Program: gdcm
Module: $RCSfile: gdcmFileHelper.cxx,v $
Language: C++
- Date: $Date: 2005/02/21 17:45:41 $
- Version: $Revision: 1.18 $
+
+ Date: $Date: 2005/04/19 09:58:19 $
+ Version: $Revision: 1.33 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include <fstream>
+/*
+// ----------------------------- WARNING -------------------------
+
+These lines will be moved to the document-to-be 'User's Guide'
+
+// To read an image, user needs a gdcm::File
+gdcm::File *f1 = new gdcm::File(fileName);
+// user can now check some values
+std::string v = f1->GetEntryValue(groupNb,ElementNb);
+// to get the pixels, user needs a gdcm::FileHelper
+gdcm::FileHelper *fh1 = new gdcm::FileHelper(f1);
+// user may ask not to convert Palette to RGB
+uint8_t *pixels = fh1->GetImageDataRaw();
+int imageLength = fh1->GetImageDataRawSize();
+// He can now use the pixels, create a new image, ...
+uint8_t *userPixels = ...
+
+To re-write the image, user re-uses the gdcm::FileHelper
+
+fh1->SetImageData( userPixels, userPixelsLength);
+fh1->SetTypeToRaw(); // Even if it was possible to convert Palette to RGB
+ // (WriteMode is set)
+
+fh1->SetWriteTypeToDcmExpl(); // he wants Explicit Value Representation
+ // Little Endian is the default
+ // no other value is allowed
+ (-->SetWriteType(ExplicitVR);)
+ -->WriteType = ExplicitVR;
+fh1->Write(newFileName); // overwrites the file, if any
+
+// or :
+fh1->WriteDcmExplVR(newFileName);
+
+
+// ----------------------------- WARNING -------------------------
+
+These lines will be moved to the document-to-be 'Developer's Guide'
+
+WriteMode : WMODE_RAW / WMODE_RGB
+WriteType : ImplicitVR, ExplicitVR, ACR, ACR_LIBIDO
+
+fh1->Write(newFileName);
+ SetWriteFileTypeToImplicitVR() / SetWriteFileTypeToExplicitVR();
+ (modifies TransferSyntax)
+ SetWriteToRaw(); / SetWriteToRGB();
+ (modifies, when necessary : photochromatic interpretation,
+ samples per pixel, Planar configuration,
+ bits allocated, bits stored, high bit -ACR 24 bits-
+ Pixels element VR, pushes out the LUT )
+ CheckWriteIntegrity();
+ (checks user given pixels length)
+ FileInternal->Write(fileName,WriteType)
+ fp = opens file(fileName);
+ ComputeGroup0002Length(writetype);
+ BitsAllocated 12->16
+ RemoveEntryNoDestroy(palettes, etc)
+ Document::WriteContent(fp, writetype);
+ RestoreWrite();
+ (moves back to the File all the archived elements)
+ RestoreWriteFileType();
+ (pushes back group 0002, with TransferSyntax)
+*/
+
+
+
namespace gdcm
{
*/
bool FileHelper::WriteRawData(std::string const &fileName)
{
- std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
+ std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
if (!fp1)
{
gdcmWarningMacro( "Fail to open (write) file:" << fileName.c_str());
SetWriteFileTypeToImplicitVR();
CheckMandatoryElements();
break;
+ case Unknown: // should never happen; ExplicitVR is the default value
case ExplicitVR:
SetWriteFileTypeToExplicitVR();
CheckMandatoryElements();
break;
case ACR:
case ACR_LIBIDO:
+ // Just to avoid further trouble if user create a file ex-nihilo,
+ // wants to write it as an ACR-NEMA file,
+ // and forget to create any Entry belonging to group 0008
+ // (shame on him !)
+ // We add Recognition Code (RET)
+ if ( ! FileInternal->GetValEntry(0x0008, 0x0010) )
+ FileInternal->InsertValEntry("", 0x0008, 0x0010);
SetWriteFileTypeToACR();
- break;
- default:
- SetWriteFileTypeToExplicitVR();
+ SetWriteFileTypeToImplicitVR();
CheckMandatoryElements();
+ break;
+
}
// --------------------------------------------------------------
// just before writting ...
/// \todo the best trick would be *change* the recognition code
/// but pb expected if user deals with, e.g. COMPLEX images
+
if( WriteType == ACR_LIBIDO )
{
SetWriteToLibido();
RestoreWrite();
RestoreWriteFileType();
+ RestoreWriteMandatory();
// --------------------------------------------------------------
// Special Patch to allow gdcm to re-write ACR-LibIDO formated images
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);
*/
void FileHelper::RestoreWriteFileType()
{
- // group 0002 may be pushed out for ACR-NEMA writting purposes
- Archive->Restore(0x0002,0x0000);
- Archive->Restore(0x0002,0x0001);
- Archive->Restore(0x0002,0x0002);
- Archive->Restore(0x0002,0x0003);
- Archive->Restore(0x0002,0x0010);//only TransferSyntax was pushed out/restored
- Archive->Restore(0x0002,0x0012);
- Archive->Restore(0x0002,0x0013);
- Archive->Restore(0x0002,0x0016);
- Archive->Restore(0x0002,0x0100);
- Archive->Restore(0x0002,0x0102);
}
/**
Archive->Restore(0x0028,0x0010);
Archive->Restore(0x0028,0x0011);
Archive->Restore(0x0008,0x0010);
+
+ // Restore 'LibIDO-special' entries, if any
+ Archive->Restore(0x0028,0x0015);
+ Archive->Restore(0x0028,0x0016);
+ Archive->Restore(0x0028,0x0017);
+ Archive->Restore(0x0028,0x00199);
}
/**
DocEntry *oldE = FileInternal->GetDocEntry(group, elem);
BinEntry *newE;
- if( oldE )
+ if( oldE )
if( oldE->GetVR()!=vr )
oldE = NULL;
}
/**
- * \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 left them.
+ *
+ * \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
+ // 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);
e_0002_0001->SetBinArea((uint8_t*)Util::GetFileMetaInformationVersion(),
false);
e_0002_0001->SetLength(2);
+ Archive->Push(e_0002_0001);
ValEntry *e_0002_0002 = CopyValEntry(0x0002,0x0002);
// [Secondary Capture Image Storage]
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 *e_0002_0012 = CopyValEntry(0x0002,0x0012);
e_0002_0012->SetValue(Util::CreateUniqueUID());
// --- Check UID-related Entries ---
// If 'SOP Class UID' exists ('true DICOM' image)
+ // 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
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 *e_0008_1150 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x1150) );
e_0008_1150->SetValue( e_0008_0016->GetValue());
sqi->AddEntry(e_0008_1150);
// temporarily replaces any previous 'Source Image Sequence'
Archive->Push(s);
- // 'Image Type'
+ // '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
- ValEntry *e_0008_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
+ e_0008_0016 = new ValEntry(
Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0016) );
// [Secondary Capture Image Storage]
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 *e_0008_0018 = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0018) );
+ 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 *e_0020_000e = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
- e_0020_000e->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e_0020_000e);
-
- // new value for 'Study Instance UID'
- // TODO prevoir flag pour figer la valeurd'un appel a l'autre
- // calculer nouvelle valeur a chaque fois
- // reutiliser mla valeur image origine
-
- ValEntry *e_0020_000d = new ValEntry(
- Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
- e_0020_000d->SetValue( Util::CreateUniqueUID() );
- Archive->Push(e_0020_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;
- // Modality
- e = FileInternal->GetValEntry(0x0008, 0x0060);
- if ( !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 = InsertValEntry("OT", 0x0008, 0x0060);
- Archive->Push(e);
+ e_0020_000e = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000e) );
+ e_0020_000e->SetValue(Util::CreateUniqueUID() );
+ Archive->Push(e_0020_000e);
}
- // Manufacturer
- e = FileInternal->GetValEntry(0x0008, 0x0070);
- if ( !e )
+
+ // '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 )
{
- e = InsertValEntry("GDCM Factory", 0x0008, 0x0070);
- Archive->Push(e);
+ e_0020_000d = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0020, 0x000d) );
+ e_0020_000d->SetValue(Util::CreateUniqueUID() );
+ Archive->Push(e_0020_000d);
}
- // Institution Name
- e = FileInternal->GetValEntry(0x0008, 0x0070);
- if ( !e )
+
+ // Modality : if missing we set it to 'OTher'
+ ValEntry *e_0008_0060 = FileInternal->GetValEntry(0x0008, 0x0060);
+ if ( !e_0008_0060 )
{
- e = InsertValEntry("GDCM Hospital",0x0008, 0x0080);
- Archive->Push(e);
- }
- // Institution Adress
- e = FileInternal->GetValEntry(0x0008, 0x0081);
- if ( !e )
+ e_0008_0060 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0060) );
+ e_0008_0060->SetValue("OT");
+ Archive->Push(e_0008_0060);
+ }
+
+ // Manufacturer : if missing we set it to 'GDCM Factory'
+ ValEntry *e_0008_0070 = FileInternal->GetValEntry(0x0008, 0x0070);
+ if ( !e_0008_0070 )
{
- e = InsertValEntry("@ GDCM", 0x0008, 0x0081);
- Archive->Push(e);
- }
- // Patient's Name
- e = FileInternal->GetValEntry(0x0010, 0x0010);
- if ( !e )
+ e_0008_0070 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0070) );
+ e_0008_0070->SetValue("GDCM Factory");
+ Archive->Push(e_0008_0070);
+ }
+
+ // Institution Name : if missing we set it to 'GDCM Hospital'
+ ValEntry *e_0008_0080 = FileInternal->GetValEntry(0x0008, 0x0080);
+ if ( !e_0008_0080 )
{
- e = InsertValEntry("GDCM^patient", 0x0010, 0x0010);
- Archive->Push(e);
- }
- // Patient's ID
- e = FileInternal->GetValEntry(0x0010, 0x0020);
- if ( !e )
+ e_0008_0080 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0080) );
+ e_0008_0080->SetValue("GDCM Hospital");
+ Archive->Push(e_0008_0080);
+ }
+
+ // Patient's Name : if missing, we set it to 'GDCM^Patient'
+ ValEntry *e_0010_0010 = FileInternal->GetValEntry(0x0010, 0x0010);
+ if ( !e_0010_0010 )
{
- e = InsertValEntry("GDCM_patient_ID",0x0010, 0x0020);
- Archive->Push(e);
- }
+ e_0010_0010 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0010) );
+ e_0010_0010->SetValue("GDCM^Patient");
+ Archive->Push(e_0010_0010);
+ }
- // Patient's Birth Date
- e = FileInternal->GetValEntry(0x0010, 0x0030);
- if ( !e )
+ // Patient's Birth Date : 'type 2' entry -> must exist, value not mandatory
+ ValEntry *e_0010_0030 = FileInternal->GetValEntry(0x0010, 0x0030);
+ if ( !e_0010_0030 )
{
- e = InsertValEntry("",0x0010, 0x0030);
- Archive->Push(e);
+ e_0010_0030 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0030) );
+ e_0010_0030->SetValue("");
+ Archive->Push(e_0010_0030);
}
- // Patient's Sex
- e = FileInternal->GetValEntry(0x0010, 0x0040);
- if ( !e )
+ // Patient's Sex :'type 2' entry -> must exist, value not mandatory
+ ValEntry *e_0010_0040 = FileInternal->GetValEntry(0x0010, 0x0040);
+ if ( !e_0010_0040 )
{
- e = InsertValEntry("",0x0010, 0x0040);
- Archive->Push(e);
+ e_0010_0040 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0010, 0x0040) );
+ e_0010_0040->SetValue("");
+ Archive->Push(e_0010_0040);
}
- // Referring Physician's Name
- e = FileInternal->GetValEntry(0x0008, 0x0090);
- if ( !e )
+ // Referring Physician's Name :'type 2' entry -> must exist, value not mandatory
+ ValEntry *e_0008_0090 = FileInternal->GetValEntry(0x0008, 0x0090);
+ if ( !e_0008_0090 )
{
- e = InsertValEntry("",0x0008, 0x0090);
- Archive->Push(e);
+ e_0008_0090 = new ValEntry(
+ Global::GetDicts()->GetDefaultPubDict()->GetEntry(0x0008, 0x0090) );
+ e_0008_0090->SetValue("");
+ Archive->Push(e_0008_0090);
}
+
+ // 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)
+ ValEntry *e_0028_0008 = FileInternal->GetValEntry(0x0028, 0x0008);
+ if ( !e_0028_0008 )
+ {
+ Archive->Push(0x0020, 0X0052);
+ }
}
+/**
+ * \brief Restore in the File the initial group 0002
+ */
+void FileHelper::RestoreWriteMandatory()
+{
+ // group 0002 may be pushed out for ACR-NEMA writting purposes
+ Archive->Restore(0x0002,0x0000);
+ Archive->Restore(0x0002,0x0001);
+ Archive->Restore(0x0002,0x0002);
+ Archive->Restore(0x0002,0x0003);
+ Archive->Restore(0x0002,0x0012);
+ Archive->Restore(0x0002,0x0013);
+ Archive->Restore(0x0002,0x0016);
+ Archive->Restore(0x0002,0x0100);
+ Archive->Restore(0x0002,0x0102);
+}
+
//-----------------------------------------------------------------------------
// Private
/**
WriteMode = WMODE_RAW;
WriteType = ExplicitVR;
- PixelReadConverter = new PixelReadConvert;
+ PixelReadConverter = new PixelReadConvert;
PixelWriteConverter = new PixelWriteConvert;
Archive = new DocEntryArchive( FileInternal );
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff