X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=bbtk_creaVtk_PKG%2Fsrc%2FbbcreaVtkReadMHDPlane.cxx;h=3b8fb24e373d5cd7593918fec5c2dd7b83b67077;hb=2076b540c52e3c4c62304f0cc99e4155256a138e;hp=cc881a84823e71b1c6307151a1d97d3218324645;hpb=3e0821360400df4c51def3efe9960d85be0f7104;p=creaVtk.git

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx
index cc881a8..3b8fb24 100644
--- a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx
+++ b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx
@@ -6,6 +6,23 @@
 
 #include "stdio.h"
 
+
+#define _LARGEFILE64_SOURCE
+
+#include <stdio.h>
+#include <sys/types.h>
+
+#if defined(_WIN32)
+#else
+#include <unistd.h>
+#endif // defined(_WIN32)
+
+#include <stdlib.h>
+#include <errno.h>
+#include <string.h>
+#include <sys/stat.h>
+#include <fcntl.h>
+
 namespace bbcreaVtk
 {
 
@@ -14,9 +31,9 @@ BBTK_BLACK_BOX_IMPLEMENTATION(ReadMHDPlane,bbtk::AtomicBlackBox);
 //===== 
 // Before editing this file, make sure it's a file of your own (i.e.: it wasn't generated from xml description; if so : your modifications will be lost)
 //===== 
-void ReadMHDPlane::Process()
-{
 
+void ReadMHDPlane::ReadNormalMHD()
+{
 // THE MAIN PROCESSING METHOD BODY
 //   Here we simply set the input 'In' value to the output 'Out'
 //   And print out the output value
@@ -32,69 +49,332 @@ void ReadMHDPlane::Process()
 //    bbSetOutputOut( bbGetInputIn() );
 //    std::cout << "Output value = " <<bbGetOutputOut() << std::endl;
 
+	std::string inputfilename;
 
+	if (bbGetInputDirectionPlane()=="XY")
+	{
+		inputfilename=bbGetInputFileName();
+	} // if XY
+
+
+	if ((bbGetInputDirectionPlane()=="YZ") || (bbGetInputDirectionPlane()=="ZX"))
+	{
 
+		//-- Split FileName
+  		std::size_t found		=	bbGetInputFileName().find_last_of("/\\");
+		std::string path		=	bbGetInputFileName().substr(0,found+1);
+		std::string filename	=	bbGetInputFileName().substr(found+1);
+#ifdef _WIN32
+		path=path+"YZ_ZX\\";
+#else
+		path=path+"YZ_ZX/";
+#endif
+	
+	
+		if (bbGetInputDirectionPlane()=="YZ") 
+		{ 
+			inputfilename = path+filename+"_YZ.mhd";  
+		} // if YZ
 
-	long int newHeaderSize;
-    	std::string newFileName=bbGetInputFileName()+"-OneSlice";
+		if (bbGetInputDirectionPlane()=="ZX")
+		{
+			inputfilename = path+filename+"_ZX.mhd";
+		} // XZ
+	} // if YZ || XZ
+
+	vtkImageData *newImage;
+	long long int newHeaderSize;
+    std::string newFileName=inputfilename+"-OneSlice";
 
     int sx,sy,sz;
     char mystring[250];
     char strTmp[20];
-    FILE *ffOut	= fopen(newFileName.c_str(),"w+");
-    FILE *ffIn	= fopen(bbGetInputFileName().c_str(),"r+");
-
-    while(!feof(ffIn))
-    {
-        strcpy(mystring,"\n");
-        fgets(mystring,250,ffIn);
-        if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
-        if (strncmp("DimSize",mystring,6)==0) 
+	bool ok=true;
+    FILE *ffIn	= fopen(inputfilename.c_str(),"r");
+	if (ffIn!=NULL)
 	{
-		sscanf(mystring,"%s %s %d %d",strTmp, strTmp, &sx, &sy);
-		sprintf(mystring,"DimSize = %d %d\n",sx,sy);
-    		newHeaderSize = sx*sy*bbGetInputSlice();
-	}
-        if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
-        if (strncmp("ElementType = MET_SHORT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; }
-        if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) { newHeaderSize=newHeaderSize*2; }
-        if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
-        if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
-        if (strncmp("ElementDataFile",mystring,15)==0) 
+	    FILE *ffOut	= fopen(newFileName.c_str(),"w");
+
+    	while(!feof(ffIn))
+    	{
+    	    strcpy(mystring,"\n");
+   			fgets(mystring,250,ffIn);
+   	     	if (strncmp("NDims",mystring,5)==0) {strcpy(mystring,"NDims = 2\n");}
+        	if (strncmp("DimSize",mystring,6)==0) 
+			{
+				sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
+				sprintf(mystring,"DimSize = %d %d\n",sx,sy);
+    			newHeaderSize = (long long int)sx*(long long int)sy*(long long int)bbGetInputSlice();
+				if (bbGetInputSlice()>=sz) {ok=false;}
+			} // if
+        	if (strncmp("ElementType = MET_CHAR",mystring,22)==0) 	{ newHeaderSize=newHeaderSize*1; }
+        	if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) 	{ newHeaderSize=newHeaderSize*1; }
+        	if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newHeaderSize=newHeaderSize*2; }
+        	if (strncmp("ElementType = MET_SHORT",mystring,23)==0) 	{ newHeaderSize=newHeaderSize*2; }
+        	if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) 	{ newHeaderSize=newHeaderSize*4; }
+        	if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) 	{ newHeaderSize=newHeaderSize*4; }
+        	if (strncmp("Offset",mystring,6)==0) {strcpy(mystring,"Offset = 0 0 0\n");}
+        	if (strncmp("HeaderSize",mystring,10)==0) {strcpy(mystring,"");}
+        	if (strncmp("ElementDataFile",mystring,15)==0) 
+			{
+				fprintf(ffOut,"HeaderSize = %lld\n\n", newHeaderSize );
+			} // if
+        	fprintf(ffOut,mystring); 
+    	} // while
+   		fclose(ffIn);
+   		fclose(ffOut);
+
+		if (ok==true)
+		{
+   			vtkMetaImageReader * reader = vtkMetaImageReader::New();
+   			reader->SetFileName( newFileName.c_str() );
+   			reader->Update();
+			newImage = reader->GetOutput();
+		} // if ok
+	} else {
+		ok=false;
+ 		printf("EED ERROR: Problem openin:%s\n", inputfilename.c_str() );
+ 	}
+
+	if (ok==false)
 	{
-		fprintf(ffOut,"HeaderSize = %ld\n\n", newHeaderSize );
-	}
-        fprintf(ffOut,mystring); 
-    }
-
-/*
-   fprintf(ff,"ObjectType = Image\n");
-   fprintf(ff,"NDims = 2\n");
-   fprintf(ff,"BinaryData = True\n");
-   fprintf(ff,"BinaryDataByteOrderMSB = False\n");
-   fprintf(ff,"CompressedData = False\n");
-   fprintf(ff,"TransformMatrix = 1 0 0 0 1 0 0 0 1\n");
-   fprintf(ff,"CenterOfRotation = 0 0 0\n");
-   fprintf(ff,"ElementSpacing = 0.7 0.7 0.7\n");
-   fprintf(ff,"DimSize = 512 512\n");
-   fprintf(ff,"AnatomicalOrientation = ???\n");
-   fprintf(ff,"ElementType = MET_SHORT\n");
-   fprintf(ff,"ElementNumberOfChannels = 1\n");
-   fprintf(ff,"Offset = 0 0 0\n");
-   fprintf(ff,"HeaderSize = %ld\n", newHeaderSize );
-   fprintf(ff,"ElementDataFile = inspi1_ana.raw\n");
-*/
-
-   fclose(ffIn);
-   fclose(ffOut);
-
-
-   vtkMetaImageReader * reader = vtkMetaImageReader::New();
-   reader->SetFileName( newFileName.c_str() );
-   reader->Update();
-   
-   bbSetOutputOut( reader->GetOutput() );
+		int i;
+		int sizeX, sizeY, sizeZ;
+		sizeX = 200;
+		sizeY = sizeX;
+		sizeZ = 1;
+		newImage = vtkImageData::New();
+   		newImage->Initialize();
+   		newImage->SetScalarTypeToUnsignedChar();
+   		newImage->SetSpacing( 1,1,1 );
+   		newImage->SetDimensions(  sizeX,sizeY,sizeZ );
+   		newImage->SetWholeExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
+   		newImage->SetExtent(0,  sizeX-1,0,sizeY-1,0,sizeZ-1 );
+   		newImage->SetNumberOfScalarComponents(1);
+   		newImage->AllocateScalars();
+   		newImage->Update();
+		memset ( (void*)newImage->GetScalarPointer(), 0, sizeX*sizeY*1 );
+   		for (i=0; i<sizeX; i++)
+   		{
+			newImage->SetScalarComponentFromDouble(i,i,0, 0, 255 );
+			newImage->SetScalarComponentFromDouble(i,sizeY-1-i,0, 0, 255 );
+  		} // for i
+	} // if ok
+
+	bbSetOutputOut( newImage );
+
+}
+
+void ReadMHDPlane::Read64lseek()
+{
+
+	int 		dimX=-1,dimY=-1,dimZ=-1;
+	int 		dim=-1;
+	std::string formattype("VOID");
+	std::string elementdatafile("VOID");
+	float	 	spcX=-1,spcY=-1,spcZ=-1;
+	float 		ox=-1,oy=-1,oz=-1;
+	long int 	headersize=0;
+
+	vtkImageData *newImage;
+
+	char mystring[250];
+	char strTmp[30];
+	char strTmp2[30];
+	FILE *ffIn	= fopen(bbGetInputFileName().c_str(),"r");
+	long long dataSize;
+
+
+
+	if (ffIn!=NULL)
+	{
+		newImage = vtkImageData::New();
+
+		while(!feof(ffIn))
+		{
+    	    strcpy(mystring,"\n");
+   			fgets(mystring,250,ffIn);
+   	     	if (strncmp("NDims",mystring,5)==0) 			{ sscanf(mystring,"%s %s %d"		,strTmp, strTmp, &dim); 				}
+        	if (strncmp("DimSize",mystring,6)==0) 			{ sscanf(mystring,"%s %s %d %d %d"	,strTmp, strTmp, &dimX, &dimY,&dimZ);	} 
+			if (strncmp("ElementType",mystring,11)==0) 		{ sscanf(mystring,"%s %s %s"		,strTmp, strTmp, strTmp2); formattype=strTmp2;			}
+			if (strncmp("ElementSpacing",mystring,11)==0) 	{ sscanf(mystring,"%s %s %f %f %f"	,strTmp, strTmp, &spcX,&spcY,&spcZ);	}
+         	if (strncmp("Offset",mystring,6)==0) 			{ sscanf(mystring,"%s %s %f %f %f"	,strTmp, strTmp, &ox, &oy, &oz);		}
+        	if (strncmp("HeaderSize",mystring,10)==0) 		{ sscanf(mystring,"%s %s %ld"		,strTmp, strTmp, &headersize);			}
+			if (strncmp("ElementDataFile",mystring,15)==0) 	{ sscanf(mystring,"%s %s %s"		,strTmp, strTmp, strTmp2); elementdatafile=strTmp2;		}
+
+        	if (strncmp("ElementType = MET_CHAR",mystring,22)==0) 	{ newImage->SetScalarTypeToChar(); 			dataSize=sizeof(char); 			}
+        	if (strncmp("ElementType = VTK_CHAR",mystring,22)==0) 	{ newImage->SetScalarTypeToChar(); 			dataSize=sizeof(char); 			}
+        	if (strncmp("ElementType = MET_UCHAR",mystring,23)==0) 	{ newImage->SetScalarTypeToUnsignedChar();	dataSize=sizeof(unsigned char); }
+        	if (strncmp("ElementType = VTK_UNSIGNED_CHAR",mystring,31)==0) 	{ newImage->SetScalarTypeToUnsignedChar();	dataSize=sizeof(unsigned char); }
+        	if (strncmp("ElementType = MET_USHORT",mystring,24)==0) { newImage->SetScalarTypeToUnsignedShort();	dataSize=sizeof(unsigned short);}
+        	if (strncmp("ElementType = VTK_UNSIGNED_SHORT",mystring,32)==0) { newImage->SetScalarTypeToUnsignedShort();	dataSize=sizeof(unsigned short);}
+        	if (strncmp("ElementType = MET_SHORT",mystring,23)==0) 	{ newImage->SetScalarTypeToShort();			dataSize=sizeof(short); 		}
+        	if (strncmp("ElementType = VTK_SHORT",mystring,23)==0) 	{ newImage->SetScalarTypeToShort();			dataSize=sizeof(short); 		}
+        	if (strncmp("ElementType = MET_FLOAT",mystring,23)==0) 	{ newImage->SetScalarTypeToFloat();			dataSize=sizeof(float); 		}
+        	if (strncmp("ElementType = VTK_FLOAT",mystring,23)==0) 	{ newImage->SetScalarTypeToFloat();			dataSize=sizeof(float); 		}
+        	if (strncmp("ElementType = MET_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();		dataSize=sizeof(double); 		}
+        	if (strncmp("ElementType = VTK_DOUBLE",mystring,24)==0) { newImage->SetScalarTypeToDouble();		dataSize=sizeof(double); 		}
+
+    	} // while
+   		fclose(ffIn);
 
+   		newImage->Initialize();
+
+
+		int fd;
+		long long ret;
+		std::size_t found;
+		std::string filename;
+		found					=	bbGetInputFileName().find_last_of("/\\");
+		filename 				= bbGetInputFileName().substr(0,found+1) + elementdatafile ;
+		long long pos;
+
+		long long lsize			= dimX*dimY*1 *dataSize;
+
+
+#if defined(_WIN32)
+		   _sopen_s( &fd, filename.c_str(), _O_RDONLY, _SH_DENYNO, 0 );
+#else
+		fd = open ( filename.c_str() ,  O_RDONLY|O_LARGEFILE );
+#endif // defined(_WIN32)
+
+
+
+		if (fd < 0)
+		{
+			printf("EED ReadMHDPlane::Read64lseek \n");
+			fprintf(stderr, "%s\n", strerror(errno));
+			exit(1);
+		}
+
+		if (bbGetInputDirectionPlane()=="XY") 
+		{ 
+	   		newImage->SetSpacing( spcX,spcY,spcZ );
+	   		newImage->SetDimensions(  dimX,dimY,1 );
+	   		newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,0 );
+	   		newImage->SetExtent(0,  dimX-1,0,dimY-1,0,0 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			pos = dimX*dimY*(long long)bbGetInputSlice()*dataSize;
+
+
+
+#if defined(_WIN32)
+			if (_lseeki64( fd, pos, SEEK_SET ) < 0)
+#else
+			if (lseek64(fd, pos, SEEK_SET) < 0) 
+#endif // defined(_WIN32)
+
+			{
+				printf("EED ReadMHDPlane::Read64lseek \n");
+				fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
+				exit(1);
+			}
+
+			if ((ret = read(fd, newImage->GetScalarPointer() , lsize)) < 0) 
+			{
+				fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+				exit(1);
+			}
+		}  // if PLANE XY
+
+		/*
+		if (bbGetInputDirectionPlane()=="XZ") 
+		{ 
+			long long int j;
+	   		newImage->SetSpacing( spcX,spcZ,spcY );
+	   		newImage->SetDimensions(  dimX,dimZ,1 );
+	   		newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,0 );
+	   		newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,0 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			long long sizeBytesPlane = dimX*dimY*dataSize;
+			pos = dimX*(long long int)bbGetInputSlice()*dataSize;
+			void *pImage = newImage->GetScalarPointer();
+			for (j=0;j<dimZ;j++)
+			{
+printf("EED EED ReadMHDPlane::Read64lseek XZ j=%d \n", j);
+				if (lseek64(fd, pos + j*sizeBytesPlane , SEEK_SET) < 0) 
+				{
+					printf("EED ReadMHDPlane::Read64lseek \n");
+					fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
+					exit(1);
+				}
+
+				if ((ret = read(fd, pImage , dimX*dataSize)) < 0) 
+				{
+					fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+					exit(1);
+				}
+				pImage=pImage+dimX*dataSize;
+			} // for j
+		}  // if PLANE XZ
+
+
+		if (bbGetInputDirectionPlane()=="YZ") 
+		{ 
+			long long int j;
+			long long int i;
+	   		newImage->SetSpacing( spcY,spcZ,spcX );
+	   		newImage->SetDimensions(  dimY,dimZ,1 );
+	   		newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,0 );
+	   		newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,0 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			long long sizeBytesPlane = dimX*dimY*dataSize;
+//			pos = dimX*(long long int)bbGetInputSlice()*dataSize;
+			void *pImage;
+			for (j=0;j<dimZ;j++)
+			{
+printf("EED EED ReadMHDPlane::Read64lseek YZ i=%d j=%d \n", i,j);
+				for (i=0;i<dimY;i++)
+				{
+					pos = ((long long int)bbGetInputSlice() + i*dimX + j*dimX*dimY)*dataSize ;
+					if (lseek64(fd, pos  , SEEK_SET) < 0) 
+					{
+						printf("EED ReadMHDPlane::Read64lseek \n");
+						fprintf(stderr, "Failed seeking to %lld, %s\n", pos, strerror(errno));
+						exit(1);
+					}
+
+					pImage=newImage->GetScalarPointer(i, j,0 );
+					if ((ret = read(fd, pImage , dataSize)) < 0) 
+					{
+						fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+						exit(1);
+					}
+				}
+			} // for j
+		}  // if PLANE YZ
+		*/
+	
+#if defined(_WIN32)
+		_close (fd);
+#else
+		close (fd);
+#endif // defined(_WIN32)
+
+		bbSetOutputOut( newImage );
+	} // if
+
+
+}
+
+
+void ReadMHDPlane::Process()
+{
+	if (bbGetInputType()==0)
+	{
+		ReadNormalMHD();
+	}	
+
+	if (bbGetInputType()==1)
+	{
+		Read64lseek();
+	}	
 
 }
 //===== 
@@ -107,6 +387,8 @@ void ReadMHDPlane::bbUserSetDefaultValues()
 //    Here we initialize the input 'In' to 0
    bbSetInputFileName("");
    bbSetInputSlice(0);
+   bbSetInputType(0);
+   bbSetInputDirectionPlane("XY");
   
 }
 //=====