Mercurial > hg > orthanc
annotate OrthancServer/OrthancFindRequestHandler.cpp @ 807:566a2fb3c1fb
update/delete modalities
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 07 May 2014 15:54:23 +0200 |
parents | 557575fd93e9 |
children | 401a9633e492 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
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4 * Belgium |
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5 * |
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6 * This program is free software: you can redistribute it and/or |
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7 * modify it under the terms of the GNU General Public License as |
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8 * published by the Free Software Foundation, either version 3 of the |
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9 * License, or (at your option) any later version. |
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10 * |
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11 * In addition, as a special exception, the copyright holders of this |
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12 * program give permission to link the code of its release with the |
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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14 * that use the same license as the "OpenSSL" library), and distribute |
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15 * the linked executables. You must obey the GNU General Public License |
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16 * in all respects for all of the code used other than "OpenSSL". If you |
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17 * modify file(s) with this exception, you may extend this exception to |
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18 * your version of the file(s), but you are not obligated to do so. If |
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19 * you do not wish to do so, delete this exception statement from your |
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20 * version. If you delete this exception statement from all source files |
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21 * in the program, then also delete it here. |
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22 * |
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23 * This program is distributed in the hope that it will be useful, but |
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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26 * General Public License for more details. |
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27 * |
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28 * You should have received a copy of the GNU General Public License |
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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30 **/ |
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31 |
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32 #include "OrthancFindRequestHandler.h" |
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33 |
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34 #include <glog/logging.h> |
608 | 35 #include <boost/regex.hpp> |
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36 |
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37 #include "../Core/DicomFormat/DicomArray.h" |
608 | 38 #include "ServerToolbox.h" |
618 | 39 #include "OrthancInitialization.h" |
795 | 40 #include "FromDcmtkBridge.h" |
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41 |
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42 namespace Orthanc |
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43 { |
615 | 44 static bool IsWildcard(const std::string& constraint) |
45 { | |
46 return (constraint.find('-') != std::string::npos || | |
47 constraint.find('*') != std::string::npos || | |
48 constraint.find('\\') != std::string::npos || | |
49 constraint.find('?') != std::string::npos); | |
50 } | |
51 | |
608 | 52 static bool ApplyRangeConstraint(const std::string& value, |
53 const std::string& constraint) | |
54 { | |
610 | 55 size_t separator = constraint.find('-'); |
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56 std::string lower, upper, v; |
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57 Toolbox::ToLowerCase(lower, constraint.substr(0, separator)); |
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58 Toolbox::ToLowerCase(upper, constraint.substr(separator + 1)); |
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59 Toolbox::ToLowerCase(v, value); |
610 | 60 |
61 if (lower.size() == 0 && upper.size() == 0) | |
62 { | |
63 return false; | |
64 } | |
65 | |
66 if (lower.size() == 0) | |
67 { | |
68 return v <= upper; | |
69 } | |
70 | |
71 if (upper.size() == 0) | |
72 { | |
73 return v >= lower; | |
74 } | |
75 | |
76 return (v >= lower && v <= upper); | |
608 | 77 } |
78 | |
79 | |
80 static bool ApplyListConstraint(const std::string& value, | |
81 const std::string& constraint) | |
82 { | |
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83 std::string v1; |
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84 Toolbox::ToLowerCase(v1, value); |
608 | 85 |
86 std::vector<std::string> items; | |
87 Toolbox::TokenizeString(items, constraint, '\\'); | |
88 | |
89 for (size_t i = 0; i < items.size(); i++) | |
90 { | |
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91 std::string lower; |
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92 Toolbox::ToLowerCase(lower, items[i]); |
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93 if (lower == v1) |
608 | 94 { |
95 return true; | |
96 } | |
97 } | |
98 | |
99 return false; | |
100 } | |
101 | |
102 | |
103 static bool Matches(const std::string& value, | |
104 const std::string& constraint) | |
105 { | |
106 // http://www.itk.org/Wiki/DICOM_QueryRetrieve_Explained | |
107 // http://dicomiseasy.blogspot.be/2012/01/dicom-queryretrieve-part-i.html | |
108 | |
109 if (constraint.find('-') != std::string::npos) | |
110 { | |
111 return ApplyRangeConstraint(value, constraint); | |
112 } | |
113 | |
114 if (constraint.find('\\') != std::string::npos) | |
115 { | |
116 return ApplyListConstraint(value, constraint); | |
117 } | |
118 | |
119 if (constraint.find('*') != std::string::npos || | |
120 constraint.find('?') != std::string::npos) | |
121 { | |
122 // TODO - Cache the constructed regular expression | |
123 boost::regex pattern(Toolbox::WildcardToRegularExpression(constraint), | |
124 boost::regex::icase /* case insensitive search */); | |
125 return boost::regex_match(value, pattern); | |
126 } | |
127 else | |
128 { | |
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129 std::string v, c; |
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130 Toolbox::ToLowerCase(v, value); |
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131 Toolbox::ToLowerCase(c, constraint); |
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132 return v == c; |
608 | 133 } |
134 } | |
135 | |
136 | |
137 static bool LookupOneInstance(std::string& result, | |
138 ServerIndex& index, | |
139 const std::string& id, | |
140 ResourceType type) | |
141 { | |
142 if (type == ResourceType_Instance) | |
143 { | |
144 result = id; | |
145 return true; | |
146 } | |
147 | |
148 std::string childId; | |
149 | |
150 { | |
151 std::list<std::string> children; | |
152 index.GetChildInstances(children, id); | |
153 | |
656 | 154 if (children.empty()) |
608 | 155 { |
156 return false; | |
157 } | |
158 | |
159 childId = children.front(); | |
160 } | |
161 | |
162 return LookupOneInstance(result, index, childId, GetChildResourceType(type)); | |
163 } | |
164 | |
165 | |
166 static bool Matches(const Json::Value& resource, | |
167 const DicomArray& query) | |
168 { | |
169 for (size_t i = 0; i < query.GetSize(); i++) | |
170 { | |
171 if (query.GetElement(i).GetValue().IsNull() || | |
172 query.GetElement(i).GetTag() == DICOM_TAG_QUERY_RETRIEVE_LEVEL || | |
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173 query.GetElement(i).GetTag() == DICOM_TAG_SPECIFIC_CHARACTER_SET || |
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174 query.GetElement(i).GetTag() == DICOM_TAG_MODALITIES_IN_STUDY) |
608 | 175 { |
176 continue; | |
177 } | |
178 | |
179 std::string tag = query.GetElement(i).GetTag().Format(); | |
180 std::string value; | |
181 if (resource.isMember(tag)) | |
182 { | |
183 value = resource.get(tag, Json::arrayValue).get("Value", "").asString(); | |
184 } | |
185 | |
186 if (!Matches(value, query.GetElement(i).GetValue().AsString())) | |
187 { | |
188 return false; | |
189 } | |
190 } | |
191 | |
192 return true; | |
193 } | |
194 | |
195 | |
196 static void AddAnswer(DicomFindAnswers& answers, | |
197 const Json::Value& resource, | |
198 const DicomArray& query) | |
199 { | |
200 DicomMap result; | |
201 | |
202 for (size_t i = 0; i < query.GetSize(); i++) | |
203 { | |
204 if (query.GetElement(i).GetTag() != DICOM_TAG_QUERY_RETRIEVE_LEVEL && | |
205 query.GetElement(i).GetTag() != DICOM_TAG_SPECIFIC_CHARACTER_SET) | |
206 { | |
207 std::string tag = query.GetElement(i).GetTag().Format(); | |
208 std::string value; | |
209 if (resource.isMember(tag)) | |
210 { | |
211 value = resource.get(tag, Json::arrayValue).get("Value", "").asString(); | |
212 result.SetValue(query.GetElement(i).GetTag(), value); | |
213 } | |
722 | 214 else |
215 { | |
216 result.SetValue(query.GetElement(i).GetTag(), ""); | |
217 } | |
608 | 218 } |
219 } | |
220 | |
221 answers.Add(result); | |
222 } | |
223 | |
224 | |
615 | 225 static bool ApplyModalitiesInStudyFilter(std::list<std::string>& filteredStudies, |
226 const std::list<std::string>& studies, | |
612 | 227 const DicomMap& input, |
228 ServerIndex& index) | |
229 { | |
615 | 230 filteredStudies.clear(); |
612 | 231 |
232 const DicomValue& v = input.GetValue(DICOM_TAG_MODALITIES_IN_STUDY); | |
233 if (v.IsNull()) | |
234 { | |
235 return false; | |
236 } | |
237 | |
238 // Move the allowed modalities into a "std::set" | |
239 std::vector<std::string> tmp; | |
240 Toolbox::TokenizeString(tmp, v.AsString(), '\\'); | |
241 | |
242 std::set<std::string> modalities; | |
243 for (size_t i = 0; i < tmp.size(); i++) | |
244 { | |
245 modalities.insert(tmp[i]); | |
246 } | |
247 | |
248 // Loop over the studies | |
615 | 249 for (std::list<std::string>::const_iterator |
656 | 250 it = studies.begin(); it != studies.end(); ++it) |
612 | 251 { |
252 try | |
253 { | |
254 // We are considering a single study. Check whether one of | |
255 // its child series matches one of the modalities. | |
256 Json::Value study; | |
615 | 257 if (index.LookupResource(study, *it, ResourceType_Study)) |
612 | 258 { |
259 // Loop over the series of the considered study. | |
260 for (Json::Value::ArrayIndex j = 0; j < study["Series"].size(); j++) // (*) | |
261 { | |
262 Json::Value series; | |
263 if (index.LookupResource(series, study["Series"][j].asString(), ResourceType_Series)) | |
264 { | |
265 // Get the modality of this series | |
266 if (series["MainDicomTags"].isMember("Modality")) | |
267 { | |
268 std::string modality = series["MainDicomTags"]["Modality"].asString(); | |
269 if (modalities.find(modality) != modalities.end()) | |
270 { | |
271 // This series of the considered study matches one | |
272 // of the required modalities. Take the study into | |
273 // consideration for future filtering. | |
615 | 274 filteredStudies.push_back(*it); |
612 | 275 |
276 // We have finished considering this study. Break the study loop at (*). | |
277 break; | |
278 } | |
279 } | |
280 } | |
281 } | |
282 } | |
283 } | |
284 catch (OrthancException&) | |
285 { | |
286 // This resource has probably been deleted during the find request | |
287 } | |
288 } | |
289 | |
290 return true; | |
291 } | |
292 | |
293 | |
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294 namespace |
615 | 295 { |
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296 class CandidateResources |
615 | 297 { |
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298 private: |
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299 ServerIndex& index_; |
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300 ModalityManufacturer manufacturer_; |
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301 ResourceType level_; |
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302 bool isFilterApplied_; |
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303 std::set<std::string> filtered_; |
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304 |
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305 static void ListToSet(std::set<std::string>& target, |
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306 const std::list<std::string>& source) |
615 | 307 { |
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308 for (std::list<std::string>::const_iterator |
716 | 309 it = source.begin(); it != source.end(); ++it) |
615 | 310 { |
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311 target.insert(*it); |
615 | 312 } |
313 } | |
314 | |
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315 void ApplyExactFilter(const DicomTag& tag, const std::string& value) |
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316 { |
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317 LOG(INFO) << "Applying exact filter on tag " |
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318 << FromDcmtkBridge::GetName(tag) << " (value: " << value << ")"; |
615 | 319 |
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320 std::list<std::string> resources; |
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321 index_.LookupTagValue(resources, tag, value, level_); |
615 | 322 |
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323 if (isFilterApplied_) |
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324 { |
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325 std::set<std::string> s; |
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326 ListToSet(s, resources); |
615 | 327 |
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328 std::set<std::string> tmp = filtered_; |
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329 filtered_.clear(); |
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331 for (std::set<std::string>::const_iterator |
716 | 332 it = tmp.begin(); it != tmp.end(); ++it) |
665 | 333 { |
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334 if (s.find(*it) != s.end()) |
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335 { |
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336 filtered_.insert(*it); |
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337 } |
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338 } |
665 | 339 } |
340 else | |
341 { | |
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342 assert(filtered_.empty()); |
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343 isFilterApplied_ = true; |
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344 ListToSet(filtered_, resources); |
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345 } |
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346 } |
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347 |
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348 public: |
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349 CandidateResources(ServerIndex& index, |
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350 ModalityManufacturer manufacturer) : |
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351 index_(index), |
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352 manufacturer_(manufacturer), |
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353 level_(ResourceType_Patient), |
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354 isFilterApplied_(false) |
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355 { |
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356 } |
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357 |
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358 ResourceType GetLevel() const |
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359 { |
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360 return level_; |
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361 } |
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362 |
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363 void GoDown() |
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364 { |
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365 assert(level_ != ResourceType_Instance); |
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366 |
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367 if (isFilterApplied_) |
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368 { |
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369 std::set<std::string> tmp = filtered_; |
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370 |
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371 filtered_.clear(); |
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372 |
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373 for (std::set<std::string>::const_iterator |
716 | 374 it = tmp.begin(); it != tmp.end(); ++it) |
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375 { |
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376 std::list<std::string> children; |
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377 index_.GetChildren(children, *it); |
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378 ListToSet(filtered_, children); |
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379 } |
665 | 380 } |
381 | |
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382 switch (level_) |
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383 { |
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384 case ResourceType_Patient: |
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385 level_ = ResourceType_Study; |
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386 break; |
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387 |
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388 case ResourceType_Study: |
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389 level_ = ResourceType_Series; |
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390 break; |
615 | 391 |
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392 case ResourceType_Series: |
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393 level_ = ResourceType_Instance; |
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394 break; |
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395 |
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396 default: |
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397 throw OrthancException(ErrorCode_InternalError); |
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398 } |
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399 } |
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400 |
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401 void Flatten(std::list<std::string>& resources) const |
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402 { |
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403 resources.clear(); |
615 | 404 |
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405 if (isFilterApplied_) |
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406 { |
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407 for (std::set<std::string>::const_iterator |
716 | 408 it = filtered_.begin(); it != filtered_.end(); ++it) |
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409 { |
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410 resources.push_back(*it); |
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411 } |
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412 } |
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413 else |
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414 { |
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415 Json::Value tmp; |
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416 index_.GetAllUuids(tmp, level_); |
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417 for (Json::Value::ArrayIndex i = 0; i < tmp.size(); i++) |
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418 { |
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419 resources.push_back(tmp[i].asString()); |
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420 } |
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421 } |
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422 } |
615 | 423 |
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424 void ApplyFilter(const DicomTag& tag, const DicomMap& query) |
615 | 425 { |
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426 if (query.HasTag(tag)) |
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427 { |
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428 const DicomValue& value = query.GetValue(tag); |
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429 if (!value.IsNull()) |
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430 { |
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431 std::string value = query.GetValue(tag).AsString(); |
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432 if (!IsWildcard(value)) |
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433 { |
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434 ApplyExactFilter(tag, value); |
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435 } |
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436 } |
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437 } |
615 | 438 } |
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439 }; |
615 | 440 } |
441 | |
442 | |
618 | 443 void OrthancFindRequestHandler::Handle(DicomFindAnswers& answers, |
665 | 444 const DicomMap& input, |
445 const std::string& callingAETitle) | |
565
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446 { |
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447 /** |
665 | 448 * Retrieve the manufacturer of this modality. |
449 **/ | |
450 | |
451 ModalityManufacturer manufacturer; | |
452 | |
453 { | |
806 | 454 RemoteModalityParameters modality; |
665 | 455 |
806 | 456 if (!LookupDicomModalityUsingAETitle(modality, callingAETitle)) |
665 | 457 { |
458 throw OrthancException("Unknown modality"); | |
459 } | |
806 | 460 |
461 manufacturer = modality.GetManufacturer(); | |
665 | 462 } |
463 | |
464 | |
465 /** | |
565
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466 * Retrieve the query level. |
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467 **/ |
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468 |
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469 const DicomValue* levelTmp = input.TestAndGetValue(DICOM_TAG_QUERY_RETRIEVE_LEVEL); |
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470 if (levelTmp == NULL) |
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471 { |
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472 throw OrthancException(ErrorCode_BadRequest); |
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473 } |
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474 |
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475 ResourceType level = StringToResourceType(levelTmp->AsString().c_str()); |
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476 |
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477 if (level != ResourceType_Patient && |
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478 level != ResourceType_Study && |
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479 level != ResourceType_Series && |
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480 level != ResourceType_Instance) |
565
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481 { |
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482 throw OrthancException(ErrorCode_NotImplemented); |
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483 } |
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484 |
665 | 485 |
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486 DicomArray query(input); |
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487 LOG(INFO) << "DICOM C-Find request at level: " << EnumerationToString(level); |
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488 |
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489 for (size_t i = 0; i < query.GetSize(); i++) |
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490 { |
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491 if (!query.GetElement(i).GetValue().IsNull()) |
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492 { |
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493 LOG(INFO) << " " << query.GetElement(i).GetTag() |
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494 << " " << FromDcmtkBridge::GetName(query.GetElement(i).GetTag()) |
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495 << " = " << query.GetElement(i).GetValue().AsString(); |
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496 } |
565
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497 } |
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498 |
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499 |
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500 /** |
615 | 501 * Retrieve the candidate resources for this query level. Whenever |
502 * possible, we avoid returning ALL the resources for this query | |
503 * level, as it would imply reading the JSON file on the harddisk | |
504 * for each of them. | |
608 | 505 **/ |
506 | |
714
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507 CandidateResources candidates(context_.GetIndex(), manufacturer); |
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508 |
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509 for (;;) |
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510 { |
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511 switch (candidates.GetLevel()) |
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512 { |
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513 case ResourceType_Patient: |
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514 candidates.ApplyFilter(DICOM_TAG_PATIENT_ID, input); |
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515 break; |
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516 |
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517 case ResourceType_Study: |
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518 candidates.ApplyFilter(DICOM_TAG_STUDY_INSTANCE_UID, input); |
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519 candidates.ApplyFilter(DICOM_TAG_ACCESSION_NUMBER, input); |
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520 break; |
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521 |
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522 case ResourceType_Series: |
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523 candidates.ApplyFilter(DICOM_TAG_SERIES_INSTANCE_UID, input); |
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524 break; |
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525 |
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526 case ResourceType_Instance: |
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527 candidates.ApplyFilter(DICOM_TAG_SOP_INSTANCE_UID, input); |
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528 break; |
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529 |
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530 default: |
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531 throw OrthancException(ErrorCode_InternalError); |
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532 } |
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533 |
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534 if (candidates.GetLevel() == level) |
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535 { |
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536 break; |
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537 } |
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538 |
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539 candidates.GoDown(); |
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540 } |
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541 |
615 | 542 std::list<std::string> resources; |
714
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543 candidates.Flatten(resources); |
608 | 544 |
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545 LOG(INFO) << "Number of candidate resources after exact filtering: " << resources.size(); |
611
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546 |
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547 /** |
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548 * Apply filtering on modalities for studies, if asked (this is an |
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549 * extension to standard DICOM) |
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550 * http://www.medicalconnections.co.uk/kb/Filtering_on_and_Retrieving_the_Modality_in_a_C_FIND |
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551 **/ |
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552 |
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553 if (level == ResourceType_Study && |
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554 input.HasTag(DICOM_TAG_MODALITIES_IN_STUDY)) |
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555 { |
615 | 556 std::list<std::string> filtered; |
612 | 557 if (ApplyModalitiesInStudyFilter(filtered, resources, input, context_.GetIndex())) |
611
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558 { |
612 | 559 resources = filtered; |
611
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560 } |
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561 } |
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562 |
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563 |
608 | 564 /** |
565 * Loop over all the resources for this query level. | |
565
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566 **/ |
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567 |
615 | 568 for (std::list<std::string>::const_iterator |
656 | 569 resource = resources.begin(); resource != resources.end(); ++resource) |
565
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570 { |
608 | 571 try |
565
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572 { |
608 | 573 std::string instance; |
615 | 574 if (LookupOneInstance(instance, context_.GetIndex(), *resource, level)) |
565
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575 { |
615 | 576 Json::Value info; |
577 context_.ReadJson(info, instance); | |
608 | 578 |
615 | 579 if (Matches(info, query)) |
608 | 580 { |
615 | 581 AddAnswer(answers, info, query); |
608 | 582 } |
565
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583 } |
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584 } |
608 | 585 catch (OrthancException&) |
586 { | |
611
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587 // This resource has probably been deleted during the find request |
608 | 588 } |
565
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589 } |
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590 } |
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591 } |
682
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592 |
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593 |
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594 |
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595 /** |
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596 * TODO : Case-insensitive match for PN value representation (Patient |
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597 * Name). Case-senstive match for all the other value representations. |
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598 * |
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599 * Reference: DICOM PS 3.4 |
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600 * - C.2.2.2.1 ("Single Value Matching") |
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601 * - C.2.2.2.4 ("Wild Card Matching") |
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602 * http://medical.nema.org/Dicom/2011/11_04pu.pdf ( |
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603 **/ |