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comparison Plugins/Samples/GdcmDecoding/Plugin.cpp @ 983:80d4f1618b33 plugins

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Sample plugin to replace DCMTK by GDCM when decoding images
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 01 Jul 2014 12:01:58 +0200
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children 0bfdfc0c6b9b
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982:5983e59ac670 983:80d4f1618b33
1 /**
2 * Orthanc - A Lightweight, RESTful DICOM Store
3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
4 * Belgium
5 *
6 * Permission is hereby granted, free of charge, to any person
7 * obtaining a copy of this software and associated documentation
8 * files (the "Software"), to deal in the Software without
9 * restriction, including without limitation the rights to use, copy,
10 * modify, merge, publish, distribute, sublicense, and/or sell copies
11 * of the Software, and to permit persons to whom the Software is
12 * furnished to do so, subject to the following conditions:
13 *
14 * The above copyright notice and this permission notice shall be
15 * included in all copies or substantial portions of the Software.
16 *
17 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
18 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
19 * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
20 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
21 * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
22 * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
23 * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
24 * SOFTWARE.
25 **/
26
27
28 #include <map>
29 #include <string>
30 #include <stdexcept>
31 #include <sstream>
32
33 #include "OrthancContext.h"
34 #include "../../../Core/ImageFormats/ImageProcessing.h"
35
36 #include <gdcmReader.h>
37 #include <gdcmImageReader.h>
38
39
40 static bool GetOrthancPixelFormat(Orthanc::PixelFormat& format,
41 const gdcm::Image& image)
42 {
43 if (image.GetPlanarConfiguration() != 0 &&
44 image.GetPixelFormat().GetSamplesPerPixel() != 1)
45 {
46 OrthancContext::GetInstance().LogError("Planar configurations are not supported");
47 return false;
48 }
49
50 if (image.GetPixelFormat().GetSamplesPerPixel() == 1)
51 {
52 switch (image.GetPixelFormat().GetScalarType())
53 {
54 case gdcm::PixelFormat::UINT8:
55 format = Orthanc::PixelFormat_Grayscale8;
56 return true;
57
58 case gdcm::PixelFormat::UINT16:
59 format = Orthanc::PixelFormat_Grayscale16;
60 return true;
61
62 case gdcm::PixelFormat::INT16:
63 format = Orthanc::PixelFormat_SignedGrayscale16;
64 return true;
65
66 default:
67 return false;
68 }
69 }
70 else if (image.GetPixelFormat().GetSamplesPerPixel() == 3 &&
71 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
72 {
73 format = Orthanc::PixelFormat_RGB24;
74 }
75 else if (image.GetPixelFormat().GetSamplesPerPixel() == 4 &&
76 image.GetPixelFormat().GetScalarType() == gdcm::PixelFormat::UINT8)
77 {
78 format = Orthanc::PixelFormat_RGBA32;
79 }
80
81 return false;
82 }
83
84
85 ORTHANC_PLUGINS_API int32_t DecodeImage(OrthancPluginRestOutput* output,
86 const char* url,
87 const OrthancPluginHttpRequest* request)
88 {
89 std::string instance(request->groups[0]);
90 std::string outputFormat(request->groups[1]);
91 OrthancContext::GetInstance().LogWarning("Using GDCM to decode instance " + instance);
92
93 // Download the request DICOM instance from Orthanc into a memory buffer
94 std::string dicom;
95 OrthancContext::GetInstance().GetDicomForInstance(dicom, instance);
96
97 // Prepare a memory stream over the DICOM instance
98 std::stringstream stream(dicom);
99
100 // Parse the DICOM instance using GDCM
101 gdcm::ImageReader imageReader;
