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comparison OrthancFramework/Sources/Images/NumpyWriter.cpp @ 4834:bec432ee1094

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download of numpy arrays from the REST API
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 26 Nov 2021 19:03:32 +0100
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children f3f93695d6df
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4833:970092a67897 4834:bec432ee1094
1 /**
2 * Orthanc - A Lightweight, RESTful DICOM Store
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
4 * Department, University Hospital of Liege, Belgium
5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
7 *
8 * This program is free software: you can redistribute it and/or
9 * modify it under the terms of the GNU Lesser General Public License
10 * as published by the Free Software Foundation, either version 3 of
11 * the License, or (at your option) any later version.
12 *
13 * This program is distributed in the hope that it will be useful, but
14 * WITHOUT ANY WARRANTY; without even the implied warranty of
15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
16 * Lesser General Public License for more details.
17 *
18 * You should have received a copy of the GNU Lesser General Public
19 * License along with this program. If not, see
20 * <http://www.gnu.org/licenses/>.
21 **/
22
23
24 #include "NumpyWriter.h"
25
26 #if ORTHANC_ENABLE_ZLIB == 1
27 # include "../Compression/ZipWriter.h"
28 #endif
29
30 #if ORTHANC_SANDBOXED == 0
31 # include "../SystemToolbox.h"
32 #endif
33
34 #include "../OrthancException.h"
35 #include "../Toolbox.h"
36
37 #include <boost/lexical_cast.hpp>
38
39 namespace Orthanc
40 {
41 void NumpyWriter::WriteHeader(ChunkedBuffer& target,
42 unsigned int depth,
43 unsigned int width,
44 unsigned int height,
45 PixelFormat format)
46 {
47 // https://numpy.org/devdocs/reference/generated/numpy.lib.format.html
48 static const unsigned char VERSION[] = {
49 0x93, 'N', 'U', 'M', 'P', 'Y',
50 0x01 /* major version: 1 */,
51 0x00 /* minor version: 0 */
52 };
53
54 std::string datatype;
55
56 switch (Toolbox::DetectEndianness())
57 {
58 case Endianness_Little:
59 datatype = "<";
60 break;
61
62 case Endianness_Big:
63 datatype = ">";
64 break;
65
66 default:
67 throw OrthancException(ErrorCode_InternalError);
68 }
69
70 unsigned int channels;
71
72 switch (format)
73 {
74 case PixelFormat_Grayscale8:
75 datatype += "u1";
76 channels = 1;
77 break;
78
79 case PixelFormat_Grayscale16:
80 datatype += "u2";
81 channels = 1;
82 break;
83
84 case PixelFormat_SignedGrayscale16:
85 datatype += "s2";
86 channels = 1;
87 break;
88
89 case PixelFormat_RGB24:
90 datatype += "u1";
91 channels = 3;
92 break;
93
94 case PixelFormat_Float32:
95 datatype += "f4";
96 channels = 1;
97 break;
98
99 default:
100 throw OrthancException(ErrorCode_NotImplemented);
101 }
102
103 std::string depthString;
104 if (depth != 0)
105 {
106 depthString = boost::lexical_cast<std::string>(depth) + ", ";
107 }
108
109 const std::string info = ("{'descr': '" + datatype + "', 'fortran_order': False, " +
110 "'shape': (" + depthString + boost::lexical_cast<std::string>(height) +
111 "," + boost::lexical_cast<std::string>(width) +
112 "," + boost::lexical_cast<std::string>(channels) + "), }");
113
114 const uint16_t minimumLength = sizeof(VERSION) + sizeof(uint16_t) + info.size() + 1 /* trailing '\n' */;
115
116 // The length of the header must be evenly divisible by 64. This
117 // loop could be optimized by a "ceil()" operation, but we keep
118 // the code as simple as possible
119 uint16_t length = 64;
120 while (length < minimumLength)
121 {
122 length += 64;
123 }
124
125 uint16_t countZeros = length - minimumLength;
126 uint16_t headerLength = info.size() + countZeros + 1 /* trailing '\n' */;
127 uint8_t highByte = headerLength / 256;
128 uint8_t lowByte = headerLength % 256;
129
130 target.AddChunk(VERSION, sizeof(VERSION));
131 target.AddChunk(&lowByte, 1);
132 target.AddChunk(&highByte, 1);
133 target.AddChunk(info);
134 target.AddChunk(std::string(countZeros, ' '));
135 target.AddChunk("\n");
136 }
137
138
139 void NumpyWriter::WritePixels(ChunkedBuffer& target,
140 const ImageAccessor& image)
141 {
142 size_t rowSize = image.GetBytesPerPixel() * image.GetWidth();
143
144 for (unsigned int y = 0; y < image.GetHeight(); y++)
145 {
146 target.AddChunk(image.GetConstRow(y), rowSize);
147 }
148 }
149
150
151 void NumpyWriter::Finalize(std::string& target,
152 ChunkedBuffer& source,
153 bool compress)
154 {
155 if (compress)
156 {
157 #if ORTHANC_ENABLE_ZLIB == 1
158 // This is the default name of the first array if arrays are
159 // specified as positional arguments in "numpy.savez()"
160 // https://numpy.org/doc/stable/reference/generated/numpy.savez.html
161 const char* ARRAY_NAME = "arr_0";
162
163 std::string uncompressed;
164 source.Flatten(uncompressed);
165
166 const bool isZip64 = (uncompressed.size() >= 1lu * 1024lu * 1024lu * 1024lu);
167
168 ZipWriter writer;
169 writer.SetMemoryOutput(target, isZip64);
170 writer.Open();
171 writer.OpenFile(ARRAY_NAME);
172 writer.Write(uncompressed);
173 writer.Close();
174 #else
175 throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
176 #endif
177 }
178 else
179 {
180 source.Flatten(target);
181 }
182 }
183
184
185 #if ORTHANC_SANDBOXED == 0
186 void NumpyWriter::WriteToFileInternal(const std::string& filename,
187 unsigned int width,
188 unsigned int height,
189 unsigned int pitch,
190 PixelFormat format,
191 const void* buffer)
192 {
193 std::string content;
194 WriteToMemoryInternal(content, width, height, pitch, format, buffer);
195
196 SystemToolbox::WriteFile(content, filename);
197 }
198 #endif
199
200
201 void NumpyWriter::WriteToMemoryInternal(std::string& content,
202 unsigned int width,
203 unsigned int height,
204 unsigned int pitch,
205 PixelFormat format,
206 const void* buffer)
207 {
208 ChunkedBuffer chunks;
209 WriteHeader(chunks, 0 /* no depth */, width, height, format);
210
211 ImageAccessor image;
212 image.AssignReadOnly(format, width, height, pitch, buffer);
213 WritePixels(chunks, image);
214
215 Finalize(content, chunks, compressed_);
216 }
217
218
219 NumpyWriter::NumpyWriter()
220 {
221 compressed_ = false;
222 }
223
224
225 void NumpyWriter::SetCompressed(bool compressed)
226 {
227 #if ORTHANC_ENABLE_ZLIB == 1
228 compressed_ = compressed;
229 #else
230 if (compressed)
231 {
232 throw OrthancException(ErrorCode_InternalError, "Orthanc was compiled without support for zlib");
233 }
234 #endif
235 }
236 }