", mock_stream.captured[2])
         self.assertTrue(mock_stream.is_closed)
@@ -319,11 +320,31 @@ def test_save_csv_norm(self):
             self.model.save_csv(mock_path, True)
 
         mock_path.open.assert_called_once_with("w")
-        self.assertIn("# tof_index,all,all_open,all_norm,roi,roi_open,roi_norm", mock_stream.captured[0])
+        self.assertIn("tof_index,all,all_open,all_norm,roi,roi_open,roi_norm", mock_stream.captured[0])
         self.assertIn("0.0,0.0,2.0,0.0,0.0,2.0,0.0", mock_stream.captured[1])
         self.assertIn("1.0,1.0,2.0,0.5,1.0,2.0,0.5", mock_stream.captured[2])
         self.assertTrue(mock_stream.is_closed)
 
+    def test_save_csv_norm_with_tof_loaded(self):
+        stack, _ = self._set_sample_stack(with_tof=True)
+        norm = ImageStack(np.full([10, 11, 12], 2))
+        stack.data[:, :, :5] *= 2
+        self.model.set_normalise_stack(norm)
+
+        mock_stream, mock_path = self._make_mock_path_stream()
+        with mock.patch.object(self.model, "save_roi_coords"):
+            self.model.save_csv(mock_path, True)
+
+        mock_path.open.assert_called_once_with("w")
+        self.assertIn("tof_index,Wavelength,ToF,Energy,all,all_open,all_norm,roi,roi_open,roi_norm",
+                      mock_stream.captured[0])
+        self.assertIn("#,Angstrom,Microseconds,MeV,Counts,Counts,Counts", mock_stream.captured[1])
+        self.assertIn("0.0,0.0,0.0,inf,0.0,2.0,0.0,0.0,2.0,0.0", mock_stream.captured[2])
+        self.assertIn(
+            "1.0,7.064346392065392,100000.0,2.9271405738026552,1.4166666666666667,2.0,0.7083333333333334,1.4166666666666667,2.0,0.7083333333333334",
+            mock_stream.captured[3])
+        self.assertTrue(mock_stream.is_closed)
+
     def test_WHEN_roi_name_generator_called_THEN_correct_names_returned_visible_to_model(self):
         self.assertEqual(self.model.roi_name_generator(), "roi")
         self.assertEqual(self.model.roi_name_generator(), "roi_1")