Merge branch 'develop' into 'master'

Develop in Master

See merge request !9

.gitignore

@@ -85,3 +85,4 @@ scripts/stefan copy/
 scripts/stefan/
 test.py
 /Release/
+build*

.gitlab-ci.yml

@@ -25,6 +25,7 @@ configure-linux:
   script:
     - mkdir -p build
     - cd build
+    - which git
     - cmake -DCMAKE_BUILD_TYPE=Debug -DBoost_NO_SYSTEM_PATHS=true -DBOOST_ROOT=~/boost_1_61_0  ..
     - echo "configure | ${CI_PROJECT_DIR}"
   stage: configure
@@ -48,7 +49,8 @@ make-linux:
     - cd build
     - make -j$nproc
     - echo "compile | ${CI_PROJECT_DIR}"
-
+  tags:
+    - linux
 
 after_script:
   - echo "End CI" # todo: run report script

Analysis.cpp

@@ -71,10 +71,10 @@ Analysis::Analysis()
      _building = NULL;
      _projectRootDir="";
      _deltaF=5;   // half of the time interval that used to calculate instantaneous velocity of ped i. Here v_i = (X(t+deltaF) - X(t+deltaF))/(2*deltaF).   X is location.
-     _DoesUseMethodA = false; 						// Method A (Zhang2011a)
-     _DoesUseMethodB = false; 			// Method B (Zhang2011a)
-     _DoesUseMethodC = false; 					// Method C //calculate and save results of classic in separate file
-     _DoesUseMethodD = false;  					// Method D--Voronoi method
+     _DoesUseMethodA = false;                                           // Method A (Zhang2011a)
+     _DoesUseMethodB = false;                   // Method B (Zhang2011a)
+     _DoesUseMethodC = false;                                   // Method C //calculate and save results of classic in separate file
+     _DoesUseMethodD = false;                                   // Method D--Voronoi method
      _cutByCircle = false;  //Adjust whether cut each original voronoi cell by a circle
      _getProfile = false;   // Whether make field analysis or not
      _outputGraph = false;   // Whether output the data for plot the fundamental diagram each frame
@@ -119,27 +119,6 @@ void Analysis::InitArgs(ArgumentParser* args)
 {
      string s = "Parameter:\n";
 
-     switch (args->GetLog()) {
-     case 0:
-          // no log file
-          //Log = new OutputHandler();
-          break;
-     case 1:
-          if(Log) delete Log;
-          Log = new STDIOHandler();
-          break;
-     case 2: {
-          char name[CLENGTH]="";
-          sprintf(name,"%s.P0.dat",args->GetErrorLogFile().c_str());
-          if(Log) delete Log;
-          Log = new FileHandler(name);
-     }
-          break;
-     default:
-          Log->Write("Wrong option for Log file!");
-          exit(0);
-     }
-
      if(args->GetIsMethodA()) {
           _DoesUseMethodA = true;
           vector<int> Measurement_Area_IDs = args->GetAreaIDforMethodA();
@@ -188,6 +167,7 @@ void Analysis::InitArgs(ArgumentParser* args)
      _getProfile = args->GetIsGetProfile();
      _outputGraph = args->GetIsOutputGraph();
      _plotGraph = args->GetIsPlotGraph();
+     _plotIndex = args->GetIsPlotIndex();
      _isOneDimensional=args->GetIsOneDimensional();
      _vComponent = args->GetVComponent();
      _IgnoreBackwardMovement =args->GetIgnoreBackwardMovement();
@@ -273,7 +253,9 @@ std::map<int, polygon_2d> Analysis::ReadGeometry(const std::string& geometryFile
      _highVertexY = geo_maxY;
      _lowVertexX = geo_minX;
      _lowVertexY = geo_minY;
-     //cout<<"INFO: \tGeometry polygon is:\t"<<dsv(geoPoly)<<endl;
+     // using boost::geometry::dsv;
+     // cout<<"INFO: \tGeometry polygon is:\t" << dsv(geoPoly[1])<<endl;
+
      return geoPoly;
 }
 
@@ -375,7 +357,7 @@ int Analysis::RunAnalysis(const string& filename, const string& path)
                     Log->Write("INFO:\tSuccess with Method C using measurement area id %d!\n",_areaForMethod_C[i]->_id);
                     if(_plotTimeseriesC[i])
                     {
-                         string parameters_Timeseries="python3 \""+_scriptsLocation+"/_Plot_timeseries_rho_v.py\" -p \""+ _projectRootDir+VORO_LOCATION + "\" -n "+filename+
+                         string parameters_Timeseries="python \""+_scriptsLocation+"/_Plot_timeseries_rho_v.py\" -p \""+ _projectRootDir+VORO_LOCATION + "\" -n "+filename+
                               " -f "+boost::lexical_cast<std::string>(data.GetFps());
                          int res=system(parameters_Timeseries.c_str());
                          Log->Write("INFO:\t time series result: %d ",res);
@@ -403,6 +385,7 @@ int Analysis::RunAnalysis(const string& filename, const string& path)
                method_D.SetGridSize(_grid_size_X, _grid_size_Y);
                method_D.SetOutputVoronoiCellData(_outputGraph);
                method_D.SetPlotVoronoiGraph(_plotGraph);
+               method_D.SetPlotVoronoiIndex(_plotIndex);
                method_D.SetDimensional(_isOneDimensional);
                method_D.SetCalculateProfiles(_getProfile);
                method_D.SetTrajectoriesLocation(path);
@@ -417,7 +400,7 @@ int Analysis::RunAnalysis(const string& filename, const string& path)
                     Log->Write("INFO:\tSuccess with Method D using measurement area id %d!\n",_areaForMethod_D[i]->_id);
                     if(_plotTimeseriesD[i])
                     {
-                         string parameters_Timeseries="python3 \""+_scriptsLocation+"/_Plot_timeseries_rho_v.py\" -p \""+ _projectRootDir+VORO_LOCATION + "\" -n "+filename+
+                         string parameters_Timeseries="python \""+_scriptsLocation+"/_Plot_timeseries_rho_v.py\" -p \""+ _projectRootDir+VORO_LOCATION + "\" -n "+filename+
                               " -f "+boost::lexical_cast<std::string>(data.GetFps());
                          int res=system(parameters_Timeseries.c_str());
                          Log->Write("INFO:\t time series result: %d ",res);
@@ -493,9 +476,5 @@ int Analysis::mkpath(char* file_path, mode_t mode)
      }
      return 0;
 }
-
+// delete
 #endif
-
-
-
-

Analysis.h

@@ -2,7 +2,7 @@
  * \file        Analysis.h
  * \date        Oct 10, 2014
  * \version     v0.7
- * \copyright   <2009-2015> Forschungszentrum J�lich GmbH. All rights reserved.
+ * \copyright   <2009-2015> Forschungszentrum Jülich GmbH. All rights reserved.
  *
  * \section License
  * This file is part of JuPedSim.
@@ -133,7 +133,11 @@ private:
      int _circleEdges;
      bool _getProfile;        // Whether make field analysis or not
      bool _outputGraph;       // Whether output the data for plot the voronoi diagram each frame
-     bool _plotGraph;       // Whether plot the voronoi diagram each frame
+     bool _plotGraph;       // Whether plot the voronoi diagram each
+                            // frame. if (outputGraph==true)
+     bool _plotIndex;       // Whether plot the voronoi diagram each
+                            // frame with index of pedesrians
+                            // if (outputGraph==true and _polotGraph==true)
      std::vector<bool> _plotTimeseriesA;
      std::vector<bool> _plotTimeseriesC;
      std::vector<bool> _plotTimeseriesD;

CHANGELOG.md

 # Change Log
 All notable changes to `jpsreport` will be documented in this file.
-## v0.8.2 [unreleased]
 
+## v0.8.3 [unreleased]
 ### Added
+- Option to output log in a file instead of the screen fe66fa49
+  ```
+  <logfile>log.txt</logfile>
+  ```
+- Output useful debug information like date, git and compiler versions. !6 and discussion in #79 
+- Option to plot Voronoi diagrams with index instead of little blue circles `plot_index`. Use as:
+  ```xml
+  <output_voronoi_cells enabled="true" plot_graphs="true" plot_index="true"/>
+  ```
+- new format of returned polygons `"index | polygon"` 6fa459ad9ffe5a07699c05b655bcf90f114ed635
+- Exit if `framerate` is not found. c1308ef8
 
-- Use the effective distance in method B in case `length_in_movement_direction` is not defined.  (2c321cef) 
+### Changed
+- Pass Matrix by reference bff89e48
+- Better fonts in plot scripts. 56d6a8f7
+
+
+### Fixed
+- Ignore empty line in traj file. 3a3ae04e
+- Fixes for profile plots. a8a1414c
+- Fix parsing of framerate. 2ad0b01d
+
+## v0.8.2 [06.11.2017]
+
+### Added
+
+- Use the effective distance in method B in case `length_in_movement_direction` is not defined.  (2c321cef)
 - Added an error warning when the number of agents in the trajectory is not corresponding to total ids or the ped ids are not continuous in the first frame.
 
 ### Changed
-- Code does not come with Boost anymore. User should install Boost before using jpsreport. (2c0c69f3) 
+- Code does not come with Boost anymore. User should install Boost before using jpsreport. (2c0c69f3)
 - use boost matrix instead of double pointers (9ff5c978)
 - Use own index numbers (9a0d8ec8)
 - Use Python3 in scripts.
 
-### Fixed 
-- Fixed SegFault due to reading files from different OS. (9a42c9dd)
-
+### Fixed
+- Fix SegFault due to reading files from different OS. (9a42c9dd)
 
 ## v0.8.1 [11.10.2016]
 
@@ -23,7 +47,7 @@ All notable changes to `jpsreport` will be documented in this file.
 
 - Two options `startframe` and `stopframe` are added for each measurement area for method D to assign the time periods for analysis.
 
-- Individual density based on Voronoi method is added for one dimensional case in the output file (Individual headway is moved to the 5th column). 
+- Individual density based on Voronoi method is added for one dimensional case in the output file (Individual headway is moved to the 5th column).
 
 - z-position of each measurement area can be assigned in inifile so that the trajectories in geometries with several floors can be analyzed.
 
@@ -66,7 +90,7 @@ All notable changes to `jpsreport` will be documented in this file.
 
 - Issue a warning when the voronoi cell cannot be calculated.
 
-- A warning will will be given and the program stops if trajectory for a given pedestrian ID is not continuous. 
+- A warning will will be given and the program stops if trajectory for a given pedestrian ID is not continuous.
 
 
 ### Changed
@@ -93,7 +117,7 @@ All notable changes to `jpsreport` will be documented in this file.
 
 - when path of trajectory is not given absolutely, the default location is the same folder with the inifile
 
-	
+
 ## v0.7
 
 ### Added
@@ -108,38 +132,38 @@ All notable changes to `jpsreport` will be documented in this file.
 
 - Changed name of some variables in configuration file:
 
-	**measurementAreas**                --->  **measurement_areas**
-    
-	**Length_in_movement_direction**	---> **length_in_movement_direction**
-	
-	**useXComponent**		            ---> **use_x_component**
-	
-	**useYComponent**		            ---> **use_y_component**
-	
-	**halfFrameNumberToUse**            ---> **frame_step**
-	
-	**timeInterval**	                ---> **frame_interval**
-	
-	**measurementArea**	                ---> **measurement_area**
-	
-	**outputGraph**	                    ---> **output_graph**
-	
-	**individualFDdata**	            ---> **individual_FD**
-	
-	**cutByCircle** 	                ---> **cut_by_circle**
-	
-	**getProfile** 		                ---> **profiles**
-	
-	**scale_x**			                ---> **grid_size_x**
-	
-	**scale_y**			                ---> **grid_size_y**
+    **measurementAreas**                --->  **measurement_areas**
+
+    **Length_in_movement_direction**	---> **length_in_movement_direction**
+
+    **useXComponent**                   ---> **use_x_component**
+
+    **useYComponent**                   ---> **use_y_component**
+
+    **halfFrameNumberToUse**            ---> **frame_step**
+
+    **timeInterval**                    ---> **frame_interval**
+
+    **measurementArea**                 ---> **measurement_area**
+
+    **outputGraph**                     ---> **output_graph**
+
+    **individualFDdata**                ---> **individual_FD**
+
+    **cutByCircle**                     ---> **cut_by_circle**
+
+    **getProfile**                      ---> **profiles**
+
+    **scale_x**                         ---> **grid_size_x**
+
+    **scale_y**                         ---> **grid_size_y**
 - Changed the data type of frame rate (fps) from integer to float
 
-- Changed the way for dealing with pedestrian outside geometry. In old version JPSreport stops when some pedestrians are outside geometry but now it continue working by 
+- Changed the way for dealing with pedestrian outside geometry. In old version JPSreport stops when some pedestrians are outside geometry but now it continue working by
 removing these pedestrians from the list.
 
 - More than one sub rooms in one geometry can be analysed independently.
-	
+
 ### Fixed
-	
-- Fixed bug for dealing with obstacles inside geometry.
+
+- Fixed bug for dealing with obstacles inside geometry.
\ No newline at end of file

CMakeLists.txt

@@ -20,6 +20,56 @@ if (Boost_NO_SYSTEM_PATHS)
   set(CMAKE_LIBRARY_PATH ${CMAKE_LIBRARY_PATH} ${BOOST_LIBRARY_DIRS})
 endif (Boost_NO_SYSTEM_PATHS)
 
+
+find_package(Git REQUIRED) # no need for this msg. It comes from cmake.findgit()
+
+find_program(GIT_SCM git DOC "Git version control")
+mark_as_advanced(GIT_SCM)
+find_file(GITDIR NAMES .git PATHS ${CMAKE_SOURCE_DIR} NO_DEFAULT_PATH)
+if (GIT_SCM AND GITDIR)
+
+# the commit's SHA1, and whether the building workspace was dirty or not
+# describe --match=NeVeRmAtCh --always --tags --abbrev=40 --dirty
+execute_process(COMMAND
+  "${GIT_EXECUTABLE}" --no-pager describe --tags --always --dirty
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_SHA1
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+# branch
+execute_process(
+  COMMAND "${GIT_EXECUTABLE}" rev-parse --abbrev-ref HEAD
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_BRANCH
+  OUTPUT_STRIP_TRAILING_WHITESPACE
+)
+
+# the date of the commit
+execute_process(COMMAND
+  "${GIT_EXECUTABLE}" log -1 --format=%ad --date=local
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_DATE
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+# the subject of the commit
+execute_process(COMMAND
+  "${GIT_EXECUTABLE}" log -1 --format=%s
+  WORKING_DIRECTORY "${CMAKE_SOURCE_DIR}"
+  OUTPUT_VARIABLE GIT_COMMIT_SUBJECT
+  ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+
+
+add_definitions("-DGIT_COMMIT_HASH=\"${GIT_SHA1}\"")
+add_definitions("-DGIT_COMMIT_DATE=\"${GIT_DATE}\"")
+add_definitions("-DGIT_COMMIT_SUBJECT=\"${GIT_COMMIT_SUBJECT}\"")
+add_definitions("-DGIT_BRANCH=\"${GIT_BRANCH}\"")
+
+else()
+    message(STATUS "Not in a git repo")
+endif()
+
+
 #set(EXECUTABLE_OUTPUT_PATH "../")
 #INCLUDE_DIRECTORIES("./")
 # message( STATUS "CMAKE_BINARY_DIR: " ${CMAKE_BINARY_DIR} )
@@ -29,12 +79,13 @@ set(CMAKE_TEST_DIR ${CMAKE_SOURCE_DIR}/Utest)
 
 set(JPSREPORT_MAJOR_VERSION 0)
 set(JPSREPORT_MINOR_VERSION 8)
-set(JPSREPORT_PATCH_VERSION 2)
+set(JPSREPORT_PATCH_VERSION 3)
 set(JPSREPORT_VERSION
   ${JPSREPORT_MAJOR_VERSION}.${JPSREPORT_MINOR_VERSION}.${JPSREPORT_PATCH_VERSION})
 message( STATUS "JPSREPORT_VERSION: " ${JPSREPORT_VERSION} )
+add_definitions("-DJPSREPORT_VERSION=\"${JPSREPORT_VERSION}\"")
 if(NOT CMAKE_BUILD_TYPE)
-  set (CMAKE_BUILD_TYPE Release) 
+  set (CMAKE_BUILD_TYPE Release)
 endif(NOT CMAKE_BUILD_TYPE)
 message( STATUS "CMAKE_BUILD_TYPE: " ${CMAKE_BUILD_TYPE} )
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${CMAKE_SOURCE_DIR}/bin")
@@ -74,7 +125,7 @@ endif(NOT DEFINED PROCESSOR_COUNT)
 
 if(PROCESSOR_COUNT)
   # add 1 should be magic! http://www.kitware.com/blog/home/post/63
-  #math(EXPR PROCESSOR_COUNT "${PROCESSOR_COUNT} + 1") 
+  #math(EXPR PROCESSOR_COUNT "${PROCESSOR_COUNT} + 1")
   message( STATUS "PROCESSOR_COUNT " ${PROCESSOR_COUNT})
   set(CTEST_BUILD_FLAGS "-j${PROCESSOR_COUNT}")
 endif(PROCESSOR_COUNT)
@@ -102,7 +153,6 @@ if(BUILD_TESTING)
 endif(BUILD_TESTING)
 
 set(source_files
-  getRSS.c
   Analysis.cpp
   IO/OutputHandler.cpp
   general/ArgumentParser.cpp
@@ -116,45 +166,45 @@ set(source_files
   methods/Method_B.cpp
   methods/Method_C.cpp
   methods/Method_D.cpp
-  geometry/Building.cpp  
-  geometry/Line.cpp      
-  geometry/Point.cpp    
+  geometry/Building.cpp
+  geometry/Line.cpp
+  geometry/Point.cpp
   geometry/Transition.cpp
-  geometry/Crossing.cpp  
-  geometry/NavLine.cpp   
-  geometry/Room.cpp     
+  geometry/Crossing.cpp
+  geometry/NavLine.cpp
+  geometry/Room.cpp
   geometry/Wall.cpp
-  geometry/Hline.cpp     
-  geometry/Obstacle.cpp  
+  geometry/Hline.cpp
+  geometry/Obstacle.cpp
   geometry/SubRoom.cpp
   geometry/Goal.cpp
-)  
+)
 set (  header_files
   Analysis.h
-  methods/MeasurementArea.h   
+  methods/MeasurementArea.h
   methods/VoronoiDiagram.h
   methods/PedData.h
   methods/Method_A.h
   methods/Method_B.h
   methods/Method_C.h
-  methods/Method_D.h  
+  methods/Method_D.h
   IO/OutputHandler.h
   general/ArgumentParser.h
   general/Macros.h
   tinyxml/tinyxml.h
   tinyxml/tinystr.h
-  geometry/Building.h  
-  geometry/Line.h      
-  geometry/Point.h    
+  geometry/Building.h
+  geometry/Line.h
+  geometry/Point.h
   geometry/Transition.h
-  geometry/Crossing.h  
-  geometry/NavLine.h   
-  geometry/Room.h     
+  geometry/Crossing.h
+  geometry/NavLine.h
+  geometry/Room.h
   geometry/Wall.h
-  geometry/Hline.h     
-  geometry/Obstacle.h  
+  geometry/Hline.h
+  geometry/Obstacle.h
   geometry/SubRoom.h
-  geometry/Goal.h  
+  geometry/Goal.h
   )
 
 
@@ -205,19 +255,25 @@ message( STATUS "Boost_INCLUDE_DIR: " ${Boost_INCLUDE_DIR} )
 message( STATUS "Boost_LIBRARY_DIR: " ${Boost_LIBRARY_DIR} )
 
 include_directories(${Boost_INCLUDE_DIR})
-link_directories(${Boost_LIBRARY_DIR})
+#link_directories(${Boost_LIBRARY_DIR})
+
+if (WIN32)
+find_library (PSAPI Psapi PATH_SUFFIXES "x64")
+message (STATUS "PSAPI: ${PSAPI}")
+endif()
 
 add_library ( geometrycore STATIC ${source_files} )
 add_executable(
-	jpsreport main.cpp
+        jpsreport main.cpp
 )
-target_link_libraries( jpsreport ${Boost_LIBRARIES} )
-target_link_libraries( jpsreport geometrycore )
+
 
 if(WIN32)
 target_link_libraries (jpsreport wsock32)
+target_link_libraries( jpsreport ${PSAPI} )
 endif()
 
+target_link_libraries( jpsreport geometrycore )
 
 # ----------------------------- cTest ------------------------------------------
 if(BUILD_TESTING)
@@ -228,11 +284,11 @@ if(BUILD_TESTING)
   include(CTest) #adding Dart support
 
   #test if code compiles and runs default setting. Takes about 30 seconds
-  add_test (jpsreport_compile ${CMAKE_CTEST_COMMAND} 
+  add_test (jpsreport_compile ${CMAKE_CTEST_COMMAND}
   --build-and-test "${CMAKE_SOURCE_DIR}" "${EXECUTABLE_OUTPUT_PATH}" #"${CMAKE_BINARY_DIR}"
   --build-generator ${CMAKE_GENERATOR}
   --build-makeprogram ${CMAKE_MAKE_PROGRAM} -j${PROCESSOR_COUNT}
-  --build-two-config  
+  --build-two-config
   --build-exe-dir ${EXECUTABLE_OUTPUT_PATH}  # todo wo soll der exe hin?: ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}
   --build-project JPSreport
   --test-command jpsreport --ini=${CMAKE_TEST_DIR}/files/input_UO_180.xml

demos/HowTo.ipynb

+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Getting started with `JPSreport`\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "`JPSreport` needs three different files as input: \n",
+    "- A trajectory file (txt or xml) (see [documentation](http://www.jupedsim.org/jpsreport/2016-11-03-trajectory))\n",
+    "- A geometry file (see [documentation](http://www.jupedsim.org/jpsreport/2016-11-02-geometry)) \n",
+    "- and a project file, called inifile (see [documentation](http://www.jupedsim.org/jpsreport/2016-11-01-inifile))\n",
+    "\n",
+    "For example in **demos/bottleneck** we can find the following files:"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Calling `JPSreport` without an inifile yields:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {