Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2006/02/16 21:27:41 $
- Version: $Revision: 1.94 $
+ Date: $Date: 2007/08/28 09:29:26 $
+ Version: $Revision: 1.123 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmSeqEntry.h"
#include "gdcmSQItem.h"
#include "gdcmDataEntry.h"
+#include "gdcmDocEntry.h"
#include "gdcmFile.h"
#include "gdcmPixelReadConvert.h"
#include "gdcmPixelWriteConvert.h"
#include "gdcmDocEntryArchive.h"
#include "gdcmDictSet.h"
#include "gdcmOrientation.h"
-
+
#if defined(__BORLANDC__)
#include <mem.h> // for memset
#endif
// user may also decide he doesn't want to load some parts of the header
gdcm::File *f = new gdcm::File();
f->SetFileName(fileName);
- f->SetLoadMode(LD_NOSEQ); // or
- f->SetLoadMode(LD_NOSHADOW); // or
+ f->SetLoadMode(LD_NOSEQ); // or
+ f->SetLoadMode(LD_NOSHADOW); // or
f->SetLoadMode(LD_NOSEQ | LD_NOSHADOW); // or
f->SetLoadMode(LD_NOSHADOWSEQ);
f->Load();
+// To decide whether it's an 'image of interest for him, or not,
// user can now check some values
std::string v = f->GetEntryValue(groupNb,ElementNb);
// to get the pixels, user needs a gdcm::FileHelper
gdcm::FileHelper *fh = new gdcm::FileHelper(f);
-// user may ask not to convert Palette to RGB
+
+// 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->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
- // Little Endian is the default
- // no other value is allowed
+ // (WriteMode is set)
+
+// If user wants to write the file as MONOCHROME1 (0=white)
+fh->SetPhotometricInterpretationToMonochrome1();
+
+fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
+ // 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'
WriteMode : WMODE_RAW / WMODE_RGB
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)
-fh1->Write(newFileName);
- SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR();
- (modifies TransferSyntax)
+fh->SetWriteType( ImplicitVR/ExplicitVR/ACR/ACR_LIBIDO/JPEG/JPEG2000)
+
+fh->Write(newFileName);
+ CheckMandatoryElements(); // Checks existing ones / Add missing ones
+ Fix VR if unknown elements
+ SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR(); /
+ SetWriteFileTypeToACR() / SetWriteFileTypeToJPEG() / SetWriteFileTypeToJ2K()
+ (Modifies TransferSyntax if any; Pushes to the Archives old one)
SetWriteToRaw(); / SetWriteToRGB();
- (modifies, when necessary : photochromatic interpretation,
- samples per pixel, Planar configuration,
- bits allocated, bits stored, high bit -ACR 24 bits-
- Pixels element VR, pushes out the LUT )
+ (Modifies and pushes to the Archive, when necessary : photochr. interp.,
+ samples per pixel, Planar configuration,
+ bits allocated, bits stored, high bit -ACR 24 bits-
+ Pixels element VR, pushes out the LUT )
+ SetWriteToRaw()
+ Sets Photometric Interpretation
+ DataEntry *pixel =CopyDataEntry(7fe0,0010,VR)
+ Sets VR, BinArea, Length for PixelData
+ if MONOCHROME1
+ ConvertFixGreyLevels
+ Archive->Push(photInt);
+ Archive->Push(pixel);
+ photInt->Delete();
+ pixel->Delete();
+ SetWriteToRGB()
+ if NumberOfScalarComponents==1
+ SetWriteToRaw(); return;
+ PixelReadConverter->BuildRGBImage()
+ DataEntry *pixel =CopyDataEntry(7fe0,0010,VR)
+ Archives spp, planConfig,photInt, pixel
+ Pushes out any LUT
CheckWriteIntegrity();
(checks user given pixels length)
FileInternal->Write(fileName,WriteType)
- fp = opens file(fileName);
- ComputeGroup0002Length( );
- BitsAllocated 12->16
- RemoveEntry(palettes, etc)
+ fp = opens file(fileName); // out|binary
+ ComputeGroup0002Length( );
Document::WriteContent(fp, writetype);
+ writes Dicom File Preamble not ACR-NEMA
+ ElementSet::WriteContent(fp, writetype);
+ writes recursively all DataElements
RestoreWrite();
- (moves back to the File all the archived elements)
- RestoreWriteFileType();
- (pushes back group 0002, with TransferSyntax)
+ (moves back to the gdcm::File all the archived elements)
*/
-namespace gdcm
+namespace GDCM_NAME_SPACE
{
typedef std::map<uint16_t, int> GroupHT; // Hash Table
//-------------------------------------------------------------------------
}
/**
- * \brief Accesses an existing DataEntry through it's (group, element)
- * and modifies it's content with the given value.
+ * \brief Accesses an existing DataEntry through its (group, element)
+ * and modifies its content with the given value.
* @param content new value (string) to substitute with
* @param group group number of the Dicom Element to modify
* @param elem element number of the Dicom Element to modify
/**
- * \brief Accesses an existing DataEntry through it's (group, element)
- * and modifies it's content with the given value.
+ * \brief Accesses an existing DataEntry through its (group, element)
+ * and modifies its content with the given value.
* @param content new value (void* -> uint8_t*) to substitute with
* @param lgth new value length
* @param group group number of the Dicom Element to modify
* @param content (string) value to be set
* @param group Group number of the Entry
* @param elem Element number of the Entry
+ * @param vr Value Representation of the DataElement to be inserted
* \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryString(std::string const &content,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
- return FileInternal->InsertEntryString(content, group, elem);
+ return FileInternal->InsertEntryString(content, group, elem, vr);
}
/**
* \brief Modifies the value of a given DataEntry when it exists.
