Merge pull request #1064 from KrisThielemans/TOF_mashing

allow specifying TOF mashing for STIR

CHANGES.md

@@ -8,6 +8,11 @@
 * documentation
   - revision of READMEs for the examples
 
+* Require STIR 5.0
+
+* sirf.STIR.AcquisitionData constructor taking a scanner now has an extra optional argument
+  tof_mash_factor (defaulting to 1). This is only functional if a STIR version supporting TOF is used.
+
 ## v3.3.0
 
 * Added a new acquisition model `SPECTUBMatrix` for (simple) usage in SPECT.

src/CMakeLists.txt

@@ -87,9 +87,9 @@ if (DISABLE_STIR)
 else()
   find_package(STIR REQUIRED)
   message(STATUS "STIR version found: ${STIR_VERSION}")
-  if (STIR_VERSION  VERSION_LESS 4.1.0)
-    # Note: we support both version 4 and 5, so cannot put the version in the find_package statement
-    message(FATAL_ERROR "SIRF requires STIR version at least 4.1.0")
+  if (STIR_VERSION  VERSION_LESS 5.0.0)
+    # Note: we support both version 5 and 6, so cannot put the version in the find_package statement
+    message(FATAL_ERROR "SIRF requires STIR version at least 5.0.0")
   endif()
   if (STIR_WITH_NiftyPET_PROJECTOR)
     set(NiftyPET_BOOL_STR "1")

src/xSTIR/cSTIR/cstir.cpp

@@ -780,14 +780,17 @@ const int num_tof_bins_to_combine
 
 extern "C"
 void* cSTIR_acquisitionDataFromScannerInfo
-(const char* scanner, int span, int max_ring_diff, int view_mash_factor)
+(const char* scanner, int span, int max_ring_diff, int view_mash_factor, int tof_mash_factor)
 {
 	try{
                 stir::shared_ptr<ExamInfo> sptr_ei(new ExamInfo());
         sptr_ei->imaging_modality = ImagingModality::PT;
 		stir::shared_ptr<stir::ProjDataInfo> sptr_pdi =
 			PETAcquisitionData::proj_data_info_from_scanner
 			(scanner, span, max_ring_diff, view_mash_factor);
+#if STIR_VERSION >= 050000
+                sptr_pdi->set_tof_mash_factor(tof_mash_factor);
+#endif
 		PETAcquisitionDataInFile::init();
 		std::shared_ptr<PETAcquisitionData> sptr_t =
 			PETAcquisitionData::storage_template();

src/xSTIR/cSTIR/include/sirf/STIR/cstir.h

@@ -109,7 +109,7 @@ extern "C" {
 		const int num_tof_bins_to_combine
 		);
 	void* cSTIR_acquisitionDataFromScannerInfo
-		(const char* scanner, int span, int max_ring_diff, int view_mash_factor);
+        (const char* scanner, int span, int max_ring_diff, int view_mash_factor, int tof_mash_factor);
 	void* cSTIR_getAcquisitionDataDimensions(const void* ptr_acq, PTR_INT ptr_dim);
 	void* cSTIR_getAcquisitionData(const void* ptr_acq, PTR_FLOAT ptr_data);
 	void* cSTIR_setAcquisitionData(void* ptr_acq, PTR_FLOAT ptr_data);

src/xSTIR/mSTIR/+sirf/+STIR/AcquisitionData.m

@@ -54,15 +54,15 @@ function set_storage_scheme(scheme)
     end
     methods
         function self = AcquisitionData...
-                (arg, span, max_ring_diff, view_mash_factor)
+                (arg, span, max_ring_diff, view_mash_factor, tof_mash_factor)
 %***SIRF*** AcquisitionData(arg) creates a new AcquisitionData object 
 %           from a file or scanner or another AcquisitionData object;
 %           arg:  file or scanner name or AcquisitionData object.
 %           if a scanner name is used, additional arguments can be
 %           given to specify the data size, e.g.:
 %                acq=AcquisitionData('Siemens_mMR',span,max_ring_diff,view_mash_factor);
 %           Defaults are: 
-%                span=1, max_ring_diff=-1 (i.e. all), view_mash_factor=1
+%                span=1, max_ring_diff=-1 (i.e. all), view_mash_factor=1, tof_mash_factor=1
             self.handle_ = [];
             self.name = 'AcquisitionData';
             self.read_only = false;
@@ -71,6 +71,9 @@ function set_storage_scheme(scheme)
             elseif ischar(arg)
                 i = strfind(arg, '.');
                 if isempty(i)
+                    if nargin < 5
+                        tof_mash_factor = 1;
+                    end
                     if nargin < 4
                         view_mash_factor = 1;
                     end
@@ -82,7 +85,7 @@ function set_storage_scheme(scheme)
                     end
                     self.handle_ = calllib...
                         ('mstir', 'mSTIR_acquisitionDataFromScannerInfo',...
-                        arg, span, max_ring_diff, view_mash_factor);
+                        arg, span, max_ring_diff, view_mash_factor, tof_mash_factor);
                     status = calllib('miutilities', 'mExecutionStatus', ...
                         self.handle_);
                     if status ~= 0

src/xSTIR/pSTIR/STIR.py

@@ -870,7 +870,7 @@ def set_resolution_model(self, collimator_sigma_0_in_mm, collimator_slope_in_mm,
 class AcquisitionData(DataContainer):
     """Class for PET acquisition data."""
 
-    def __init__(self, src=None, span=1, max_ring_diff=-1, view_mash_factor=1):
+    def __init__(self, src=None, span=1, max_ring_diff=-1, view_mash_factor=1, tof_mash_factor=1):
         """Creates new AcquisitionData.
 
         Can create object from a file or another AcquisitionData object.
@@ -893,7 +893,7 @@ def __init__(self, src=None, span=1, max_ring_diff=-1, view_mash_factor=1):
             else:
                 # src is a scanner name
                 self.handle = pystir.cSTIR_acquisitionDataFromScannerInfo(
-                    src, span, max_ring_diff, view_mash_factor)
+                    src, span, max_ring_diff, view_mash_factor, tof_mash_factor)
                 if pyiutil.executionStatus(self.handle) != 0:
                     msg = pyiutil.executionError(self.handle)
                     if msg == 'Unknown scanner':