1
|
|
|
<?php |
2
|
|
|
/** |
3
|
|
|
Copyright (C) 2018-2020 KANOUN Salim |
4
|
|
|
This program is free software; you can redistribute it and/or modify |
5
|
|
|
it under the terms of the Affero GNU General Public v.3 License as published by |
6
|
|
|
the Free Software Foundation; |
7
|
|
|
This program is distributed in the hope that it will be useful, |
8
|
|
|
but WITHOUT ANY WARRANTY; without even the implied warranty of |
9
|
|
|
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
10
|
|
|
Affero GNU General Public Public for more details. |
11
|
|
|
You should have received a copy of the Affero GNU General Public Public along |
12
|
|
|
with this program; if not, write to the Free Software Foundation, Inc., |
13
|
|
|
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
14
|
|
|
*/ |
15
|
|
|
|
16
|
|
|
/** |
17
|
|
|
* Fill Orthanc_Studies and Orthanc_Series table to link DICOM Orthanc storage with the web plateform |
18
|
|
|
* Used in the validation process of the upload |
19
|
|
|
*/ |
20
|
|
|
|
21
|
|
|
class Fill_Orthanc_Table { |
22
|
|
|
|
23
|
|
|
private $linkpdo; |
24
|
|
|
private $username; |
25
|
|
|
private $studyOrthancObject; |
26
|
|
|
private $visitObject; |
27
|
|
|
|
28
|
|
|
|
29
|
|
|
public function __construct($id_visit, String $username, PDO $linkpdo) { |
30
|
|
|
$this->username=$username; |
31
|
|
|
$this->linkpdo=$linkpdo; |
32
|
|
|
$this->visitObject=new Visit($id_visit, $linkpdo); |
33
|
|
|
} |
34
|
|
|
|
35
|
|
|
/** |
36
|
|
|
* return study details of a study stored in Orthanc |
37
|
|
|
* @param String $studyID |
38
|
|
|
* @return array |
39
|
|
|
*/ |
40
|
|
|
public function parseData(String $studyID) { |
41
|
|
|
$studyData=new Orthanc_Study($studyID, null, null); |
42
|
|
|
$studyData->retrieveStudyData(); |
43
|
|
|
$this->studyOrthancObject=$studyData; |
44
|
|
|
$studyDetails=get_object_vars($studyData); |
45
|
|
|
return $studyDetails; |
46
|
|
|
} |
47
|
|
|
|
48
|
|
|
/** |
49
|
|
|
* Fill data in the database, write data for study and for each series |
50
|
|
|
* Once done trigger the change upload status of visit to update upload status and eventually skip |
51
|
|
|
* local form and/or QC |
52
|
|
|
*/ |
53
|
|
|
public function fillDB($anonFromOrthancStudyId) { |
54
|
|
|
|
55
|
|
|
//Check that original OrthancID is unknown for this study |
56
|
|
|
if ($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId)) { |
57
|
|
|
try { |
58
|
|
|
//Fill la database |
59
|
|
|
$this->addToDbStudy($anonFromOrthancStudyId); |
60
|
|
|
|
61
|
|
|
foreach ($this->studyOrthancObject->orthancSeries as $serie) { |
62
|
|
|
//Fill series database |
63
|
|
|
$this->addtoDbSerie($serie); |
64
|
|
|
} |
65
|
|
|
$this->visitObject->changeUploadStatus(Visit::DONE, $this->username); |
66
|
|
|
|
67
|
|
|
} catch (Exception $e1) { |
68
|
|
|
throw new Exception("Error during import ".$e1->getMessage()); |
69
|
|
|
} |
70
|
|
|
} else { |
71
|
|
|
throw new Exception("Error during import Study Already Known"); |
72
|
|
|
} |
73
|
|
|
} |
74
|
|
|
|
75
|
|
|
/** |
76
|
|
|
* Private function to write into Orthanc_Studies DB |
77
|
|
|
* @param string $anonFromOrthancStudyId |
78
|
|
|
*/ |
79
|
|
|
private function addToDbStudy(string $anonFromOrthancStudyId) { |
80
|
|
|
$studyAcquisitionDate2=$this->parseDateTime($this->studyOrthancObject->studyDate, 1); |
81
|
|
|
$studyAcquisitionTime2=$this->parseDateTime($this->studyOrthancObject->studyTime, 2); |
82
|
|
|
|
83
|
|
|
if ($studyAcquisitionDate2 != null && $studyAcquisitionTime2 != null) { |
|
|
|
|
84
|
|
|
$acquisitionDateTime=$studyAcquisitionDate2." ".$studyAcquisitionTime2; |
85
|
|
|
} |
86
|
|
|
|
87
|
|
|
$addBdd=$this->linkpdo->prepare('INSERT INTO orthanc_studies (id_visit, |
88
|
|
|
uploader, |
89
|
|
|
upload_date, |
90
|
|
|
acquisition_date, |
91
|
|
|
acquisition_time, |
92
|
|
|
acquisition_datetime, |
93
|
|
|
study_orthanc_id, |
94
|
|
|
anon_from_orthanc_id, |
95
|
|
|
study_uid, |
96
|
|
|
study_description, |
97
|
|
|
patient_orthanc_id, |
98
|
|
|
patient_name, |
99
|
|
|
patient_id, |
100
|
|
|
number_of_series, |
101
|
|
|
number_of_instances, |
102
|
|
|
disk_size, |
103
|
|
|
uncompressed_disk_size) |
104
|
|
|
VALUES(:id_visit, |
105
|
|
|
:uploader, |
106
|
|
|
:upload_date, |
107
|
|
|
:acquisition_date, |
108
|
|
|
:acquisition_time, |
109
|
|
|
:acquisition_datetime, |
110
|
|
|
:study_orthanc_id, |
111
|
|
|
:anon_from_orthanc_id, |
112
|
|
|
:study_uid, |
113
|
|
|
:study_description, |
114
|
|
|
:patient_orthanc_id, |
115
|
|
|
:patient_name, |
116
|
|
|
:patient_id, |
117
|
|
|
:number_of_series, |
118
|
|
|
:number_of_instances, |
119
|
|
|
:disk_size, |
120
|
|
|
:uncompressed_disk_size) |
121
|
|
|
|
122
|
|
|
ON DUPLICATE KEY UPDATE uploader=:uploader, |
123
|
|
|
upload_date=:upload_date, |
124
|
|
|
acquisition_date=:acquisition_date, |
125
|
|
|
acquisition_time=:acquisition_time, |
126
|
|
|
acquisition_datetime=:acquisition_datetime, |
127
|
|
|
anon_from_orthanc_id=:anon_from_orthanc_id, |
128
|
|
|
study_uid=:study_uid, |
129
|
|
|
study_description=:study_description, |
130
|
|
|
patient_orthanc_id=:patient_orthanc_id, |
131
|
|
|
patient_name=:patient_name, |
132
|
|
|
patient_id=:patient_id, |
133
|
|
|
number_of_series=:number_of_series, |
134
|
|
|
number_of_instances=:number_of_instances, |
135
|
|
|
disk_size=:disk_size, |
136
|
|
|
uncompressed_disk_size=:uncompressed_disk_size, |
137
|
|
|
deleted=0 '); |
138
|
|
|
|
139
|
|
|
$addBdd->execute(array( |
140
|
|
|
'id_visit'=>$this->visitObject->id_visit, |
141
|
|
|
'uploader'=>$this->username, |
142
|
|
|
'upload_date'=>date("Y-m-d H:i:s"), |
143
|
|
|
'acquisition_date'=>$this->studyOrthancObject->studyDate, |
144
|
|
|
'acquisition_time'=>$this->studyOrthancObject->studyTime, |
145
|
|
|
'acquisition_datetime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null, |
146
|
|
|
'study_orthanc_id'=>$this->studyOrthancObject->studyOrthancID, |
147
|
|
|
'anon_from_orthanc_id'=>$anonFromOrthancStudyId, |
148
|
|
|
'study_uid'=>$this->studyOrthancObject->studyInstanceUID, |
149
|
|
|
'study_description'=>$this->studyOrthancObject->studyDescription, |
150
|
|
|
'patient_orthanc_id'=>$this->studyOrthancObject->parentPartientOrthancID, |
151
|
|
|
'patient_name'=>$this->studyOrthancObject->parentPatientName, |
152
|
|
|
'patient_id'=>$this->studyOrthancObject->parentPatientID, |
153
|
|
|
'number_of_series'=>$this->studyOrthancObject->numberOfSeriesInStudy, |
154
|
|
|
'number_of_instances'=>$this->studyOrthancObject->countInstances, |
155
|
|
|
'disk_size'=>$this->studyOrthancObject->diskSizeMb, |
156
|
|
|
'uncompressed_disk_size'=>$this->studyOrthancObject->uncompressedSizeMb |
157
|
|
|
)); |
158
|
|
|
|
159
|
|
|
} |
160
|
|
|
|
161
|
|
|
/** |
162
|
|
|
* Private function to write into the Orthanc_Series DB |
163
|
|
|
* @param Orthanc_Serie $serie |
164
|
|
|
*/ |
165
|
|
|
private function addtoDbSerie(Orthanc_Serie $serie) { |
166
|
|
|
|
167
|
|
|
$serieAcquisitionDate2=$this->parseDateTime($serie->seriesDate, 1); |
168
|
|
|
$serieAcquisitionTime2=$this->parseDateTime($serie->seriesTime, 2); |
169
|
|
|
|
170
|
|
|
if ($serieAcquisitionDate2 != null && $serieAcquisitionTime2 != null) { |
|
|
|
|
171
|
|
|
$acquisitionDateTime=$serieAcquisitionDate2." ".$serieAcquisitionTime2; |
172
|
|
|
} |
173
|
|
|
|
174
|
|
|
$addBddSeries=$this->linkpdo->prepare('INSERT INTO orthanc_series ( |
175
|
|
|
study_orthanc_id, |
176
|
|
|
modality, |
177
|
|
|
acquisition_date, |
178
|
|
|
acquisition_time, |
179
|
|
|
acquisition_datetime, |
180
|
|
|
series_description, |
181
|
|
|
injected_dose, |
182
|
|
|
radiopharmaceutical, |
183
|
|
|
half_life, |
184
|
|
|
injected_time, |
185
|
|
|
injected_activity, |
186
|
|
|
series_orthanc_id, |
187
|
|
|
number_of_instances, |
188
|
|
|
serie_uid, |
189
|
|
|
serie_number, |
190
|
|
|
patient_weight, |
191
|
|
|
serie_disk_size, |
192
|
|
|
serie_uncompressed_disk_size, |
193
|
|
|
manufacturer, |
194
|
|
|
model_name, |
195
|
|
|
injected_datetime) |
196
|
|
|
VALUES( :Study_Orthanc_ID, |
197
|
|
|
:Modality, |
198
|
|
|
:Acquisition_Date, |
199
|
|
|
:Acquisition_Time, |
200
|
|
|
:Acquisition_DateTime, |
201
|
|
|
:Series_Description, |
202
|
|
|
:Injected_Dose, |
203
|
|
|
:Radiopharmaceutical, |
204
|
|
|
:HalfLife, |
205
|
|
|
:Injected_Time, |
206
|
|
|
:Injected_Activity, |
207
|
|
|
:Series_Orthanc_ID, |
208
|
|
|
:Number_Instances, |
209
|
|
|
:Serie_UID, |
210
|
|
|
:Serie_Number, |
211
|
|
|
:Patient_Weight, |
212
|
|
|
:Serie_Disk_Size, |
213
|
|
|
:Serie_Uncompressed_Disk_Size, |
214
|
|
|
:Manufacturer, |
215
|
|
|
:Model_Name, :Injected_DateTime) |
216
|
|
|
ON DUPLICATE KEY UPDATE study_orthanc_id=:Study_Orthanc_ID, modality=:Modality, acquisition_date=:Acquisition_Date, acquisition_time=:Acquisition_Time, acquisition_datetime=:Acquisition_DateTime, series_description=:Series_Description, injected_dose=:Injected_Dose, radiopharmaceutical=:Radiopharmaceutical, half_life=:HalfLife, injected_time=:Injected_Time, injected_activity=:Injected_Activity, number_of_instances=:Number_Instances, serie_number=:Serie_Number, patient_weight=:Patient_Weight, serie_disk_size=:Serie_Disk_Size, serie_uncompressed_disk_size=:Serie_Uncompressed_Disk_Size, manufacturer=:Manufacturer, model_name=:Model_Name, deleted=0, injected_datetime=:Injected_DateTime'); |
217
|
|
|
|
218
|
|
|
$value=array( |
219
|
|
|
'Study_Orthanc_ID'=>$this->studyOrthancObject->studyOrthancID, |
220
|
|
|
'Modality'=>$serie->modality, |
221
|
|
|
'Acquisition_Date'=>$serie->seriesDate, |
222
|
|
|
'Acquisition_Time'=>$serie->seriesTime, |
223
|
|
|
'Acquisition_DateTime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null, |
224
|
|
|
'Series_Description'=> $serie->seriesDescription, |
225
|
|
|
'Injected_Dose'=> is_numeric($serie->injectedDose) ? $serie->injectedDose : null, |
226
|
|
|
'Radiopharmaceutical'=> $serie->radiopharmaceutical, |
227
|
|
|
'HalfLife'=> is_numeric($serie->halfLife) ? $serie->halfLife : null, |
228
|
|
|
'Injected_Time'=> $serie->injectedTime, |
229
|
|
|
'Injected_DateTime'=> $this->parseDateTime($serie->injectedDateTime, 0), |
230
|
|
|
'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity : null, |
231
|
|
|
'Series_Orthanc_ID'=> $serie->serieOrthancID, |
232
|
|
|
'Number_Instances'=> $serie->numberOfInstanceInOrthanc, |
233
|
|
|
'Serie_UID'=> $serie->seriesInstanceUID, |
234
|
|
|
'Serie_Number'=> $serie->seriesNumber, |
235
|
|
|
'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight : null, |
236
|
|
|
'Serie_Disk_Size'=> $serie->diskSizeMb, |
237
|
|
|
'Serie_Uncompressed_Disk_Size' => $serie->uncompressedSizeMb, |
238
|
|
|
'Manufacturer'=> $serie->seriesManufacturer, |
239
|
|
|
'Model_Name'=>$serie->seriesModelName |
240
|
|
|
); |
241
|
|
|
|
242
|
|
|
$addBddSeries->execute($value); |
243
|
|
|
|
244
|
|
|
} |
245
|
|
|
|
246
|
|
|
/** |
247
|
|
|
* Parse a DICOM date or Time string and return a string ready to send to database |
248
|
|
|
* Return null if non parsable |
249
|
|
|
* @param string $string |
250
|
|
|
* @param type 0=dateTime, 1=Date, 2=Time |
|
|
|
|
251
|
|
|
* return formated date for db saving, null if parse failed |
252
|
|
|
*/ |
253
|
|
|
private function parseDateTime($string, int $type) { |
254
|
|
|
$parsedDateTime=null; |
255
|
|
|
|
256
|
|
|
//If contain time split the ms (after.) which are not constant |
257
|
|
|
if ($type == 0 || $type == 2) { |
258
|
|
|
if (strpos($string, ".")) { |
259
|
|
|
$timeWithoutms=explode(".", $string); |
260
|
|
|
$string=$timeWithoutms[0]; |
261
|
|
|
} |
262
|
|
|
|
263
|
|
|
} |
264
|
|
|
|
265
|
|
|
if ($type == 2) { |
266
|
|
|
$dateObject=DateTime::createFromFormat('His', $string); |
267
|
|
|
if ($dateObject !== false) { |
268
|
|
|
$parsedDateTime=$dateObject->format('H:i:s'); |
269
|
|
|
} |
270
|
|
|
} else if ($type == 1) { |
271
|
|
|
$dateObject=DateTime::createFromFormat('Ymd', $string); |
272
|
|
|
if ($dateObject !== false) { |
273
|
|
|
$parsedDateTime=$dateObject->format('Y-m-d'); |
274
|
|
|
} |
275
|
|
|
} else if ($type == 0) { |
276
|
|
|
$dateObject=DateTime::createFromFormat('YmdHis', $string); |
277
|
|
|
if ($dateObject !== false) { |
278
|
|
|
$parsedDateTime=$dateObject->format('Y-m-d H:i:s'); |
279
|
|
|
} |
280
|
|
|
} |
281
|
|
|
|
282
|
|
|
return $parsedDateTime; |
283
|
|
|
|
284
|
|
|
} |
285
|
|
|
|
286
|
|
|
} |
287
|
|
|
|
288
|
|
|
|