fix GSM methods for python wrapper (#198)

.github/workflows/main.yml

@@ -26,7 +26,7 @@ jobs:
         mkdir build
         cd build
         cmake  -DCMAKE_BUILD_TYPE=Release ../ -DCMAKE_INSTALL_PREFIX=$HOME/usr
-        cmake --build . --target install -- -j2
+        cmake --build . --target install -- -j
       
     - name: tests
       run: |
@@ -61,7 +61,7 @@ jobs:
           tar -xzf gsl-latest.tar.gz -C $HOME/gsl-latest
           mv $HOME/gsl-latest/** $HOME/gsl-latest/gsl
           mkdir $HOME/usr
-          cd $HOME/gsl-latest/gsl/ && emconfigure ./configure --prefix=$HOME/usr --disable-shared && emmake make -j2 && emmake make install
+          cd $HOME/gsl-latest/gsl/ && emconfigure ./configure --prefix=$HOME/usr --disable-shared && emmake make -j && emmake make install
           ls -al $HOME/usr/lib/
           
       - name: Compile libamtrack webassembly package

README.md

@@ -1,5 +1,3 @@
-[![Build Status](https://travis-ci.org/libamtrack/library.svg?branch=master)](https://travis-ci.org/libamtrack/library)
-
 # 1. WHAT IS LIBAMTRACK?
 
 * libamtrack provides computational routines for the prediction of detector response and radiobiological efficiency in heavy charged particle beams.
@@ -11,8 +9,6 @@
 * libamtrack is free, open-source software under GNU GPL licence.
 * libamtrack is intended to facilitate the comparison of and the communication on amorphous track models for particle beam research.
 
-libamtrack's main website: http://libamtrack.dkfz.org
-
 
 # 2. HOW CAN I USE LIBAMTRACK?
 
@@ -43,8 +39,6 @@ This should be the very last alternative - THE FACT THAT YOU ARE LOOKING AT THIS
 Everybody is welcome to read, use and modify (preferably to improve) the code according to GNU GPL 3.
 
 
-
 # 4. WHERE DO I FIND DOCUMENTATION ON LIBAMTRACK?
 
-- The libamtrack manual is found here: /docs/libamtrackManual.pdf
-- On the webpage: libamtrack.dkfz.org
+- The libamtrack manual is found here: /docs/libamtrackManual.pdf

distributions/Python/pyamtrack/make_wheel_package.sh

@@ -3,7 +3,13 @@
 # get the tool which aids making wheel package
 # it will automatically generate python wrapper for decorated (doxygen) C code
 rm -rf cBinder || exit 1
-git clone https://github.com/Tetrite/cBinder.git || exit 1
+if [ -d "$DIR" ]; then
+    echo "cBinder already exists"
+    cd cBinder || exit 1
+    git pull || exit 1
+else
+    git clone https://github.com/Tetrite/cBinder.git || exit 1
+fi
 
 # copy source files and headers to local folder, so the docker container can access them
 rm -rf libamtrack || exit 1
@@ -13,20 +19,28 @@ cp -rf ../../../include libamtrack/ || exit 1
 cp -rf ../../../src libamtrack/ || exit 1
 
 # get necessary dependency (latest) version of GSL library
-rm -f gsl.tar.gz || exit 1
-wget --quiet "http://ftpmirror.gnu.org/gnu/gsl/gsl-latest.tar.gz" --output-document=gsl.tar.gz || exit 1
+if [ -d "gsl-latest" ]; then
+    echo "gsl-latest already exists"
+else
+    rm -f gsl.tar.gz || exit 1
+    wget --quiet "http://ftpmirror.gnu.org/gnu/gsl/gsl-latest.tar.gz" --output-document=gsl.tar.gz || exit 1
 
-# unpack into gsl-x.y directory
-rm -rf gsl-?.* || exit 1
-tar -zxf gsl.tar.gz || exit 1
+    # unpack into gsl-x.y directory
+    rm -rf gsl-?.* || exit 1
+    tar -zxf gsl.tar.gz || exit 1
+
+    # move into gsl-latest directory
+    rm -rf gsl-latest || exit 1
+    mv gsl-?.* gsl-latest || exit 1
+fi
 
-# move into gsl-latest directory
-rm -rf gsl-latest || exit 1
-mv gsl-?.* gsl-latest || exit 1
 
 # make directory for GSL installation
-rm -rf gsl || exit 1
-mkdir gsl || exit 1
+if [ -d "gsl" ]; then
+    echo "gsl already exists"
+else
+    mkdir gsl || exit 1
+fi
 
 # run the docker process which using manylinux1 machine (SLC6 based) will compile
 # the C extensions using old enough libraries

example/demo/CMakeLists.txt

@@ -10,4 +10,12 @@ add_executable (${PROJECT_NAME} ${SOURCE_FILES} )
 
 target_link_libraries( ${PROJECT_NAME} LINK_PUBLIC amtrack ${GSL_LIBRARIES})
 
+# Visual Studio does not need or want you to explicitly request linking the math library.
+# You must avoid adding it as a link library when building for Windows.
+# see https://stackoverflow.com/questions/54935559/linking-math-library-in-cmake-file-on-windows-and-linux
+IF (NOT WIN32)
+  target_link_libraries (${PROJECT_NAME} m)
+ENDIF()
+
+
 install(TARGETS ${PROJECT_NAME} DESTINATION bin)

include/AT_Algorithms_GSM.h

@@ -234,18 +234,19 @@ void AT_run_GSM_method(  const long  number_of_field_components,
  * @param[in]  material_no                               index number for detector material
  * @see          AT_DataMaterial.h for definition
  * @param[in]  rdd_model                                 index number for chosen radial dose distribution
- * @param[in]  rdd_parameter                             parameters for chosen radial dose distribution (array of size depending on chosen model)
+ * @param[in]  rdd_parameter                             parameters for chosen radial dose distribution (array of size 3)
  * @see          AT_RDD.h for definition
  * @param[in]  er_model                                  index number for chosen electron-range model
  * @see          AT_ElectronRange.h for definition
- * @param[in] stopping_power_source_no                   TODO
- * @param[in] nX                                         TODO
- * @param[in] pixel_size_m                               TODO
- * @param[in] number_of_bins                             TODO
- * @param[in] dose_bin_centers_Gy                        TODO
- * @param[out] random_number_generator_seed              TODO
- * @param[out] zero_dose_fraction                        TODO
- * @param[out] dose_frequency_Gy                         TODO
+ * @param[in]      stopping_power_source_no         stopping power source number (PSTAR,...)
+ * @see AT_DataMaterial.h for definition
+ * @param[in] nX                                         number of pixels along one side
+ * @param[in] pixel_size_m                               pixel size [m]
+ * @param[in] number_of_bins                             number of bins in the histogram
+ * @param[in] dose_bin_centers_Gy                        edges in the output dose histogram (array of size number_of_bins)
+ * @param[out] random_number_generator_seed              seed for the random number generator
+ * @param[out] zero_dose_fraction                        fraction of pixels with zero dose
+ * @param[out] dose_frequency_Gy                         values in the output dose histogram (array of size number_of_bins)
  */
 void AT_GSM_local_dose_distrib( const long  number_of_field_components,
     const double   E_MeV_u[],

src/AT_Algorithms_GSM.c

@@ -233,7 +233,11 @@ void AT_GSM_local_dose_distrib_from_dose_grid( const long     nX,
         bin_no = AT_histoOld_bin_no(	number_of_bins,
 									bin_centers_Gy,
 									grid[i][j]);
-        frequency[bin_no]  += 1.0;
+        // user could provide bins not spanning whole dose range
+        // we skip the values outside the range
+        if((bin_no >= 0) && (bin_no < number_of_bins)){
+          frequency[bin_no] += 1.0;
+        }
       }
     }
   }