Merge remote-tracking branch 'refs/remotes/origin/master' into issues_A

Author: dcwhite

src/Core/IEPlugin/CMakeLists.txt

@@ -32,6 +32,7 @@ SET(Core_IEPlugin_SRCS
   CurveField_Plugin.cc
   #DIF_Plugin.cc
   EcgsimFileToMatrix_Plugin.cc
+  #IgbFileToMatrix_Plugin.cc
   #EcgsimFileToTriSurf_Plugin.cc
   #HexVolField_Plugin.cc
   IEPluginInit.cc
@@ -60,6 +61,7 @@ SET(Core_IEPlugin_HEADERS
   CurveField_Plugin.h
   #DIF_Plugin.h
   EcgsimFileToMatrix_Plugin.h
+  IgbFileToMatrix_Plugin.h
   #EcgsimFileToTriSurf_Plugin.h
   #HexVolField_Plugin.h
   #MRC_Plugin.h

src/Core/IEPlugin/IEPluginInit.cc

@@ -32,6 +32,7 @@
 #include <Core/IEPlugin/SimpleTextFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/EcgsimFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/PointCloudField_Plugin.h>
+#include <Core/IEPlugin/IGBFileToMatrix_Plugin.h>
 #include <Core/IEPlugin/CurveField_Plugin.h>
 #include <Core/IEPlugin/TriSurfField_Plugin.h>
 #include <Core/IEPlugin/TetVolField_Plugin.h>
@@ -65,6 +66,7 @@ void IEPluginManager::Initialize()
   static FieldIEPluginLegacyAdapter CurveField_plugin("CurveField", "*.pts *.pos *.edge", "", TextToCurveField_reader, CurveFieldToTextBaseIndexZero_writer);
 
   static MatrixIEPluginLegacyAdapter EcgsimFileMatrix_plugin("ECGSimFile", "", "", EcgsimFileMatrix_reader, EcgsimFileMatrix_writer);
+  //static MatrixIEPluginLegacyAdapter IgbFileMatrix_plugin("IGBFile", "*.igb", "*.igb", IgbFileMatrix_reader, IgbFileMatrix_writer);
 
   static FieldIEPluginLegacyAdapter TriSurfField_plugin("TriSurfField", "*.fac *.tri *.pts *.pos", "", TextToTriSurfField_reader, TriSurfFieldToTextBaseIndexZero_writer);
   static FieldIEPluginLegacyAdapter TriSurfFieldBaseIndexOne_plugin("TriSurfField[BaseIndex 1]", "*.fac *.pts", "", nullptr, TriSurfFieldToTextBaseIndexOne_writer);

src/Core/IEPlugin/IgbFileToMatrix_Plugin.cc

@@ -0,0 +1,267 @@
+/*
+   For more information, please see: http://software.sci.utah.edu
+
+   The MIT License
+
+   Copyright (c) 2015 Scientific Computing and Imaging Institute,
+   University of Utah.
+
+   
+   Permission is hereby granted, free of charge, to any person obtaining a
+   copy of this software and associated documentation files (the "Software"),
+   to deal in the Software without restriction, including without limitation
+   the rights to use, copy, modify, merge, publish, distribute, sublicense,
+   and/or sell copies of the Software, and to permit persons to whom the
+   Software is furnished to do so, subject to the following conditions:
+
+   The above copyright notice and this permission notice shall be included
+   in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+   OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+   THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+   FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+   DEALINGS IN THE SOFTWARE.
+*/
+
+/*
+ *  EcgsimFileToMatrix_Plugin.cc
+ *
+ *  Written by:
+ *   Jeroen Stinstra
+ *   Department of Computer Science
+ *   University of Utah
+ *
+ */
+ 
+
+#include <Core/ImportExport/Matrix/MatrixIEPlugin.h>
+#include <Core/IEPlugin/IgbmFileToMatrix_Plugin.h>
+#include <Core/Datatypes/DenseMatrix.h>
+#include <Core/Datatypes/MatrixTypeConversions.h>
+#include <Core/Utils/Legacy/StringUtil.h>
+#include <Core/Logging/LoggerInterface.h>
+#include <Core/ImportExport/Matrix/MatrixIEPlugin.h>
+#include <Core/Datatypes/DenseMatrix.h>
+
+#include <iostream>
+#include <fstream>
+#include <sstream>
+
+using namespace SCIRun;
+using namespace SCIRun::Core;
+using namespace SCIRun::Core::Logging;
+using namespace SCIRun::Core::Datatypes;
+
+MatrixHandle SCIRun::IgbFileMatrix_reader(LoggerHandle pr, const char *filename)
+{
+  DenseMatrixHandle result;
+
+  int ncols = 0;
+  int nrows = 0;
+  int line_ncols = 0;
+  int header_rows = 0;
+  int header_cols = 0;
+
+  std::string line;
+  double data;
+
+  // STAGE 1 - SCAN THE FILE TO DETERMINE THE DIMENSIONS OF THE MATRIX
+  // AND CHECK THE FILE'S INTEGRITY.
+
+  {
+    std::ifstream inputfile;
+    inputfile.exceptions( std::ifstream::badbit );
+
+    try
+    {
+      inputfile.open(filename);
+
+      // get header information
+      getline(inputfile,line,'\n');
+      for (size_t p = 0;p<line.size();p++)
+      {
+        if ((line[p] == '\t')||(line[p] == ',')||(line[p]=='"')) line[p] = ' ';
+      }
+      std::istringstream iss(line);
+      iss >> header_rows;
+      iss >> header_cols; 
+
+      while( getline(inputfile,line,'\n'))
+      {
+        if (line.size() > 0)
+        {
+          // block out comments
+          if ((line[0] == '#')||(line[0] == '%')) continue;
+        }
+                  
+        // replace comma's and tabs with white spaces
+        for (size_t p = 0;p<line.size();p++)
+        {
+          if ((line[p] == '\t')||(line[p] == ',')||(line[p]=='"')) line[p] = ' ';
+        }
+        std::istringstream iss(line);
+        iss.exceptions( std::ifstream::failbit | std::ifstream::badbit);
+
+        try
+        {
+          line_ncols = 0;
+          while(1)
+          {
+            iss >> data;
+            line_ncols++;
+          }
+        }
+        catch(...)
+        {
+        }
+
+        if (line_ncols > 0)
+        {
+          nrows++;
+          if (ncols > 0)
+          {
+            if (ncols != line_ncols)
+            {
+              if (pr) pr->error("Improper format of text file, not every line contains the same amount of numbers");
+              return (result);
+            }
+          }
+          else
+          {
+            ncols = line_ncols;
+          }
+        }
+      }
+
+      if(ncols*nrows != header_cols*header_rows)
+      {
+        if (pr) pr->error("Data does not match header information.");
+        return(result);
+      }
+    }
+    catch (...)
+    {
+      if (pr) pr->error("Could not open file: "+std::string(filename));
+      return (result);
+    }
+    
+    inputfile.close();
+  }
+
+  // STAGE 2 - NOW ACTUALLY READ AND STORE THE MATRIX
+
+  {
+    std::ifstream inputfile;
+    inputfile.exceptions( std::ifstream::badbit );
+
+    result.reset(new DenseMatrix(header_rows,header_cols));
+    if (!result)
+    {
+      if (pr) pr->error("Could not allocate matrix");
+      return(result);
+    }
+    
+    double* dataptr = result->data();
+    int k = 0;
+
+    try
+    {
+      inputfile.open(filename);
+    
+      // get header information
+      getline(inputfile,line,'\n');
+
+      while( getline(inputfile,line,'\n'))
+      {
+        if (line.size() > 0)
+        {
+          // block out comments
+          if ((line[0] == '#')||(line[0] == '%')) continue;
+        }
+                                          
+        // replace comma's and tabs with white spaces
+        for (size_t p = 0;p<line.size();p++)
+        {
+          if ((line[p] == '\t')||(line[p] == ',')||(line[p]=='"')) line[p] = ' ';
+        }
+        std::istringstream iss(line);
+        iss.exceptions( std::ifstream::failbit | std::ifstream::badbit);
+        try
+        {
+          while(1)
+          {
+            iss >> data;
+            dataptr[k++] = data;
+          }
+        }
+        catch(...)
+        {
+        }
+      }
+    }
+    catch (...)
+    {
+      if (pr) pr->error("Could not open and read data in file: " + std::string(filename));
+      return (result);
+    }
+    
+    inputfile.close();
+  }
+  return(result);
+}
+
+
+bool SCIRun::IgbFileMatrix_writer(LoggerHandle pr, MatrixHandle matrixInput, const char *filename)
+{
+
+  std::ofstream outputfile;
+  outputfile.exceptions( std::ofstream::failbit | std::ofstream::badbit );
+
+  DenseMatrixHandle matrix = castMatrix::toDense(matrixInput);
+  
+  if (!matrix)
+  {
+    if (pr) pr->error("Empty matrix detected");
+    return(false);
+  }
+
+  double* dataptr = matrix->data();
+  if (!dataptr)
+  {
+    if (pr) pr->error("Empty matrix detected");
+    return(false);
+  }
+
+  try
+  {
+    outputfile.open(filename);
+  }
+  catch (...)
+  {
+    if (pr) pr->error("Could not open file: "+std::string(filename));
+    return (false);
+  }
+    
+  // output header line
+  //int rows = matrix->nrows();
+  //int cols = matrix->ncols();
+  outputfile << matrix->nrows() << " " << matrix->ncols() << std::endl;
+
+  size_t k = 0;
+  for (int p=0; p<matrix->nrows(); p++)  
+  {
+    for (int q=0; q<matrix->ncols(); q++)  
+    {
+      outputfile << dataptr[k++] << " ";
+    }
+    outputfile << "\n";
+  }  
+  
+  return (true);
+}
+
+
+

src/Core/IEPlugin/IgbFileToMatrix_Plugin.h

@@ -0,0 +1,43 @@
+/*
+  For more information, please see: http://software.sci.utah.edu
+
+  The MIT License
+
+  Copyright (c) 2015 Scientific Computing and Imaging Institute,
+  University of Utah.
+
+  
+  Permission is hereby granted, free of charge, to any person obtaining a
+  copy of this software and associated documentation files (the "Software"),
+  to deal in the Software without restriction, including without limitation
+  the rights to use, copy, modify, merge, publish, distribute, sublicense,
+  and/or sell copies of the Software, and to permit persons to whom the
+  Software is furnished to do so, subject to the following conditions:
+
+  The above copyright notice and this permission notice shall be included
+  in all copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+  DEALINGS IN THE SOFTWARE.
+*/
+
+#ifndef CORE_IEPLUGIN_IGBFILETOMATRIX_PLUGIN_H__
+#define CORE_IEPLUGIN_IGBFILETOMATRIX_PLUGIN_H__
+
+#include <Core/Logging/LoggerFwd.h>
+#include <Core/Datatypes/DatatypeFwd.h>
+#include <Core/IEPlugin/share.h>
+
+namespace SCIRun 
+{
+  SCISHARE Core::Datatypes::MatrixHandle IgbFileMatrix_reader(Core::Logging::LoggerHandle pr, const char *filename);
+
+  SCISHARE bool IgbFileMatrix_writer(Core::Logging::LoggerHandle pr, Core::Datatypes::MatrixHandle fh, const char* filename);
+}
+
+#endif