Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/06/22 08:11:23 $
- Version: $Revision: 1.243 $
+ Date: $Date: 2005/07/19 14:43:48 $
+ Version: $Revision: 1.250 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
-#include <stdio.h> //sscanf
#include <vector>
+#include <stdio.h> //sscanf
+#include <stdlib.h> // for atoi
namespace gdcm
{
* @param filename name of the file whose header we want to analyze
*/
File::File( std::string const &filename )
- :Document(filename)
+ :Document( )
{
RLEInfo = new RLEFramesInfo;
JPEGInfo = new JPEGFragmentsInfo;
- Load( filename );
+ Load( filename ); // gdcm::Document is first Loaded, then the 'File part'
}
/**
//-----------------------------------------------------------------------------
// Public
-
/**
* \brief Loader
- * @param fileName file to be open for parsing
* @return false if file cannot be open or no swap info was found,
* or no tag was found.
*/
-bool File::Load( std::string const &fileName )
+bool File::Load( )
+{
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+
+/**
+ * \brief Does the Loading Job (internal use only)
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ */
+bool File::DoTheLoadingJob( )
{
- this->Document::Load( fileName );
// for some ACR-NEMA images GrPixel, NumPixel is *not* 7fe0,0010
// We may encounter the 'RETired' (0x0028, 0x0200) tag
gdcmWarningMacro("Wrong Image Dimensions" << res);
return false; // Image Dimensions
}
+ bool b0028_0100 = true;
if ( !GetDocEntry(0x0028, 0x0100) )
{
gdcmWarningMacro("Bits Allocated (0028|0100) not found");
- return false; // "Bits Allocated"
+ //return false; // "Bits Allocated"
+ b0028_0100 = false;
}
+ bool b0028_0101 = true;
if ( !GetDocEntry(0x0028, 0x0101) )
{
gdcmWarningMacro("Bits Stored (0028|0101) not found");
- return false; // "Bits Stored"
+ //return false; // "Bits Stored"
+ b0028_0101 = false;
}
+ bool b0028_0102 = true;
if ( !GetDocEntry(0x0028, 0x0102) )
{
gdcmWarningMacro("Hight Bit (0028|0102) not found");
- return false; // "High Bit"
+ //return false; // "High Bit"
+ b0028_0102 = false;
}
+ bool b0028_0103 = true;
if ( !GetDocEntry(0x0028, 0x0103) )
{
gdcmWarningMacro("Pixel Representation (0028|0103) not found");
- return false; // "Pixel Representation" i.e. 'Sign'
+ //return false; // "Pixel Representation" i.e. 'Sign' ( 0 : unsigned, 1 : signed)
+ b0028_0103 = false;
+ }
+
+ if ( !b0028_0100 && !b0028_0101 && !b0028_0102 && !b0028_0103)
+ {
+ gdcmWarningMacro("Too much mandatory Tags missing !");
+ return false;
}
+
if ( !GetDocEntry(GrPixel, NumPixel) )
{
gdcmWarningMacro("Pixel Dicom Element " << std::hex <<
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;
+ 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("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;
+ < strModality.length()) return RTDOSE;
else if ( strModality.find("RTIMAGE")
- < strModality.length()) return RTIMAGE;
+ < strModality.length()) return RTIMAGE;
else if ( strModality.find("RTPLAN")
- < strModality.length()) return 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;
+ < 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;
else
{
return Unknow;
}
}
-
return Unknow;
}
{
return 0;
}
-
return atoi( strSize.c_str() );
}
return 0;
}
- // The Rows (0028,0010) entry was optional for ACR/NEMA. It might
- // hence be a signal (1D image). So we default to 1:
+ // The Rows (0028,0010) entry was optional for ACR/NEMA.
+ // (at least some images didn't have it.)
+ // 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
+ * 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).
*/
{
return atoi( strSize2.c_str() );
}
-
return 1;
}
/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * (first in 0018,1164 : ImagerPixelSpacing)
+ * \brief gets the info from 0018,1164 : ImagerPixelSpacing
+ * then 0028,0030 : Pixel Spacing
* else 1.0
* @return X dimension of a pixel
*/
int nbValues;
// To follow David Clunie's advice, we first check ImagerPixelSpacing
- // (never saw any image with that field :-(
const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
if ( strImagerPixelSpacing != GDCM_UNFOUND )
}
}
-
const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
if ( strSpacing == GDCM_UNFOUND )
xspacing = 1.0;
return xspacing;
-
}
- // to avoid troubles with David Clunie's-like images
+ // to avoid troubles with David Clunie's-like images (at least one)
if ( xspacing == 0. && yspacing == 0.)
return 1.;
}
/**
- * \brief gets the info from 0028,0030 : Pixel Spacing
- * (first in 0018,1164 : ImagerPixelSpacing)
+ * \brief gets the info from 0018,1164 : ImagerPixelSpacing
+ * then from 0028,0030 : Pixel Spacing
* else 1.0
* @return Y dimension of a pixel
*/
float yspacing = 1.;
int nbValues;
// To follow David Clunie's advice, we first check ImagerPixelSpacing
- // (never saw any image with that field :-(
const std::string &strImagerPixelSpacing = GetEntryValue(0x0018,0x1164);
if ( strImagerPixelSpacing != GDCM_UNFOUND )
// overlapping (Spacing between Slices < Slice Thickness)
// disjointes (Spacing between Slices > Slice Thickness)
// Slice Thickness : epaisseur de tissus sur laquelle est acquis le signal
- // It only concerns the MRI guys, not people wanting to visualize volmues
- // If Spacing Between Slices is Missing,
+ // It only concerns the MRI guys, not people wanting to visualize volumes
+ // If Spacing Between Slices is missing,
// we suppose slices joint together
const std::string &strSpacingBSlices = GetEntryValue(0x0018,0x0088);
}
}
- std::string strSliceLocation = GetEntryValue(0x0020,0x1041); // for *very* old ACR-NEMA images
+ // for *very* old ACR-NEMA images
+ std::string strSliceLocation = GetEntryValue(0x0020,0x1041);
if ( strSliceLocation != GDCM_UNFOUND )
{
if ( sscanf( strSliceLocation.c_str(), "%f ", &zImPos) != 1)
/**
* \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
+ * @param iop adress of the (6)float array to receive values
* @return cosines of image orientation patient
*/
void File::GetImageOrientationPatient( float iop[6] )
/**
* \brief Retrieve the number of Bits Allocated
- * (8, 12 -compacted ACR-NEMA files, 16, ...)
+ * (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 !
*/
/**
* \brief Retrieve the high bit position.
- * \warning The method defaults to 0 when information is Missing.
+ * \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.
+ * @return The high bit position when present. 0 when missing.
*/
int File::GetHighBitPosition()
{
/**
* \brief Retrieve the number of Samples Per Pixel
- * (1 : gray level, 3 : RGB -1 or 3 Planes-)
+ * (1 : gray level, 3 : RGB/YBR -1 or 3 Planes-)
* @return The encountered number of Samples Per Pixel, 1 by default.
- * (Gray level Pixels)
+ * (we assume Gray level Pixels)
*/
int File::GetSamplesPerPixel()
{
int File::GetPixelSize()
{
// 0028 0100 US IMG Bits Allocated
- // (in order no to be messed up by old RGB images)
+ // (in order no to be messed up by old ACR-NEMA RGB images)
// if (File::GetEntryValue(0x0028,0x0100) == "24")
// return 3;
* - 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 + photochromatic interp ="RGB "
+ * + Planar Configuration = 0
* @return 0S if nothing found. NOT USABLE file. The caller has to check
*/
std::string File::GetPixelType()
* \brief Check whether the pixels are signed (1) or UNsigned (0) data.
* \warning The method defaults to false (UNsigned) when tag 0028|0103
* is missing.
- * The responsability of checking this value is left to the caller.
+ * The responsability of checking this value is left to the caller
+ * (NO transformation is performed on the pixels to make then >0)
* @return True when signed, false when UNsigned
*/
bool File::IsSignedPixelData()
* 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)
+ * @return 1 if Gray level, 3 if Color (RGB, YBR, *or PALETTE COLOR*)
*/
int File::GetNumberOfScalarComponents()
{
/**
* \brief Adds the characteristics of a new element we want to anonymize
- *
+ * @param group Group number of the target tag.
+ * @param elem Element number of the target tag.
+ * @param value new value (string) to substitute with
*/
void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
std::string const &value)
-
{
Element el;
el.Group = group;
}
/**
- * \brief anonymize a File (removes Patient's personal info passed with
+ * \brief anonymize a File (remove Patient's personal info passed with
* AddAnonymizeElement()
*/
bool File::AnonymizeFile()
* (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 writetype Type of the File to be written
+ * @param writetype type of the file to be written
* (ACR, ExplicitVR, ImplicitVR)
*/
bool File::Write(std::string fileName, FileType writetype)
rleSegmentOffsetTable[k] = ReadInt32();
}
- // Deduce from both the RLE Header and the frameLength the
- // fragment length, and again store this info in a
- // RLEFramesInfo.
+ // Deduce from both RLE Header and frameLength
+ // the fragment length, and again store this info
+ // in a RLEFramesInfo.
long rleSegmentLength[15];
// skipping (not reading) RLE Segments
if ( nbRleSegments > 1)
RLEInfo->AddFrame(newFrame);
}
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the item :
if ( !ReadTag(0xfffe, 0xe0dd) )
{
gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
SkipBytes(fragmentLength);
}
- // Make sure that at the end of the item we encounter a 'Sequence
- // Delimiter Item':
+ // Make sure that we encounter a 'Sequence Delimiter Item'
+ // at the end of the item :
if ( !ReadTag(0xfffe, 0xe0dd) )
{
gdcmWarningMacro( "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).
+ * tag is (TestGroup, TestElem).
* \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
+ * (TestGroup, TestElem) 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.
+ * @param testGroup The expected group of the tag.
+ * @param testElem The expected Element of the tag.
* @return True on success, false otherwise.
*/
-bool File::ReadTag(uint16_t testGroup, uint16_t testElement)
+bool File::ReadTag(uint16_t testGroup, uint16_t testElem)
{
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;
+ uint16_t itemTagElem;
try
{
- itemTagGroup = ReadInt16();
- itemTagElement = ReadInt16();
+ itemTagGroup = ReadInt16();
+ itemTagElem = ReadInt16();
}
catch ( FormatError e )
{
//std::cerr << e << std::endl;
return false;
}
- if ( itemTagGroup != testGroup || itemTagElement != testElement )
+ if ( itemTagGroup != testGroup || itemTagElem != testElem )
{
gdcmWarningMacro( "Wrong Item Tag found:"
<< " We should have found tag ("
- << std::hex << testGroup << "," << testElement << ")" << std::endl
+ << std::hex << testGroup << "," << testElem << ")" << std::endl
<< " but instead we encountered tag ("
- << std::hex << itemTagGroup << "," << itemTagElement << ")"
+ << std::hex << itemTagGroup << "," << itemTagElem << ")"
<< " at address: " << " 0x(" << (unsigned int)currentPosition << ")"
) ;
Fp->seekg(positionOnEntry, std::ios::beg);
* 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.
+ * @param testGroup The expected Group of the tag.
+ * @param testElem 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)
+uint32_t File::ReadTagLength(uint16_t testGroup, uint16_t testElem)
{
- if ( !ReadTag(testGroup, testElement) )
+ if ( !ReadTag(testGroup, testElem) )
{
return 0;
}
}
}
+// These are the deprecated method that one day should be removed (after the next release)
+#ifndef GDCM_LEGACY_REMOVE
+/**
+ * \brief Loader. (DEPRECATED : not to break the API)
+ * @param fileName file to be open for parsing
+ * @return false if file cannot be open or no swap info was found,
+ * or no tag was found.
+ * @deprecated Use the Load() function instead
+ */
+bool File::Load( std::string const &fileName )
+{
+ GDCM_LEGACY_REPLACED_BODY(File::Load(std::string), "1.2",
+ File::Load());
+ SetFileName( fileName );
+ if ( ! this->Document::Load( ) )
+ return false;
+
+ return DoTheLoadingJob( );
+}
+#endif
+
//-----------------------------------------------------------------------------
// Print
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff