TIme of Flight - clean

.clang-format

@@ -0,0 +1,15 @@
+---
+Language : Cpp
+# BasedOnStyle : GNU
+AlwaysBreakAfterReturnType: TopLevelDefinitions
+AlwaysBreakTemplateDeclarations: true
+BraceWrapping:
+  SplitEmptyFunction: false
+ColumnLimit:     130
+IndentPPDirectives: AfterHash
+PointerAlignment: Left
+SortIncludes:    false
+SortUsingDeclarations: false
+SpaceBeforeParens: ControlStatements
+Standard:        Cpp11
+...

.gitattributes

@@ -1,3 +1,14 @@
+# currently empty attributes (using pre-commit)
+[attr]cppfiles
+[attr]cfiles
+[attr]pyfiles
+*.cpp  cppfiles
+*.cxx  cppfiles
+*.h  cppfiles
+*.inl  cppfiles
+*.txx  cppfiles
+*.c    cfiles
+*.py   pyfiles
 *.v     -text -diff
 *.s     -text -diff
 *.scn     -text -diff

.github/workflows/check.yml

@@ -0,0 +1,13 @@
+name: Check
+on:
+- push
+- pull_request
+jobs:
+  check:
+    runs-on: ubuntu-latest
+    name: pre-commit
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+    - run: sudo apt-get install -yqq clang-format
+    - uses: pre-commit/action@v2.0.0

.gitignore

@@ -84,4 +84,7 @@ install_manifest.txt
 # other stuff
 .cache
 *.idea
-*.user
+*.user
+
+build
+out

.pre-commit-config.yaml

@@ -0,0 +1,6 @@
+repos:
+-   repo: git://github.com/doublify/pre-commit-clang-format
+    rev: 62302476d0da01515660132d76902359bed0f782
+    hooks:
+    -   id: clang-format
+        files: \.(c|cc|cxx|cpp|h|hpp|hxx|inl|txx)$

CMakeLists.txt

@@ -123,6 +123,10 @@ if(NOT DISABLE_CERN_ROOT)
   endif()
 endif()
 
+if(NOT DISABLE_HDF5_SUPPORT)
+    find_package(HDF5 COMPONENTS CXX)
+endif()
+
 if(NOT DISABLE_AVW)
   find_package(AVW)
 endif()

documentation/devel/README.md

@@ -0,0 +1,8 @@
+# Information specific for developers
+
+Please check files here for information/code practices for developers.
+
+- Do read our [contribution guidelines](../../CONTRIBUTING.md)
+- Set your editor settings appropriately: [instructions](editor-settings.md)
+- Install git hooks for serious development: [instructions](git-hooks.md)
+- Read the documentation, including the STIR developers guide

documentation/devel/editor-settings.md

@@ -0,0 +1,5 @@
+# Developer documentation: editor settings
+
+White-spaces and indentation with multiple developers are a pain. Please adhere to
+our white-space policy, which we try to enforce via [clang-format](https://clang.llvm.org/docs/ClangFormat.html).
+Check that site for integration with your editor/IDE.

documentation/devel/git-hooks.md

@@ -0,0 +1,28 @@
+# Developer documentation: how to install (software for) git hooks
+
+You first need to have Python and pip
+
+## Install [pre-commit](https://pre-commit.com)
+See https://pre-commit.com/#install but the following might work.
+
+    pip install pre-commit
+
+If this fails with a permission error, try adding `--user` to the command.
+
+If that fails with a message about `PyYAML` and `distutils`, try
+
+    pip install --ignore-installed PyYAML
+
+## Install clang-format
+### debian/Ubuntu
+    sudo apt install clang-format
+### MacOS
+    brew install clang-format
+### Others
+search the internet and tell us
+
+## Enable pre-commit hooks
+```sh
+cd /whereever/STIR
+pre-commit install
+```

examples/C++/General_Reconstruction/General_Reconstruction.cxx

@@ -5,53 +5,40 @@
 #include <iostream>
 START_NAMESPACE_STIR
 
-General_Reconstruction::
-General_Reconstruction()
-{
-    this->set_defaults();
-}
+General_Reconstruction::General_Reconstruction() { this->set_defaults(); }
 
 void
-General_Reconstruction::set_defaults()
-{
-
-}
+General_Reconstruction::set_defaults() {}
 
 void
-General_Reconstruction::initialise_keymap()
-{
-    this->parser.add_start_key("General reconstruction");
-    this->parser.add_stop_key("End General reconstruction");
+General_Reconstruction::initialise_keymap() {
+  this->parser.add_start_key("General reconstruction");
+  this->parser.add_stop_key("End General reconstruction");
 
-    this->parser.add_parsing_key("reconstruction method", &this->reconstruction_method_sptr);
+  this->parser.add_parsing_key("reconstruction method", &this->reconstruction_method_sptr);
 }
 
 bool
-General_Reconstruction::post_processing()
-{
-    return false;
+General_Reconstruction::post_processing() {
+  return false;
 }
 
 Succeeded
-General_Reconstruction::process_data()
-{
-    HighResWallClockTimer t;
-    t.reset();
-    t.start();
-
-        //return reconstruction_object.reconstruct() == Succeeded::yes ?
-        //    EXIT_SUCCESS : EXIT_FAILURE;
-        if (reconstruction_method_sptr->reconstruct() == Succeeded::yes)
-          {
-            t.stop();
-            std::cout << "Total Wall clock time: " << t.value() << " seconds" << std::endl;
-            return Succeeded::yes;
-          }
-        else
-          {
-            t.stop();
-            return Succeeded::no;
-          }
+General_Reconstruction::process_data() {
+  HighResWallClockTimer t;
+  t.reset();
+  t.start();
+
+  // return reconstruction_object.reconstruct() == Succeeded::yes ?
+  //    EXIT_SUCCESS : EXIT_FAILURE;
+  if (reconstruction_method_sptr->reconstruct() == Succeeded::yes) {
+    t.stop();
+    std::cout << "Total Wall clock time: " << t.value() << " seconds" << std::endl;
+    return Succeeded::yes;
+  } else {
+    t.stop();
+    return Succeeded::no;
+  }
 }
 
 END_NAMESPACE_STIR

examples/C++/General_Reconstruction/General_Reconstruction.h

@@ -16,31 +16,26 @@
 #include "stir/CartesianCoordinate3D.h"
 #include "Reconstruction.h"
 
-
 START_NAMESPACE_STIR
 
 class Succeeded;
 
-class General_Reconstruction : public ParsingObject
-{
+class General_Reconstruction : public ParsingObject {
 public:
-    //!
-    //! \brief General_Reconstuction
-    //! \details Default constructor
-    General_Reconstruction();
+  //!
+  //! \brief General_Reconstuction
+  //! \details Default constructor
+  General_Reconstruction();
 
-    virtual Succeeded process_data();
-protected:
+  virtual Succeeded process_data();
 
-    void set_defaults();
-    void initialise_keymap();
-    bool post_processing();
+protected:
+  void set_defaults();
+  void initialise_keymap();
+  bool post_processing();
 
 private:
-
-    shared_ptr < Reconstruction < DiscretisedDensity < 3, float > > >
-        reconstruction_method_sptr;
-
+  shared_ptr<Reconstruction<DiscretisedDensity<3, float>>> reconstruction_method_sptr;
 };
 
 END_NAMESPACE_STIR

examples/C++/src/demo1.cxx

@@ -6,20 +6,20 @@
   \brief A simple program that backprojects some projection data.
 
   It illustrates
-	- basic interaction with the user,
-	- reading of images and projection data
-	- construction of a specified type of back-projector,
-	- how to use back-project all projection data
-	- output of images
+        - basic interaction with the user,
+        - reading of images and projection data
+        - construction of a specified type of back-projector,
+        - how to use back-project all projection data
+        - output of images
 
   See README.txt in the directory where this file is located.
 
-  \author Kris Thielemans      
+  \author Kris Thielemans
 */
 /*
     Copyright (C) 2004- 2011, Hammersmith Imanet Ltd
 
-    This software is distributed under the terms 
+    This software is distributed under the terms
     of the GNU General  Public Licence (GPL)
     See STIR/LICENSE.txt for details
 */
@@ -33,25 +33,20 @@
 #include "stir/utilities.h"
 #include "stir/Succeeded.h"
 
-int main()
-{
+int
+main() {
   using namespace stir;
- 
+
   /////////////// input sinogram
-  const std::string input_filename =
-    ask_filename_with_extension("Input file",".hs");
+  const std::string input_filename = ask_filename_with_extension("Input file", ".hs");
 
-  shared_ptr<ProjData> 
-    proj_data_sptr(ProjData::read_from_file(input_filename));
-  shared_ptr<ProjDataInfo> 
-    proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
+  shared_ptr<ProjData> proj_data_sptr(ProjData::read_from_file(input_filename));
+  shared_ptr<ProjDataInfo> proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
 
   /////////////// template image (for sizes etc)
-  const std::string template_filename =
-    ask_filename_with_extension("Template image file",".hv");
+  const std::string template_filename = ask_filename_with_extension("Template image file", ".hv");
 
-  shared_ptr<DiscretisedDensity<3,float> > 
-    density_sptr(read_from_file<DiscretisedDensity<3,float> >(template_filename));
+  shared_ptr<DiscretisedDensity<3, float>> density_sptr(read_from_file<DiscretisedDensity<3, float>>(template_filename));
 
   density_sptr->fill(0);
 

examples/C++/src/demo2.cxx

@@ -4,23 +4,23 @@
   \file
   \ingroup examples
   \brief A small modification of demo1.cxx to ask the user for the
-	back projector she wants to use.
+        back projector she wants to use.
 
   It illustrates
-	- how to ask the user for objects for which different types
-	  exist (e.g. back-projector, forward-projectors, image processors 
-	  etc), anything based on the RegisteredObject hierarchy.
-	- that STIR is able to select basic processing units at run-time
-	- how to use the (very) basic display facilities in STIR
+        - how to ask the user for objects for which different types
+          exist (e.g. back-projector, forward-projectors, image processors
+          etc), anything based on the RegisteredObject hierarchy.
+        - that STIR is able to select basic processing units at run-time
+        - how to use the (very) basic display facilities in STIR
 
   See README.txt in the directory where this file is located.
 
-  \author Kris Thielemans      
+  \author Kris Thielemans
 */
 /*
     Copyright (C) 2004- 2012, Hammersmith Imanet Ltd
 
-    This software is distributed under the terms 
+    This software is distributed under the terms
     of the GNU General  Public Licence (GPL)
     See STIR/LICENSE.txt for details
 */
@@ -34,31 +34,25 @@
 #include "stir/Succeeded.h"
 #include "stir/display.h"
 
-int main()
-{
+int
+main() {
   using namespace stir;
- 
+
   /////////////// input sinogram
-  const std::string input_filename =
-    ask_filename_with_extension("Input file",".hs");
+  const std::string input_filename = ask_filename_with_extension("Input file", ".hs");
 
-  shared_ptr<ProjData> 
-    proj_data_sptr(ProjData::read_from_file(input_filename));
-  shared_ptr<ProjDataInfo> 
-    proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
+  shared_ptr<ProjData> proj_data_sptr(ProjData::read_from_file(input_filename));
+  shared_ptr<ProjDataInfo> proj_data_info_sptr(proj_data_sptr->get_proj_data_info_sptr()->clone());
 
   /////////////// template image (for sizes etc)
-  const std::string template_filename =
-    ask_filename_with_extension("Template image file",".hv");
+  const std::string template_filename = ask_filename_with_extension("Template image file", ".hv");
 
-  shared_ptr<DiscretisedDensity<3,float> > 
-    density_sptr(read_from_file<DiscretisedDensity<3,float> >(template_filename));
+  shared_ptr<DiscretisedDensity<3, float>> density_sptr(read_from_file<DiscretisedDensity<3, float>>(template_filename));
 
   density_sptr->fill(0);
 
   /////////////// back project
-  shared_ptr<BackProjectorByBin> back_projector_sptr
-    (BackProjectorByBin::ask_type_and_parameters());
+  shared_ptr<BackProjectorByBin> back_projector_sptr(BackProjectorByBin::ask_type_and_parameters());
 
   back_projector_sptr->set_up(proj_data_info_sptr, density_sptr);