Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2006/02/08 10:13:55 $
- Version: $Revision: 1.91 $
+ Date: $Date: 2006/04/20 16:12:11 $
+ Version: $Revision: 1.101 $
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
fh->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
// (WriteMode is set)
-fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
+fh->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
// Little Endian is the default
// no other value is allowed
(-->SetWriteType(ExplicitVR);)
* \return false if DataEntry not found
*/
bool FileHelper::SetEntryString(std::string const &content,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem)
{
return FileInternal->SetEntryString(content, group, elem);
}
* \return false if DataEntry not found
*/
bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem)
{
return FileInternal->SetEntryBinArea(content, lgth, group, elem);
}
* failed).
*/
DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
- uint16_t group, uint16_t elem)
+ uint16_t group, uint16_t elem)
{
return FileInternal->InsertEntryBinArea(binArea, lgth, group, elem);
}
* - DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
* @return Pointer to newly allocated pixel data.
* (uint8_t is just for prototyping. feel free to cast)
- * NULL if alloc fails
+ * NULL if alloc fails
*/
uint8_t *FileHelper::GetImageDataRaw ()
{
#ifndef GDCM_LEGACY_REMOVE
/*
- * \ brief Useless function, since PixelReadConverter forces us
+ * \brief Useless function, since PixelReadConverter forces us
* copy the Pixels anyway.
* Reads the pixels from disk (uncompress if necessary),
* Transforms YBR pixels, if any, into RGB pixels
* Transforms single Grey plane + 3 Palettes into a RGB Plane
* Copies at most MaxSize bytes of pixel data to caller allocated
* memory space.
- * \ warning This function allows people that want to build a volume
+ * \warning This function allows people that want to build a volume
* from an image stack *not to* have, first to get the image pixels,
* and then move them to the volume area.
* It's absolutely useless for any VTK user since vtk chooses
* to load the image line by line, starting from the end.
* VTK users have to call GetImageData
*
- * @ param destination Address (in caller's memory space) at which the
+ * @param destination Address (in caller's memory space) at which the
* pixel data should be copied
- * @ param maxSize Maximum number of bytes to be copied. When MaxSize
+ * @param maxSize Maximum number of bytes to be copied. When MaxSize
* is not sufficient to hold the pixel data the copy is not
* executed (i.e. no partial copy).
- * @ return On success, the number of bytes actually copied. Zero on
+ * @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)
*/
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:
- SetWriteFileTypeToExplicitVR();
+
+ // 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.
+
+
+ e = FileInternal->GetFirstEntry();
+ while (e != 0)
+ {
+ if (e->GetVR() == " ")
+ {
+ SetWriteTypeToDcmImplVR();
+ SetWriteFileTypeToImplicitVR();
+ flag = true;
+ break;
+ }
+ e = FileInternal->GetNextEntry();
+ }
+
+ if (!flag)
+ {
+ SetWriteFileTypeToExplicitVR();
+ }
break;
+
+ SetWriteFileTypeToExplicitVR(); // to see JPRx
+ 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 may be either ExplicitVR or ImplicitVR
case JPEG:
SetWriteFileTypeToJPEG();
- std::cerr << "Writting as JPEG" << std::endl;
break;
}
- CheckMandatoryElements();
-
+
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
//
check = FileInternal->Write(fileName,WriteType);
}
- RestoreWrite();
- RestoreWriteFileType();
- RestoreWriteMandatory();
+ RestoreWrite();
+ // RestoreWriteFileType();
+ // RestoreWriteMandatory();
+
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
size_t decSize = FileInternal->GetXSize()
* FileInternal->GetYSize()
* FileInternal->GetZSize()
+ * FileInternal->GetTSize()
* FileInternal->GetSamplesPerPixel()
* ( numberBitsAllocated / 8 );
size_t rgbSize = decSize;
}
else
{
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
if (FileInternal->HasLUT() )
{
photInt->SetString("PALETTE COLOR ");
{
PixelReadConverter->BuildRGBImage();
- DataEntry *spp = CopyDataEntry(0x0028,0x0002);
+ DataEntry *spp = CopyDataEntry(0x0028,0x0002,"US");
spp->SetString("3 ");
- DataEntry *planConfig = CopyDataEntry(0x0028,0x0006);
+ DataEntry *planConfig = CopyDataEntry(0x0028,0x0006,"US");
planConfig->SetString("0 ");
- DataEntry *photInt = CopyDataEntry(0x0028,0x0004);
+ DataEntry *photInt = CopyDataEntry(0x0028,0x0004,"CS");
photInt->SetString("RGB ");
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);
*/
void FileHelper::RestoreWrite()
{
+
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);
+
}
/**
}
/**
- * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ * \brief Sets in the File the TransferSyntax to 'JPEG'
*/
void FileHelper::SetWriteFileTypeToJPEG()
{
std::string ts = Util::DicomString(
Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
- DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010,"UI");
tss->SetString(ts);
Archive->Push(tss);
tss->Delete();
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ */
void FileHelper::SetWriteFileTypeToExplicitVR()
{
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();
}
{
std::string rows, columns;
- DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
- DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
-
+ //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(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.
+ FILTERED_IMAGE
-3) user created a new image, using existing images (eg MIP, MPR, cartography image)
--4) user anonymized an image without processing the pixels.
-
+ CREATED_IMAGE
+-4) user modified/added some tags *without processing* the pixels (anonymization..
+ UNMODIFIED_PIXELS_IMAGE
+
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.
-------------------------------------------------------------------------------------*/
-
+
void FileHelper::CheckMandatoryElements()
{
std::string sop = Util::CreateUniqueUID();
-
+
+ // --------------------- For Meta Elements ---------------------
// just to remember : 'official' 0002 group
if ( WriteType != ACR && WriteType != ACR_LIBIDO )
{
// 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(),
false);
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);
+ CopyMandatoryEntry(0x0002,0x0003,sop,"UI");
// 'Implementation Class UID'
// FIXME : in all examples we have, 0x0002,0x0012 is not so long :
- // semms to be Root UID + 4 digits (?)
- CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
+ // seems to be Root UID + 4 digits (?)
+ 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
+ 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 ;-)
int nbBitsAllocated = FileInternal->GetBitsAllocated();
if ( nbBitsAllocated == 0 || nbBitsAllocated > 32)
{
- 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");
{
pixelSpacing = "1.0\\1.0";
// if missing, Pixel Spacing forced to "1.0\1.0"
- CopyMandatoryEntry(0x0028,0x0030,pixelSpacing);
+ CopyMandatoryEntry(0x0028,0x0030,pixelSpacing,"DS");
}
// '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
+ 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);
+ CheckMandatoryEntry(0x0018,0x1164,pixelSpacing,"DS");
// Samples Per Pixel (type 1) : default to grayscale
- CheckMandatoryEntry(0x0028,0x0002,"1");
-
- // --- Check UID-related Entries ---
+ CheckMandatoryEntry(0x0028,0x0002,"1","US");
- // 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) );
- 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();
-
- sis->AddSQItem(sqi,1);
- sqi->Delete();
-
- // temporarily replaces any previous 'Source Image Sequence'
- Archive->Push(sis);
- sis->Delete();
+ // --- Check UID-related Entries ---
- // 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");
-
- }
-
// At the end, not to overwrite the original ones,
// 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
// SI = Scanned Image
// DRW = Drawing
// SYN = Synthetic Image
-
- CheckMandatoryEntry(0x0008,0x0064,"SYN");
- }
- // ---- The user will never have to take any action on the following ----
+ 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'
//SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
// 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)
std::string ori = o->GetOrientation ( FileInternal );
o->Delete();
if (ori != "\\" && ori != GDCM_UNFOUND)
- CheckMandatoryEntry(0x0020,0x0020,ori);
+ CheckMandatoryEntry(0x0020,0x0020,ori,"CS");
else
- CheckMandatoryEntry(0x0020,0x0020,"");
-
+ 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,"");
-
- // Remove some inconstencies (probably some more will be added)
+ CheckMandatoryEntry(0x0008,0x0090,"","PN");
- // if (0028 0008)Number of Frames exists
- // Push out (0020 0052),Frame of Reference UID
- // (only meaningfull within a Serie)
-
- // Well ...
- // Maybe not!
- // dciodvfy complains when missing (Type 1 element)
- /// todo add it when missing (?)
- /*
- DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008);
- if ( !e_0028_0008 )
- {
- Archive->Push(0x0020, 0x0052);
- }
- */
-
+ /*
// 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
-*/
+*/
+
}
-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();
void FileHelper::Initialize()
{
UserFunction = 0;
- KeepMediaStorageSOPClassUID = false;
+ ContentType = USER_OWN_IMAGE;
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff