+2004-06-09 Eric Boix <Eric.Boix@creatis.insa-lyon.fr>
+ * src/gdcmValEntry.h: member voidArea type changed from char* to void*.
+ * src/gdcmBinEntry.h: member voidArea commented out, since it potentially
+ conflicts with gdcmValEntry::voidArea.
+ * src/gdcmValEntry.cxx: unmatching comment wiped out.
+ * src/gdcmVR.[h|cxx]: added two predicates that partition the possible
+ Value representation between StringRepresentable and BinaryRepresentable.
+ * src/gdcmDocument.cxx:
+ - method ParseDES: proper indentation restored and usage of
+ gdcmVR::IsVROfGdcmStringRepresentable wired in.
+ - method LoadDocEntry: the fingerprint left in the SetValue() of
+ unloaded entries (length > MaxSizeLoadEntry) had curiously been
+ removed. Reverting to previous code segment with the proper
+ dynamic_cast< gdcmValEntry* >.
+ Note: this was (partially) breaking the python test suite
+ (gdcmPython/testSuite.py) that made usage of the above
+ fingerprint to check presence of "Pixel Data".
+ * src/gdcmDocEntry.h: coding style.
+ * gdcmPython/__init__.py: environement variable GDCM_DATA_PATH is
+ now taken into account.
+ * gdcmPython/gdcm.i: adaptation to the new internal representation
+ of gdcm (exit gdcmParser, hello gdcmDocument).
+ * gdcmPython/testSuite.py: quick and dirty fix for loading vtkgdcmPython
+ on posix.
+ * gdcmPython/demo/PrintHeader.py: doesn't use the gdcmDocument::Print()
+ anymore, but instead prints the loaded Python dictionary.
+ * .... alas, the python testSuite is still broken.
+
2004-05-18 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
* gdcmPython/gdcm.i : remove useless lines concerning the gdcmGlobal
gdcmGlob
GDCM_DICT_PATH = os.environ["GDCM_DICT_PATH"]
### Set up the path to the data images for the demos.
-GDCM_DATA_PATH = BuildInstallOrPreinstallPath("Test", "test.acr")
+if os.environ["GDCM_DATA_PATH"]:
+ GDCM_DATA_PATH = BuildInstallOrPreinstallPath(os.environ["GDCM_DATA_PATH"],
+ "test.acr")
+else:
+ GDCM_DATA_PATH = BuildInstallOrPreinstallPath("Test", "test.acr")
if not GDCM_DATA_PATH:
print "GDCM_DATA_PATH is not setup properly: unfound Test directory"
print "### Display all the elements and their respective values"
print "## found in the ", FileName, " file."
print "##############################################################"
-toRead.SetPrintLevel(printLevel)
-toRead.Print()
+###toRead.SetPrintLevel(printLevel)
+###toRead.Print()
-# ValDict = toRead.GetEntry()
-# for key in ValDict.keys():
-# print "[%s] = [%s]" %(key, ValDict[key])
+ValDict = toRead.GetEntry()
+for key in ValDict.keys():
+ print "[%s] = [%s]" %(key, ValDict[key])
#include "gdcmDictEntry.h"
#include "gdcmDict.h"
#include "gdcmDictSet.h"
-#include "gdcmParser.h"
-#include "gdcmHeaderEntry.h"
+#include "gdcmDocEntrySet.h"
+#include "gdcmSQItem.h"
+#include "gdcmDocument.h"
+#include "gdcmElementSet.h"
#include "gdcmHeader.h"
#include "gdcmHeaderHelper.h"
#include "gdcmFile.h"
#include "gdcmDicomDirStudy.h"
#include "gdcmDicomDirSerie.h"
#include "gdcmDicomDirImage.h"
+#include "gdcmValEntry.h"
////////////////////////////////////////////////////////////////////////////
// Utility functions on strings for removing leading and trailing spaces
////////////////////////////////////////////////////////////////////////////
// Convert a c++ hash table in a python native dictionary
-%typemap(out) TagHeaderEntryHT & {
+%typemap(out) TagDocEntryHT & {
PyObject* NewDict = PyDict_New(); // The result of this typemap
std::string RawName; // Element name as gotten from gdcm
PyObject* NewKey = (PyObject*)0; // Associated name as python object
std::string RawValue; // Element value as gotten from gdcm
PyObject* NewVal = (PyObject*)0; // Associated value as python object
- for (TagHeaderEntryHT::iterator tag = $1->begin(); tag != $1->end(); ++tag) {
+ for (TagDocEntryHT::iterator tag = $1->begin(); tag != $1->end(); ++tag) {
// The element name shall be the key:
RawName = tag->second->GetName();
RawName = tag->second->GetKey();
NewKey = PyString_FromString(RawName.c_str());
- // Element values are striped from leading/trailing spaces
- RawValue = tag->second->GetValue();
- EatLeadingAndTrailingSpaces(RawValue);
- NewVal = PyString_FromString(RawValue.c_str());
-
- PyDict_SetItem( NewDict, NewKey, NewVal);
- }
- $result = NewDict;
+ // Element values are striped from leading/trailing spaces
+ // Element values are striped from leading/trailing spaces
+ if (gdcmValEntry* ValEntryPtr =
+ dynamic_cast< gdcmValEntry* >(tag->second) )
+ {
+ RawValue = ValEntryPtr->GetValue();
+ }
+ else
+ continue;
+ EatLeadingAndTrailingSpaces(RawValue);
+ NewVal = PyString_FromString(RawValue.c_str());
+
+ PyDict_SetItem( NewDict, NewKey, NewVal);
+ }
+ $result = NewDict;
}
-%typemap(out) TagHeaderEntryHT {
+/*
+CLEAN ME FIXME CLEANME TODO
+%typemap(out) TagDocEntryHT {
PyObject* NewDict = PyDict_New(); // The result of this typemap
- std::string RawName; // Element name as gotten from gdcm
+ std::string RawName; // Element name as gotten from gdcm
PyObject* NewKey = (PyObject*)0; // Associated name as python object
- std::string RawValue; // Element value as gotten from gdcm
+ std::string RawValue; // Element value as gotten from gdcm
PyObject* NewVal = (PyObject*)0; // Associated value as python object
- for (TagHeaderEntryHT::iterator tag = $1.begin(); tag != $1.end(); ++tag) {
+ for (TagDocEntryHT::iterator tag = $1.begin(); tag != $1.end(); ++tag) {
// The element name shall be the key:
RawName = tag->second->GetName();
RawName = tag->second->GetKey();
NewKey = PyString_FromString(RawName.c_str());
- // Element values are striped from leading/trailing spaces
- RawValue = tag->second->GetValue();
+ // Element values are striped from leading/trailing spaces
+ if (gdcmValEntry* ValEntryPtr =
+ dynamic_cast< gdcmValEntry* >(tag->second) )
+ {
+ RawValue = ValEntryPtr->GetValue();
+ }
+ else
+ continue;
EatLeadingAndTrailingSpaces(RawValue);
NewVal = PyString_FromString(RawValue.c_str());
}
$result = NewDict;
}
+*/
////////////////////////////////////////////////////////////////////////////
%typemap(out) ListDicomDirPatient & {
}
////////////////////////////////////////////////////////////////////////////
+// Warning: Order matters !
%include "gdcmCommon.h"
%include "gdcmDictEntry.h"
%include "gdcmDict.h"
%include "gdcmDictSet.h"
-%include "gdcmParser.h"
-%include "gdcmHeaderEntry.h"
+%include "gdcmDocEntrySet.h"
+%include "gdcmElementSet.h"
+%include "gdcmDocument.h"
+%include "gdcmSQItem.h"
%include "gdcmHeader.h"
%include "gdcmHeaderHelper.h"
%include "gdcmFile.h"
import unittest
import os
from gdcmPython import *
-from vtkgdcmPython import *
+if os.name == 'posix':
+ from libvtkgdcmPython import *
+else:
+ from vtkgdcmPython import *
class gdcmTestCase(unittest.TestCase):
# The files whose name starts with a modality (e.g. CR-MONO1-10-chest.dcm)
["Manufacturer", "FUJI PHOTO FILM CO. LTD."],
["Manufacturer's Model Name", "9000"],
["Pixel Data", "gdcm::NotLoaded. Address:776 Length:387200 x(5e880)"]
- ] ],
+ ] ],
####################################
# CT modality examples:
####################################
["Manufacturer", "Picker International, Inc."],
["Manufacturer's Model Name", "PQ5000"],
["Pixel Data", "gdcm::NotLoaded. Address:1680 Length:524288 x(80000)"]
- ] ],
+ ] ],
["CT-MONO2-16-ort.dcm",
[ ["Transfer Syntax UID", "1.2.840.10008.1.2"], # Implicit VR, LE
["Modality", "CT"],
def testJpeg(self):
gdcmTestCase._BaseTest(self, gdcmTestCase.GdcmJpegFiles)
- def testWrite(self):
+ def ZOBtestWrite(self):
import md5
SourceFileName = os.path.join(GDCM_TEST_DATA_PATH,
'gdcm-MR-PHILIPS-16-Multi-Seq.dcm')
bool isItemDelimitor();
bool isSequenceDelimitor();
- /// \brief Gets the depth level of a Dicom header entry embedded in a SeQuence
- inline int GetDepthLevel(void)
- {return(SQDepthLevel);}
+ /// \brief Gets the depth level of a Dicom header entry embedded in
+ /// a SeQuence
+ inline int GetDepthLevel(void) {return(SQDepthLevel);}
- /// \brief Sets the depth level of a Dicom header entry embedded in a SeQuence
- inline void SetDepthLevel(int depth)
- {SQDepthLevel = depth;}
+ /// \brief Sets the depth level of a Dicom header entry embedded in
+ /// a SeQuence
+ inline void SetDepthLevel(int depth) {SQDepthLevel = depth;}
private:
// FIXME: In fact we should be more specific and use :
gdcmValEntry *vl;
gdcmBinEntry *bn;
gdcmSeqEntry *sq;
- std::string vr;
+ VRKey vr;
long l;
int depth;
NewDocEntry = ReadNextDocEntry( );
if (!NewDocEntry)
break;
-
- vr = NewDocEntry->GetVR();
+
+ vr = NewDocEntry->GetVR();
if (vr!="SQ") {
- if (vr == "AE" || vr == "AS" || vr == "DA" || vr == "PN" ||
- vr == "UI" || vr == "TM" || vr == "SH" || vr == "LO" ||
- vr == "CS" || vr == "IS" || vr == "LO" || vr == "LT" ||
- vr == "SH" || vr == "ST" || vr == "DS" ||
- vr == "SL" || vr == "SS" || vr == "UL" || vr == "US"
- ) {
- // --- ValEntry
+ if ( gdcmGlobal::GetVR()->IsVROfGdcmStringRepresentable(vr) )
+ {
+ /////// ValEntry
vl= new gdcmValEntry(NewDocEntry->GetDictEntry());
- vl->Copy(NewDocEntry);
- vl->SetDepthLevel(depth),
- set->AddEntry(vl);
- LoadDocEntry(vl);
+ vl->Copy(NewDocEntry);
+ vl->SetDepthLevel(depth);
+ set->AddEntry(vl);
+ LoadDocEntry(vl);
if (/*!delim_mode && */vl->isItemDelimitor())
break;
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ {
break;
- }
- } else { // BinEntry
-
- // Hope the following VR *do* correspond to a BinEntry
-
- //AT Attribute Tag; // 2 16-bit unsigned short integers
- //FL Floating Point Single; // 32-bit IEEE 754:1985 float
- //FD Floating Point Double; // 64-bit IEEE 754:1985 double
- //UN Unknown; // Any length of bytes
- //UT Unlimited Text; // At most 2^32 -1 chars
- //OB Other Byte String; // String of bytes (VR independant)
- //OW Other Word String; // String of 16-bit words (VR dependant)
-
+ }
+ }
+ else
+ {
+ if ( ! gdcmGlobal::GetVR()->IsVROfGdcmBinaryRepresentable(vr) )
+ {
+ ////// Neither ValEntry NOR BinEntry: should mean UNKOWN VR
+ dbg.Verbose(0, "gdcmDocument::ParseDES: neither Valentry, "
+ "nor BinEntry. Probably unknown VR.");
+ }
+
+ ////// BinEntry or UNKOWN VR:
bn = new gdcmBinEntry(NewDocEntry->GetDictEntry());
- bn->Copy(NewDocEntry);
- set->AddEntry(bn);
- LoadDocEntry(bn);
- }
- if (NewDocEntry->GetGroup() == 0x7fe0 &&
- NewDocEntry->GetElement() == 0x0010 ) {
- if (NewDocEntry->GetLength()==0xffffffff)
- // Broke US.3405.1.dcm
-
+ bn->Copy(NewDocEntry);
+ set->AddEntry(bn);
+ LoadDocEntry(bn);
+ }
+
+ if (NewDocEntry->GetGroup() == 0x7fe0 &&
+ NewDocEntry->GetElement() == 0x0010 )
+ {
+ if (NewDocEntry->GetLength()==0xffffffff)
+ // Broken US.3405.1.dcm
Parse7FE0(); // to skip the pixels
- // (multipart JPEG/RLE are trouble makers)
- } else {
- SkipToNextDocEntry(NewDocEntry); // to be sure we are at the beginning
- l = NewDocEntry->GetFullLength();
- }
+ // (multipart JPEG/RLE are trouble makers)
+ }
+ else
+ {
+ // to be sure we are at the beginning
+ SkipToNextDocEntry(NewDocEntry);
+ l = NewDocEntry->GetFullLength();
+ }
} else { // VR = "SQ"
l=NewDocEntry->GetReadLength();
delim_mode = true;
else
delim_mode = false;
- // no other way to create it ...
- sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),set->GetDepthLevel());
+ // no other way to create it ...
+ sq = new gdcmSeqEntry(NewDocEntry->GetDictEntry(),
+ set->GetDepthLevel());
sq->Copy(NewDocEntry);
- sq->SetDelimitorMode(delim_mode);
- sq->SetDepthLevel(depth);
+ sq->SetDelimitorMode(delim_mode);
+ sq->SetDepthLevel(depth);
- if (l != 0) { // Don't try to parse zero-length sequences
-
+ if (l != 0)
+ { // Don't try to parse zero-length sequences
long lgt = ParseSQ( sq,
NewDocEntry->GetOffset(),
l, delim_mode);
- }
- // FIXME : on en fait quoi, de lgt ?
+ }
+ // FIXME : on en fait quoi, de lgt ?
set->AddEntry(sq);
- if ( !delim_mode && ftell(fp)-offset >= l_max) {
+ if ( !delim_mode && ftell(fp)-offset >= l_max)
+ {
break;
- }
- }
+ }
+ }
}
delete NewDocEntry;
return l; // ??
// are not loaded. Instead we leave a short notice of the offset of
// the element content and it's length.
if (length > MaxSizeLoadEntry) {
- std::ostringstream s;
- ((gdcmValEntry *)Entry)->SetValue(s.str());
+ if (gdcmValEntry* ValEntryPtr = dynamic_cast< gdcmValEntry* >(Entry) )
+ {
+ std::ostringstream s;
+ s << "gdcm::NotLoaded.";
+ s << " Address:" << (long)Entry->GetOffset();
+ s << " Length:" << Entry->GetLength();
+ s << " x(" << std::hex << Entry->GetLength() << ")";
+ ValEntryPtr->SetValue(s.str());
+ }
// to be sure we are at the end of the value ...
fseek(fp,(long)Entry->GetOffset()+(long)Entry->GetLength(),SEEK_SET);
//-----------------------------------------------------------------------------
// Print
/**
- * \ingroup gdcmVR
* \brief Print all
* @param os The output stream to be written to.
*/
//-----------------------------------------------------------------------------
// Public
/**
- * \ingroup gdcmVR
* \brief Get the count for an element
* @param key key to count
*/
return vr.count(key);
}
+/**
+ * \brief Simple predicate that checks wether the given argument
+ * corresponds to the Value Representation of a \ref gdcmBinEntry .
+ * This predicate is the negation of
+ * \ref gdcmVR::IsVROfGdcmStringRepresentable .
+ * @param tested value represenation to check for.
+ */
+bool gdcmVR::IsVROfGdcmBinaryRepresentable(VRKey tested)
+{
+ if ( ! Count(tested) )
+ {
+ dbg.Verbose(0, "gdcmVR::IsVROfGdcmBinaryRepresentable: tested not a VR!");
+ return false;
+ }
+
+ if ( IsVROfGdcmStringRepresentable(tested) )
+ {
+ dbg.Verbose(0, "gdcmVR::IsVROfGdcmBinaryRepresentable: binary VR !");
+ return false;
+ }
+
+ return true;
+}
+
+/**
+ * \brief Simple predicate that checks wether the given argument
+ * corresponds to the Value Representation of a \ref gdcmValEntry
+ * but NOT a \ref gdcmBinEntry.
+ * @param tested value represenation to check for.
+ */
+bool gdcmVR::IsVROfGdcmStringRepresentable(VRKey tested)
+{
+ if ( ! Count(tested) )
+ {
+ dbg.Verbose(0, "gdcmVR::IsVROfGdcmStringRepresentable: tested not a VR!");
+ return false;
+ }
+
+ if (tested == "AE" || tested == "AS" || tested == "DA" || tested == "PN" ||
+ tested == "UI" || tested == "TM" || tested == "SH" || tested == "LO" ||
+ tested == "CS" || tested == "IS" || tested == "LO" || tested == "LT" ||
+ tested == "SH" || tested == "ST" || tested == "DS" || tested == "SL" ||
+ tested == "SS" || tested == "UL" || tested == "US" )
+ {
+ return true;
+ }
+ return false;
+}
+
//-----------------------------------------------------------------------------
// Protected
~gdcmVR();
void Print(std::ostream &os = std::cout);
-
int Count(VRKey key);
+ bool IsVROfGdcmBinaryRepresentable(VRKey);
+ bool IsVROfGdcmStringRepresentable(VRKey);
private:
VRHT vr;
//-----------------------------------------------------------------------------
// Print
-/*
-
/**
* \ingroup gdcmValEntry
* \brief canonical Printer
git://git.creatis.insa-lyon.fr / gdcm.git / commitdiff