Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/11/30 13:42:19 $
- Version: $Revision: 1.85 $
+ Date: $Date: 2006/03/29 16:09:48 $
+ Version: $Revision: 1.98 $
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
#include <fstream>
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)
{
+ 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;
+
case ACR:
case ACR_LIBIDO:
// NOTHING is done here just for LibIDO.
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();
// --------------------------------------------------------------
size_t decSize = FileInternal->GetXSize()
* FileInternal->GetYSize()
* FileInternal->GetZSize()
+ * FileInternal->GetTSize()
* FileInternal->GetSamplesPerPixel()
* ( numberBitsAllocated / 8 );
size_t rgbSize = decSize;
}
/**
- * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ * \brief Sets in the File the TransferSyntax to 'JPEG'
*/
void FileHelper::SetWriteFileTypeToJPEG()
{
tss->Delete();
}
+/**
+ * \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
+ */
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
DataEntry *tss = CopyDataEntry(0x0002,0x0010);
tss->SetString(ts);
-
Archive->Push(tss);
tss->Delete();
}
DataEntry *tss = CopyDataEntry(0x0002,0x0010);
tss->SetString(ts);
-
Archive->Push(tss);
tss->Delete();
}
/* -------------------------------------------------------------------------------------
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.
+ 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)
+ 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)
+0008 0012 Instance Creation Date
+0008 0013 Instance Creation Time
+0008 0018 SOP Instance UID
+are *always* created with the current values; user has *no* possible intervention on
+them.
+
+'Serie Instance UID'(0x0020,0x000e)
+'Study Instance UID'(0x0020,0x000d) are kept as is if already exist,
+ created if it doesn't.
+ The user is allowed to create his own Series/Studies,
+ 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 allow him to do that
+
+ None of the 'shadow elements' are droped out.
+
+
+1)
+'Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image).
+
+1)3)
+'Media Storage SOP Class UID' (0x0002,0x0002)
+'SOP Class UID' (0x0008,0x0016) are set to
+ [Secondary Capture Image Storage]
+'Image Type' (0x0008,0x0008) is forced to "DERIVED\PRIMARY"
+Conversion Type (0x0008,0x0064) is forced to 'SYN' (Synthetic Image)
+
+2)4)
+If 'SOP Class UID' exists in the native image ('true DICOM' image)
+ we create the 'Source Image Sequence' SeqEntry (0x0008, 0x2112)
+ --> 'Referenced SOP Class UID' (0x0008, 0x1150)
+ whose value is the original 'SOP Class UID'
+ --> '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
+ or the Series, (or the Study ?) he used to created his image
+ (MIP, MPR, cartography image, ...)
+ These info should be stored (?)
+ 0008 1110 SQ 1 Referenced Study Sequence
+ 0008 1115 SQ 1 Referenced Series Sequence
+ 0008 1140 SQ 1 Referenced Image Sequence
+
+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)
+
+
+Bellow follows the full description (hope so !) of the consistency checks performed
+by gdcm::FileHelper::CheckMandatoryElements()
-->'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 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.
(a fully user created image belongs to *no* modality)
--> Bits Stored, Bits Allocated, Hight Bit Position are checked for consistency
--> Pixel Spacing (0x0028,0x0030) is defaulted to "1.0\1.0"
--> Samples Per Pixel (0x0028,0x0002) is defaulted to 1 (grayscale)
+
--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
---> Instance Creation Date, Instance Creation Time, Study Date, Study Time
- are force to current Date and Time
-
---> Conversion Type (0x0008,0x0064)
- is forced to 'SYN' (Synthetic Image)
+--> Instance Creation Date, Instance Creation Time are forced to current Date and Time
+
+--> Study Date, Study Time are defaulted to current Date and Time
+ (they remain unchanged if they exist)
--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
- Image Orientation (Patient) : (0020|0037)
+ Image Orientation (Patient) : (0020|0037) or from
+ Image Orientation (RET) : (0020 0035)
--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
are created, with empty value if there are 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 )
{
// Always modify the value
// Push the entries to the archive.
CopyMandatoryEntry(0x0002,0x0000,"0");
-
+
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");
+ }
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");
+ }
+
// 'Media Storage SOP Instance UID'
CopyMandatoryEntry(0x0002,0x0003,sop);
// 'Implementation Class UID'
// FIXME : in all examples we have, 0x0002,0x0012 is not so long :
- // semms to be Root UID + 4 digits (?)
+ // seems to be Root UID + 4 digits (?)
CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
// 'Implementation Version Name'
CopyMandatoryEntry(0x0002,0x0013,version);
}
+ // --------------------- For DataSet ---------------------
+
+ 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");
+ }
+ 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");
+ }
+
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
Archive->Push(0x0028,0x0016);
}
std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
- if ( pixelSpacing == GDCM_UNKNOWN )
+ if ( pixelSpacing == GDCM_UNFOUND )
+ {
pixelSpacing = "1.0\\1.0";
- else
// if missing, Pixel Spacing forced to "1.0\1.0"
- CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
-
+ CopyMandatoryEntry(0x0028,0x0030,pixelSpacing);
+ }
+
// '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);
-
+ 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);
+
// Samples Per Pixel (type 1) : default to grayscale
CheckMandatoryEntry(0x0028,0x0002,"1");
-
+
// --- Check UID-related Entries ---
- // If 'SOP Class UID' exists ('true DICOM' image)
+
+ if ( ContentType != USER_OWN_IMAGE) // when it's not a user made image
+ {
+ // 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 )
- {
+
+ 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) );
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");
-
- }
+ // 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");
+ }
+ }
// 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)
+ if ( ContentType == USER_OWN_IMAGE)
+ {
// 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"); // 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());
CopyMandatoryEntry(0x0008,0x0013,time);
// Study Date
- CopyMandatoryEntry(0x0008,0x0020,date);
+ CheckMandatoryEntry(0x0008,0x0020,date);
// Study Time
- CopyMandatoryEntry(0x0008,0x0030,time);
+ CheckMandatoryEntry(0x0008,0x0030,time);
// Accession Number
//CopyMandatoryEntry(0x0008,0x0050,"");
gdcm::Orientation *o = gdcm::Orientation::New();
std::string ori = o->GetOrientation ( FileInternal );
o->Delete();
- if (ori != "\\" )
+ if (ori != "\\" && ori != GDCM_UNFOUND)
CheckMandatoryEntry(0x0020,0x0020,ori);
else
CheckMandatoryEntry(0x0020,0x0020,"");
-
+
+ // Default Patient Position to HFS
+ CheckMandatoryEntry(0x0018,0x5100,"HFS");
+
// Modality : if missing we set it to 'OTher'
CheckMandatoryEntry(0x0008,0x0060,"OT");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
CheckMandatoryEntry(0x0008,0x0090,"");
-
- // Remove some inconstencies (probably some more will be added)
- // if (0028 0008)Number of Frames exists
- // Push out (0020 0052),Frame of Reference UID
- // (only meaningfull within a Serie)
- 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::Initialize()
{
UserFunction = 0;
- KeepMediaStorageSOPClassUID = false;
+ ContentType = USER_OWN_IMAGE;
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff