Switch Time of Flight units in Spectrum Viewer

docs/release_notes/next/feature-2151-spectrum-viewer-ToF-units

@@ -0,0 +1 @@
+#2151: Neutron wavelength, energy and tof units can be selected in the Spectrum Viewer

mantidimaging/core/utility/unit_conversion.py

@@ -0,0 +1,28 @@
+# Copyright (C) 2024 ISIS Rutherford Appleton Laboratory UKRI
+# SPDX - License - Identifier: GPL-3.0-or-later
+from __future__ import annotations
+
+import numpy as np
+
+
+class UnitConversion:
+    # target_to_camera_dist = 56 m taken from https://scripts.iucr.org/cgi-bin/paper?S1600576719001730
+    neutron_mass: float = 1.674927211e-27  # [kg]
+    planck_h: float = 6.62606896e-34  # [JHz-1]
+    angstrom: float = 1e-10  # [m]
+    mega_electro_volt: float = 1.60217662e-19 / 1e6
+
+    def __init__(self, data_to_convert: np.ndarray, target_to_camera_dist: float = 56) -> None:
+        self.tof_data_to_convert = data_to_convert
+        self.target_to_camera_dist = target_to_camera_dist
+        self.velocity = self.target_to_camera_dist / self.tof_data_to_convert
+
+    def tof_seconds_to_wavelength(self) -> np.ndarray:
+        wavelength = self.planck_h / (self.neutron_mass * self.velocity)
+        wavelength_angstroms = wavelength / self.angstrom
+        return wavelength_angstroms
+
+    def tof_seconds_to_energy(self) -> np.ndarray:
+        energy = self.neutron_mass * self.velocity / 2
+        energy_evs = energy / self.mega_electro_volt
+        return energy_evs

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -16,6 +16,7 @@
 from mantidimaging.core.io.instrument_log import LogColumn
 from mantidimaging.core.utility.sensible_roi import SensibleROI
 from mantidimaging.core.utility.progress_reporting import Progress
+from mantidimaging.core.utility.unit_conversion import UnitConversion
 
 if TYPE_CHECKING:
     from mantidimaging.gui.windows.spectrum_viewer.presenter import SpectrumViewerWindowPresenter
@@ -32,6 +33,13 @@ class SpecType(Enum):
     SAMPLE_NORMED = 3
 
 
+class ToFUnitMode(Enum):
+    IMAGE_NUMBER = 1
+    TOF_US = 2
+    WAVELENGTH = 3
+    ENERGY = 4
+
+
 class ErrorMode(Enum):
     STANDARD_DEVIATION = "Standard Deviation"
     PROPAGATED = "Propagated"
@@ -55,14 +63,24 @@ class SpectrumViewerWindowModel:
     _stack: ImageStack | None = None
     _normalise_stack: ImageStack | None = None
     tof_range: tuple[int, int] = (0, 0)
+    tof_plot_range: tuple[float, float] | tuple[int, int] = (0, 0)
     _roi_ranges: dict[str, SensibleROI]
+    tof_mode: ToFUnitMode
+    tof_data: np.ndarray | None = None
+    tof_range_full: tuple[int, int] = (0, 0)
 
     def __init__(self, presenter: SpectrumViewerWindowPresenter):
         self.presenter = presenter
         self._roi_id_counter = 0
         self._roi_ranges = {}
         self.special_roi_list = [ROI_ALL]
 
+        self.tof_data = self.get_stack_time_of_flight()
+        if self.tof_data is None:
+            self.tof_mode = ToFUnitMode.IMAGE_NUMBER
+        else:
+            self.tof_mode = ToFUnitMode.WAVELENGTH
+
     def roi_name_generator(self) -> str:
         """
         Returns a new Unique ID for newly created ROIs
@@ -94,6 +112,8 @@ def set_stack(self, stack: ImageStack | None) -> None:
             return
         self._roi_id_counter = 0
         self.tof_range = (0, stack.data.shape[0] - 1)
+        self.tof_range_full = self.tof_range
+        self.tof_data = self.get_stack_time_of_flight()
         self.set_new_roi(ROI_ALL)
 
     def set_new_roi(self, name: str) -> None:
@@ -441,3 +461,21 @@ def remove_all_roi(self) -> None:
         Remove all ROIs from the model
         """
         self._roi_ranges = {}
+
+    def set_relevant_tof_units(self) -> None:
+        if self._stack is not None:
+            self.tof_data = self.get_stack_time_of_flight()
+            if self.tof_mode == ToFUnitMode.IMAGE_NUMBER or self.tof_data is None:
+                self.tof_plot_range = (0, self._stack.data.shape[0] - 1)
+                self.tof_range = (0, self._stack.data.shape[0] - 1)
+                self.tof_data = np.arange(self.tof_range[0], self.tof_range[1] + 1)
+            else:
+                units = UnitConversion(self.tof_data)
+                if self.tof_mode == ToFUnitMode.TOF_US:
+                    self.tof_data = self.tof_data * 1e6
+                elif self.tof_mode == ToFUnitMode.WAVELENGTH:
+                    self.tof_data = units.tof_seconds_to_wavelength()
+                elif self.tof_mode == ToFUnitMode.ENERGY:
+                    self.tof_data = units.tof_seconds_to_energy()
+                self.tof_plot_range = (self.tof_data.min(), self.tof_data.max())
+                self.tof_range = (0, self.tof_data.size)

mantidimaging/gui/windows/spectrum_viewer/presenter.py

@@ -7,10 +7,15 @@
 from typing import TYPE_CHECKING
 
 from logging import getLogger
+
+import numpy as np
+from PyQt5.QtCore import QSignalBlocker
+
 from mantidimaging.core.data.dataset import StrictDataset
 from mantidimaging.gui.dialogs.async_task import start_async_task_view, TaskWorkerThread
 from mantidimaging.gui.mvp_base import BasePresenter
-from mantidimaging.gui.windows.spectrum_viewer.model import SpectrumViewerWindowModel, SpecType, ROI_RITS, ErrorMode
+from mantidimaging.gui.windows.spectrum_viewer.model import SpectrumViewerWindowModel, SpecType, ROI_RITS, ErrorMode, \
+    ToFUnitMode
 
 if TYPE_CHECKING:
     from mantidimaging.gui.windows.spectrum_viewer.view import SpectrumViewerWindowView  # pragma: no cover
@@ -62,6 +67,8 @@ def handle_stack_changed(self) -> None:
             except RuntimeError:
                 norm_stack = None
             self.model.set_normalise_stack(norm_stack)
+        self.reset_units_menu()
+        self.handle_tof_unit_change()
         self.show_new_sample()
         self.redraw_all_rois()
 
@@ -81,9 +88,12 @@ def handle_sample_change(self, uuid: UUID | None) -> None:
         if uuid is None:
             self.model.set_stack(None)
             self.view.clear()
+            self.view.tof_mode_select_group.setEnabled(False)
             return
 
         self.model.set_stack(self.main_window.get_stack(uuid))
+        self.reset_units_menu()
+        self.handle_tof_unit_change()
         normalise_uuid = self.view.get_normalise_stack()
         if normalise_uuid is not None:
             try:
@@ -98,6 +108,19 @@ def handle_sample_change(self, uuid: UUID | None) -> None:
         self.show_new_sample()
         self.view.on_visibility_change()
 
+    def reset_units_menu(self):
+        self.model.tof_mode = ToFUnitMode.IMAGE_NUMBER
+        for action in self.view.tof_mode_select_group.actions():
+            with QSignalBlocker(action):
+                if action.objectName() == 'Image Index':
+                    action.setChecked(True)
+                else:
+                    action.setChecked(False)
+        if self.model.tof_data is None:
+            self.view.tof_mode_select_group.setEnabled(False)
+        else:
+            self.view.tof_mode_select_group.setEnabled(True)
+
     def handle_normalise_stack_change(self, normalise_uuid: UUID | None) -> None:
         if normalise_uuid == self.current_norm_stack_uuid:
             return
@@ -135,13 +158,22 @@ def show_new_sample(self) -> None:
         averaged_image = self.model.get_averaged_image()
         assert averaged_image is not None
         self.view.set_image(averaged_image)
-        self.view.spectrum_widget.spectrum_plot_widget.add_range(*self.model.tof_range)
+        self.view.spectrum_widget.spectrum_plot_widget.add_range(*self.model.tof_plot_range)
+        self.view.spectrum_widget.spectrum_plot_widget.set_image_index_range_label(*self.model.tof_range)
         self.view.auto_range_image()
         if self.view.get_roi_properties_spinboxes():
             self.view.set_roi_properties()
 
     def handle_range_slide_moved(self, tof_range) -> None:
-        self.model.tof_range = tof_range
+        self.model.tof_plot_range = tof_range
+        if self.model.tof_mode == ToFUnitMode.IMAGE_NUMBER:
+            self.model.tof_range = (int(tof_range[0]), int(tof_range[1]))
+        else:
+            image_index_min = np.abs(self.model.tof_data - tof_range[0]).argmin()
+            image_index_max = np.abs(self.model.tof_data - tof_range[1]).argmin()
+            self.model.tof_range = tuple(sorted((image_index_min, image_index_max)))
+        self.view.spectrum_widget.spectrum_plot_widget.set_image_index_range_label(*self.model.tof_range)
+        self.view.spectrum_widget.spectrum_plot_widget.set_tof_range_label(*self.model.tof_plot_range)
         averaged_image = self.model.get_averaged_image()
         assert averaged_image is not None
         self.view.set_image(averaged_image, autoLevels=False)
@@ -312,3 +344,16 @@ def do_remove_roi(self, roi_name: str | None = None) -> None:
     def handle_export_tab_change(self, index: int) -> None:
         self.export_mode = ExportMode(index)
         self.view.on_visibility_change()
+
+    def handle_tof_unit_change(self) -> None:
+        selected_mode = self.view.tof_mode_select_group.checkedAction().text()
+        self.model.tof_mode = self.view.allowed_modes[selected_mode]["mode"]
+        self.model.set_relevant_tof_units()
+        self.view.spectrum_widget.spectrum_plot_widget.set_tof_axis_label(
+            self.view.allowed_modes[selected_mode]["label"])
+        self.view.spectrum_widget.spectrum.clearPlots()
+        self.view.spectrum_widget.spectrum.update()
+        self.view.show_visible_spectrums()
+        self.view.spectrum_widget.spectrum_plot_widget.add_range(*self.model.tof_plot_range)
+        self.view.spectrum_widget.spectrum_plot_widget.set_image_index_range_label(*self.model.tof_range)
+        self.view.auto_range_image()

mantidimaging/gui/windows/spectrum_viewer/spectrum_widget.py

@@ -7,7 +7,7 @@
 from PyQt5.QtCore import pyqtSignal, Qt, QSignalBlocker
 from PyQt5.QtGui import QColor
 from PyQt5.QtWidgets import QColorDialog, QAction, QMenu, QSplitter, QWidget, QVBoxLayout
-from pyqtgraph import ROI, GraphicsLayoutWidget, LinearRegionItem, PlotItem, mkPen
+from pyqtgraph import ROI, GraphicsLayoutWidget, LinearRegionItem, PlotItem, mkPen, ViewBox
 
 from mantidimaging.core.utility.close_enough_point import CloseEnoughPoint
 from mantidimaging.core.utility.sensible_roi import SensibleROI
@@ -121,7 +121,6 @@ def __init__(self) -> None:
         self.image = self.image_widget.image
         self.spectrum_plot_widget = SpectrumPlotWidget()
         self.spectrum = self.spectrum_plot_widget.spectrum
-
         self.splitter = QSplitter(Qt.Vertical)
         self.splitter.addWidget(self.image_widget)
         self.splitter.addWidget(self.spectrum_plot_widget)
@@ -272,31 +271,40 @@ class SpectrumPlotWidget(GraphicsLayoutWidget):
     def __init__(self) -> None:
         super().__init__()
 
-        self.spectrum = self.addPlot()
+        self.vb = ViewBox()
+        self.spectrum = self.addPlot(viewbox=self.vb)
         self.nextRow()
         self._tof_range_label = self.addLabel()
+        self.nextRow()
+        self._image_index_range_label = self.addLabel()
         self.range_control = LinearRegionItem()
         self.range_control.sigRegionChanged.connect(self._handle_tof_range_changed)
         self.ci.layout.setRowStretchFactor(0, 1)
 
-    def get_tof_range(self) -> tuple[int, int]:
+    def get_tof_range(self) -> tuple[float, float]:
         r_min, r_max = self.range_control.getRegion()
-        return int(r_min), int(r_max)
+        return r_min, r_max
 
     def _handle_tof_range_changed(self) -> None:
         tof_range = self.get_tof_range()
-        self._set_tof_range_label(tof_range[0], tof_range[1])
+        self.set_tof_range_label(tof_range[0], tof_range[1])
         self.range_changed.emit(tof_range)
 
-    def add_range(self, range_min: int, range_max: int) -> None:
+    def add_range(self, range_min: int | float, range_max: int | float) -> None:
         with QSignalBlocker(self.range_control):
             self.range_control.setBounds((range_min, range_max))
             self.range_control.setRegion((range_min, range_max))
         self.spectrum.addItem(self.range_control)
-        self._set_tof_range_label(range_min, range_max)
+        self.set_tof_range_label(range_min, range_max)
+
+    def set_tof_range_label(self, range_min: float, range_max: float) -> None:
+        self._tof_range_label.setText(f'ToF range: {range_min:.3f} - {range_max:.3f}')
+
+    def set_image_index_range_label(self, range_min: int, range_max: int) -> None:
+        self._image_index_range_label.setText(f'Image index range: {range_min} - {range_max}')
 
-    def _set_tof_range_label(self, range_min: int, range_max: int) -> None:
-        self._tof_range_label.setText(f'ToF range: {range_min} - {range_max}')
+    def set_tof_axis_label(self, tof_axis_label: str) -> None:
+        self.spectrum.setLabel('bottom', text=tof_axis_label)
 
 
 class SpectrumProjectionWidget(GraphicsLayoutWidget):

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

@@ -6,7 +6,7 @@
 from pathlib import Path
 from unittest import mock
 
-from PyQt5.QtWidgets import QPushButton
+from PyQt5.QtWidgets import QPushButton, QActionGroup
 from parameterized import parameterized
 
 from mantidimaging.core.data.dataset import StrictDataset, MixedDataset
@@ -34,6 +34,8 @@ def setUp(self) -> None:
         self.view.exportButton = mock.create_autospec(QPushButton)
         self.view.exportButtonRITS = mock.create_autospec(QPushButton)
         self.view.addBtn = mock.create_autospec(QPushButton)
+        self.view.tof_mode_select_group = mock.create_autospec(QActionGroup)
+        self.view.allowed_modes = mock.create_autospec(dict)
         self.presenter = SpectrumViewerWindowPresenter(self.view, self.main_window)
 
     def test_get_dataset_id_for_stack_no_stack_id(self):
@@ -53,6 +55,7 @@ def test_handle_sample_change_has_flat_before(self):
         self.presenter.main_window.get_stack = mock.Mock(return_value=generate_images())
         self.presenter.show_new_sample = mock.Mock()
         self.view.try_to_select_relevant_normalise_stack = mock.Mock()
+        self.presenter.handle_tof_unit_change = mock.Mock()
 
         self.presenter.handle_sample_change(uuid.uuid4())
         self.view.try_to_select_relevant_normalise_stack.assert_called_once_with('Flat_before')
@@ -67,6 +70,7 @@ def test_handle_sample_change_has_flat_after(self):
         self.presenter.show_new_sample = mock.Mock()
         self.view.try_to_select_relevant_normalise_stack = mock.Mock()
 
+        self.presenter.handle_tof_unit_change = mock.Mock()
         self.presenter.handle_sample_change(uuid.uuid4())
         self.view.try_to_select_relevant_normalise_stack.assert_called_once_with('Flat_after')
         self.presenter.show_new_sample.assert_called_once()
@@ -88,6 +92,7 @@ def test_handle_sample_change_dataset_unchanged(self):
         self.presenter.main_window.get_dataset = mock.Mock()
         self.presenter.main_window.get_stack = mock.Mock(return_value=generate_images())
         self.presenter.show_new_sample = mock.Mock()
+        self.presenter.handle_tof_unit_change = mock.Mock()
 
         self.presenter.handle_sample_change(uuid.uuid4())
         self.presenter.main_window.get_dataset.assert_not_called()
@@ -100,6 +105,7 @@ def test_handle_sample_change_to_MixedDataset(self):
         self.presenter.main_window.get_stack = mock.Mock(return_value=generate_images())
         self.presenter.show_new_sample = mock.Mock()
         self.view.try_to_select_relevant_normalise_stack = mock.Mock()
+        self.presenter.handle_tof_unit_change = mock.Mock()
 
         self.presenter.handle_sample_change(uuid.uuid4())
         self.presenter.main_window.get_dataset.assert_called_once()
@@ -112,6 +118,7 @@ def test_handle_sample_change_no_flat(self):
         self.presenter.main_window.get_stack = mock.Mock(return_value=generate_images())
         self.presenter.show_new_sample = mock.Mock()
         self.view.try_to_select_relevant_normalise_stack = mock.Mock()
+        self.presenter.handle_tof_unit_change = mock.Mock()
 
         self.presenter.handle_sample_change(uuid.uuid4())
         self.presenter.main_window.get_dataset.assert_called_once()
@@ -158,7 +165,7 @@ def test_WHEN_has_stack_has_bad_norm_THEN_buttons_set(self, normalise_issue, has
 
     def test_WHEN_show_sample_call_THEN_add_range_set(self):
         self.presenter.model.set_stack(generate_images([10, 5, 5]))
-        self.presenter.model.tof_range = (0, 9)
+        self.presenter.model.tof_plot_range = (0, 9)
         self.presenter.show_new_sample()
         self.view.spectrum_widget.spectrum_plot_widget.add_range.assert_called_once_with(0, 9)
 

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

@@ -104,7 +104,8 @@ def test_WHEN_set_roi_alpha_called_THEN_set_roi_visibility_flags_called(self, _,
     def test_WHEN_add_range_called_THEN_region_and_label_set_correctly(self, _, range_min, range_max):
         self.spectrum_plot_widget.add_range(range_min, range_max)
         self.assertEqual(self.spectrum_plot_widget.range_control.getRegion(), (range_min, range_max))
-        self.assertEqual(self.spectrum_plot_widget._tof_range_label.text, f"ToF range: {range_min} - {range_max}")
+        self.assertEqual(self.spectrum_plot_widget._tof_range_label.text,
+                         f"ToF range: {range_min:.3f} - {range_max:.3f}")
 
     def test_WHEN_get_roi_called_THEN_SensibleROI_returned(self):
         spectrum_roi = SpectrumROI("roi",
@@ -136,8 +137,8 @@ def test_WHEN_remove_roi_called_THEN_roi_removed_from_roi_dict(self):
         self.assertNotIn(spectrum_roi, self.spectrum_widget.image.vb.addedItems)
 
     def test_WHEN_set_tof_range_called_THEN_range_control_set_correctly(self):
-        self.spectrum_plot_widget._set_tof_range_label(0, 100)
-        self.assertEqual(self.spectrum_plot_widget._tof_range_label.text, "ToF range: 0 - 100")
+        self.spectrum_plot_widget.set_tof_range_label(0, 100)
+        self.assertEqual(self.spectrum_plot_widget._tof_range_label.text, "ToF range: 0.000 - 100.000")
 
     def test_WHEN_rename_roi_called_THEN_roi_renamed(self):
         spectrum_roi = SpectrumROI("roi_1",