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UCL / STIR

Software for Tomographic Image Reconstruction
http://stir.sourceforge.net/
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Feature suggestions for ProjData Visualization #1320

Open robbietuk opened 10 months ago

robbietuk commented 10 months ago

Relevant directory: https://github.com/UCL/STIR/tree/master/examples/python/projdata_visualisation

1319 Added a TOF slider. The following are suggestions of changes to be made to ProjData Visualization

Further TOF improvements:

General

robbietuk commented 10 months ago

Suggestion: Add error handling for loading projdata with no binary or error when reading binary. The error should be displayed in the application window.

$ python3 examples/python/projdata_visualisation/ProjDataVisualisation.py 
ProjDataVisualisationBackend.load_data: Loading data from file: /home/rts/devel/stir/examples/PET_simulation/scatter_template.hs

WARNING: 
Interfile warning: I did not recognise the scanner neither from 
'originating_system' or 'number of detectors per ring' and 'number of rings'.

WARNING: Interfile warning: 'default_bin size (cm)' invalid.

WARNING: Interfile warning: 'axial crystals per singles unit' invalid.

WARNING: Interfile warning: 'transaxial crystals per singles unit' invalid.

WARNING: Interfile warning: 'distance between crystals in axial direction (cm)' invalid.

WARNING: Interfile warning: 'distance between crystals in transaxial direction (cm)' invalid.

WARNING: Interfile warning: 'distance between blocks in axial direction (cm)' invalid.

WARNING: Interfile warning: 'distance between blocks in transaxial direction (cm)' invalid.

WARNING: Scanner unknown: transaxial block info is not set (probably irrelevant unless you use a projector or normalisation that needs this block info)

WARNING: Scanner unknown: transaxial bucket info is not set (probably irrelevant unless you use dead-time correction that needs this info)

WARNING: Scanner unknown: axial block info is not set (probably irrelevant unless you use a projector or normalisation that needs this block info)

WARNING: Scanner unknown: axial bucket info is not set (probably irrelevant unless you use dead-time correction that needs this info)

WARNING: Scanner unknown: transaxial singles_unit info is not set (probably irrelevant unless you use dead-time correction that needs this info)

WARNING: Scanner unknown: axial singles_unit info is not set (probably irrelevant unless you use dead-time correction that needs this info)

WARNING: Interfile parsing ended up with the following scanner:
Scanner parameters:=
  Scanner type := unknown
  Number of rings                          := 8
  Number of detectors per ring             := 64
  Inner ring diameter (cm)                 := 88.62
  Average depth of interaction (cm)        := 0.84
  Distance between rings (cm)              := 1.962
  Default bin size (cm)                    := -1
  View offset (degrees)                    := 0
  Maximum number of non-arc-corrected bins := 35
  Default number of arc-corrected bins     := 0
  Energy resolution         := 0.16
  Reference energy (in keV) := 511
  Number of blocks per bucket in transaxial direction         := 0
  Number of blocks per bucket in axial direction              := 0
  Number of crystals per block in axial direction             := 0
  Number of crystals per block in transaxial direction        := 0
  Number of detector layers                                   := 1
  Number of crystals per singles unit in axial direction      := -1
  Number of crystals per singles unit in transaxial direction := -1
  Scanner geometry (BlocksOnCylindrical/Cylindrical/Generic)  := Cylindrical
End scanner parameters:=

WARNING: read_data: error after reading from stream.

ERROR: ProjDataFromStream: error reading data
ProjDataVisualisationBackend.load_data: Error loading data from file: /home/rts/devel/stir/examples/PET_simulation/scatter_template.hs
Traceback (most recent call last):
  File "/home/rts/devel/stir/examples/python/projdata_visualisation/ProjDataVisualisation.py", line 239, in browse_file_system_for_projdata
    self.load_projdata(filename[0])
  File "/home/rts/devel/stir/examples/python/projdata_visualisation/ProjDataVisualisation.py", line 260, in load_projdata
    self.refresh_UI_configuration()
  File "/home/rts/devel/stir/examples/python/projdata_visualisation/ProjDataVisualisation.py", line 167, in refresh_UI_configuration
    self.update_display_image()
  File "/home/rts/devel/stir/examples/python/projdata_visualisation/ProjDataVisualisation.py", line 182, in update_display_image
    image = self.get_sinogram_numpy_array()
  File "/home/rts/devel/stir/examples/python/projdata_visualisation/ProjDataVisualisation.py", line 226, in get_sinogram_numpy_array
    self.stir_interface.segment_data.get_sinogram(self.get_bin().axial_pos_num))
AttributeError: 'NoneType' object has no attribute 'get_sinogram'
robbietuk commented 10 months ago

Add a checkbox to sum over TOF indices, as suggested https://github.com/UCL/STIR/pull/1319#issuecomment-1887589084

I have to give up soon but here is a note on this. Adding a checkbox should be done to the ModeSelectionGroupBox, as added in #1321. Segments are unique for each TOF index and so requires a new segment to be loaded.

    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.segment_data = self.stir_interface.get_segment_data(new_segment_num, new_timing_pos)
        self.UI_controller_UI_change_trigger()

To sum each TOF index, we would need to load every TOF bins segment, convert to numpy and sum. It would be more convenient to do this on the cpp side.