-2005-04-31 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
+2005-02-07 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
+ * gdcmPython/gdcm.i : bug fix. Now string are correctly converted in python
+ string type
+ * src/gdcmDict.h : remove commented code
+ * src/gdcmDocument.cxx : initialize values
+ * src/gdcmFile.cxx : bug fix when reading values
+ * gdcmPython/demo/ : change file names. Remove useless files
+
+2005-02-04 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
* src/gdcmFile.cxx : remove the default array of initialization.
The static array contained pointers to non-static values (comming from
strings). To have coherences, when creating files, these values can't be
static. So, the array can't be static, too ! To simplify, the array have
been replaced by repeted lines to insert values in the File
-2005-03-31 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
+2005-02-03 Benoit Regrain <Benoit.Regrain@creatis.insa-lyon.fr>
* src/gdcmBinEntry.cxx : bug fix for BIG_ENDIAN part when writing the content
* gdcmPython/gdcm.i : rename gdcmHeader to gdcmHelper
ADD_TEST(Python-PrintDict ${PYTHON_EXECUTABLE}
${GDCM_BINARY_DIR}/gdcmPython/demo/PrintDict.py
)
- ADD_TEST(Python-PrintHeader ${PYTHON_EXECUTABLE}
- ${GDCM_BINARY_DIR}/gdcmPython/demo/PrintHeader.py
+ ADD_TEST(Python-PrintFile ${PYTHON_EXECUTABLE}
+ ${GDCM_BINARY_DIR}/gdcmPython/demo/PrintFile.py
)
ADD_TEST(Python-PrintDicomDir ${PYTHON_EXECUTABLE}
${GDCM_BINARY_DIR}/gdcmPython/demo/PrintDicomDir.py
# Copy all the demo directory content to the cmake bin
# Without it, tests can't be launched
CONFIGURE_FILE(
- ${GDCM_SOURCE_DIR}/gdcmPython/demo/PrintHeader.py.in
- ${GDCM_BINARY_DIR}/gdcmPython/demo/PrintHeader.py
+ ${GDCM_SOURCE_DIR}/gdcmPython/demo/PrintFile.py.in
+ ${GDCM_BINARY_DIR}/gdcmPython/demo/PrintFile.py
)
CONFIGURE_FILE(
+++ /dev/null
-from gdcmPython import *
-import sys
-
-### Get filename from command line or default it
-try:
- fileName = sys.argv[1]
-except IndexError:
- fileName = os.path.join(GDCM_DATA_PATH, "DICOMDIR")
-
-try:
- printLevel = int(sys.argv[2])
-except IndexError:
- printLevel = 1
-
-### Build the header element list
-dicomdir = gdcmDicomDir(fileName)
-if not dicomdir.IsReadable():
- print "The '", fileName, "' DicomDir is not readable with gdcm. Sorry."
- sys.exit()
-
-print "##############################################################"
-print "## Display all the elements and their respective values"
-print "## found in the ", fileName, " file."
-print "##############################################################"
-dicomdir.SetPrintLevel(-1)
-dicomdir.Print()
-
+++ /dev/null
-from gdcmPython.core import *
-import sys
-import os
-
-### Get filename from command line or default it
-try:
- fileName = sys.argv[1]
-except IndexError:
- fileName = os.path.join(GDCM_DATA_PATH, "test.acr")
-
-try:
- printLevel = int(sys.argv[2])
-except IndexError:
- printLevel = 1
-
-#if not os.path.isfile(FileName):
-# print "Cannot open file ", FileName
-# sys.exit()
-
-# On debugging purposes uncomment the next line
-#s = raw_input("Hit any key in this window to exit")
-
-### Build the header element list
-print fileName, type(fileName)
-header = gdcm.Header(fileName)
-if not header.IsReadable():
- print "The '", fileName, "' file is not readable with gdcm. Sorry."
- sys.exit()
-
-print "##############################################################"
-print "### Display all the elements and their respective values"
-print "## found in the ", fileName, " file."
-print "##############################################################"
-
-header.InitTraversal()
-val=header.GetNextEntry()
-while(val):
- val.Print()
- print ""
- val=header.GetNextEntry()
-val=None
-
+++ /dev/null
-## A small demo that displays with VTK a dicom image parsed with gdcm.
-## Warning: the parsing of header of the dicom file is done with gdcm
-## but the process of in-memory loading of the image is performed
-## by vtkImageReader (classical vtk operator). Since vtkImageReader
-## has no special knowledge of Dicom file format, this demo
-## will only work for a restrained sub-set of Dicom files (basically
-## non compressed and with "HighBit + 1 != BitsStored").
-## When those conditions are not met try using vtkgdcmReader.py...
-import sys
-import vtk
-from gdcmPython import gdcmHeader
-
-class vtkHistogram:
- '''Some medical images might have a poor dynamic. This is because
- some additional visual tags-like the patient name- are sometimes
- written/drawn on top of the image : to avoid interference with
- the image itself, the level used for this additional text is
- usually way above the maximum level of the image. Hence we use
- some cumulative histograme die-hard technique to remove some
- arbitrary small portion of the dynamic.'''
- def __init__(self, imagereader):
- self.vtkReader = imagereader
- self.__Histo = None
- self.__CumulHisto = None
- self.__LevelMin = self.vtkReader.GetOutput().GetScalarRange()[0]
- self.__LevelMax = self.vtkReader.GetOutput().GetScalarRange()[1]
- self.__NumberOfBins = 255 # See VTKImageAccumulate
- self.__Spacing = (self.__LevelMax - self.__LevelMin)/self.__NumberOfBins
-
- def ComputeHisto(self):
- self.__Histo = vtk.vtkImageAccumulate()
- self.__Histo.SetComponentExtent(0, self.__NumberOfBins, 0, 0, 0, 0)
- self.__Histo.SetInput(self.vtkReader.GetOutput())
- self.__Histo.SetComponentSpacing(self.__Spacing, 0.0, 0.0)
- self.__Histo.Update()
-
- def ComputeCumulativeHisto(self):
- ''' Compyte the Cumulative histogram of the image.'''
- if not self.__Histo:
- self.ComputeHisto()
- self.__CumulHisto = []
- histo = self.__Histo.GetOutput()
- self.__CumulHisto.append(int(histo.GetScalarComponentAsDouble(0,0,0,0)))
- for i in range(1, self.__NumberOfBins):
- value = int(histo.GetScalarComponentAsDouble(i,0,0,0))
- self.__CumulHisto.append( self.__CumulHisto[i-1] + value)
-
- def GetTruncateLevels(self, LostPercentage):
- ''' Compute the level below which (respectively above which)
- the LostPercentage percentage of the pixels shall be disregarded.
- '''
- if LostPercentage < 0.0 or LostPercentage >1.0:
- print " vtkHistogram::GetTruncateLevels: defaulting to 5%"
- LostPercentage = 0.05
- if not self.__CumulHisto:
- self.ComputeCumulativeHisto()
- NumPixels = self.__CumulHisto[self.__NumberOfBins - 1]
- NumLostPixels = NumPixels * LostPercentage
- AboveLevel = None
- BelowLevel = None
- # FIXME : not really clean loop...
- for i in range(0, self.__NumberOfBins-1):
- if not BelowLevel:
- if self.__CumulHisto[i] > NumLostPixels:
- BelowLevel = self.__LevelMin + self.__Spacing * i
- if not AboveLevel:
- if self.__CumulHisto[i] > NumPixels - NumLostPixels:
- AboveLevel = self.__LevelMin + self.__Spacing * i
- if not AboveLevel or not BelowLevel:
- print " vtkHistogram::GetTruncateLevels: Mistakes were made..."
- return BelowLevel, AboveLevel
-
-class vtkGdcmImage(gdcmHeader):
- ''' All informations required for VTK display
- * VTK pipeline
- * Lut (or associated Window/Level reductive control parameters)'''
- def __init__(self, filename):
- gdcmHeader.__init__(self, filename)
- self.filename = filename
- # LUT reductive parameters
- self.__LevelMin = 0 # Minimum value of pixel intensity
- self.__LevelMax = 0 # Maximun value of pixel intensity
- self.__Level = 0 # Current Level value (treshold below
- # which the image is represented as black)
- self.__Window = 0 # Width of displayed pixels (linearly).
- # Above Level + Window pixel are represented
- # as white.
- self.__VTKplaneActor = None
- self.vtkSetup()
-
- def VTKreaderSetup(self):
- self.__VTKReader = vtk.vtkImageReader()
- self.__VTKReader.SetFileName(self.filename)
- type = self.GetPixelType()
- if type == "8U":
- self.__VTKReader.SetDataScalarTypeToUnsignedChar()
- elif type == "8S":
- self.__VTKReader.SetDataScalarTypeTodChar()
- elif type == "16U":
- self.__VTKReader.SetDataScalarTypeToUnsignedShort()
- elif type == "16S":
- self.__VTKReader.SetDataScalarTypeToShort()
- self.__VTKReader.SetDataByteOrderToLittleEndian()
- #self.__VTKReader.SetDataByteOrderToBigEndian()
- else:
- print "vtkGdcmImage::VTKreaderSetup: unkown encoding:", type
- sys.exit()
- self.__VTKReader.SetHeaderSize(self.GetPixelOffset())
- self.__VTKReader.SetDataExtent (0, self.GetXSize()-1,
- 0, self.GetYSize()-1,
- 1, 1)
- self.__VTKReader.UpdateWholeExtent()
-
- def vtkSetup(self, orgx = -0.5, orgy = -0.5,
- ix = 0.5, iy = -0.5, jx = -0.5, jy = 0.5):
- # ImageReader ---> Texture \
- # | ==> PlaneActor
- # PlaneSource ---> PolyDataMapper /
- self.VTKreaderSetup()
- ### LookupTable
- self.__VTKtable = vtk.vtkLookupTable()
- self.__VTKtable.SetNumberOfColors(1000)
- self.__VTKtable.SetTableRange(0,1000)
- self.CallibrateWindowLevel() # calls the SetTableRange
- self.__VTKtable.SetSaturationRange(0,0)
- self.__VTKtable.SetHueRange(0,1)
- self.__VTKtable.SetValueRange(0,1)
- self.__VTKtable.SetAlphaRange(1,1)
- self.__VTKtable.Build()
- ### Texture
- self.__VTKtexture = vtk.vtkTexture()
- self.__VTKtexture.SetInput(self.__VTKReader.GetOutput())
- self.__VTKtexture.InterpolateOn()
- self.__VTKtexture.SetLookupTable(self.__VTKtable)
- ### PlaneSource
- self.__VTKplane = vtk.vtkPlaneSource()
- self.__VTKplane.SetOrigin( orgx, orgy, 0.0)
- self.__VTKplane.SetPoint1( ix, iy, 0.0)
- self.__VTKplane.SetPoint2( jx, jy, 0.0)
- ### PolyDataMapper
- self.__VTKplaneMapper = vtk.vtkPolyDataMapper()
- self.__VTKplaneMapper.SetInput(self.__VTKplane.GetOutput())
- ### Actor
- self.__VTKplaneActor = vtk.vtkActor()
- self.__VTKplaneActor.SetTexture(self.__VTKtexture)
- self.__VTKplaneActor.SetMapper(self.__VTKplaneMapper)
- self.__VTKplaneActor.PickableOn()
-
- def CallibrateWindowLevel(self):
- vtkreader = self.__VTKReader
- self.__LevelMin = vtkreader.GetOutput().GetScalarRange()[0]
- self.__LevelMax = vtkreader.GetOutput().GetScalarRange()[1]
- histo = vtkHistogram(vtkreader)
- self.__Level, above = histo.GetTruncateLevels(0.05)
- self.__Window = above - self.__Level
- self.__VTKtable.SetTableRange(self.__Level,
- self.__Level + self.__Window)
-
- def GetVTKActor(self):
- return self.__VTKplaneActor
-
-######################################################################
-import os
-from gdcmPython import GDCM_DATA_PATH
-
-### Get filename from command line or default it
-try:
- FileName = sys.argv[1]
-except IndexError:
- FileName = os.path.join(GDCM_DATA_PATH, "test.acr")
-
-if not os.path.isfile(FileName):
- print "Cannot open file ", FileName
- sys.exit()
-
-### The default vtkImageReader is unable to read some type of images:
-check = gdcmHeader(FileName)
-if not check.IsReadable():
- print "The ", FileName, " file is not "
- print " readable with gdcm. Sorry."
- sys.exit()
-check = check.GetEntry()
-try:
- HighBit = check["High Bit"]
- if len(HighBit) == 0 or HighBit == "gdcm::Unfound":
- raise KeyError
-except KeyError:
- print "Gdcm couldn't find the Bits Allocated Dicom tag in file ", FileName
- sys.exit()
-try:
- BitsStored = check["Bits Stored"]
- if len(BitsStored) == 0 or BitsStored == "gdcm::Unfound":
- raise KeyError
-except KeyError:
- print "Gdcm couldn't find the Bits Stored Dicom tag in file ", FileName
- sys.exit()
-if int(HighBit) + 1 != int(BitsStored):
- print "vtkImageReader cannot read the file ", FileName
- print " because the High Bit is offseted from the BitsStored."
- print " You should consider using vtkGdcmReader as opposed to the"
- print " vtkImageReader python class present in this demo. Please"
- print " see gdcmPython/demo/vtkGdcmReader.py for a demo."
- sys.exit()
-
-### Display in a vtk RenderWindow
-image = vtkGdcmImage(FileName)
-ren = vtk.vtkRenderer()
-renwin = vtk.vtkRenderWindow()
-renwin.AddRenderer(ren)
-iren = vtk.vtkRenderWindowInteractor()
-iren.SetRenderWindow(renwin)
-ren.AddActor(image.GetVTKActor())
-ren.SetBackground(0,0,0.5)
-renwin.Render()
-iren.Start()
+++ /dev/null
-## This demo illustrates the usage of the python-wrappers of vtkGdcmReader
-## native C++ vtk class. vtkGdcmReader.cxx is a C++ level wrapper of
-## gdcm which offers a vtk class vtkGdcmReader (inheriting from vtkImageReader,
-## see gdcm/vtk/vtkGdcmReader.cxx). vtkgdcmPython wraps this class for
-## python (by using vtk wrappers).
-from vtk import *
-from gdcmPython import *
-from gdcmPython.vtkgdcmPython import *
-import sys
-
-### Get filename from command line or default it
-try:
- FileName = sys.argv[1]
-except IndexError:
- FileName = os.path.join(GDCM_DATA_PATH, "test.acr")
-
-### Build the header element list
-test = gdcmHeader(FileName)
-if not test.IsReadable():
- print "The ", FileName, " file is not readable with gdcm. Sorry."
- sys.exit()
-del test
-toDisplay = vtkGdcmReader()
-toDisplay.AddFileName(FileName)
-###toDisplay.DebugOn()
-
-VTKtable = vtkLookupTable()
-VTKtable.SetNumberOfColors(1000)
-VTKtable.SetTableRange(0,1000)
-VTKtable.SetSaturationRange(0,0)
-VTKtable.SetHueRange(0,1)
-VTKtable.SetValueRange(0,1)
-VTKtable.SetAlphaRange(1,1)
-VTKtable.Build()
-
-VTKtexture = vtkTexture()
-VTKtexture.SetInput(toDisplay.GetOutput())
-VTKtexture.InterpolateOn()
-VTKtexture.SetLookupTable(VTKtable)
-
-VTKplane = vtkPlaneSource()
-VTKplane.SetOrigin( -0.5, -0.5, 0.0)
-VTKplane.SetPoint1( 0.5, -0.5, 0.0)
-VTKplane.SetPoint2( -0.5, 0.5, 0.0)
-
-VTKplaneMapper = vtkPolyDataMapper()
-VTKplaneMapper.SetInput(VTKplane.GetOutput())
-
-VTKplaneActor = vtkActor()
-VTKplaneActor.SetTexture(VTKtexture)
-VTKplaneActor.SetMapper(VTKplaneMapper)
-VTKplaneActor.PickableOn()
-
-ren = vtkRenderer()
-renwin = vtkRenderWindow()
-renwin.AddRenderer(ren)
-iren = vtkRenderWindowInteractor()
-iren.SetRenderWindow(renwin)
-ren.AddActor(VTKplaneActor)
-ren.SetBackground(0,0,0.5)
-renwin.Render()
-iren.Start()
-
-
-
//////////////////// STL string versus Python str ////////////////////////
// Convertion returning a C++ string.
-%typemap(out) string, std::string
+%typemap(out) std::string
{
$result = PyString_FromString(($1).c_str());
}
+%typemap(out) string
+{
+ $result = PyString_FromString(($1).c_str());
+}
+
+%typemap(out) std::string const &
+{
+ $result = PyString_FromString(($1)->c_str());
+}
+
// Convertion of incoming Python str to STL string
%typemap(python, in) const std::string, std::string
{
Program: gdcm
Module: $RCSfile: gdcmDict.h,v $
Language: C++
- Date: $Date: 2005/02/02 15:07:41 $
- Version: $Revision: 1.37 $
+ Date: $Date: 2005/02/07 09:51:03 $
+ Version: $Revision: 1.38 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
//-----------------------------------------------------------------------------
typedef std::string DictKey;
typedef std::map<TagKey, DictEntry> TagKeyHT;
-//typedef std::list<std::string> EntryNamesList;
-//typedef std::map<std::string,
-// std::list<std::string> > EntryNamesByCatMap;
//-----------------------------------------------------------------------------
/**
* \brief Dict acts a memory representation of a dicom dictionary i.e.
Program: gdcm
Module: $RCSfile: gdcmDocument.cxx,v $
Language: C++
- Date: $Date: 2005/02/06 14:39:35 $
- Version: $Revision: 1.224 $
+ Date: $Date: 2005/02/07 09:51:03 $
+ Version: $Revision: 1.225 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
return 0;
}
- uint16_t zero;
+ uint16_t zero = 0;
Fp->read((char*)&zero, (size_t)2);
if( Fp->eof() )
{
//DICOM
Fp->seekg(126L, std::ios::cur);
- char dicm[4];
+ char dicm[4] = {' ',' ',' ',' '};
Fp->read(dicm, (size_t)4);
if( Fp->eof() )
{
Program: gdcm
Module: $RCSfile: gdcmFile.cxx,v $
Language: C++
- Date: $Date: 2005/02/06 14:39:35 $
- Version: $Revision: 1.213 $
+ Date: $Date: 2005/02/07 09:51:03 $
+ Version: $Revision: 1.214 $
Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
l'Image). All rights reserved. See Doc/License.txt or
float xspacing, yspacing;
const std::string &strSpacing = GetEntryValue(0x0028,0x0030);
- if ( strSpacing == GDCM_UNFOUND )
+ if( strSpacing == GDCM_UNFOUND )
{
gdcmWarningMacro( "Unfound Pixel Spacing (0028,0030)" );
return 1.;
if( ( nbValues = sscanf( strSpacing.c_str(),
"%f\\%f", &yspacing, &xspacing)) != 2 )
{
+ // if no values, xspacing is set to 1.0
+ if( nbValues == 0 )
+ xspacing = 1.0;
// if single value is found, xspacing is defaulted to yspacing
- if ( nbValues == 1 )
- {
+ if( nbValues == 1 )
xspacing = yspacing;
- }
if ( xspacing == 0.0 )
xspacing = 1.0;
}
// if sscanf cannot read any float value, it won't affect yspacing
- sscanf( strSpacing.c_str(), "%f", &yspacing);
+ int nbValues = sscanf( strSpacing.c_str(), "%f", &yspacing);
+
+ // if no values, xspacing is set to 1.0
+ if( nbValues == 0 )
+ yspacing = 1.0;
if ( yspacing == 0.0 )
yspacing = 1.0;
projects / gdcm.git / commitdiff