102 imageReader.SetStream(stream);
103 if (!imageReader.Read())
104 {
105 OrthancContext::GetInstance().LogError("GDCM cannot extract an image from this DICOM instance");
106 return -1; // Error
107 }
108
109 gdcm::Image& image = imageReader.GetImage();
110
111 // Log information about the decoded image
112 char tmp[1024];
113 sprintf(tmp, "Image format: %dx%d %s with %d color channel(s)", image.GetRows(), image.GetColumns(),
114 image.GetPixelFormat().GetScalarTypeAsString(), image.GetPixelFormat().GetSamplesPerPixel());
115 OrthancContext::GetInstance().LogWarning(tmp);
116
117 // Create a read-only accessor to the bitmap decoded by GDCM
118 Orthanc::PixelFormat format;
119 if (!GetOrthancPixelFormat(format, image))
120 {
121 OrthancContext::GetInstance().LogError("This sample plugin does not support this image format");
122 return -1; // Error
123 }
124
125 Orthanc::ImageAccessor decodedImage;
126 std::vector<char> decodedBuffer(image.GetBufferLength());
127
128 if (decodedBuffer.size())
129 {
130 image.GetBuffer(&decodedBuffer[0]);
131 unsigned int pitch = image.GetColumns() * ::Orthanc::GetBytesPerPixel(format);
132 decodedImage.AssignWritable(format, image.GetColumns(), image.GetRows(), pitch, &decodedBuffer[0]);
133 }
134 else
135 {
136 // Empty image
137 decodedImage.AssignWritable(format, 0, 0, 0, NULL);
138 }
139
140
141 // Convert the pixel format from GDCM to the format requested by the REST query
142 Orthanc::ImageBuffer converted;
143 converted.SetWidth(decodedImage.GetWidth());
144 converted.SetHeight(decodedImage.GetHeight());
145
146 if (outputFormat == "preview")
147 {
148 if (format == Orthanc::PixelFormat_RGB24 ||
149 format == Orthanc::PixelFormat_RGBA32)
150 {
151 // Do not rescale color image
152 converted.SetFormat(Orthanc::PixelFormat_RGB24);
153 }
154 else
155 {
156 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
157
158 // Rescale the image to the [0,255] range
159 int64_t a, b;
160 Orthanc::ImageProcessing::GetMinMaxValue(a, b, decodedImage);
161
162 float offset = -a;
163 float scaling = 255.0f / static_cast<float>(b - a);
164 Orthanc::ImageProcessing::ShiftScale(decodedImage, offset, scaling);
165 }
166 }
167 else if (outputFormat == "image-uint8")
168 {
169 converted.SetFormat(Orthanc::PixelFormat_Grayscale8);
170 }
171 else if (outputFormat == "image-uint16")
172 {
173 converted.SetFormat(Orthanc::PixelFormat_Grayscale16);
174 }
175 else if (outputFormat == "image-int16")
176 {
177 converted.SetFormat(Orthanc::PixelFormat_SignedGrayscale16);
178 }
179 else
180 {
181 OrthancContext::GetInstance().LogError("Unknown output format: " + outputFormat);
182 return -1;
183 }
184
185 Orthanc::ImageAccessor convertedAccessor(converted.GetAccessor());
186 Orthanc::ImageProcessing::Convert(convertedAccessor, decodedImage);
187
188
189 // Compress the converted image as a PNG file
190 OrthancContext::GetInstance().CompressAndAnswerPngImage(output, convertedAccessor);
191
192 return 0; // Success
193 }
194
195
196 extern "C"
197 {
198 ORTHANC_PLUGINS_API int32_t OrthancPluginInitialize(OrthancPluginContext* context)
199 {
200 OrthancContext::GetInstance().Initialize(context);
201 OrthancContext::GetInstance().LogWarning("Initializing GDCM decoding");
202 OrthancContext::GetInstance().Register("/instances/([^/]+)/(preview|image-uint8|image-uint16|image-int16)", DecodeImage);
203 return 0;
204 }
205
206 ORTHANC_PLUGINS_API void OrthancPluginFinalize()
207 {
208 OrthancContext::GetInstance().LogWarning("Finalizing GDCM decoding");
209 OrthancContext::GetInstance().Finalize();
210 }
211
212 ORTHANC_PLUGINS_API const char* OrthancPluginGetName()
213 {
214 return "gdcm-decoding";
215 }
216
217 ORTHANC_PLUGINS_API const char* OrthancPluginGetVersion()
218 {
219 return "1.0";
220 }
221 }