Merge pull request #1273 from SyneRBI/v3.8.0prep

Preparation branch for version 3.8.0

CHANGES.md

@@ -3,11 +3,16 @@
 ## v3.8.0
 
 * SIRF/STIR (PET and SPECT)
-  - use direct STIR operations for arrays, potentially resulting in speed-up when using STIR 6.2 or later.
+  - use direct STIR operations for arrays, potentially resulting in speed-up when using STIR 6.2 or later
+  - fixed STIR linking problems by adding STIR_REGISTRIES to Reg executables
+  - added `compute_attenuation_factors` method to AcquisitionSensitivityModel
   - added means for setting maximal and minimal value for scale factor in stir::ScatterEstimation
 
+* MR
+  - fixed density_weight shape issue caused by upgrading numpy to version 2.0
+
 * CMake/building:
-- set CMP0074 policy to NEW, i.e. honour <packagename>_ROOT env variables
+  - set CMP0074 policy to NEW, i.e. honour <packagename>_ROOT env variables
 
 ## v3.7.0
 
@@ -27,7 +32,7 @@
 
 * PET:
   - incorporated into SIRF data processing utilities from SyneRBI-Challenge.
-  - Added method modality() to AcquisitionData classes.
+  - added method modality() to AcquisitionData classes.
 
 ## v3.7.0
 

CMakeLists.txt

@@ -61,7 +61,7 @@ endif()
 
 ####### Set Version number etc
 set(VERSION_MAJOR   3 )
-set(VERSION_MINOR   7 )
+set(VERSION_MINOR   8 )
 set(VERSION_PATCH   0 )
 mark_as_advanced(VERSION_MAJOR VERSION_MINOR VERSION_PATCH)
 

doc/DeveloperGuide.md

@@ -27,7 +27,7 @@
 # Overview <a name="Overview"></a>
 
 The SIRF (Synergistic Image Reconstruction Framework) software is an Open Source toolkit for the reconstruction of PET and MRI raw data. The aim is to provide code simple enough to easily perform a reconstruction, yet powerful enough to be able to handle real, full-size datasets. Our strategy in achieving this aim is to employ available Open Source reconstruction software written in advanced programming languages such as C++ and provide basic-user-friendly interfaces to it written in script languages, primarily Matlab and Python. This document describes in detail the interfacing principles and structure in order to facilitate the contributions to SIRF from any interested developer.
-This Developer's Guide is for version 3.7 of SIRF. The software can be found on [https://github.com/CCPSyneRBI](https://github.com/CCPSyneRBI).
+This Developer's Guide is for version 3.8 of SIRF. The software can be found on [https://github.com/CCPSyneRBI](https://github.com/CCPSyneRBI).
 
 # SIRF structure <a name="SIRF_structure"></a>
 

doc/UserGuide.md

@@ -32,7 +32,7 @@
 
 The SIRF (Synergistic Image Reconstruction Framework) software is an Open Source toolkit for the reconstruction of PET and MRI raw data. The aim is to provide code simple enough to easily perform a reconstruction, yet powerful enough to be able to handle real, full-size datasets. Our strategy in achieving this aim is to employ available Open Source reconstruction software written in advanced programming languages such as C++ and provide basic-user-friendly interfaces to it written in script languages, primarily Matlab and Python. The interface style permits a reconstruction to be performed in stages, allowing the user to inspect or modify data, or insert their own code. 
 
-This User’s Guide describes version 3.7 of SIRF. The software can be found on [https://github.com/SyneRBI](https://github.com/SyneRBI).
+This User’s Guide describes version 3.8 of SIRF. The software can be found on [https://github.com/SyneRBI](https://github.com/SyneRBI).
 
 ## General architecture <a name="General_architecture"></a>
 
@@ -44,7 +44,7 @@ At present, you should only use the C++, MATLAB and Python interfaces. The under
 
 ### MRI <a name="MRI"></a>
 
-SIRF expects raw MR data in the ISMRMRD format. We use [siemens_to_ismrmrd](https://github.com/ismrmrd/siemens_to_ismrmrd) for this. This enables raw data from Siemens mMR Biograph PET-MR scanners to be converted to ISMRMRD format. For more details of how to export the raw MR data from Siemens PET-MR scanners and how to convert the data to ISMRMRD please see the wiki: [https://github.com/SyneRBI/SIRF/wiki/MR-raw-data](https://github.com/SyneRBI/SIRF/wiki/MR-raw-data).  
+SIRF expects raw MR data in the ISMRMRD format. We use [siemens_to_ismrmrd](https://github.com/ismrmrd/siemens_to_ismrmrd) for this. This enables raw data from Siemens mMR Biograph PET-MR scanners to be converted to ISMRMRD format. For more details of how to export the raw MR data from Siemens PET-MR scanners and how to convert the data to ISMRMRD please see the wiki: [https://github.com/SyneRBI/SIRF/wiki/MR-raw-data](https://github.com/SyneRBI/SIRF/wiki/MR-raw-data).
 
 Converters for data from other scanners are available from [https://github.com/ismrmrd](https://github.com/ismrmrd) but we have not tried these yet.