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b/Thoracic Organs Segmentation code/OpticalFlow3D/cimgmatlab.h |
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/************************************************************************* |
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* cimgmatlab.h |
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* ------------- |
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* |
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* cimgmatlab.h is a "plugin" for the CImg library that allows to convert |
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* CImg<T> images from/to MATLAB arrays, so that CImg can be used to write |
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* MATLAB mex files. It also swaps the "x" and "y" coordinates when going |
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* from / to MATLAB array, i.e. the usual image-processing annoying MATLAB |
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* behaviour of considering images as matrices. |
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* |
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* Added to the CImg<T> class are: |
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* |
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* - a constructor : CImg(const mxArray *matlabArray, bool vdata = false) |
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* the vdata serves to decide whether a 3D matlab array should give |
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* rise to a 3D CImg object or a "2D vectorial" one. |
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* |
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* - a assignment operator : CImg & operator=(const mxArray *matlabArray) |
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* (I use myself extremely seldom and might remove it in the future). |
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* |
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* - a routine converting a CImg image to a matlab array: |
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* mxArray *toMatlab(mxClassID classID = mxDOUBLE_CLASS, |
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* bool squeeze = false) const |
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* the squeeze argument serves the opposite purpose than the vdata from |
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* the constructor. |
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* |
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* For a bit more documentation, the manual is this header, see the more |
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* detailed comments in the source code (i.e. RTFM) |
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* |
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* |
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* Its usage should be straightforward: |
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* |
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* - file cimgmatlab.h must be in a directory that the compiler can locate. |
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* - prior to include CImg.h, mex.h must be included first, else it will |
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* result in a compiler error. |
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* - after the inclusion of mex.h, one must define the macro cimg_plugin as |
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* "cimgmatlab.h" or <cimgmatlab.h> or <CImg/plugins/cimgmatlab.h> or |
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* a variation that matches your local installation of CImg package and |
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* plugins probably via the appropriate specification of the include path |
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* "-Ipath/to/cimg/and/plugins" at mex cmdline. |
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* |
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* You would probably have this kind of declaration: |
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* |
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* // The begining of my fantastic mex file code... |
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* #include <mex.h> |
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* ... |
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* #define cimg_plugin <cimgmatlab.h> |
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* #include <CImg.h> |
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* ... |
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* // and now I can implement my new killer MATLAB function! |
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* .... |
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* |
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* |
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* Copyright (c) 2004-2008 Francois Lauze |
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* Licence: the Gnu Lesser General Public License |
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* http://www.gnu.org/licenses/lgpl.html |
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* |
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* MATLAB is copyright of The MathWorks, Inc, http://www.mathworks.com |
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* |
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* Any comments, improvements and potential bug corrections are welcome, so |
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* write to me at francois@diku.dk, or use CImg forums, I promise I'll try |
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* to read them once in a while. BTW who modified the cpMatlabData with the |
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* cimg::type<t>::is_float() test (good idea!) |
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* |
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***************************************************************************/ |
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#define CIMGMATLAB_VER 0102 |
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#ifndef mex_h |
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#error the file mex.h must be included prior to inclusion of cimgmatlab.h |
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#endif |
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#ifndef cimg_version |
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#error cimgmatlab.h requires that CImg.h is included! |
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#endif |
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/********************************************************** |
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* introduction of mwSize and mwIndex types in relatively * |
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* recent versions of matlab, 7.3.0 from what I gathered. * |
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* here is hopefully a needed fix for older versions * |
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**********************************************************/ |
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#if !defined(MX_API_VER) || MX_API_VER < 0x7030000 |
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typedef int mwSize; |
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#endif |
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/********************************************************* |
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* begin of included methods * |
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* They are just added as member functions / constructor * |
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* for the CImg<T> class. * |
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*********************************************************/ |
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private: |
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/********************************************************************** |
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* internally used to transfer MATLAB array values to CImg<> objects, |
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* check wether the array type is a "numerical" one (including logical) |
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*/ |
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static int isNumericalClassID(mxClassID id) |
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{ |
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// all these constants are defined in matrix.h included by mex.h |
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switch (id) { |
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case mxLOGICAL_CLASS: |
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case mxDOUBLE_CLASS: |
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case mxSINGLE_CLASS: |
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case mxINT8_CLASS: |
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case mxUINT8_CLASS: |
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case mxINT16_CLASS: |
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case mxUINT16_CLASS: |
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case mxINT32_CLASS: |
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case mxUINT32_CLASS: |
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case mxINT64_CLASS: |
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case mxUINT64_CLASS: |
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return 1; |
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default: |
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return 0; |
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} |
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} |
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/*************************************************** |
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* driving routine that will copy the content of |
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* a MATLAB array to this->data |
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* The type names used are defined in matlab c/c++ |
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* header file tmwtypes.h |
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*/ |
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void makeImageFromMatlabData(const mxArray *matlabArray, mxClassID classID) |
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{ |
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if (classID == mxLOGICAL_CLASS) |
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{ |
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// logical type works a bit differently than the numerical types |
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mxLogical *mdata = mxGetLogicals(matlabArray); |
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cpMatlabData((const mxLogical *)mdata); |
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} |
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else |
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{ |
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void *mdata = (void *)mxGetPr(matlabArray); |
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switch (classID) { |
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case mxDOUBLE_CLASS: |
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cpMatlabData((const real64_T *)mdata); |
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break; |
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case mxSINGLE_CLASS: |
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cpMatlabData((const real32_T *)mdata); |
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break; |
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case mxINT8_CLASS: |
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cpMatlabData((const int8_T *)mdata); |
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break; |
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case mxUINT8_CLASS: |
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cpMatlabData((const uint8_T *)mdata); |
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break; |
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case mxINT16_CLASS: |
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cpMatlabData((const int16_T *)mdata); |
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break; |
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case mxUINT16_CLASS: |
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cpMatlabData((const uint16_T *)mdata); |
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break; |
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case mxINT32_CLASS: |
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cpMatlabData((const int32_T *)mdata); |
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break; |
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case mxUINT32_CLASS: |
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cpMatlabData((const uint32_T *)mdata); |
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break; |
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case mxINT64_CLASS: |
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cpMatlabData((const int64_T *)mdata); |
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break; |
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case mxUINT64_CLASS: |
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cpMatlabData((const uint64_T *)mdata); |
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break; |
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} |
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} |
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} |
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/*********************************************************** |
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* the actual memory copy and base type conversion is then |
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* performed by this routine that handles the annoying x-y |
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* problem of MATLAB when dealing with images: we switch |
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* line and column storage: the MATLAB A(x,y) becomes the |
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* CImg img(y,x) |
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*/ |
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template <typename t> void cpMatlabData(const t* mdata) |
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{ |
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if (cimg::type<t>::is_float()) |
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{ |
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cimg_forXYZV(*this, x, y, z, v) |
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{ |
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(*this)(x, y, z, v) = (T)(mdata[((v*depth + z)*width+x)*height+y]); |
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} |
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} |
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else |
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{ |
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cimg_forXYZV(*this, x, y, z, v) |
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{ |
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(*this)(x, y, z, v) = (T)(int)(mdata[((v*depth + z)*width+x)*height+y]); |
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} |
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} |
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} |
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public: |
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/****************************************************************** |
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* Consruct a CImg<T> object from a MATLAB mxArray. |
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* The MATLAB array must be AT MOST 4-dimensional. The boolean |
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* argument vdata is employed in the case the the input mxArray |
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* has dimension 3, say M x N x K. In that case, if vdata is true, |
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* the last dimension is assumed to be "vectorial" and the |
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* resulting CImg<T> object has dimension N x M x 1 x K. Otherwise, |
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* the resulting object has dimension N x M x K x 1. |
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* When MATLAB array has dimension 2 or 4, vdata has no effects. |
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* No shared memory mechanisms are used, it would be the easiest |
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* to crash Matlab (from my own experience...) |
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*/ |
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CImg(const mxArray *matlabArray, bool vdata = false) |
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: is_shared(false) |
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{ |
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mwSize nbdims = mxGetNumberOfDimensions(matlabArray); |
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mxClassID classID = mxGetClassID(matlabArray); |
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if (nbdims > 4 || !isNumericalClassID(classID)) |
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{ |
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data=NULL; |
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width=height=depth=dim=0; |
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#if cimg_debug>1 |
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cimg::warn("MATLAB array is more than 4D or/and " |
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"not numerical, returning null image."); |
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#endif |
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} |
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else |
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{ |
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const mwSize *dims = mxGetDimensions(matlabArray); |
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depth = dim = 1; |
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width = (unsigned)dims[1]; |
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height = (unsigned)dims[0]; |
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if (nbdims == 4) |
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{ |
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depth = (unsigned)dims[2]; |
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dim = (unsigned)dims[3]; |
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} |
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else if (nbdims == 3) |
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{ |
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if (vdata) |
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{ |
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dim = (unsigned)dims[2]; |
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} |
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else |
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{ |
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depth = (unsigned)dims[2]; |
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} |
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} |
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data = new T[size()]; |
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makeImageFromMatlabData(matlabArray, classID); |
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} |
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} |
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248 |
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/******************************************************************* |
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* operator=(). Copy mxMarray data mArray into the current image |
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* Works as the previous constructor, but without the vdata stuff. |
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* don't know if it is of any use... |
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*/ |
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CImg & operator=(const mxArray *matlabArray) |
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{ |
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int nbdims = (int)mxGetNumberOfDimensions(matlabArray); |
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int classID = mxGetClassID(matlabArray); |
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if (nbdims > 4 || !isNumericalClassID(classID)) |
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{ |
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delete [] data; |
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data = NULL; |
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width=height=depth=dim=0; |
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#if cimg_debug>1 |
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cimg::warn("MATLAB array is more than 4D or/and " |
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"not numerical, returning null image."); |
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#endif |
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} |
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else |
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{ |
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const mwSize *dims = mxGetDimensions(matlabArray); |
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depth = dim = 1; |
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width = (unsigned)dims[1]; |
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height = (unsigned)dims[0]; |
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if (nbdims > 2) |
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{ |
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depth = (unsigned)dims[2]; |
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} |
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if (nbdims > 3) |
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{ |
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dim = (unsigned)dims[3]; |
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} |
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282 |
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delete [] data; |
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data = new T[size()]; |
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285 |
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makeImageFromMatlabData(matlabArray, classID); |
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} |
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} |
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289 |
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private: |
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/***************************************************************** |
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* private routines used for transfering a CImg<T> to a mxArray |
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* here also, we have to exchange the x and y dims so we get the |
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* expected MATLAB array. |
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295 |
*/ |
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template <typename c> void populate_maltlab_array(c *mdata) const |
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297 |
{ |
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cimg_forXYZV(*this, x, y, z, v) |
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299 |
{ |
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mdata[((v*depth + z)*width+x)*height+y] = (c)(*this)(x, y, z, v); |
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301 |
} |
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302 |
} |
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303 |
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304 |
/************************************************* |
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305 |
* the specialized version for "logical" entries |
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306 |
*/ |
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307 |
void populate_maltlab_array(mxLogical *mdata) const |
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{ |
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cimg_forXYZV(*this, x, y, z, v) |
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310 |
{ |
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311 |
mdata[((v*depth + z)*width+x)*height+y] = (mxLogical)((*this)(x, y, z, v)!=0); |
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312 |
} |
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313 |
} |
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314 |
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315 |
public: |
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316 |
/****************************************** |
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317 |
* export a CImg image to a MATLAB array. |
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318 |
**/ |
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319 |
mxArray *toMatlab(mxClassID classID = mxDOUBLE_CLASS, bool squeeze = false) const |
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320 |
{ |
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321 |
if (!isNumericalClassID(classID)) |
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322 |
{ |
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323 |
#if cimg_debug>1 |
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324 |
cimg::warn("Invalid MATLAB Class Id Specified."); |
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325 |
#endif |
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326 |
return NULL; |
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327 |
} |
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328 |
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329 |
mwSize dims[4]; |
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330 |
dims[0] = (mwSize)height; |
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331 |
dims[1] = (mwSize)width; |
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332 |
dims[2] = (mwSize)depth; |
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333 |
dims[3] = (mwSize)dim; |
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334 |
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335 |
if (squeeze && depth == 1) |
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336 |
{ |
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337 |
dims[2] = (mwSize)dim; |
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338 |
dims[3] = (mwSize)1; |
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339 |
} |
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340 |
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341 |
mxArray *matlabArray = mxCreateNumericArray((mwSize)4, dims, classID, mxREAL); |
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342 |
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343 |
if (classID == mxLOGICAL_CLASS) |
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344 |
{ |
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345 |
mxLogical *mdata = mxGetLogicals(matlabArray); |
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346 |
populate_maltlab_array(mdata); |
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347 |
} |
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348 |
else |
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349 |
{ |
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350 |
void *mdata = mxGetPr(matlabArray); |
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351 |
switch (classID) { |
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352 |
case mxDOUBLE_CLASS: |
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353 |
populate_maltlab_array((real64_T *)mdata); |
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354 |
break; |
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355 |
case mxSINGLE_CLASS: |
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356 |
populate_maltlab_array((real32_T *)mdata); |
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357 |
break; |
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358 |
case mxINT8_CLASS: |
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359 |
populate_maltlab_array((int8_T *)mdata); |
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360 |
break; |
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361 |
case mxUINT8_CLASS: |
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362 |
populate_maltlab_array((uint8_T *)mdata); |
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363 |
break; |
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364 |
case mxINT16_CLASS: |
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365 |
populate_maltlab_array((int16_T *)mdata); |
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366 |
break; |
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367 |
case mxUINT16_CLASS: |
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368 |
populate_maltlab_array((uint16_T *)mdata); |
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369 |
break; |
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370 |
case mxINT32_CLASS: |
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371 |
populate_maltlab_array((int32_T *)mdata); |
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372 |
break; |
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373 |
case mxUINT32_CLASS: |
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374 |
populate_maltlab_array((uint32_T *)mdata); |
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375 |
break; |
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376 |
case mxINT64_CLASS: |
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377 |
populate_maltlab_array((int64_T *)mdata); |
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378 |
break; |
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379 |
case mxUINT64_CLASS: |
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380 |
populate_maltlab_array((uint64_T *)mdata); |
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381 |
break; |
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|
382 |
} |
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|
383 |
} |
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|
384 |
return matlabArray; |
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|
385 |
} |
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|
386 |
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|
387 |
// end of cimgmatlab.h |