Program: gdcm
Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/02/28 16:34:55 $
- Version: $Revision: 1.21 $
+
+ Date: $Date: 2005/03/02 17:18:32 $
+ Version: $Revision: 1.22 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
}
/**
- * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
+ * \brief Points the internal pointer to the callers inData
+ * image representation, BUT WITHOUT COPYING THE DATA.
+ * 'image' Pixels are presented as C-like 2D arrays : line per line.
+ * 'volume'Pixels are presented as C-like 3D arrays : plane per plane
* \warning Since the pixels are not copied, it is the caller's responsability
* not to deallocate its data before gdcm uses them (e.g. with
* the Write() method )
}
/**
- * \brief Set the image data defined by the user, BUT WITHOUT COPYING THE DATA.
+ * \brief Set the image data defined by the user
* \warning When writting the file, this data are get as default data to write
- * \warning Since the pixels are not copied, it is the caller's responsability
- * not to deallocate its data before gdcm uses them (e.g. with
- * the Write() method )
* @param inData user supplied pixel area (uint8_t* is just for the compiler.
* user is allowed to pass any kind of pixels since the size is
* given in bytes)
Archive->Push(0x0002,0x0001);
Archive->Push(0x0002,0x0002);
Archive->Push(0x0002,0x0003);
- Archive->Push(0x0002,0x0010);// Only TransferSyntax was pushed out !
+ Archive->Push(0x0002,0x0010);
Archive->Push(0x0002,0x0012);
Archive->Push(0x0002,0x0013);
Archive->Push(0x0002,0x0016);
Archive->Restore(0x0002,0x0001);
Archive->Restore(0x0002,0x0002);
Archive->Restore(0x0002,0x0003);
- Archive->Restore(0x0002,0x0010);//only TransferSyntax was pushed out/restored
+ Archive->Restore(0x0002,0x0010);
Archive->Restore(0x0002,0x0012);
Archive->Restore(0x0002,0x0013);
Archive->Restore(0x0002,0x0016);
}
/**
- * \brief Checks the Mandatory Elements
- * adds the mandatory Entries if not found
- * (when user asks to write as a DICOM file, an ACR-NEMA file
- * he read before)
+ * \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 ...)
+ *
+ * Just before writting :
+ * - we check the Entries
+ * - we create the mandatory entries if they are missing
+ * - we modify the values if necessary
+ * - 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
+ *
+ * \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 ...)
+ * - read the whole PS 3.3 Part of DICOM (890 pages)
+ * and write a *full* checker (probably one method per Modality ...)
+ * Any contribution is welcome.
+ * - write a user callable full checker, to allow post reading
+ * and/or pre writting image consistency check.
*/
+
void FileHelper::CheckMandatoryElements()
{
// just to remember : 'official' 0002 group
//0002 0016 AE 1 Source Application Entity Title
//0002 0100 UI 1 Private Information Creator
//0002 0102 OB 1 Private Information
-
-
+
// Create them if not found
- ValEntry *e0002_0000 = CopyValEntry(0x0002,0x0000);
- e0002_0000->SetValue("0"); // for the moment
- Archive->Push(e0002_0000);
+ // Always modify the value
+ // Push the entries to the archive.
+
+ ValEntry *e_0002_0000 = CopyValEntry(0x0002,0x0000);
+ e_0002_0000->SetValue("0"); // for the moment
+ Archive->Push(e_0002_0000);
-/* BinEntry *e0002_0001 = CopyBinEntry(0x0002,0x0001, "OB");
- e0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),false);
- e0002_0001->SetLength(2);*/
-
-/* ValEntry *e0002_0002 = CopyValEntry(0x0002,0x0002);
- // [Secondary Capture Image Storage]
- e0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7");
- Archive->Push(e0002_0002);*/
+ BinEntry *e_0002_0001 = CopyBinEntry(0x0002,0x0001, "OB");
+ e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
+ false);
+ e_0002_0001->SetLength(2);
+
+ ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002);
+ // [Secondary Capture Image Storage]
+ e_0002_0002->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ Archive->Push(e_0002_0002);
// 'Media Stored SOP Instance UID'
-/* ValEntry *e0002_0003 = CopyValEntry(0x0002,0x0003);
- e0002_0003->SetValue(Util::CreateUniqueUID());
- Archive->Push(e0002_0003); */
-
-/* ValEntry *e0002_0010 = CopyValEntry(0x0002,0x0010);
- //[Explicit VR - Little Endian]
- e0002_0010->SetValue("1.2.840.10008.1.2.1");
- Archive->Push(e0002_0010);*/
+ ValEntry *e_0002_0003 = CopyValEntry(0x0002,0x0003);
+ e_0002_0003->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e_0002_0003);
+
+ ValEntry *e_0002_0010 = CopyValEntry(0x0002,0x0010);
+ //[Explicit VR - Little Endian]
+ e_0002_0010->SetValue("1.2.840.10008.1.2.1");
+ Archive->Push(e_0002_0010);
// 'Implementation Class UID'
-/* ValEntry *e0002_0012 = CopyValEntry(0x0002,0x0012);
- e0002_0012->SetValue(Util::CreateUniqueUID());
- Archive->Push(e0002_0012); */
+ ValEntry *e_0002_0012 = CopyValEntry(0x0002,0x0012);
+ e_0002_0012->SetValue(Util::CreateUniqueUID());
+ Archive->Push(e_0002_0012);
// 'Implementation Version Name'
- ValEntry *e0002_0013 = CopyValEntry(0x0002,0x0013);
- e0002_0013->SetValue("GDCM 1.0");
- Archive->Push(e0002_0013);
+ ValEntry *e_0002_0013 = CopyValEntry(0x0002,0x0013);
+ e_0002_0013->SetValue("GDCM 1.0");
+ Archive->Push(e_0002_0013);
//'Source Application Entity Title' Not Mandatory
- //ValEntry *e0002_0016 = CopyValEntry(0x0002,0x0016);
- // e0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7");
- // Archive->Push(e0002_0016);
+ //ValEntry *e_0002_0016 = CopyValEntry(0x0002,0x0016);
+ // e_0002_0016->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ // Archive->Push(e_0002_0016);
// Push out 'LibIDO-special' entries, if any
Archive->Push(0x0028,0x0015);
// --- Check UID-related Entries ---
// If 'SOP Class UID' exists ('true DICOM' image)
- ValEntry *e0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016);
- if ( e0008_0016 != 0 )
+ // we create the 'Source Image Sequence' SeqEntry
+ // to hold informations about the Source Image
+
+ ValEntry *e_0008_0016 = FileInternal->GetValEntry(0x0008, 0x0016);
+ if ( e_0008_0016 != 0 )
{
-/* // Create 'Source Image Sequence' SeqEntry
+ // Create 'Source Image Sequence' SeqEntry
SeqEntry *s = new SeqEntry (
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x2112) );
SQItem *sqi = new SQItem(1);
// (we assume 'SOP Instance UID' exists too)
// create 'Referenced SOP Class UID'
- ValEntry *e0008_1150 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
- e0008_1150->SetValue( e0008_0016->GetValue());
- sqi->AddEntry(e0008_1150);
+ ValEntry *e_0008_1150 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
+ e_0008_1150->SetValue( e_0008_0016->GetValue());
+ sqi->AddEntry(e_0008_1150);
// create 'Referenced SOP Instance UID'
- ValEntry *e0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
- ValEntry *e0008_1155 = new ValEntry(
+ ValEntry *e_0008_0018 = FileInternal->GetValEntry(0x0008, 0x0018);
+ ValEntry *e_0008_1155 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1155) );
- e0008_1155->SetValue( e0008_0018->GetValue());
- sqi->AddEntry(e0008_1155);
+ e_0008_1155->SetValue( e_0008_0018->GetValue());
+ sqi->AddEntry(e_0008_1155);
s->AddSQItem(sqi,1);
// temporarily replaces any previous 'Source Image Sequence'
Archive->Push(s);
- // 'Image Type'
- ValEntry *e0008_0008 = CopyValEntry(0x0008,0x0008);
- e0008_0008->SetValue("DERIVED\\PRIMARY");
- Archive->Push(e0008_0008);*/
+ // 'Image Type' (The written image is no longer an 'ORIGINAL' one)
+ ValEntry *e_0008_0008 = CopyValEntry(0x0008,0x0008);
+ e_0008_0008->SetValue("DERIVED\\PRIMARY");
+ Archive->Push(e_0008_0008);
}
else
{
- // SOP Class UID
-/* e0008_0016 = new ValEntry(
+ // 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
+ ValEntry *e_0008_0016 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0016) );
// [Secondary Capture Image Storage]
- e0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
- Archive->Push(e0008_0016); */
+ e_0008_0016 ->SetValue("1.2.840.10008.5.1.4.1.1.7");
+ Archive->Push(e_0008_0016);
}
+// ---- The user will never have to take any action on the following ----.
+
// new value for 'SOP Instance UID'
- ValEntry *e0008_0018 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
- e0008_0018->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e0008_0018);
+ ValEntry *e_0008_0018 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
+ e_0008_0018->SetValue( Util::CreateUniqueUID() );
+ Archive->Push(e_0008_0018);
// Instance Creation Date
- ValEntry *e0008_0012 = CopyValEntry(0x0008,0x0012);
+ ValEntry *e_0008_0012 = CopyValEntry(0x0008,0x0012);
std::string date = Util::GetCurrentDate();
- e0008_0012->SetValue(date.c_str());
- Archive->Push(e0008_0012);
+ e_0008_0012->SetValue(date.c_str());
+ Archive->Push(e_0008_0012);
// Instance Creation Time
- ValEntry *e0008_0013 = CopyValEntry(0x0008,0x0013);
+ ValEntry *e_0008_0013 = CopyValEntry(0x0008,0x0013);
std::string time = Util::GetCurrentTime();
- e0008_0013->SetValue(time.c_str());
- Archive->Push(e0008_0013);
-
-/* // new value for 'Serie Instance UID'
- // TODO prevoir booleen pour figer la valeur d'un appel a l'autre
- // calculer nouvelle valeur a chaque fois
-
- ValEntry *e0020_000e = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
- e0020_000e->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e0020_000e);
-
- // new value for 'Study Instance UID'
- // TODO prevoir flag pour figer la valeur d'un appel a l'autre
- // calculer nouvelle valeur a chaque fois
- // reutiliser la valeur image origine
-
- ValEntry *e0020_000d = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
- e0020_000d->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e0020_000d);
-*/
+ e_0008_0013->SetValue(time.c_str());
+ Archive->Push(e_0008_0013);
// ----- Add Mandatory Entries if missing ---
// Entries whose type is 1 are mandatory, with a mandatory value
-// Entries whose type is 1c are ?
+// 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 ?
+// Entries whose type is 2c are mandatory-inside-a-Sequence
// Entries whose type is 3 are optional
-// ValEntry *e;
+ // 'Serie Instance UID'
+ // Keep the value if exists
+ // 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
+ ValEntry *e_0020_000e = FileInternal->GetValEntry(0x0020, 0x000e);
+ if ( !e_0020_000e )
+ {
+ e_0020_000e = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
+ e_0020_000e->SetValue(Util::CreateUniqueUID() );
+ Archive->Push(e_0020_000e);
+ }
- // Modality
-/* ValEntry *e0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
- if ( !e0008_0060 )
+ // '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
+ ValEntry *e_0020_000d = FileInternal->GetValEntry(0x0020, 0x000d);
+ if ( !e_0020_000d )
{
- e0008_0060 = new ValEntry(
+ e_0020_000d = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
+ e_0020_000d->SetValue(Util::CreateUniqueUID() );
+ Archive->Push(e_0020_000d);
+ }
+
+ // Modality : if missing we set it to 'OTher'
+ ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
+ if ( !e_0008_0060 )
+ {
+ e_0008_0060 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) );
- e0008_0060->SetValue("OT");
- Archive->Push(e0008_0060);
+ e_0008_0060->SetValue("OT");
+ Archive->Push(e_0008_0060);
}
- // Manufacturer
- ValEntry *e0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
- if ( !e0008_0070 )
+ // Manufacturer : if missing we set it to 'GDCM Factory'
+ ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
+ if ( !e_0008_0070 )
{
- e0008_0070 = new ValEntry(
+ e_0008_0070 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) );
- e0008_0070->SetValue("GDCM Factory");
- Archive->Push(e0008_0070);
- }
+ e_0008_0070->SetValue("GDCM Factory");
+ Archive->Push(e_0008_0070);
+ }
- // Institution Name
- ValEntry *e0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
- if ( !e0008_0080 )
+ // Institution Name : if missing we set it to 'GDCM Hospital'
+ ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
+ if ( !e_0008_0080 )
{
- e0008_0080 = new ValEntry(
+ e_0008_0080 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) );
- e0008_0080->SetValue("GDCM Hospital");
- Archive->Push(e0008_0080);
- }
+ e_0008_0080->SetValue("GDCM Hospital");
+ Archive->Push(e_0008_0080);
+ }
- // Patient's Name
- ValEntry *e0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
- if ( !e0010_0010 )
+ // Patient's Name : if missing, we set it to 'GDCM^Patient'
+ ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
+ if ( !e_0010_0010 )
{
- e0010_0010 = new ValEntry(
+ e_0010_0010 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) );
- e0010_0010->SetValue("GDCM_Patient");
- Archive->Push(e0010_0010);
- }
+ e_0010_0010->SetValue("GDCM^Patient");
+ Archive->Push(e_0010_0010);
+ }
- // Patient's ID
+ // Patient's ID : if missing, we set it to 'GDCM_Patient_ID'
ValEntry *e_0010_0020 = FileInternal->GetValEntry(0x0010, 0x0020);
- if ( !e )
+ if ( !e_0010_0020 )
{
e_0010_0020 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0020) );
Archive->Push(e_0010_0020);
}
- // Patient's Birth Date
+ // Patient's Birth Date :'type 2' entry -> must exist, value not mandatory
ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030);
if ( !e_0010_0030 )
{
Archive->Push(e_0010_0030);
}
- // Patient's Sex
+ // Patient's Sex :'type 2' entry -> must exist, value not mandatory
ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040);
if ( !e_0010_0040 )
{
Archive->Push(e_0010_0040);
}
- // Referring Physician's Name
+ // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090);
if ( !e_0008_0090 )
{
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) );
e_0008_0090->SetValue("");
Archive->Push(e_0008_0090);
- }*/
+ }
+
+ // Remove some inconstencies (probably some more will be added)
+
+ // Push out (0020 0052),Frame of Reference UID
+ // if (0028 0008)Number of Frames exists
+ // (0020 0052),Frame of Reference UID only meaningfull within a Serie
+ ValEntry *e_0028_0008 = FileInternal->GetValEntry(0x0028, 0x0008);
+ if ( !e_0028_0008 )
+ {
+ Archive->Push(0x0020, 0X0052);
+ }
}
//-----------------------------------------------------------------------------
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
- PixelReadConverter = new PixelReadConvert;
+ PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
Archive = new DocEntryArchive( FileInternal );
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