Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/02/04 13:15:41 $
- Version: $Revision: 1.210 $
+ Date: $Date: 2005/02/06 14:39:35 $
+ Version: $Revision: 1.213 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
// 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,
+// as the Z coordinate,
// 0. for all the coordinates if nothing is found
//
// ---------------------------------------------------------------
#include "gdcmTS.h"
#include "gdcmValEntry.h"
#include "gdcmBinEntry.h"
+#include "gdcmSeqEntry.h"
#include "gdcmRLEFramesInfo.h"
#include "gdcmJPEGFragmentsInfo.h"
if ( strSpacing == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Pixel Spacing (0028,0030)" );
+ gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
return 1.;
}
if ( xspacing == 0.)
{
- gdcmVerboseMacro("gdcmData/CT-MONO2-8-abdo.dcm problem");
+ gdcmWarningMacro("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 );
if ( strSpacing == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Pixel Spacing (0028,0030)");
+ gdcmWarningMacro("Unfound Pixel Spacing (0028,0030)");
return 1.;
}
if ( strSpacingBSlices == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Spacing Between Slices (0018,0088)");
+ gdcmWarningMacro("Unfound Spacing Between Slices (0018,0088)");
const std::string &strSliceThickness = GetEntryValue(0x0018,0x0050);
if ( strSliceThickness == GDCM_UNFOUND )
{
- gdcmVerboseMacro("Unfound Slice Thickness (0018,0050)");
+ gdcmWarningMacro("Unfound Slice Thickness (0018,0050)");
return 1.;
}
else
if ( strImPos == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ gdcmWarningMacro( "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)");
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
return 0.;
}
}
if ( strImPos == GDCM_UNFOUND)
{
- gdcmVerboseMacro( "Unfound Image Position Patient (0020,0032)");
+ gdcmWarningMacro( "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)");
+ gdcmWarningMacro( "Unfound Image Position (RET) (0020,0030)");
return 0.;
}
}
{
if( sscanf( strImPos.c_str(), "%f\\%f\\%f", &xImPos, &yImPos, &zImPos) != 3)
{
- gdcmVerboseMacro( "Wrong Image Position Patient (0020,0032)");
+ gdcmWarningMacro( "Wrong Image Position Patient (0020,0032)");
return 0.; // bug in the element 0x0020,0x0032
}
else
if( sscanf( strImPos.c_str(),
"%f\\%f\\%f", &xImPos, &yImPos, &zImPos ) != 3 )
{
- gdcmVerboseMacro( "Wrong Image Position (RET) (0020,0030)");
+ gdcmWarningMacro( "Wrong Image Position (RET) (0020,0030)");
return 0.; // bug in the element 0x0020,0x0032
}
else
{
if( sscanf( strSliceLocation.c_str(), "%f", &zImPos) != 1)
{
- gdcmVerboseMacro( "Wrong Slice Location (0020,1041)");
+ gdcmWarningMacro( "Wrong Slice Location (0020,1041)");
return 0.; // bug in the element 0x0020,0x1041
}
else
return zImPos;
}
}
- gdcmVerboseMacro( "Unfound Slice Location (0020,1041)");
+ gdcmWarningMacro( "Unfound Slice Location (0020,1041)");
std::string strLocation = GetEntryValue(0x0020,0x0050);
if ( strLocation != GDCM_UNFOUND )
{
if( sscanf( strLocation.c_str(), "%f", &zImPos) != 1)
{
- gdcmVerboseMacro( "Wrong Location (0020,0050)");
+ gdcmWarningMacro( "Wrong Location (0020,0050)");
return 0.; // bug in the element 0x0020,0x0050
}
else
return zImPos;
}
}
- gdcmVerboseMacro( "Unfound Location (0020,0050)");
+ gdcmWarningMacro( "Unfound Location (0020,0050)");
return 0.; // Hopeless
}
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." );
+ gdcmWarningMacro( "Wrong Image Orientation Patient (0020,0037). Less than 6 values were found." );
}
}
//For ACR-NEMA
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." );
+ gdcmWarningMacro( "wrong Image Orientation Patient (0020,0035). Less than 6 values were found." );
}
}
}
/**
* \brief Retrieve the number of Bits Stored (actually used)
- * (as opposite to number of Bits Allocated)
+ * (as opposed 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 !
*/
std::string strSize = GetEntryValue( 0x0028, 0x0101 );
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro("(0028,0101) is supposed to be mandatory");
+ gdcmWarningMacro("(0028,0101) is supposed to be mandatory");
return 0; // It's supposed to be mandatory
// the caller will have to check
}
std::string strSize = GetEntryValue(0x0028,0x0100);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0100) is supposed to be mandatory");
+ gdcmWarningMacro( "(0028,0100) is supposed to be mandatory");
return 0; // It's supposed to be mandatory
// the caller will have to check
}
std::string strSize = GetEntryValue( 0x0028, 0x0102 );
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0102) is supposed to be mandatory");
+ gdcmWarningMacro( "(0028,0102) is supposed to be mandatory");
return 0;
}
return atoi( strSize.c_str() );
const std::string &strSize = GetEntryValue(0x0028,0x0002);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0002) is supposed to be mandatory");
+ gdcmWarningMacro( "(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
}
std::string strSize = GetEntryValue(0x0028,0x0006);
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : Planar Configuration (0028,0006)");
+ gdcmWarningMacro( "Not found : Planar Configuration (0028,0006)");
return 0;
}
return atoi( strSize.c_str() );
{
return 8;
}
- gdcmVerboseMacro( "Unknown pixel type");
+ gdcmWarningMacro( "Unknown pixel type");
return 0;
}
std::string bitsAlloc = GetEntryValue(0x0028, 0x0100); // Bits Allocated
if ( bitsAlloc == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Missing Bits Allocated (0028,0100)");
+ gdcmWarningMacro( "Missing Bits Allocated (0028,0100)");
bitsAlloc = "16"; // default and arbitrary value, not to polute the output
}
if (sign == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Missing Pixel Representation (0028,0103)");
+ gdcmWarningMacro( "Missing Pixel Representation (0028,0103)");
sign = "U"; // default and arbitrary value, not to polute the output
}
else if ( sign == "0" )
std::string strSize = GetEntryValue( 0x0028, 0x0103 );
if ( strSize == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "(0028,0103) is supposed to be mandatory");
+ gdcmWarningMacro( "(0028,0103) is supposed to be mandatory");
return false;
}
int sign = atoi( strSize.c_str() );
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : Photometric Interpretation (0028,0004)");
+ gdcmWarningMacro( "Not found : Photometric Interpretation (0028,0004)");
}
return false;
}
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : Palette color (0028,0004)");
+ gdcmWarningMacro( "Not found : Palette color (0028,0004)");
}
return false;
}
}
if ( PhotometricInterp == GDCM_UNFOUND )
{
- gdcmVerboseMacro( "Not found : YBR Full (0028,0004)");
+ gdcmWarningMacro( "Not found : YBR Full (0028,0004)");
}
return false;
}
if( sscanf( strRescInter.c_str(), "%f", &resInter) != 1 )
{
// bug in the element 0x0028,0x1052
- gdcmVerboseMacro( "Rescale Intercept (0028,1052) is empty." );
+ gdcmWarningMacro( "Rescale Intercept (0028,1052) is empty." );
}
}
if( sscanf( strRescSlope.c_str(), "%f", &resSlope) != 1)
{
// bug in the element 0x0028,0x1053
- gdcmVerboseMacro( "Rescale Slope (0028,1053) is empty.");
+ gdcmWarningMacro( "Rescale Slope (0028,1053) is empty.");
}
}
}
else
{
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
return 0;
}
}
}
else
{
-#ifdef GDCM_DEBUG
- std::cout << "Big trouble : Pixel Element ("
- << std::hex << GrPixel<<","<< NumPixel<< ") NOT found"
- << std::endl;
-#endif //GDCM_DEBUG
+ gdcmDebugMacro( "Big trouble : Pixel Element ("
+ << std::hex << GrPixel<<","<< NumPixel<< ") NOT found" );
return 0;
}
}
+
/**
- * \brief anonymize a File (removes Patient's personal info)
- * (read the code to see which ones ...)
+ * \brief Adds the characteristics of a new element we want to anonymize
+ *
*/
-bool File::AnonymizeFile()
-{
- // If exist, replace by spaces
- SetValEntry (" ",0x0010, 0x2154); // Telephone
- SetValEntry (" ",0x0010, 0x1040); // Adress
- SetValEntry (" ",0x0010, 0x0020); // Patient ID
+void File::AddAnonymizeElement (uint16_t group, uint16_t elem,
+ std::string const &value)
+
+{
+ Element el;
+ el.Group = group;
+ el.Elem = elem;
+ el.Value = value;
+ AnonymizeList.push_back(el);
+}
- 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 )
+/**
+ * \brief Overwrites in the file the values of the DicomElements
+ * held in the list
+ */
+void File::AnonymizeNoLoad()
+{
+ std::fstream *fp = new std::fstream(Filename.c_str(),
+ std::ios::in | std::ios::out | std::ios::binary);
+ // TODO : FIXME
+ // how to white out disk space if longer than 50 ?
+ char spaces[50] = " ";
+
+ gdcm::DocEntry *d;
+ uint32_t offset;
+ uint32_t lgth;
+ uint32_t lgtToWrite;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
+
+ offset = d->GetOffset();
+ lgth = d->GetLength();
+ fp->seekp( offset, std::ios::beg );
+
+ if ( (*it).Value == "" )
{
- InsertValEntry(studyInstanceUID, 0x0010, 0x0010);
+ lgtToWrite = lgth > 50 ? 50 : lgth;
+ fp->write( spaces, lgtToWrite );
}
else
{
- InsertValEntry("anonymised", 0x0010, 0x0010);
+ // TODO : FIXME
+ // how to white out disk space if longer than 50 ?
+ (*it).Value = (*it).Value + spaces;
+ lgtToWrite = lgth > (*it).Value.length() ? (*it).Value.length() : lgth;
+ fp->write( (char *)(*it).Value.c_str(), lgtToWrite );
+
+ }
+ fp->close();
+ delete fp;
+ }
+}
+
+/**
+ * \brief anonymize a File (removes Patient's personal info passed with
+ * AddAnonymizeElement()
+ */
+bool File::AnonymizeFile()
+{
+ // If Anonymisation list is empty, let's perform some basic anonymisation
+ if ( AnonymizeList.begin() == AnonymizeList.end() )
+ {
+ // If exist, replace by spaces
+ SetValEntry (" ",0x0010, 0x2154); // Telephone
+ SetValEntry (" ",0x0010, 0x1040); // Adress
+ SetValEntry (" ",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 )
+ {
+ SetValEntry(studyInstanceUID, 0x0010, 0x0010);
+ }
+ else
+ {
+ SetValEntry("anonymised", 0x0010, 0x0010);
+ }
}
}
+ else
+ {
+ gdcm::DocEntry *d;
+ for (ListElements::iterator it = AnonymizeList.begin();
+ it != AnonymizeList.end();
+ ++it)
+ {
+ d = GetDocEntry( (*it).Group, (*it).Elem);
+
+ if ( dynamic_cast<BinEntry *>(d)
+ || dynamic_cast<SeqEntry *>(d) )
+ continue;
+
+ SetValEntry ((*it).Value, (*it).Group, (*it).Elem);
+ }
+}
- // Just for fun :-(
- // (if any) remove or replace all the stuff that contains a Date
+ // In order to make definitively impossible any further identification
+ // remove or replace all the stuff that contains a Date
//0008 0012 DA ID Instance Creation Date
//0008 0020 DA ID Study Date
std::ios::out | std::ios::binary);
if (*fp == NULL)
{
- gdcmVerboseMacro("Failed to open (write) File: " << fileName.c_str());
+ gdcmWarningMacro("Failed to open (write) File: " << fileName.c_str());
return false;
}
if ( GetPixelSize() == 16 )
{
uint16_t *im16 = (uint16_t *)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
+ int lgth = b->GetLength();
+ for( int i = 0; i < lgth / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
if ( GetPixelSize() == 16 )
{
uint16_t *im16 = (uint16_t*)b->GetBinArea();
- int lgr = b->GetLength();
- for( int i = 0; i < lgr / 2; i++ )
+ int lgth = b->GetLength();
+ for( int i = 0; i < lgth / 2; i++ )
{
im16[i]= (im16[i] >> 8) | (im16[i] << 8 );
}
if ( nbRleSegments > 16 )
{
// There should be at most 15 segments (refer to RLEFrame class)
- gdcmVerboseMacro( "Too many segments.");
+ gdcmWarningMacro( "Too many segments.");
}
uint32_t rleSegmentOffsetTable[16];
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- gdcmVerboseMacro( "No sequence delimiter item at end of RLE item sequence");
+ gdcmWarningMacro( "No sequence delimiter item at end of RLE item sequence");
}
}
// Delimiter Item':
if ( !ReadTag(0xfffe, 0xe0dd) )
{
- gdcmVerboseMacro( "No sequence delimiter item at end of JPEG item sequence");
+ gdcmWarningMacro( "No sequence delimiter item at end of JPEG item sequence");
}
}
}
if ( itemTagGroup != testGroup || itemTagElement != testElement )
{
- gdcmVerboseMacro( "Wrong Item Tag found:"
+ gdcmWarningMacro( "Wrong Item Tag found:"
<< " We should have found tag ("
<< std::hex << testGroup << "," << testElement << ")" << std::endl
<< " but instead we encountered tag ("
long currentPosition = Fp->tellg();
uint32_t itemLength = ReadInt32();
{
- gdcmVerboseMacro( "Basic Item Length is: "
+ gdcmWarningMacro( "Basic Item Length is: "
<< itemLength << std::endl
<< " at address: " << std::hex << (unsigned int)currentPosition);
}
{
uint32_t individualLength = str2num( &basicOffsetTableItemValue[i],
uint32_t);
- gdcmVerboseMacro( "Read one length: " <<
+ gdcmWarningMacro( "Read one length: " <<
std::hex << individualLength );
}
#endif //GDCM_DEBUG
git://git.creatis.insa-lyon.fr / gdcm.git / blobdiff