- /*=========================================================================
+/*=========================================================================
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2004/11/24 16:39:18 $
- Version: $Revision: 1.162 $
+ Date: $Date: 2005/01/24 16:44:54 $
+ Version: $Revision: 1.199 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
=========================================================================*/
#include "gdcmFile.h"
-#include "gdcmDebug.h"
+#include "gdcmGlobal.h"
#include "gdcmUtil.h"
+#include "gdcmDebug.h"
+#include "gdcmTS.h"
+#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
-#include <fstream>
+#include <stdio.h> //sscanf
+
+#include <vector>
namespace gdcm
{
-typedef std::pair<TagDocEntryHT::iterator,TagDocEntryHT::iterator> IterHT;
-
-//-------------------------------------------------------------------------
+//-----------------------------------------------------------------------------
// Constructor / Destructor
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header 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
- * (see GetImageData, GetImageDataRaw)
- * \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
- * user sets an a posteriori shadow dictionary (efficiency can be
- * seen as a side effect).
- * @param header already built Header
+ * \brief Constructor
+ * @param filename name of the file whose header we want to analyze
*/
-File::File(Header *header)
+File::File( std::string const &filename ):
+ Document( filename )
+{
+ // 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
+ // the group that contains the pixel data (hence the "Pixel Data"
+ // is found by indirection through the "Image Location").
+ // Inside the group pointed by "Image Location" the searched element
+ // is conventionally the element 0x0010 (when the norm is respected).
+ // When the "Image Location" is missing we default to group 0x7fe0.
+ // Note: this IS the right place for the code
+
+ // Image Location
+ const std::string &imgLocation = GetEntryValue(0x0028, 0x0200);
+ if ( imgLocation == GDCM_UNFOUND )
+ {
+ // default value
+ GrPixel = 0x7fe0;
+ }
+ else
+ {
+ GrPixel = (uint16_t) atoi( imgLocation.c_str() );
+ }
+
+ // sometimes Image Location value doesn't follow
+ // the supposed processor endianness.
+ // see gdcmData/cr172241.dcm
+ if ( GrPixel == 0xe07f )
+ {
+ GrPixel = 0x7fe0;
+ }
+
+ if ( GrPixel != 0x7fe0 )
+ {
+ // This is a kludge for old dirty Philips imager.
+ NumPixel = 0x1010;
+ }
+ else
+ {
+ NumPixel = 0x0010;
+ }
+
+ // Now, we know GrPixel and NumPixel.
+ // Let's create a VirtualDictEntry to allow a further VR modification
+ // and force VR to match with BitsAllocated.
+ DocEntry *entry = GetDocEntry(GrPixel, NumPixel);
+ if ( entry != 0 )
+ {
+
+ 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'
+ if ( GetBitsAllocated() == 8 || GetBitsAllocated() == 24 )
+ PixelVR = "OB";
+ else
+ PixelVR = "OW";
+
+ 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()
{
- HeaderInternal = header;
- SelfHeader = false;
- Initialise();
+ InitializeDefaultFile();
}
/**
- * \brief Constructor dedicated to deal with the *pixels* area of a ACR/DICOMV3
- * file (Header 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
- * (see GetImageData, GetImageDataRaw)
- * \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
+ * \brief Canonical destructor.
*/
-File::File(std::string const & filename )
+File::~File ()
{
- HeaderInternal = new Header( filename );
- SelfHeader = true;
- Initialise();
}
/**
- * \brief Factorization for various forms of constructors.
+ * \brief Performs some consistency checking on various 'File related'
+ * (as opposed to 'DicomDir related') entries
+ * then writes in a file all the (Dicom Elements) included the Pixels
+ * @param fileName file name to write to
+ * @param filetype Type of the File to be written
+ * (ACR, ExplicitVR, ImplicitVR)
*/
-void File::Initialise()
+bool File::Write(std::string fileName, FileType filetype)
{
- WriteMode = WMODE_DECOMPRESSED;
- WriteType = WTYPE_IMPL_VR;
+ std::ofstream *fp = new std::ofstream(fileName.c_str(),
+ std::ios::out | std::ios::binary);
+ if (*fp == NULL)
+ {
+ gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
+ return false;
+ }
- PixelConverter = new PixelConvert;
- Archive = new DocEntryArchive( HeaderInternal );
+ // Bits Allocated
+ if ( GetEntryValue(0x0028,0x0100) == "12")
+ {
+ SetEntryValue("16", 0x0028,0x0100);
+ }
+
+ /// \todo correct 'Pixel group' Length if necessary
- if ( HeaderInternal->IsReadable() )
+ int i_lgPix = GetEntryLength(GrPixel, NumPixel);
+ if (i_lgPix != -2)
{
- ImageDataSizeRaw = ComputeDecompressedPixelDataSizeFromHeader();
- if ( HeaderInternal->HasLUT() )
+ // no (GrPixel, NumPixel) element
+ std::string s_lgPix = Util::Format("%d", i_lgPix+12);
+ s_lgPix = Util::DicomString( s_lgPix.c_str() );
+ Insert(s_lgPix,GrPixel, 0x0000);
+ }
+
+ // FIXME : should be nice if we could move it to File
+ // (or in future gdcmPixelData class)
+
+ // Drop Palette Color, if necessary
+
+ if ( GetEntryValue(0x0028,0x0002).c_str()[0] == '3' )
+ {
+ // if SamplesPerPixel = 3, sure we don't need any LUT !
+ // Drop 0028|1101, 0028|1102, 0028|1103
+ // Drop 0028|1201, 0028|1202, 0028|1203
+
+ DocEntry *e = GetDocEntry(0x0028,0x01101);
+ if (e)
{
- ImageDataSize = 3 * ImageDataSizeRaw;
+ RemoveEntryNoDestroy(e);
}
- else
+ e = GetDocEntry(0x0028,0x1102);
+ if (e)
{
- ImageDataSize = ImageDataSizeRaw;
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1103);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x01201);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1202);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
+ }
+ e = GetDocEntry(0x0028,0x1203);
+ if (e)
+ {
+ RemoveEntryNoDestroy(e);
}
-
- PixelConverter->GrabInformationsFromHeader( HeaderInternal );
}
- SaveInitialValues();
-}
-
-/**
- * \brief canonical destructor
- * \note If the Header was created by the File constructor,
- * it is destroyed by the File
- */
-File::~File()
-{
- if( PixelConverter )
- {
- delete PixelConverter;
- }
- if( Archive )
+/*
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Super Super hack that will make gdcm a BOMB ! but should
+ // Fix temporarily the dashboard
+ BinEntry *b = GetBinEntry(GrPixel,NumPixel);
+ if ( GetPixelSize() == 16 )
{
- delete Archive;
+ uint16_t *im16 = (uint16_t*)b->GetBinArea();
+ int lgr = b->GetLength();
+ for( int i = 0; i < lgr / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
}
+#endif //GDCM_WORDS_BIGENDIAN
+*/
+
+ Document::WriteContent(fp,filetype);
- if( SelfHeader )
+/*
+#ifdef GDCM_WORDS_BIGENDIAN
+ // Flip back the pixel ... I told you this is a hack
+ if ( GetPixelSize() == 16 )
{
- delete HeaderInternal;
+ uint16_t *im16 = (uint16_t*)b->GetBinArea();
+ int lgr = b->GetLength();
+ for( int i = 0; i < lgr / 2; i++ )
+ {
+ im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
+ }
}
- HeaderInternal = 0;
-}
+#endif //GDCM_WORDS_BIGENDIAN
+*/
-/**
- * \brief Sets some initial values for the Constructor
- * \warning not end user intended
- */
-void File::SaveInitialValues()
-{
- PixelRead = -1; // no ImageData read yet.
- Pixel_Data = 0;
+ fp->close();
+ delete fp;
+
+ return true;
}
//-----------------------------------------------------------------------------
// Print
+
//-----------------------------------------------------------------------------
// Public
/**
- * \brief computes the length (in bytes) we must ALLOCATE to receive the
- * image(s) pixels (multiframes taken into account)
- * \warning : it is NOT the group 7FE0 length
- * (no interest for compressed images).
- */
-int File::ComputeDecompressedPixelDataSizeFromHeader()
-{
- // see PS 3.3-2003 : C.7.6.3.2.1
- //
- // MONOCHROME1
- // MONOCHROME2
- // PALETTE COLOR
- // RGB
- // HSV (Retired)
- // ARGB (Retired)
- // CMYK (Retired)
- // YBR_FULL
- // YBR_FULL_422 (no LUT, no Palette)
- // YBR_PARTIAL_422
- // YBR_ICT
- // YBR_RCT
-
- // LUT's
- // ex : gdcm-US-ALOKA-16.dcm
- // 0028|1221 [OW] [Segmented Red Palette Color Lookup Table Data]
- // 0028|1222 [OW] [Segmented Green Palette Color Lookup Table Data]
- // 0028|1223 [OW] [Segmented Blue Palette Color Lookup Table Data]
-
- // ex : OT-PAL-8-face.dcm
- // 0028|1201 [US] [Red Palette Color Lookup Table Data]
- // 0028|1202 [US] [Green Palette Color Lookup Table Data]
- // 0028|1203 [US] [Blue Palette Color Lookup Table Data]
-
- int numberBitsAllocated = HeaderInternal->GetBitsAllocated();
- // Number of "Bits Allocated" is fixed to 16 when:
- // - it is not defined (i.e. it's value is 0)
- // - it's 12, since we will expand the image to 16 bits (see
- // PixelConvert::ConvertDecompress12BitsTo16Bits() )
- if ( numberBitsAllocated == 0 || numberBitsAllocated == 12 )
- {
- numberBitsAllocated = 16;
- }
-
- int DecompressedSize = HeaderInternal->GetXSize()
- * HeaderInternal->GetYSize()
- * HeaderInternal->GetZSize()
- * ( numberBitsAllocated / 8 )
- * HeaderInternal->GetSamplesPerPixel();
-
- return DecompressedSize;
-}
-
-/// Accessor to \ref ImageDataSize
-size_t File::GetImageDataSize()
+ * \brief This predicate, based on hopefully reasonable heuristics,
+ * decides whether or not the current File was properly parsed
+ * and contains the mandatory information for being considered as
+ * a well formed and usable Dicom/Acr File.
+ * @return true when File is the one of a reasonable Dicom/Acr file,
+ * false otherwise.
+ */
+bool File::IsReadable()
{
- if ( ! GetDecompressed() )
+ if( !Document::IsReadable() )
{
- // If the decompression failed nothing can be done.
- return 0;
+ return false;
}
-
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+
+ const std::string &res = GetEntryValue(0x0028, 0x0005);
+ if ( res != GDCM_UNFOUND && atoi(res.c_str()) > 4 )
{
- return PixelConverter->GetRGBSize();
+ return false; // Image Dimensions
}
- else
+ if ( !GetDocEntry(0x0028, 0x0100) )
+ {
+ return false; // "Bits Allocated"
+ }
+ if ( !GetDocEntry(0x0028, 0x0101) )
+ {
+ return false; // "Bits Stored"
+ }
+ if ( !GetDocEntry(0x0028, 0x0102) )
+ {
+ return false; // "High Bit"
+ }
+ if ( !GetDocEntry(0x0028, 0x0103) )
{
- // When no LUT or LUT conversion fails, return the decompressed
- return PixelConverter->GetDecompressedSize();
+ return false; // "Pixel Representation" i.e. 'Sign'
}
+
+ return true;
}
-/// Accessor to \ref ImageDataSizeRaw
-size_t File::GetImageDataSizeRaw()
+/**
+ * \brief Retrieve the number of columns of image.
+ * @return The encountered size when found, 0 by default.
+ * 0 means the file is NOT USABLE. The caller will have to check
+ */
+int File::GetXSize()
{
- if ( ! GetDecompressed() )
+ const std::string &strSize = GetEntryValue(0x0028,0x0011);
+ if ( strSize == GDCM_UNFOUND )
{
- // If the decompression failed nothing can be done.
return 0;
}
- return PixelConverter->GetDecompressedSize();
+
+ return atoi( strSize.c_str() );
}
/**
- * \brief - Allocates necessary memory,
- * - Reads the pixels from disk (uncompress if necessary),
- * - Transforms YBR pixels, if any, into RGB pixels
- * - Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * - 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.
- * NULL if alloc fails
+ * \brief Retrieve the number of lines of image.
+ * \warning The defaulted value is 1 as opposed to File::GetXSize()
+ * @return The encountered size when found, 1 by default
+ * (The ACR-NEMA file contains a Signal, not an Image).
*/
-uint8_t* File::GetImageData()
+int File::GetYSize()
{
- if ( ! GetDecompressed() )
+ const std::string &strSize = GetEntryValue(0x0028,0x0010);
+ if ( strSize != GDCM_UNFOUND )
+ {
+ return atoi( strSize.c_str() );
+ }
+ if ( IsDicomV3() )
{
- // If the decompression failed nothing can be done.
return 0;
}
-
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+
+ // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
+ // hence be a signal (1D image). So we default to 1:
+ return 1;
+}
+
+/**
+ * \brief Retrieve the number of planes of volume or the number
+ * of frames of a multiframe.
+ * \warning When present we consider the "Number of Frames" as the third
+ * dimension. When Missing we consider the third dimension as
+ * being the ACR-NEMA "Planes" tag content.
+ * @return The encountered size when found, 1 by default (single image).
+ */
+int File::GetZSize()
+{
+ // Both DicomV3 and ACR/Nema consider the "Number of Frames"
+ // as the third dimension.
+ const std::string &strSize = GetEntryValue(0x0028,0x0008);
+ if ( strSize != GDCM_UNFOUND )
{
- return PixelConverter->GetRGB();
+ return atoi( strSize.c_str() );
}
- else
+
+ // We then consider the "Planes" entry as the third dimension
+ const std::string &strSize2 = GetEntryValue(0x0028,0x0012);
+ if ( strSize2 != GDCM_UNFOUND )
{
- // When no LUT or LUT conversion fails, return the decompressed
- return PixelConverter->GetDecompressed();
- }
-}
-
-/**
- * \brief
- * Read the pixels from disk (uncompress if necessary),
- * Transforms YBR pixels, if any, into RGB pixels
- * Transforms 3 planes R, G, B, if any, into a single RGB Plane
- * Transforms single Grey plane + 3 Palettes into a RGB Plane
- * Copies at most MaxSize bytes of pixel data to caller allocated
- * memory space.
- * \warning This function allows people that want to build a volume
- * from an image stack *not to* have, first to get the image pixels,
- * and then move them to the volume area.
- * It's absolutely useless for any VTK user since vtk chooses
- * to invert the lines of an image, that is the last line comes first
- * (for some axis related reasons?). Hence he will have
- * to load the image line by line, starting from the end.
- * VTK users have to call GetImageData
- *
- * @param destination Address (in caller's memory space) at which the
- * pixel data should be copied
- * @param maxSize Maximum number of bytes to be copied. When MaxSize
- * is not sufficient to hold the pixel data the copy is not
- * executed (i.e. no partial copy).
- * @return On success, the number of bytes actually copied. Zero on
- * failure e.g. MaxSize is lower than necessary.
- */
-size_t File::GetImageDataIntoVector (void* destination, size_t maxSize)
-{
- if ( ! GetDecompressed() )
- {
- // If the decompression failed nothing can be done.
- return 0;
+ return atoi( strSize2.c_str() );
}
- if ( HeaderInternal->HasLUT() && PixelConverter->BuildRGBImage() )
+ return 1;
+}
+
+/**
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return X dimension of a pixel
+ */
+float File::GetXSpacing()
+{
+ float xspacing, yspacing;
+ const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
+ return 1.;
+ }
+
+ int nbValues;
+ if( ( nbValues = sscanf( strSpacing.c_str(),
+ "%f\\%f", &yspacing, &xspacing)) != 2 )
{
- if ( PixelConverter->GetRGBSize() > maxSize )
+ // if single value is found, xspacing is defaulted to yspacing
+ if ( nbValues == 1 )
{
- dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return 0;
+ xspacing = yspacing;
}
- memcpy( destination,
- (void*)PixelConverter->GetRGB(),
- PixelConverter->GetRGBSize() );
- return PixelConverter->GetRGBSize();
+
+ if ( xspacing == 0.0 )
+ xspacing = 1.0;
+
+ return xspacing;
+
}
- // Either no LUT conversion necessary or LUT conversion failed
- if ( PixelConverter->GetDecompressedSize() > maxSize )
+ // to avoid troubles with David Clunie's-like images
+ if ( xspacing == 0. && yspacing == 0.)
+ return 1.;
+
+ if ( xspacing == 0.)
{
- dbg.Verbose(0, "File::GetImageDataIntoVector: pixel data bigger"
- "than caller's expected MaxSize");
- return 0;
+ gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
+ // seems to be a bug in the header ...
+ nbValues = sscanf( strSpacing.c_str(), "%f\\0\\%f", &yspacing, &xspacing);
+ gdcmAssertMacro( nbValues == 2 );
}
- memcpy( destination,
- (void*)PixelConverter->GetDecompressed(),
- PixelConverter->GetDecompressedSize() );
- return PixelConverter->GetDecompressedSize();
+
+ return xspacing;
}
/**
- * \brief Allocates necessary memory,
- * Transforms YBR pixels (if any) into RGB pixels
- * Transforms 3 planes R, G, B (if any) into a single RGB Plane
- * 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.
- * \ NULL if alloc fails
+ * \brief gets the info from 0028,0030 : Pixel Spacing
+ * else 1.0
+ * @return Y dimension of a pixel
+ */
+float File::GetYSpacing()
+{
+ float yspacing = 1.;
+ std::string strSpacing = GetEntryValue(0x0028,0x0030);
+
+ if ( strSpacing == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
+ return 1.;
+ }
+
+ // if sscanf cannot read any float value, it won't affect yspacing
+ sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ if ( yspacing == 0.0 )
+ yspacing = 1.0;
+
+ return yspacing;
+}
+
+/**
+ * \brief gets the info from 0018,0088 : Space Between Slices
+ * else from 0018,0050 : Slice Thickness
+ * else 1.0
+ * @return Z dimension of a voxel-to be
*/
-uint8_t* File::GetImageDataRaw ()
+float File::GetZSpacing()
{
- return GetDecompressed();
+ // Spacing Between Slices : distance entre le milieu de chaque coupe
+ // Les coupes peuvent etre :
+ // jointives (Spacing between Slices = Slice Thickness)
+ // chevauchantes (Spacing between Slices < Slice Thickness)
+ // disjointes (Spacing between Slices > Slice Thickness)
+ // Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
+ // ca interesse le physicien de l'IRM, pas le visualisateur de volumes ...
+ // Si le Spacing Between Slices est Missing,
+ // on suppose que les coupes sont jointives
+
+ const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
+
+ if ( strSpacingBSlices == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
+ const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
+ if ( strSliceThickness == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)");
+ return 1.;
+ }
+ else
+ {
+ // if no 'Spacing Between Slices' is found,
+ // we assume slices join together
+ // (no overlapping, no interslice gap)
+ // if they don't, we're fucked up
+ return (float)atof( strSliceThickness.c_str() );
+ }
+ }
+ //else
+ return (float)atof( strSpacingBSlices.c_str() );
}
-uint8_t* File::GetDecompressed()
+/**
+ *\brief gets the info from 0028,1052 : Rescale Intercept
+ * @return Rescale Intercept
+ */
+float File::GetRescaleIntercept()
{
- uint8_t* decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
+ float resInter = 0.;
+ /// 0028 1052 DS IMG Rescale Intercept
+ const std::string &strRescInter = GetEntryValue(0x0028,0x1052);
+ if ( strRescInter != GDCM_UNFOUND )
{
- // The decompressed image migth not be loaded yet:
- std::ifstream* fp = HeaderInternal->OpenFile();
- PixelConverter->ReadAndDecompressPixelData( fp );
- if(fp) HeaderInternal->CloseFile();
- decompressed = PixelConverter->GetDecompressed();
- if ( ! decompressed )
+ if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
{
- dbg.Verbose(0, "File::GetDecompressed: read/decompress of "
- "pixel data apparently went wrong.");
- return 0;
+ // bug in the element 0x0028,0x1052
+ gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
}
}
- return decompressed;
+ return resInter;
}
/**
- * \brief Points the internal Pixel_Data 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 it's data before gdcm uses them (e.g. with
- * the Write() method.
- * @param inData user supplied pixel area
- * @param expectedSize total image size, in Bytes
- *
- * @return boolean
+ *\brief gets the info from 0028,1053 : Rescale Slope
+ * @return Rescale Slope
*/
-bool File::SetImageData(uint8_t* inData, size_t expectedSize)
+float File::GetRescaleSlope()
{
- HeaderInternal->SetImageDataSize( expectedSize );
-// FIXME : if already allocated, memory leak !
- Pixel_Data = inData;
- ImageDataSize = ImageDataSizeRaw = expectedSize;
- PixelRead = 1;
-// FIXME : 7fe0, 0010 IS NOT set ...
- return true;
+ float resSlope = 1.;
+ //0028 1053 DS IMG Rescale Slope
+ std::string strRescSlope = GetEntryValue(0x0028,0x1053);
+ if ( strRescSlope != GDCM_UNFOUND )
+ {
+ if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
+ {
+ // bug in the element 0x0028,0x1053
+ gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
+ }
+ }
+
+ return resSlope;
}
/**
- * \brief Writes on disk A SINGLE Dicom file
- * NO test is performed on processor "Endiannity".
- * It's up to the user to call his Reader properly
- * @param fileName name of the file to be created
- * (any already existing file is over written)
- * @return false if write fails
+ * \brief This function is intended to user who doesn't want
+ * to have to manage a LUT and expects to get an RBG Pixel image
+ * (or a monochrome one ...)
+ * \warning to be used with GetImagePixels()
+ * @return 1 if Gray level, 3 if Color (RGB, YBR or PALETTE COLOR)
*/
-
-bool File::WriteRawData(std::string const & fileName)
+int File::GetNumberOfScalarComponents()
{
- std::ofstream fp1(fileName.c_str(), std::ios::out | std::ios::binary );
- if (!fp1)
+ if ( GetSamplesPerPixel() == 3 )
{
- dbg.Verbose(2, "Fail to open (write) file:", fileName.c_str());
- return false;
+ return 3;
}
- fp1.write((char*)Pixel_Data, ImageDataSize);
- fp1.close();
+
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( GetEntryValue(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ std::string strPhotometricInterpretation = GetEntryValue(0x0028,0x0004);
- return true;
+ if ( ( strPhotometricInterpretation == "PALETTE COLOR ") )
+ {
+ if ( HasLUT() )// PALETTE COLOR is NOT enough
+ {
+ return 3;
+ }
+ else
+ {
+ return 1;
+ }
+ }
+
+ // beware of trailing space at end of string
+ // DICOM tags are never of odd length
+ if ( strPhotometricInterpretation == GDCM_UNFOUND ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME1") ||
+ Util::DicomStringEqual(strPhotometricInterpretation, "MONOCHROME2") )
+ {
+ return 1;
+ }
+ else
+ {
+ // we assume that *all* kinds of YBR are dealt with
+ return 3;
+ }
}
/**
- * \brief Writes on disk A SINGLE Dicom file,
- * using the Implicit Value Representation convention
- * NO test is performed on processor "Endiannity".
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \brief This function is intended to user that DOESN'T want
+ * to get RGB pixels image when it's stored as a PALETTE COLOR image
+ * - the (vtk) user is supposed to know how deal with LUTs -
+ * \warning to be used with GetImagePixelsRaw()
+ * @return 1 if Gray level, 3 if Color (RGB or YBR - NOT 'PALETTE COLOR' -)
*/
-
-bool File::WriteDcmImplVR (std::string const & fileName)
+int File::GetNumberOfScalarComponentsRaw()
{
- SetWriteTypeToDcmImplVR();
- return Write(fileName);
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ if ( File::GetEntryValue(0x0028,0x0100) == "24" )
+ {
+ return 3;
+ }
+
+ // we assume that *all* kinds of YBR are dealt with
+ return GetSamplesPerPixel();
}
+//
+// -------------- Remember ! ----------------------------------
+//
+// Image Position Patient (0020,0032):
+// If not found (ACR_NEMA) we try Image Position (0020,0030)
+// If not found (ACR-NEMA), we consider Slice Location (0020,1041)
+// or Location (0020,0050)
+// as the Z coordinate,
+// 0. for all the coordinates if nothing is found
+
+// \todo find a way to inform the caller nothing was found
+// \todo How to tell the caller a wrong number of values was found?
+//
+// ---------------------------------------------------------------
+//
+
/**
-* \brief Writes on disk A SINGLE Dicom file,
- * using the Explicit Value Representation convention
- * NO test is performed on processor "Endiannity". * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner X position
*/
-
-bool File::WriteDcmExplVR (std::string const & fileName)
+float File::GetXOrigin()
{
- SetWriteTypeToDcmExplVR();
- return Write(fileName);
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
+
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
+ {
+ return 0.;
+ }
+
+ return xImPos;
}
/**
- * \brief Writes on disk A SINGLE Dicom file,
- * using the ACR-NEMA convention
- * NO test is performed on processor "Endiannity".
- * (a l'attention des logiciels cliniques
- * qui ne prennent en entrée QUE des images ACR ...
- * \warning if a DICOM_V3 header is supplied,
- * groups < 0x0008 and shadow groups are ignored
- * \warning NO TEST is performed on processor "Endiannity".
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @return false if write fails
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else 0.
+ * @return up-left image corner Y position
*/
-
-bool File::WriteAcr (std::string const & fileName)
+float File::GetYOrigin()
{
- SetWriteTypeToAcr();
- return Write(fileName);
-}
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
-bool File::Write(std::string const& fileName)
-{
- switch(WriteType)
+ if ( strImPos == GDCM_UNFOUND)
+ {
+ gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Unfound Image Position (RET) (0020,0030)");
+ /// \todo How to tell the caller nothing was found ?
+ return 0.;
+ }
+ }
+
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3 )
{
- case WTYPE_IMPL_VR:
- return WriteBase(fileName,ImplicitVR);
- case WTYPE_EXPL_VR:
- return WriteBase(fileName,ExplicitVR);
- case WTYPE_ACR:
- return WriteBase(fileName,ACR);
+ return 0.;
}
- return(false);
+
+ return yImPos;
}
-//-----------------------------------------------------------------------------
-// Protected
/**
- * \brief NOT a end user inteded function
- * (used by WriteDcmExplVR, WriteDcmImplVR, WriteAcr, etc)
- * @param fileName name of the file to be created
- * (any already existing file is overwritten)
- * @param type file type (ExplicitVR, ImplicitVR, ...)
- * @return false if write fails
+ * \brief gets the info from 0020,0032 : Image Position Patient
+ * else from 0020,0030 : Image Position (RET)
+ * else from 0020,1041 : Slice Location
+ * else from 0020,0050 : Location
+ * else 0.
+ * @return up-left image corner Z position
*/
-bool File::WriteBase (std::string const & fileName, FileType type)
+float File::GetZOrigin()
{
-/* if ( PixelRead == -1 && type != ExplicitVR)
+ float xImPos, yImPos, zImPos;
+ std::string strImPos = GetEntryValue(0x0020,0x0032);
+
+ if ( strImPos != GDCM_UNFOUND )
{
- return false;
- }*/
+ if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
+ {
+ gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
- std::ofstream* fp1 = new std::ofstream(fileName.c_str(),
- std::ios::out | std::ios::binary);
- if (fp1 == NULL)
+ strImPos = GetEntryValue(0x0020,0x0030); // For ACR-NEMA images
+ if ( strImPos != GDCM_UNFOUND )
{
- dbg.Verbose(2, "Failed to open (write) File: " , fileName.c_str());
- return false;
+ if( sscanf( strImPos.c_str(),
+ "%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
+ {
+ gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
+ return 0.; // bug in the element 0x0020,0x0032
+ }
+ else
+ {
+ return zImPos;
+ }
}
- switch(WriteMode)
- {
- case WMODE_NATIVE :
- SetWriteToNative();
- break;
- case WMODE_DECOMPRESSED :
- SetWriteToDecompressed();
- break;
- case WMODE_RGB :
- SetWriteToRGB();
- break;
- }
-
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // if recognition code tells us we dealt with a LibIDO image
- // we reproduce on disk the switch between lineNumber and columnNumber
- // 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 ( HeaderInternal->GetFileType() == ACR_LIBIDO)
- {
- SetWriteToLibido();
- }*/
- // ----------------- End of Special Patch ----------------
-
- HeaderInternal->Write(fp1, type);
+ std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
+ if ( strSliceLocation != GDCM_UNFOUND )
+ {
+ if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
+ return 0.; // bug in the element 0x0020,0x1041
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
- // --------------------------------------------------------------
- // Special Patch to allow gdcm to re-write ACR-LibIDO formated images
- //
- // ...and we restore the Header to be Dicom Compliant again
- // just after writting
-/* if ( HeaderInternal->GetFileType() == ACR_LIBIDO )
+ std::string strLocation = GetEntryValue(0x0020,0x0050);
+ if ( strLocation != GDCM_UNFOUND )
{
- RestoreWriteFromLibido();
- }*/
- // ----------------- End of Special Patch ----------------
+ if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
+ {
+ gdcmVerboseMacro( "Wrong Location (0020,0050)");
+ return 0.; // bug in the element 0x0020,0x0050
+ }
+ else
+ {
+ return zImPos;
+ }
+ }
+ gdcmVerboseMacro( "Unfound Location (0020,0050)");
+
+ return 0.; // Hopeless
+}
- RestoreWrite();
+/**
+ * \brief gets the info from 0020,0013 : Image Number else 0.
+ * @return image number
+ */
+int File::GetImageNumber()
+{
+ // The function i atoi() takes the address of an area of memory as
+ // parameter and converts the string stored at that location to an integer
+ // using the external decimal to internal binary conversion rules. This may
+ // be preferable to sscanf() since atoi() is a much smaller, simpler and
+ // faster function. sscanf() can do all possible conversions whereas
+ // atoi() can only do single decimal integer conversions.
+ //0020 0013 IS REL Image Number
+ std::string strImNumber = GetEntryValue(0x0020,0x0013);
+ if ( strImNumber != GDCM_UNFOUND )
+ {
+ return atoi( strImNumber.c_str() );
+ }
+ return 0; //Hopeless
+}
+/**
+ * \brief gets the info from 0008,0060 : Modality
+ * @return Modality Type
+ */
+ModalityType File::GetModality()
+{
+ // 0008 0060 CS ID Modality
+ std::string strModality = GetEntryValue(0x0008,0x0060);
+ if ( strModality != GDCM_UNFOUND )
+ {
+ if ( strModality.find("AU") < strModality.length()) return AU;
+ else if ( strModality.find("AS") < strModality.length()) return AS;
+ else if ( strModality.find("BI") < strModality.length()) return BI;
+ else if ( strModality.find("CF") < strModality.length()) return CF;
+ else if ( strModality.find("CP") < strModality.length()) return CP;
+ else if ( strModality.find("CR") < strModality.length()) return CR;
+ else if ( strModality.find("CT") < strModality.length()) return CT;
+ else if ( strModality.find("CS") < strModality.length()) return CS;
+ else if ( strModality.find("DD") < strModality.length()) return DD;
+ else if ( strModality.find("DF") < strModality.length()) return DF;
+ else if ( strModality.find("DG") < strModality.length()) return DG;
+ else if ( strModality.find("DM") < strModality.length()) return DM;
+ else if ( strModality.find("DS") < strModality.length()) return DS;
+ else if ( strModality.find("DX") < strModality.length()) return DX;
+ else if ( strModality.find("ECG") < strModality.length()) return ECG;
+ else if ( strModality.find("EPS") < strModality.length()) return EPS;
+ else if ( strModality.find("FA") < strModality.length()) return FA;
+ else if ( strModality.find("FS") < strModality.length()) return FS;
+ else if ( strModality.find("HC") < strModality.length()) return HC;
+ else if ( strModality.find("HD") < strModality.length()) return HD;
+ else if ( strModality.find("LP") < strModality.length()) return LP;
+ else if ( strModality.find("LS") < strModality.length()) return LS;
+ else if ( strModality.find("MA") < strModality.length()) return MA;
+ else if ( strModality.find("MR") < strModality.length()) return MR;
+ else if ( strModality.find("NM") < strModality.length()) return NM;
+ else if ( strModality.find("OT") < strModality.length()) return OT;
+ else if ( strModality.find("PT") < strModality.length()) return PT;
+ else if ( strModality.find("RF") < strModality.length()) return RF;
+ else if ( strModality.find("RG") < strModality.length()) return RG;
+ else if ( strModality.find("RTDOSE") < strModality.length()) return RTDOSE;
+ else if ( strModality.find("RTIMAGE") < strModality.length()) return RTIMAGE;
+ else if ( strModality.find("RTPLAN") < strModality.length()) return RTPLAN;
+ else if ( strModality.find("RTSTRUCT") < strModality.length()) return RTSTRUCT;
+ else if ( strModality.find("SM") < strModality.length()) return SM;
+ else if ( strModality.find("ST") < strModality.length()) return ST;
+ else if ( strModality.find("TG") < strModality.length()) return TG;
+ else if ( strModality.find("US") < strModality.length()) return US;
+ else if ( strModality.find("VF") < strModality.length()) return VF;
+ else if ( strModality.find("XA") < strModality.length()) return XA;
+ else if ( strModality.find("XC") < strModality.length()) return XC;
- fp1->close ();
- delete fp1;
+ else
+ {
+ /// \todo throw error return value ???
+ /// specified <> unknown in our database
+ return Unknow;
+ }
+ }
- return true;
+ return Unknow;
}
/**
- * \brief Access to the underlying \ref PixelConverter RGBA LUT
+ * \brief Retrieve the number of Bits Stored (actually used)
+ * (as opposite to number of Bits Allocated)
+ * @return The encountered number of Bits Stored, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
*/
-uint8_t* File::GetLutRGBA()
+int File::GetBitsStored()
{
- return PixelConverter->GetLutRGBA();
+ std::string strSize = GetEntryValue( 0x0028, 0x0101 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro("(0028,0101) is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
}
-//-----------------------------------------------------------------------------
-// Private
/**
- * \brief Set the pixel datas in the good entry of the Header
+ * \brief Retrieve the high bit position.
+ * \warning The method defaults to 0 when information is Missing.
+ * The responsability of checking this value is left to the caller.
+ * @return The high bit positin when present. 0 when Missing.
*/
-void File::SetPixelData(uint8_t* data)
+int File::GetHighBitPosition()
{
- GetHeader()->SetEntryByNumber( GDCM_BINLOADED,
- GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
+ std::string strSize = GetEntryValue( 0x0028, 0x0102 );
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
+}
- // Will be 7fe0, 0010 in standard case
- DocEntry* currentEntry = GetHeader()->GetDocEntryByNumber(GetHeader()->GetGrPixel(), GetHeader()->GetNumPixel());
- if ( currentEntry )
+/**
+ * \brief Check whether the pixels are signed or UNsigned data.
+ * \warning The method defaults to false (UNsigned) when information is Missing.
+ * The responsability of checking this value is left to the caller.
+ * @return True when signed, false when UNsigned
+ */
+bool File::IsSignedPixelData()
+{
+ std::string strSize = GetEntryValue( 0x0028, 0x0103 );
+ if ( strSize == GDCM_UNFOUND )
{
- if ( BinEntry* binEntry = dynamic_cast<BinEntry *>(currentEntry) )
- // Flag is to false because datas are kept in the gdcmPixelConvert
- binEntry->SetBinArea( data, false );
+ gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory");
+ return false;
}
+ int sign = atoi( strSize.c_str() );
+ if ( sign == 0 )
+ {
+ return false;
+ }
+ return true;
}
-void File::SetWriteToNative()
+/**
+ * \brief Retrieve the number of Bits Allocated
+ * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ * @return The encountered number of Bits Allocated, 0 by default.
+ * 0 means the file is NOT USABLE. The caller has to check it !
+ */
+int File::GetBitsAllocated()
{
-// Nothing to do
+ std::string strSize = GetEntryValue(0x0028,0x0100);
+ if ( strSize == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory");
+ return 0; // It's supposed to be mandatory
+ // the caller will have to check
+ }
+ return atoi( strSize.c_str() );
}
-void File::SetWriteToDecompressed()
+/**
+ * \brief Retrieve the number of Samples Per Pixel
+ * (1 : gray level, 3 : RGB -1 or 3 Planes-)
+ * @return The encountered number of Samples Per Pixel, 1 by default.
+ * (Gray level Pixels)
+ */
+int File::GetSamplesPerPixel()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
+ const std::string& strSize = GetEntryValue(0x0028,0x0002);
+ if ( strSize == GDCM_UNFOUND )
{
- SetWriteToRGB();
- }
- else
+ gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory");
+ return 1; // Well, it's supposed to be mandatory ...
+ // but sometimes it's missing : *we* assume Gray pixels
+ }
+ return atoi( strSize.c_str() );
+}
+
+/**
+ * \brief Check whether this a monochrome picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "MONOCHROME1" or "MONOCHROME2". False otherwise.
+ */
+bool File::IsMonochrome()
+{
+ const std::string& PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( Util::DicomStringEqual(PhotometricInterp, "MONOCHROME1")
+ || Util::DicomStringEqual(PhotometricInterp, "MONOCHROME2") )
{
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- if(HeaderInternal->HasLUT())
- {
- photInt->SetValue("PALETTE COLOR ");
- photInt->SetLength(14);
- }
- else
- {
- photInt->SetValue("MONOCHROME1 ");
- photInt->SetLength(12);
- }
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)");
+ }
+ return false;
+}
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- if(Pixel_Data)
- {
- pixel->SetBinArea(Pixel_Data,false);
- pixel->SetLength(ImageDataSize);
- }
- else
- {
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
- }
+/**
+ * \brief Check whether this a "PALETTE COLOR" picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "PALETTE COLOR". False otherwise.
+ */
+bool File::IsPaletteColor()
+{
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "PALETTE COLOR " )
+ {
+ return true;
+ }
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : Palette color (0028,0004)");
+ }
+ return false;
+}
- Archive->Push(photInt);
- Archive->Push(pixel);
+/**
+ * \brief Check whether this a "YBR_FULL" color picture or not by accessing
+ * the "Photometric Interpretation" tag ( 0x0028, 0x0004 ).
+ * @return true when "YBR_FULL". False otherwise.
+ */
+bool File::IsYBRFull()
+{
+ std::string PhotometricInterp = GetEntryValue( 0x0028, 0x0004 );
+ if ( PhotometricInterp == "YBR_FULL" )
+ {
+ return true;
}
+ if ( PhotometricInterp == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
+ }
+ return false;
}
-void File::SetWriteToRGB()
+/**
+ * \brief Retrieve the Planar Configuration for RGB images
+ * (0 : RGB Pixels , 1 : R Plane + G Plane + B Plane)
+ * @return The encountered Planar Configuration, 0 by default.
+ */
+int File::GetPlanarConfiguration()
{
- if(HeaderInternal->GetNumberOfScalarComponents()==3 && !HeaderInternal->HasLUT())
+ std::string strSize = GetEntryValue(0x0028,0x0006);
+ if ( strSize == GDCM_UNFOUND )
{
- PixelConverter->BuildRGBImage();
-
- ValEntry* spp = CopyValEntry(0x0028,0x0002);
- spp->SetValue("3 ");
- spp->SetLength(2);
+ gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
+ return 0;
+ }
+ return atoi( strSize.c_str() );
+}
- ValEntry* planConfig = CopyValEntry(0x0028,0x0006);
- planConfig->SetValue("0 ");
- planConfig->SetLength(2);
+/**
+ * \brief Return the size (in bytes) of a single pixel of data.
+ * @return The size in bytes of a single pixel of data; 0 by default
+ * 0 means the file is NOT USABLE; the caller will have to check
+ */
+int File::GetPixelSize()
+{
+ // 0028 0100 US IMG Bits Allocated
+ // (in order no to be messed up by old RGB images)
+ // if (File::GetEntryValue(0x0028,0x0100) == "24")
+ // return 3;
- ValEntry* photInt = CopyValEntry(0x0028,0x0004);
- photInt->SetValue("RGB ");
- photInt->SetLength(4);
+ std::string pixelType = GetPixelType();
+ if ( pixelType == "8U" || pixelType == "8S" )
+ {
+ return 1;
+ }
+ if ( pixelType == "16U" || pixelType == "16S")
+ {
+ return 2;
+ }
+ if ( pixelType == "32U" || pixelType == "32S")
+ {
+ return 4;
+ }
+ if ( pixelType == "FD" )
+ {
+ return 8;
+ }
+ gdcmVerboseMacro( "Unknown pixel type");
+ return 0;
+}
- BinEntry* pixel = CopyBinEntry(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
- pixel->SetValue(GDCM_BINLOADED);
- if(Pixel_Data)
- {
- pixel->SetBinArea(Pixel_Data,false);
- pixel->SetLength(ImageDataSize);
- }
- else if(PixelConverter->GetRGB())
- {
- pixel->SetBinArea(PixelConverter->GetRGB(),false);
- pixel->SetLength(PixelConverter->GetRGBSize());
- }
- else // Decompressed data
- {
- pixel->SetBinArea(PixelConverter->GetDecompressed(),false);
- pixel->SetLength(PixelConverter->GetDecompressedSize());
- }
+/**
+ * \brief Build the Pixel Type of the image.
+ * Possible values are:
+ * - 8U unsigned 8 bit,
+ * - 8S signed 8 bit,
+ * - 16U unsigned 16 bit,
+ * - 16S signed 16 bit,
+ * - 32U unsigned 32 bit,
+ * - 32S signed 32 bit,
+ * - FD floating double 64 bits (Not kosher DICOM, but so usefull!)
+ * \warning 12 bit images appear as 16 bit.
+ * 24 bit images appear as 8 bit
+ * @return 0S if nothing found. NOT USABLE file. The caller has to check
+ */
+std::string File::GetPixelType()
+{
+ std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
+ if ( bitsAlloc == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)");
+ bitsAlloc = "16"; // default and arbitrary value, not to polute the output
+ }
- Archive->Push(spp);
- Archive->Push(planConfig);
- Archive->Push(photInt);
- Archive->Push(pixel);
+ if ( bitsAlloc == "64" )
+ {
+ return "FD";
+ }
+ else if ( bitsAlloc == "12" )
+ {
+ // It will be unpacked
+ bitsAlloc = "16";
+ }
+ else if ( bitsAlloc == "24" )
+ {
+ // (in order no to be messed up
+ bitsAlloc = "8"; // by old RGB images)
+ }
- // For old ACR-NEMA
- // Thus, we have a RGB image and the bits allocated = 24 and
- // samples per pixels = 1 (in the read file)
- if(HeaderInternal->GetBitsAllocated()==24)
- {
- ValEntry* bitsAlloc = CopyValEntry(0x0028,0x0100);
- bitsAlloc->SetValue("8 ");
- bitsAlloc->SetLength(2);
+ std::string sign = GetEntryValue(0x0028, 0x0103);//"Pixel Representation"
- ValEntry* bitsStored = CopyValEntry(0x0028,0x0101);
- bitsStored->SetValue("8 ");
- bitsStored->SetLength(2);
+ if (sign == GDCM_UNFOUND )
+ {
+ gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)");
+ sign = "U"; // default and arbitrary value, not to polute the output
+ }
+ else if ( sign == "0" )
+ {
+ sign = "U";
+ }
+ else
+ {
+ sign = "S";
+ }
+ return bitsAlloc + sign;
+}
- ValEntry* highBit = CopyValEntry(0x0028,0x0102);
- highBit->SetValue("7 ");
- highBit->SetLength(2);
- Archive->Push(bitsAlloc);
- Archive->Push(bitsStored);
- Archive->Push(highBit);
- }
+/**
+ * \brief Recover the offset (from the beginning of the file)
+ * of *image* pixels (not *icone image* pixels, if any !)
+ * @return Pixel Offset
+ */
+size_t File::GetPixelOffset()
+{
+ DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetOffset();
}
else
{
- SetWriteToDecompressed();
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
}
}
-void File::RestoreWrite()
+/// \todo TODO : unify those two (previous one and next one)
+/**
+ * \brief Recover the pixel area length (in Bytes)
+ * @return Pixel Element Length, as stored in the header
+ * (NOT the memory space necessary to hold the Pixels
+ * -in case of embeded compressed image-)
+ * 0 : NOT USABLE file. The caller has to check.
+ */
+size_t File::GetPixelAreaLength()
{
- Archive->Restore(0x0028,0x0002);
- Archive->Restore(0x0028,0x0004);
- Archive->Restore(0x0028,0x0006);
- Archive->Restore(GetHeader()->GetGrPixel(),GetHeader()->GetNumPixel());
-
- // For old ACR-NEMA (24 bits problem)
- Archive->Restore(0x0028,0x0100);
- Archive->Restore(0x0028,0x0101);
- Archive->Restore(0x0028,0x0102);
+ DocEntry* pxlElement = GetDocEntry(GrPixel,NumPixel);
+ if ( pxlElement )
+ {
+ return pxlElement->GetLength();
+ }
+ else
+ {
+#ifdef GDCM_DEBUG
+ std::cout << "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
+ << std::endl;
+#endif //GDCM_DEBUG
+ return 0;
+ }
}
-void File::SetWriteToLibido()
+/**
+ * \brief tells us if LUT are used
+ * \warning Right now, 'Segmented xxx Palette Color Lookup Table Data'
+ * are NOT considered as LUT, since nobody knows
+ * how to deal with them
+ * Please warn me if you know sbdy that *does* know ... jprx
+ * @return true if LUT Descriptors and LUT Tables were found
+ */
+bool File::HasLUT()
{
- ValEntry *oldRow = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0010));
- ValEntry *oldCol = dynamic_cast<ValEntry *>(HeaderInternal->GetDocEntryByNumber(0x0028, 0x0011));
-
- if( oldRow && oldCol )
+ // Check the presence of the LUT Descriptors, and LUT Tables
+ // LutDescriptorRed
+ if ( !GetDocEntry(0x0028,0x1101) )
+ {
+ return false;
+ }
+ // LutDescriptorGreen
+ if ( !GetDocEntry(0x0028,0x1102) )
+ {
+ return false;
+ }
+ // LutDescriptorBlue
+ if ( !GetDocEntry(0x0028,0x1103) )
+ {
+ return false;
+ }
+ // Red Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1201) )
{
- std::string rows, columns;
+ return false;
+ }
+ // Green Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1202) )
+ {
+ return false;
+ }
+ // Blue Palette Color Lookup Table Data
+ if ( !GetDocEntry(0x0028,0x1203) )
+ {
+ return false;
+ }
- ValEntry *newRow=new ValEntry(oldRow->GetDictEntry());
- ValEntry *newCol=new ValEntry(oldCol->GetDictEntry());
+ // FIXME : (0x0028,0x3006) : LUT Data (CTX dependent)
+ // NOT taken into account, but we don't know how to use it ...
+ return true;
+}
- newRow->Copy(oldCol);
- newCol->Copy(oldRow);
+/**
+ * \brief gets the info from 0028,1101 : Lookup Table Desc-Red
+ * else 0
+ * @return Lookup Table number of Bits , 0 by default
+ * when (0028,0004),Photometric Interpretation = [PALETTE COLOR ]
+ * @ return bit number of each LUT item
+ */
+int File::GetLUTNbits()
+{
+ std::vector<std::string> tokens;
+ int lutNbits;
+
+ //Just hope Lookup Table Desc-Red = Lookup Table Desc-Red
+ // = Lookup Table Desc-Blue
+ // Consistency already checked in GetLUTLength
+ std::string lutDescription = GetEntryValue(0x0028,0x1101);
+ if ( lutDescription == GDCM_UNFOUND )
+ {
+ return 0;
+ }
- newRow->SetValue(oldCol->GetValue());
- newCol->SetValue(oldRow->GetValue());
+ tokens.clear(); // clean any previous value
+ Util::Tokenize ( lutDescription, tokens, "\\" );
+ //LutLength=atoi(tokens[0].c_str());
+ //LutDepth=atoi(tokens[1].c_str());
- Archive->Push(newRow);
- Archive->Push(newCol);
- }
+ lutNbits = atoi( tokens[2].c_str() );
+ tokens.clear();
+
+ return lutNbits;
}
-void File::RestoreWriteFromLibido()
+
+//-----------------------------------------------------------------------------
+// Protected
+
+/**
+ * \brief anonymize a File (removes Patient's personal info)
+ * (read the code to see which ones ...)
+ */
+bool File::AnonymizeFile()
{
- Archive->Restore(0x0028,0x0010);
- Archive->Restore(0x0028,0x0011);
+ // If exist, replace by spaces
+ SetEntryValue (" ",0x0010, 0x2154); // Telephone
+ SetEntryValue (" ",0x0010, 0x1040); // Adress
+ SetEntryValue (" ",0x0010, 0x0020); // Patient ID
+
+ DocEntry* patientNameHE = GetDocEntry (0x0010, 0x0010);
+
+ if ( patientNameHE ) // we replace it by Study Instance UID (why not)
+ {
+ std::string studyInstanceUID = GetEntryValue (0x0020, 0x000d);
+ if ( studyInstanceUID != GDCM_UNFOUND )
+ {
+ Insert(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ Insert("anonymised", 0x0010, 0x0010);
+ }
+ }
+
+ // Just for fun :-(
+ // (if any) remove or replace all the stuff that contains a Date
+
+//0008 0012 DA ID Instance Creation Date
+//0008 0020 DA ID Study Date
+//0008 0021 DA ID Series Date
+//0008 0022 DA ID Acquisition Date
+//0008 0023 DA ID Content Date
+//0008 0024 DA ID Overlay Date
+//0008 0025 DA ID Curve Date
+//0008 002a DT ID Acquisition Datetime
+//0018 9074 DT ACQ Frame Acquisition Datetime
+//0018 9151 DT ACQ Frame Reference Datetime
+//0018 a002 DT ACQ Contribution Date Time
+//0020 3403 SH REL Modified Image Date (RET)
+//0032 0032 DA SDY Study Verified Date
+//0032 0034 DA SDY Study Read Date
+//0032 1000 DA SDY Scheduled Study Start Date
+//0032 1010 DA SDY Scheduled Study Stop Date
+//0032 1040 DA SDY Study Arrival Date
+//0032 1050 DA SDY Study Completion Date
+//0038 001a DA VIS Scheduled Admission Date
+//0038 001c DA VIS Scheduled Discharge Date
+//0038 0020 DA VIS Admitting Date
+//0038 0030 DA VIS Discharge Date
+//0040 0002 DA PRC Scheduled Procedure Step Start Date
+//0040 0004 DA PRC Scheduled Procedure Step End Date
+//0040 0244 DA PRC Performed Procedure Step Start Date
+//0040 0250 DA PRC Performed Procedure Step End Date
+//0040 2004 DA PRC Issue Date of Imaging Service Request
+//0040 4005 DT PRC Scheduled Procedure Step Start Date and Time
+//0040 4011 DT PRC Expected Completion Date and Time
+//0040 a030 DT PRC Verification Date Time
+//0040 a032 DT PRC Observation Date Time
+//0040 a120 DT PRC DateTime
+//0040 a121 DA PRC Date
+//0040 a13a DT PRC Referenced Datetime
+//0070 0082 DA ??? Presentation Creation Date
+//0100 0420 DT ??? SOP Autorization Date and Time
+//0400 0105 DT ??? Digital Signature DateTime
+//2100 0040 DA PJ Creation Date
+//3006 0008 DA SSET Structure Set Date
+//3008 0024 DA ??? Treatment Control Point Date
+//3008 0054 DA ??? First Treatment Date
+//3008 0056 DA ??? Most Recent Treatment Date
+//3008 0162 DA ??? Safe Position Exit Date
+//3008 0166 DA ??? Safe Position Return Date
+//3008 0250 DA ??? Treatment Date
+//300a 0006 DA RT RT Plan Date
+//300a 022c DA RT Air Kerma Rate Reference Date
+//300e 0004 DA RT Review Date
+
+ return true;
}
-ValEntry* File::CopyValEntry(uint16_t group,uint16_t element)
+/**
+ * \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] )
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- ValEntry* newE;
+ std::string strImOriPat;
+ //iop is supposed to be float[6]
+ iop[0] = iop[1] = iop[2] = iop[3] = iop[4] = iop[5] = 0.;
- if(oldE)
+ // 0020 0037 DS REL Image Orientation (Patient)
+ if ( (strImOriPat = GetEntryValue(0x0020,0x0037)) != GDCM_UNFOUND )
{
- newE = new ValEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
+ 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." );
+ }
}
- else
+ //For ACR-NEMA
+ // 0020 0035 DS REL Image Orientation (RET)
+ else if ( (strImOriPat = GetEntryValue(0x0020,0x0035)) != GDCM_UNFOUND )
{
- newE = GetHeader()->NewValEntryByNumber(group,element);
+ 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." );
+ }
}
-
- return(newE);
}
-BinEntry* File::CopyBinEntry(uint16_t group,uint16_t element)
+/**
+ * \brief Initialize a default DICOM File that should contain all the
+ * field require by other reader. DICOM standard does not
+ * explicitely defines those fields, heuristic has been choosen.
+ * This is not perfect as we are writting a CT image...
+ */
+void File::InitializeDefaultFile()
{
- DocEntry* oldE = HeaderInternal->GetDocEntryByNumber(group, element);
- BinEntry* newE;
-
- if(oldE)
+ typedef struct
{
- newE = new BinEntry(oldE->GetDictEntry());
- newE->Copy(oldE);
- }
- else
+ const char *value;
+ uint16_t group;
+ uint16_t elem;
+ } DICOM_DEFAULT_VALUE;
+
+ std::string date = Util::GetCurrentDate();
+ std::string time = Util::GetCurrentTime();
+ std::string uid = Util::CreateUniqueUID();
+ std::string uidMedia = uid;
+ std::string uidClass = uid + ".1";
+ std::string uidInst = uid + ".10";
+ std::string uidStudy = uid + ".100";
+ std::string uidSerie = uid + ".1000";
+
+ static DICOM_DEFAULT_VALUE defaultvalue[] = {
+ { "146 ", 0x0002, 0x0000}, // Meta Element Group Length // FIXME: how to recompute ?
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0002, 0x0002}, // Media Storage SOP Class UID (CT Image Storage)
+ { uidClass.c_str(), 0x0002, 0x0003}, // Media Storage SOP Instance UID
+ { "1.2.840.10008.1.2.1 ", 0x0002, 0x0010}, // Transfer Syntax UID (Explicit VR Little Endian)
+ { uidClass.c_str(), 0x0002, 0x0012}, // META Implementation Class UID
+ { "GDCM", 0x0002, 0x0016}, // Source Application Entity Title
+
+ { date.c_str(), 0x0008, 0x0012}, // Instance Creation Date
+ { time.c_str(), 0x0008, 0x0013}, // Instance Creation Time
+ { "1.2.840.10008.5.1.4.1.1.2", 0x0008, 0x0016}, // SOP Class UID
+ { uidInst.c_str(), 0x0008, 0x0018}, // SOP Instance UID
+ { "CT", 0x0008, 0x0060}, // Modality
+ { "GDCM", 0x0008, 0x0070}, // Manufacturer
+ { "GDCM", 0x0008, 0x0080}, // Institution Name
+ { "http://www-creatis.insa-lyon.fr/Public/Gdcm", 0x0008, 0x0081}, // Institution Address
+
+ { "GDCM", 0x0010, 0x0010}, // Patient's Name
+ { "GDCMID", 0x0010, 0x0020}, // Patient ID
+
+ { uidStudy.c_str(), 0x0020, 0x000d}, // Study Instance UID
+ { uidSerie.c_str(), 0x0020, 0x000e}, // Series Instance UID
+ { "1", 0x0020, 0x0010}, // StudyID
+ { "1", 0x0020, 0x0011}, // SeriesNumber
+
+ { "1", 0x0028, 0x0002}, // Samples per pixel 1 or 3
+ { "MONOCHROME1", 0x0028, 0x0004}, // photochromatic interpretation
+ { "0", 0x0028, 0x0010}, // nbRows
+ { "0", 0x0028, 0x0011}, // nbCols
+ { "8", 0x0028, 0x0100}, // BitsAllocated 8 or 12 or 16
+ { "8", 0x0028, 0x0101}, // BitsStored <= BitsAllocated
+ { "7", 0x0028, 0x0102}, // HighBit <= BitsAllocated - 1
+ { "0", 0x0028, 0x0103}, // Pixel Representation 0(unsigned) or 1(signed)
+ { 0, 0, 0 }
+ };
+
+ // default value
+ // Special case this is the image (not a string)
+ GrPixel = 0x7fe0;
+ NumPixel = 0x0010;
+ Insert(0, 0, GrPixel, NumPixel);
+
+ // All remaining strings:
+ unsigned int i = 0;
+ DICOM_DEFAULT_VALUE current = defaultvalue[i];
+ while( current.value )
{
- newE = GetHeader()->NewBinEntryByNumber(group,element);
+ Insert(current.value, current.group, current.elem);
+ current = defaultvalue[++i];
}
+}
- return(newE);
-}
+//-----------------------------------------------------------------------------
+// Private
//-----------------------------------------------------------------------------
-} // end namespace gdcm
+} // end namespace gdcm
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff