Merge pull request #1493 from csukuangfj:improve-hdf
Alexander Alekhin
7 years ago
commit
f03e415e64
16 changed files with 809 additions and 174 deletions
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// This file is part of OpenCV project.
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// It is subject to the license terms in the LICENSE file found in the top-level directory
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// of this distribution and at http://opencv.org/license.html.
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/**
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* @file create_groups.cpp |
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* @author Fangjun Kuang <csukuangfj dot at gmail dot com> |
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* @date December 2017 |
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* |
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* @brief It demonstrates how to create HDF5 groups and subgroups. |
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* |
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* Basic steps: |
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* 1. Use hdf::open to create a HDF5 file |
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* 2. Use HDF5::hlexists to check if a group exists or not |
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* 3. Use HDF5::grcreate to create a group by specifying its name |
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* 4. Use hdf::close to close a HDF5 file after modifying it |
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* |
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*/ |
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//! [tutorial]
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#include <iostream> |
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#include <opencv2/core.hpp> |
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#include <opencv2/hdf.hpp> |
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using namespace cv; |
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int main() |
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{ |
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//! [create_group]
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//! [tutorial_create_file]
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Ptr<hdf::HDF5> h5io = hdf::open("mytest.h5"); |
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//! [tutorial_create_file]
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//! [tutorial_create_group]
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// "/" means the root group, which is always present
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if (!h5io->hlexists("/Group1")) |
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h5io->grcreate("/Group1"); |
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else |
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std::cout << "/Group1 has already been created, skip it.\n"; |
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//! [tutorial_create_group]
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//! [tutorial_create_subgroup]
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// Note that Group1 has been created above, otherwise exception will occur
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if (!h5io->hlexists("/Group1/SubGroup1")) |
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h5io->grcreate("/Group1/SubGroup1"); |
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else |
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std::cout << "/Group1/SubGroup1 has already been created, skip it.\n"; |
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//! [tutorial_create_subgroup]
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//! [tutorial_close_file]
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h5io->close(); |
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//! [tutorial_close_file]
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//! [create_group]
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return 0; |
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} |
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//! [tutorial]
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// This file is part of OpenCV project.
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// It is subject to the license terms in the LICENSE file found in the top-level directory
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// of this distribution and at http://opencv.org/license.html.
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/**
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* @file create_read_write.cpp |
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* @author Fangjun Kuang <csukuangfj dot at gmail dot com> |
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* @date December 2017 |
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* |
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* @brief It demonstrates how to create a dataset, how |
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* to write a cv::Mat to the dataset and how to |
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* read a cv::Mat from it. |
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* |
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*/ |
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#ifdef __GNUC__ |
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# pragma GCC diagnostic ignored "-Wmissing-declarations" |
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# if defined __clang__ || defined __APPLE__ |
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# pragma GCC diagnostic ignored "-Wmissing-prototypes" |
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# pragma GCC diagnostic ignored "-Wextra" |
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# endif |
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#endif |
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//! [tutorial]
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#include <iostream> |
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#include <opencv2/core.hpp> |
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#include <opencv2/hdf.hpp> |
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using namespace cv; |
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void write_root_group_single_channel() |
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{ |
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String filename = "root_group_single_channel.h5"; |
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String dataset_name = "/single"; // Note that it is a child of the root group /
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// prepare data
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Mat data; |
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data = (cv::Mat_<float>(2, 3) << 0, 1, 2, 3, 4, 5, 6); |
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//! [tutorial_open_file]
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Ptr<hdf::HDF5> h5io = hdf::open(filename); |
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//! [tutorial_open_file]
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//! [tutorial_write_root_single_channel]
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// write data to the given dataset
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// the dataset "/single" is created automatically, since it is a child of the root
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h5io->dswrite(data, dataset_name); |
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//! [tutorial_write_root_single_channel]
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//! [tutorial_read_dataset]
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Mat expected; |
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h5io->dsread(expected, dataset_name); |
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//! [tutorial_read_dataset]
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//! [tutorial_check_result]
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double diff = norm(data - expected); |
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CV_Assert(abs(diff) < 1e-10); |
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//! [tutorial_check_result]
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h5io->close(); |
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} |
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void write_single_channel() |
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{ |
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String filename = "single_channel.h5"; |
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String parent_name = "/data"; |
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String dataset_name = parent_name + "/single"; |
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// prepare data
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Mat data; |
