Load incompatible Mat file as weights dialog will crash GeoDa GeoDaCe…

…nter#2265
lixun910 · Oct 29, 2020 · 8b1053b · 8b1053b
1 parent de3a34a
commit 8b1053b
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Showing 11 changed files with 105 additions and 79 deletions.
diff --git a/Algorithms/distmatrix.cpp b/Algorithms/distmatrix.cpp
@@ -56,7 +56,7 @@ float* gpu_distmatrix(const char* cl_path, int rows, int columns, double** data,
     fp = fopen(cl_path, "r");
     if (!fp) {
         fprintf(stderr, "Failed to load kernel.\n");
-        exit(1);
+        return 0;
     }
     source_str = (char*)malloc(MAX_SOURCE_SIZE);
     source_size = fread( source_str, 1, MAX_SOURCE_SIZE, fp);

diff --git a/Algorithms/tsne.cpp b/Algorithms/tsne.cpp
@@ -119,7 +119,10 @@ void TSNE::run(boost::lockfree::queue<int>& tsne_queue,
     double* dY    = (double*) malloc(N * no_dims * sizeof(double));
     double* uY    = (double*) calloc(N * no_dims , sizeof(double));
     double* gains = (double*) malloc(N * no_dims * sizeof(double));
-    if (dY == NULL || uY == NULL || gains == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (dY == NULL || uY == NULL || gains == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
     for (int i = 0; i < N * no_dims; i++) {
         gains[i] = 1.0;
     }
@@ -296,7 +299,8 @@ double TSNE::computeGradient(int* inp_row_P, int* inp_col_P, double* inp_val_P,
     double C = 0.;
 
     if (pos_f == NULL || neg_f == NULL) { 
-        fprintf(stderr, "Memory allocation failed!\n"); exit(1); 
+        fprintf(stderr, "Memory allocation failed!\n");
+        return 0;
     }
 
 #ifdef _OPENMP
@@ -401,7 +405,10 @@ void TSNE::computeGaussianPerplexity(double* X, int N, int D, int** _row_P, int*
     *_row_P = (int*)    malloc((N + 1) * sizeof(int));
     *_col_P = (int*)    calloc(N * K, sizeof(int));
     *_val_P = (double*) calloc(N * K, sizeof(double));
-    if (*_row_P == NULL || *_col_P == NULL || *_val_P == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (*_row_P == NULL || *_col_P == NULL || *_val_P == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
 
     /*
         row_P -- offsets for `col_P` (i)
@@ -534,7 +541,10 @@ void TSNE::symmetrizeMatrix(int** _row_P, int** _col_P, double** _val_P, int N)
 
     // Count number of elements and row counts of symmetric matrix
     int* row_counts = (int*) calloc(N, sizeof(int));
-    if (row_counts == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (row_counts == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
     for (int n = 0; n < N; n++) {
         for (int i = row_P[n]; i < row_P[n + 1]; i++) {
 
@@ -563,15 +573,21 @@ void TSNE::symmetrizeMatrix(int** _row_P, int** _col_P, double** _val_P, int N)
     int*    sym_row_P = (int*)    malloc((N + 1) * sizeof(int));
     int*    sym_col_P = (int*)    malloc(no_elem * sizeof(int));
     double* sym_val_P = (double*) malloc(no_elem * sizeof(double));
-    if (sym_row_P == NULL || sym_col_P == NULL || sym_val_P == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (sym_row_P == NULL || sym_col_P == NULL || sym_val_P == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
 
     // Construct new row indices for symmetric matrix
     sym_row_P[0] = 0;
     for (int n = 0; n < N; n++) sym_row_P[n + 1] = sym_row_P[n] + row_counts[n];
 
     // Fill the result matrix
     int* offset = (int*) calloc(N, sizeof(int));
-    if (offset == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (offset == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
     for (int n = 0; n < N; n++) {
         for (int i = row_P[n]; i < row_P[n + 1]; i++) {                                 // considering element(n, col_P[i])
 
@@ -628,7 +644,10 @@ void TSNE::zeroMean(double* X, int N, int D) {
 
     // Compute data mean
     double* mean = (double*) calloc(D, sizeof(double));
-    if (mean == NULL) { fprintf(stderr, "Memory allocation failed!\n"); exit(1); }
+    if (mean == NULL) {
+        fprintf(stderr, "Memory allocation failed!\n");
+        return;
+    }
     for (int n = 0; n < N; n++) {
         for (int d = 0; d < D; d++) {
             mean[d] += X[n * D + d];

diff --git a/Regression/ML_im.cpp b/Regression/ML_im.cpp
@@ -2544,7 +2544,8 @@ double goldeno(const double left, const double right, const SparseMatrix &w,
     Lco(y, lag, X, w, f1, sol);
     Lco(y, lag, X, w, f2, sol);
     Lco(y, lag, X, w, -0.0586045, sol);
-    exit(0);
+
+    //exit(0);
     //  while (fabs(x3-x0) > tol*(fabs(x1)+fabs(x2)))  {			// here tol is used as RELATIVE accuracy
     while (fabs(x3-x0) > TOLERANCE)  {							// here tol is used as an ABSOLUTE accuracy
         if (f1 < f2)  {

diff --git a/Regression/SparseMatrix.cpp b/Regression/SparseMatrix.cpp
@@ -92,12 +92,12 @@ void SparseMatrix::createGAL(const GalElement* my_gal, int obs)
             int oix = row[r].getIx(cnt);
             if (oix < key[0].first || oix > key[dim-1].first)  {
 				wxMessageBox("Error: value does not exist in the weights file");
-				exit(0);
+                return;
             }
             int lx = ik[ oix - key[0].first ];
             if (lx < 0) {
 				wxMessageBox("Error: value does not exist in the weights file");
-				exit(0);
+                return;
             }
             this->row[r].setIx(cnt, lx);
         }

diff --git a/ShapeOperations/PolysToContigWeights.cpp b/ShapeOperations/PolysToContigWeights.cpp
@@ -340,7 +340,7 @@ void PartitionM::initIx(const int incl, const double lwr, const double upr)  {
     if (lower < 0 || upper > cells || incl < 0 || incl >= elements)
     {
         //     cout << "PartM: incl= " << incl << " l= " << lwr << "  " << upr;
-        exit(1);
+        return;
     }
 
 

diff --git a/io/MatfileReader.cpp b/io/MatfileReader.cpp
@@ -40,7 +40,7 @@ pair<EDataType, EMatrixClass> classify(char* data, bool endianSwap) {
     if (static_cast<EDataType>(dataType) != miMATRIX)
         return make_pair(static_cast<EDataType>(dataType), mxINVALID);
     // miMATRIX must not be small element
-    assert(!isSmallDataElement);
+    //assert(!isSmallDataElement);
 
     ArrayFlags* af = new ArrayFlags(data+8, endianSwap);
 
@@ -147,16 +147,13 @@ DataElement* parse(char* data, bool endianSwap) {
             break;
         default:
             cerr << "invalid EMatrixClass!\n";
-            exit(1);
         }
         break;
     default:
         cerr << "invalid EDataType!\n";
-        exit(1);
     }
     if (!de) {
         cerr << "failed to parse!\n";
-        exit(1);
     }
     return de;
 }
@@ -216,14 +213,12 @@ CompressedDataElement::CompressedDataElement(char* data, bool endianSwap) :
             _decompressedData = new char[size];
             if (!_decompressedData) {
                 cerr << "FlatDataElement::parseData new failed!\n";
-                exit(1);
             }
             rsize = size;
             res = uncompress(reinterpret_cast<unsigned char*>(_decompressedData), &size,
                              reinterpret_cast<unsigned char*>(data), _numberOfBytes);
         } else {
             cerr << "FlatDataElement::parseData uncompress failed!\n";
-            exit(1);
         }
     }
     _decompressedSize = static_cast<uint32_t>(rsize);
@@ -255,7 +250,7 @@ NumericArray<T>::NumericArray(char* data, bool endianSwap) :
         parseImag(data);
         data += _imag->totalBytes();
     }
-    assert(data == start+_numberOfBytes+8);
+    //assert(data == start+_numberOfBytes+8);
 }
 
 template <typename T>
@@ -283,7 +278,7 @@ SparseArray<T>::SparseArray(char* data, bool endianSwap) :
         parseImag(data);
         data += _imag->totalBytes();
     }
-    assert(data == start+_numberOfBytes+8);
+    //assert(data == start+_numberOfBytes+8);
 }
 
 Cell::Cell(char* data, bool endianSwap) : MatrixDataElement(endianSwap), _cells() {
@@ -303,11 +298,11 @@ Cell::Cell(char* data, bool endianSwap) : MatrixDataElement(endianSwap), _cells(
     while(data < start + _numberOfBytes + 8) {
         // create matrix and add to _cells
         cell = dynamic_cast<MatrixDataElement*>(parse(data, endianSwap));
-        assert(cell);
+        //assert(cell);
         _cells.push_back(cell);
         data += cell->totalBytes();
     }
-    assert(data == start+_numberOfBytes+8);
+    //assert(data == start+_numberOfBytes+8);
 }
 
 Struct::Struct(char* data, bool endianSwap) :
@@ -332,11 +327,11 @@ Struct::Struct(char* data, bool endianSwap) :
     while(data < start + _numberOfBytes + 8) {
         // create matrix and add to _fields
         field = dynamic_cast<MatrixDataElement*>(parse(data, endianSwap));
-        assert(field);
+        //assert(field);
         _fields.push_back(field);
         data += field->totalBytes();
     }
-    assert(data == start+_numberOfBytes+8);
+    //assert(data == start+_numberOfBytes+8);
 }
 
 Object::Object(char* data, bool endianSwap) : _className(NULL), Struct(endianSwap) {
@@ -362,11 +357,11 @@ Object::Object(char* data, bool endianSwap) : _className(NULL), Struct(endianSwa
     while(data < start + _numberOfBytes + 8) {
         // create matrix and add to _fields
         field = dynamic_cast<MatrixDataElement*>(parse(data, endianSwap));
-        assert(field);
+        //assert(field);
         _fields.push_back(field);
         data += field->totalBytes();
     }
-    assert(data == start+_numberOfBytes+8);
+    //assert(data == start+_numberOfBytes+8);
 }
 
 
@@ -376,13 +371,13 @@ MatfileReader::MatfileReader(std::ifstream& inputStream)
     //_inputStream.open(_matfile.c_str(), ios_base::in | ios_base::binary);
     if(!_inputStream.is_open()) {
         cerr << "open " << _matfile.c_str() << " error!\n";
-        exit(1);
     }
 }
 
 MatfileReader::~MatfileReader() {
-    for (int i = 0; i < _dataElements.size(); ++i)
+    for (int i = 0; i < _dataElements.size(); ++i)  {
         delete _dataElements[i];
+    }
 }
 
 void MatfileReader::parseHeader() {
@@ -392,15 +387,16 @@ void MatfileReader::parseHeader() {
     memcpy(&_subsysDataOffset, _header+116, 8);
     memcpy(&_version, _header+124, 2);
     _endianIndicator.assign(_header+126, 2);
-    if (_endianIndicator.compare("IM"))
+    if (_endianIndicator.compare("IM")) {
         _endianSwap = true;
-    else
+    } else {
         _endianSwap = false;
+    }
 }
 
-void MatfileReader::parseDataElement() {
+bool MatfileReader::parseDataElement() {
     if (_inputStream.eof())
-        return;
+        return false;
     uint32_t dataType;
     uint32_t numberOfBytes;
     bool isSmallDataElement;
@@ -417,27 +413,36 @@ void MatfileReader::parseDataElement() {
     }
     char* data = NULL;
     DataElement* de = NULL;
-    if (isSmallDataElement)
+    if (isSmallDataElement) {
         de = parse(tag, _endianSwap);
-    else {
+        if (de == NULL) {
+            return false;
+        }
+    } else {
         data = new char[numberOfBytes+8];
         if (!data) {
-            cerr << "MatfileReader::parseDataElement new failed!\n";
-            exit(1);
+            //cerr << "MatfileReader::parseDataElement new failed!\n";
+            return false;
         }
         memcpy(data, tag, 8);
         _inputStream.read(reinterpret_cast<char*>(data+8), numberOfBytes);
         de = parse(data, _endianSwap);
     }
-    assert(de);
+    //assert(de);
+    if (de == NULL) {
+        return false;
+    }
     _dataElements.push_back(de);
     // padding
-    if (numberOfBytes % 8)
+    if (numberOfBytes % 8) {
         _inputStream.ignore(8 - numberOfBytes % 8);
+    }
+    return true;
 }
 
 void MatfileReader::parseAllDataElements() {
     gotoData();
-    while (!_inputStream.eof())
+    while (!_inputStream.eof()) {
         parseDataElement();
+    }
 }
diff --git a/io/MatfileReader.h b/io/MatfileReader.h
@@ -354,7 +354,7 @@ class MatfileReader
     void gotoHeader() { _inputStream.seekg(0, ios_base::beg); }
     void gotoData() { _inputStream.seekg(128, ios_base::beg); }
     void parseHeader();
-    void parseDataElement();
+    bool parseDataElement();
     void parseAllDataElements();
     bool eof() { return _inputStream.eof(); }
 

diff --git a/io/matlab_mat.cpp b/io/matlab_mat.cpp
@@ -30,12 +30,14 @@ GalElement* ReadMatAsGal(const wxString& fname, TableInterface* table_int)
     }
     MatfileReader mmr(istream);
     mmr.parseHeader();
-    // cout << mmr->descriptiveText() << endl;
-    // cout << mmr->subsysDataOffset() << endl;
-    // cout << mmr->version() << endl;
-    // cout << mmr->endianIndicator() << endl;
+    //cout << mmr.descriptiveText() << endl;
+    //cout << mmr.subsysDataOffset() << endl;
+    //cout << mmr.version() << endl;
+    //cout << mmr.endianIndicator() << endl;
     mmr.gotoData();
-    mmr.parseDataElement();
+    if (mmr.parseDataElement()  ==  false) {
+        throw WeightsNotValidException();
+    }
     vector<DataElement*> des = mmr.dataElements();
     // cout << des[0]->dataType() << endl;
     DataElement* de = des[0];
-Original file line number
+Diff line change
@@ Expand Up @@
         if (lower < 0 || upper > cells || incl < 0 || incl >= elements)
         {
             //     cout << "PartM: incl= " << incl << " l= " << lwr << "  " << upr;
-            exit(1);
+            return;
         }
@@ Expand Down @@