DimensionReduction.cpp

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#include <DimensionReduction.h>
#include <TopoMap.h>
 
#include <map>
 
#define VALUE_TO_STRING(x) #x
#define VALUE(x) VALUE_TO_STRING(x)
 
#ifdef TTK_ENABLE_SCIKIT_LEARN
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#include <Python.h>
#include <numpy/arrayobject.h>
#endif
 
using namespace std;
using namespace ttk;
 
DimensionReduction::DimensionReduction() {
  this->setDebugMsgPrefix("DimensionReduction");
 
  // default backend
  this->setInputMethod(METHOD::MDS);
 
#ifdef TTK_ENABLE_SCIKIT_LEARN
  auto finalize_callback = []() { Py_Finalize(); };
 
  if(!Py_IsInitialized()) {
    Py_Initialize();
    atexit(finalize_callback);
  }
 
  const char *version = Py_GetVersion();
  if(version[0] >= '3') {
    this->printMsg("Initializing Python " + std::to_string(version[0])
                   + std::to_string(version[1]) + std::to_string(version[2]));
  } else {
    this->printErr("Python 3 + is required :" + std::string{version}
                   + " is provided.");
  }
 
  majorVersion_ = version[0];
#endif
}
 
int DimensionReduction::execute(
  std::vector<std::vector<double>> &outputEmbedding,
  const std::vector<double> &inputMatrix,
  const int nRows,
  const int nColumns,
  int *insertionTimeForTopomap) const {
 
#ifndef TTK_ENABLE_SCIKIT_LEARN
  TTK_FORCE_USE(nColumns);
#endif
 
  Timer t;
 
  if(this->Method == METHOD::TOPOMAP) {
    TopoMap topomap(
      this->topomap_AngularSampleNb, topomap_CheckMST, topomap_Strategy);
    topomap.setDebugLevel(this->debugLevel_);
    topomap.setThreadNumber(this->threadNumber_);
 
    std::vector<double> coordsTopomap(2 * nRows);
    topomap.execute<double>(coordsTopomap.data(), insertionTimeForTopomap,
                            inputMatrix, IsInputADistanceMatrix, nRows);
    outputEmbedding.resize(2);
    outputEmbedding[0].resize(nRows);
    outputEmbedding[1].resize(nRows);
    for(int i = 0; i < nRows; i++) {
      outputEmbedding[0][i] = coordsTopomap[2 * i];
      outputEmbedding[1][i] = coordsTopomap[2 * i + 1];
    }
 
    this->printMsg(
      "Computed TopoMap", 1.0, t.getElapsedTime(), this->threadNumber_);
    return 0;
  }
 
#ifdef TTK_ENABLE_SCIKIT_LEARN
#ifndef TTK_ENABLE_KAMIKAZE
  if(majorVersion_ < '3')
    return -1;
  if(ModulePath.empty())
    return -2;
  if(ModuleName.empty())
    return -3;
  if(FunctionName.empty())
    return -4;
#endif
 
  const int numberOfComponents = std::max(2, this->NumberOfComponents);
 
  const int numberOfNeighbors = std::max(1, this->NumberOfNeighbors);
 
  // declared here to avoid crossing initialization with goto
  vector<PyObject *> gc;
  PyObject *pArray;
  PyObject *pPath;
  PyObject *pSys;
  PyObject *pName;
  PyObject *pModule;
  PyObject *pFunc;
  PyObject *pMethod;
  PyObject *pNumberOfComponents;
  PyObject *pNumberOfNeighbors;
  PyObject *pJobs;
  PyObject *pIsDeterministic;
  PyObject *pReturn;
  PyObject *pNRows;
  PyObject *pNColumns;
  PyObject *pEmbedding;
  PyObject *pSEParams;
  PyObject *pLLEParams;
  PyObject *pMDSParams;
  PyObject *pTSNEParams;
  PyObject *pISOParams;
  PyObject *pPCAParams;
  PyObject *pParams;
  PyArrayObject *npArr;
  PyArrayObject *npEmbedding;
 
  string modulePath;
 
  if(PyArray_API == nullptr) {
#ifndef __clang_analyzer__
    import_array1(-1);
#endif // __clang_analyzer__
  }
  if(PyArray_API == nullptr) {
    return -5;
  }
 
  // convert the input matrix into a NumPy array.
  const int numberOfDimensions = 2;
  npy_intp dimensions[2]{nRows, nColumns};
 
  std::vector<std::string> methodToString{
    "SE", "LLE", "MDS", "t-SNE", "IsoMap", "PCA"};
 
  pArray = PyArray_SimpleNewFromData(numberOfDimensions, dimensions, NPY_DOUBLE,
                                     const_cast<double *>(inputMatrix.data()));
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pArray) {
    this->printErr("Python: failed to convert the array.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pArray);
 
  npArr = reinterpret_cast<PyArrayObject *>(pArray);
 
  pSys = PyImport_ImportModule("sys");
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pSys) {
    this->printErr("Python: failed to load the sys module.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pSys);
 
  pPath = PyObject_GetAttrString(pSys, "path");
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pPath) {
    this->printErr("Python: failed to get the path variable.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pPath);
 
  if(ModulePath == "default")
    modulePath = VALUE(TTK_SCRIPTS_PATH);
  else
    modulePath = ModulePath;
 
  this->printMsg("Loading Python script from: " + modulePath);
  PyList_Append(pPath, PyUnicode_FromString(modulePath.data()));
 
  // set other parameters
  pNumberOfComponents = PyLong_FromLong(numberOfComponents);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pNumberOfComponents) {
    this->printErr("Python: cannot convert pNumberOfComponents.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pNumberOfComponents);
 
  pNumberOfNeighbors = PyLong_FromLong(numberOfNeighbors);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pNumberOfNeighbors) {
    this->printErr("Python: cannot convert pNumberOfNeighbors.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pNumberOfNeighbors);
 
  pMethod = PyLong_FromLong(static_cast<long>(this->Method));
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pMethod) {
    this->printErr("Python: cannot convert pMethod.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pMethod);
 
  if(threadNumber_ > 1 && this->Method == METHOD::MDS) { // MDS
    this->printWrn(
      "MDS is known to be instable when used with multiple threads");
  }
  pJobs = PyLong_FromLong(threadNumber_);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pJobs) {
    this->printErr("Python: cannot convert pJobs.");
    goto collect_garbage;
  }
#endif
 
  pIsDeterministic = PyLong_FromLong(static_cast<long>(this->IsDeterministic));
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pIsDeterministic) {
    this->printErr("Python: cannot convert pIsDeterministic.");
    goto collect_garbage;
  }
#endif
 
  // load module
  pName = PyUnicode_FromString(ModuleName.data());
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pName) {
    this->printErr("Python: moduleName parsing failed.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pName);
 
  pModule = PyImport_Import(pName);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pModule) {
    this->printErr("Python: module import failed.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pModule);
 
  // configure function
  pFunc = PyObject_GetAttrString(pModule, FunctionName.data());
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pFunc) {
    this->printErr("Python: functionName parsing failed.");
    goto collect_garbage;
  }
 
  if(!PyCallable_Check(pFunc)) {
    this->printErr("Python: function call failed.");
    goto collect_garbage;
  }
#endif
 
  pSEParams = PyList_New(0);
  PyList_Append(pSEParams, PyUnicode_FromString(se_Affinity.data()));
  PyList_Append(pSEParams, PyFloat_FromDouble(se_Gamma));
  PyList_Append(pSEParams, PyUnicode_FromString(se_EigenSolver.data()));
 
  pLLEParams = PyList_New(0);
  PyList_Append(pLLEParams, PyFloat_FromDouble(lle_Regularization));
  PyList_Append(pLLEParams, PyUnicode_FromString(lle_EigenSolver.data()));
  PyList_Append(pLLEParams, PyFloat_FromDouble(lle_Tolerance));
  PyList_Append(pLLEParams, PyLong_FromLong(lle_MaxIteration));
  PyList_Append(pLLEParams, PyUnicode_FromString(lle_Method.data()));
  PyList_Append(pLLEParams, PyFloat_FromDouble(lle_HessianTolerance));
  PyList_Append(pLLEParams, PyFloat_FromDouble(lle_ModifiedTolerance));
  PyList_Append(
    pLLEParams, PyUnicode_FromString(lle_NeighborsAlgorithm.data()));
 
  pMDSParams = PyList_New(0);
  PyList_Append(pMDSParams, PyBool_FromLong(mds_Metric));
  PyList_Append(pMDSParams, PyLong_FromLong(mds_Init));
  PyList_Append(pMDSParams, PyLong_FromLong(mds_MaxIteration));
  PyList_Append(pMDSParams, PyLong_FromLong(mds_Verbose));
  PyList_Append(pMDSParams, PyFloat_FromDouble(mds_Epsilon));
  PyList_Append(pMDSParams, PyUnicode_FromString(mds_Dissimilarity.data()));
 
  pTSNEParams = PyList_New(0);
  PyList_Append(pTSNEParams, PyFloat_FromDouble(tsne_Perplexity));
  PyList_Append(pTSNEParams, PyFloat_FromDouble(tsne_Exaggeration));
  PyList_Append(pTSNEParams, PyFloat_FromDouble(tsne_LearningRate));
  PyList_Append(pTSNEParams, PyLong_FromLong(tsne_MaxIteration));
  PyList_Append(pTSNEParams, PyLong_FromLong(tsne_MaxIterationProgress));
  PyList_Append(pTSNEParams, PyFloat_FromDouble(tsne_GradientThreshold));
  PyList_Append(pTSNEParams, PyUnicode_FromString(tsne_Metric.data()));
  PyList_Append(pTSNEParams, PyUnicode_FromString(tsne_Init.data()));
  PyList_Append(pTSNEParams, PyLong_FromLong(tsne_Verbose));
  PyList_Append(pTSNEParams, PyUnicode_FromString(tsne_Method.data()));
  PyList_Append(pTSNEParams, PyFloat_FromDouble(tsne_Angle));
 
  pISOParams = PyList_New(0);
  PyList_Append(pISOParams, PyUnicode_FromString(iso_EigenSolver.data()));
  PyList_Append(pISOParams, PyFloat_FromDouble(iso_Tolerance));
  PyList_Append(pISOParams, PyLong_FromLong(iso_MaxIteration));
  PyList_Append(pISOParams, PyUnicode_FromString(iso_PathMethod.data()));
  PyList_Append(
    pISOParams, PyUnicode_FromString(iso_NeighborsAlgorithm.data()));
  PyList_Append(pISOParams, PyUnicode_FromString(iso_Metric.data()));
 
  pPCAParams = PyList_New(0);
  PyList_Append(pPCAParams, PyBool_FromLong(pca_Copy));
  PyList_Append(pPCAParams, PyBool_FromLong(pca_Whiten));
  PyList_Append(pPCAParams, PyUnicode_FromString(pca_SVDSolver.data()));
  PyList_Append(pPCAParams, PyFloat_FromDouble(pca_Tolerance));
  PyList_Append(pPCAParams, PyUnicode_FromString(pca_MaxIteration.data()));
 
  pParams = PyList_New(0);
  gc.push_back(pParams);
 
  PyList_Append(pParams, pSEParams);
  PyList_Append(pParams, pLLEParams);
  PyList_Append(pParams, pMDSParams);
  PyList_Append(pParams, pTSNEParams);
  PyList_Append(pParams, pISOParams);
  PyList_Append(pParams, pPCAParams);
 
  pReturn = PyObject_CallFunctionObjArgs(
    pFunc, npArr, pMethod, pNumberOfComponents, pNumberOfNeighbors, pJobs,
    pIsDeterministic, pParams, NULL);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pReturn) {
    this->printErr("Python: function returned invalid object.");
    goto collect_garbage;
  }
#endif
  gc.push_back(pReturn);
 
  pNRows = PyList_GetItem(pReturn, 0);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pNRows) {
    this->printErr("Python: function returned invalid number of rows");
    goto collect_garbage;
  }
#endif
 
  pNColumns = PyList_GetItem(pReturn, 1);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pNColumns) {
    this->printErr("Python: function returned invalid number of columns.");
    goto collect_garbage;
  }
#endif
 
  pEmbedding = PyList_GetItem(pReturn, 2);
#ifndef TTK_ENABLE_KAMIKAZE
  if(!pEmbedding) {
    this->printErr("Python: function returned invalid embedding data.");
    goto collect_garbage;
  }
#endif
 
  if(PyLong_AsLong(pNRows) == nRows
     and PyLong_AsLong(pNColumns) == numberOfComponents) {
    npEmbedding = reinterpret_cast<PyArrayObject *>(pEmbedding);
 
    outputEmbedding.resize(numberOfComponents);
    for(int i = 0; i < numberOfComponents; ++i) {
      outputEmbedding[i].resize(nRows);
      if(PyArray_TYPE(npEmbedding) == NPY_FLOAT) {
        float *c_out = reinterpret_cast<float *>(PyArray_DATA(npEmbedding));
        for(int j = 0; j < nRows; ++j)
          outputEmbedding[i][j] = c_out[i * nRows + j];
      } else if(PyArray_TYPE(npEmbedding) == NPY_DOUBLE) {
        double *c_out = reinterpret_cast<double *>(PyArray_DATA(npEmbedding));
        for(int j = 0; j < nRows; ++j)
          outputEmbedding[i][j] = c_out[i * nRows + j];
      }
    }
  }
 
  // normal control-flow
  for(auto i : gc)
    Py_DECREF(i);
 
  this->printMsg("Computed " + methodToString[static_cast<int>(this->Method)],
                 1.0, t.getElapsedTime(), this->threadNumber_);
 
  return 0;
 
  // error control-flow
#ifndef TTK_ENABLE_KAMIKAZE
collect_garbage:
#endif
  for(auto i : gc)
    Py_DECREF(i);
  return -6;
 
#endif
 
  return 0;
}