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data = (cv::Mat_<float>(2, 3) << 0, 1, 2, 3, 4, 5); |
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Ptr<hdf::HDF5> h5io = hdf::open(filename); |
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//! [tutorial_create_dataset]
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// first we need to create the parent group
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if (!h5io->hlexists(parent_name)) h5io->grcreate(parent_name); |
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// create the dataset if it not exists
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if (!h5io->hlexists(dataset_name)) h5io->dscreate(data.rows, data.cols, data.type(), dataset_name); |
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//! [tutorial_create_dataset]
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// the following is the same with the above function write_root_group_single_channel()
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h5io->dswrite(data, dataset_name); |
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Mat expected; |
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h5io->dsread(expected, dataset_name); |
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double diff = norm(data - expected); |
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CV_Assert(abs(diff) < 1e-10); |
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h5io->close(); |
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} |
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/*
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* creating, reading and writing multiple-channel matrices |
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* are the same with single channel matrices |
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*/ |
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void write_multiple_channels() |
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{ |
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String filename = "two_channels.h5"; |
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String parent_name = "/data"; |
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String dataset_name = parent_name + "/two_channels"; |
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// prepare data
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Mat data(2, 3, CV_32SC2); |
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for (size_t i = 0; i < data.total()*data.channels(); i++) |
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((int*) data.data)[i] = (int)i; |
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Ptr<hdf::HDF5> h5io = hdf::open(filename); |
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// first we need to create the parent group
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if (!h5io->hlexists(parent_name)) h5io->grcreate(parent_name); |
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// create the dataset if it not exists
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if (!h5io->hlexists(dataset_name)) h5io->dscreate(data.rows, data.cols, data.type(), dataset_name); |
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// the following is the same with the above function write_root_group_single_channel()
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h5io->dswrite(data, dataset_name); |
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Mat expected; |
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h5io->dsread(expected, dataset_name); |
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double diff = norm(data - expected); |
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CV_Assert(abs(diff) < 1e-10); |
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h5io->close(); |
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} |
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int main() |
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{ |
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write_root_group_single_channel(); |
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write_single_channel(); |
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write_multiple_channels(); |
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return 0; |
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} |
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//! [tutorial]
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@ -0,0 +1,212 @@ |
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// This file is part of OpenCV project.
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// It is subject to the license terms in the LICENSE file found in the top-level directory
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// of this distribution and at http://opencv.org/license.html.
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/**
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* @file test_hdf5.cpp |
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* @author Fangjun Kuang <csukuangfj dot at gmail dot com> |
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* @date December 2017 |
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* |
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*/ |
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#include<stdio.h> // for remove() |
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#include "test_precomp.hpp" |
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#include <vector> |
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using namespace cv; |
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struct HDF5_Test : public testing::Test |
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{ |
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virtual void SetUp() |
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{ |
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m_filename = "test.h5"; |
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// 0 1 2
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// 3 4 5
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m_single_channel.create(2, 3, CV_32F); |
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for (size_t i = 0; i < m_single_channel.total(); i++) |
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{ |
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((float*)m_single_channel.data)[i] = i; |
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} |
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// 0 1 2 3 4 5
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// 6 7 8 9 10 11
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m_two_channels.create(2, 3, CV_32SC2); |
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for (size_t i = 0; i < m_two_channels.total()*m_two_channels.channels(); i++) |
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{ |
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((int*)m_two_channels.data)[i] = (int)i; |
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} |
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} |
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//! Remove the hdf5 file
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void reset() |
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{ |
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remove(m_filename.c_str()); |
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} |
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String m_filename; //!< filename for testing
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Ptr<hdf::HDF5> m_hdf_io; //!< HDF5 file pointer
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Mat m_single_channel; //!< single channel matrix for test
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Mat m_two_channels; //!< two-channel matrix for test
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}; |
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TEST_F(HDF5_Test, create_a_single_group) |
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{ |
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reset(); |
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String group_name = "parent"; |
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m_hdf_io = hdf::open(m_filename); |
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m_hdf_io->grcreate(group_name); |
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EXPECT_EQ(m_hdf_io->hlexists(group_name), true); |
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EXPECT_EQ(m_hdf_io->hlexists("child"), false); |
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m_hdf_io->close(); |
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} |
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TEST_F(HDF5_Test, create_a_child_group) |
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{ |
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reset(); |
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String parent = "parent"; |
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String child = parent + "/child"; |
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m_hdf_io = hdf::open(m_filename); |
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m_hdf_io->grcreate(parent); |
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m_hdf_io->grcreate(child); |
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EXPECT_EQ(m_hdf_io->hlexists(parent), true); |
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EXPECT_EQ(m_hdf_io->hlexists(child), true); |
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m_hdf_io->close(); |
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} |
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TEST_F(HDF5_Test, create_dataset) |
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{ |
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reset(); |
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String dataset_single_channel = "/single"; |
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String dataset_two_channels = "/dual"; |
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m_hdf_io = hdf::open(m_filename); |
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m_hdf_io->dscreate(m_single_channel.rows, |
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m_single_channel.cols, |
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m_single_channel.type(), |
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dataset_single_channel); |
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m_hdf_io->dscreate(m_two_channels.rows, |
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m_two_channels.cols, |
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m_two_channels.type(), |
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dataset_two_channels); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true); |
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std::vector<int> dims; |
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dims = m_hdf_io->dsgetsize(dataset_single_channel, hdf::HDF5::H5_GETDIMS); |
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EXPECT_EQ(dims.size(), (size_t)2); |
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EXPECT_EQ(dims[0], m_single_channel.rows); |
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EXPECT_EQ(dims[1], m_single_channel.cols); |
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dims = m_hdf_io->dsgetsize(dataset_two_channels, hdf::HDF5::H5_GETDIMS); |
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EXPECT_EQ(dims.size(), (size_t)2); |
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EXPECT_EQ(dims[0], m_two_channels.rows); |
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EXPECT_EQ(dims[1], m_two_channels.cols); |
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int type; |
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type = m_hdf_io->dsgettype(dataset_single_channel); |
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EXPECT_EQ(type, m_single_channel.type()); |
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type = m_hdf_io->dsgettype(dataset_two_channels); |
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EXPECT_EQ(type, m_two_channels.type()); |
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m_hdf_io->close(); |
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} |
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TEST_F(HDF5_Test, write_read_dataset_1) |
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{ |
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reset(); |
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String dataset_single_channel = "/single"; |
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String dataset_two_channels = "/dual"; |
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m_hdf_io = hdf::open(m_filename); |
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// since the dataset is under the root group, it is created by dswrite() automatically.
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m_hdf_io->dswrite(m_single_channel, dataset_single_channel); |
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m_hdf_io->dswrite(m_two_channels, dataset_two_channels); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true); |
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// read single channel matrix
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Mat single; |
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m_hdf_io->dsread(single, dataset_single_channel); |
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EXPECT_EQ(single.type(), m_single_channel.type()); |
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EXPECT_EQ(single.size(), m_single_channel.size()); |
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EXPECT_NEAR(norm(single-m_single_channel), 0, 1e-10); |
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// read dual channel matrix
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Mat dual; |
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m_hdf_io->dsread(dual, dataset_two_channels); |
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EXPECT_EQ(dual.type(), m_two_channels.type()); |
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EXPECT_EQ(dual.size(), m_two_channels.size()); |
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EXPECT_NEAR(norm(dual-m_two_channels), 0, 1e-10); |
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m_hdf_io->close(); |
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} |
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TEST_F(HDF5_Test, write_read_dataset_2) |
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{ |
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reset(); |
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// create the dataset manually if it is not inside
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// the root group
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String parent = "/parent"; |
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String dataset_single_channel = parent + "/single"; |
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String dataset_two_channels = parent + "/dual"; |
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m_hdf_io = hdf::open(m_filename); |
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m_hdf_io->grcreate(parent); |
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EXPECT_EQ(m_hdf_io->hlexists(parent), true); |
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m_hdf_io->dscreate(m_single_channel.rows, |
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m_single_channel.cols, |
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m_single_channel.type(), |
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dataset_single_channel); |
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m_hdf_io->dscreate(m_two_channels.rows, |
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m_two_channels.cols, |
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m_two_channels.type(), |
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dataset_two_channels); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true); |
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m_hdf_io->dswrite(m_single_channel, dataset_single_channel); |
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m_hdf_io->dswrite(m_two_channels, dataset_two_channels); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_single_channel), true); |
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EXPECT_EQ(m_hdf_io->hlexists(dataset_two_channels), true); |
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// read single channel matrix
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Mat single; |
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m_hdf_io->dsread(single, dataset_single_channel); |
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EXPECT_EQ(single.type(), m_single_channel.type()); |
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EXPECT_EQ(single.size(), m_single_channel.size()); |
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EXPECT_NEAR(norm(single-m_single_channel), 0, 1e-10); |
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// read dual channel matrix
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Mat dual; |
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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(); |
||||||
|
} |
||||||
@ -0,0 +1,7 @@ |
|||||||
|
// 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") |
||||||
@ -0,0 +1,20 @@ |
|||||||
|
// 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 |
||||||
@ -0,0 +1,85 @@ |
|||||||
|
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: |
||||||
|
|
||||||
|
 |
||||||
|
|
||||||
|
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 |
||||||
@ -0,0 +1,73 @@ |
|||||||
|
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. |
||||||
|
|
||||||
|
 |
||||||
|
|
||||||
|
 |
||||||
|
|
||||||
|
 |
||||||
|
|
||||||
|
|
||||||
|
[1]: https://github.com/opencv/opencv_contrib/tree/master/modules/hdf/samples/create_read_write_datasets.cpp |
||||||
@ -0,0 +1,24 @@ |
|||||||
|
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. |
||||||
Loading…
Reference in new issue