latest from coda-oss and nitro

externals/coda-oss/UnitTest/pch.h

@@ -46,9 +46,12 @@
 #include <future>
 #include <cassert>
 #include <tuple>
+#include <complex>
+#include <stdexcept>
 
 #include "CppUnitTest.h"
 
+#include "coda_oss/span.h"
 #include "gsl/gsl.h"
 #include "import/sys.h"
 #include "import/math.h"
@@ -58,6 +61,7 @@
 #include "import/mem.h"
 #include <mem/SharedPtr.h>
 #include <mem/AutoPtr.h>
+#include <mem/ComplexView.h>
 #include "import/cli.h"
 #include "polygon/DrawPolygon.h"
 #include "polygon/PolygonMask.h"

externals/coda-oss/modules/c++/coda-oss-lite.vcxproj

@@ -116,6 +116,7 @@
     <ClInclude Include="mem\include\mem\Align.h" />
     <ClInclude Include="mem\include\mem\AutoPtr.h" />
     <ClInclude Include="mem\include\mem\BufferView.h" />
+    <ClInclude Include="mem\include\mem\ComplexView.h" />
     <ClInclude Include="mem\include\mem\ScopedAlignedArray.h" />
     <ClInclude Include="mem\include\mem\ScopedArray.h" />
     <ClInclude Include="mem\include\mem\ScopedCloneablePtr.h" />

externals/coda-oss/modules/c++/coda-oss-lite.vcxproj.filters

@@ -720,6 +720,9 @@
     <ClInclude Include="mem\include\mem\AutoPtr.h">
       <Filter>mem</Filter>
     </ClInclude>
+    <ClInclude Include="mem\include\mem\ComplexView.h">
+      <Filter>mem</Filter>
+    </ClInclude>
   </ItemGroup>
   <ItemGroup>
     <ClCompile Include="pch.cpp" />

externals/coda-oss/modules/c++/hdf5.lite/include/hdf5/lite/Read.h

@@ -45,6 +45,7 @@ namespace lite
 {
 
 CODA_OSS_API types::RowCol<size_t> readFile(coda_oss::filesystem::path, std::string datasetName, std::vector<double>&);
+CODA_OSS_API types::RowCol<size_t> readFile(coda_oss::filesystem::path, std::string datasetName, std::vector<float>&);
 
 }
 }

externals/coda-oss/modules/c++/hdf5.lite/source/Info.cpp

@@ -146,7 +146,7 @@ static hdf5::lite::GroupInfo groupInfo_(coda_oss::filesystem::path filename, std
 }
 hdf5::lite::GroupInfo hdf5::lite::groupInfo(coda_oss::filesystem::path filename, std::string loc)
 {
-    return details::try_catch_H5Exceptions(groupInfo_, filename, loc);
+    return details::try_catch_H5Exceptions(groupInfo_, __FILE__, __LINE__, filename, loc);
 }
 hdf5::lite::FileInfo hdf5::lite::fileInfo(coda_oss::filesystem::path filename)
 {
@@ -208,5 +208,5 @@ static hdf5::lite::DatasetInfo datasetInfo_(coda_oss::filesystem::path filename,
 }
 hdf5::lite::DatasetInfo hdf5::lite::datasetInfo(coda_oss::filesystem::path filename, std::string loc)
 {
-    return details::try_catch_H5Exceptions(datasetInfo_, filename, loc);
+    return details::try_catch_H5Exceptions(datasetInfo_, __FILE__, __LINE__, filename, loc);
 }

externals/coda-oss/modules/c++/hdf5.lite/source/Read.cpp

@@ -51,15 +51,14 @@ inline types::RowCol<size_t> readDataset_(const H5::DataSet& dataset, std::vecto
     static_assert(sizeof(float) * 8 == 32, "'float' should be 32-bits"); // IEEE_F32LE
     return readDatasetT(dataset, H5T_FLOAT, H5::PredType::IEEE_F32LE, result);
 }
-
 inline types::RowCol<size_t> readDataset_(const H5::DataSet& dataset, std::vector<double>& result)
 {
     static_assert(sizeof(double) * 8 == 64, "'double' should be 64-bits"); // IEEE_F64LE
     return readDatasetT(dataset, H5T_FLOAT, H5::PredType::IEEE_F64LE, result);
 }
-
+template<typename T>
 static types::RowCol<size_t> readFile_(const coda_oss::filesystem::path& fileName, const std::string& datasetName,
-                                std::vector<double>& result)
+                                std::vector<T>& result)
 {
     /*
      * Open the specified file and the specified dataset in the file.
@@ -68,8 +67,14 @@ static types::RowCol<size_t> readFile_(const coda_oss::filesystem::path& fileNam
     const auto dataset = file.openDataSet(datasetName);
     return readDataset_(dataset, result);
 }
+
 types::RowCol<size_t> hdf5::lite::readFile(coda_oss::filesystem::path fileName, std::string datasetName,
     std::vector<double>& result)
 {
-    return details::try_catch_H5Exceptions(readFile_, fileName, datasetName, result); 
+    return details::try_catch_H5Exceptions(readFile_<double>, __FILE__, __LINE__, fileName, datasetName, result); 
+}
+types::RowCol<size_t> hdf5::lite::readFile(coda_oss::filesystem::path fileName, std::string datasetName,
+    std::vector<float>& result)
+{
+    return details::try_catch_H5Exceptions(readFile_<float>, __FILE__, __LINE__, fileName, datasetName, result); 
 }

externals/coda-oss/modules/c++/hdf5.lite/source/hdf5.lite.cpp

@@ -22,7 +22,12 @@
 
 #include "hdf5.lite.h"
 
-void hdf5::lite::details::try_catch_H5Exceptions_(std::function<void(void*)> f, void* context)
+inline except::Context make_Context(const H5::Exception& error,  const char* file, int line)
+{
+    return except::Context(error.getDetailMsg(), file, line, error.getFuncName());
+}
+
+void hdf5::lite::details::try_catch_H5Exceptions_(std::function<void(void*)> f, const char* file, int line, void* context)
 {
     try
     {
@@ -34,28 +39,28 @@ void hdf5::lite::details::try_catch_H5Exceptions_(std::function<void(void*)> f,
 
         f(context);
     }
+
     // catch failure caused by the H5File operations
     catch (const H5::FileIException& error)
     {
-        const except::Context ctx(error.getDetailMsg(), __FILE__, __LINE__, error.getFuncName());
-        throw except::IOException(ctx);
+        throw except::IOException(make_Context(error, file, line));
     }
+
     // catch failure caused by the DataSet operations
     catch (const H5::DataSetIException& error)
     {
-        const except::Context ctx(error.getDetailMsg(), __FILE__, __LINE__, error.getFuncName());
-        throw hdf5::lite::DataSetException(ctx);
+        throw hdf5::lite::DataSetException(make_Context(error, file, line));
     }
+
     // catch failure caused by the DataSpace operations
     catch (const H5::DataSpaceIException& error)
     {
-        const except::Context ctx(error.getDetailMsg(), __FILE__, __LINE__, error.getFuncName());
-        throw hdf5::lite::DataSpaceException(ctx);
+        throw hdf5::lite::DataSpaceException(make_Context(error, file, line));
     }
+
     // catch failure caused by the DataType operations
     catch (const H5::DataTypeIException& error)
     {
-        const except::Context ctx(error.getDetailMsg(), __FILE__, __LINE__, error.getFuncName());
-        throw hdf5::lite::DataTypeException(ctx);
+        throw hdf5::lite::DataTypeException(make_Context(error, file, line));
     }
 }

externals/coda-oss/modules/c++/hdf5.lite/source/hdf5.lite.h

@@ -39,21 +39,21 @@ namespace lite
 namespace details
 {
 // Call the given function, converting H5 exceptions to our own.
-void try_catch_H5Exceptions_(std::function<void(void*)> f, void* context = nullptr);
+void try_catch_H5Exceptions_(std::function<void(void*)> f, const char* file, int line, void* context = nullptr);
 
 template <typename R, typename... Args>
 R return_type_of(R (*)(Args...));
 
 template<typename TFunc, typename ...TArgs>
-auto try_catch_H5Exceptions(TFunc f, TArgs&&... args)
+auto try_catch_H5Exceptions(TFunc f, const char* file, int line, TArgs&&... args)
 {
     // Figure out return type by "calling" the function at compile-time
     // https://stackoverflow.com/a/53673522/8877
     decltype(return_type_of(f)) retval; 
 
     // "Hide" the arguments inside of a lambda
     auto call_f = [&](void*) { retval = f(std::forward<TArgs>(args)...); };
-    details::try_catch_H5Exceptions_(call_f);
+    details::try_catch_H5Exceptions_(call_f, file, line, &retval /*context*/);
     return retval;
 }
 

externals/coda-oss/modules/c++/hdf5.lite/unittests/create_123_barfoo_catdog_cx.m

@@ -0,0 +1,55 @@
+% https://www.mathworks.com/help/matlab/ref/h5write.html
+mydata = rand(10, 1);
+
+h5create('123_barfoo_catdog_cx.h5', '/1/bar/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/bar/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/bar/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/bar/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/bar/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/bar/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/bar/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/bar/dog/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/foo/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/foo/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/foo/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/foo/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/foo/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/foo/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/1/foo/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/1/foo/dog/r', mydata)
+
+h5create('123_barfoo_catdog_cx.h5', '/2/bar/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/bar/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/bar/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/bar/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/bar/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/bar/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/bar/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/bar/dog/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/foo/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/foo/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/foo/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/foo/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/foo/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/foo/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/2/foo/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/2/foo/dog/r', mydata)
+
+h5create('123_barfoo_catdog_cx.h5', '/3/bar/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/bar/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/bar/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/bar/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/bar/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/bar/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/bar/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/bar/dog/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/foo/cat/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/foo/cat/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/foo/cat/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/foo/cat/r', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/foo/dog/i', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/foo/dog/i', mydata)
+h5create('123_barfoo_catdog_cx.h5', '/3/foo/dog/r', [10, 1])
+h5write('123_barfoo_catdog_cx.h5', '/3/foo/dog/r', mydata)
+
+h5disp('123_barfoo_catdog_cx.h5')

externals/coda-oss/modules/c++/hdf5.lite/unittests/test_hdf5info.cpp

@@ -34,6 +34,7 @@ static std::filesystem::path find_unittest_file(const std::filesystem::path& nam
     static const auto unittests = std::filesystem::path("modules") / "c++" / "hdf5.lite" / "unittests";
     return sys::test::findGITModuleFile("coda-oss", unittests, name);
 }
+
 TEST_CASE(test_hdf5Info_IOException)
 {
     static const std::filesystem::path path = "does not exist . h5";
@@ -55,6 +56,16 @@ TEST_CASE(test_hdf5FileInfo)
     static const auto path = find_unittest_file("example.h5");
 
     // https://www.mathworks.com/help/matlab/ref/h5info.html
+    /*
+    info = struct with fields:
+          Filename: '/mathworks/devel/bat/Bdoc22b/build/matlab/toolbox/matlab/demos/example.h5'
+              Name: '/'
+            Groups: [4x1 struct]
+          Datasets: []
+         Datatypes: []
+             Links: []
+        Attributes: [2x1 struct]
+    */
     const auto info = hdf5::lite::fileInfo(path);
     TEST_ASSERT_EQ(path.string(), info.filename);
     TEST_ASSERT_EQ("/", info.name);
@@ -71,7 +82,16 @@ TEST_CASE(test_hdf5GroupInfo)
 
     // https://www.mathworks.com/help/matlab/ref/h5info.html
     const auto info = hdf5::lite::groupInfo(path, "/g4");
-
+    /*
+    info = struct with fields:
+      Filename: '/mathworks/devel/bat/Bdoc22b/build/matlab/toolbox/matlab/demos/example.h5'
+          Name: '/g4'
+        Groups: []
+      Datasets: [4x1 struct]
+     Datatypes: []
+         Links: []
+    Attributes: []
+    */
     TEST_ASSERT_EQ(path.string(), info.filename);
     TEST_ASSERT_EQ("/g4", info.name);
     TEST_ASSERT_TRUE(info.groups.empty());
@@ -87,21 +107,104 @@ TEST_CASE(test_hdf5DatasetInfo)
 
     // https://www.mathworks.com/help/matlab/ref/h5info.html
     const auto info = hdf5::lite::datasetInfo(path, "/g4/time");
-
+    /*
+    info = struct with fields:
+      Filename: '/mathworks/devel/bat/Bdoc22b/build/matlab/toolbox/matlab/demos/example.h5'
+          Name: 'time'
+      Datatype: [1x1 struct]
+     Dataspace: [1x1 struct]
+     ChunkSize: 10
+     FillValue: 0
+       Filters: []
+    Attributes: [2x1 struct]    
+    */
     TEST_ASSERT_EQ(path.string(), info.filename);
     TEST_ASSERT_EQ("time", info.name);
     TEST_ASSERT(info.datatype.h5Class == hdf5::lite::Class::Float);
     //TEST_ASSERT(info.dataspace == hdf5::lite::Class::Float);
-    // TEST_ASSERT(info.chunkSize == hdf5::lite::Class::Float);
-    // TEST_ASSERT(info.fillValue == hdf5::lite::Class::Float);
+    //TEST_ASSERT_EQ(info.chunkSize, 10);
+    //TEST_ASSERT_EQ(info.fillValue, 0);
     //TEST_ASSERT_TRUE(info.filters.empty());
     //TEST_ASSERT_EQ(info.attributes.size(), 2);
 }
 
+static void read_complex(const std::string& testName,
+    const std::filesystem::path& path, const std::string& datasetPath)
+{
+    const auto i_info = hdf5::lite::datasetInfo(path, datasetPath + "/i");
+    TEST_ASSERT(i_info.datatype.h5Class == hdf5::lite::Class::Float);
+
+    const auto r_info = hdf5::lite::datasetInfo(path, datasetPath + "/r");
+    TEST_ASSERT(r_info.datatype.h5Class == hdf5::lite::Class::Float);
+}
+
+TEST_CASE(test_hdf5Info_nested)
+{
+    /*
+    Group '/' 
+    Group '/1' 
+        Group '/1/bar' 
+            Group '/1/bar/cat' 
+                Dataset 'i' 
+                    Size:  10x1
+                    MaxSize:  10x1
+                    Datatype:   H5T_IEEE_F64LE (double)
+                    ChunkSize:  []
+                    Filters:  none
+                    FillValue:  0.000000
+    */
+
+    // outer groups: 1, 2, 3
+    // sub groups: bar, foo
+    // sub-sub groups: cat, dog
+    // data: i (float array), r (float array)
+    static const auto path = find_unittest_file("123_barfoo_catdog_cx.h5");
+
+    // https://www.mathworks.com/help/matlab/ref/h5info.html
+    const auto info = hdf5::lite::fileInfo(path);
+    TEST_ASSERT_EQ(path.string(), info.filename);
+    TEST_ASSERT_EQ("/", info.name);
+    TEST_ASSERT_TRUE(info.datasets.empty());
+    TEST_ASSERT_TRUE(info.datatypes.empty());
+
+    const std::vector<std::string> expectedOuterGroupNames{"1" , "2", "3"};
+    TEST_ASSERT_EQ(info.groups.size(), expectedOuterGroupNames.size());
+    for (size_t outer = 0; outer < info.groups.size(); outer++)
+    {
+        const auto groupName = info.groups[outer].name;
+        TEST_ASSERT_EQ(groupName, expectedOuterGroupNames[outer]);
+
+        const auto subGroupInfo = hdf5::lite::groupInfo(path, "/" + groupName);
+
+        const std::vector<std::string> expectedSubGroupNames{"bar", "foo"};
+        TEST_ASSERT_EQ(subGroupInfo.groups.size(), expectedSubGroupNames.size());
+        for (size_t sub = 0; sub < subGroupInfo.groups.size(); sub++)
+        {
+            const auto subGroupName = subGroupInfo.groups[sub].name;
+            TEST_ASSERT_EQ(subGroupName, expectedSubGroupNames[sub]);
+
+            const auto subSubGroupInfo = hdf5::lite::groupInfo(path, "/" + groupName + "/" + subGroupName);
+
+            const std::vector<std::string> expectedSubSubGroupNames{"cat", "dog"};
+            TEST_ASSERT_EQ(subSubGroupInfo.groups.size(), expectedSubSubGroupNames.size());
+            for (size_t subsub = 0; subsub < subSubGroupInfo.groups.size(); subsub++)
+            {
+                const auto subSubGroupName = subSubGroupInfo.groups[subsub].name;
+                TEST_ASSERT_EQ(subSubGroupName, expectedSubSubGroupNames[subsub]);
+
+                const auto datasetPath =  "/" + groupName + "/" + subGroupName + "/" + subSubGroupName;
+                read_complex(testName, path, datasetPath);
+            }
+        }
+    }
+}
+
 TEST_MAIN(
     TEST_CHECK(test_hdf5Info_IOException);
 
     TEST_CHECK(test_hdf5FileInfo);
     TEST_CHECK(test_hdf5GroupInfo);
     TEST_CHECK(test_hdf5DatasetInfo);
+
+    TEST_CHECK(test_hdf5Info_nested);
 )