* Creates it with the given value when unexistant.
* A copy of the binArea is made to be kept in the Document.
- * @param binArea (binary)value to be set
+ * @param binArea (binary) value to be set
* @param lgth new value length
* @param group Group number of the Entry
* @param elem Element number of the Entry
+ * @param vr Value Representation of the DataElement to be inserted
* \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem,
+ VRKey const &vr )
{
- return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem);
+ return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem, vr);
}
/**
return GetRaw();
}
-#ifndef GDCM_LEGACY_REMOVE
+//#ifndef GDCM_LEGACY_REMOVE
/*
* \brief Useless function, since PixelReadConverter forces us
* copy the Pixels anyway.
* @return On success, the number of bytes actually copied. Zero on
* failure e.g. MaxSize is lower than necessary.
*/
+ /*
size_t FileHelper::GetImageDataIntoVector (void *destination, size_t maxSize)
{
if ( ! GetRaw() )
PixelReadConverter->GetRawSize() );
return PixelReadConverter->GetRawSize();
}
-#endif
+*/
+//#endif
/**
* \brief Points the internal pointer to the callers inData
* 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)
{
- SetUserData(inData, 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);
+ }
+ else if( WriteType == JPEG )
+ {
+ PixelWriteConverter->SetCompressJPEGUserData(inData, expectedSize, FileInternal);
+ }
+ else
+ {
+ PixelWriteConverter->SetUserData(inData, expectedSize);
+ }
+ */
+ // Just try!
PixelWriteConverter->SetUserData(inData, expectedSize);
}
* @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:
SetWriteFileTypeToImplicitVR();
break;
+
case Unknown: // should never happen; ExplicitVR is the default value
case ExplicitVR:
+
+ // We let DocEntry::WriteContent to put vr=UN for undocumented Shadow Groups !
SetWriteFileTypeToExplicitVR();
- break;
+
+ break;
case ACR:
case ACR_LIBIDO:
// NOTHING is done here just for LibIDO.
// (shame on him !)
// We add Recognition Code (RET)
if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
- FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010);
+ FileInternal->InsertEntryString("ACR-NEMA V1.0 ",
+ 0x0008, 0x0010, "LO");
SetWriteFileTypeToACR();
// SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
+
+ /// \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;
}
- CheckMandatoryElements();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
break;
}
- bool check = CheckWriteIntegrity(); // verifies length
- if (WriteType == JPEG ) check = true;
+ bool check;
+ if (WriteType == JPEG || WriteType == JPEG2000)
+ check = true;
+ else
+ check = CheckWriteIntegrity(); // verifies length
+
if (check)
{
check = FileInternal->Write(fileName,WriteType);
}
RestoreWrite();
- RestoreWriteFileType();
- RestoreWriteMandatory();
+ // RestoreWriteFileType();
+ // RestoreWriteMandatory();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//-----------------------------------------------------------------------------
// Protected
/**
- * \brief Checks the write integrity
- *
- * The tests made are :
- * - verify the size of the image to write with the possible write
- * when the user set an image data
+ * \brief Verifies the size of the user given PixelData
* @return true if check is successfull
*/
bool FileHelper::CheckWriteIntegrity()
size_t decSize = FileInternal->GetXSize()
* FileInternal->GetYSize()
* FileInternal->GetZSize()
+ * FileInternal->GetTSize()
* FileInternal->GetSamplesPerPixel()
* ( numberBitsAllocated / 8 );
size_t rgbSize = decSize;
break;
}
}
-
return true;
}
* \brief Updates the File to write RAW data (as opposed to RGB data)
* (modifies, when necessary, photochromatic interpretation,
* bits allocated, Pixels element VR)
+ * WARNING : if SetPhotometricInterpretationToMonochrome1() was called
+ * before Pixel Elements is modified :-(
*/
void FileHelper::SetWriteToRaw()
{
}
else
{
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ // 0x0028,0x0004 : Photometric Interpretation
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
if (FileInternal->HasLUT() )
{
photInt->SetString("PALETTE COLOR ");
}
else
{
- photInt->SetString("MONOCHROME2 ");
+ if (GetPhotometricInterpretation() == 2)
+ photInt->SetString("MONOCHROME2 "); // 0 = Black
+ else
+ photInt->SetString("MONOCHROME1 "); // 0 = White !
}
PixelWriteConverter->SetReadData(PixelReadConverter->GetRaw(),
vr = "OW";
if ( FileInternal->GetBitsAllocated()==24 ) // For RGB ACR files
vr = "OB";
+ // For non RAW data. Mainly JPEG/JPEG2000
+ if( WriteType == JPEG || WriteType == JPEG2000)
+ {
+ vr = "OW";
+ }
+
DataEntry *pixel =
CopyDataEntry(GetFile()->GetGrPixel(),GetFile()->GetNumPixel(),vr);
pixel->SetFlag(DataEntry::FLAG_PIXELDATA);
pixel->SetBinArea(PixelWriteConverter->GetData(),false);
- pixel->SetLength(PixelWriteConverter->GetDataSize());
+ pixel->SetLength(
+ static_cast< uint32_t >(PixelWriteConverter->GetDataSize()) );
+
+ if (!FileInternal->HasLUT() && GetPhotometricInterpretation() == 1)
+ {
+ ConvertFixGreyLevels( pixel->GetBinArea(), pixel->GetLength() );
+ }
Archive->Push(photInt);
Archive->Push(pixel);
{
PixelReadConverter->BuildRGBImage();
- DataEntry *spp = CopyDataEntry(0x0028,0x0002);
- spp->SetString("3 ");
+ DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
+ spp->SetString("3 "); // Don't drop trailing space
- DataEntry *planConfig = CopyDataEntry(0x0028,0x0006);
- planConfig->SetString("0 ");
+ DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
+ planConfig->SetString("0 "); // Don't drop trailing space
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
- photInt->SetString("RGB ");
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
+ photInt->SetString("RGB "); // Don't drop trailing space
if ( PixelReadConverter->GetRGB() )
{
// samples per pixels = 1 (in the read file)
if ( FileInternal->GetBitsAllocated()==24 )
{
- DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100);
+ DataEntry *bitsAlloc = CopyDataEntry(0x0028,0x0100,"US");
bitsAlloc->SetString("8 ");
- DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101);
+ DataEntry *bitsStored = CopyDataEntry(0x0028,0x0101,"US");
bitsStored->SetString("8 ");
- DataEntry *highBit = CopyDataEntry(0x0028,0x0102);
+ DataEntry *highBit = CopyDataEntry(0x0028,0x0102,"US");
highBit->SetString("7 ");
Archive->Push(bitsAlloc);
{
Archive->Restore(0x0028,0x0002);
Archive->Restore(0x0028,0x0004);
+
Archive->Restore(0x0028,0x0006);
Archive->Restore(GetFile()->GetGrPixel(),GetFile()->GetNumPixel());
// For the Palette Color Lookup Table UID
Archive->Restore(0x0028,0x1203);
-
// group 0002 may be pushed out for ACR-NEMA writting purposes
Archive->Restore(0x0002,0x0000);
Archive->Restore(0x0002,0x0001);
Archive->Restore(0x0002,0x0016);
Archive->Restore(0x0002,0x0100);
Archive->Restore(0x0002,0x0102);
+
}
/**
Archive->Push(0x0002,0x0102);
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'JPEG2000'
+ */
+void FileHelper::SetWriteFileTypeToJPEG2000()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::JPEG2000Lossless) );
+
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
+ tss->SetString(ts);
+
+ Archive->Push(tss);
+ tss->Delete();
+}
+
/**
* \brief Sets in the File the TransferSyntax to 'JPEG'
- */
+ */
void FileHelper::SetWriteFileTypeToJPEG()
{
- std::string ts = Util::DicomString(
- Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGLosslessProcess14_1) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
Archive->Push(tss);
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ExplicitVRLittleEndian) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
-
Archive->Push(tss);
tss->Delete();
}
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::ImplicitVRLittleEndian) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
-
Archive->Push(tss);
tss->Delete();
}
-
-/**
- * \brief Restore in the File the initial group 0002
- */
-void FileHelper::RestoreWriteFileType()
-{
-}
-
/**
* \brief Set the Write not to Libido format
*/
{
std::string rows, columns;
- DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
- DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
+ DataEntry *newRow=DataEntry::New(0x0028, 0x0010, "US");
+ DataEntry *newCol=DataEntry::New(0x0028, 0x0011, "US");
newRow->Copy(oldCol);
newCol->Copy(oldRow);
newCol->Delete();
}
- DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
Archive->Push(libidoCode);
libidoCode->Delete();
{
if ( recCode->GetString() == "ACRNEMA_LIBIDO_1.1" )
{
- DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
+ DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010,"LO");
libidoCode->SetString("");
Archive->Push(libidoCode);
libidoCode->Delete();
* @param group Group number of the Entry
* @param elem Element number of the Entry
* @param vr Value Representation of the Entry
- * FIXME : what is it used for?
* \return pointer to the new Bin Entry (NULL when creation failed).
*/
DataEntry *FileHelper::CopyDataEntry(uint16_t group, uint16_t elem,
- const TagName &vr)
+ const VRKey &vr)
{
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
DataEntry *newE;
if ( oldE )
{
- newE = DataEntry::New(oldE->GetDictEntry());
+ newE = DataEntry::New(group, elem, vr);
newE->Copy(oldE);
}
else
To be moved to User's guide / WIKI ?
We have to deal with 4 *very* different cases :
--1) user created ex nihilo his own image and wants to write it as a Dicom image.
+-1) user created ex nihilo his own image and wants to write it as a Dicom image.
+ USER_OWN_IMAGE
-2) user modified the pixels of an existing image.
--3) user created a new image, using existing images (eg MIP, MPR, cartography image)
--4) user anonymized an image without processing the pixels.
-
+ FILTERED_IMAGE
+-3) user created a new image, using a set of existing images (eg MIP, MPR, cartography image)
+ CREATED_IMAGE
+-4) user modified/added some tags *without processing* the pixels (anonymization...)
+ UNMODIFIED_PIXELS_IMAGE
+-Probabely some more to be added.
+
gdcm::FileHelper::CheckMandatoryElements() deals automatically with these cases.
1)2)3)4)
keeping the same 'Serie Instance UID' / 'Study Instance UID' for various images
Warning :
The user shouldn't add any image to a 'Manufacturer Serie'
- but there is no way no to allowed him to do that
+ but there is no way no to allow him to do that
None of the 'shadow elements' are droped out.
1)
-'Modality' (0x0008,0x0060) is defaulted to "OT" (other) if missing.
'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
-'Study Date', 'Study Time' are defaulted to current Date and Time.
-1)2)3)
+1)3)
'Media Storage SOP Class UID' (0x0002,0x0002)
'SOP Class UID' (0x0008,0x0016) are set to
[Secondary Capture Image Storage]
0008 1115 SQ 1 Referenced Series Sequence
0008 1140 SQ 1 Referenced Image Sequence
-4) When user *knows* he didn't modified the pixels, he may ask the writer to keep some
-informations unchanged :
+4) When user *knows* he didn't modified the pixels, we keep some informations unchanged :
'Media Storage SOP Class UID' (0x0002,0x0002)
'SOP Class UID' (0x0008,0x0016)
'Image Type' (0x0008,0x0008)
'Conversion Type' (0x0008,0x0064)
-He has to use gdcm::FileHelper::SetKeepMediaStorageSOPClassUID(true)
-(probabely name has to be changed)
Bellow follows the full description (hope so !) of the consistency checks performed
-->'Media Storage SOP Class UID' (0x0002,0x0002)
--->'SOP Class UID' (0x0008,0x0016) are set to
+-->'SOP Class UID' (0x0008,0x0016) are defaulted to
[Secondary Capture Image Storage]
- (Potentialy, the image was modified by user, and post-processed;
- it's no longer a 'native' image)
- Except if user told he wants to keep MediaStorageSOPClassUID,
- when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
-
--> 'Image Type' (0x0008,0x0008)
is forced to "DERIVED\PRIMARY"
(The written image is no longer an 'ORIGINAL' one)
- Except if user told he wants to keep MediaStorageSOPClassUID,
- when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
+ Except if user knows he didn't modify the image (e.g. : he just anonymized the file)
--> Conversion Type (0x0008,0x0064)
- is forced to 'SYN' (Synthetic Image)
- Except if user told he wants to keep MediaStorageSOPClassUID,
- when *he* knows he didn't modify the image (e.g. : he just anonymized the file)
+ is defaulted to 'SYN' (Synthetic Image)
+ when *he* knows he created his own image ex nihilo
--> 'Modality' (0x0008,0x0060)
is defaulted to "OT" (other) if missing.
--> Patient ID, Patient's Birth Date, Patient's Sex, (Type 2)
--> Referring Physician's Name (Type 2)
- are created, with empty value if there are missing.
+ are created, with empty value if there are missing.
-------------------------------------------------------------------------------------*/
{
std::string sop = Util::CreateUniqueUID();
+ // --------------------- For Meta Elements ---------------------
// just to remember : 'official' 0002 group
if ( WriteType != ACR && WriteType != ACR_LIBIDO )
{
//0002 0000 UL 1 Meta Group Length
//0002 0001 OB 1 File Meta Information Version
- //0002 0002 UI 1 Media Stored SOP Class UID
- //0002 0003 UI 1 Media Stored SOP Instance UID
+ //0002 0002 UI 1 Media Storage SOP Class UID
+ //0002 0003 UI 1 Media Storage SOP Instance UID
//0002 0010 UI 1 Transfer Syntax UID
//0002 0012 UI 1 Implementation Class UID
//0002 0013 SH 1 Implementation Version Name
//0002 0016 AE 1 Source Application Entity Title
//0002 0100 UI 1 Private Information Creator
//0002 0102 OB 1 Private Information
-
+
+ // Push out 'ACR-NEMA-special' entries, if any
+ Archive->Push(0x0008,0x0001); // Length to End
+ Archive->Push(0x0008,0x0010); // Recognition Code
+ Archive->Push(0x0028,0x0005); // Image Dimension
+
// Create them if not found
// Always modify the value
// Push the entries to the archive.
- CopyMandatoryEntry(0x0002,0x0000,"0");
+ CopyMandatoryEntry(0x0002,0x0000,"0","UL");
DataEntry *e_0002_0001 = CopyDataEntry(0x0002,0x0001, "OB");
e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
Archive->Push(e_0002_0001);
e_0002_0001->Delete();
- if ( KeepMediaStorageSOPClassUID)
- // It up to the use to *know* whether he modified the pixels or not.
- // he is allowed to keep the original 'Media Storage SOP Class UID'
- CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
+ if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
+ {
+ // we keep the original 'Media Storage SOP Class UID', we default it if missing
+ CheckMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
else
- // Potentialy this is a post-processed image
+ {
+ // It's *not* an image comming straight from a source. We force
// 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
- CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
+ CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
+
+ // 'Media Storage SOP Instance UID'
+ CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
- // 'Media Storage SOP Instance UID'
- CopyMandatoryEntry(0x0002,0x0003,sop);
-
// 'Implementation Class UID'
// FIXME : in all examples we have, 0x0002,0x0012 is not so long :
// seems to be Root UID + 4 digits (?)
- CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
+ CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID(),"UI");
// 'Implementation Version Name'
std::string version = "GDCM ";
version += Util::GetVersion();
- CopyMandatoryEntry(0x0002,0x0013,version);
+ CopyMandatoryEntry(0x0002,0x0013,version,"SH");
}
+ // --------------------- For DataSet ---------------------
+
+ 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)
+ // we create the 'Source Image Sequence' SeqEntry
+ // to hold informations about the Source Image
+
+ DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
+ if ( e_0008_0016 )
+ {
+ // 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 '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");
+ }
+ }
+
+ if ( ContentType == FILTERED_IMAGE || ContentType == UNMODIFIED_PIXELS_IMAGE)
+ {
+ // we keep the original 'Media Storage SOP Class UID', we default it if missing (it should be present !)
+ CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7","UI");
+ }
+ else
+ {
+ // It's *not* an image comming straight from a source. We force
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7", "UI");
+ }
+
+ Archive->Push(0x0028,0x005); // [Image Dimensions (RET)
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
Archive->Push(0x0028,0x0016);
Archive->Push(0x0028,0x0017);
- Archive->Push(0x0028,0x00199);
+ Archive->Push(0x0028,0x0198); // very old versions
+ Archive->Push(0x0028,0x0199);
+
+ // Replace deprecated 0028 0012 US Planes
+ // by new 0028 0008 IS Number of Frames
+
+ ///\todo : find if there is a rule!
+ DataEntry *e_0028_0012 = FileInternal->GetDataEntry(0x0028, 0x0012);
+ if ( e_0028_0012 )
+ {
+ CopyMandatoryEntry(0x0028, 0x0008,e_0028_0012->GetString(),"IS");
+ Archive->Push(0x0028,0x0012);
+ }
// Deal with the pb of (Bits Stored = 12)
// - we're gonna write the image as Bits Stored = 16
if ( FileInternal->GetEntryString(0x0028,0x0100) == "12")
{
- CopyMandatoryEntry(0x0028,0x0100,"16");
+ CopyMandatoryEntry(0x0028,0x0100,"16","US");
}
// Check if user wasn't drunk ;-)
std::ostringstream s;
// check 'Bits Allocated' vs decent values
int nbBitsAllocated = FileInternal->GetBitsAllocated();
- if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
+ if ( (nbBitsAllocated == 0 || nbBitsAllocated > 32)
+ || ( nbBitsAllocated > 8 && nbBitsAllocated <16) )
{
- CopyMandatoryEntry(0x0028,0x0100,"16");
+ CopyMandatoryEntry(0x0028,0x0100,"16","US");
gdcmWarningMacro("(0028,0100) changed from "
<< nbBitsAllocated << " to 16 for consistency purpose");
nbBitsAllocated = 16;
{
s.str("");
s << nbBitsAllocated;
- CopyMandatoryEntry(0x0028,0x0101,s.str());
+ CopyMandatoryEntry(0x0028,0x0101,s.str(),"US");
gdcmWarningMacro("(0028,0101) changed from "
<< nbBitsStored << " to " << nbBitsAllocated
<< " for consistency purpose" );
{
s.str("");
s << nbBitsStored - 1;
- CopyMandatoryEntry(0x0028,0x0102,s.str());
+ CopyMandatoryEntry(0x0028,0x0102,s.str(),"US");
gdcmWarningMacro("(0028,0102) changed from "
<< highBitPosition << " to " << nbBitsAllocated-1
<< " for consistency purpose");
}
- std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
- if ( pixelSpacing == GDCM_UNFOUND )
+ // check Pixel Representation (default it as 0 -unsigned-)
+
+ DataEntry *e_0028_0103 = FileInternal->GetDataEntry(0x0028, 0x0103);
+ if ( !e_0028_0103 )
{
- pixelSpacing = "1.0\\1.0";
- // if missing, Pixel Spacing forced to "1.0\1.0"
- CopyMandatoryEntry(0x0028,0x0030,pixelSpacing);
+ gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be mandatory");
+ CopyMandatoryEntry(0x0028, 0x0103,"0","US");
+ }
+ else
+ {
+ int sign = (int)e_0028_0103->GetValue(0);
+ if (sign !=1 && sign !=0)
+ {
+ gdcmWarningMacro("PixelRepresentation (0028,0103) is supposed to be =1 or =0");
+ CopyMandatoryEntry(0x0028, 0x0103,"0","US");
+ }
}
-
- // 'Imager Pixel Spacing' : defaulted to 'Pixel Spacing'
- // --> This one is the *legal* one !
- // FIXME : we should write it only when we are *sure* the image comes from
- // an imager (see also 0008,0x0064)
- CheckMandatoryEntry(0x0018,0x1164,pixelSpacing);
-
- // Samples Per Pixel (type 1) : default to grayscale
- CheckMandatoryEntry(0x0028,0x0002,"1");
-
- // --- Check UID-related Entries ---
-
- // If 'SOP Class UID' exists ('true DICOM' image)
- // we create the 'Source Image Sequence' SeqEntry
- // to hold informations about the Source Image
- DataEntry *e_0008_0016 = FileInternal->GetDataEntry(0x0008, 0x0016);
- if ( e_0008_0016 )
+ std::string pixelAspectRatio = FileInternal->GetEntryString(0x0028,0x0034);
+ if ( pixelAspectRatio == GDCM_UNFOUND ) // avoid conflict with pixelSpacing !
{
- // Create 'Source Image Sequence' SeqEntry
- SeqEntry *sis = SeqEntry::New (
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(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) );
- e_0008_1150->SetString( e_0008_0016->GetString());
- sqi->AddEntry(e_0008_1150);
- e_0008_1150->Delete();
-
- // 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) );
- e_0008_1155->SetString( e_0008_0018->GetString());
- sqi->AddEntry(e_0008_1155);
- e_0008_1155->Delete();
+ 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
+
+// See page 73 of ACR-NEMA_300-1988.pdf !
+
+// 0020,0020 : Patient Orientation :
+Patient direction of the first row and
+column of the images. The first entry id the direction of the raws, given by the
+direction of the last pixel in the first row from the first pixel in tha row.
+the second entry is the direction of the columns, given by the direction of the
+last pixel in the first column from the first pixel in that column.
+L : Left, F : Feet, A : Anterior, P : Posterior.
