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/************************************************************************ |
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* |
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* Copyright (C) 2009-2023 IRCAD France |
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* Copyright (C) 2012-2019 IHU Strasbourg |
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* |
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* This file is part of Sight. |
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* |
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* Sight is free software: you can redistribute it and/or modify it under |
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* the terms of the GNU Lesser General Public License as published by |
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* the Free Software Foundation, either version 3 of the License, or |
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* (at your option) any later version. |
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* |
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* Sight is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public |
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* License along with Sight. If not, see <https://www.gnu.org/licenses/>. |
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* |
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***********************************************************************/ |
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// cspell:ignore NOLINT |
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#include "filter/dicom/splitter/tag_value_splitter.hpp" |
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#include "filter/dicom/exceptions/filter_failure.hpp" |
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#include "filter/dicom/registry/macros.hpp" |
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#include <dcmtk/config/osconfig.h> |
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#include <dcmtk/dcmdata/dcdeftag.h> |
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#include <dcmtk/dcmdata/dcfilefo.h> |
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#include <dcmtk/dcmdata/dcistrmb.h> |
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#include <dcmtk/dcmimgle/dcmimage.h> |
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#include <dcmtk/dcmnet/diutil.h> |
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SIGHT_REGISTER_DICOM_FILTER(sight::filter::dicom::splitter::tag_value_splitter); |
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namespace sight::filter::dicom::splitter |
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{ |
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const std::string tag_value_splitter::FILTER_NAME = "Tag value splitter"; |
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const std::string tag_value_splitter::FILTER_DESCRIPTION = |
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"Split instances according to a tag value."; |
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//----------------------------------------------------------------------------- |
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tag_value_splitter::tag_value_splitter() : |
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m_tag(DCM_UndefinedTagKey) |
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{ |
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} |
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//----------------------------------------------------------------------------- |
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tag_value_splitter::~tag_value_splitter() |
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= default; |
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//----------------------------------------------------------------------------- |
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std::string tag_value_splitter::get_name() const |
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{ |
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return tag_value_splitter::FILTER_NAME; |
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} |
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//----------------------------------------------------------------------------- |
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std::string tag_value_splitter::get_description() const |
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{ |
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return tag_value_splitter::FILTER_DESCRIPTION; |
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} |
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//----------------------------------------------------------------------------- |
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bool tag_value_splitter::is_configuration_required() const |
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{ |
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return true; |
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} |
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//----------------------------------------------------------------------------- |
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tag_value_splitter::dicom_series_container_t tag_value_splitter::apply( |
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const data::dicom_series::sptr& _series, |
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const core::log::logger::sptr& _logger |
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) const |
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{ |
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if(m_tag == DCM_UndefinedTagKey) |
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{ |
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const std::string msg = "Unable to split the series, the specified tag is not valid."; |
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throw sight::filter::dicom::exceptions::filter_failure(msg); |
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} |
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dicom_series_container_t result; |
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using instance_container_t = std::vector<core::memory::buffer_object::sptr>; |
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using instance_group_container = std::map<std::string, instance_container_t>; |
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// Create a container to store the groups of instances |
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instance_group_container group_container; |
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OFCondition status; |
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OFString data; |
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for(const auto& item : _series->get_dicom_container()) |
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{ |
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const core::memory::buffer_object::sptr buffer_obj = item.second; |
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const std::size_t buff_size = buffer_obj->size(); |
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core::memory::buffer_object::lock_t lock(buffer_obj); |
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char* buffer = static_cast<char*>(lock.buffer()); |
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DcmInputBufferStream is; |
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is.setBuffer(buffer, offile_off_t(buff_size)); |
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is.setEos(); |
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DcmFileFormat file_format; |
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file_format.transferInit(); |
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if(!file_format.read(is).good()) |
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{ |
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SIGHT_THROW( |
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"Unable to read Dicom file '" << buffer_obj->get_stream_info().fs_file.string() << "' " |
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<< "(slice: '" << item.first << "')" |
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); |
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} |
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file_format.loadAllDataIntoMemory(); |
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file_format.transferEnd(); |
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DcmDataset* dataset = file_format.getDataset(); |
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// Get the value of the instance |
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dataset->findAndGetOFStringArray(m_tag, data); |
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const std::string value = data.c_str(); // NOLINT(readability-redundant-string-cstr) |
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// Add the instance to the group |
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group_container[value].push_back(buffer_obj); |
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} |
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for(const auto& group : group_container) |
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{ |
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// Copy the series |
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data::dicom_series::sptr dicom_series = std::make_shared<data::dicom_series>(); |
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dicom_series->shallow_copy(_series); |
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dicom_series->clear_dicom_container(); |
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std::size_t index = 0; |
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// Add the paths to the series |
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for(const core::memory::buffer_object::sptr& buffer : group.second) |
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{ |
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dicom_series->add_binary(index++, buffer); |
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} |
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// Set number of instances |
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dicom_series->set_number_of_instances(dicom_series->get_dicom_container().size()); |
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result.push_back(dicom_series); |
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} |
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if(result.size() > 1) |
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{ |
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std::stringstream ss; |
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ss << "Series has been split according to the tag value (" |
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<< std::hex << std::setfill('0') << std::setw(4) << m_tag.getGroup() << "," |
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<< std::hex << std::setfill('0') << std::setw(4) << m_tag.getElement() << ")."; |
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_logger->warning(ss.str()); |
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} |
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return result; |
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} |
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} // namespace sight::filter::dicom::splitter |
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