Program: gdcm
Module: $RCSfile: exExtractOverlaysACR.cxx,v $
Language: C++
- Date: $Date: 2007/09/12 10:43:47 $
- Version: $Revision: 1.1 $
+ Date: $Date: 2007/09/14 08:23:34 $
+ Version: $Revision: 1.2 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmCommon.h"
#include "gdcmDebug.h"
#include "gdcmDocEntry.h"
+#include "gdcmArgMgr.h"
+
#include <iostream>
-#include <stdio.h> // for fseek... FIXME
#include <stdlib.h> // for atoi
-#include "gdcmArgMgr.h"
-
- // WARNING :
- // unfinished : DO NOT to be used as is !
+ /* SIEMENS_GBS_III-16-ACR_NEMA_1.acr
- /*
// Example (sorry, we've got no more than this one ...)
-V 0028|0010[US] [Rows] [256] x(100)
-V 0028|0011[US] [Columns] [256] x(100)
-V 0028|0030[DS] [Pixel Spacing] [01.56\1.56]
-V 0028|0100[US] [Bits Allocated] [16] x(10)
-V 0028|0101[US] [Bits Stored] [12] x(c)
-V 0028|0102[US] [High Bit] [11] x(b)
-V 0028|0103[US] [Pixel Representation] [0] x(0)
+0028|0010[US] [Rows] [256] x(100)
+0028|0011[US] [Columns] [256] x(100)
+0028|0030[DS] [Pixel Spacing] [01.56\1.56]
+0028|0100[US] [Bits Allocated] [16] x(10)
+0028|0101[US] [Bits Stored] [12] x(c)
+0028|0102[US] [High Bit] [11] x(b)
+0028|0103[US] [Pixel Representation] [0] x(0)
-V 6000|0000[UL] [Group Length] [96] x(60)
-V 6000|0010[US] [Rows] [256] x(100)
-V 6000|0011[US] [Columns] [256] x(100)
-V 6000|0040[CS] [Overlay Type] [R ]
-V 6000|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
-V 6000|0100[US] [Overlay Bits Allocated] [16] x(10)
-V 6000|0102[US] [Overlay Bit Position] [12] x(c)
+6000|0000[UL] [Group Length] [96] x(60)
+6000|0010[US] [Rows] [256] x(100)
+6000|0011[US] [Columns] [256] x(100)
+6000|0040[CS] [Overlay Type] [R ]
+6000|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+6000|0100[US] [Overlay Bits Allocated] [16] x(10)
+6000|0102[US] [Overlay Bit Position] [12] x(c)
...
...
-V 6006|0000[UL] [Group Length] [96] x(60)
-V 6006|0010[US] [Rows] [256] x(100)
-V 6006|0011[US] [Columns] [256] x(100)
-V 6006|0040[CS] [Overlay Type] [R ]
-V 6006|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
-V 6006|0100[US] [Overlay Bits Allocated] [16] x(10)
-V 6006|0102[US] [Overlay Bit Position] [15] x(f)
+6006|0000[UL] [Group Length] [96] x(60)
+6006|0010[US] [Rows] [256] x(100)
+6006|0011[US] [Columns] [256] x(100)
+6006|0040[CS] [Overlay Type] [R ]
+6006|0050[SS] [Overlay Origin] [23601\8241] x(5c31)
+6006|0100[US] [Overlay Bits Allocated] [16] x(10)
+6006|0102[US] [Overlay Bit Position] [15] x(f)
*/
int main(int argc, char *argv[])
-{
+{
START_USAGE(usage)
" \n exExtractOverlaysACR :\n ",
" Extract ACR-NEMA style overlays from an image ",
- " usage: exExtractOverlaysACR filein=inputDirectoryName [debug] ",
+ " usage: exExtractOverlaysACR filein=inputFileName [debug] ",
" debug : developper wants to run the program in 'debug mode' ",
FINISH_USAGE
delete am;
return 0;
}
-
- // "SIEMENS_GBS_III-16-ACR_NEMA_1.acr"
-
- const char *fileName = am->ArgMgrWantString("filein", usage);
+
+ const char *fileName = am->ArgMgrWantString("filein", usage);
if (am->ArgMgrDefined("debug"))
GDCM_NAME_SPACE::Debug::DebugOn();
delete am; // we don't need Argument Manager any longer
+ // ========================== Now, we can do the job! ================
- // ========================== Now, we can do the job! ================
-
GDCM_NAME_SPACE::File *f;
-
// ============================================================
// Read the input image.
// ============================================================
- //std::cout << argv[1] << std::endl;
-
f = GDCM_NAME_SPACE::File::New( );
f->SetLoadMode(GDCM_NAME_SPACE::LD_NOSEQ | GDCM_NAME_SPACE::LD_NOSHADOW);
f->SetFileName( fileName );
bool res = f->Load();
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- {
- std::cout << "---------------------------------------------" << std::endl;
- f->Print();
- std::cout << "---------------------------------------------" << std::endl;
- }
+
if (!res) {
std::cout << "Sorry, " << fileName <<" not a gdcm-readable "
<< "DICOM / ACR File"
f->Delete();
return 0;
}
- std::cout << " ... is readable " << std::endl;
+ std::cout << fileName << " ... is readable " << std::endl;
// ============================================================
// Check whether image contains Overlays ACR-NEMA style.
f->Delete();
return 0;
}
- std::cout << " File is read! " << std::endl;
+ std::cout << fileName << " is read! " << std::endl;
// ============================================================
// Load the pixels in memory.
// ============================================================
- int nx = f->GetXSize();
- int ny = f->GetYSize();
-
GDCM_NAME_SPACE::FileHelper *fh1 = GDCM_NAME_SPACE::FileHelper::New(f);
fh1->SetKeepOverlays(true);
uint16_t *pixels = (uint16_t *)fh1->GetImageDataRaw();
int lgt = fh1->GetImageDataRawSize();
-
+
if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Pixels read as expected : length = " << lgt << std::endl;
-
+ std::cout << "Pixels read as expected : length = " << lgt << std::endl;
+
// ============================================================
// Prepare the stuff
// ============================================================
-
- uint8_t *tabPixels = new uint8_t[nx*ny]; // uint8 is enought to hold 1 bit !
-
- uint16_t currentOvlGroup = 0x6000;
+
+ unsigned int nx = f->GetXSize();
+ unsigned int ny = f->GetYSize();
+ unsigned int nxy=nx*ny;
+ uint16_t currentOvlGroup;
+ int i;
+
+ std::ostringstream str;
+
+ uint8_t *outputData = new uint8_t[nxy]; // uint8 is enought to hold 1 bit !
+
std::string strOvlBitPosition;
int ovlBitPosition;
uint16_t mask;
- int i = 0;
uint16_t overlayLocation;
- std::ostringstream str;
-
std::string strOverlayLocation;
-
+
GDCM_NAME_SPACE::File *fileToBuild = 0;
GDCM_NAME_SPACE::FileHelper *fh = 0;
// ============================================================
-// Get each overlay Bit into an image
+// Get each overlay Bit into the image
// ============================================================
- for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
+ for(i=0, currentOvlGroup=0x6000; i<32; i+=2 ,currentOvlGroup+=2)
{
if ( (strOvlBitPosition = f->GetEntryString(currentOvlGroup, 0x0102))
== GDCM_NAME_SPACE::GDCM_UNFOUND )
continue;
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Current Overlay Group " << std::hex << currentOvlGroup
+
+ if( GDCM_NAME_SPACE::Debug::GetWarningFlag() )
+ std::cout << "Current Overlay Group " << std::hex << currentOvlGroup
<< " OvlBitPosition " << strOvlBitPosition << std::endl;
-
+
strOverlayLocation = f->GetEntryString(currentOvlGroup, 0x0200);
if ( strOverlayLocation != GDCM_NAME_SPACE::GDCM_UNFOUND )
{
continue;
}
}
+
+ // ============================================================
+ // DICOM Overlay Image data generation
+ // ============================================================
+
ovlBitPosition = atoi(strOvlBitPosition.c_str());
mask = 1 << ovlBitPosition;
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Mask :[" <<std::hex << mask << "]" << std::endl;
- for (int j=0; j<nx*ny ; j++)
+
+ if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
+ std::cout << "Mask :[" <<std::hex << mask << "]" << std::endl;
+ for (int j=0; j<nxy; j++)
{
if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
if (pixels[j] >= 0x1000)// if it contains at least one overlay bit
printf("%d : %04x\n",j, pixels[j]);
if ( (pixels[j] & mask) == 0 )
- tabPixels[j] = 0;
+ outputData[j] = 0;
else
- tabPixels[j] = 128;
+ outputData[j] = 128;
}
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "About to built empty file" << std::endl;
+ // ============================================================
+ // Write a new file
+ // ============================================================
fileToBuild = GDCM_NAME_SPACE::File::New();
-
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "Finish to built empty file" << std::endl;
-
str.str("");
str << nx;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0011); // Columns
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0011, "US"); // Columns
str.str("");
str << ny;
- fileToBuild->InsertEntryString(str.str(),0x0028,0x0010); // Rows
+ fileToBuild->InsertEntryString(str.str(),0x0028,0x0010, "US"); // Rows
- fileToBuild->InsertEntryString("8",0x0028,0x0100); // Bits Allocated
- fileToBuild->InsertEntryString("8",0x0028,0x0101); // Bits Stored
- fileToBuild->InsertEntryString("7",0x0028,0x0102); // High Bit
- fileToBuild->InsertEntryString("0",0x0028,0x0103); // Pixel Representation
- fileToBuild->InsertEntryString("1",0x0028,0x0002); // Samples per Pixel
+ fileToBuild->InsertEntryString("8",0x0028,0x0100, "US"); // Bits Allocated
+ fileToBuild->InsertEntryString("8",0x0028,0x0101, "US"); // Bits Stored
+ fileToBuild->InsertEntryString("7",0x0028,0x0102, "US"); // High Bit
+ fileToBuild->InsertEntryString("0",0x0028,0x0103, "US"); // Pixel Representation
+ fileToBuild->InsertEntryString("1",0x0028,0x0002, "US"); // Samples per Pixel
+ fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004, "LO");
- fileToBuild->InsertEntryString("MONOCHROME2 ",0x0028,0x0004);
+ // feel free to add any field (Dicom Data Entry) you like, here.
+ // ...
// Other mandatory fields will be set automatically,
// just before Write(), by FileHelper::CheckMandatoryElements()
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "-------------About to built FileHelper" << std::endl;
-
fh = GDCM_NAME_SPACE::FileHelper::New(fileToBuild);
- if( GDCM_NAME_SPACE::Debug::GetDebugFlag() )
- std::cout << "-------------Finish to built FileHelper" << std::endl;
-
- fh->SetImageData(tabPixels,nx*ny);
+ fh->SetImageData(outputData,nx*ny);
fh->SetWriteTypeToDcmExplVR();
std::ostringstream tmp;
{
std::cout << "Failed\n"
<< "File [" << str.str() << "] is unwrittable" << std::endl;
- /*
- fh->Delete();
- if (fileToBuild)
- fileToBuild->Delete();
- delete pixels;
- delete tabPixels;
- return 0;
- */
}
else
{
std::cout << "File written successfully [" << str.str() << "]" << std::endl;
}
- }
-
+
+ } // end on loop on 60xx
+
if (f)
fh->Delete();
if (fileToBuild)
fileToBuild->Delete();
f->Delete();
delete pixels;
- delete tabPixels;
+ delete outputData;
return 0;
}
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff