1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
|
/************************************************************************
*
* Copyright (C) 2009-2022 IRCAD France
* Copyright (C) 2012-2018 IHU Strasbourg
*
* This file is part of Sight.
*
* Sight is free software: you can redistribute it and/or modify it under
* the terms of the GNU Lesser General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Sight is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with Sight. If not, see <https://www.gnu.org/licenses/>.
*
***********************************************************************/
#include "io/dicom/helper/DicomSeriesDBWriter.hpp"
#include "io/dicom/helper/DicomAnonymizer.hpp"
#include "io/dicom/helper/DicomSeriesWriter.hpp"
#include <core/jobs/Aggregator.hpp>
#include <core/jobs/Job.hpp>
#include <core/jobs/Observer.hpp>
#include <data/DicomSeries.hpp>
#include <data/Series.hpp>
#include <data/SeriesDB.hpp>
#include <io/zip/WriteDirArchive.hpp>
namespace sight::io::dicom
{
namespace helper
{
//------------------------------------------------------------------------------
DicomSeriesDBWriter::DicomSeriesDBWriter(io::base::writer::IObjectWriter::Key key) :
m_aggregator(core::jobs::Aggregator::New("Writing Dicom series"))
{
}
//------------------------------------------------------------------------------
DicomSeriesDBWriter::~DicomSeriesDBWriter()
{
}
//------------------------------------------------------------------------------
std::string DicomSeriesDBWriter::extension() const
{
return "";
}
//------------------------------------------------------------------------------
core::jobs::Aggregator::sptr DicomSeriesDBWriter::getAggregator()
{
return m_aggregator;
}
//------------------------------------------------------------------------------
void DicomSeriesDBWriter::setAnonymizer(const DicomAnonymizer::sptr& anonymizer)
{
m_anonymizer = anonymizer;
}
//------------------------------------------------------------------------------
void DicomSeriesDBWriter::setProducer(std::string producer)
{
m_producer = producer;
}
//------------------------------------------------------------------------------
std::string getSubPath(int index)
{
std::stringstream ss;
ss << std::setfill('0') << std::setw(3) << index;
return ss.str();
}
//------------------------------------------------------------------------------
void DicomSeriesDBWriter::write()
{
data::SeriesDB::csptr seriesDB = this->getConcreteObject();
SIGHT_ASSERT("Unable to retrieve associated SeriesDB", seriesDB);
io::zip::IWriteArchive::sptr writeArchive = io::zip::WriteDirArchive::New(this->getFolder());
const auto nbSeries = seriesDB->getContainer().size();
int processedSeries = 0;
for(data::Series::sptr series : seriesDB->getContainer())
{
const data::DicomSeries::sptr& dicomSeries = data::DicomSeries::dynamicCast(series);
core::jobs::Job::sptr job =
core::jobs::Job::New(
"Write Dicom series",
[&, dicomSeries](core::jobs::Job& runningJob)
{
if(!runningJob.cancelRequested())
{
m_anonymizer->resetIndex();
io::dicom::helper::DicomSeriesWriter::sptr writer = io::dicom::helper::DicomSeriesWriter::New();
writer->setObject(dicomSeries);
writer->setAnonymizer(m_anonymizer);
writer->setOutputArchive(writeArchive, nbSeries > 1 ? getSubPath(processedSeries++) : "");
runningJob.addCancelHook(
[&](core::jobs::IJob& subJob)
{
writer->getJob()->cancel();
});
writer->getJob()->addDoneWorkHook(
[&](core::jobs::IJob& subJob, std::uint64_t oldWork)
{
runningJob.doneWork(subJob.getDoneWorkUnits());
});
try
{
writer->write();
}
catch(std::exception& e)
{
runningJob.log(std::string("Failed to write series :\n") + e.what());
}
catch(...)
{
runningJob.log("An unexpected error occurred while writing series");
}
}
},
core::thread::getDefaultWorker()
);
m_aggregator->addCancelHook(
[&](core::jobs::IJob& subJob)
{
job->cancel();
});
m_aggregator->add(job);
}
auto futureAG = m_aggregator->run();
futureAG.wait();
}
//------------------------------------------------------------------------------
} // namespace helper
} // namespace sight::io::dicom
|
