refactored nixgen to mkarray

Author: asobolev

nix_mx.cc

@@ -9,7 +9,7 @@
 #include "handle.h"
 #include "arguments.h"
 #include "struct.h"
-#include "nix2mx.h"
+#include "mknix.h"
 
 #include "nixfile.h"
 #include "nixsection.h"

src/nixdataarray.cc

@@ -1,14 +1,13 @@
 #include "nixdataarray.h"
-#include "nixgen.h"
-
+#include "mkarray.h"
 #include "mex.h"
 
 #include <nix.hpp>
 
 #include "handle.h"
 #include "arguments.h"
 #include "struct.h"
-#include "nix2mx.h"
+#include "mknix.h"
 
 namespace nixdataarray {
 
@@ -44,7 +43,7 @@ namespace nixdataarray {
     void read_all(const extractor &input, infusor &output)
     {
         nix::DataArray da = input.entity<nix::DataArray>(1);
-        mxArray *data = nixgen::dataset_read_all(da);
+        mxArray *data = make_mx_array(da);
         output.set(0, data);
     }
 

src/nixdimensions.cc

@@ -1,11 +1,5 @@
-#include "nixtag.h"
-#include "nixgen.h"
-
-#include "mex.h"
-
 #include <nix.hpp>
-
-#include "handle.h"
+#include "mex.h"
 #include "arguments.h"
 #include "struct.h"
 

src/nixgen.cc

@@ -1,5 +1,5 @@
 #include "nixmultitag.h"
-#include "nixgen.h"
+#include "mkarray.h"
 
 #include "mex.h"
 
@@ -49,7 +49,7 @@ namespace nixmultitag {
         double p_index = input.num<double>(2);
         double f_index = input.num<double>(3);
 
-        mxArray *data = nixgen::dataset_read_all(currObj.retrieveData(p_index, f_index));
+        mxArray *data = make_mx_array(currObj.retrieveData(p_index, f_index));
         output.set(0, data);
     }
 
@@ -58,7 +58,7 @@ namespace nixmultitag {
         double p_index = input.num<double>(2);
         double f_index = input.num<double>(3);
 
-        mxArray *data = nixgen::dataset_read_all(currObj.retrieveFeatureData(p_index, f_index));
+        mxArray *data = make_mx_array(currObj.retrieveFeatureData(p_index, f_index));
         output.set(0, data);
     }
 

src/nixgen.h

@@ -6,7 +6,7 @@
 #include "handle.h"
 #include "arguments.h"
 #include "struct.h"
-#include "nix2mx.h"
+#include "mknix.h"
 
 
 namespace nixsection {

src/nixmultitag.cc

@@ -1,5 +1,5 @@
 #include "nixtag.h"
-#include "nixgen.h"
+#include "mkarray.h"
 
 #include "mex.h"
 
@@ -50,15 +50,15 @@ namespace nixtag {
         nix::Tag currObj = input.entity<nix::Tag>(1);
         double index = input.num<double>(2);
 
-        mxArray *data = nixgen::dataset_read_all(currObj.retrieveData(index));
+        mxArray *data = make_mx_array(currObj.retrieveData(index));
         output.set(0, data);
     }
 
     void retrieve_feature_data(const extractor &input, infusor &output) {
         nix::Tag currObj = input.entity<nix::Tag>(1);
         double index = input.num<double>(2);
 
-        mxArray *data = nixgen::dataset_read_all(currObj.retrieveFeatureData(index));
+        mxArray *data = make_mx_array(currObj.retrieveFeatureData(index));
         output.set(0, data);
     }
 

src/nixsection.cc

@@ -5,7 +5,7 @@
 #include "handle.h"
 #include "datatypes.h"
 #include "mkarray.h"
-#include "nix2mx.h"
+#include "mknix.h"
 #include <stdexcept>
 
 // *** argument helpers ***
@@ -199,6 +199,13 @@ class extractor : public argument_helper<const mxArray> {
 		return l[0];
 	}
 
+    template<typename T>
+    T get(size_t pos) const {
+        check_size(pos);
+
+        return mx_array_to_nix(array[pos]);
+    }
+
     template<typename T>
     T entity(size_t pos) const {
         return hdl(pos).get<T>();

src/nixtag.cc

@@ -1,4 +1,35 @@
 #include "mkarray.h"
+#include "mex.h"
+#include <nix.hpp>
+
+mxArray* make_mx_array(const nix::DataSet &da) {
+    nix::NDSize size = da.dataExtent();
+    const size_t len = size.size();
+    std::vector<mwSize> dims(len);
+
+    //NB: matlab is column-major, while HDF5 is row-major
+    //    data is correct with this, but dimensions don't
+    //    agree with the file anymore. Transpose it in matlab
+    //    (DataArray.read_all)
+    for (size_t i = 0; i < len; i++) {
+        dims[len - (i + 1)] = static_cast<mwSize>(size[i]);
+    }
+
+    nix::DataType da_type = da.dataType();
+    DType2 dtype = dtype_nix2mex(da_type);
+
+    if (!dtype.is_valid) {
+        throw std::domain_error("Unsupported data type");
+    }
+
+    mxArray *data = mxCreateNumericArray(dims.size(), dims.data(), dtype.cid, dtype.clx);
+    double *ptr = mxGetPr(data);
+
+    nix::NDSize offset(size.size(), 0);
+    da.getData(da_type, ptr, size, offset);
+
+    return data;
+}
 
 mxArray* make_mx_array(const nix::NDSize &size)
 {