[med-svn] [pymia] 01/02: Imported Upstream version 0.1.4
Gert Wollny
gert-guest at moszumanska.debian.org
Wed Dec 4 16:09:28 UTC 2013
This is an automated email from the git hooks/post-receive script.
gert-guest pushed a commit to branch master
in repository pymia.
commit 99e390ea7471fe3b26c1027c7c8f964167b0dd52
Author: Gert Wollny <gw.fossdev at gmail.com>
Date: Wed Dec 4 17:04:20 2013 +0100
Imported Upstream version 0.1.4
---
AUTHORS | 3 +
COPYING | 676 +++++++++++++++++++++++++++++++++++++++++++++++++
ChangeLog | 18 ++
PKG-INFO | 17 ++
README | 39 +++
setup.py | 86 +++++++
src/mia_conversions.hh | 441 ++++++++++++++++++++++++++++++++
src/mia_python.cc | 369 +++++++++++++++++++++++++++
8 files changed, 1649 insertions(+)
diff --git a/AUTHORS b/AUTHORS
new file mode 100644
index 0000000..3849d5f
--- /dev/null
+++ b/AUTHORS
@@ -0,0 +1,3 @@
+Gert Wollny <gw.fossdev dot gmail dot com>
+
+
diff --git a/COPYING b/COPYING
new file mode 100644
index 0000000..4432540
--- /dev/null
+++ b/COPYING
@@ -0,0 +1,676 @@
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+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+ <one line to give the program's name and a brief idea of what it does.>
+ Copyright (C) <year> <name of author>
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ <program> Copyright (C) <year> <name of author>
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+
diff --git a/ChangeLog b/ChangeLog
new file mode 100644
index 0000000..1c54b77
--- /dev/null
+++ b/ChangeLog
@@ -0,0 +1,18 @@
+Version 0.1.4
+=============
+
+ * move the segmentation tool into different package since it
+ does not work with python3
+ * remove direct (deprecated) access to array objects
+
+Version 0.1.3
+=============
+
+ * mia modules support for python 3
+ * move to python distutils as build tool
+ * change drawn star rays to six Closes [tickets-pymia:#1]
+
+Version 0.1.2
+=============
+
+ * first public release
diff --git a/PKG-INFO b/PKG-INFO
new file mode 100644
index 0000000..ec976d5
--- /dev/null
+++ b/PKG-INFO
@@ -0,0 +1,17 @@
+Metadata-Version: 1.1
+Name: pymia
+Version: 0.1.4
+Summary: Functions for mediacal image analysis
+Home-page: http://mia.sourceforge.net/
+Author: Gert Wollny
+Author-email: gw.fossdev at gmail.com
+License: GNU General Public License
+Description: This package provides a module for gray scale image processing and a tool for basic image segmentation
+Platform: Linux
+Platform: BSD
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: GNU General Public License
+Classifier: Operating System :: POSIX
+Classifier: Programming Language :: Python
+Classifier: Topic :: Science :: Image Processing
diff --git a/README b/README
new file mode 100644
index 0000000..d30994c
--- /dev/null
+++ b/README
@@ -0,0 +1,39 @@
+This is the python interface for the MIA library. It uses numpy to
+represent images, and currently, filters and image registration is
+supported.
+
+ Compiling the interface:
+
+The build system utilizes python distutils. To compile the interface
+the compiler must support the -std=c++11 compiler flag.
+Building the interface then build down to running
+
+ python setup.py build
+
+Note, that you wil need mia >= 2.0.10 to be installed.
+
+
+ Using the python interface:
+
+Given that MyImage is a 2D or 3D numpy array of scalar values, one may
+run a filter chain like
+
+ import mia
+
+ MyFilteredImage = mia.filter(MyImage, ["filter1:param1=a",
+ "filter2:param1=b,param2=c", ...])
+
+For the availabe filters see the user reference of MIA.
+
+
+Similarly, the image registration can be run with images Moving and Reference,
+using a spline based transformation with a coefficient rate of 5 pixels, 2
+multi-resolution levels and an nlopt based optimizer:
+
+ import mia
+ Registered = mia.register_images(src=Moving, ref=Reference,
+ transform="spline:rate=5", cost=["image:cost=ssd", "divcurl:weight=10.0"],
+ mglevels=2, optimizer="nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300")
+
+
+The result image is stored in Registered. Currently, the transformation is lost.
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..d2f02b1
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,86 @@
+#
+# Copyright (c) Madrid 2008
+# BIT, ETSI Telecomunicacion, UPM
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 2 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+#
+#
+#
+
+
+from distutils.core import setup
+from distutils.extension import Extension
+
+import numpy
+import subprocess
+
+#
+# as seen on
+# http://code.activestate.com/recipes/502261-python-distutils-pkg-config/
+
+def pkgconfig(*packages, **kw):
+ flag_map = {'-I': 'include_dirs', '-L': 'library_dirs', '-l': 'libraries'}
+
+ s = subprocess.check_output(['pkg-config','--libs', '--cflags', ' '.join(packages)]).decode('utf-8')
+ for token in s.split():
+
+ if token[:2] in flag_map:
+ kw.setdefault(flag_map.get(token[:2]), []).append(token[2:])
+ else: # throw others to extra_link_args
+ kw.setdefault('extra_link_args', []).append(token)
+
+ for k, v in kw.items(): # remove duplicated
+ kw[k] = list(set(v))
+
+ return kw
+
+
+depvars = pkgconfig('mia3d-2.0')
+print(depvars)
+depvars['include_dirs'].append(numpy.get_include())
+
+
+extension = Extension('mia',
+ ['src/mia_python.cc'],
+ extra_compile_args = ['-std=c++11'],
+ depends = ["numpy"],
+ **depvars)
+
+
+
+setup(name='pymia',
+ version='0.1.4',
+ description='Functions for mediacal image analysis ',
+ long_description='This package provides a module for gray scale image processing and a tool for basic image segmentation' ,
+ author='Gert Wollny',
+ author_email='gw.fossdev at gmail.com',
+ license = "GNU General Public License",
+ platforms = ["Linux", "BSD"],
+ url='http://mia.sourceforge.net/',
+ ext_modules = [extension],
+ classifiers=[
+ 'Development Status :: 4 - Beta',
+ 'Intended Audience :: Developers',
+ 'License :: OSI Approved :: GNU General Public License',
+ 'Operating System :: POSIX',
+ 'Programming Language :: Python',
+ 'Topic :: Science :: Image Processing',
+ ],
+ )
+
+
+
+
+
diff --git a/src/mia_conversions.hh b/src/mia_conversions.hh
new file mode 100644
index 0000000..31ffe5c
--- /dev/null
+++ b/src/mia_conversions.hh
@@ -0,0 +1,441 @@
+ /* -*- mia-c++ -*-
+ *
+ * Copyright (c) Leipzig, Madrid 1999-2012 Gert Wollny
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ */
+
+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
+
+#include <Python.h>
+#include <numpy/arrayobject.h>
+#include <mia/core/msgstream.hh>
+#include <mia/core/errormacro.hh>
+#include <mia/2d/image.hh>
+#include <mia/3d/image.hh>
+#include <miaconfig.h>
+
+NS_MIA_BEGIN
+
+using std::unique_ptr;
+using std::runtime_error;
+using std::invalid_argument;
+
+/// \cond INTERNAL
+
+/**
+ This is the placeholder temnplate of the creation of an image from a numpy array.
+ It needs to be specified for the actual image type.
+ \tparam in input pixel type
+ \tparam out output pixel type
+ \tparam Image the image type
+*/
+
+template <typename in, typename out, template <class> class Image>
+struct get_image {
+ static Image<out> apply(PyArrayObject *input) {
+ static_assert(sizeof(in) == 0, "If you end up here, you need to add a new instanciation of get_image structure");
+ }
+};
+
+
+/**
+ This is the line copy if the input and output data is of the same size and not boolean
+ (Boolean is special in the STL vector implementation)
+ \tparam Image the image type
+ \tparam the pixel type
+*/
+template <template <class> class Image, typename T>
+struct __dispatch_copy_line {
+ static void apply(typename Image<T>::iterator out, char *data, int size) {
+ memcpy(&out[0], data, size);
+ }
+};
+
+/**
+ This is the line copy if the data represents boolean
+ \tparam Image the image type
+ \tparam the pixel type
+*/
+
+template <template <class> class Image>
+struct __dispatch_copy_line<Image, bool> {
+ static void apply(typename Image<bool>::iterator out, char *data, int size) {
+ copy(data, data+size, out);
+ }
+};
+
+/**
+ This structure is the template specialization of get_image for 2D images.
+ \tparam in input pixel type
+ \tparam out output pixel type
+ */
+template <typename in, typename out>
+struct get_image<in, out, T2DImage > {
+ static typename T2DImage<out>::Pointer apply(PyArrayObject *input) {
+ TRACE_FUNCTION;
+ typedef typename T2DImage<out>::dimsize_type Dimsize;
+
+ const npy_intp *dimensions = PyArray_DIMS(input);
+ Dimsize size(dimensions[1], dimensions[0]);
+ T2DImage<out> *result = new T2DImage<out>(size);
+ typename T2DImage<out>::Pointer presult(result);
+
+ cvdebug() << "Create mia image of size " << size
+ << " type " << __type_descr<out>::value
+ << "\n";
+
+ /////////////////////////////////////////////////////////////////////////////////////////
+ // this code is taken from the on-line example about iterators and adapted to my needs
+ // http://docs.scipy.org/doc/numpy/reference/c-api.iterator.html#simple-iteration-example
+ //
+ auto iter = NpyIter_New(input, NPY_ITER_READONLY|
+ NPY_ITER_EXTERNAL_LOOP|
+ NPY_ITER_REFS_OK,NPY_KEEPORDER, NPY_NO_CASTING,
+ NULL);
+ unique_ptr<NpyIter, int (*)(NpyIter *p)> piter(iter, NpyIter_Deallocate);
+ if (!iter)
+ throw runtime_error("Unable create iterater for input array");
+
+ auto iternext = NpyIter_GetIterNext(iter, NULL);
+ if (iternext == NULL)
+ throw runtime_error("Unable to iterate over input array");
+
+ auto innerstride = NpyIter_GetInnerStrideArray(iter)[0];
+ auto itemsize = NpyIter_GetDescrArray(iter)[0]->elsize;
+ auto innersizeptr = NpyIter_GetInnerLoopSizePtr(iter);
+ auto dataptrarray = NpyIter_GetDataPtrArray(iter);
+
+ if (innerstride == sizeof(out)) {
+ // fast copy if stride is equal to target item size
+ size_t y = 0;
+ do {
+ __dispatch_copy_line<T2DImage, out>::apply(result->begin_at(0,y), dataptrarray[0], itemsize * (*innersizeptr));
+ ++y;
+ } while (iternext(iter));
+ } else {
+ auto ir = result->begin();
+ do {
+ npy_intp size = *innersizeptr;
+ char *src = dataptrarray[0];
+ for(npy_intp i = 0; i < size; i++, src += innerstride, ++ir) {
+ *ir = *(in*)src;
+ }
+ } while (iternext(iter));
+ }
+ //
+ // End of copying
+ ////////////////////////////////////////////////////////////////
+ return presult;
+ }
+};
+
+
+/**
+ This structure is the template specialization of get_image for 3D images.
+ \tparam in input pixel type
+ \tparam out output pixel type
+ */
+template <typename in, typename out>
+struct get_image<in, out, T3DImage > {
+ static typename T3DImage<out>::Pointer apply(PyArrayObject *input) {
+ TRACE_FUNCTION;
+ typedef typename T3DImage<out>::dimsize_type Dimsize;
+
+ const npy_intp *dimensions = PyArray_DIMS(input);
+ Dimsize size(dimensions[2], dimensions[1], dimensions[0]);
+
+ cvdebug() << "Create mia image of size " << size
+ << " and type " << __type_descr<out>::value << "\n";
+
+ T3DImage<out> *result = new T3DImage<out>(size);
+ typename T3DImage<out>::Pointer presult(result);
+
+ /////////////////////////////////////////////////////////////////////////////////////////
+ // this code is taken from the on-line example about iterators and adapted to my needs
+ // http://docs.scipy.org/doc/numpy/reference/c-api.iterator.html#simple-iteration-example
+ //
+ auto iter = NpyIter_New(input, NPY_ITER_READONLY|
+ NPY_ITER_EXTERNAL_LOOP|
+ NPY_ITER_REFS_OK,
+ NPY_KEEPORDER,
+ NPY_NO_CASTING,
+ NULL);
+ unique_ptr<NpyIter, int (*)(NpyIter *p)> piter(iter, NpyIter_Deallocate);
+ if (!iter)
+ throw runtime_error("Unable create iterater for input array");
+
+ auto iternext = NpyIter_GetIterNext(iter, NULL);
+ if (iternext == NULL)
+ throw runtime_error("Unable to iterate over input array");
+
+ auto innerstride = NpyIter_GetInnerStrideArray(iter)[0];
+ auto itemsize = NpyIter_GetDescrArray(iter)[0]->elsize;
+ auto innersizeptr = NpyIter_GetInnerLoopSizePtr(iter);
+ auto dataptrarray = NpyIter_GetDataPtrArray(iter);
+
+ if (innerstride == sizeof(out)) {
+ // fast copy if stride is equal to item size
+ size_t z = 0;
+ size_t y = 0;
+
+ do {
+ __dispatch_copy_line<T3DImage, out>::apply(result->begin_at(0,y,z), dataptrarray[0], itemsize * (*innersizeptr));
+ ++y;
+ if ( y >= size.y )
+ ++z;
+ } while (iternext(iter));
+ } else {
+ auto ir = result->begin();
+ do {
+ npy_intp size = *innersizeptr;
+ char *src = dataptrarray[0];
+ for(npy_intp i = 0; i < size; i++, src += innerstride, ++ir) {
+ *ir = *(in*)src;
+ }
+ } while (iternext(iter));
+ }
+ //
+ // End of copying
+ ////////////////////////////////////////////////////////////////
+ return presult;
+ }
+};
+
+/**
+ \cond internal
+ Provide a mapping from C++ types to the numpy type constants
+*/
+
+template <typename T>
+struct __mia_pixel_type_numarray_id {
+ static const int value;
+ static const char *name;
+};
+
+template <typename T>
+const char *__mia_pixel_type_numarray_id<T>::name = "NPY_USERDEF";
+
+template <typename T>
+const int __mia_pixel_type_numarray_id<T>::value = NPY_USERDEF;
+
+
+#define SPECIALICE_ID(type, VALUE) \
+template <> \
+struct __mia_pixel_type_numarray_id<type> { \
+ static const int value; \
+ static const char *name; \
+}; \
+ \
+ \
+const char *__mia_pixel_type_numarray_id<type>::name = #VALUE; \
+const int __mia_pixel_type_numarray_id<type>::value = VALUE;
+
+SPECIALICE_ID(bool, NPY_BOOL);
+SPECIALICE_ID(signed char, NPY_BYTE);
+SPECIALICE_ID(unsigned char, NPY_UBYTE);
+SPECIALICE_ID(signed short, NPY_SHORT);
+SPECIALICE_ID(unsigned short, NPY_USHORT);
+SPECIALICE_ID(signed int, NPY_INT);
+SPECIALICE_ID(unsigned int, NPY_UINT);
+SPECIALICE_ID(signed long, NPY_LONG);
+SPECIALICE_ID(unsigned long, NPY_ULONG);
+SPECIALICE_ID(float, NPY_FLOAT);
+SPECIALICE_ID(double, NPY_DOUBLE);
+
+
+
+/**
+ The MIA filter object to convert a 2D or 3D image to a PyArrayObject
+
+
+*/
+struct FConvertToPyArray: public TFilter<PyArrayObject*> {
+ template <typename T>
+ PyArrayObject * operator () (const T2DImage<T>& image) const;
+
+ template <typename T>
+ PyArrayObject * operator () (const T3DImage<T>& image) const;
+
+};
+
+
+template <template <class> class Image, typename T>
+struct __dispatch_py_array_copy {
+ static void apply(char *output, const Image<T>& image) {
+ memcpy(output, &image.begin()[0], image.size() * sizeof(T));
+ }
+};
+
+template <template <class> class Image>
+struct __dispatch_py_array_copy<Image, bool> {
+ static void apply(char *output, const Image<bool>& image) {
+ copy(image.begin(), image.end(), output);
+ }
+};
+
+
+
+template <typename T>
+PyArrayObject * FConvertToPyArray::operator () (const T2DImage<T>& image) const
+{
+ TRACE_FUNCTION;
+ npy_intp dims[2];
+ dims[1] = image.get_size().x;
+ dims[0] = image.get_size().y;
+ cvdebug() << "Create array of size " << image.get_size() << " numpy type " << __mia_pixel_type_numarray_id<T>::name <<"\n";
+ PyArrayObject* out_array = (PyArrayObject*)(PyArray_SimpleNew(2, dims, __mia_pixel_type_numarray_id<T>::value));
+ if (!out_array) {
+ throw create_exception<runtime_error>("Unable to create output array of type '",
+ __mia_pixel_type_numarray_id<T>::value, "' and size ", image.get_size());
+ }
+ __dispatch_py_array_copy<T2DImage, T>::apply(PyArray_BYTES(out_array), image);
+ return out_array;
+}
+
+template <typename T>
+PyArrayObject * FConvertToPyArray::operator () (const T3DImage<T>& image) const
+{
+ TRACE_FUNCTION;
+ npy_intp dims[3];
+ dims[2] = image.get_size().x;
+ dims[1] = image.get_size().y;
+ dims[0] = image.get_size().z;
+ cvdebug() << "Create array of size " << image.get_size()
+ << " numpy type " << __mia_pixel_type_numarray_id<T>::name << "("
+ <<__mia_pixel_type_numarray_id<T>::value<<")\n";
+
+ PyArrayObject* out_array = (PyArrayObject*)(PyArray_SimpleNew(3, dims, __mia_pixel_type_numarray_id<T>::value));
+ if (!out_array) {
+ throw runtime_error("Unable to create output array");
+ }
+ __dispatch_py_array_copy<T3DImage, T>::apply(PyArray_BYTES(out_array), image);
+ return out_array;
+}
+
+
+/// \endcond
+
+/**
+ This template function creates a MIA image of the given template type from a PyArrayObject
+ (numpy.array) Currently, attributes are not kept.
+
+ \tparam Output image type, must be given explicitely
+ \param input input python array
+ \remark currently, on 64 bit machines, the long type (which is the standard int type in
+ Python will be copied to int. This may clobber the data.
+
+ */
+
+template <template <class> class Image>
+typename Image<int>::Pointer mia_image_from_pyarray(PyArrayObject *input)
+{
+ TRACE_FUNCTION;
+ cvdebug() << "Get image numpy type " << PyArray_DESCR(input)->type_num
+ << "and is "
+ << ( PyArray_IS_C_CONTIGUOUS(input) ? " c-array " : " fortran array" )
+ <<"\n";
+ switch (PyArray_DESCR(input)->type_num) {
+ case NPY_BOOL: return get_image<signed char, bool, Image>::apply(input);
+ case NPY_BYTE: return get_image<signed char, signed char, Image>::apply(input);
+ case NPY_UBYTE: return get_image<unsigned char, unsigned char, Image>::apply(input);
+ case NPY_SHORT: return get_image<signed short, signed short, Image>::apply(input);
+ case NPY_USHORT: return get_image<unsigned short, unsigned short, Image>::apply(input);
+ case NPY_INT: return get_image<signed int, signed int, Image>::apply(input);
+ case NPY_UINT: return get_image<unsigned int, unsigned int, Image>::apply(input);
+#ifdef LONG_64BIT
+ case NPY_LONG: return get_image<signed long, signed long, Image>::apply(input);
+ case NPY_ULONG: return get_image<unsigned long, unsigned long, Image>::apply(input);
+#endif
+ case NPY_FLOAT: return get_image<float, float, Image>::apply(input);
+ case NPY_DOUBLE: return get_image<double, double, Image>::apply(input);
+ default:
+ throw create_exception<invalid_argument>("mia doesn't support images of type ",
+ PyArray_DESCR(input)->type_num,
+ ", If this is int64 then you are probably on a 32 bit platform.");
+ }
+}
+
+/**
+ Convert a MIA image to a python PyArrayObject (numpy.array)
+ \tparam image
+
+*/
+
+
+template <typename Image>
+PyArrayObject * mia_pyarray_from_image(const Image& image)
+{
+ TRACE_FUNCTION;
+ FConvertToPyArray convert;
+ cvdebug() << "Image pixel type = " << image.get_pixel_type() << "\n";
+ return mia::filter(convert, image);
+}
+
+#define PYTHON_MIA_CALL_self_args(NAME) \
+ static PyObject *NAME##call(PyObject *self, PyObject *args); \
+ static PyObject *NAME(PyObject *self, PyObject *args) \
+ { \
+ std::ostringstream msg; \
+ try { \
+ return NAME##call(self, args); \
+ } \
+ catch (std::runtime_error& x) { \
+ msg << "mia runtime error:'" << x.what() << "'"; \
+ } \
+ catch (std::invalid_argument& x) { \
+ msg << "mia invalid argument:'" << x.what() << "'"; \
+ } \
+ catch (std::exception& x) { \
+ msg << "mia exception: '" << x.what() << "'"; \
+ } \
+ catch (...) { \
+ msg << "mia: unknown error"; \
+ } \
+ PyErr_SetString(MiaError, msg.str().c_str()); \
+ return NULL; \
+ } \
+ static PyObject *NAME##call(PyObject */*self*/, PyObject *args)
+
+#define PYTHON_MIA_CALL_self_args_kwdict(NAME) \
+ static PyObject *NAME##call(PyObject *self, PyObject *args, PyObject *keywds); \
+ static PyObject *NAME(PyObject *self, PyObject *args, PyObject *keywds) \
+ { \
+ std::ostringstream msg; \
+ try { \
+ return NAME##call(self, args, keywds); \
+ } \
+ catch (std::runtime_error& x) { \
+ msg << "mia runtime error:'" << x.what() << "'"; \
+ } \
+ catch (std::invalid_argument& x) { \
+ msg << "mia invalid argument:'" << x.what() << "'"; \
+ } \
+ catch (std::exception& x) { \
+ msg << "mia exception: '" << x.what() << "'"; \
+ } \
+ catch (...) { \
+ msg << "mia: unknown error"; \
+ } \
+ PyErr_SetString(MiaError, msg.str().c_str()); \
+ return NULL; \
+ } \
+ static PyObject *NAME##call(PyObject */*self*/, PyObject *args, PyObject *kwdict)
+
+
+
+
+NS_MIA_END
diff --git a/src/mia_python.cc b/src/mia_python.cc
new file mode 100644
index 0000000..b621bb6
--- /dev/null
+++ b/src/mia_python.cc
@@ -0,0 +1,369 @@
+/* -*- mia-c++ -*-
+ *
+ * Copyright (c) Leipzig, Madrid 1999-2012 Gert Wollny
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ */
+#include <Python.h>
+#include "mia_conversions.hh"
+#include <mia/2d/filter.hh>
+#include <mia/2d/imageio.hh>
+#include <mia/2d/nonrigidregister.hh>
+#include <mia/3d/filter.hh>
+#include <mia/3d/imageio.hh>
+#include <mia/3d/nonrigidregister.hh>
+
+
+
+#if PY_MAJOR_VERSION >= 3
+#define IS_PYTHON3
+#endif
+
+
+using namespace std;
+using namespace mia;
+
+static PyObject *MiaError;
+
+static PyArrayObject *run_filters_2d(PyArrayObject *input, const vector<string>& filter_list)
+{
+ TRACE_FUNCTION;
+ auto image = mia_image_from_pyarray<T2DImage>(input);
+ auto result = C2DImageFilterChain(filter_list).run(image);
+ return mia_pyarray_from_image(*result);
+}
+
+static PyArrayObject *run_filters_3d(PyArrayObject *input, const vector<string>& filter_list)
+{
+ TRACE_FUNCTION;
+ auto image = mia_image_from_pyarray<T3DImage>(input);
+ auto result = C3DImageFilterChain(filter_list).run(image);
+ return mia_pyarray_from_image(*result);
+}
+
+#ifdef IS_PYTHON3
+std::string as_string(PyObject *obj)
+{
+ auto h2 = PyUnicode_AsUTF8String(obj);
+ if (!h2) {
+ throw create_exception<invalid_argument>("mia.get_strings_in_list: non-string value in list");
+ }
+ std::string s(PyBytes_AsString(h2));
+ Py_DECREF(h2);
+ return s;
+}
+#else
+std::string as_string(PyObject *obj)
+{
+ auto s = PyString_AsString(obj);
+ if (!s)
+ throw create_exception<invalid_argument>("mia.get_strings_in_list: non-string value in list");
+ return std::string(s);
+}
+#endif
+
+
+static vector<string> get_strings_in_list(PyObject *obj)
+{
+ vector<string> result_list;
+ if ( PyList_Check(obj)) {
+ auto length = PyList_Size(obj);
+ result_list.reserve(length);
+ for (Py_ssize_t i = 0; i < length; ++i) {
+ auto help = PyList_GET_ITEM(obj,i);
+ result_list.push_back(as_string(help));
+ }
+ } else {
+ result_list.push_back(as_string(obj));
+ }
+ return result_list;
+}
+
+PYTHON_MIA_CALL_self_args(run_filters)
+{
+ PyArrayObject *py_resultarray = NULL;
+ PyArrayObject *py_inputarray;
+ PyObject *py_filterlist;
+
+
+ /* parse input */
+ if (!PyArg_ParseTuple(args,"O!O",&PyArray_Type, &py_inputarray, &py_filterlist))
+ return NULL;
+
+ auto filter_list = get_strings_in_list(py_filterlist);
+
+ switch (PyArray_NDIM(py_inputarray)) {
+ case 2: py_resultarray = run_filters_2d(py_inputarray, filter_list);
+ break;
+ case 3: py_resultarray = run_filters_3d(py_inputarray, filter_list);
+ break;
+ default:
+ throw create_exception<invalid_argument>("mia dosn't support images of ",
+ PyArray_NDIM(py_inputarray), " dimensions");
+ }
+
+ // return result
+ return PyArray_Return(py_resultarray);
+}
+
+PYTHON_MIA_CALL_self_args(set_verbose)
+{
+ const char *verbosity;
+ if (!PyArg_ParseTuple(args,"s", &verbosity))
+ return NULL;
+
+ cverb.set_verbosity(g_verbose_dict.get_value( verbosity) );
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+
+template <typename Handler>
+PyObject *load_image(const Handler& handler, PyObject *args)
+{
+ const char *filename;
+ if (!PyArg_ParseTuple(args,"s", &filename))
+ return NULL;
+
+ auto images = handler.load(filename);
+ if (images && !images->empty()) {
+ if (images->size() == 1)
+ return (PyObject*)mia_pyarray_from_image(*(*images)[0]);
+ else {
+ PyObject* output = PyList_New(images->size());
+ for(size_t i = 0; i < images->size(); ++i) {
+ auto img = mia_pyarray_from_image(*(*images)[i]);
+ PyList_SetItem(output, i, (PyObject*)img);
+ }
+ return output;
+ }
+ }
+ throw create_exception<runtime_error>("No images found in '", filename, "'");
+}
+
+PYTHON_MIA_CALL_self_args(load_image2d)
+{
+ return load_image(C2DImageIOPluginHandler::instance(), args);
+}
+
+PYTHON_MIA_CALL_self_args(load_image3d)
+{
+ return load_image(C3DImageIOPluginHandler::instance(), args);
+}
+
+PYTHON_MIA_CALL_self_args(set_filter_plugin_cache)
+{
+ int enabled;
+ if (!PyArg_ParseTuple(args,"i", &enabled))
+ return NULL;
+
+ C2DFilterPluginHandler::instance().set_caching(enabled);
+ C3DFilterPluginHandler::instance().set_caching(enabled);
+
+ Py_INCREF(Py_None);
+ return Py_None;
+}
+
+struct SRegistrationParameters {
+ const char *transform;
+ PyObject *cost;
+
+ // predefined
+ int mg_levels;
+ const char *optimizer;
+ const char *refiner;
+};
+
+template <int dim>
+struct register_images_d {
+ typedef typename dimension_traits<dim>::PTransformationFactory PTransformationFactory;
+ typedef typename dimension_traits<dim>::PFullCost PFullCost;
+ typedef typename dimension_traits<dim>::FullCostList FullCostList;
+ typedef typename FactoryTrait<PTransformationFactory>::type TransformationFactoryHandler;
+ typedef typename FactoryTrait<PFullCost>::type FullCostHandler;
+ typedef typename dimension_traits<dim>::PImage PImage;
+
+ static PyObject *apply(PImage src, PImage ref, const SRegistrationParameters& p);
+};
+
+template <int dim>
+PyObject *register_images_d<dim>::apply(PImage src, PImage ref, const SRegistrationParameters& p)
+{
+ if (src->get_size() != ref->get_size())
+ cvwarn() << "mia.register_images: Images are of different size, this hasnÄt beed tested\n";
+
+ auto transform_creator = TransformationFactoryHandler::instance().produce(p.transform);
+ auto optimizer = produce_minimizer(p.optimizer);
+ auto cost_list = get_strings_in_list(p.cost);
+
+ if (cost_list.empty())
+ throw invalid_argument("mia.register_images: Got empty cost function list");
+
+ FullCostList costs;
+ for (auto i = cost_list.begin(); i != cost_list.end(); ++i)
+ costs.push(FullCostHandler::instance().produce(*i));
+
+
+ TNonrigidRegister<dim> nrr(costs, optimizer, transform_creator, p.mg_levels);
+ if (p.refiner) {
+ auto refiner = produce_minimizer(p.refiner);
+ nrr.set_refinement_minimizer(refiner);
+ }
+
+ auto transform = nrr.run(src, ref);
+ auto result = (*transform)(*src);
+
+ // currently the transformation type is not defined, return only the transformed image
+ return (PyObject *)mia_pyarray_from_image(*result);
+}
+
+PYTHON_MIA_CALL_self_args_kwdict(register_images)
+{
+ SRegistrationParameters p = {
+ NULL, NULL, 3,
+ "nlopt:opt=ld-var1,xtola=0.001,ftolr=0.001,maxiter=300",
+ NULL
+ };
+
+ // keywords:
+ // study - source or floating image
+ // reference - reference image
+ // transform = transformation
+ // cost - list of cost functions
+
+ // multigrid - number of multigrid levels
+ // optimizer - optimizer string
+ // refiner - refinement
+ static const char *kwlist[] = {"src", "ref", "transform", "cost",
+ "mglevels", "optimizer", "refiner", NULL};
+
+ PyArrayObject *src = NULL;
+ PyArrayObject *ref = NULL;
+
+ if (!PyArg_ParseTupleAndKeywords(args, kwdict, "O!O!sO|iss",
+ const_cast<char**>(kwlist),
+ &PyArray_Type, &src, &PyArray_Type, &ref,
+ &p.transform, &p.cost, &p.mg_levels, &p.optimizer, &p.refiner))
+ return NULL;
+
+ if (PyArray_NDIM(src) != PyArray_NDIM(ref)) {
+ throw create_exception<invalid_argument>("Images must be of the same dimensions, but the source "
+ "is of dimension ", PyArray_NDIM(src), " and the reference of dimension ", PyArray_NDIM(ref));
+ }
+ switch (PyArray_NDIM(src)) {
+ case 2: {
+ auto miasrc = mia_image_from_pyarray<T2DImage>(src);
+ auto miaref = mia_image_from_pyarray<T2DImage>(ref);
+ return register_images_d<2>::apply(miasrc, miaref, p);
+ }
+ case 3: {
+ auto miasrc = mia_image_from_pyarray<T3DImage>(src);
+ auto miaref = mia_image_from_pyarray<T3DImage>(ref);
+ return register_images_d<3>::apply(miasrc, miaref, p);
+ }
+ default:
+ throw create_exception<invalid_argument>("mia dosn't support images of ",
+ PyArray_NDIM(src), " dimensions");
+ }
+}
+
+
+static struct PyMethodDef mia_methods[]={
+ { "load_image2d", load_image2d, METH_VARARGS, "loads one or more images from a file. "
+ "If the file contains only one images, it is returned directly as numpy.array, "
+ "otherwise a list of numpy.array objects is returned." },
+ { "load_image3d", load_image3d, METH_VARARGS, "loads one or more images from a file. "
+ "If the file contains only one images, it is returned directly as numpy.array, "
+ "otherwise a list of numpy.array objects is returned." },
+ { "filter", run_filters, METH_VARARGS, "run the given filter(s) on an input image. "
+ "The image must be given as a numpy.array of scalar values. Either you give one filter "
+ "as string, or a series of filters as list. If no filter as given then you must give at "
+ "least an empty list."},
+ { "register_images", (PyCFunction)register_images, METH_VARARGS | METH_KEYWORDS,
+ "run the registration of the image 'src' to the image 'ref' allowing for the transformation "
+ "'transform' and optimizing cost functions 'cost'. Use 'mglevels' multi-resolution levels "
+ " for registration and optimize by using 'optimizer'. A refinement optimizer 'refiner' can be given "
+ "for post-iteration."},
+ { "set_filter_plugin_cache", set_filter_plugin_cache, METH_VARARGS, "Enable or disable the "
+ "2D and 3D filter plugin caches"},
+ { "set_verbose", set_verbose, METH_VARARGS, "set the verbosity of the MIA output" },
+ { NULL, NULL, 0, NULL} /* stop mark */
+};
+
+/* ----------- module initialization -------------------------- */
+
+#ifdef IS_PYTHON3
+
+
+
+static struct PyModuleDef moduledef = {
+ PyModuleDef_HEAD_INIT,
+ "mia",
+ NULL,
+ 0,
+ mia_methods,
+ NULL,
+ NULL,
+ NULL,
+ NULL
+};
+
+#endif
+
+#ifdef IS_PYTHON3
+extern "C"
+PyObject *
+PyInit_mia(void){
+ PyObject *m,*d ;
+
+ m = PyModule_Create(&moduledef);
+
+
+ /* initialize exception object */
+ d=PyModule_GetDict(m) ; /* get module dictionary */
+ MiaError=PyErr_NewException(const_cast<char*>("mia.error"),NULL,NULL) ;
+ PyDict_SetItemString(d,"error",MiaError) ;
+
+ import_array();
+
+ if (PyErr_Occurred()) /* something went wrong ?*/
+ Py_FatalError("can't initialize module mia") ;
+ return m;
+
+}
+
+
+
+#else
+
+extern "C"
+PyMODINIT_FUNC
+initmia() {
+ PyObject *m,*d ;
+
+ m=Py_InitModule("mia", mia_methods);
+
+ /* initialize exception object */
+ d=PyModule_GetDict(m) ; /* get module dictionary */
+ MiaError=PyErr_NewException(const_cast<char*>("mia.error"),NULL,NULL) ;
+ PyDict_SetItemString(d,"error",MiaError) ;
+
+ import_array();
+
+ if (PyErr_Occurred()) /* something went wrong ?*/
+ Py_FatalError("can't initialize module mia") ;
+}
+#endif
+
--
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