Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/10/18 08:35:50 $
- Version: $Revision: 1.60 $
+ Date: $Date: 2005/10/26 08:28:58 $
+ Version: $Revision: 1.76 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
fp = opens file(fileName);
ComputeGroup0002Length( );
BitsAllocated 12->16
- RemoveEntryNoDestroy(palettes, etc)
+ RemoveEntry(palettes, etc)
Document::WriteContent(fp, writetype);
RestoreWrite();
(moves back to the File all the archived elements)
*/
FileHelper::FileHelper( )
{
- FileInternal = new File( );
- SelfHeader = true;
+ FileInternal = File::New( );
Initialize();
}
*/
FileHelper::FileHelper(File *header)
{
- FileInternal = header;
- SelfHeader = false;
- Initialize();
- if ( FileInternal->IsReadable() )
- {
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
- }
-}
+ gdcmAssertMacro(header);
-#ifndef GDCM_LEGACY_REMOVE
-/**
- * \brief DEPRECATED : use SetFilename() + SetLoadMode() + Load() methods
- * Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (gdcm::File only deals with the ... header)
- * Opens (in read only and when possible) an existing file and checks
- * for DICOM compliance. Returns NULL on failure.
- * It will be up to the user to load the pixels into memory
- * \note the in-memory representation of all available tags found in
- * the DICOM header is post-poned to first header information access.
- * This avoid a double parsing of public part of the header when
- * one sets an a posteriori shadow dictionary (efficiency can be
- * seen as a side effect).
- * @param filename file to be opened for parsing
- * @deprecated use SetFilename() + Load() methods
- */
-FileHelper::FileHelper(std::string const &filename )
-{
- FileInternal = new File( );
- FileInternal->SetFileName( filename );
- FileInternal->Load();
- SelfHeader = true;
+ FileInternal = header;
+ FileInternal->Register();
Initialize();
if ( FileInternal->IsReadable() )
{
PixelReadConverter->GrabInformationsFromFile( FileInternal );
}
}
-#endif
/**
* \brief canonical destructor
delete Archive;
}
- if ( SelfHeader )
- {
- delete FileInternal;
- }
- FileInternal = 0;
+ FileInternal->Unregister();
}
//-----------------------------------------------------------------------------
/**
* \brief Sets the LoadMode of the internal gdcm::File as a boolean string.
- * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ
- *... (nothing more, right now)
+ * NO_SEQ, NO_SHADOW, NO_SHADOWSEQ ... (nothing more, right now)
* WARNING : before using NO_SHADOW, be sure *all* your files
* contain accurate values in the 0x0000 element (if any)
* of *each* Shadow Group. The parser will fail if the size is wrong !
}
/**
- * \brief Get the size of the image data
+ * \brief Get the size of the image data.
* If the image could be converted to RGB using a LUT,
* this transformation is not taken into account by GetImageDataRawSize
* (use GetImageDataSize if you wish)
}
/**
- * \brief - Allocates necessary memory,
+ * \brief brings pixels into memory :
+ * - Allocates necessary memory,
* - Reads the pixels from disk (uncompress if necessary),
* - Transforms YBR pixels, if any, into RGB pixels,
* - Transforms 3 planes R, G, B, if any, into a single RGB Plane
* - Transforms single Grey plane + 3 Palettes into a RGB Plane
* - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
* @return Pointer to newly allocated pixel data.
+ * (uint8_t is just for prototyping. feel free to cast)
* NULL if alloc fails
*/
uint8_t *FileHelper::GetImageData()
}
/**
- * \brief Allocates necessary memory,
- * Transforms YBR pixels (if any) into RGB pixels
- * Transforms 3 planes R, G, B (if any) into a single RGB Plane
- * Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
- * DOES NOT transform Grey plane + 3 Palettes into a RGB Plane
+ * \brief brings pixels into memory :
+ * - Allocates necessary memory,
+ * - Transforms YBR pixels (if any) into RGB pixels
+ * - Transforms 3 planes R, G, B (if any) into a single RGB Plane
+ * - Copies the pixel data (image[s]/volume[s]) to newly allocated zone.
+ * - 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
*/
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)
// (shame on him !)
