Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2007/08/21 12:51:09 $
- Version: $Revision: 1.120 $
+ Date: $Date: 2007/10/25 07:52:59 $
+ Version: $Revision: 1.136 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmDocEntryArchive.h"
#include "gdcmDictSet.h"
#include "gdcmOrientation.h"
-
+
+
+
+#include <algorithm> // for transform?
+
#if defined(__BORLANDC__)
- #include <mem.h> // for memset
+ #include <mem.h> // for memset
+ #include <ctype.h> //for toupper
+ #include <math.h>
#endif
#include <fstream>
// to get the pixels, user needs a gdcm::FileHelper
gdcm::FileHelper *fh = new gdcm::FileHelper(f);
+
// user may ask not to convert Palette (if any) to RGB
uint8_t *pixels = fh->GetImageDataRaw();
int imageLength = fh->GetImageDataRawSize();
+
// He can now use the pixels, create a new image, ...
uint8_t *userPixels = ...
-To re-write the image, user re-uses the gdcm::FileHelper
+//To re-write the image, user re-uses the gdcm::FileHelper
+gdcm::File *fh = new gdcm::FileHelper();
-fh->SetImageData( userPixels, userPixelsLength);
fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
// (WriteMode is set)
fh->SetPhotometricInterpretationToMonochrome1();
fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
- // Little Endian is the default
- // no other value is allowed
+ // Little Endian is the default,
+ // bigendian not supported for writting
(-->SetWriteType(ExplicitVR);)
-->WriteType = ExplicitVR;
+fh->SetWriteTypeToJPEG(); // lossless compression
+fh->SetWriteTypeToJPEG2000(); // lossless compression
+
+fh->SetImageData( userPixels, userPixelsLength);
+or
+fh->SetUserData( userPixels, userPixelsLength); // this one performs compression, when required
+
fh->Write(newFileName); // overwrites the file, if any
-// or :
-fh->WriteDcmExplVR(newFileName);
-// ----------------------------- WARNING -------------------------
These lines will be moved to the document-to-be 'Developer's Guide'
WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
PhotometricInterpretation : MONOCHROME2 (0=black), MONOCHROME2 (0=white)
-
+fh->SetImageData( userPixels, userPixelsLength);
+or
+fh->SetUserData( userPixels, userPixelsLength);
+ PixelWriteConverter->SetUserData(inData, expectedSize);
+
+
fh->SetWriteMode(WMODE_RAW / WMODE_RGB)
fh->SetWriteType( ImplicitVR/ExplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000)
* not to deallocate its data before gdcm uses them (e.g. with
* the Write() method )
* @param inData user supplied pixel area (uint8_t* is just for the compiler.
- * user is allowed to pass any kind of pixelsn since the size is
+ * user is allowed to pass any kind of pixels since the size is
* given in bytes)
* @param expectedSize total image size, *in Bytes*
*/
void FileHelper::SetImageData(uint8_t *inData, size_t expectedSize)
{
PixelWriteConverter->SetUserData(inData, expectedSize);
+ /// \todo : shouldn't we call SetCompressJPEGUserData/SetCompressJPEG2000UserData
+ /// here, too?
}
/**
*/
void FileHelper::SetUserData(uint8_t *inData, size_t expectedSize)
{
+ // Shouldn't we move theese lines to FileHelper::Write()?
+/*
if( WriteType == JPEG2000 )
{
PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
{
PixelWriteConverter->SetUserData(inData, expectedSize);
}
+ */
+ // Just try!
+ PixelWriteConverter->SetUserData(inData, expectedSize);
}
/**
}
/**
- * \brief Access to the underlying \ref PixelReadConverter RGBA LUT
+ * \brief Access to the underlying PixelReadConverter RGBA LUT
*/
uint8_t* FileHelper::GetLutRGBA()
{
}
/**
- * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Number
+ * \brief Access to the underlying PixelReadConverter RGBA LUT Item Number
*/
int FileHelper::GetLutItemNumber()
{
}
/**
- * \brief Access to the underlying \ref PixelReadConverter RGBA LUT Item Size
+ * \brief Access to the underlying PixelReadConverter RGBA LUT Item Size
*/
int FileHelper::GetLutItemSize()
{
* @return false if write fails
*/
bool FileHelper::Write(std::string const &fileName)
-{
+{
CheckMandatoryElements(); //called once, here !
- bool flag = false;
- DocEntry *e;
switch(WriteType)
{
case ImplicitVR:
case Unknown: // should never happen; ExplicitVR is the default value
case ExplicitVR:
-
- // User should ask gdcm to write an image in Explicit VR mode
- // only when he is sure *all* the VR of *all* the DataElements is known.
- // i.e : when there are *only* Public Groups
- // or *all* the Shadow Groups are fully described in the relevant Shadow
- // Dictionnary
- // Let's just *dream* about it; *never* trust a user !
- // We turn to Implicit VR if at least the VR of one element is unknown.
- // Better we let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
-
-/*
- e = FileInternal->GetFirstEntry();
- while (e != 0)
- {
- if (e->GetVR() == " ")
- {
- SetWriteTypeToDcmImplVR();
- SetWriteFileTypeToImplicitVR();
- flag = true;
- break;
- }
- e = FileInternal->GetNextEntry();
- }
-
- if (!flag)
- {
- SetWriteFileTypeToExplicitVR();
- }
- break;
-*/
-
+ // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
SetWriteFileTypeToExplicitVR();
break;
// SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
- /// \todo FIXME : JPEG may be either ExplicitVR or ImplicitVR
+ /// \todo FIXME : JPEG/JPEG2000 may be either ExplicitVR or ImplicitVR
case JPEG:
SetWriteFileTypeToJPEG();
+ // was :
+ //PixelWriteConverter->SetCompressJPEGUserData(
+ // inData, expectedSize, FileInternal);
+ PixelWriteConverter->SetCompressJPEGUserData(
+ PixelWriteConverter->GetUserData(),
+ PixelWriteConverter->GetUserDataSize(),FileInternal);
break;
case JPEG2000:
+ /// \todo Maybe we should consider doing the compression here !
+ // PixelWriteConverter->SetCompressJPEG2000UserData(inData, expectedSize, FileInternal);
+
SetWriteFileTypeToJPEG2000();
+ PixelWriteConverter->SetCompressJPEG2000UserData(
+ PixelWriteConverter->GetUserData(),
+ PixelWriteConverter->GetUserDataSize(),
+ FileInternal);
break;
}
break;
}
- bool check = CheckWriteIntegrity(); // verifies length
+ bool check;
if (WriteType == JPEG || WriteType == JPEG2000)
check = true;
+ else
+ check = CheckWriteIntegrity(); // verifies length
if (check)
{
int numberBitsAllocated = FileInternal->GetBitsAllocated();
if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
{
- gdcmWarningMacro( "numberBitsAllocated changed from "
- << numberBitsAllocated << " to 16 "
+ gdcmWarningMacro( "numberBitsAllocated changed from "
+ << numberBitsAllocated << " to 16 "
<< " for consistency purpose" );
numberBitsAllocated = 16;
}
size_t decSize = FileInternal->GetXSize()
- * FileInternal->GetYSize()
+ * FileInternal->GetYSize()
* FileInternal->GetZSize()
* FileInternal->GetTSize()
* FileInternal->GetSamplesPerPixel()
if ( FileInternal->HasLUT() )
rgbSize = decSize * 3;
+ size_t userDataSize = PixelWriteConverter->GetUserDataSize();
switch(WriteMode)
{
case WMODE_RAW :
- if ( decSize!=PixelWriteConverter->GetUserDataSize() )
+ if ( abs((long)(decSize-userDataSize))>1) // ignore padding zero
{
gdcmWarningMacro( "Data size (Raw) is incorrect. Should be "
<< decSize << " / Found :"
- << PixelWriteConverter->GetUserDataSize() );
+ << userDataSize );
return false;
}
break;
case WMODE_RGB :
- if ( rgbSize!=PixelWriteConverter->GetUserDataSize() )
+ if ( abs((long)(rgbSize-userDataSize))>1) // ignore padding zero
{
gdcmWarningMacro( "Data size (RGB) is incorrect. Should be "
- << decSize << " / Found "
- << PixelWriteConverter->GetUserDataSize() );
+ << rgbSize << " / Found "
+ << userDataSize );
return false;
}
break;
* (modifies, when necessary, photochromatic interpretation,
* bits allocated, Pixels element VR)
* WARNING : if SetPhotometricInterpretationToMonochrome1() was called
- * before Pixel Elements if modified :-(
+ * before Pixel Elements is modified :-(
*/
void FileHelper::SetWriteToRaw()
{
vr = "OW";
if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
vr = "OB";
- // For non RAW data. Mainly JPEG
+ // For non RAW data. Mainly JPEG/JPEG2000
if( WriteType == JPEG || WriteType == JPEG2000)
{
vr = "OW";
PixelReadConverter->BuildRGBImage();
DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
- spp->SetString("3 ");
+ spp->SetString("3 "); // Don't drop trailing space
DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
- planConfig->SetString("0 ");
+ planConfig->SetString("0 "); // Don't drop trailing space
DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
- photInt->SetString("RGB ");
+ photInt->SetString("RGB "); // Don't drop trailing space
if ( PixelReadConverter->GetRGB() )
{
-4) user modified/added some tags *without processing* the pixels (anonymization...)
UNMODIFIED_PIXELS_IMAGE
-Probabely some more to be added.
+ --> Set it with FileHelper::SetContentType(int);
gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
--> 'Referenced SOP Instance UID' (0x0008, 0x1155)
whose value is the original 'SOP Class UID'
-3) TODO : find a trick to allow user to pass to the writter the list of the Dicom images
+3) TO DO : find a trick to allow user to pass to the writter the list of the Dicom images
or the Series, (or the Study ?) he used to created his image
(MIP, MPR, cartography image, ...)
These info should be stored (?)
// --------------------- For DataSet ---------------------
+ // check whether 0018|0015 [CS] [Body Part Examined] value is UPPER CASE
+ // (avoid dciodvfy to complain!)
+ DataEntry *e_0018_0015 = FileInternal->GetDataEntry(0x0018, 0x0015);
+ if ( e_0018_0015)
+ {
+ std::string bodyPartExamined = e_0018_0015->GetString();
+ std::transform(bodyPartExamined.begin(), bodyPartExamined.end(), bodyPartExamined.begin(),
+ (int(*)(int)) toupper);
+ CopyMandatoryEntry(0x0018,0x0015,bodyPartExamined,"CS");
+ }
+
if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
{
-
- gdcmDebugMacro( "USER_OWN_IMAGE (1)");
- // If 'SOP Class UID' exists ('true DICOM' image)
+ // If 'SOP Class UID' and 'SOP Instance UID' exist ('true DICOM' image)
// we create the 'Source Image Sequence' SeqEntry
// to hold informations about the Source Image
-
+
+ // 'SOP Instance UID'
DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
- if ( e_0008_0016 )
+ //
+ DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
+ if ( e_0008_0016 && e_0008_0018)
{
- // Create 'Source Image Sequence' SeqEntry
-// SeqEntry *sis = SeqEntry::New (
-// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
- SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
- SQItem *sqi = SQItem::New(1);
- // (we assume 'SOP Instance UID' exists too)
- // create 'Referenced SOP Class UID'
-// DataEntry *e_0008_1150 = DataEntry::New(
-// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
- DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
- e_0008_1150->SetString( e_0008_0016->GetString());
- sqi->AddEntry(e_0008_1150);
- e_0008_1150->Delete();
+ // Create 'Source Image Sequence' SeqEntry
+ SeqEntry *sis = SeqEntry::New (0x0008, 0x2112);
+ SQItem *sqi = SQItem::New(1);
- // create 'Referenced SOP Instance UID'
- DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
-// DataEntry *e_0008_1155 = DataEntry::New(
-// Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
- DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
- e_0008_1155->SetString( e_0008_0018->GetString());
- sqi->AddEntry(e_0008_1155);
- e_0008_1155->Delete();
-
- sis->AddSQItem(sqi,1);
- sqi->Delete();
-
- // temporarily replaces any previous 'Source Image Sequence'
- Archive->Push(sis);
- sis->Delete();
-
- // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
- if ( ContentType == FILTERED_IMAGE)
- // the user *knows* he just modified the pixels
- // the image is no longer an 'Original' one
- CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
+ // create 'Referenced SOP Class UID' from 'SOP Class UID'
+
+ DataEntry *e_0008_1150 = DataEntry::New(0x0008, 0x1150, "UI");
+ e_0008_1150->SetString( e_0008_0016->GetString());
+ sqi->AddEntry(e_0008_1150);
+ e_0008_1150->Delete();
+
+ // create 'Referenced SOP Instance UID' from 'SOP Instance UID'
+ // DataEntry *e_0008_0018 = FileInternal->GetDataEntry(0x0008, 0x0018);
+
+ DataEntry *e_0008_1155 = DataEntry::New(0x0008, 0x1155, "UI");
+ e_0008_1155->SetString( e_0008_0018->GetString());
+ sqi->AddEntry(e_0008_1155);
+ e_0008_1155->Delete();
+
+ sis->AddSQItem(sqi,1);
+ sqi->Delete();
+
+ // temporarily replaces any previous 'Source Image Sequence'
+ Archive->Push(sis);
+ sis->Delete();
+ // FIXME : is 'Image Type' *really* depending on the presence of 'SOP Class UID'?
+
+ if ( ContentType == FILTERED_IMAGE) // the user *knows* he just modified the pixels
+ {
+ DataEntry *e_0008_0008 = FileInternal->GetDataEntry(0x0008, 0x0008);
+ if ( e_0008_0008)
+ {
+ std::string imageType = e_0008_0008->GetString();
+ std::string::size_type p = imageType.find("ORIGINAL");
+ if (p == 0) // image is ORIGINAL one
+ {
+ // the image is no longer an 'Original' one
+ CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
+ }
+ // if Image Type was not ORIGINAL\..., we keep it.
+ }
+ else // 0008_0008 was missing, wee add it.
+ {
+ CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY","CS");
+ }
+ }
}
}
}
}
- std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
- if ( pixelSpacing == GDCM_UNFOUND )
+ std::string pixelAspectRatio = FileInternal->GetEntryString(0x0028,0x0034);
+ if ( pixelAspectRatio == GDCM_UNFOUND ) // avoid conflict with pixelSpacing !
{
- pixelSpacing = "1.0\\1.0";
- // if missing, Pixel Spacing forced to "1.0\1.0"
- CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
- }
-
- // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
- // --> This one is the *legal* one !
- if ( ContentType != USER_OWN_IMAGE)
- // we write it only when we are *sure* the image comes from
- // an imager (see also 0008,0x0064)
- CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
-
+ std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
+ if ( pixelSpacing == GDCM_UNFOUND )
+ {
+ pixelSpacing = "1.0\\1.0";
+ // if missing, Pixel Spacing forced to "1.0\1.0"
+ CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
+ }
+
+ // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
+ // --> This one is the *legal* one !
+ if ( ContentType != USER_OWN_IMAGE)
+ // we write it only when we are *sure* the image comes from
+ // an imager (see also 0008,0x0064)
+ CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
+ }
/*
///Exact meaning of RETired fields
PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
Archive = new DocEntryArchive( FileInternal );
+
+ KeepOverlays = false;
}
/**
/* Probabely something to be added to use Rescale Slope/Intercept
-Have a look ,at ITK code !
+Have a look at ITK code !
// Internal function to rescale pixel according to Rescale Slope/Intercept
template<class TBuffer, class TSource>
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff