Enter Time of Flight user properties in Spectrum Viewer

mantidimaging/core/utility/unit_conversion.py

@@ -11,18 +11,42 @@ class UnitConversion:
     planck_h: float = 6.62606896e-34  # [JHz-1]
     angstrom: float = 1e-10  # [m]
     mega_electro_volt: float = 1.60217662e-19 / 1e6
+    target_to_camera_dist: float = 56  # [m]
+    data_offset: float = 0  # [us]
+    tof_data_to_convert: np.ndarray
+    velocity: np.ndarray
 
-    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 __init__(self, data_to_convert: np.ndarray | None = None) -> None:
+        if data_to_convert is not None:
+            self.set_data_to_convert(data_to_convert)
 
     def tof_seconds_to_wavelength(self) -> np.ndarray:
+        self.check_data()
         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:
+        self.check_data()
         energy = self.neutron_mass * self.velocity / 2
         energy_evs = energy / self.mega_electro_volt
         return energy_evs
+
+    def tof_seconds_to_us(self) -> np.ndarray:
+        self.check_data()
+        return (self.tof_data_to_convert + self.data_offset) * 1e6
+
+    def set_target_to_camera_dist(self, target_to_camera_dist: float) -> None:
+        self.target_to_camera_dist = target_to_camera_dist
+
+    def set_data_to_convert(self, data_to_convert: np.ndarray) -> None:
+        self.tof_data_to_convert = data_to_convert
+
+    def check_data(self) -> None:
+        if self.tof_data_to_convert is None:
+            raise TypeError("Data is not present")
+        else:
+            self.velocity = self.target_to_camera_dist / (self.tof_data_to_convert + self.data_offset)
+
+    def set_data_offset(self, data_offset: float) -> None:
+        self.data_offset = data_offset * 1e-6

mantidimaging/gui/ui/spectrum_viewer.ui

@@ -6,8 +6,8 @@
    <rect>
     <x>0</x>
     <y>0</y>
-    <width>905</width>
-    <height>752</height>
+    <width>1001</width>
+    <height>766</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -391,7 +391,78 @@
          </widget>
         </item>
         <item>
-         <spacer name="PropertiesSpacer">
+         <widget class="QGroupBox" name="tofPropertiesGroupBox">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Expanding" vsizetype="MinimumExpanding">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="minimumSize">
+           <size>
+            <width>300</width>
+            <height>84</height>
+           </size>
+          </property>
+          <property name="title">
+           <string>Time of Flight Properties</string>
+          </property>
+          <widget class="QLabel" name="label_3">
+           <property name="geometry">
+            <rect>
+             <x>10</x>
+             <y>31</y>
+             <width>101</width>
+             <height>16</height>
+            </rect>
+           </property>
+           <property name="text">
+            <string>Flight path:</string>
+           </property>
+          </widget>
+          <widget class="QLabel" name="label_4">
+           <property name="geometry">
+            <rect>
+             <x>10</x>
+             <y>50</y>
+             <width>91</width>
+             <height>20</height>
+            </rect>
+           </property>
+           <property name="text">
+            <string>Time delay: </string>
+           </property>
+          </widget>
+          <widget class="QDoubleSpinBox" name="flightPathSpinBox">
+           <property name="geometry">
+            <rect>
+             <x>80</x>
+             <y>30</y>
+             <width>211</width>
+             <height>19</height>
+            </rect>
+           </property>
+           <property name="suffix">
+            <string/>
+           </property>
+          </widget>
+          <widget class="QDoubleSpinBox" name="timeDelaySpinBox">
+           <property name="geometry">
+            <rect>
+             <x>80</x>
+             <y>50</y>
+             <width>211</width>
+             <height>19</height>
+            </rect>
+           </property>
+           <property name="suffix">
+            <string/>
+           </property>
+          </widget>
+         </widget>
+        </item>
+        <item>
+         <spacer name="verticalSpacer">
           <property name="orientation">
            <enum>Qt::Vertical</enum>
           </property>

mantidimaging/gui/windows/spectrum_viewer/model.py

@@ -81,6 +81,8 @@ def __init__(self, presenter: SpectrumViewerWindowPresenter):
         else:
             self.tof_mode = ToFUnitMode.WAVELENGTH
 
+        self.units = UnitConversion()
+
     def roi_name_generator(self) -> str:
         """
         Returns a new Unique ID for newly created ROIs
@@ -470,12 +472,12 @@ def set_relevant_tof_units(self) -> None:
                 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)
+                self.units.set_data_to_convert(self.tof_data)
                 if self.tof_mode == ToFUnitMode.TOF_US:
-                    self.tof_data = self.tof_data * 1e6
+                    self.tof_data = self.units.tof_seconds_to_us()
                 elif self.tof_mode == ToFUnitMode.WAVELENGTH:
-                    self.tof_data = units.tof_seconds_to_wavelength()
+                    self.tof_data = self.units.tof_seconds_to_wavelength()
                 elif self.tof_mode == ToFUnitMode.ENERGY:
-                    self.tof_data = units.tof_seconds_to_energy()
+                    self.tof_data = self.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

@@ -109,6 +109,12 @@ def handle_sample_change(self, uuid: UUID | None) -> None:
         self.view.on_visibility_change()
 
     def reset_units_menu(self):
+        if self.model.tof_data is None:
+            self.view.tof_mode_select_group.setEnabled(False)
+            self.view.tofPropertiesGroupBox.setEnabled(False)
+        else:
+            self.view.tof_mode_select_group.setEnabled(True)
+            self.view.tofPropertiesGroupBox.setEnabled(True)
         self.model.tof_mode = ToFUnitMode.IMAGE_NUMBER
         for action in self.view.tof_mode_select_group.actions():
             with QSignalBlocker(action):
@@ -349,11 +355,25 @@ 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"])
+        tof_axis_label = self.view.allowed_modes[selected_mode]["label"]
+        self.view.spectrum_widget.spectrum_plot_widget.set_tof_axis_label(tof_axis_label)
+        self.refresh_spectrum_plot()
+
+    def refresh_spectrum_plot(self) -> None:
         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()
+
+    def handle_flight_path_change(self) -> None:
+        self.model.units.set_target_to_camera_dist(self.view.flightPathSpinBox.value())
+        self.model.set_relevant_tof_units()
+        self.refresh_spectrum_plot()
+
+    def handle_time_delay_change(self) -> None:
+        self.model.tof_data = self.model.get_stack_time_of_flight()
+        self.model.units.set_data_offset(self.view.timeDelaySpinBox.value())
+        self.model.set_relevant_tof_units()
+        self.refresh_spectrum_plot()

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, QActionGroup
+from PyQt5.QtWidgets import QPushButton, QActionGroup, QGroupBox
 from parameterized import parameterized
 
 from mantidimaging.core.data.dataset import StrictDataset, MixedDataset
@@ -35,7 +35,7 @@ def setUp(self) -> None:
         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.view.tofPropertiesGroupBox = mock.create_autospec(QGroupBox)
         self.presenter = SpectrumViewerWindowPresenter(self.view, self.main_window)
 
     def test_get_dataset_id_for_stack_no_stack_id(self):

mantidimaging/gui/windows/spectrum_viewer/view.py

@@ -7,7 +7,7 @@
 
 from PyQt5.QtGui import QPixmap
 from PyQt5.QtWidgets import QCheckBox, QVBoxLayout, QFileDialog, QPushButton, QLabel, QAbstractItemView, QHeaderView, \
-    QTabWidget, QComboBox, QSpinBox, QTableWidget, QTableWidgetItem, QGroupBox, QActionGroup, QAction
+    QTabWidget, QComboBox, QSpinBox, QTableWidget, QTableWidgetItem, QGroupBox, QActionGroup, QAction, QDoubleSpinBox
 from PyQt5.QtCore import QSignalBlocker, Qt
 
 from mantidimaging.core.utility import finder
@@ -58,6 +58,10 @@ class SpectrumViewerWindowView(BaseMainWindowView):
 
     number_roi_properties_procced: int = 0
 
+    tofPropertiesGroupBox: QGroupBox
+    flightPathSpinBox: QDoubleSpinBox
+    timeDelaySpinBox: QDoubleSpinBox
+
     def __init__(self, main_window: MainWindowView):
         super().__init__(None, 'gui/ui/spectrum_viewer.ui')
 
@@ -200,6 +204,16 @@ def __init__(self, main_window: MainWindowView):
         self.current_roi = self.last_clicked_roi = self.roi_table_model.roi_names()[0]
         self.set_roi_properties()
 
+        self.flightPathSpinBox.setMinimum(0)
+        self.flightPathSpinBox.setMaximum(1e10)
+        self.flightPathSpinBox.setValue(56)
+        self.flightPathSpinBox.setSuffix(" m")
+        self.timeDelaySpinBox.setMaximum(1e10)
+        self.timeDelaySpinBox.setSuffix(" \u03BCs")
+
+        self.flightPathSpinBox.valueChanged.connect(self.presenter.handle_flight_path_change)
+        self.timeDelaySpinBox.valueChanged.connect(self.presenter.handle_time_delay_change)
+
         def on_row_change(item, _) -> None:
             """
             Handle cell change in table view and update selected ROI and