Merge branch 'sprint_2' into 'hs-worms/TOP-2021'

[MERGE #40] Sprint 2

See merge request top/21s/sivert-vis/sivert-vis-project!19

src/core/dataHandler/WDataSetCSV.cpp

@@ -24,7 +24,7 @@
 
 #include "WDataSetCSV.h"
 
-WDataSetCSV::WDataSetCSV( WDataSetCSV::Content header, WDataSetCSV::Content data )
+WDataSetCSV::WDataSetCSV( WDataSetCSV::ContentSPtr header, WDataSetCSV::ContentSPtr data )
     : m_header( header ), m_data( data )
 {
 }
@@ -37,12 +37,12 @@ WDataSetCSV::~WDataSetCSV()
 {
 }
 
-WDataSetCSV::Content WDataSetCSV::getHeader()
+WDataSetCSV::ContentSPtr WDataSetCSV::getHeader()
 {
     return m_header;
 }
 
-WDataSetCSV::Content WDataSetCSV::getData()
+WDataSetCSV::ContentSPtr WDataSetCSV::getData()
 {
     return m_data;
 }

src/core/dataHandler/WDataSetCSV.h

@@ -39,7 +39,12 @@ public:
     /**
      * represents a vector containing a vector of strings.
      */
-    typedef std::vector< std::vector<std::string> > Content;
+    typedef std::vector< std::vector< std::string > > Content;
+
+    /**
+     * represents a pointer to the Content
+     */
+    typedef boost::shared_ptr< std::vector< std::vector< std::string > > > ContentSPtr;
 
     /**
      * Construct WDataSetCSV object
@@ -47,7 +52,7 @@ public:
      * \param header Column names of the CSV file.
      * \param data Data content of the CSV file.
      */
-    explicit WDataSetCSV( Content header, Content data );
+    explicit WDataSetCSV( WDataSetCSV::ContentSPtr header, WDataSetCSV::ContentSPtr data );
 
     /**
      * The standard constructor.
@@ -64,25 +69,25 @@ public:
      *
      * \return m_header as WDataSetCSV::Content object
      */
-    WDataSetCSV::Content getHeader();
+    WDataSetCSV::ContentSPtr getHeader();
 
     /**
      * Getter method to receive csv data
      *
      * \return m_data as WDataSetCSV::Content object
      */
-    WDataSetCSV::Content getData();
+    WDataSetCSV::ContentSPtr getData();
 
 private:
     /**
      * Stores the column titles of a loaded CSV file.
      */
-    Content m_header;
+    WDataSetCSV::ContentSPtr m_header;
 
     /**
      * Stores the data of a loaded CSV file.
      */
-    Content m_data;
+    WDataSetCSV::ContentSPtr m_data;
 };
 
 #endif  // WDATASETCSV_H

src/core/dataHandler/test/WDataSetPointsAndSizes_test.h

@@ -28,7 +28,7 @@
 #include <vector>
 
 #include <boost/shared_ptr.hpp>
-#include <cxxtest/Testsuite.h>
+#include <cxxtest/TestSuite.h>
 #include "../WDataSetPointsAndSizes.h"
 
 

src/modules/converterCSV/WMConverterCSV.cpp

-//---------------------------------------------------------------------------
-//
-// Project: OpenWalnut ( http://www.openwalnut.org )
-//
-// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
-// For more information see http://www.openwalnut.org/copying
-//
-// This file is part of OpenWalnut.
-//
-// OpenWalnut is free software: you can redistribute it and/or modify
-// it under the terms of the GNU Lesser General Public License as published by
-// the Free Software Foundation, either version 3 of the License, or
-// (at your option) any later version.
-//
-// OpenWalnut is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-// GNU Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public License
-// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
-//
-//---------------------------------------------------------------------------
-
-#include <string>
-#include <vector>
-
-#include "WMConverterCSV.h"
-
-W_LOADABLE_MODULE( WMConverterCSV )
-
-WMConverterCSV::WMConverterCSV():
-        WModule()
-{
-}
-
-WMConverterCSV::~WMConverterCSV()
-{
-}
-
-const std::string WMConverterCSV::getName() const
-{
-    return "FilterProtonData";
-}
-
-const std::string WMConverterCSV::getDescription() const
-{
-    return "Converter CSV-data To WDataSetPoints and WDataSetFibers";
-}
-
-boost::shared_ptr< WModule > WMConverterCSV::factory() const
-{
-    return boost::shared_ptr< WModule >( new WMConverterCSV() );
-}
-
-const char** WMConverterCSV::getXPMIcon() const
-{
-    return NULL;
-}
-
-void WMConverterCSV::moduleMain()
-{
-    m_moduleState.setResetable( true, true );
-    m_moduleState.add( m_input->getDataChangedCondition() );
-
-    ready();
-
-    waitRestored();
-
-
-    while( !m_shutdownFlag() )
-    {
-        m_moduleState.wait();
-
-        boost::shared_ptr< WDataSetCSV > dataset = m_input->getData();
-        WDataSetCSV::Content m_csvHeader = dataset->getHeader();
-        WDataSetCSV::Content m_csvData = dataset->getData();
-
-        setPointsOutOfCSVData( m_csvHeader, m_csvData );
-        setFibersOutOfCSVData( m_csvHeader, m_csvData );
-    }
-}
-
-void WMConverterCSV::connectors()
-{
-    m_input = WModuleInputData< WDataSetCSV >::createAndAdd( shared_from_this(), "in", "CSV_input" );
-
-    m_output_points = boost::shared_ptr< WModuleOutputData< WDataSet > >(
-            new WModuleOutputData< WDataSet >(
-                    shared_from_this(),
-                    "output points",
-                    "Output CSV data as Point data" )
-
-    );
-
-    m_output_fibers = boost::shared_ptr< WModuleOutputData< WDataSet > >(
-            new WModuleOutputData< WDataSet >(
-                    shared_from_this(),
-                    "output fibers",
-                    "Output CSV data as Fiber data" )
-
-    );
-
-    addConnector( m_output_points );
-    addConnector( m_output_fibers );
-
-    WModule::connectors();
-}
-
-void WMConverterCSV::properties()
-{
-}
-
-int WMConverterCSV::getColumnNumberByName( std::string columnNameToMatch, std::vector<std::string> headerToSearchIn )
-{
-    int pos = 0;
-    for( std::vector<std::string>::iterator it = headerToSearchIn.begin(); it != headerToSearchIn.end(); it++ )
-    {
-        if( *it == columnNameToMatch ) return pos;
-        pos++;
-    }
-    return pos;
-}
-
-
-void WMConverterCSV::setFibersOutOfCSVData( WDataSetCSV::Content header, WDataSetCSV::Content data )
-{
-    SPFloatVector m_vertices = SPFloatVector( new std::vector<float>() );
-    SPSizeVector m_lineStartIndexes = SPSizeVector( new std::vector < size_t >() );
-    SPSizeVector m_lineLengths  = SPSizeVector( new std::vector < size_t >() );
-    SPSizeVector m_verticesReverse = SPSizeVector( new std::vector < size_t >() );
-
-    SPFloatVector m_colors = SPFloatVector( new std::vector< float >() );
-
-    std::vector< int > eventIDs;
-    std::vector< float > edeps;
-
-    int xPosIndex = getColumnNumberByName( "posX", header.at( 0 ) );
-    int yPosIndex = getColumnNumberByName( "posY", header.at( 0 ) );
-    int zPosIndex = getColumnNumberByName( "posZ", header.at( 0 ) );
-    int eventIDIndex = getColumnNumberByName( "eventID", header.at( 0 ) );
-    int parentIDIndex = getColumnNumberByName( "parentID", header.at( 0 ) );
-    int edepIndex = getColumnNumberByName( "edep", header.at( 0 ) );
-
-    float maxEdep = 0.0;
-
-    for( WDataSetCSV::Content::iterator dataRow = data.begin(); dataRow != data.end(); dataRow++ )
-    {
-        float posX, posY, posZ, edep;
-        int eventID;
-
-        if( dataRow->empty() )
-        {
-            continue;
-        }
-
-        if(std::stoi( dataRow->at(parentIDIndex ) ) != 0 )
-        {
-            continue;
-        }
-
-        posX = boost::lexical_cast< float >( dataRow->at( xPosIndex ) );
-        posY = boost::lexical_cast< float >( dataRow->at( yPosIndex ) );
-        posZ = boost::lexical_cast< float >( dataRow->at( zPosIndex ) );
-        eventID = std::stoi( dataRow->at( eventIDIndex ) );
-        edep = boost::lexical_cast< float >( dataRow->at( edepIndex ) );
-
-        if( edep > maxEdep )
-        {
-            maxEdep = edep;
-        }
-
-        m_vertices->push_back( posX );
-        m_vertices->push_back( posY );
-        m_vertices->push_back( posZ );
-        eventIDs.push_back( eventID );
-        edeps.push_back( edep );
-    }
-
-    for( std::vector< float >::iterator currentEdep = edeps.begin(); currentEdep != edeps.end(); currentEdep++ )
-    {
-        *currentEdep = *currentEdep / maxEdep;
-
-        m_colors->push_back( *currentEdep * 1000 );
-        m_colors->push_back( *currentEdep * 100 );
-        m_colors->push_back( *currentEdep * 10 );
-    }
-
-    int fiberLength = 0;
-    int fiberStartIndex = 0;
-    int reversePos = 0;
-    int currentEventID = eventIDs.at( 0 );
-
-    m_lineStartIndexes->push_back( fiberStartIndex );
-
-    for(std::vector<int>::iterator eID = eventIDs.begin(); eID != eventIDs.end(); eID++ )
-    {
-        if(currentEventID != *eID )
-        {
-            currentEventID = *eID;
-            m_lineStartIndexes->push_back( fiberStartIndex );
-            m_lineLengths->push_back( fiberLength );
-            fiberLength = 0;
-            reversePos++;
-        }
-        fiberLength++;
-        fiberStartIndex++;
-        m_verticesReverse->push_back( reversePos );
-    }
-
-    m_lineLengths->push_back( fiberLength );
-
-    m_fibers = boost::shared_ptr< WDataSetFibers >(
-            new WDataSetFibers(
-                    m_vertices,
-                    m_lineStartIndexes,
-                    m_lineLengths,
-                    m_verticesReverse
-            )
-    );
-
-    m_fibers->addColorScheme( m_colors, "Energy deposition", "Color fibers based on their energy." );
-
-    m_output_fibers->updateData( m_fibers );
-}
-
-void WMConverterCSV::setPointsOutOfCSVData( WDataSetCSV::Content header, WDataSetCSV::Content data )
-{
-    SPFloatVector m_vertices = SPFloatVector( new std::vector< float >() );
-    SPFloatVector m_colors = SPFloatVector( new std::vector< float >() );
-    SPFloatVector m_sizes = SPFloatVector( new std::vector< float >() );
-
-    int xPosIndex = getColumnNumberByName( "posX", header.at( 0 ) );
-    int yPosIndex = getColumnNumberByName( "posY", header.at( 0 ) );
-    int zPosIndex = getColumnNumberByName( "posZ", header.at( 0 ) );
-    int edepIndex = getColumnNumberByName( "edep", header.at( 0 ) );
-
-    float posX, posY, posZ, edep;
-    for(WDataSetCSV::Content::iterator dataRow = data.begin(); dataRow != data.end(); dataRow++ )
-    {
-        if( dataRow->empty() )
-        {
-            continue;
-        }
-
-        posX = boost::lexical_cast< float >( dataRow->at( xPosIndex ) );
-        posY = boost::lexical_cast< float >( dataRow->at( yPosIndex ) );
-        posZ = boost::lexical_cast< float >( dataRow->at( zPosIndex ) );
-        edep = boost::lexical_cast< float >( dataRow->at( edepIndex ) );
-
-        m_vertices->push_back( posX );
-        m_vertices->push_back( posY );
-        m_vertices->push_back( posZ );
-
-        m_sizes->push_back( edep );
-
-        // TODO(robin.eschbach): disable this, when #35 is done
-        m_colors->push_back( 0 );
-        m_colors->push_back( 0 );
-        m_colors->push_back( 0 );
-    }
-
-    m_points = boost::shared_ptr< WDataSetPointsAndSizes >(
-            new WDataSetPointsAndSizes(
-                    m_vertices,
-                    m_colors,
-                    m_sizes
-            )
-    );
-
-    m_output_points->updateData( m_points );
-}

src/modules/data/io/WReaderCSV.cpp

@@ -43,15 +43,15 @@ boost::shared_ptr< WDataSetCSV > WReaderCSV::read()
     std::string cell;
 
     std::vector< std::string >  row;
-    WDataSetCSV::Content header;
-    WDataSetCSV::Content data;
+    WDataSetCSV::ContentSPtr header = WDataSetCSV::ContentSPtr( new WDataSetCSV::Content() );
+    WDataSetCSV::ContentSPtr data = WDataSetCSV::ContentSPtr( new WDataSetCSV::Content() );
 
     std::fstream file;
     file.open( m_fname );
 
     if( !file.is_open() )
     {
-        //throw()
+        throw WException( "File could not be opened!" );
     }
 
     while( std::getline( file, col ) )
@@ -63,13 +63,13 @@ boost::shared_ptr< WDataSetCSV > WReaderCSV::read()
         {
             row.push_back( cell );
         }
-        data.push_back( row );
+        data->push_back( row );
     }
 
     file.close();
 
-    header.push_back( data.at( 0 ) );
-    data.erase( data.begin() );
+    header->push_back( data->at( 0 ) );
+    data->erase( data->begin() );
 
     return boost::shared_ptr< WDataSetCSV >( new WDataSetCSV( header, data ) );
 }

src/modules/data/io/WReaderCSV.h

@@ -55,7 +55,8 @@ public:
     /**
      * Read the file and create a dataset as a vector.
      *
-     * \return pointer to a WDataSetCSV
+     * \return pointer to a WDataSetCSV.
+     * \throws WException If the file could not be opened.
      */
     virtual boost::shared_ptr< WDataSetCSV > read();
 };

src/modules/filterProtonData/WMConverterIndexes.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#include "WMConverterIndexes.h"
+
+WMConverterIndexes::WMConverterIndexes()
+{
+}
+
+void WMConverterIndexes::update( WMProtonData::SPtr protonData )
+{
+    m_parentID = protonData->getColumnIndex( "parentID" );
+    m_posX = protonData->getColumnIndex( "posX" );
+    m_posY = protonData->getColumnIndex( "posY" );
+    m_posZ = protonData->getColumnIndex( "posZ" );
+    m_edep = protonData->getColumnIndex( "edep" );
+    m_PDGEncoding = protonData->getColumnIndex( "PDGEncoding" );
+    m_eventID = protonData->getColumnIndex( "eventID" );
+}
+
+int WMConverterIndexes::getParentID()
+{
+    return m_parentID;
+}
+
+int WMConverterIndexes::getPosX()
+{
+    return m_posX;
+}
+
+int WMConverterIndexes::getPosY()
+{
+    return m_posY;
+}
+
+int WMConverterIndexes::getPosZ()
+{
+    return m_posZ;
+}
+
+int WMConverterIndexes::getEdep()
+{
+    return m_edep;
+}
+
+int WMConverterIndexes::getPDGEncoding()
+{
+    return m_PDGEncoding;
+}
+
+int WMConverterIndexes::getEventID()
+{
+    return m_eventID;
+}

src/modules/filterProtonData/WMConverterIndexes.h

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.
+//
+// OpenWalnut is free software: you can redistribute it and/or modify
+// it under the terms of the GNU Lesser General Public License as published by
+// the Free Software Foundation, either version 3 of the License, or
+// (at your option) any later version.
+//
+// OpenWalnut is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+// GNU Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public License
+// along with OpenWalnut. If not, see <http://www.gnu.org/licenses/>.
+//
+//---------------------------------------------------------------------------
+
+#ifndef WMCONVERTERINDEXES_H
+#define WMCONVERTERINDEXES_H
+
+#include <boost/shared_ptr.hpp>
+
+#include "WMProtonData.h"
+
+/**
+ * Holds the indexes of the columns and is able to update them.
+ */
+class WMConverterIndexes
+{
+public:
+    /**
+     * A shared_ptr to this class.
+     */
+    typedef boost::shared_ptr< WMConverterIndexes > SPtr;
+
+    /**
+     * Empty constructor for class creation.
+     */
+    WMConverterIndexes();
+
+    /**
+     * Updates the indexes based on the data given.
+     * \param protonData The data which contains the columns.
+     */
+    void update( WMProtonData::SPtr protonData );
+
+    /**
+     * Gets the parentID index as integer.
+     * \return int The parentID index.
+     */
+    int getParentID();
+
+    /**
+     * Gets the posX index as integer.
+     * \return int The posX index.
+     */
+    int getPosX();
+
+
+    /**
+     * Gets the posY index as integer.
+     * \return int The posY index.
+     */
+    int getPosY();
+
+    /**
+     * Gets the posZ index as integer.
+     * \return int The posZ index.
+     */
+    int getPosZ();
+
+    /**
+     * Gets the edep index as integer.
+     * \return int The edep index.
+     */
+    int getEdep();
+
+    /**
+     * Gets the PDGEncoding index as integer.
+     * \return int The PDGEncoding index.
+     */
+    int getPDGEncoding();
+
+    /**
+     * Gets the eventID index as integer.
+     * \return int The eventID index.
+     */
+    int getEventID();
+
+private:
+    int m_parentID = -1;    //<! The parentID index.
+
+    int m_posX = -1;    //<! The posX index.
+
+    int m_posY = -1;    //<! The posY index.
+
+    int m_posZ = -1;    //<! The posZ index.
+
+    int m_edep = -1;    //<! The edep index.
+
+    int m_PDGEncoding = -1; //<! The PDGEncoding index.
+
+    int m_eventID = -1; //<! The eventID index.
+};
+
+#endif  // WMCONVERTERINDEXES_H

src/modules/filterProtonData/WMConverterVectors.cpp

+//---------------------------------------------------------------------------
+//
+// Project: OpenWalnut ( http://www.openwalnut.org )
+//
+// Copyright 2009 OpenWalnut Community, BSV@Uni-Leipzig and CNCF@MPI-CBS
+// For more information see http://www.openwalnut.org/copying
+//
+// This file is part of OpenWalnut.