Merge pull request #111 from mpsonntag/dims

Various bug fixes

LGTM

Author: gicmo

+nix/Block.m

@@ -53,6 +53,14 @@
         end;
 
         function da = create_data_array(obj, name, nixtype, datatype, shape)
+            %-- Quick fix to enable alias range dimension with
+            %-- 1D data arrays created with this function.
+            %-- e.g. size([1 2 3]) returns shape [1 3], which would not
+            %-- be accepted when trying to add an alias range dimension.
+            if(shape(1) == 1)
+                shape(2:size(shape,2));
+            end;
+            
             errorStruct.identifier = 'Block:unsupportedDataType';
             if(~isa(datatype, 'nix.DataType'))
                 errorStruct.message = 'Please provide a valid nix.DataType';

+nix/DataArray.m

@@ -65,11 +65,11 @@
             dim = nix.RangeDimension(nix_mx(func_name, obj.nix_handle));
         end
 
-        function delCheck = delete_dimension(obj, index)
-            func_name = strcat(obj.alias, '::delete_dimension');
-            delCheck = nix_mx(func_name, obj.nix_handle, index);
+        function delCheck = delete_dimensions(obj)
+            func_name = strcat(obj.alias, '::delete_dimensions');
+            delCheck = nix_mx(func_name, obj.nix_handle);
         end;
-        
+
         % -----------------
         % Data access methods
         % -----------------

nix_mx.cc

@@ -184,7 +184,7 @@ void mexFunction(int            nlhs,
             .reg("create_range_dimension", &nix::DataArray::createRangeDimension)
             .reg("create_alias_range_dimension", &nix::DataArray::createAliasRangeDimension)
             .reg("create_sampled_dimension", &nix::DataArray::createSampledDimension);
-        methods->add("DataArray::delete_dimension", nixdataarray::delete_dimension);
+        methods->add("DataArray::delete_dimensions", nixdataarray::delete_dimensions);
         methods->add("DataArray::readAll", nixdataarray::read_all);
         methods->add("DataArray::writeAll", nixdataarray::write_all);
         methods->add("DataArray::addSource", nixdataarray::add_source);

src/nixdataarray.cc

@@ -52,8 +52,26 @@ namespace nixdataarray {
         nix::DataArray da = input.entity<nix::DataArray>(1);
         nix::DataType dtype = input.dtype(2);
 
-        nix::NDSize count = input.ndsize(2);
-        nix::NDSize offset(0);
+        const mxArray *arr = input.get_mx_array(2);
+
+        mwSize ndims = mxGetNumberOfDimensions(arr);
+        const mwSize *dims = mxGetDimensions(arr);
+        
+        mwSize tmp = ndims;
+        
+        // Quick fix for writing data arrays that have exactly one row.
+        // This fix does not resolve more complex arrays that have a 
+        // last dimension of exactly one row.
+        if (dims[ndims-1] == 1) {
+            ndims--;
+        }
+        nix::NDSize count(ndims);
+
+        for (mwSize i = 0; i < ndims; i++) {
+            count[(ndims - i) - 1] = static_cast<nix::ndsize_t>(dims[i]);
+        }
+
+        nix::NDSize offset(count.size(), 0);
         double *ptr = input.get_raw(2);
 
         if (dtype == nix::DataType::String) {
@@ -63,11 +81,10 @@ namespace nixdataarray {
         }
     }
 
-    void delete_dimension(const extractor &input, infusor &output) {
+    void delete_dimensions(const extractor &input, infusor &output) {
         nix::DataArray da = input.entity<nix::DataArray>(1);
 
-        const size_t idx = static_cast<size_t>(input.num<double>(2));
-        bool res = da.deleteDimension(idx);
+        bool res = da.deleteDimensions();
 
         output.set(0, res);
     }

src/nixdataarray.h

@@ -15,8 +15,8 @@ namespace nixdataarray {
 
     void write_all(const extractor &input, infusor &output);
 
-    void delete_dimension(const extractor &input, infusor &output);
+    void delete_dimensions(const extractor &input, infusor &output);
 
 } // namespace nixdataarray
 
-#endif
+#endif

src/utils/arguments.h

@@ -18,9 +18,9 @@ class argument_helper {
 
     bool check_size(size_t pos, bool fatal = false) const {
         bool res = pos + 1 > number;
-		if (!res && fatal) {
-			throw std::out_of_range("argument position is out of bounds");
-		}
+        if (!res && fatal) {
+            throw std::out_of_range("argument position is out of bounds");
+        }
         return res;
     }
 
@@ -49,7 +49,7 @@ class argument_helper {
     size_t number;
 };
 
-class extractor : public argument_helper<const mxArray> {
+class extractor : public argument_helper < const mxArray > {
 public:
     extractor(const mxArray **arr, int n) : argument_helper(arr, n) { }
 
@@ -76,7 +76,7 @@ class extractor : public argument_helper<const mxArray> {
     nix::NDSize ndsize(size_t pos) const {
         return mx_to_ndsize(array[pos]);
     }
-    
+
     nix::DataType dtype(size_t pos) const {
         return dtype_mex2nix(array[pos]);
     }
@@ -97,7 +97,7 @@ class extractor : public argument_helper<const mxArray> {
     }
 
     handle hdl(size_t pos) const {
-		handle h = handle(num<uint64_t>(pos));
+        handle h = handle(num<uint64_t>(pos));
         return h;
     }
 
@@ -114,24 +114,28 @@ class extractor : public argument_helper<const mxArray> {
         return mxGetPr(array[pos]);
     }
 
+    const mxArray *get_mx_array(size_t pos) const {
+        return array[pos];
+    }
+
 private:
 };
 
 template<>
 inline std::vector<std::string> extractor::vec(size_t pos) const {
-	return mx_to_strings(array[pos]);
+    return mx_to_strings(array[pos]);
 }
 
 
 class infusor : public argument_helper<mxArray> {
 public:
     infusor(mxArray **arr, int n) : argument_helper(arr, n) { }
 
-	template<typename T>
-	void set(size_t pos, T &&value) {
-		mxArray *array = make_mx_array(std::forward<T>(value));
-		set(pos, array);
-	}
+    template<typename T>
+    void set(size_t pos, T &&value) {
+        mxArray *array = make_mx_array(std::forward<T>(value));
+        set(pos, array);
+    }
 
     void set(size_t pos, mxArray *arr) {
         array[pos] = arr;

tests/TestDataArray.m

@@ -149,7 +149,7 @@
     charData = ['a' 'b' 'c' 'd' 'e'];
     cellData = {1 2 3 4 5};
 
-    da = b.create_data_array('numericArray', typeDA, nix.DataType.Double, [1 5]);
+    da = b.create_data_array('numericArray', typeDA, nix.DataType.Double, 5);
     da.write_all(numData);
     assert(isequal(da.read_all(), numData));
 
@@ -185,7 +185,7 @@
     numData = [1 2 3 4 5];
     charData = ['a' 'b' 'c' 'd' 'e'];
 
-    da = b.create_data_array('logicalArray', typeDA, nix.DataType.Bool, [1 5]);
+    da = b.create_data_array('logicalArray', typeDA, nix.DataType.Bool, 5);
     da.write_all(logData);
     assert(isequal(da.read_all, logData));
     try
@@ -213,7 +213,7 @@
 
     numData = [1.3 2.4143 3.9878 4.1239 5];
 
-    da = b.create_data_array('floatArray', typeDA, nix.DataType.Float, [1 5]);
+    da = b.create_data_array('floatArray', typeDA, nix.DataType.Float, 5);
     da.write_all(numData);
     assert(isequal(da.read_all, single(numData)));
 
@@ -332,16 +332,7 @@
     assert(isequal(f.blocks{1}.dataArrays{1}.dimensions{3}.ticks, ticks));
     assert(~da.dimensions{3}.isAlias);
 
-    da.delete_dimension(2);
-    assert(length(da.dimensions) == 2);
-    assert(strcmp(da.dimensions{1}.dimensionType, 'set'));
-    assert(strcmp(da.dimensions{2}.dimensionType, 'range'));
-
-    da.delete_dimension(1);
-    assert(length(da.dimensions) == 1);
-    assert(strcmp(da.dimensions{1}.dimensionType, 'range'));
-    
-    da.delete_dimension(1);
+    da.delete_dimensions();
     assert(isempty(da.dimensions));
 
     try

tests/TestTag.m

@@ -319,7 +319,7 @@
 function [] = test_retrieve_data( varargin )
     f = nix.File(fullfile(pwd, 'tests', 'test.h5'), nix.FileMode.ReadOnly);
     b = f.blocks{1};
-    tag = b.tags{1};
+    tag = b.open_tag('Arm movement epoch Trial 001');
 
     data = tag.retrieve_data(1);
     assert(~isempty(data));