// We add Recognition Code (RET)
if ( ! FileInternal->GetDataEntry(0x0008, 0x0010) )
- FileInternal->InsertEntryString("", 0x0008, 0x0010);
+ FileInternal->InsertEntryString("ACR-NEMA V1.0 ", 0x0008, 0x0010);
SetWriteFileTypeToACR();
// SetWriteFileTypeToImplicitVR(); // ACR IS implicit VR !
break;
+ case JPEG:
+ SetWriteFileTypeToJPEG();
+ std::cerr << "Writting as JPEG" << std::endl;
+ break;
}
CheckMandatoryElements();
}
bool check = CheckWriteIntegrity(); // verifies length
+ if (WriteType == JPEG ) check = true;
if (check)
{
check = FileInternal->Write(fileName,WriteType);
Archive->Push(photInt);
Archive->Push(pixel);
+
+ photInt->Delete();
+ pixel->Delete();
}
}
Archive->Push(photInt);
Archive->Push(pixel);
+ spp->Delete();
+ planConfig->Delete();
+ photInt->Delete();
+ pixel->Delete();
+
// Remove any LUT
Archive->Push(0x0028,0x1101);
Archive->Push(0x0028,0x1102);
Archive->Push(bitsAlloc);
Archive->Push(bitsStored);
Archive->Push(highBit);
+
+ bitsAlloc->Delete();
+ bitsStored->Delete();
+ highBit->Delete();
}
}
else
/**
* \brief Sets in the File the TransferSyntax to 'Explicit VR Little Endian"
*/
+void FileHelper::SetWriteFileTypeToJPEG()
+{
+ std::string ts = Util::DicomString(
+ Global::GetTS()->GetSpecialTransferSyntax(TS::JPEGBaselineProcess1) );
+
+ DataEntry *tss = CopyDataEntry(0x0002,0x0010);
+ tss->SetString(ts);
+
+ Archive->Push(tss);
+ tss->Delete();
+}
+
void FileHelper::SetWriteFileTypeToExplicitVR()
{
std::string ts = Util::DicomString(
tss->SetString(ts);
Archive->Push(tss);
+ tss->Delete();
}
/**
tss->SetString(ts);
Archive->Push(tss);
+ tss->Delete();
}
{
std::string rows, columns;
- DataEntry *newRow=new DataEntry(oldRow->GetDictEntry());
- DataEntry *newCol=new DataEntry(oldCol->GetDictEntry());
+ DataEntry *newRow=DataEntry::New(oldRow->GetDictEntry());
+ DataEntry *newCol=DataEntry::New(oldCol->GetDictEntry());
newRow->Copy(oldCol);
newCol->Copy(oldRow);
Archive->Push(newRow);
Archive->Push(newCol);
+
+ newRow->Delete();
+ newCol->Delete();
}
DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
libidoCode->SetString("ACRNEMA_LIBIDO_1.1");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
/**
DataEntry *libidoCode = CopyDataEntry(0x0008,0x0010);
libidoCode->SetString("");
Archive->Push(libidoCode);
+ libidoCode->Delete();
}
}
}
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
DataEntry *newE;
- if ( oldE && vr != GDCM_UNKNOWN )
- if ( oldE->GetVR()!=vr )
+ if ( oldE && vr != GDCM_VRUNKNOWN )
+ if ( oldE->GetVR() != vr )
oldE = NULL;
if ( oldE )
{
- newE = new DataEntry(oldE->GetDictEntry());
+ newE = DataEntry::New(oldE->GetDictEntry());
newE->Copy(oldE);
}
else
* The writing process will restore the entries as they where before
* entering FileHelper::CheckMandatoryElements, so the user will always
* see the entries just as he left them.
+ * \note
+ * - Entries whose type is 1 are mandatory, with a mandatory value
+ * - Entries whose type is 1c are mandatory-inside-a-Sequence,
+ * with a mandatory value
+ * - Entries whose type is 2 are mandatory, with an optional value
+ * - Entries whose type is 2c are mandatory-inside-a-Sequence,
+ * with an optional value
+ * - Entries whose type is 3 are optional
*
* \todo : - warn the user if we had to add some entries :
* even if a mandatory entry is missing, we add it, with a default value
* - write a user callable full checker, to allow post reading
* and/or pre writting image consistency check.
*/
+
+/* -------------------------------------------------------------------------------------
+To be moved to User's guide / WIKI ?
+
+
+-->'Media Storage SOP Class UID' (0x0002,0x0002)
+-->'SOP Class UID' (0x0008,0x0016) are set to
+ [Secondary Capture Image Storage]
+ (Potentialy, the image was modified by user, and post-processed;
+ it's no longer a 'native' image)
+
+--> 'Image Type' (0x0008,0x0008)
+ is forced to "DERIVED\PRIMARY"
+ (The written image is no longer an 'ORIGINAL' one)
+
+--> 'Modality' (0x0008,0x0060)
+ is defaulted to "OT" (other) if missing.
+ (a fully user created image belongs to *no* modality)
+
+--> 'Media Storage SOP Instance UID' (0x0002,0x0003)
+--> 'Implementation Class UID' (0x0002,0x0012)
+ are automatically generated; no user intervention possible
+
+--> '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 allowed him to do that
+
+
+--> 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'
+
+--> 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)
+
+--> 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)
+
+--> Study ID, Series Number, Instance Number, Patient Orientation (Type 2)
+ are created, with empty value if there are missing.
+
+--> Manufacturer, Institution Name, Patient's Name, (Type 2)
+ are defaulted with a 'gdcm' value.
+
+--> 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.
+
+ -------------------------------------------------------------------------------------*/
void FileHelper::CheckMandatoryElements()
{
+ std::string sop = Util::CreateUniqueUID();
+
// just to remember : 'official' 0002 group
if ( WriteType != ACR && WriteType != ACR_LIBIDO )
{
false);
e_0002_0001->SetLength(2);
Archive->Push(e_0002_0001);
+ e_0002_0001->Delete();
- // 'Media Stored SOP Class UID'
- // [Secondary Capture Image Storage]
- CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
+ // Potentialy post-processed image --> [Secondary Capture Image Storage]
+ // 'Media Storage SOP Class UID'
+ CopyMandatoryEntry(0x0002,0x0002,"1.2.840.10008.5.1.4.1.1.7");
- // 'Media Stored SOP Instance UID'
- CopyMandatoryEntry(0x0002,0x0003,Util::CreateUniqueUID());
-
+ // 'Media Storage SOP Instance UID'
+ CopyMandatoryEntry(0x0002,0x0003,sop);
+
// 'Implementation Class UID'
CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
<< highBitPosition << " to " << nbBitsAllocated-1
<< " for consistency purpose");
}
+
+ // Pixel Spacing : defaulted to 1.0\1.0
+ CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
+
+ // 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 ( e_0008_0016 )
{
// Create 'Source Image Sequence' SeqEntry
- SeqEntry *sis = new SeqEntry (
+ SeqEntry *sis = SeqEntry::New (
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
- SQItem *sqi = new SQItem(1);
+ SQItem *sqi = SQItem::New(1);
// (we assume 'SOP Instance UID' exists too)
// create 'Referenced SOP Class UID'
- DataEntry *e_0008_1150 = new DataEntry(
+ 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 = new DataEntry(
+ 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();
- sis->AddSQItem(sqi,1);
// 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'?
+
// 'Image Type' (The written image is no longer an 'ORIGINAL' one)
CopyMandatoryEntry(0x0008,0x0008,"DERIVED\\PRIMARY");
- }
- else
- {
- // There was no 'SOP Class UID'.
- // the source image was NOT a true Dicom one.
- // We consider the image is a 'Secondary Capture' one
- // SOP Class UID
- // [Secondary Capture Image Storage]
- SetMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
}
+ // 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);
+
+ // whether a 'SOP Class UID' already exists or not in the original image
+ // the gdcm written image *is* a [Secondary Capture Image Storage] !
+ // 'SOP Class UID' : [Secondary Capture Image Storage]
+ CopyMandatoryEntry(0x0008,0x0016,"1.2.840.10008.5.1.4.1.1.7");
+
// ---- The user will never have to take any action on the following ----.
// new value for 'SOP Instance UID'
- SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
+ //SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
// Instance Creation Date
- CopyMandatoryEntry(0x0008,0x0012,Util::GetCurrentDate().c_str());
+ const std::string &date = Util::GetCurrentDate();
+ CopyMandatoryEntry(0x0008,0x0012,date);
// Instance Creation Time
- CopyMandatoryEntry(0x0008,0x0013,Util::GetCurrentTime().c_str());
+ const std::string &time = Util::GetCurrentTime();
+ CopyMandatoryEntry(0x0008,0x0013,time);
+
+ // Study Date
+ CopyMandatoryEntry(0x0008,0x0020,date);
+ // Study Time
+ CopyMandatoryEntry(0x0008,0x0030,time);
+
+ // Accession Number
+ CopyMandatoryEntry(0x0008,0x0050,"");
+
+ // Conversion Type.
+ // Other possible values are :
+ // See PS 3.3, Page 408
+
+ // DV = Digitized Video
+ // DI = Digital Interface
+ // DF = Digitized Film
+ // WSD = Workstation
+ // SD = Scanned Document
+ // SI = Scanned Image
+ // DRW = Drawing
+ // SYN = Synthetic Image
+
+ // FIXME : Must we Force Value, or Default value ?
+ // Is it Type 1 for any Modality ?
+ // --> Answer seems to be NO :-(
+ CopyMandatoryEntry(0x0008,0x0064,"SYN");
// ----- Add Mandatory Entries if missing ---
-// Entries whose type is 1 are mandatory, with a mandatory value
-// Entries whose type is 1c are mandatory-inside-a-Sequence
-// Entries whose type is 2 are mandatory, with a optional value
-// Entries whose type is 2c are mandatory-inside-a-Sequence
-// Entries whose type is 3 are optional
+ // Entries whose type is 1 are mandatory, with a mandatory value
+ // Entries whose type is 1c are mandatory-inside-a-Sequence,
+ // with a mandatory value
+ // Entries whose type is 2 are mandatory, with an optional value
+ // Entries whose type is 2c are mandatory-inside-a-Sequence,
+ // with an optional value
+ // Entries whose type is 3 are optional
+
+ // 'Study Instance UID'
+ // Keep the value if exists
+ // The user is allowed to create his own Study,
+ // 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());
// 'Serie Instance UID'
// Keep the value if exists
// but there is no way no to allowed him to do that
CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID());
- // 'Study Instance UID'
- // Keep the value if exists
- // The user is allowed to create his own Study,
- // 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());
+ // Study ID
+ CheckMandatoryEntry(0x0020,0x0010,"");
+
+ // Series Number
+ CheckMandatoryEntry(0x0020,0x0011,"");
+ // Instance Number
+ CheckMandatoryEntry(0x0020,0x0013,"");
+
+ // Patient Orientation FIXME 1\0\0\0\1\0 or empty ?
+ CheckMandatoryEntry(0x0020,0x0020,"");
+
// Modality : if missing we set it to 'OTher'
CheckMandatoryEntry(0x0008,0x0060,"OT");
// Patient's Name : if missing, we set it to 'GDCM^Patient'
CheckMandatoryEntry(0x0010,0x0010,"GDCM^Patient");
+ // Patient ID
+ CheckMandatoryEntry(0x0010,0x0020,"");
+
// Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
CheckMandatoryEntry(0x0010,0x0030,"");
// Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
CheckMandatoryEntry(0x0008,0x0090,"");
-
- // Pixel Spacing : defaulted to 1.0\1.0
- CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
// Remove some inconstencies (probably some more will be added)
DataEntry *e_0028_0008 = FileInternal->GetDataEntry(0x0028, 0x0008);
if ( !e_0028_0008 )
{
- Archive->Push(0x0020, 0X0052);
+ Archive->Push(0x0020, 0x0052);
}
}
DataEntry *entry = FileInternal->GetDataEntry(group,elem);
if ( !entry )
{
- entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
entry->SetString(value);
Archive->Push(entry);
+ entry->Delete();
}
}
void FileHelper::SetMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
{
- DataEntry *entry = new DataEntry(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
+ DataEntry *entry = DataEntry::New(Global::GetDicts()->GetDefaultPubDict()->GetEntry(group,elem));
entry->SetString(value);
Archive->Push(entry);
+ entry->Delete();
}
void FileHelper::CopyMandatoryEntry(uint16_t group,uint16_t elem,std::string value)
DataEntry *entry = CopyDataEntry(group,elem);
entry->SetString(value);
Archive->Push(entry);
+ entry->Delete();
}
/**
Archive->Restore(0x0020,0x000d);
Archive->Restore(0x0020,0x000e);
-
}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff