--- /dev/null
+/*=========================================================================
+
+ Program: gdcm
+ Module: $RCSfile: PatchHeader.cxx,v $
+ Language: C++
+ Date: $Date: 2005/08/28 17:10:49 $
+ Version: $Revision: 1.1 $
+
+ Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
+ l'Image). All rights reserved. See Doc/License.txt or
+ http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the above copyright notices for more information.
+
+=========================================================================*/
+#include "gdcmFile.h"
+#include "gdcmFileHelper.h"
+#include "gdcmCommon.h"
+#include "gdcmDebug.h"
+#include "gdcmDirList.h"
+#include "gdcmDocEntry.h"
+#include "gdcmArgMgr.h"
+
+#include <iostream>
+
+// ------------------------------------------------------------------------
+// gdcm mechanisms don't allow user to read an image
+// whose header contains wrong physical info (say : wrong Row Number ...)
+// and re-write with a right value.
+// This program does the job by brutally overwritting the wrong values.
+// It may be usefull to save a set of images ...
+// (It dosn't allow to *add* a missing field)
+// ------------------------------------------------------------------------
+
+// global variables will be seen inside any function.
+
+gdcm::File *f;
+std::fstream *fp;
+
+uint16_t samplesperpixel;
+uint16_t planarconfiguration;
+uint16_t size;
+uint16_t rows;
+uint16_t columns;
+uint16_t planes;
+uint16_t bitsallocated;
+uint16_t bitsstored;
+uint16_t highbit;
+uint16_t pixelrepresentation;
+
+bool bsamplesperpixel;
+bool bplanarconfiguration;
+bool bsize;
+bool brows;
+bool bcolumns;
+bool bplanes;
+bool bbitsallocated;
+bool bbitsstored;
+bool bhighbit;
+bool bpixelrepresentation;
+
+void update()
+{
+ uint32_t offset;
+ gdcm::DocEntry *d;
+ //
+ // Fields to replace.
+ //
+
+ // Samples Per Pixel
+ if (bsamplesperpixel)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0002);
+ if (d)
+ {
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&samplesperpixel, 2 );
+ }
+ }
+ // Rows
+ if (brows)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0010);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&rows, 2 );
+ }
+ // Columns
+ if (bcolumns)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0011);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&columns, 2 );
+ }
+ // Planes
+ if (bplanes)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0012);
+ if (d)
+ {
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&planes, 2 );
+ }
+ }
+ // Bits Allocated
+ if (bbitsallocated)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0100);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&bitsallocated, 2 );
+ }
+
+ // Bits Stored
+ if (bbitsstored)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0101);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&bitsstored, 2 );
+ }
+
+ // High Bit
+ if (bhighbit)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0102);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&highbit, 2 );
+ }
+
+ // Pixel Representation
+ if (bpixelrepresentation)
+ {
+ d = f->GetDocEntry( 0x0028, 0x0103);
+ offset = d->GetOffset();
+ fp->seekp( offset, std::ios::beg );
+ fp->write( (char *)&pixelrepresentation, 2 );
+ }
+}
+
+int main(int argc, char *argv[])
+{
+ START_USAGE(usage)
+ "\n PatchHeader :\n ",
+ " Allows aware user to patch an image header, without loading image. ",
+ " Warning : the image(s) is/are overwritten ",
+ " to preserve image(s) integrity, use a copy. ",
+ " WARNING : *NO CHECK* is performed on the new values. ",
+ " Use only if you are sure the original values are wrong ",
+ " *and* your values are right... ",
+ "usage: PatchHeader {filein=inputFileName|dirin=inputDirectoryName} ",
+ " [ { [size=] | [rows=][columns=] } ] [planes=] ",
+ " [bitsallocated=] [bitsstored=] ",
+ " [highbit=] [samplesperpixel=] ",
+ " [pixelrepresentation=] [samplesperpixel=] ",
+ " [ { [noshadowseq] | [noshadow][noseq] } ] [debug] ",
+ " ",
+ " inputFileName : Name of the (single) file user wants to modify ",
+ " inputDirectoryName : user wants to modify *all* the files ",
+ " within the directory ",
+ " size : new (square) size, to owerwrite old (wrong) one ",
+ " or ",
+ " rows : new Rows number, to owerwrite old (wrong) one ",
+ " columns : new Columns number, to owerwrite old (wrong) one ",
+ " planes : new Planes number, ... ",
+ " bitsallocated : new Bits Allocated number, ... ",
+ " bitsstored : new Bits Stored number, ... ",
+ " highbit : new High Bit number, ... ",
+ " samplesperpixel : new Samples Per Pixel, ... ",
+ " pixelrepresentation : new Pixel Representation, ... ",
+ " ",
+ " noshadowseq: user doesn't want to load Private Sequences ",
+ " noshadow : user doesn't want to load Private groups (odd number) ",
+ " noseq : user doesn't want to load Sequences ",
+ " debug : user wants to run the program in 'debug mode' ",
+ FINISH_USAGE
+
+ // ----- Initialize Arguments Manager ------
+
+ gdcm::ArgMgr *am = new gdcm::ArgMgr(argc, argv);
+
+ if (am->ArgMgrDefined("usage") || argc == 1)
+ {
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+ char *fileName = am->ArgMgrGetString("filein",(char *)0);
+ char *dirName = am->ArgMgrGetString("dirin",(char *)0);
+
+ if ( (fileName == 0 && dirName == 0)
+ ||
+ (fileName != 0 && dirName != 0) )
+ {
+ std::cout <<std::endl
+ << "Either 'filein=' or 'dirin=' must be present;"
+ << std::endl << "Not both" << std::endl;
+ am->ArgMgrUsage(usage); // Display 'usage'
+ delete am;
+ return 0;
+ }
+
+bsamplesperpixel = am->ArgMgrDefined("samplesperpixel");
+ if ( bsamplesperpixel )
+ samplesperpixel = am->ArgMgrWantInt("samplesperpixel",usage);
+
+ planarconfiguration = am->ArgMgrDefined("planarconfiguration");
+ if ( bplanarconfiguration )
+ planarconfiguration = am->ArgMgrWantInt("planarconfiguration",usage);
+
+ bsize = am->ArgMgrDefined("size");
+ brows = am->ArgMgrDefined("rows");
+ bcolumns = am->ArgMgrDefined("columns");
+
+ if (bsize && (brows || bcolumns) )
+ {
+ printf ("Use 'SIZE=...' or 'ROWS=... COLUMNS=...'\n");
+ printf ("Not both\n");
+ delete am;
+ return 0;
+ }
+
+ if ( bsize )
+ size = am->ArgMgrWantInt("size",usage);
+
+ if ( brows )
+ rows = am->ArgMgrWantInt("rows",usage);
+
+ if ( bcolumns )
+ columns = am->ArgMgrWantInt("columns",usage);
+
+ if (bsize)
+ {
+ brows = bcolumns = true;
+ rows = columns = size;
+ }
+ bplanes = am->ArgMgrDefined("planes");
+ if ( bplanes )
+ planes = am->ArgMgrWantInt("planes",usage);
+
+ bbitsallocated = am->ArgMgrDefined("bitsallocated");
+ if ( bbitsallocated )
+ bitsallocated = am->ArgMgrWantInt("bitsallocated",usage);
+
+ bbitsstored = am->ArgMgrDefined("bitsstored");
+ if ( bbitsstored )
+ bitsstored = am->ArgMgrWantInt("bitsstored",usage);
+
+ bhighbit = am->ArgMgrDefined("highbit");
+ if ( bhighbit )
+ highbit = am->ArgMgrWantInt("highbit",usage);
+
+ bpixelrepresentation = am->ArgMgrDefined("pixelrepresentation");
+ if ( bpixelrepresentation )
+ pixelrepresentation = am->ArgMgrWantInt("pixelrepresentation",usage);
+
+ if (am->ArgMgrDefined("debug"))
+ gdcm::Debug::DebugOn();
+
+ int loadMode = 0x00000000;
+ if ( am->ArgMgrDefined("noshadowseq") )
+ loadMode |= NO_SHADOWSEQ;
+ else
+ {
+ if ( am->ArgMgrDefined("noshadow") )
+ loadMode |= NO_SHADOW;
+ if ( am->ArgMgrDefined("noseq") )
+ loadMode |= NO_SEQ;
+ }
+
+ /* if unused Param we give up */
+ if ( am->ArgMgrPrintUnusedLabels() )
+ {
+ am->ArgMgrUsage(usage);
+ delete am;
+ return 0;
+ }
+
+ delete am; // ------ we don't need Arguments Manager any longer ------
+
+
+ if ( fileName != 0 ) // ====== Deal with a single file ======
+ {
+
+ //
+ // Parse the input file.
+ //
+
+ f = new gdcm::File( );
+ f->SetLoadMode(loadMode);
+ f->SetFileName( fileName );
+ bool res = f->Load();
+
+ // gdcm::File::IsReadable() is no usable here, because we deal with
+ // any kind of gdcm::Readable *document*
+ // not only gdcm::File (as opposed to gdcm::DicomDir)
+ if ( !res )
+ {
+ std::cout <<std::endl
+ << "Sorry, " << fileName <<" not a gdcm-readable "
+ << "DICOM / ACR Document"
+ << std::endl;
+ delete f;
+ return 1;
+ }
+ std::cout << fileName << " is readable " << std::endl;
+
+ //
+ // No need to load the pixels in memory.
+ // File will be overwritten
+ //
+
+ // open the file
+ fp = new std::fstream(fileName,
+ std::ios::in | std::ios::out | std::ios::binary);
+
+ update ();
+
+ fp->close();
+ delete fp;
+ delete f;
+ return 0;
+
+ }
+ else // ====== Deal with a (single Patient) Directory ======
+ {
+ std::cout << "dirName [" << dirName << "]" << std::endl;
+ gdcm::DirList dirList(dirName,1); // gets recursively the file list
+ gdcm::DirListType fileList = dirList.GetFilenames();
+ for( gdcm::DirListType::iterator it = fileList.begin();
+ it != fileList.end();
+ ++it )
+ {
+ f = new gdcm::File( );
+ f->SetLoadMode(loadMode);
+ f->SetFileName( it->c_str() );
+ bool res = f->Load();
+
+ if ( !res )
+ {
+ delete f;
+ continue;
+ }
+
+ // open the file
+ fp = new std::fstream(it->c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ update();
+
+
+ fp->close();
+ delete fp;
+ delete f;
+ }
+ }
+ return 0;
+}
+
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff