Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/10/26 06:08:24 $
- Version: $Revision: 1.75 $
+ Date: $Date: 2006/01/19 11:46:45 $
+ Version: $Revision: 1.88 $
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(File *header)
{
+ gdcmAssertMacro(header);
+
FileInternal = header;
- header->Register();
+ FileInternal->Register();
Initialize();
if ( FileInternal->IsReadable() )
{
- PixelReadConverter->GrabInformationsFromFile( FileInternal );
+ PixelReadConverter->GrabInformationsFromFile( FileInternal, this );
}
}
}
FileInternal->Unregister();
- FileInternal = 0;
}
//-----------------------------------------------------------------------------
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)
/**
* \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 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 ...)
/* -------------------------------------------------------------------------------------
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.
+-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.
+
+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 allowed 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)
+'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, he may ask the writer to 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
+by gdcm::FileHelper::CheckMandatoryElements()
+
-->'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)
+
+ --> 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)
+
--> 'Modality' (0x0008,0x0060)
is defaulted to "OT" (other) if missing.
(a fully user created image belongs to *no* modality)
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)
+ --> '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)
-
+--> Imager Pixel Spacing (0x0018,0x1164) : defaulted to Pixel Spacing value
+
+--> 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) 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.
// 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'
<< " for consistency purpose");
}
- // Pixel Spacing : defaulted to 1.0\1.0
- CheckMandatoryEntry(0x0028,0x0030,"1.0\\1.0");
-
+ 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);
+ }
+
+ // '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 ---
+ // --- Check UID-related Entries ---
// If 'SOP Class UID' exists ('true DICOM' image)
// we create the 'Source Image Sequence' SeqEntry
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)
+ 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(0x0008,0x0013,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,"");
+ //CopyMandatoryEntry(0x0008,0x0050,"");
+ CheckMandatoryEntry(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,
- // 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");
{
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);
Archive->Restore(0x0020,0x000e);
}
+
+/**
+ * \brief CallStartMethod
+ */
+void FileHelper::CallStartMethod()
+{
+ Progress = 0.0f;
+ Abort = false;
+ CommandManager::ExecuteCommand(this,CMD_STARTPROGRESS);
+}
+
+/**
+ * \brief CallProgressMethod
+ */
+void FileHelper::CallProgressMethod()
+{
+ CommandManager::ExecuteCommand(this,CMD_PROGRESS);
+}
+
+/**
+ * \brief CallEndMethod
+ */
+void FileHelper::CallEndMethod()
+{
+ Progress = 1.0f;
+ CommandManager::ExecuteCommand(this,CMD_ENDPROGRESS);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
void FileHelper::Initialize()
{
UserFunction = 0;
-
+ KeepMediaStorageSOPClassUID = false;
+
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;