X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=bbtk_creaVtk_PKG%2Fsrc%2FbbcreaVtkReadMHDPlane.cxx;h=58486f2bbfa4cbcb6a0712d47dcb02209348bbc9;hb=b5336cb50d214351673b863554714c5b2fa728a1;hp=5436547076db319eee239fe021624f225e3af6d2;hpb=f1922fd6bea6c9a0c3c105f6c093f1f5bce01c3e;p=creaVtk.git

diff --git a/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx b/bbtk_creaVtk_PKG/src/bbcreaVtkReadMHDPlane.cxx
index 5436547..58486f2 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 +31,37 @@ 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()
+
+
+vtkImageData* ReadMHDPlane::CreateDefaultImage()
 {
+	int i;
+	int sizeX, sizeY, sizeZ;
+	sizeX = 200;
+	sizeY = sizeX;
+	sizeZ = 1;
+	vtkImageData *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
+	return newImage;
+} 
 
+
+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 +77,377 @@ void ReadMHDPlane::Process()
 //    bbSetOutputOut( bbGetInputIn() );
 //    std::cout << "Output value = " <<bbGetOutputOut() << std::endl;
 
+	std::string inputfilename;
+	int slice;
+	int width;
 
+	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
 
+		if (bbGetInputDirectionPlane()=="ZX")
+		{
+			inputfilename = path+filename+"_ZX.mhd";
+		} // XZ
+	} // if YZ || XZ
 
-	long int newHeaderSize;
-    	std::string newFileName=bbGetInputFileName()+"-OneSlice";
+	width = bbGetInputWidth();
+	if (width<=0 ) { width=1; }
 
-    int sx,sy;
+	slice = bbGetInputSlice();
+	if (slice<0 ) { slice=0; }
+
+
+	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)
+	{
+	    FILE *ffOut	= fopen(newFileName.c_str(),"w");
+
+    	while(!feof(ffIn))
+    	{
+    	    strcpy(mystring,"\n");
+   			fgets(mystring,250,ffIn);
+   	     	if (strncmp("NDims",mystring,5)==0) 
+			{
+				if (width==1) 
+				{ 
+					strcpy(mystring,"NDims = 2\n"); 
+				} else {
+					strcpy(mystring,"NDims = 3\n"); 
+				}
+			}
+        	if (strncmp("DimSize",mystring,6)==0) 
+			{
+				sscanf(mystring,"%s %s %d %d %d",strTmp, strTmp, &sx, &sy,&sz);
+
+				if (width==1) 
+				{ 
+					sprintf(mystring,"DimSize = %d %d\n",sx,sy);
+				} else {
+					sprintf(mystring,"DimSize = %d %d %d\n",sx,sy,width);
+				}
+
+    			newHeaderSize = (long long int)sx*(long long int)sy*(long long int)slice;
+				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)
 	{
-		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) 
+		newImage=CreateDefaultImage();
+	} // if ok
+
+	bbSetOutputOut( newImage );
+}
+
+
+
+
+
+void ReadMHDPlane::Read64lseek()
+{
+	int 		slice;
+	int 		width;
+
+	width = bbGetInputWidth();
+	if (width<=0 ) { width=1; }
+
+	slice = bbGetInputSlice();
+	if (slice<0 ) { slice=0; }
+
+	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=NULL;
+
+	char mystring[250];
+	char strTmp[30];
+	char strTmp2[30];
+	FILE *ffIn	= fopen(bbGetInputFileName().c_str(),"r");
+printf("EED ReadMHDPlane::Read64lseek filename %s %p\n", bbGetInputFileName().c_str(), ffIn );
+	long long dataSize;
+
+	if (ffIn!=NULL)
 	{
-		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() );
+		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,14)==0) 	{ sscanf(mystring,"%s %s %f %f %f"	,strTmp, strTmp, &spcX,&spcY,&spcZ);	}
+			if (strncmp("ElementSize",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_UINT",mystring,24)==0) 			{ newImage->SetScalarTypeToUnsignedInt();	dataSize=sizeof(unsigned int);	}
+        	if (strncmp("ElementType = VTK_UNSIGNED_INT",mystring,32)==0) 	{ newImage->SetScalarTypeToUnsignedInt();	dataSize=sizeof(unsigned int);	}
+        	if (strncmp("ElementType = MET_INT",mystring,24)==0) 			{ newImage->SetScalarTypeToInt();			dataSize=sizeof(int);			}
+        	if (strncmp("ElementType = VTK_INT",mystring,32)==0) 			{ newImage->SetScalarTypeToInt();			dataSize=sizeof(int);			}
+        	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_LONG",mystring,23)==0) 			{ newImage->SetScalarTypeToLong();			dataSize=sizeof(long); 			}
+        	if (strncmp("ElementType = VTK_LONG",mystring,23)==0) 			{ newImage->SetScalarTypeToLong();			dataSize=sizeof(long); 			}
+        	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*width *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   WARNNING! raw file not exist\n");
+			fprintf(stderr, "%s\n", strerror(errno));
+			newImage=CreateDefaultImage();
+//			exit(1);
+		} 	
+		
+
+		if ((bbGetInputDirectionPlane()=="XY") && (fd>=0)) 
+		{ 
+	   		newImage->SetSpacing( spcX,spcY,spcZ );
+	   		newImage->SetDimensions(  dimX,dimY,width );
+	   		newImage->SetWholeExtent(0,  dimX-1,0,dimY-1,0,width-1 );
+	   		newImage->SetExtent(0,  dimX-1,0,dimY-1,0,width-1 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			pos = dimX*dimY*(long long)slice*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") && (fd>=0))
+		{ 
+	   		newImage->SetSpacing( spcX,spcZ,spcY );
+	   		newImage->SetDimensions(  dimX,dimZ,width );
+	   		newImage->SetWholeExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
+	   		newImage->SetExtent(0,  dimX-1,0,dimZ-1,0,width-1 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			int iWidth;
+			for (iWidth=0;iWidth<width;iWidth++)
+			{
+				copy_XZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
+			}
+		}  // if PLANE XZ
+
+		if ((bbGetInputDirectionPlane()=="YZ") && (fd>=0))
+		{ 
+	   		newImage->SetSpacing( spcY,spcZ,spcX );
+	   		newImage->SetDimensions(  dimY,dimZ,width );
+	   		newImage->SetWholeExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
+	   		newImage->SetExtent(0,  dimY-1,0,dimZ-1,0,width-1 );
+	   		newImage->SetNumberOfScalarComponents(1);
+	   		newImage->AllocateScalars();
+	   		newImage->Update();
+			int iWidth;
+			for (iWidth=0;iWidth<width;iWidth++)
+			{
+				copy_YZ_plane(fd,newImage,slice+iWidth,iWidth,dimX,dimY,dimZ,dataSize);
+			}
+
+		}  // if PLANE YZ	
+#if defined(_WIN32)
+		_close (fd);
+#else
+		close (fd);
+#endif // defined(_WIN32)
+	} else {
+		newImage=CreateDefaultImage();
+	} // if  ffIn
+
+	bbSetOutputOut( newImage );
+}
+
+
+void ReadMHDPlane::copy_YZ_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
+{
+	long long int j;
+	long long int i;
+	long long 	ret;
+	long long 	pos;
+	long long sizeBytesPlane = dimX*dimY*dataSize;
+	char *pImage;
+	for (j=0;j<dimZ;j++)
+	{
+		for (i=0;i<dimY;i++)
+		{
+			pos = ((long long int)slice+iWidth + i*dimX + j*dimX*dimY)*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);
+			}
+
+			pImage=(char*)(newImage->GetScalarPointer(i, dimZ-1-j,iWidth ));
+			if ((ret = read(fd, pImage , dataSize)) < 0) 
+			{
+				fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+				exit(1);
+			}
+			} // for i
+		} // for j
+}
+
+
+void ReadMHDPlane::copy_XZ_plane(int fd,vtkImageData *newImage,int slice,int iWidth,int dimX,int dimY,int dimZ,int dataSize)
+{
+	long long int j;
+	long long 	ret;
+	long long 	pos;
+	pos = dimX*(long long int)slice*dataSize;
+	long long sizeBytesPlane = dimX*dimY*dataSize;
+	char *pImage = (char*)( newImage->GetScalarPointer(0,0,iWidth) );
+	for (j=dimZ-1;j>=0;j--)
+	{
+#if defined(_WIN32)
+		if (_lseeki64( fd, pos + j*sizeBytesPlane , SEEK_SET ) < 0)
+#else
+		if (lseek64(fd, pos + j*sizeBytesPlane , 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, pImage , dimX*dataSize)) < 0) 
+		{
+			fprintf(stderr, "Failed reading: %s\n", strerror(errno));
+			exit(1);
+		}
+		pImage = pImage+dimX*dataSize;
+	} // for j
+}
+
+
+
+void ReadMHDPlane::Process()
+{
+	if (bbGetInputType()==0)
+	{
+		ReadNormalMHD();
+	}	
+
+	if (bbGetInputType()==1)
+	{
+		Read64lseek();
+	}	
 
 }
 //===== 
@@ -107,6 +460,9 @@ void ReadMHDPlane::bbUserSetDefaultValues()
 //    Here we initialize the input 'In' to 0
    bbSetInputFileName("");
    bbSetInputSlice(0);
+   bbSetInputType(1);
+   bbSetInputWidth(1);
+   bbSetInputDirectionPlane("XY");
   
 }
 //=====