+2003-05-21 Eric Boix <Eric.Boix@creatis.insa-lyon.fr> with JPR
+ * Added python wrappers of vtkGdcmReader vtk class (see the
+ source in vtk/vtkGdcmReader.cxx) :
+ - vtk/Makefile.am now builds a library
+ - gdcmPython/Makefile.am now builds vtkgdcmPython a second import
+ python library (as opposed to _gdcm.so wich are the python
+ wrappers of gdcm). vtkgdcmPython.so uses the vtk python wrappers
+ (vtkWrapPython and vtkWrapPythonInit utility) to build vtkgdcmPython
+ import library.
+ - configure.in has an additional flag --enable-vtk that needs
+ to be set to enable compilation of vtk related code, that is:
+ + vtk/vtkGdcmReader.so and
+ + vtk/testvtkGdcmReader C++ demo of vtk wrappers of gdcm)
+ + gdcmPython/vtkgdcmPython.so (see above)
+ - gdcmPython/demo/vtkGdcmDemo.py corrected (some images cannot
+ be read when compressed or when HighBit + 1 != BitsStored),
+ - gdcmPython/demo/vtkGdcmReader.py added. This demo illustrates
+ the usage of the python wrapper of vtkGdcmReader vtk class.
+ * vtk/vtkGdcmReader.cxx: bug fixed (thanks to Benoit Regrain).
+
2003-05-12 Eric Boix <Eric.Boix@creatis.insa-lyon.fr> with JPR
* src/gdcmHeader>[h/cxx] added gdcmHeader::GetPixelSize()
* vtk/vtkGdcmReader.cxx now properly inports the image in the
AC_SUBST(HAVE_DOXYGEN)
dnl Let people disable the doxygen stuff.
-AC_ARG_ENABLE(docygen, [ --enable-doxygen Use doxygen to build documentation (default=auto)], enable_doxygen="$enableval",
-enable_doxygen=auto)
+AC_ARG_ENABLE(docygen,
+ [ --enable-doxygen Use doxygen to build documentation (default=auto)],
+ [enable_doxygen="$enableval"],
+ [enable_doxygen=auto])
if test x$enable_doxygen = xauto ; then
if test x$DOXYGEN = xtrue ; then
dnl Checks for Python
AC_ARG_ENABLE(python,
- [ --enable-python Enable Python language support (default=no).],,
- [enable_python="no"])
+ [ --enable-python Enable Python language support (default=no).],
+ ,
+ [enable_python="no"])
dnl AC_MSG_RESULT($enable_python)
build_python=no
if test "yes" = "$enable_python"; then
dnl Checks for vtk
AC_ARG_ENABLE(vtk,
- [ --enable-vtk Enable vtk extensions support (default=no).],,
- [enable_vtk="no"])
+ [ --enable-vtk Enable vtk extensions support (default=no).],
+ ,
+ [enable_vtk="no"])
AM_CONDITIONAL(BUILD_VTK, test x$enable_vtk = xyes)
dnl produce Makefile.in files
## Process this file with automake to produce Makefile.in
-## $(top_builddir) is required for idtypes.h
-GDCM_INC = -I$(top_srcdir)/src -I$(top_builddir)
-SWIG_INC = $(GLIB_CFLAGS) $(PYTHON_INCLUDES) $(GDCM_INC)
-INCLUDES = $(GDCM_INC) $(PYTHON_INCLUDES)
+### VTK related
+VTK_INC = -I/usr/include/vtk
+LIBS_VTK=-L/usr/lib/vtk \
+ -lvtkCommon -lvtkIO -lvtkFiltering -lvtkRendering -lvtkGraphics \
+ -lvtkImaging -lvtkpng -lvtkzlib -lvtkjpeg -lvtkexpat -lvtktiff \
+ -lvtkftgl -lvtkfreetype
+LIBS_VTK_PYTHON= $(LIBS_VTK) \
+ -lvtkCommonPython -lvtkIOPython -lvtkFilteringPython \
+ -lvtkRenderingPython -lvtkGraphicsPython -lvtkImagingPython
+### Gdcm itself:
+GDCM_INC = -I$(top_srcdir)/src -I$(top_builddir)
+### Vtk wrappers of gdcm relate:
+VTKGDCM_DIR = $(top_srcdir)/vtk/
+VTKGDCM_INC = -I$(VTKGDCM_DIR)
+### Swig related (for wrapping Gdcm):
+SWIG_INC = $(PYTHON_INCLUDES) $(GDCM_INC)
-LIBADDS = $(top_builddir)/src/libgdcm.la -lstdc++
-
-### Non default rules
+### The resulting include path:
+INCLUDES = $(GDCM_INC) $(PYTHON_INCLUDES) $(VTK_INC) $(VTKGDCM_INC)
+### Since maude_LDFLAGS cannot be defined conditionaly:
pygdcm_la_LDFLAGS = -module -avoid-version -L$(top_builddir)/src/.libs
+vtkgdcmPython_la_LDFLAGS = -module -avoid-version
+############################################################
if BUILD_PYTHON
pythondir = $(prefix)/lib/python${PYTHON_VERSION}/site-packages/gdcm
-python_LTLIBRARIES = pygdcm.la
+if BUILD_VTK
+GDCMVTKLIB = vtkgdcmPython.la
+endif
+python_LTLIBRARIES = pygdcm.la $(GDCMVTKLIB)
+
+############ Gdcm python wrappers:
pygdcm_la_SOURCES = gdcm_wrap.cxx
-pygdcm_la_LIBADD = $(LIBADDS)
+pygdcm_la_LIBADD = $(top_builddir)/src/libgdcm.la -lstdc++
gdcm_wrap.cxx: $(srcdir)/gdcm.i
$(SWIG) -python -c++ $(SWIG_INC) -o $@ $<
-MOSTLYCLEANFILES = $(pygdcm_la_SOURCES)
-BUILT_SOURCES = gdcm_wrap.cxx
-CLEANFILES = gdcm_wrap.cxx
+############ Vtk wrappers of Gdcm wrapped for python
+if BUILD_VTK
+PYTHON_LIB_BASENAME=vtkgdcmPython
+
+# Python wrappers
+PYTHON_WRAPPER = vtkWrapPython
+PYTHON_WRAPPER_INIT=./vtkWrapPythonInit
+PWFLAGS=hints
+
+vtkgdcmPython_la_SOURCES = \
+ vtkGdcmReaderPython.cxx \
+ vtkGdcmInit.cxx
+vtkgdcmPython_la_LIBADD = $(top_builddir)/vtk/libvtkgdcm.la \
+ $(LIBS_VTK_PYTHON)
+
+vtkGdcmReaderPython.cxx: $(VTKGDCM_DIR)/vtkGdcmReader.h
+ $(PYTHON_WRAPPER) $< $(PWFLAGS) $@
+
+vtkGdcmInit.cxx : $(VTKGDCM_DIR)/vtkGdcmReader.h $(PYTHON_WRAPPER_INIT)
+ $(PYTHON_WRAPPER_INIT) $(PYTHON_LIB_BASENAME) \
+ vtkGdcmReader.h \
+ > $@
+
+$(PYTHON_WRAPPER_INIT) : vtkWrapPythonInit.c
+ gcc -o $@ $<
+endif### BUILD_PYTHON #######################################
+
+############ Automake general usage classics:
+MOSTLYCLEANFILES = $(pygdcm_la_SOURCES) $(vtkgdcmPython_la_SOURCES)
+BUILT_SOURCES = $(pygdcm_la_SOURCES) $(vtkgdcmPython_la_SOURCES)
+CLEANFILES = gdcm_wrap.cxx gdcm.py gdcm.pyc vtkWrapPythonInit
dist-hook:
rm -f $(distdir)/gdcm_wrap.cxx
-## A small demo that displays with VTK an image parsed with gdcm.
+## 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
sys.exit()
check = check.GetPubElVal()
try:
- BitsAlloc = check["Bits Allocated"]
- if len(BitsAlloc) == 0 or BitsAlloc == "gdcm::Unfound":
+ 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
except KeyError:
print "Gdcm couldn't find the Bits Stored Dicom tag in file ", FileName
sys.exit()
-if BitsAlloc != BitsStored:
+if int(HighBit) + 1 != int(BitsStored):
print "vtkImageReader cannot read the file ", FileName
- print " because the Bits Allocated and the Bits stored don't match."
+ 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
--- /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.SetFileName(FileName)
+toDisplay.UpdateWholeExtent()
+
+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()
+
+
+
--- /dev/null
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+char *names[1000];
+char *kitName;
+int anindex = 0;
+
+/* warning this code is also in getclasses.cxx under pcmaker */
+void stuffit()
+{
+ int i;
+
+ for (i = 0; i < anindex; i++)
+ {
+ fprintf(stdout,"extern \"C\" { PyObject *PyVTKClass_%sNew(char *); }\n",
+ names[i]);
+ }
+
+ fprintf(stdout,"\nstatic PyMethodDef Py%s_ClassMethods[] = {\n",
+ kitName);
+ fprintf(stdout,"{NULL, NULL}};\n\n");
+
+ fprintf(stdout,"extern \"C\" { void init%s();}\n\n",kitName);
+
+ /* module init function */
+ fprintf(stdout,"void init%s()\n{\n",kitName);
+ fprintf(stdout," PyObject *m, *d, *c;\n\n");
+ fprintf(stdout," static char modulename[] = \"%s\";\n",kitName);
+ fprintf(stdout," m = Py_InitModule(modulename, Py%s_ClassMethods);\n",
+ kitName);
+
+ fprintf(stdout," d = PyModule_GetDict(m);\n");
+ fprintf(stdout," if (!d) Py_FatalError(\"can't get dictionary for module %s!\");\n\n",
+ kitName);
+
+ for (i = 0; i < anindex; i++)
+ {
+ fprintf(stdout," if ((c = PyVTKClass_%sNew(modulename)))\n",names[i]);
+ fprintf(stdout," if (-1 == PyDict_SetItemString(d, \"%s\", c))\n",
+ names[i]);
+ fprintf(stdout," Py_FatalError(\"can't add class %s to dictionary!\");\n\n",
+ names[i]);
+ }
+ fprintf(stdout,"}\n\n");
+}
+
+int main(int argc,char *argv[])
+{
+ int i,j;
+ char tmp[128];
+ FILE *file;
+
+ if (argc < 3)
+ {
+ fprintf(stderr,"Usage: %s kit_name file1 file2 file3 ...\n",argv[0]);
+ exit(1);
+ }
+
+ kitName = strdup(argv[1]);
+
+ /* fill in the correct arrays */
+ for (i = 2, j = 0; i < argc; i++)
+ {
+ strcpy(tmp,argv[i]);
+ strcpy(tmp+strlen(tmp)-2,"Python.cxx");
+ file = fopen(tmp,"r");
+ if (file)
+ {
+ fgets(tmp,22,file);
+ fclose(file);
+ }
+ if (strcmp(tmp,"// python wrapper for") != 0)
+ {
+ continue;
+ }
+ /* remove the .h and store */
+ names[j] = strdup(argv[i]);
+ names[j++][strlen(argv[i])-2] = '\0';
+ }
+ anindex = j;
+
+ fprintf(stdout,"#include <string.h>\n");
+ fprintf(stdout,"#include \"Python.h\"\n\n");
+
+ stuffit();
+
+ return 0;
+}
+
Makefile.in
Makefile
vtkgdcmdemo
+*.la
+*.lo
-lvtkCommon -lvtkIO -lvtkFiltering -lvtkRendering -lvtkGraphics \
-lvtkImaging -lvtkpng -lvtkzlib -lvtkjpeg -lvtkexpat -lvtktiff \
-lvtkftgl -lvtkfreetype
+LIBS_VTK_PYTHON= $(LIBS_VTK) \
+ -lvtkCommonPython -lvtkIOPython -lvtkFilteringPython \
+ -lvtkRenderingPython -lvtkGraphicsPython -lvtkImagingPython
INCLUDE_VTK=-I/usr/include/vtk
LIBS_X11= -L/usr/X11R6/lib -lX11 -lXt -lSM -lICE -lXext -lGL
-## $(x_ldflags)
-## $(x_libs)
+#LIBS_X11= $(x_ldflags) $(x_libs)
-INCLUDES = \
- -I. \
+INCLUDES = \
+ -I. \
-I$(top_srcdir)/src \
+ $(PYTHON_INCLUDES) \
$(INCLUDE_VTK)
LDADD = \
if BUILD_VTK
noinst_PROGRAMS = vtkgdcmdemo
vtkgdcmdemo_SOURCES = testvtkGdcmReader.cxx vtkGdcmReader.cxx
+vtkgdcmdemo_LDADD = $(LDADD)
+lib_LTLIBRARIES = libvtkgdcm.la
+libvtkgdcm_la_SOURCES = vtkGdcmReader.cxx
+libvtkgdcm_la_LIBADD = $(LDADD)
else
all:
endif
-
-
-// $Header: /cvs/public/gdcm/vtk/Attic/testvtkGdcmReader.cxx,v 1.2 2003/05/12 14:32:43 frog Exp $
+// $Header: /cvs/public/gdcm/vtk/Attic/testvtkGdcmReader.cxx,v 1.3 2003/05/21 08:21:17 frog Exp $
#include "vtkRenderer.h"
#include "vtkRenderWindow.h"
vtkImageData *ima = reader->GetOutput();
taille=ima->GetDimensions();
x = taille[0]; y = taille[1];
- cout << "Taille de l'image en X=" << x << " et en Y=" << y << endl;
+ cout << "Dimensions of the picture as read with gdcm: "
+ << x << " x " << y << endl;
vtkLookupTable *VTKtable = vtkLookupTable::New();
VTKtable->SetNumberOfColors(1000);
-// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.2 2003/05/12 14:32:43 frog Exp $
+// $Header: /cvs/public/gdcm/vtk/vtkGdcmReader.cxx,v 1.3 2003/05/21 08:21:17 frog Exp $
#include "vtkGdcmReader.h"
#include "vtkByteSwap.h"
#include <stdio.h>
Source += LineSize;
Destination -= LineSize;
}
-
+ // The "size" of the vtkScalars data is expressed in number of points,
+ // and is not the memory size representing those points:
+ size = size / GdcmFile.GetPixelSize();
data->GetPointData()->GetScalars()->SetVoidArray(mem, size, 0);
this->Modified();
projects / gdcm.git / commitdiff