Building igl statically and moving to the dep scripts
Fixing dep build script on Windows and removing some warnings. Use bundled igl by default. Not building with the dependency scripts if not explicitly stated. This way, it will stay in Fix the libigl patch to include C source files in header only mode.
This commit is contained in:
tamasmeszaros
579
src/libigl/igl/matlab/MatlabWorkspace.h
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579
src/libigl/igl/matlab/MatlabWorkspace.h
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@@ -0,0 +1,579 @@
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// This file is part of libigl, a simple c++ geometry processing library.
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//
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// Copyright (C) 2013 Alec Jacobson <alecjacobson@gmail.com>
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//
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// This Source Code Form is subject to the terms of the Mozilla Public License
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// v. 2.0. If a copy of the MPL was not distributed with this file, You can
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// obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef IGL_MATLAB_MATLAB_WORKSPACE_H
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#define IGL_MATLAB_MATLAB_WORKSPACE_H
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#include <Eigen/Dense>
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#include <Eigen/Sparse>
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#include <mat.h>
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#include <string>
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#include <vector>
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namespace igl
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{
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namespace matlab
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{
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// It would be really great to replicate this for a simple XML-based
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// workspace.
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//
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// Class which contains data of a matlab workspace which can be written to a
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// .mat file and loaded from matlab
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//
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// This depends on matlab at compile time (though it shouldn't necessarily
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// have to) but it does not depend on running the matlab engine at run-time.
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//
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// Known bugs: Treats all matrices as doubles (this may actually be desired
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// for some "index" matrices since matlab's sparse command takes doubles
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// rather than int class matrices). It is of course not desired when dealing
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// with logicals or uint's for images.
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class MatlabWorkspace
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{
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private:
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// KNOWN BUG: Why not use a map? Any reason to allow duplicate names?
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//
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// List of names
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std::vector<std::string> names;
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// List of data pointers
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std::vector<mxArray*> data;
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public:
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MatlabWorkspace();
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~MatlabWorkspace();
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// Clear names and data of variables in workspace
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inline void clear();
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// Save current list of variables
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//
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// Inputs:
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// path path to .mat file
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// Returns true on success, false on failure
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inline bool write(const std::string & path) const;
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// Load list of variables from .mat file
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//
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// Inputs:
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// path path to .mat file
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// Returns true on success, false on failure
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inline bool read(const std::string & path);
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// Assign data to a variable name in the workspace
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//
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// Template:
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// DerivedM eigen matrix (e.g. MatrixXd)
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// Inputs:
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// M data (usually a matrix)
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// name variable name to save into work space
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// Returns true on success, false on failure
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//
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// Known Bugs: Assumes Eigen is using column major ordering
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template <typename DerivedM>
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inline MatlabWorkspace& save(
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const Eigen::PlainObjectBase<DerivedM>& M,
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const std::string & name);
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// Template:
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// MT sparse matrix type (e.g. double)
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template <typename MT>
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inline MatlabWorkspace& save(
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const Eigen::SparseMatrix<MT>& M,
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const std::string & name);
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// Templates:
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// ScalarM scalar type, e.g. double
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template <typename ScalarM>
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inline MatlabWorkspace& save(
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const std::vector<std::vector<ScalarM> > & vM,
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const std::string & name);
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// Templates:
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// ScalarV scalar type, e.g. double
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template <typename ScalarV>
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inline MatlabWorkspace& save(
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const std::vector<ScalarV> & vV,
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const std::string & name);
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// NOTE: Eigen stores quaternions coefficients as (i,j,k,1), but most of
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// our matlab code stores them as (1,i,j,k) This takes a quaternion and
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// saves it as a (1,i,j,k) row vector
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//
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// Templates:
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// Q quaternion type
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template <typename Q>
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inline MatlabWorkspace& save(
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const Eigen::Quaternion<Q> & q,
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const std::string & name);
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inline MatlabWorkspace& save(
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const double d,
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const std::string & name);
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// Same as save() but adds 1 to each element, useful for saving "index"
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// matrices like lists of faces or elements
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template <typename DerivedM>
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inline MatlabWorkspace& save_index(
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const Eigen::DenseBase<DerivedM>& M,
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const std::string & name);
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template <typename ScalarM>
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inline MatlabWorkspace& save_index(
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const std::vector<std::vector<ScalarM> > & vM,
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const std::string & name);
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template <typename ScalarV>
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inline MatlabWorkspace& save_index(
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const std::vector<ScalarV> & vV,
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const std::string & name);
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// Find a certain matrix by name.
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//
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// KNOWN BUG: Outputs the first found (not necessarily unique lists).
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//
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// Template:
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// DerivedM eigen matrix (e.g. MatrixXd)
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// Inputs:
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// name exact name of matrix as string
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// Outputs:
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// M matrix
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// Returns true only if found.
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template <typename DerivedM>
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inline bool find(
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const std::string & name,
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Eigen::PlainObjectBase<DerivedM>& M);
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template <typename MT>
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inline bool find(
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const std::string & name,
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Eigen::SparseMatrix<MT>& M);
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inline bool find(
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const std::string & name,
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double & d);
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inline bool find(
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const std::string & name,
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int & v);
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// Subtracts 1 from all entries
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template <typename DerivedM>
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inline bool find_index(
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const std::string & name,
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Eigen::PlainObjectBase<DerivedM>& M);
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};
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}
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}
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// Implementation
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// Be sure that this is not compiled into libigl.a
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// http://stackoverflow.com/a/3318993/148668
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// IGL
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#include "igl/list_to_matrix.h"
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// MATLAB
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#include "mat.h"
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// STL
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#include <iostream>
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#include <algorithm>
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#include <vector>
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inline igl::matlab::MatlabWorkspace::MatlabWorkspace():
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names(),
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data()
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{
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}
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inline igl::matlab::MatlabWorkspace::~MatlabWorkspace()
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{
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// clean up data
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clear();
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}
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inline void igl::matlab::MatlabWorkspace::clear()
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{
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for_each(data.begin(),data.end(),&mxDestroyArray);
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data.clear();
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names.clear();
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}
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inline bool igl::matlab::MatlabWorkspace::write(const std::string & path) const
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{
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using namespace std;
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MATFile * mat_file = matOpen(path.c_str(), "w");
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if(mat_file == NULL)
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{
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fprintf(stderr,"Error opening file %s\n",path.c_str());
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return false;
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}
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assert(names.size() == data.size());
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// loop over names and data
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for(int i = 0;i < (int)names.size(); i++)
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{
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// Put variable as LOCAL variable
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int status = matPutVariable(mat_file,names[i].c_str(), data[i]);
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if(status != 0)
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{
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cerr<<"^MatlabWorkspace::save Error: matPutVariable ("<<names[i]<<
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") failed"<<endl;
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return false;
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}
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}
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if(matClose(mat_file) != 0)
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{
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fprintf(stderr,"Error closing file %s\n",path.c_str());
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return false;
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}
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return true;
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}
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inline bool igl::matlab::MatlabWorkspace::read(const std::string & path)
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{
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using namespace std;
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MATFile * mat_file;
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mat_file = matOpen(path.c_str(), "r");
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if (mat_file == NULL)
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{
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cerr<<"Error: failed to open "<<path<<endl;
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return false;
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}
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int ndir;
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const char ** dir = (const char **)matGetDir(mat_file, &ndir);
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if (dir == NULL) {
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cerr<<"Error reading directory of file "<< path<<endl;
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return false;
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}
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mxFree(dir);
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// Must close and reopen
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if(matClose(mat_file) != 0)
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{
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cerr<<"Error: failed to close file "<<path<<endl;
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return false;
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}
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mat_file = matOpen(path.c_str(), "r");
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if (mat_file == NULL)
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{
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cerr<<"Error: failed to open "<<path<<endl;
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return false;
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}
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/* Read in each array. */
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for (int i=0; i<ndir; i++)
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{
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const char * name;
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mxArray * mx_data = matGetNextVariable(mat_file, &name);
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if (mx_data == NULL)
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{
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cerr<<"Error: matGetNextVariable failed in "<<path<<endl;
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return false;
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}
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const int dims = mxGetNumberOfDimensions(mx_data);
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assert(dims == 2);
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if(dims != 2)
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{
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fprintf(stderr,"Variable '%s' has %d ≠ 2 dimensions. Skipping\n",
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name,dims);
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mxDestroyArray(mx_data);
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continue;
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}
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// don't destroy
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names.push_back(name);
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data.push_back(mx_data);
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}
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if(matClose(mat_file) != 0)
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{
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cerr<<"Error: failed to close file "<<path<<endl;
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return false;
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}
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return true;
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}
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// Treat everything as a double
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template <typename DerivedM>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const Eigen::PlainObjectBase<DerivedM>& M,
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const std::string & name)
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{
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using namespace std;
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const int m = M.rows();
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const int n = M.cols();
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mxArray * mx_data = mxCreateDoubleMatrix(m,n,mxREAL);
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data.push_back(mx_data);
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names.push_back(name);
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// Copy data immediately
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// Use Eigen's map and cast to copy
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Eigen::Map< Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> >
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map(mxGetPr(mx_data),m,n);
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map = M.template cast<double>();
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return *this;
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}
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// Treat everything as a double
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template <typename MT>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const Eigen::SparseMatrix<MT>& M,
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const std::string & name)
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{
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using namespace std;
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const int m = M.rows();
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const int n = M.cols();
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// THIS WILL NOT WORK FOR ROW-MAJOR
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assert(n==M.outerSize());
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const int nzmax = M.nonZeros();
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mxArray * mx_data = mxCreateSparse(m, n, nzmax, mxREAL);
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data.push_back(mx_data);
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names.push_back(name);
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// Copy data immediately
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double * pr = mxGetPr(mx_data);
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mwIndex * ir = mxGetIr(mx_data);
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mwIndex * jc = mxGetJc(mx_data);
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// Iterate over outside
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int k = 0;
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for(int j=0; j<M.outerSize();j++)
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{
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jc[j] = k;
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// Iterate over inside
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for(typename Eigen::SparseMatrix<MT>::InnerIterator it (M,j); it; ++it)
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{
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pr[k] = it.value();
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ir[k] = it.row();
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k++;
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}
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}
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jc[M.outerSize()] = k;
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return *this;
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}
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template <typename ScalarM>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const std::vector<std::vector<ScalarM> > & vM,
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const std::string & name)
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{
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Eigen::MatrixXd M;
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list_to_matrix(vM,M);
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return this->save(M,name);
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}
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template <typename ScalarV>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const std::vector<ScalarV> & vV,
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const std::string & name)
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{
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Eigen::MatrixXd V;
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list_to_matrix(vV,V);
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return this->save(V,name);
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}
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template <typename Q>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const Eigen::Quaternion<Q> & q,
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const std::string & name)
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{
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Eigen::Matrix<Q,1,4> qm;
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qm(0,0) = q.w();
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qm(0,1) = q.x();
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qm(0,2) = q.y();
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qm(0,3) = q.z();
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return save(qm,name);
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}
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save(
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const double d,
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const std::string & name)
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{
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Eigen::VectorXd v(1);
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v(0) = d;
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return save(v,name);
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}
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template <typename DerivedM>
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inline igl::matlab::MatlabWorkspace&
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igl::matlab::MatlabWorkspace::save_index(
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const Eigen::DenseBase<DerivedM>& M,
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const std::string & name)
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{
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DerivedM Mp1 = M;
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Mp1.array() += 1;
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return this->save(Mp1,name);
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}
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template <typename ScalarM>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save_index(
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const std::vector<std::vector<ScalarM> > & vM,
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const std::string & name)
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{
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Eigen::MatrixXd M;
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list_to_matrix(vM,M);
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return this->save_index(M,name);
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}
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template <typename ScalarV>
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inline igl::matlab::MatlabWorkspace& igl::matlab::MatlabWorkspace::save_index(
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const std::vector<ScalarV> & vV,
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const std::string & name)
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{
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Eigen::MatrixXd V;
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list_to_matrix(vV,V);
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return this->save_index(V,name);
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}
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template <typename DerivedM>
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inline bool igl::matlab::MatlabWorkspace::find(
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const std::string & name,
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Eigen::PlainObjectBase<DerivedM>& M)
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||||
{
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||||
using namespace std;
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const int i = std::find(names.begin(), names.end(), name)-names.begin();
|
||||
if(i>=(int)names.size())
|
||||
{
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||||
return false;
|
||||
}
|
||||
assert(i<=(int)data.size());
|
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mxArray * mx_data = data[i];
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assert(!mxIsSparse(mx_data));
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assert(mxGetNumberOfDimensions(mx_data) == 2);
|
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//cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
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const int m = mxGetM(mx_data);
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const int n = mxGetN(mx_data);
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// Handle vectors: in the sense that anything found becomes a column vector,
|
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// whether it was column vector, row vector or matrix
|
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if(DerivedM::IsVectorAtCompileTime)
|
||||
{
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assert(m==1 || n==1 || (m==0 && n==0));
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M.resize(m*n,1);
|
||||
}else
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||||
{
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M.resize(m,n);
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}
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assert(mxGetNumberOfElements(mx_data) == M.size());
|
||||
// Use Eigen's map and cast to copy
|
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M = Eigen::Map< Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> >
|
||||
(mxGetPr(mx_data),M.rows(),M.cols()).cast<typename DerivedM::Scalar>();
|
||||
return true;
|
||||
}
|
||||
|
||||
template <typename MT>
|
||||
inline bool igl::matlab::MatlabWorkspace::find(
|
||||
const std::string & name,
|
||||
Eigen::SparseMatrix<MT>& M)
|
||||
{
|
||||
using namespace std;
|
||||
using namespace Eigen;
|
||||
const int i = std::find(names.begin(), names.end(), name)-names.begin();
|
||||
if(i>=(int)names.size())
|
||||
{
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||||
return false;
|
||||
}
|
||||
assert(i<=(int)data.size());
|
||||
mxArray * mx_data = data[i];
|
||||
// Handle boring case where matrix is actually an empty dense matrix
|
||||
if(mxGetNumberOfElements(mx_data) == 0)
|
||||
{
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||||
M.resize(0,0);
|
||||
return true;
|
||||
}
|
||||
assert(mxIsSparse(mx_data));
|
||||
assert(mxGetNumberOfDimensions(mx_data) == 2);
|
||||
//cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
|
||||
const int m = mxGetM(mx_data);
|
||||
const int n = mxGetN(mx_data);
|
||||
// TODO: It should be possible to directly load the data into the sparse
|
||||
// matrix without going through the triplets
|
||||
// Copy data immediately
|
||||
double * pr = mxGetPr(mx_data);
|
||||
mwIndex * ir = mxGetIr(mx_data);
|
||||
mwIndex * jc = mxGetJc(mx_data);
|
||||
vector<Triplet<MT> > MIJV;
|
||||
const int nnz = mxGetNzmax(mx_data);
|
||||
MIJV.reserve(nnz);
|
||||
// Iterate over outside
|
||||
int k = 0;
|
||||
for(int j=0; j<n;j++)
|
||||
{
|
||||
// Iterate over inside
|
||||
while(k<(int)jc[j+1])
|
||||
{
|
||||
//cout<<ir[k]<<" "<<j<<" "<<pr[k]<<endl;
|
||||
assert((int)ir[k]<m);
|
||||
assert((int)j<n);
|
||||
MIJV.push_back(Triplet<MT >(ir[k],j,pr[k]));
|
||||
k++;
|
||||
}
|
||||
}
|
||||
M.resize(m,n);
|
||||
M.setFromTriplets(MIJV.begin(),MIJV.end());
|
||||
|
||||
return true;
|
||||
}
|
||||
|
||||
inline bool igl::matlab::MatlabWorkspace::find(
|
||||
const std::string & name,
|
||||
int & v)
|
||||
{
|
||||
using namespace std;
|
||||
const int i = std::find(names.begin(), names.end(), name)-names.begin();
|
||||
if(i>=(int)names.size())
|
||||
{
|
||||
return false;
|
||||
}
|
||||
assert(i<=(int)data.size());
|
||||
mxArray * mx_data = data[i];
|
||||
assert(!mxIsSparse(mx_data));
|
||||
assert(mxGetNumberOfDimensions(mx_data) == 2);
|
||||
//cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
|
||||
assert(mxGetNumberOfElements(mx_data) == 1);
|
||||
copy(
|
||||
mxGetPr(mx_data),
|
||||
mxGetPr(mx_data)+mxGetNumberOfElements(mx_data),
|
||||
&v);
|
||||
return true;
|
||||
}
|
||||
|
||||
inline bool igl::matlab::MatlabWorkspace::find(
|
||||
const std::string & name,
|
||||
double & d)
|
||||
{
|
||||
using namespace std;
|
||||
const int i = std::find(names.begin(), names.end(), name)-names.begin();
|
||||
if(i>=(int)names.size())
|
||||
{
|
||||
return false;
|
||||
}
|
||||
assert(i<=(int)data.size());
|
||||
mxArray * mx_data = data[i];
|
||||
assert(!mxIsSparse(mx_data));
|
||||
assert(mxGetNumberOfDimensions(mx_data) == 2);
|
||||
//cout<<name<<": "<<mxGetM(mx_data)<<" "<<mxGetN(mx_data)<<endl;
|
||||
assert(mxGetNumberOfElements(mx_data) == 1);
|
||||
copy(
|
||||
mxGetPr(mx_data),
|
||||
mxGetPr(mx_data)+mxGetNumberOfElements(mx_data),
|
||||
&d);
|
||||
return true;
|
||||
}
|
||||
|
||||
template <typename DerivedM>
|
||||
inline bool igl::matlab::MatlabWorkspace::find_index(
|
||||
const std::string & name,
|
||||
Eigen::PlainObjectBase<DerivedM>& M)
|
||||
{
|
||||
if(!find(name,M))
|
||||
{
|
||||
return false;
|
||||
}
|
||||
M.array() -= 1;
|
||||
return true;
|
||||
}
|
||||
|
||||
|
||||
//template <typename Data>
|
||||
//bool igl::matlab::MatlabWorkspace::save(const Data & M, const std::string & name)
|
||||
//{
|
||||
// using namespace std;
|
||||
// // If I don't know the type then I can't save it
|
||||
// cerr<<"^MatlabWorkspace::save Error: Unknown data type. "<<
|
||||
// name<<" not saved."<<endl;
|
||||
// return false;
|
||||
//}
|
||||
|
||||
#endif
|
||||
|
||||
Reference in New Issue
Block a user