UCL · KrisThielemans · Apr 22, 2020 · Jul 11, 2019 · Jul 11, 2019 · Apr 21, 2020
diff --git a/documentation/release_4.0.htm b/documentation/release_4.0.htm
@@ -159,6 +159,8 @@ <h3>New functionality</h3>
 <li><tt>list_image_values</tt> now has options to print coordinates in LPS as opposed to indices, print in CSV, or suppress the title row.</li>
 <li><tt>list_lm_countrates</tt> is a new list mode utility to output total counts per specified time interval.</li>
 <li>List-mode classes for Siemens ECAT8 (32-bit).</li>
+<li>Normalisation class for Siemens ECAT8, allowing for the <i>virtual</i> crystals. This needed 2 extra functions in <code>Scanner</code>
+to know how many virtual crystals there are.</li>
 <li>add Verbosity level (currently only to be set from interactive languages)</li>
 <li>Added the anatomical parallel level sets (PLS) prior. If an uniform anatomical image is provided it will work as a (smoothed) total variation (TV) prior. </li>
 <li>We added <code>SeparableGaussianArrayFilter</code> and <code>SeparableGaussianImageFilter</code> (based on old code in <tt>experimental</tt> which has now been removed). This filter constructs the kernel by sampling a Gaussian. It is therefore different from the Metz filter with power 0, as that is constructed by sampling a Gaussian in frequency space (and can therefore have negative values in image space).</li>

diff --git a/src/IO/CMakeLists.txt b/src/IO/CMakeLists.txt
@@ -35,6 +35,7 @@ set(${dir_LIB_SOURCES}
   MultiDynamicDiscretisedDensityOutputFileFormat
 
   GIPL_ImageFormat
+  stir_ecat_common 
 ) 
 
 # we can use IO from the itk library
@@ -49,7 +50,6 @@ if (LLN_FOUND)
  list(APPEND ${dir_LIB_SOURCES}
     ECAT7OutputFileFormat stir_ecat7 
     ECAT6OutputFileFormat 
-    stir_ecat_common 
     ECAT7ParametricDensityOutputFileFormat 
     ECAT7DynamicDiscretisedDensityOutputFileFormat 
     ECAT7DynamicDiscretisedDensityInputFileFormat

diff --git a/src/IO/InterfileHeaderSiemens.cxx b/src/IO/InterfileHeaderSiemens.cxx
@@ -2,7 +2,8 @@
     Copyright (C) 2000 PARAPET partners
     Copyright (C) 2000 - 2009-04-30, Hammersmith Imanet Ltd
     Copyright (C) 2011-07-01 - 2012, Kris Thielemans
-    Copyright (C) 2013, 2016 University College London
+    Copyright (C) 2013, 2016, 2018, 2020 University College London
+    Copyright (C) 2018 STFC
     This file is part of STIR.
 
     This file is free software; you can redistribute it and/or modify
@@ -33,6 +34,7 @@
 #include "stir/ImagingModality.h"
 #include "stir/ProjDataInfoCylindricalArcCorr.h"
 #include "stir/ProjDataInfoCylindricalNoArcCorr.h"
+#include "stir/IO/stir_ecat_common.h"
 #include <numeric>
 #include <functional>
 
@@ -269,15 +271,7 @@ bool InterfileRawDataHeaderSiemens::post_processing()
       {
         error("Interfile warning: 'number of segments' and length of 'segment table' are not consistent");
       }
-    // same order as in stir_ecat7
-    // Siemens always stores segments as 0, -1, +1, ...
-    segment_sequence.resize(num_segments);
-    segment_sequence[0] = 0;
-    for (int segment_num = 1; segment_num <= num_segments/2; ++segment_num)
-      {
-        segment_sequence[2 * segment_num - 1] = -segment_num;
-        segment_sequence[2 * segment_num] = segment_num;
-      }
+    segment_sequence = ecat::find_segment_sequence(*data_info_ptr);
     //XXX check if order here and segment_table are consistent
   }
 

diff --git a/src/IO/stir_ecat7.cxx b/src/IO/stir_ecat7.cxx
@@ -1379,15 +1379,8 @@ make_pdfs_from_matrix_aux(SUBHEADERPTR sub_header_ptr,
 
   pdi_ptr->set_num_axial_poss_per_segment(num_axial_poss_per_seg);
 
-  std::vector<int> segment_sequence_in_stream(2*max_segment_num+1);
-  // KT 25/10/2000 swapped segment order
-  // ECAT 7 always stores segments as 0, -1, +1, ...
-  segment_sequence_in_stream[0] = 0;
-  for (int segment_num = 1; segment_num<=max_segment_num; ++segment_num)
-  {
-    segment_sequence_in_stream[2*segment_num-1] = -segment_num;
-    segment_sequence_in_stream[2*segment_num] = segment_num;
-  }
+  std::vector<int> segment_sequence_in_stream =
+    find_segment_sequence_in_stream(*pdi_ptr);
 
   Matval matval;
   mat_numdoc(matrix->matnum, &matval);

diff --git a/src/IO/stir_ecat_common.cxx b/src/IO/stir_ecat_common.cxx
@@ -4,7 +4,7 @@
   \file
   \ingroup ECAT
 
-  \brief Implementation of routines which convert ECAT6 and ECAT7 things into our  building blocks and vice versa. 
+  \brief Implementation of routines which convert ECAT6, ECAT7 and ECAT8 things into our  building blocks and vice versa. 
 
   \author Kris Thielemans
   \author PARAPET project
@@ -13,6 +13,7 @@
 /*
     Copyright (C) 2000 PARAPET partners
     Copyright (C) 2000- 2009, Hammersmith Imanet Ltd
+    Copyright (C) 2020, University College London
     This file is part of STIR.
 
     This file is free software; you can redistribute it and/or modify
@@ -31,6 +32,7 @@
 #include "stir/ByteOrder.h"
 #include "stir/NumericType.h"
 #include "stir/Scanner.h" 
+#include "stir/ProjDataInfo.h"
 #include "stir/IO/stir_ecat_common.h"
 
 START_NAMESPACE_STIR
@@ -187,5 +189,21 @@ Scanner* find_scanner_from_ECAT_system_type(const short system_type)
   }
 }
 
+std::vector<int>
+find_segment_sequence(const ProjDataInfo& pdi)
+{
+  const int max_segment_num = pdi.get_max_segment_num();
+  std::vector<int> segment_sequence(2*max_segment_num+1);
+  // KT 25/10/2000 swapped segment order
+  // ECAT 7 always stores segments as 0, -1, +1, ...
+  segment_sequence[0] = 0;
+  for (int segment_num = 1; segment_num<=max_segment_num; ++segment_num)
+  {
+    segment_sequence[2*segment_num-1] = -segment_num;
+    segment_sequence[2*segment_num] = segment_num;
+  }
+  return segment_sequence;
+}
+
 END_NAMESPACE_ECAT
 END_NAMESPACE_STIR
diff --git a/src/buildblock/Scanner.cxx b/src/buildblock/Scanner.cxx
@@ -3,7 +3,7 @@
     Copyright (C) 2000 - 2010-07-21, Hammersmith Imanet Ltd
     Copyright (C) 2011, Kris Thielemans
     Copyright (C) 2010-2013, King's College London
-    Copyright (C) 2013-2016, University College London
+    Copyright (C) 2013-2016,2019, University College London
     This file is part of STIR.
 
     This file is free software; you can redistribute it and/or modify
@@ -189,9 +189,9 @@ Scanner::Scanner(Type scanner_type)
     set_params(E1080, string_list("ECAT 1080", "Biograph 16", "1080"),
                41, 336, 2* 336,
                412.0F, 7.0F, 4.0F, 2.000F, 0.0F,
-               1, 2, 41, 14, 41, 14, 1);
+               1, 2, 13+1, 13+1, 0, 0, 1);// TODO bucket/singles info?
     // Transaxial blocks have 13 physical crystals and a gap at the  
-    // 140th crystal where the counts are zero.
+    // 14th crystal where the counts are zero.
     // There are 39 rings with 13 axial crystals per block. Two virtual
     // rings are added, but contain counts after applying axial compression.
     break;
@@ -207,6 +207,16 @@ Scanner::Scanner(Type scanner_type)
                0.145f, 511.f); // TODO bucket/singles info incorrect? 224 buckets in total, but not sure how distributed
     break;
 
+  case Siemens_mCT:
+    // 13x13 blocks, 1 virtual "crystal" along axial and transaxial direction, 48 blocks along the ring, 4 blocks in axial direction
+    set_params(Siemens_mCT, string_list("Siemens mCT", "mCT", "2011", "1104" /* used in norm files */),
+               55, 400, (13+1)*48,
+               421.0F, 7.0F, 4.054F, 2.005F, 0.0F,
+               4, 1, 13+1, 13+1, 0,0, 1 ); // TODO singles info incorrect
+    // energy: 435-650
+    // 13 TOF bins
+    break;
+
   case RPT:
 
     set_params(RPT, string_list("PRT-1", "RPT"), 
@@ -598,7 +608,38 @@ set_params(Type type_v,const list<string>& list_of_names_v,
 
 }
 
+/*! \todo The current list is bound to be incomplete. would be better to stick it in set_params().
+ */
+int
+Scanner::
+get_num_virtual_axial_crystals_per_block() const
+{
+  switch(get_type())
+    {
+    case E1080:
+    case Siemens_mCT:
+      return 1;
+    default:
+      return 0;
+    }
+}
 
+/*! \todo The current list is bound to be incomplete. would be better to stick it in set_params().
+ */
+int
+Scanner::
+get_num_virtual_transaxial_crystals_per_block() const
+{
+  switch(get_type())
+    {
+    case E1080:
+    case Siemens_mCT:
+    case Siemens_mMR:
+      return 1;
+    default:
+      return 0;
+    }
+}
 
 Succeeded 
 Scanner::
@@ -654,10 +695,11 @@ check_consistency() const
 	const int dets_axial =
 	  get_num_axial_blocks() *
 	  get_num_axial_crystals_per_block();
-	if ( dets_axial != get_num_rings())
+	if ( dets_axial != (get_num_rings() + get_num_virtual_axial_crystals_per_block()))
 	  { 
-	    warning("Scanner %s: inconsistent axial block info",
-		    this->get_name().c_str()); 
+	    warning("Scanner %s: inconsistent axial block info: %d vs %d",
+		    this->get_name().c_str(),
+                    dets_axial, get_num_rings() + get_num_virtual_axial_crystals_per_block()); 
 	    return Succeeded::no; 
 	  }
       }

diff --git a/src/include/stir/IO/stir_ecat_common.h b/src/include/stir/IO/stir_ecat_common.h
@@ -33,6 +33,7 @@
 #define __stir_IO_stir_ecat_common_H__
 
 #include "stir/common.h"
+#include <vector>
 
 //*************** namespace macros
 #if !defined(STIR_NO_NAMESPACE)
@@ -68,6 +69,7 @@ START_NAMESPACE_STIR
 class NumericType;
 class ByteOrder;
 class Scanner;
+class ProjDataInfo;
 
 START_NAMESPACE_ECAT
 
@@ -115,6 +117,14 @@ short find_ECAT_system_type(const Scanner& scanner);
   Returns a Scanner(Scanner::Unknown_Scanner) object when the scanner is not recognised. */
 Scanner* find_scanner_from_ECAT_system_type(const short system_type);
 
+//! Return the sequence of how Siemens stores segments
+/*!
+  \ingroup ECAT
+   ECAT 7,8 always stores segments as 0, -1, +1, ... (numbering is in STIR convention)
+ */
+std::vector<int>
+find_segment_sequence(const ProjDataInfo& pdi);
+
 END_NAMESPACE_ECAT
 
 END_NAMESPACE_STIR

diff --git a/src/include/stir/Scanner.h b/src/include/stir/Scanner.h
@@ -2,7 +2,7 @@
     Copyright (C) 2000 PARAPET partners
     Copyright (C) 2000-2010, Hammersmith Imanet Ltd
     Copyright (C) 2011-2013, King's College London
-    Copyright (C) 2016, UCL
+    Copyright (C) 2016, 2019, UCL
 
     This file is part of STIR.
 
@@ -77,6 +77,11 @@ class Succeeded;
           collection of blocks. A \c singles_unit is then a set of crystals
           for which we can get singles rates.
 
+      A further complication is that some scanners (including many Siemens scanners) 
+      insert virtual crystals in the sinogram data (corresponding to gaps between
+      detector blocks). We currently define the blocks as the "virtual" ones,
+      but provide extra members to find out how many of these virtual crystals there are.
+
       \warning This information is only sensible for discrete detector-based scanners.
       \todo Some scanners do not have all info filled in at present. Values are then
       set to 0.
@@ -108,7 +113,7 @@ class Scanner
      to flag up an error and do some guess work in trying to recognise the scanner from 
      any given parameters.
   */
-  enum Type {E931, E951, E953, E921, E925, E961, E962, E966, E1080, Siemens_mMR, RPT,HiDAC,
+  enum Type {E931, E951, E953, E921, E925, E961, E962, E966, E1080, Siemens_mMR, Siemens_mCT, RPT,HiDAC,
 	     Advance, DiscoveryLS, DiscoveryST, DiscoverySTE, DiscoveryRX, Discovery600, Discovery690,
 	     HZLR, RATPET, PANDA, HYPERimage, nanoPET, HRRT, Allegro, GeminiTF, User_defined_scanner,
 	     Unknown_scanner};
@@ -262,6 +267,15 @@ class Scanner
   /* inline int get_num_layers_singles_units() const; */
   inline int get_num_singles_units() const;
 
+  //! \name number of "fake" crystals per block, inserted by the scanner
+  /*! Some scanners (including many Siemens scanners) insert virtual crystals in the sinogram data.
+    The other members of the class return the size of the "virtual" block. With these
+    functions you can find its true size.
+  */
+  //@{! 
+  int get_num_virtual_axial_crystals_per_block() const;
+  int get_num_virtual_transaxial_crystals_per_block() const;
+  //@}
 
   //@} (end of block/bucket info)
 

diff --git a/src/include/stir/Scanner.inl b/src/include/stir/Scanner.inl
@@ -152,7 +152,9 @@ Scanner::get_num_detector_layers() const
 int
 Scanner::get_num_axial_blocks() const
 {
-  return num_rings/num_axial_crystals_per_block;
+  // when using virtual crystals between blocks, there won't be one at the end, so we
+  // need to take this into account.
+  return (num_rings+get_num_virtual_axial_crystals_per_block())/num_axial_crystals_per_block;
 }
 
 int
@@ -194,7 +196,7 @@ Scanner::get_num_axial_singles_units() const
   if ( num_axial_crystals_per_singles_unit == 0 ) {
     return 0;
   } else {
-    return num_rings / num_axial_crystals_per_singles_unit;
+    return (num_rings+get_num_virtual_axial_crystals_per_block()) / num_axial_crystals_per_singles_unit;
   }
 }
 

diff --git a/src/listmode_buildblock/CListRecordECAT8_32bit.cxx b/src/listmode_buildblock/CListRecordECAT8_32bit.cxx
@@ -28,7 +28,7 @@
 #include "stir/Bin.h"
 #include "stir/error.h"
 #include "stir/Succeeded.h"
-
+#include "stir/IO/stir_ecat_common.h"
 #include <algorithm>
 #include <iostream>
 START_NAMESPACE_STIR
@@ -42,22 +42,13 @@ CListEventECAT8_32bit(const shared_ptr<ProjDataInfo>& proj_data_info_sptr) :
     dynamic_cast<const ProjDataInfoCylindricalNoArcCorr * const>(proj_data_info_sptr.get());
   if (proj_data_info_ptr == 0)
     error("CListEventECAT8_32bit can only be initialised with cylindrical projection data without arc-correction");
+ if (proj_data_info_ptr->get_max_ring_difference(0) != proj_data_info_ptr->get_min_ring_difference(0))
+   error("CListEventECAT8_32bit can only handle axial compression==1");
 
-  const int num_rings = this->scanner_sptr->get_num_rings();
-  const int max_ring_diff=proj_data_info_ptr->get_max_ring_difference(proj_data_info_ptr->get_max_segment_num());
-  if (proj_data_info_ptr->get_max_ring_difference(0) != proj_data_info_ptr->get_min_ring_difference(0))
-    error("CListEventECAT8_32bit can only handle axial compression==1");
-  this->segment_sequence.resize(2*max_ring_diff+1);
-  this->sizes.resize(2*max_ring_diff+1);
-  this->segment_sequence[0]=0;
-  this->sizes[0]=num_rings;
-  for (int ringdiff=1; ringdiff<=max_ring_diff; ++ringdiff)
-    {
-      this->segment_sequence[2*ringdiff-1]=-ringdiff;
-      this->segment_sequence[2*ringdiff]=ringdiff;
-      this->sizes[2*ringdiff-1]=num_rings-ringdiff;
-      this->sizes[2*ringdiff]=num_rings-ringdiff;
-    }
+ this->segment_sequence = ecat::find_segment_sequence(*proj_data_info_ptr);
+ this->sizes.resize(this->segment_sequence.size());
+ for (unsigned s=0U; s <= this->segment_sequence.size(); ++s)
+   this->sizes[s]=proj_data_info_ptr->get_num_axial_poss(segment_sequence[s]);
 }
 
 void
@@ -87,6 +78,7 @@ get_detection_position(DetectionPositionPair<>& det_pos) const
           z -= this->sizes[i];
         }
     }
+  // this is actually a compressed bin for many Siemens scanners. would have to go to det_pos somehow, or overload get_bin
   const Bin uncompressed_bin(segment_num, view_num, axial_pos_num,tang_pos_num - (num_tangential_poss/2));
   this->get_uncompressed_proj_data_info_sptr()->get_det_pos_pair_for_bin(det_pos,uncompressed_bin);  
 }