Merge pull request #1493 from csukuangfj:improve-hdf

modules/fuzzy/samples/fuzzy_filtering.cpp

@@ -11,7 +11,7 @@
  * using "kernel2" with radius 100.
  *
  * Both kernels are created from linear function, using
- * linear interpolation (parametr ft:LINEAR).
+ * linear interpolation (parameter ft:LINEAR).
  */
 
 #include "opencv2/core.hpp"
@@ -26,7 +26,7 @@ int main(void)
     // Input image
     Mat I = imread("input.png");
 
-    // Kernel cretion
+    // Kernel creation
     Mat kernel1, kernel2;
 
     ft::createKernel(ft::LINEAR, 3, kernel1, 3);

modules/hdf/include/opencv2/hdf.hpp

@@ -47,6 +47,9 @@ This module provides storage routines for Hierarchical Data Format objects.
 Hierarchical Data Format version 5
 --------------------------------------------------------
 
+In order to use it, the hdf5 library has to be installed, which
+means cmake should find it using `find_package(HDF5)` .
+
 
   @}
 */

modules/hdf/samples/create_groups.cpp

+// This file is part of OpenCV project.
+// It is subject to the license terms in the LICENSE file found in the top-level directory
+// of this distribution and at http://opencv.org/license.html.
+
+/**
+ * @file create_groups.cpp
+ * @author Fangjun Kuang <csukuangfj dot at gmail dot com>
+ * @date December 2017
+ *
+ * @brief It demonstrates how to create HDF5 groups and subgroups.
+ *
+ * Basic steps:
+ *  1. Use hdf::open to create a HDF5 file
+ *  2. Use HDF5::hlexists to check if a group exists or not
+ *  3. Use HDF5::grcreate to create a group by specifying its name
+ *  4. Use hdf::close to close a HDF5 file after modifying it
+ *
+ */
+
+//! [tutorial]
+#include <iostream>
+
+#include <opencv2/core.hpp>
+#include <opencv2/hdf.hpp>
+
+using namespace cv;
+
+int main()
+{
+    //! [create_group]
+
+    //! [tutorial_create_file]
+    Ptr<hdf::HDF5> h5io = hdf::open("mytest.h5");
+    //! [tutorial_create_file]
+
+    //! [tutorial_create_group]
+    // "/" means the root group, which is always present
+    if (!h5io->hlexists("/Group1"))
+       h5io->grcreate("/Group1");
+    else
+       std::cout << "/Group1 has already been created, skip it.\n";
+    //! [tutorial_create_group]
+
+    //! [tutorial_create_subgroup]
+    // Note that Group1 has been created above, otherwise exception will occur
+    if (!h5io->hlexists("/Group1/SubGroup1"))
+       h5io->grcreate("/Group1/SubGroup1");
+    else
+       std::cout << "/Group1/SubGroup1 has already been created, skip it.\n";
+    //! [tutorial_create_subgroup]
+
+    //! [tutorial_close_file]
+    h5io->close();
+    //! [tutorial_close_file]
+
+    //! [create_group]
+
+    return 0;
+}
+//! [tutorial]

modules/hdf/samples/create_read_write_datasets.cpp

+// This file is part of OpenCV project.
+// It is subject to the license terms in the LICENSE file found in the top-level directory
+// of this distribution and at http://opencv.org/license.html.
+
+/**
+ * @file create_read_write.cpp
+ * @author Fangjun Kuang <csukuangfj dot at gmail dot com>
+ * @date December 2017
+ *
+ * @brief It demonstrates how to create a dataset,  how
+ * to write a cv::Mat to the dataset and how to
+ * read a cv::Mat from it.
+ *
+ */
+
+#ifdef __GNUC__
+#  pragma GCC diagnostic ignored "-Wmissing-declarations"
+#  if defined __clang__ || defined __APPLE__
+#    pragma GCC diagnostic ignored "-Wmissing-prototypes"
+#    pragma GCC diagnostic ignored "-Wextra"
+#  endif
+#endif
+
+//! [tutorial]
+#include <iostream>
+
+#include <opencv2/core.hpp>
+#include <opencv2/hdf.hpp>
+
+using namespace cv;
+
+void write_root_group_single_channel()
+{
+    String filename = "root_group_single_channel.h5";
+    String dataset_name = "/single"; // Note that it is a child of the root group /
+
+    // prepare data
+    Mat data;
+    data = (cv::Mat_<float>(2, 3) << 0, 1, 2, 3, 4, 5, 6);
+
+    //! [tutorial_open_file]
+    Ptr<hdf::HDF5> h5io = hdf::open(filename);
+    //! [tutorial_open_file]
+
+    //! [tutorial_write_root_single_channel]
+    // write data to the given dataset
+    // the dataset "/single" is created automatically, since it is a child of the root
+    h5io->dswrite(data, dataset_name);
+    //! [tutorial_write_root_single_channel]
+
+    //! [tutorial_read_dataset]
+    Mat expected;
+    h5io->dsread(expected, dataset_name);
+    //! [tutorial_read_dataset]
+
+    //! [tutorial_check_result]
+    double diff = norm(data - expected);
+    CV_Assert(abs(diff) < 1e-10);
+    //! [tutorial_check_result]
+
+    h5io->close();
+}
+
+void write_single_channel()
+{
+    String filename = "single_channel.h5";
+    String parent_name = "/data";
+    String dataset_name = parent_name + "/single";
+
+    // prepare data
+    Mat data;
+    data = (cv::Mat_<float>(2, 3) << 0, 1, 2, 3, 4, 5);
+
+    Ptr<hdf::HDF5> h5io = hdf::open(filename);
+
+    //! [tutorial_create_dataset]
+    // first we need to create the parent group
+    if (!h5io->hlexists(parent_name)) h5io->grcreate(parent_name);
+
+    // create the dataset if it not exists
+    if (!h5io->hlexists(dataset_name)) h5io->dscreate(data.rows, data.cols, data.type(), dataset_name);
+    //! [tutorial_create_dataset]
+
+    // the following is the same with the above function write_root_group_single_channel()
+
+    h5io->dswrite(data, dataset_name);
+
+    Mat expected;
+    h5io->dsread(expected, dataset_name);
+
+    double diff = norm(data - expected);
+    CV_Assert(abs(diff) < 1e-10);
+
+    h5io->close();
+}
+
+/*
+ * creating, reading and writing multiple-channel matrices
+ * are the same with single channel matrices
+ */
+void write_multiple_channels()
+{
+    String filename = "two_channels.h5";
+    String parent_name = "/data";
+    String dataset_name = parent_name + "/two_channels";
+
+    // prepare data
+    Mat data(2, 3, CV_32SC2);
+    for (size_t i = 0; i < data.total()*data.channels(); i++)
+        ((int*) data.data)[i] = (int)i;
+
+    Ptr<hdf::HDF5> h5io = hdf::open(filename);
+
+    // first we need to create the parent group
+    if (!h5io->hlexists(parent_name)) h5io->grcreate(parent_name);
+
+    // create the dataset if it not exists
+    if (!h5io->hlexists(dataset_name)) h5io->dscreate(data.rows, data.cols, data.type(), dataset_name);
+
+    // the following is the same with the above function write_root_group_single_channel()
+
+    h5io->dswrite(data, dataset_name);
+
+    Mat expected;
+    h5io->dsread(expected, dataset_name);
+
+    double diff = norm(data - expected);
+    CV_Assert(abs(diff) < 1e-10);
+
+    h5io->close();
+}
+
+int main()
+{
+    write_root_group_single_channel();
+
+    write_single_channel();
+
+    write_multiple_channels();
+
+    return 0;
+}
+//! [tutorial]

modules/hdf/test/test_hdf5.cpp

+// This file is part of OpenCV project.
+// It is subject to the license terms in the LICENSE file found in the top-level directory
+// of this distribution and at http://opencv.org/license.html.
+
+/**
+ * @file test_hdf5.cpp
+ * @author Fangjun Kuang <csukuangfj dot at gmail dot com>
+ * @date December 2017
+ *
+ */
+#include<stdio.h> // for remove()
+
+#include "test_precomp.hpp"
+#include <vector>
+
+using namespace cv;
+
+struct HDF5_Test : public testing::Test
+{
+    virtual void SetUp()
+    {
+        m_filename = "test.h5";
+
+        // 0 1 2
+        // 3 4 5
+        m_single_channel.create(2, 3, CV_32F);
+        for (size_t i = 0; i < m_single_channel.total(); i++)
+        {
+            ((float*)m_single_channel.data)[i] = i;
+        }
+
+        // 0 1 2 3 4  5
+        // 6 7 8 9 10 11
+        m_two_channels.create(2, 3, CV_32SC2);
+        for (size_t i = 0; i < m_two_channels.total()*m_two_channels.channels(); i++)
+        {
+            ((int*)m_two_channels.data)[i] = (int)i;
+        }
+    }
+
+    //! Remove the hdf5 file
+    void reset()
+    {
+        remove(m_filename.c_str());
+    }
+
+    String m_filename; //!< filename for testing
+    Ptr<hdf::HDF5> m_hdf_io; //!< HDF5 file pointer
+    Mat m_single_channel; //!< single channel matrix for test
+    Mat m_two_channels; //!< two-channel matrix for test
+};
+
+TEST_F(HDF5_Test, create_a_single_group)
+{
+    reset();
+
+    String group_name = "parent";
+    m_hdf_io = hdf::open(m_filename);
+    m_hdf_io->grcreate(group_name);
+
+    EXPECT_EQ(m_hdf_io->hlexists(group_name), true);
+    EXPECT_EQ(m_hdf_io->hlexists("child"), false);
+
+    m_hdf_io->close();
+}
+
+
+TEST_F(HDF5_Test, create_a_child_group)
+{
+    reset();
+
+    String parent = "parent";
+    String child = parent + "/child";
+    m_hdf_io = hdf::open(m_filename);
+    m_hdf_io->grcreate(parent);
+    m_hdf_io->grcreate(child);
+
+    EXPECT_EQ(m_hdf_io->hlexists(parent), true);
+    EXPECT_EQ(m_hdf_io->hlexists(child), true);
+
+    m_hdf_io->close();
+}
+
+TEST_F(HDF5_Test, create_dataset)
+{
+    reset();
+
+    String dataset_single_channel = "/single";
+    String dataset_two_channels = "/dual";
+
+    m_hdf_io = hdf::open(m_filename);
+
+    m_hdf_io->dscreate(m_single_channel.rows,
+                       m_single_channel.cols,
+                       m_single_channel.type(),
+                       dataset_single_channel);
+
+    m_hdf_io->dscreate(m_two_channels.rows,
+                       m_two_channels.cols,
+                       m_two_channels.type(),
+                       dataset_two_channels);
+
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true);
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true);
+
+    std::vector<int> dims;
+
+    dims = m_hdf_io->dsgetsize(dataset_single_channel, hdf::HDF5::H5_GETDIMS);
+    EXPECT_EQ(dims.size(), (size_t)2);
+    EXPECT_EQ(dims[0], m_single_channel.rows);
+    EXPECT_EQ(dims[1], m_single_channel.cols);
+
+    dims = m_hdf_io->dsgetsize(dataset_two_channels, hdf::HDF5::H5_GETDIMS);
+    EXPECT_EQ(dims.size(), (size_t)2);
+    EXPECT_EQ(dims[0], m_two_channels.rows);
+    EXPECT_EQ(dims[1], m_two_channels.cols);
+
+    int type;
+    type = m_hdf_io->dsgettype(dataset_single_channel);
+    EXPECT_EQ(type, m_single_channel.type());
+
+    type = m_hdf_io->dsgettype(dataset_two_channels);
+    EXPECT_EQ(type, m_two_channels.type());
+
+    m_hdf_io->close();
+}
+
+
+TEST_F(HDF5_Test, write_read_dataset_1)
+{
+    reset();
+
+    String dataset_single_channel = "/single";
+    String dataset_two_channels = "/dual";
+
+    m_hdf_io = hdf::open(m_filename);
+
+    // since the dataset is under the root group, it is created by dswrite() automatically.
+    m_hdf_io->dswrite(m_single_channel, dataset_single_channel);
+    m_hdf_io->dswrite(m_two_channels, dataset_two_channels);
+
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true);
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true);
+
+    // read single channel matrix
+    Mat single;
+    m_hdf_io->dsread(single, dataset_single_channel);
+    EXPECT_EQ(single.type(), m_single_channel.type());
+    EXPECT_EQ(single.size(), m_single_channel.size());
+    EXPECT_NEAR(norm(single-m_single_channel), 0, 1e-10);
+
+    // read dual channel matrix
+    Mat dual;
+    m_hdf_io->dsread(dual, dataset_two_channels);
+    EXPECT_EQ(dual.type(), m_two_channels.type());
+    EXPECT_EQ(dual.size(), m_two_channels.size());
+    EXPECT_NEAR(norm(dual-m_two_channels), 0, 1e-10);
+
+    m_hdf_io->close();
+}
+
+TEST_F(HDF5_Test, write_read_dataset_2)
+{
+    reset();
+    // create the dataset manually if it is not inside
+    // the root group
+
+    String parent = "/parent";
+
+    String dataset_single_channel = parent + "/single";
+    String dataset_two_channels = parent + "/dual";
+
+    m_hdf_io = hdf::open(m_filename);
+
+    m_hdf_io->grcreate(parent);
+    EXPECT_EQ(m_hdf_io->hlexists(parent), true);
+
+    m_hdf_io->dscreate(m_single_channel.rows,
+                       m_single_channel.cols,
+                       m_single_channel.type(),
+                       dataset_single_channel);
+
+    m_hdf_io->dscreate(m_two_channels.rows,
+                       m_two_channels.cols,
+                       m_two_channels.type(),
+                       dataset_two_channels);
+
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true);
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true);
+
+    m_hdf_io->dswrite(m_single_channel, dataset_single_channel);
+    m_hdf_io->dswrite(m_two_channels, dataset_two_channels);
+
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true);
+    EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true);
+
+    // read single channel matrix
+    Mat single;
+    m_hdf_io->dsread(single, dataset_single_channel);
+    EXPECT_EQ(single.type(), m_single_channel.type());
+    EXPECT_EQ(single.size(), m_single_channel.size());
+    EXPECT_NEAR(norm(single-m_single_channel), 0, 1e-10);
+
+    // read dual channel matrix
+    Mat dual;
+    m_hdf_io->dsread(dual, dataset_two_channels);
+    EXPECT_EQ(dual.type(), m_two_channels.type());
+    EXPECT_EQ(dual.size(), m_two_channels.size());
+    EXPECT_NEAR(norm(dual-m_two_channels), 0, 1e-10);
+
+    m_hdf_io->close();
+}

modules/hdf/test/test_main.cpp

+// This file is part of OpenCV project.
+// It is subject to the license terms in the LICENSE file found in the top-level directory
+// of this distribution and at http://opencv.org/license.html.
+
+#include "test_precomp.hpp"
+
+CV_TEST_MAIN("cv")
\ No newline at end of file

modules/hdf/test/test_precomp.hpp

+// This file is part of OpenCV project.
+// It is subject to the license terms in the LICENSE file found in the top-level directory
+// of this distribution and at http://opencv.org/license.html.
+
+#ifdef __GNUC__
+#  pragma GCC diagnostic ignored "-Wmissing-declarations"
+#  if defined __clang__ || defined __APPLE__
+#    pragma GCC diagnostic ignored "-Wmissing-prototypes"
+#    pragma GCC diagnostic ignored "-Wextra"
+#  endif
+#endif
+
+#ifndef __OPENCV_TEST_PRECOMP_HPP__
+#define __OPENCV_TEST_PRECOMP_HPP__
+
+#include "opencv2/ts.hpp"
+#include "opencv2/core.hpp"
+#include "opencv2/hdf.hpp"
+
+#endif

modules/hdf/tutorials/create_groups/how_to_create_groups.markdown

+Creating Groups {#tutorial_hdf_create_groups}
+===============================
+
+Goal
+----
+This tutorial will show you:
+ - How to create a HDF5 file?
+ - How to create a group?
+ - How to check whether a given group exists or not?
+ - How to create a subgroup?
+
+
+Source Code
+----
+
+The following code creates two groups: `Group1` and `SubGroup1`, where
+`SubGroup1` is a child of `Group1`.
+
+You can download the code from [here][1] or find it in the file
+`modules/hdf/samples/create_groups.cpp` of the opencv_contrib source code library.
+
+@snippet samples/create_groups.cpp tutorial
+
+Explanation
+----
+
+First, we create a HDF5 file
+
+@snippet samples/create_groups.cpp tutorial_create_file
+
+If the given file does not exist, it will be created. Otherwise, it is open for read and write.
+
+Next, we create the group `Group1`
+
+@snippet samples/create_groups.cpp tutorial_create_group
+
+Note that we have to check whether `/Group1` exists or not using
+the function `hlexists` before creating it. You can not create
+a group with an existing name. Otherwise, an error will occur.
+
+Then, we create the subgroup named `Subgroup1`. In order to
+indicate that it is a sub group of `Group1`, we have to
+use the group name `/Group1/SubGroup1`:
+
+@snippet samples/create_groups.cpp tutorial_create_subgroup
+
+Note that before creating a subgroup, we have to make sure
+that its parent group exists. Otherwise, an error will occur.
+
+In the end, we have to close the file
+
+@snippet samples/create_groups.cpp tutorial_close_file
+
+Result
+----
+
+There are many tools that can be used to inspect a given HDF file, such
+as HDFView and h5dump. If you are using Ubuntu, you can install
+them with the following commands:
+
+@code
+sudo apt-get install hdf5-tools hdfview
+@endcode
+
+There are also binaries available from the The HDF Group official website <https://support.hdfgroup.org/HDF5/Tutor/tools.html>.
+
+The following figure shows the result visualized with the tool HDFView:
+
+![Figure 1: Results of creating groups and subgroups](pics/create_groups.png)
+
+The output for `h5dump` is:
+
+@code
+$ h5dump mytest.h5
+HDF5 "mytest.h5" {
+GROUP "/" {
+   GROUP "Group1" {
+      GROUP "SubGroup1" {
+      }
+   }
+}
+}
+@endcode
+
+[1]: https://github.com/opencv/opencv_contrib/tree/master/modules/hdf/samples/create_groups.cpp

modules/hdf/tutorials/create_read_write_dataset/create_read_write_dataset.markdown

+Creating, Writing and Reading Datasets {#tutorial_hdf_create_read_write_datasets}
+===============================
+
+Goal
+----
+This tutorial shows you:
+ - How to create a dataset?
+ - How to write a `cv::Mat` to a dataset?
+ - How to read a `cv::Mat` from a dataset?
+
+@note Currently, it supports only reading and writing `cv::Mat` and the matrix should be continuous
+in memory. Supports for other data types have not been implemented yet.
+
+Source Code
+----
+
+The following code demonstrates writing a single channel
+matrix and a two-channel matrix to datasets and then reading them
+back.
+
+You can download the code from [here][1] or find it in the file
+`modules/hdf/samples/create_read_write_datasets.cpp` of the opencv_contrib source code library.
+
+@snippet samples/create_read_write_datasets.cpp tutorial
+
+Explanation
+----
+
+The first step for creating a dataset is to open the file
+
+@snippet samples/create_read_write_datasets.cpp tutorial_open_file
+
+For the function `write_root_group_single_channel()`, since
+the dataset name is `/single`, which is inside the root group, we can use
+
+@snippet samples/create_read_write_datasets.cpp tutorial_write_root_single_channel
+
+to write the data directly to the dataset without the need of creating
+it beforehand. Because it is created inside `HDF5::dswrite()`
+automatically.
+
+@warning This applies only to datasets that reside inside the root group.
+
+Of course, we can create the dataset by ourselves:
+
+@snippet samples/create_read_write_datasets.cpp tutorial_create_dataset
+
+To read data from a dataset, we use
+
+@snippet samples/create_read_write_datasets.cpp tutorial_read_dataset
+
+by specifying the name of the dataset.
+
+We can check that the data read out is exactly the data written before by using
+
+@snippet samples/create_read_write_datasets.cpp tutorial_check_result
+
+Results
+----
+
+Figure 1 shows the result visualized using the tool HDFView for the file
+`root_group_sinle_channel`. The results
+of matrices for datasets that are not the direct children of the root group
+are given in Figure 2 and Figure 3, respectively.
+
+![Figure 1: Result for writing a single channel matrix to a dataset inside the root group](pics/root_group_single_channel.png)
+
+![Figure 2: Result for writing a single channel matrix to a dataset not in the root group](pics/single_channel.png)
+
+![Figure 3: Result for writing a two-channel matrix to a dataset not in the root group](pics/two_channels.png)
+
+
+[1]: https://github.com/opencv/opencv_contrib/tree/master/modules/hdf/samples/create_read_write_datasets.cpp

modules/hdf/tutorials/table_of_content_hdf.markdown

+The Hierarchical Data Format (hdf) I/O {#tutorial_table_of_content_hdf}
+=====================================
+
+Here you will know how to read and write a HDF5 file using OpenCV.
+Currently, only `cv::Mat` is supported.
+
+Note that the HDF5 library has to be installed in your system
+to use this module.
+
+-   @subpage tutorial_hdf_create_groups
+
+    *Compatibility:* \> OpenCV 3.0
+
+    *Author:* Fangjun Kuang
+
+    You will learn how to create groups and subgroups.
+
+-   @subpage tutorial_hdf_create_read_write_datasets
+
+    *Compatibility:* \> OpenCV 3.0
+
+    *Author:* Fangjun Kuang
+
+    You will learn how to create, read and write datasets.