+Up to 3 letters can be used in combination to indicate oblique planes.
+
+//0020,0030 Image Position (RET)
+x,y,z coordinates im mm of the first pixel in the image
+
+// 0020,0035 Image Orientation (RET)
+Direction cosines of the R axis of the image system with respect to the
+equipment coordinate axes x,y,z, followed by direction cosines of the C axis of
+the image system with respect to the same axes
+
+//0020,0050 Location
+An image location reference, standard for the modality (such as CT bed position),
+used to indicate position. Calculation of position for other purposes
+is only from (0020,0030) and (0020,0035)
+*/
- sis->AddSQItem(sqi,1);
- sqi->Delete();
+/*
+// if imagePositionPatient not found, default it with imagePositionRet, if any
+// if imageOrientationPatient not found, default it with imageOrientationRet, if any
- // 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 ( KeepMediaStorageSOPClassUID)
- // It up to the use to *know* whether he modified the pixels or not.
- // he is allowed to keep the original 'Media Storage SOP Class UID'
- // and 'Image Type' as well
- CheckMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
- else
- // Potentialy this is a post-processed image
- // (The written image is no longer an 'ORIGINAL' one)
- CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
+ std::string imagePositionRet = FileInternal->GetEntryString(0x0020,0x0030);
+ std::string imageOrientationRet = FileInternal->GetEntryString(0x0020,0x0035);
+ std::string imagePositionPatient = FileInternal->GetEntryString(0x0020,0x0032);
+ std::string imageOrientationPatient = FileInternal->GetEntryString(0x0020,0x0037);
+ if( imagePositionPatient == GDCM_UNFOUND && imageOrientationPatient == GDCM_UNFOUND
+ && imagePositionRet != GDCM_UNFOUND && imageOrientationRet != GDCM_UNFOUND)
+ {
+ CopyMandatoryEntry(0x0020, 0x0032,imagePositionRet,"DS");
+ Archive->Push(0x0020,0x0030);
+ CopyMandatoryEntry(0x0020, 0x0037,imageOrientationRet,"DS");
+ Archive->Push(0x0020,0x0035);
}
+*/
+ // Samples Per Pixel (type 1) : default to grayscale
+ CheckMandatoryEntry(0x0028,0x0002,"1","US");
+
+ // --- Check UID-related Entries ---
+
// At the end, not to overwrite the original ones,
- // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
+ // needed by 'Referenced SOP Instance UID', 'Referenced SOP Class UID'
// 'SOP Instance UID'
- CopyMandatoryEntry(0x0008,0x0018,sop);
-
- // the gdcm written image is a [Secondary Capture Image Storage]
- // except if user told us he dind't modify the pixels, and, therefore
- // he want to keep the 'Media Storage SOP Class UID'
-
- // 'Media Storage SOP Class UID' : [Secondary Capture Image Storage]
- if ( KeepMediaStorageSOPClassUID)
- {
- // It up to the use to *know* whether he modified the pixels or not.
- // he is allowed to keep the original 'Media Storage SOP Class UID'
- CheckMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
- }
- else
- {
- // Potentialy this is a post-processed image
- // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
- CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
-
- // FIXME : Must we Force Value, or Default value ?
- // Is it Type 1 for any Modality ?
- // --> Answer seems to be NO :-(
- // FIXME : we should write it only when we are *sure* the image
- // *does not* come from an imager (see also 0018,0x1164)
+ CopyMandatoryEntry(0x0008,0x0018,sop,"UI");
+ if ( ContentType == USER_OWN_IMAGE)
+ {
+ gdcmDebugMacro( "USER_OWN_IMAGE (2)");
// Conversion Type.
// Other possible values are :
// See PS 3.3, Page 408
-
+
// DV = Digitized Video
- // DI = Digital Interface
+ // DI = Digital Interface
// DF = Digitized Film
// WSD = Workstation
// SD = Scanned Document
// SI = Scanned Image
// DRW = Drawing
// SYN = Synthetic Image
-
- CheckMandatoryEntry(0x0008,0x0064,"SYN");
- }
-
+
+ CheckMandatoryEntry(0x0008,0x0064,"SYN","CS"); // Why not?
+ }
+/*
+ if ( ContentType == CREATED_IMAGE)
+ {
+ /// \todo : find a trick to pass the Media Storage SOP Instance UID of the images used to create the current image
+
+ }
+*/
+
// ---- The user will never have to take any action on the following ----
// new value for 'SOP Instance UID'
// Instance Creation Date
const std::string &date = Util::GetCurrentDate();
- CopyMandatoryEntry(0x0008,0x0012,date);
-
+ CopyMandatoryEntry(0x0008,0x0012,date,"DA");
+
// Instance Creation Time
const std::string &time = Util::GetCurrentTime();
- CopyMandatoryEntry(0x0008,0x0013,time);
+ CopyMandatoryEntry(0x0008,0x0013,time,"TM");
// Study Date
- CheckMandatoryEntry(0x0008,0x0020,date);
+ CheckMandatoryEntry(0x0008,0x0020,date,"DA");
// Study Time
- CheckMandatoryEntry(0x0008,0x0030,time);
+ CheckMandatoryEntry(0x0008,0x0030,time,"TM");
// Accession Number
//CopyMandatoryEntry(0x0008,0x0050,"");
- CheckMandatoryEntry(0x0008,0x0050,"");
+ CheckMandatoryEntry(0x0008,0x0050,"","SH");
// ----- Add Mandatory Entries if missing ---
// keeping the same 'Study Instance UID' for various images
// The user may add images to a 'Manufacturer Study',
// adding new Series to an already existing Study
- CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID());
+ CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID(),"UI");
// 'Serie Instance UID'
// Keep the value if exists
// keeping the same 'Serie Instance UID' for various images
// The user shouldn't add any image to a 'Manufacturer Serie'
// but there is no way no to prevent him for doing that
- CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID());
+ CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID(),"UI");
// Study ID
- CheckMandatoryEntry(0x0020,0x0010,"");
+ CheckMandatoryEntry(0x0020,0x0010,"","SH");
// Series Number
- CheckMandatoryEntry(0x0020,0x0011,"");
+ CheckMandatoryEntry(0x0020,0x0011,"","IS");
// Instance Number
- CheckMandatoryEntry(0x0020,0x0013,"");
-
+ CheckMandatoryEntry(0x0020,0x0013,"","IS");
+
// Patient Orientation
// Can be computed from (0020|0037) : Image Orientation (Patient)
- gdcm::Orientation *o = gdcm::Orientation::New();
+ GDCM_NAME_SPACE::Orientation *o = GDCM_NAME_SPACE::Orientation::New();
std::string ori = o->GetOrientation ( FileInternal );
o->Delete();
if (ori != "\\" && ori != GDCM_UNFOUND)
- CheckMandatoryEntry(0x0020,0x0020,ori);
- else
- CheckMandatoryEntry(0x0020,0x0020,"");
+ CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
+ else
+ CheckMandatoryEntry(0x0020,0x0020,"","CS");
+
+ // Default Patient Position to HFS
+ CheckMandatoryEntry(0x0018,0x5100,"HFS","CS");
// Modality : if missing we set it to 'OTher'
- CheckMandatoryEntry(0x0008,0x0060,"OT");
+ CheckMandatoryEntry(0x0008,0x0060,"OT","CS");
// Manufacturer : if missing we set it to 'GDCM Factory'
- CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory");
+ CheckMandatoryEntry(0x0008,0x0070,"GDCM Factory","LO");
// Institution Name : if missing we set it to 'GDCM Hospital'
- CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital");
+ CheckMandatoryEntry(0x0008,0x0080,"GDCM Hospital","LO");
// Patient's Name : if missing, we set it to 'GDCM^Patient'
- CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient");
+ CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient","PN");
- // Patient ID
- CheckMandatoryEntry(0x0010,0x0020,"");
+ // Patient ID : some clinical softwares *demand* it although it's a 'type 2' entry.
+ CheckMandatoryEntry(0x0010,0x0020,"gdcm ID","LO");
// Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0010,0x0030,"");
+ CheckMandatoryEntry(0x0010,0x0030,"","DA");
// Patient's Sex :'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0010,0x0040,"");
+ CheckMandatoryEntry(0x0010,0x0040,"","CS");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
- CheckMandatoryEntry(0x0008,0x0090,"");
+ CheckMandatoryEntry(0x0008,0x0090,"","PN");
+ /*
// Deal with element 0x0000 (group length) of each group.
// First stage : get all the different Groups
- /*
+
GroupHT grHT;
DocEntry *d = FileInternal->GetFirstEntry();
while(d)
CheckMandatoryEntry(it->first, 0x0000, "0");
}
// Third stage : update all 'zero level' groups length
-*/
+*/
+
+
+ if (PhotometricInterpretation == 1)
+ {
+ }
}
-void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+void FileHelper::CheckMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr )
{
DataEntry *entry = FileInternal->GetDataEntry(group,elem);
if ( !entry )
{
- entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ //entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ entry = DataEntry::New(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
entry->Delete();
- }
+ }
}
-void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+/// \todo : what is it used for ? (FileHelper::SetMandatoryEntry)
+void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
{
- DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ //DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ DataEntry *entry = DataEntry::New(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
entry->Delete();
}
-void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
+void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value,const VRKey &vr)
{
- DataEntry *entry = CopyDataEntry(group,elem);
+ DataEntry *entry = CopyDataEntry(group,elem,vr);
entry->SetString(value);
Archive->Push(entry);
entry->Delete();
Archive->Restore(0x0020,0x000e);
}
-
/**
* \brief CallStartMethod
*/
void FileHelper::Initialize()
{
UserFunction = 0;
- KeepMediaStorageSOPClassUID = false;
+ ContentType = USER_OWN_IMAGE;
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
+
+ PhotometricInterpretation = 2; // Black = 0
PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
return raw;
}
+/**
+ * \brief Deal with Grey levels i.e. re-arange them
+ * to have low values = dark, high values = bright
+ */
+void FileHelper::ConvertFixGreyLevels(uint8_t *raw, size_t rawSize)
+{
+ uint32_t i; // to please M$VC6
+ int16_t j;
+
+ // Number of Bits Allocated for storing a Pixel is defaulted to 16
+ // when absent from the file.
+ int bitsAllocated = FileInternal->GetBitsAllocated();
+ if ( bitsAllocated == 0 )
+ {
+ bitsAllocated = 16;
+ }
+
+ else if (bitsAllocated > 8 && bitsAllocated < 16 && bitsAllocated != 12)
+ {
+ bitsAllocated = 16;
+ }
+ // Number of "Bits Stored", defaulted to number of "Bits Allocated"
+ // when absent from the file.
+ int bitsStored = FileInternal->GetBitsStored();
+ if ( bitsStored == 0 )
+ {
+ bitsStored = bitsAllocated;
+ }
+
+ if (!FileInternal->IsSignedPixelData())
+ {
+ if ( bitsAllocated == 8 )
+ {
+ uint8_t *deb = (uint8_t *)raw;
+ for (i=0; i<rawSize; i++)
+ {
+ *deb = 255 - *deb;
+ deb++;
+ }
+ return;
+ }
+
+ if ( bitsAllocated == 16 )
+ {
+ uint16_t mask =1;
+ for (j=0; j<bitsStored-1; j++)
+ {
+ mask = (mask << 1) +1; // will be fff when BitsStored=12
+ }
+
+ uint16_t *deb = (uint16_t *)raw;
+ for (i=0; i<rawSize/2; i++)
+ {
+ *deb = mask - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+ else
+ {
+ if ( bitsAllocated == 8 )
+ {
+ uint8_t smask8 = 255;
+ uint8_t *deb = (uint8_t *)raw;
+ for (i=0; i<rawSize; i++)
+ {
+ *deb = smask8 - *deb;
+ deb++;
+ }
+ return;
+ }
+ if ( bitsAllocated == 16 )
+ {
+ uint16_t smask16 = 65535;
+ uint16_t *deb = (uint16_t *)raw;
+ for (i=0; i<rawSize/2; i++)
+ {
+ *deb = smask16 - *deb;
+ deb++;
+ }
+ return;
+ }
+ }
+}
+
//-----------------------------------------------------------------------------
/**
- * \brief Prints the common part of DataEntry, SeqEntry
+ * \brief Prints the FileInternal + info on PixelReadConvertor
* @param os ostream we want to print in
* @param indent (unused)
*/
//-----------------------------------------------------------------------------
} // end namespace gdcm
+
+
+/* Probabely something to be added to use Rescale Slope/Intercept
+Have a look ,at ITK code !
+
+// Internal function to rescale pixel according to Rescale Slope/Intercept
+template<class TBuffer, class TSource>
+void RescaleFunction(TBuffer* buffer, TSource *source,
+ double slope, double intercept, size_t size)
+{
+ size /= sizeof(TSource);
+
+ if (slope != 1.0 && intercept != 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]*slope + intercept);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 7: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 6: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 5: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 4: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 3: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 2: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ case 1: *buffer++ = (TBuffer)((*source++)*slope + intercept);
+ } while (--n > 0);
+ }
+ }
+ else if (slope == 1.0 && intercept != 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i] + intercept);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)(*source++ + intercept);
+ case 7: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 6: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 5: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 4: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 3: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 2: *buffer++ = (TBuffer)(*source++ + intercept);
+ case 1: *buffer++ = (TBuffer)(*source++ + intercept);
+ } while (--n > 0);
+ }
+ }
+ else if (slope != 1.0 && intercept == 0.0)
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]*slope);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)((*source++)*slope);
+ case 7: *buffer++ = (TBuffer)((*source++)*slope);
+ case 6: *buffer++ = (TBuffer)((*source++)*slope);
+ case 5: *buffer++ = (TBuffer)((*source++)*slope);
+ case 4: *buffer++ = (TBuffer)((*source++)*slope);
+ case 3: *buffer++ = (TBuffer)((*source++)*slope);
+ case 2: *buffer++ = (TBuffer)((*source++)*slope);
+ case 1: *buffer++ = (TBuffer)((*source++)*slope);
+ } while (--n > 0);
+ }
+ }
+ else
+ {
+ // Duff's device. Instead of this code:
+ //
+ // for(unsigned int i=0; i<size; i++)
+ // {
+ // buffer[i] = (TBuffer)(source[i]);
+ // }
+ //
+ // use Duff's device which exploits "fall through"
+ register size_t n = (size + 7) / 8;
+ switch ( size % 8)
+ {
+ case 0: do { *buffer++ = (TBuffer)(*source++);
+ case 7: *buffer++ = (TBuffer)(*source++);
+ case 6: *buffer++ = (TBuffer)(*source++);
+ case 5: *buffer++ = (TBuffer)(*source++);
+ case 4: *buffer++ = (TBuffer)(*source++);
+ case 3: *buffer++ = (TBuffer)(*source++);
+ case 2: *buffer++ = (TBuffer)(*source++);
+ case 1: *buffer++ = (TBuffer)(*source++);
+ } while (--n > 0);
+ }
+ }
+}
+
+
+template<class TSource>
+void RescaleFunction(ImageIOBase::IOComponentType bufferType,
+ void* buffer, TSource *source,
+ double slope, double intercept, size_t size)
+{
+ switch (bufferType)
+ {
+ case ImageIOBase::UCHAR:
+ RescaleFunction( (unsigned char *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::CHAR:
+ RescaleFunction( (char *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::USHORT:
+ RescaleFunction( (unsigned short *)buffer, source, slope, intercept,size);
+ break;
+ case ImageIOBase::SHORT:
+ RescaleFunction( (short *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::UINT:
+ RescaleFunction( (unsigned int *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::INT:
+ RescaleFunction( (int *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::FLOAT:
+ RescaleFunction( (float *)buffer, source, slope, intercept, size);
+ break;
+ case ImageIOBase::DOUBLE:
+ RescaleFunction( (double *)buffer, source, slope, intercept, size);
+ break;
+ default:
+ ::itk::OStringStream message;
+ message << "itk::ERROR: GDCMImageIO: Unknown component type : " << bufferType;
+ ::itk::ExceptionObject e(__FILE__, __LINE__, message.str().c_str(),ITK_LOCATION);
+ throw e;
+ }
+}
+*/