Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/01/26 09:49:54 $
- Version: $Revision: 1.201 $
+ Date: $Date: 2005/01/26 17:17:31 $
+ Version: $Revision: 1.202 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmTS.h"
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
-#include <stdio.h> //sscanf
+#include "gdcmRLEFramesInfo.h"
+#include "gdcmJPEGFragmentsInfo.h"
+#include <stdio.h> //sscanf
#include <vector>
namespace gdcm
* @param filename name of the file whose header we want to analyze
*/
File::File( std::string const &filename ):
- Document( filename )
+ Document( filename )
{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
+
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
// (Image Location") . This entry contains the number of
GrPixel = (uint16_t) atoi( imgLocation.c_str() );
}
- // sometimes Image Location value doesn't follow
- // the supposed processor endianness.
- // see gdcmData/cr172241.dcm
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianness.
+ // see gdcmData/cr172241.dcm
if ( GrPixel == 0xe07f )
{
GrPixel = 0x7fe0;
DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
if ( entry != 0 )
{
-
+ // Compute the RLE or JPEG info
+ OpenFile();
+ std::string ts = GetTransferSyntax();
+ Fp->seekg( entry->GetOffset(), std::ios::beg );
+ if ( Global::GetTS()->IsRLELossless(ts) )
+ ComputeRLEInfo();
+ else if ( Global::GetTS()->IsJPEG(ts) )
+ ComputeJPEGFragmentInfo();
+ CloseFile();
+
+ // Change the created dict entry
std::string PixelVR;
// 8 bits allocated is a 'O Bytes' , as well as 24 (old ACR-NEMA RGB)
// more than 8 (i.e 12, 16) is a 'O Words'
else
PixelVR = "OW";
- DictEntry* newEntry = NewVirtualDictEntry(
- GrPixel, NumPixel,
- PixelVR, "PXL", "Pixel Data");
-
+ DictEntry* newEntry = NewVirtualDictEntry(GrPixel, NumPixel,
+ PixelVR, "PXL", "Pixel Data");
+
// friend class hunting : should we *create* a new entry,
// instead of modifying its DictEntry,in order not to use 'friend' ?
entry->SetDictEntry( newEntry );
/**
* \brief Constructor used when we want to generate dicom files from scratch
*/
-File::File()
- :Document()
+File::File():
+ Document()
{
+ RLEInfo = new RLEFramesInfo;
+ JPEGInfo = new JPEGFragmentsInfo;
InitializeDefaultFile();
}
*/
File::~File ()
{
+ if( RLEInfo )
+ delete RLEInfo;
+ if( JPEGInfo )
+ delete JPEGInfo;
}
/**
return lutNbits;
}
+/**
+ * \brief gets the info from 0020,0037 : Image Orientation Patient
+ * (needed to organize DICOM files based on their x,y,z position)
+ * @param iop adress of the (6)float aray to receive values
+ * @return cosines of image orientation patient
+ */
+void File::GetImageOrientationPatient( float iop[6] )
+{
+ std::string strImOriPat;
+ //iop is supposed to be float[6]
+ iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
-//-----------------------------------------------------------------------------
-// Protected
+ // 0020 0037 DS REL Image Orientation (Patient)
+ if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
+ {
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
+ }
+ }
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
+ {
+ if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
+ &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
+ {
+ gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
+ }
+ }
+}
/**
* \brief anonymize a File (removes Patient's personal info)
return true;
}
-/**
- * \brief gets the info from 0020,0037 : Image Orientation Patient
- * (needed to organize DICOM files based on their x,y,z position)
- * @param iop adress of the (6)float aray to receive values
- * @return cosines of image orientation patient
- */
-void File::GetImageOrientationPatient( float iop[6] )
-{
- std::string strImOriPat;
- //iop is supposed to be float[6]
- iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
-
- // 0020 0037 DS REL Image Orientation (Patient)
- if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
- {
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
- {
- gdcmVerboseMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
- }
- }
- //For ACR-NEMA
- // 0020 0035 DS REL Image Orientation (RET)
- else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
- {
- if( sscanf( strImOriPat.c_str(), "%f\\%f\\%f\\%f\\%f\\%f",
- &iop[0], &iop[1], &iop[2], &iop[3], &iop[4], &iop[5]) != 6 )
- {
- gdcmVerboseMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
- }
- }
-}
-
+//-----------------------------------------------------------------------------
+// Protected
/**
* \brief Initialize a default DICOM File that should contain all the
* field require by other reader. DICOM standard does not
//-----------------------------------------------------------------------------
// Private
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment RLE encoding.
+ * Compute the RLE extra information and store it in \ref RLEInfo
+ * for later pixel retrieval usage.
+ */
+void File::ComputeRLEInfo()
+{
+ std::string ts = GetTransferSyntax();
+ if ( !Global::GetTS()->IsRLELossless(ts) )
+ {
+ return;
+ }
+
+ // Encoded pixel data: for the time being we are only concerned with
+ // Jpeg or RLE Pixel data encodings.
+ // As stated in PS 3.5-2003, section 8.2 p44:
+ // "If sent in Encapsulated Format (i.e. other than the Native Format) the
+ // value representation OB is used".
+ // Hence we expect an OB value representation. Concerning OB VR,
+ // the section PS 3.5-2003, section A.4.c p 58-59, states:
+ // "For the Value Representations OB and OW, the encoding shall meet the
+ // following specifications depending on the Data element tag:"
+ // [...snip...]
+ // - the first item in the sequence of items before the encoded pixel
+ // data stream shall be basic offset table item. The basic offset table
+ // item value, however, is not required to be present"
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Encapsulated RLE Compressed Images (see PS 3.5-2003, Annex G)
+ // Loop on the individual frame[s] and store the information
+ // on the RLE fragments in a RLEFramesInfo.
+ // Note: - when only a single frame is present, this is a
+ // classical image.
+ // - when more than one frame are present, then we are in
+ // the case of a multi-frame image.
+ long frameLength;
+ while ( (frameLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ // Parse the RLE Header and store the corresponding RLE Segment
+ // Offset Table information on fragments of this current Frame.
+ // Note that the fragment pixels themselves are not loaded
+ // (but just skipped).
+ long frameOffset = Fp->tellg();
+
+ uint32_t nbRleSegments = ReadInt32();
+ if ( nbRleSegments > 16 )
+ {
+ // There should be at most 15 segments (refer to RLEFrame class)
+ gdcmVerboseMacro( "Too many segments.");
+ }
+
+ uint32_t rleSegmentOffsetTable[16];
+ for( int k = 1; k <= 15; k++ )
+ {
+ rleSegmentOffsetTable[k] = ReadInt32();
+ }
+
+ // Deduce from both the RLE Header and the frameLength the
+ // fragment length, and again store this info in a
+ // RLEFramesInfo.
+ long rleSegmentLength[15];
+ // skipping (not reading) RLE Segments
+ if ( nbRleSegments > 1)
+ {
+ for(unsigned int k = 1; k <= nbRleSegments-1; k++)
+ {
+ rleSegmentLength[k] = rleSegmentOffsetTable[k+1]
+ - rleSegmentOffsetTable[k];
+ SkipBytes(rleSegmentLength[k]);
+ }
+ }
+
+ rleSegmentLength[nbRleSegments] = frameLength
+ - rleSegmentOffsetTable[nbRleSegments];
+ SkipBytes(rleSegmentLength[nbRleSegments]);
+
+ // Store the collected info
+ RLEFrame *newFrame = new RLEFrame;
+ newFrame->SetNumberOfFragments(nbRleSegments);
+ for( unsigned int uk = 1; uk <= nbRleSegments; uk++ )
+ {
+ newFrame->SetOffset(uk,frameOffset + rleSegmentOffsetTable[uk]);
+ newFrame->SetLength(uk,rleSegmentLength[uk]);
+ }
+ RLEInfo->AddFrame(newFrame);
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
+ }
+}
+
+/**
+ * \brief Parse pixel data from disk of [multi-]fragment Jpeg encoding.
+ * Compute the jpeg extra information (fragment[s] offset[s] and
+ * length) and store it[them] in \ref JPEGInfo for later pixel
+ * retrieval usage.
+ */
+void File::ComputeJPEGFragmentInfo()
+{
+ // If you need to, look for comments of ComputeRLEInfo().
+ std::string ts = GetTransferSyntax();
+ if ( ! Global::GetTS()->IsJPEG(ts) )
+ {
+ return;
+ }
+
+ ReadAndSkipEncapsulatedBasicOffsetTable();
+
+ // Loop on the fragments[s] and store the parsed information in a
+ // JPEGInfo.
+ long fragmentLength;
+ while ( (fragmentLength = ReadTagLength(0xfffe, 0xe000)) )
+ {
+ long fragmentOffset = Fp->tellg();
+
+ // Store the collected info
+ JPEGFragment *newFragment = new JPEGFragment;
+ newFragment->SetOffset(fragmentOffset);
+ newFragment->SetLength(fragmentLength);
+ JPEGInfo->AddFragment(newFragment);
+
+ SkipBytes(fragmentLength);
+ }
+
+ // Make sure that at the end of the item we encounter a 'Sequence
+ // Delimiter Item':
+ if ( !ReadTag(0xfffe, 0xe0dd) )
+ {
+ gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
+ }
+}
+
+/**
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag check whether this
+ * tag is (TestGroup, TestElement).
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return True on success, false otherwise.
+ */
+bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
+{
+ long positionOnEntry = Fp->tellg();
+ long currentPosition = Fp->tellg(); // On debugging purposes
+
+ //// Read the Item Tag group and element, and make
+ // sure they are what we expected:
+ uint16_t itemTagGroup;
+ uint16_t itemTagElement;
+ try
+ {
+ itemTagGroup = ReadInt16();
+ itemTagElement = ReadInt16();
+ }
+ catch ( FormatError e )
+ {
+ //std::cerr << e << std::endl;
+ return false;
+ }
+ if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ {
+ gdcmVerboseMacro( "Wrong Item Tag found:"
+ << " We should have found tag ("
+ << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << " but instead we encountered tag ("
+ << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
+ ) ;
+ Fp->seekg(positionOnEntry, std::ios::beg);
+
+ return false;
+ }
+ return true;
+}
+
+/**
+ * \brief Assuming the internal file pointer \ref Document::Fp
+ * is placed at the beginning of a tag (TestGroup, TestElement),
+ * read the length associated to the Tag.
+ * \warning On success the internal file pointer \ref Document::Fp
+ * is modified to point after the tag and it's length.
+ * On failure (i.e. when the tag wasn't the expected tag
+ * (TestGroup, TestElement) the internal file pointer
+ * \ref Document::Fp is restored to it's original position.
+ * @param testGroup The expected group of the tag.
+ * @param testElement The expected Element of the tag.
+ * @return On success returns the length associated to the tag. On failure
+ * returns 0.
+ */
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElement)
+{
+
+ if ( !ReadTag(testGroup, testElement) )
+ {
+ return 0;
+ }
+
+ //// Then read the associated Item Length
+ long currentPosition = Fp->tellg();
+ uint32_t itemLength = ReadInt32();
+ {
+ gdcmVerboseMacro( "Basic Item Length is: "
+ << itemLength << std::endl
+ << " at address: " << std::hex << (unsigned int)currentPosition);
+ }
+ return itemLength;
+}
+
+/**
+ * \brief When parsing the Pixel Data of an encapsulated file, read
+ * the basic offset table (when present, and BTW dump it).
+ */
+void File::ReadAndSkipEncapsulatedBasicOffsetTable()
+{
+ //// Read the Basic Offset Table Item Tag length...
+ uint32_t itemLength = ReadTagLength(0xfffe, 0xe000);
+
+ // When present, read the basic offset table itself.
+ // Notes: - since the presence of this basic offset table is optional
+ // we can't rely on it for the implementation, and we will simply
+ // trash it's content (when present).
+ // - still, when present, we could add some further checks on the
+ // lengths, but we won't bother with such fuses for the time being.
+ if ( itemLength != 0 )
+ {
+ char *basicOffsetTableItemValue = new char[itemLength + 1];
+ Fp->read(basicOffsetTableItemValue, itemLength);
+
+#ifdef GDCM_DEBUG
+ for (unsigned int i=0; i < itemLength; i += 4 )
+ {
+ uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
+ uint32_t);
+ gdcmVerboseMacro( "Read one length: " <<
+ std::hex << individualLength );
+ }
+#endif //GDCM_DEBUG
+
+ delete[] basicOffsetTableItemValue;
+ }
+}
//-----------------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff