Merge pull request #1319 from KrisThielemans/TOF_segment_and_vis

TOF segment bug fix, extra members and update visualation to add TOF

Author: KrisThielemans

examples/python/projdata_visualisation/BackendTools/STIRInterface.py

@@ -1,4 +1,4 @@
-# Copyright 2022 University College London
+# Copyright 2022, 2024 University College London
 
 # Author Robert Twyman
 
@@ -23,7 +23,7 @@ class ProjDataDims(Enum):
     AXIAL_POS = auto()
     VIEW_NUMBER = auto()
     TANGENTIAL_POS = auto()
-
+    TIMING_POS = auto()
 
 class ProjDataVisualisationBackend:
     """Class used as STIR interface to the projection data for ProjDataVisualisation."""
@@ -84,13 +84,14 @@ def print_segment_data_configuration(self) -> None:
             f"\tNumber of axial positions:\t\t\t{self.segment_data.get_num_axial_poss()}\n"
         )
 
-    def refresh_segment_data(self, segment_number=0) -> stir.FloatSegmentByView:
+    def refresh_segment_data(self, segment_number=0, timing_pos=0) -> stir.FloatSegmentByView:
         """Loads a segment data, from the projection data, into memory allowing for faster access."""
         if self.projdata is None:
             self.load_projdata()
 
         if self.projdata is not None:
-            self.segment_data = self.projdata.get_segment_by_view(segment_number)
+            seg_idx = stir.SegmentIndices(segment_number, timing_pos)
+            self.segment_data = self.projdata.get_segment_by_view(seg_idx)
             return self.segment_data
 
     @staticmethod
@@ -120,21 +121,16 @@ def get_limits(self, dimension: ProjDataDims, segment_number: int) -> tuple:
         elif dimension == ProjDataDims.TANGENTIAL_POS:
             return self.projdata.get_min_tangential_pos_num(), \
                    self.projdata.get_max_tangential_pos_num()
+        elif dimension == ProjDataDims.TIMING_POS:
+            return self.projdata.get_min_tof_pos_num(), \
+                   self.projdata.get_max_tof_pos_num()
         else:
             raise ValueError("Unknown sinogram dimension: " + str(dimension))
 
-    def get_num_indices(self, dimension: ProjDataDims):
+    def get_num_indices(self, dimension: ProjDataDims) -> int:
         """Returns the number of indices in the given dimension."""
-        if dimension == ProjDataDims.SEGMENT_NUM:
-            return self.projdata.get_num_segments()
-        elif dimension == ProjDataDims.AXIAL_POS:
-            return self.projdata.get_num_axial_poss(self.get_current_segment_num())
-        elif dimension == ProjDataDims.VIEW_NUMBER:
-            return self.projdata.get_num_views()
-        elif dimension == ProjDataDims.TANGENTIAL_POS:
-            return self.projdata.get_num_tangential_poss()
-        else:
-            raise ValueError("Unknown sinogram dimension: " + str(dimension))
+        limits = self.get_limits(dimension, self.get_current_segment_num())
+        return limits[1] - limits[0] + 1
 
     def get_current_segment_num(self) -> int:
         """Returns the segment number of the current segment data."""

examples/python/projdata_visualisation/BackendTools/UIGroupboxProjdataDimensions.py

@@ -1,4 +1,4 @@
-# Copyright 2022 University College London
+# Copyright 2022, 2024 University College London
 
 # Author Robert Twyman
 
@@ -42,6 +42,10 @@ def __init__(self, stir_interface: ProjDataVisualisationBackend) -> QGroupBox:
             ProjDataDims.TANGENTIAL_POS: {
                 'label': 'Tangential position',
                 'connect_method': self.tangential_pos_refresh
+            },
+            ProjDataDims.TIMING_POS: {
+                'label': 'TOF bin',
+                'connect_method': self.timing_pos_refresh
             }
         }
 
@@ -54,6 +58,7 @@ def __init__(self, stir_interface: ProjDataVisualisationBackend) -> QGroupBox:
         self.UI_slider_spinboxes[ProjDataDims.AXIAL_POS].add_item_to_layout(layout, row=2)
         self.UI_slider_spinboxes[ProjDataDims.VIEW_NUMBER].add_item_to_layout(layout, row=4)
         self.UI_slider_spinboxes[ProjDataDims.TANGENTIAL_POS].add_item_to_layout(layout, row=6)
+        self.UI_slider_spinboxes[ProjDataDims.TIMING_POS].add_item_to_layout(layout, row=8)
 
         layout.setRowStretch(5, 1)
         self.groupbox.setLayout(layout)
@@ -83,7 +88,8 @@ def segment_number_refresh(self):
         """ This function is called when the user changes the segment number value.
         Because of the way the STIR segment data is handled, the segment_data needs to change first."""
         new_segment_num = self.UI_slider_spinboxes[ProjDataDims.SEGMENT_NUM].value()
-        self.stir_interface.refresh_segment_data(new_segment_num)
+        new_timing_pos = self.UI_slider_spinboxes[ProjDataDims.TIMING_POS].value()
+        self.stir_interface.refresh_segment_data(new_segment_num, new_timing_pos)
         self.UI_controller_UI_change_trigger()
 
     def axial_pos_refresh(self):
@@ -98,6 +104,13 @@ def tangential_pos_refresh(self):
         """This function is called when the user changes the tangential position value."""
         self.UI_controller_UI_change_trigger()
 
+    def timing_pos_refresh(self):
+        """This function is called when the user changes the TOF bin value."""
+        new_segment_num = self.UI_slider_spinboxes[ProjDataDims.SEGMENT_NUM].value()
+        new_timing_pos = self.UI_slider_spinboxes[ProjDataDims.TIMING_POS].value()
+        self.stir_interface.refresh_segment_data(new_segment_num, new_timing_pos)
+        self.UI_controller_UI_change_trigger()
+
     def refresh_sliders_and_spinboxes_ranges(self) -> None:
         """Update the sliders and spinboxes ranges based upon the stir_interface projdata."""
         if self.stir_interface.projdata is None:

examples/python/projdata_visualisation/ProjDataVisualisation.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-# Copyright 2022 University College London
+# Copyright 2022, 2024 University College London
 
 # Author Robert Twyman
 
@@ -26,6 +26,7 @@
 from BackendTools.STIRInterface import ProjDataVisualisationBackend, ProjDataDims
 from BackendTools.UIGroupboxProjdataDimensions import UIGroupboxProjDataDimensions
 
+import stir
 
 class ProjDataVisualisationWidgetGallery(QDialog):
     def __init__(self, parent=None):
@@ -181,16 +182,20 @@ def update_display_image(self):
             image = self.get_sinogram_numpy_array()
             ax.title.set_text(
                 f"Sinogram - Segment: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.SEGMENT_NUM)}, "
-                f"Axial Position: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.AXIAL_POS)}")
+                f"Axial Position: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.AXIAL_POS)}, "
+                f"TOF bin: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.TIMING_POS)}")
             ax.yaxis.set_label_text("Views/projection angle")
             ax.xaxis.set_label_text("Tangential positions")
+            ax.xaxis.set_label_text("TOF bins")
         elif self.viewgram_radio_button.isChecked():
             image = self.get_viewgram_numpy_array()
             ax.title.set_text(
                 f"Sinogram - Segment: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.SEGMENT_NUM)},"
-                f"View Number: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.VIEW_NUMBER)}")
+                f"View Number: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.VIEW_NUMBER)}, "
+                f"TOF bin: {self.UI_groupbox_projdata_dimensions.value(ProjDataDims.TIMING_POS)}")
             ax.yaxis.set_label_text("Axial positions")
             ax.xaxis.set_label_text("Tangential positions")
+            ax.xaxis.set_label_text("TOF bins")
         else:
             msg = f"Error: No radio button is checked... How did you get here?\n"
             raise Exception(msg)
@@ -201,6 +206,14 @@ def update_display_image(self):
                   )
         self.display_image_matplotlib_canvas.draw()
 
+    def get_bin(self) -> stir.Bin:
+        view_num = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.VIEW_NUMBER)
+        axial_pos = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.AXIAL_POS)
+        segment_num = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.SEGMENT_NUM)
+        tangential_pos = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.TANGENTIAL_POS)
+        timing_pos = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.TIMING_POS)
+        return stir.Bin(segment_num, view_num, axial_pos, tangential_pos, timing_pos)
+
     def get_sinogram_numpy_array(self):
         """
         This function returns the sinogram numpy array based on the current UI configuration parameters for segment 
@@ -209,16 +222,14 @@ def get_sinogram_numpy_array(self):
         if self.stir_interface.projdata is None:
             return None
 
-        axial_pos = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.AXIAL_POS)
         return self.stir_interface.as_numpy(
-            self.stir_interface.segment_data.get_sinogram(axial_pos))
+            self.stir_interface.segment_data.get_sinogram(self.get_bin().axial_pos_num))
 
     def get_viewgram_numpy_array(self):
         if self.stir_interface.projdata is None:
             return None
 
-        view_num = self.UI_groupbox_projdata_dimensions.value(ProjDataDims.VIEW_NUMBER)
-        return self.stir_interface.as_numpy(self.stir_interface.segment_data.get_viewgram(view_num))
+        return self.stir_interface.as_numpy(self.stir_interface.segment_data.get_viewgram(self.get_bin().view_num))
 
     def browse_file_system_for_projdata(self):
         initial = self.projdata_filename_box.text()
@@ -256,7 +267,7 @@ def set_projdata(self, projdata):
 
 def OpenProjDataVisualisation(projdata=None):
     """
-    Function to open the ProjDataVisualisation GUI window. Will not exit pyton on window close.
+    Function to open the ProjDataVisualisation GUI window. Will not exit python on window close.
     projdata: Proj data to be visualised. Can be either a stir.ProjData object, a file path (str) or None. If None, an empty GUI will be opened.
     """
     app = QApplication([])

src/include/stir/ProjData.inl

@@ -27,13 +27,13 @@ START_NAMESPACE_STIR
 SegmentBySinogram<float>
 ProjData::get_segment_by_sinogram(const SegmentIndices& si) const
 {
-  return this->get_segment_by_sinogram(si.segment_num());
+  return this->get_segment_by_sinogram(si.segment_num(), si.timing_pos_num());
 }
 
 SegmentByView<float>
 ProjData::get_segment_by_view(const SegmentIndices& si) const
 {
-  return this->get_segment_by_view(si.segment_num());
+  return this->get_segment_by_view(si.segment_num(), si.timing_pos_num());
 }
 
 Viewgram<float> 

src/include/stir/Segment.h

@@ -23,6 +23,8 @@
 
 #include "stir/ProjDataInfo.h" 
 #include "stir/SegmentIndices.h"
+#include "stir/SinogramIndices.h"
+#include "stir/ViewgramIndices.h"
 #include "stir/shared_ptr.h"
 
 START_NAMESPACE_STIR
@@ -83,6 +85,11 @@ class Segment
   //! return a new viewgram, with data set as in the segment
   virtual Viewgram<elemT> get_viewgram(int view_num) const = 0;
 
+  //! return a new sinogram, with data set as in the segment
+  inline Sinogram<elemT> get_sinogram(const SinogramIndices& s) const;
+  //! return a new viewgram, with data set as in the segment
+  inline Viewgram<elemT> get_viewgram(const ViewgramIndices&) const;
+
   //! set data in segment according to sinogram \c s
   virtual void set_sinogram(const Sinogram<elemT>& s) = 0;
   //! set sinogram at a different axial_pos_num

src/include/stir/Segment.inl

@@ -3,7 +3,7 @@
 /*
     Copyright (C) 2000 PARAPET partners
     Copyright (C) 2000- 2007, IRSL
-    Copyright (C) 2023, University College London
+    Copyright (C) 2023, 2024 University College London
     This file is part of STIR.
 
     SPDX-License-Identifier: Apache-2.0 AND License-ref-PARAPET-license
@@ -54,4 +54,18 @@ Segment<elemT>::get_proj_data_info_sptr() const
   return proj_data_info_sptr;
 }
 
+template <typename elemT>
+Sinogram<elemT>
+Segment<elemT>::get_sinogram(const SinogramIndices& s) const
+{
+  return this->get_sinogram(s.axial_pos_num());
+}
+
+template <typename elemT>
+Viewgram<elemT>
+Segment<elemT>::get_viewgram(const ViewgramIndices& v) const
+{
+  return this->get_viewgram(v.view_num());
+}
+
 END_NAMESPACE_STIR

src/include/stir/SegmentBySinogram.h

@@ -103,22 +103,24 @@ class SegmentBySinogram : public Segment<elemT>, public Array<3,elemT>
   inline int get_min_tangential_pos_num()  const;
   //! Get maximum tangential position number
   inline int get_max_tangential_pos_num()  const;
+  using Segment<elemT>::get_sinogram;
+  using Segment<elemT>::get_viewgram;
   //! Get sinogram
-  inline Sinogram<elemT> get_sinogram(int axial_pos_num) const;
+  inline Sinogram<elemT> get_sinogram(int axial_pos_num) const override;
   //! Get viewgram
-  Viewgram<elemT> get_viewgram(int view_num) const;
+  Viewgram<elemT> get_viewgram(int view_num) const override;
   //! Set viewgram
-  void set_viewgram(const Viewgram<elemT>&);
+  void set_viewgram(const Viewgram<elemT>&) override;
   //! Set sinogram
-  inline void set_sinogram(Sinogram<elemT> const &s, int axial_pos_num);
-  inline void set_sinogram(const Sinogram<elemT>& s);
+  inline void set_sinogram(Sinogram<elemT> const &s, int axial_pos_num) override;
+  inline void set_sinogram(const Sinogram<elemT>& s) override;
 
   //! Overloading Array::grow
-  void grow(const IndexRange<3>& range);
+  void grow(const IndexRange<3>& range) override;
   //! Overloading Array::resize
-  void resize(const IndexRange<3>& range);
+  void resize(const IndexRange<3>& range) override;
 
-  virtual bool operator ==(const Segment<elemT>&) const;
+  virtual bool operator ==(const Segment<elemT>&) const override;
 };
 
 END_NAMESPACE_STIR

src/include/stir/SegmentByView.h

@@ -106,23 +106,25 @@ template <typename elemT> class SegmentByView : public Segment<elemT>, public Ar
   //! Get maximum tangetial position number
   inline int get_max_tangential_pos_num() const;
 
+  using Segment<elemT>::get_sinogram;
+  using Segment<elemT>::get_viewgram;
   //! Get sinogram
-  Sinogram<elemT> get_sinogram(int axial_pos_num) const;
+  Sinogram<elemT> get_sinogram(int axial_pos_num) const override;
   //! Get viewgram
-  inline Viewgram<elemT> get_viewgram(int view_num) const;
+  inline Viewgram<elemT> get_viewgram(int view_num) const override;
   //! Set sinogram
-  inline void set_sinogram(const Sinogram<elemT> &s);
+  inline void set_sinogram(const Sinogram<elemT> &s) override;
   //! Set sinogram
-  void set_sinogram(Sinogram<elemT> const &s, int axial_pos_num);
+  void set_sinogram(Sinogram<elemT> const &s, int axial_pos_num) override;
   //! Set viewgram
-  inline void set_viewgram(const Viewgram<elemT> &v);
+  inline void set_viewgram(const Viewgram<elemT> &v) override;
 
   //! Overloading Array::grow
-  void grow(const IndexRange<3>& range);
+  void grow(const IndexRange<3>& range) override;
   //! Overloading Array::resize
-  void resize(const IndexRange<3>& range);
+  void resize(const IndexRange<3>& range) override;
 
-  virtual bool operator ==(const Segment<elemT>&) const;
+  virtual bool operator ==(const Segment<elemT>&) const override;
 };
 
 END_NAMESPACE_STIR