Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/10/25 09:22:16 $
- Version: $Revision: 1.72 $
+ Date: $Date: 2005/11/29 17:21:35 $
+ Version: $Revision: 1.84 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmPixelWriteConvert.h"
#include "gdcmDocEntryArchive.h"
#include "gdcmDictSet.h"
+#include "gdcmOrientation.h"
#include <fstream>
namespace gdcm
{
+typedef std::map<uint16_t, int> GroupHT; // Hash Table
//-------------------------------------------------------------------------
// Constructor / Destructor
/**
*/
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 );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
}
}
-#endif
/**
* \brief canonical destructor
delete Archive;
}
- if ( SelfHeader )
- {
- delete FileInternal;
- }
- FileInternal = 0;
+ FileInternal->Unregister();
}
//-----------------------------------------------------------------------------
if ( !FileInternal->Load() )
return false;
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
return true;
}
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's 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
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryString(std::string const &content,
uint16_t group, uint16_t elem)
/**
- * \brief Accesses an existing DocEntry (i.e. a Dicom Element)
- * through it's (group, element) and modifies it's content with
- * the given value.
+ * \brief Accesses an existing DataEntry through it's (group, element)
+ * and modifies it's 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 elem element number of the Dicom Element to modify
- * \return false if DocEntry not found
+ * \return false if DataEntry not found
*/
bool FileHelper::SetEntryBinArea(uint8_t *content, int lgth,
uint16_t group, uint16_t elem)
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
- * @param content (string)value to be set
+ * \brief Modifies the value of a given DataEntry when it exists.
+ * Creates it with the given value when unexistant.
+ * @param content (string) value to be set
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryString(std::string const &content,
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it with the given value when unexistant.
+ * \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 lgth new value length
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the modified/created DataEntry (NULL when creation
* failed).
*/
DataEntry *FileHelper::InsertEntryBinArea(uint8_t *binArea, int lgth,
}
/**
- * \brief Modifies the value of a given DocEntry (Dicom entry)
- * when it exists. Creates it, empty (?!) when unexistant.
+ * \brief Adds an empty SeqEntry
+ * (remove any existing entry with same group,elem)
* @param group Group number of the Entry
* @param elem Element number of the Entry
- * \return pointer to the modified/created Dicom entry (NULL when creation
+ * \return pointer to the created SeqEntry (NULL when creation
* failed).
*/
SeqEntry *FileHelper::InsertSeqEntry(uint16_t group, uint16_t elem)
* - 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()
* - 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 ()
/**
* \brief This method is called automatically, just before writting
- * in order to produce a 'True Dicom V3' image
- * We cannot know *how* the user made the File (reading an old ACR-NEMA
- * file or a not very clean DICOM file ...)
- *
+ * in order to produce a 'True Dicom V3' image.
+ *
+ * We cannot know *how* the user made the File :
+ * (reading an old ACR-NEMA file or a not very clean DICOM file ...)
* Just before writting :
* - we check the Entries
* - we create the mandatory entries if they are missing
* - we push the sensitive entries to the Archive
* 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.
+ * see the entries just as they were before he decided to write.
+ *
+ * \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 :
+ * \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
* (we don't want to give up the writting process if user forgot to
* specify Lena's Patient ID, for instance ...)
* - 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)
+ 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)
+
+--> '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)
+--> 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)
+
+--> Patient Orientation : (0x0020,0x0020), if not present, is deduced from
+ Image Orientation (Patient) : (0020|0037)
+
+--> 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()
{
// 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);
e_0002_0001->SetLength(2);
Archive->Push(e_0002_0001);
- e_0002_0001->Delete();
+ e_0002_0001->Delete();
- // 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");
-
+ 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");
+ else
+ // Potentialy this is a post-processed image
+ // 'Media Storage SOP Class UID' --> [Secondary Capture Image Storage]
+ 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 (?)
CopyMandatoryEntry(0x0002,0x0012,Util::CreateUniqueUID());
// 'Implementation Version Name'
<< highBitPosition << " to " << nbBitsAllocated-1
<< " for consistency purpose");
}
- // --- Check UID-related Entries ---
+
+ std::string pixelSpacing = FileInternal->GetEntryString(0x0028,0x0030);
+ if ( pixelSpacing == GDCM_UNKNOWN )
+ pixelSpacing = "1.0\\1.0";
+ else
+ // if missing, Pixel Spacing forced to "1.0\1.0"
+ CopyMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
+
+ // '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
// Create 'Source Image Sequence' 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 = 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);
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();
- // 'Image Type' (The written image is no longer an 'ORIGINAL' one)
+ // 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,
// '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 ----.
+ // 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)
+
+ // 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
+
+ CheckMandatoryEntry(0x0008,0x0064,"SYN");
+ }
+
+ // ---- The user will never have to take any action on the following ----
+
// new value for 'SOP Instance UID'
//SetMandatoryEntry(0x0008,0x0018,Util::CreateUniqueUID());
CopyMandatoryEntry(0x0008,0x0030,time);
// Accession Number
- CopyMandatoryEntry(0x0008,0x0050,"");
+ //CopyMandatoryEntry(0x0008,0x0050,"");
+ CheckMandatoryEntry(0x0008,0x0050,"");
- // Conversion Type ... FIXME (type 1)
- // See PS 3.3, Page 408
- 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,
- // 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
+
+ // ----- 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,
+ // 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
+ // adding new Series to an already existing Study
CheckMandatoryEntry(0x0020,0x000d,Util::CreateUniqueUID());
// 'Serie Instance UID'
// The user is allowed to create his own Series,
// 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 allowed him to do that
+ // but there is no way no to prevent him for doing that
CheckMandatoryEntry(0x0020,0x000e,Util::CreateUniqueUID());
// Study ID
// Instance Number
CheckMandatoryEntry(0x0020,0x0013,"");
-
- // Patient Orientation FIXME 1\0\0\0\1\0 or empty ?
- CheckMandatoryEntry(0x0020,0x0020,"");
+
+ // Patient Orientation
+ // Can be computed from (0020|0037) : Image Orientation (Patient)
+ gdcm::Orientation *o = gdcm::Orientation::New();
+ std::string ori = o->GetOrientation ( FileInternal );
+ o->Delete();
+ if (ori != "\\" )
+ CheckMandatoryEntry(0x0020,0x0020,ori);
+ else
+ CheckMandatoryEntry(0x0020,0x0020,"");
// 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,"");
-
- // Pixel Spacing : defaulted to 1.0\1.0
- CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
-
- // Samples Per Pixel (type 1) ... FIXME default to grayscale ?
- CheckMandatoryEntry(0x0028,0x0002,"1");
// Remove some inconstencies (probably some more will be added)
{
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)
+ {
+ grHT[d->GetGroup()] = 0;
+ d=FileInternal->GetNextEntry();
+ }
+ // Second stage : add the missing ones (if any)
+ for (GroupHT::iterator it = grHT.begin(); it != grHT.end(); ++it)
+ {
+ 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)
Archive->Restore(0x0002,0x0100);
Archive->Restore(0x0002,0x0102);
+ // FIXME : Check if none is missing !
+
Archive->Restore(0x0008,0x0012);
Archive->Restore(0x0008,0x0013);
Archive->Restore(0x0008,0x0016);
void FileHelper::Initialize()
{
UserFunction = 0;
-
+ KeepMediaStorageSOPClassUID = false;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff