Produced by Araxis Merge on 7/10/2017 1:01:44 PM Central Daylight Time. See www.araxis.com for information about Merge. This report uses XHTML and CSS2, and is best viewed with a modern standards-compliant browser. For optimum results when printing this report, use landscape orientation and enable printing of background images and colours in your browser.
| # | Location | File | Last Modified |
|---|---|---|---|
| 1 | C:\AraxisMergeCompare\Pri_un\IV-ehmp_cif\ImagingDicomDCFUtilities\src\java\gov\va\med\imaging\dicom\dcftoolkit\utilities\reconstitution | LegacyTextFileParser.java | Thu Jun 29 17:22:24 2017 UTC |
| 2 | C:\AraxisMergeCompare\Pri_re\IV-ehmp_cif\ImagingDicomDCFUtilities\src\java\gov\va\med\imaging\dicom\dcftoolkit\utilities\reconstitution | LegacyTextFileParser.java | Thu Jul 6 15:03:16 2017 UTC |
| Description | Between Files 1 and 2 |
|
|---|---|---|
| Text Blocks | Lines | |
| Unchanged | 2 | 2150 |
| Changed | 1 | 2 |
| Inserted | 0 | 0 |
| Removed | 0 | 0 |
| Whitespace | |
|---|---|
| Character case | Differences in character case are significant |
| Line endings | Differences in line endings (CR and LF characters) are ignored |
| CR/LF characters | Not shown in the comparison detail |
No regular expressions were active.
| 1 | /** | |
| 2 | * | |
| 3 | Package: MAG - Vis tA Imaging | |
| 4 | WARNING: Per VHA D irective 2 004-038, t his routin e should n ot be modi fied. | |
| 5 | Date Cre ated: Sept ember 26, 2006 | |
| 6 | Site Nam e: Washin gton OI Fi eld Office , Silver S pring, MD | |
| 7 | Developer:
|
|
| 8 | Descript ion: | |
| 9 | ||
| 10 | ;; +-------- ---------- ---------- ---------- ---------- ---------- ---------- + | |
| 11 | ;; Property of the US Government . | |
| 12 | ;; No permis sion to co py or redi stribute t his softwa re is give n. | |
| 13 | ;; Use of un released v ersions of this soft ware requi res the us er | |
| 14 | ;; to execu te a writt en test ag reement wi th the Vis tA Imaging | |
| 15 | ;; Developm ent Office of the De partment o f Veterans Affairs, | |
| 16 | ;; telephon e (301) 73 4-0100. | |
| 17 | ;; | |
| 18 | ;; The Food and Drug A dministrat ion classi fies this software a s | |
| 19 | ;; a Class I I medical device. A s such, it may not b e changed | |
| 20 | ;; in any wa y. Modifi cations to this soft ware may r esult in a n | |
| 21 | ;; adulterat ed medical device un der 21CFR8 20, the us e of which | |
| 22 | ;; is consid ered to be a violati on of US F ederal Sta tutes. | |
| 23 | ;; +-------- ---------- ---------- ---------- ---------- ---------- ---------- + | |
| 24 | */ | |
| 25 | package go v.va.med.i maging.dic om.dcftool kit.utilit ies.recons titution; | |
| 26 | ||
| 27 | import gov .va.med.im aging.Size dInputStre am; | |
| 28 | import gov .va.med.im aging.dico m.common.i nterfaces. IDicomData Set; | |
| 29 | import gov .va.med.im aging.dico m.dcftoolk it.common. impl.Dicom DataSetImp l; | |
| 30 | import gov .va.med.im aging.exce ptions.Tex tFileExcep tion; | |
| 31 | import gov .va.med.im aging.exce ptions.Tex tFileExtra ctionExcep tion; | |
| 32 | import gov .va.med.im aging.exce ptions.Tex tFileNotFo undExcepti on; | |
| 33 | ||
| 34 | import jav a.io.Buffe redReader; | |
| 35 | import jav a.io.FileN otFoundExc eption; | |
| 36 | import jav a.io.FileR eader; | |
| 37 | import jav a.io.IOExc eption; | |
| 38 | import jav a.io.Input StreamRead er; | |
| 39 | import jav a.nio.Byte Buffer; | |
| 40 | import jav a.nio.Shor tBuffer; | |
| 41 | import jav a.util.Arr ayList; | |
| 42 | import jav a.util.Has hMap; | |
| 43 | import jav a.util.Ite rator; | |
| 44 | import jav a.util.reg ex.Pattern ; | |
| 45 | ||
| 46 | import org .apache.lo g4j.Logger ; | |
| 47 | ||
| 48 | import com .lbs.DCS.A ttributeTa g; | |
| 49 | import com .lbs.DCS.D CM; | |
| 50 | import com .lbs.DCS.D CSExceptio n; | |
| 51 | import com .lbs.DCS.D icomCSElem ent; | |
| 52 | import com .lbs.DCS.D icomDataDi ctionary; | |
| 53 | import com .lbs.DCS.D icomDataSe t; | |
| 54 | import com .lbs.DCS.D icomElemen t; | |
| 55 | import com .lbs.DCS.D icomElemen tFactory; | |
| 56 | import com .lbs.DCS.D icomFDElem ent; | |
| 57 | import com .lbs.DCS.D icomFLElem ent; | |
| 58 | import com .lbs.DCS.D icomOBElem ent; | |
| 59 | import com .lbs.DCS.D icomOWElem ent; | |
| 60 | import com .lbs.DCS.D icomSLElem ent; | |
| 61 | import com .lbs.DCS.D icomSQElem ent; | |
| 62 | import com .lbs.DCS.D icomSSElem ent; | |
| 63 | import com .lbs.DCS.D icomULElem ent; | |
| 64 | import com .lbs.DCS.D icomUSElem ent; | |
| 65 | ||
| 66 | /** | |
| 67 | * | |
| 68 | * Text Fi le Parser class. Thi s parser i s specific to the Vi sta Imagin g Legacy | |
| 69 | * environ ment. The class wil l parse th e Text fil e passed f rom Archiv ing | |
| 70 | * and bui ld a new D icomDataSe t from the Text file informati on. Then the class shall | |
| 71 | * wrap th e DicomDat aSet objec t into a g eneric Dic omDataSet object. T he wrappin g allows | |
| 72 | * the Dic omDataSet object to be passed to the Dic om Generic Layer. | |
| 73 | * | |
| 74 | * @author William P eterson | |
| 75 | * extende d by Csaba Titton | |
| 76 | * for Vi X streamin g | |
| 77 | */ | |
| 78 | ||
| 79 | //NOTE 000 8,1032/000 8,0103 and | |
| 80 | // 0040 ,0260/0008 ,0103 and | |
| 81 | // 0040 ,0275/0040 ,0008/0008 ,0103 has no value i n output14 .dcm. Inve stigated t he issue. | |
| 82 | // Th is is acce ptable acc ording to the DICOM Standard. | |
| 83 | ||
| 84 | public cla ss LegacyT extFilePar ser { | |
| 85 | /* | |
| 86 | * Cre ate a Dico mDataSet o bject. Th is object is DCF Too lkit speci fic. | |
| 87 | */ | |
| 88 | privat e DicomDat aSet dicom DataSet = null; | |
| 89 | ||
| 90 | privat e IDicomDa taSet tool kitDDS = n ull; | |
| 91 | ||
| 92 | privat e Original PixelDataI nfo origin alPixelDat a = null; | |
| 93 | ||
| 94 | privat e static L ogger logg er = Logge r.getLogge r (LegacyT extFilePar ser.class) ; | |
| 95 | privat e static L ogger test Logger = L ogger.getL ogger("JUN IT_TEST"); | |
| 96 | ||
| 97 | ||
| 98 | /** | |
| 99 | * Con structor | |
| 100 | */ | |
| 101 | public LegacyTex tFileParse r() { | |
| 102 | su per(); | |
| 103 | } | |
| 104 | ||
| 105 | /** | |
| 106 | * Inv oke method to create a DicomDa taSet base d on a Tex t file. | |
| 107 | * | |
| 108 | * @pa ram textFi lename rep resents th e name (an d path) of the Text file. | |
| 109 | * @re turn repre sents the encapsulat ed DicomDa taSet that is safe f or DicomGe neric Laye r. | |
| 110 | * @th rows TextF ileNotFoun dException | |
| 111 | * @th rows TextF ileExcepti on | |
| 112 | * @th rows TextF ileExtract ionExcepti on | |
| 113 | */ | |
| 114 | public IDicomDat aSet creat eDicomData Set(String textFilen ame, Origi nalPixelDa taInfo pix elData) | |
| 115 | throws T extFileNot FoundExcep tion, Text FileExcept ion, | |
| 116 | TextFile Extraction Exception{ | |
| 117 | ||
| 118 | lo gger.info( this.getCl ass().getN ame()+": D icom Toolk it Layer: " + | |
| 119 | "... parsing Te xt file in to DicomDa taSet."); | |
| 120 | lo gger.debug ("Text Fil e: "+ text Filename); | |
| 121 | th is.origina lPixelData = pixelDa ta; | |
| 122 | Bu fferedRead er buffer = null; | |
| 123 | tr y{ | |
| 124 | //Get Te xt file. | |
| 125 | //JUNIT Create tes t to verif y how this fails if not correc t permissi ons. | |
| 126 | buffer = new Buffe redReader( new FileRe ader(textF ilename)); | |
| 127 | //Invoke parser. | |
| 128 | this.par seTextFile (buffer, t rue); | |
| 129 | //REMIND ER Find ou t why I ha ve the fol lowing lin e. It doe s not make sense, bu t | |
| 130 | // I do n't want t o change i t now. Un sure of ef fects if o mitted. | |
| 131 | pixelDat a = this.o riginalPix elData; | |
| 132 | //encaps ulate Dico mDataSet o bject. | |
| 133 | return ( this.encap sulateDico mDataSet() ); | |
| 134 | } | |
| 135 | ca tch(FileNo tFoundExce ption noFi le){ | |
| 136 | logger.e rror(noFil e.getMessa ge()); | |
| 137 | logger.e rror(this. getClass() .getName() +": Dicom Toolkit la yer: " + | |
| 138 | "Exception thrown wh ile attemp ting to op en "+textF ilename+". "); | |
| 139 | throw ne w TextFile NotFoundEx ception("C ould not f ind or ope n "+textFi lename+"." , noFile); | |
| 140 | } | |
| 141 | fi nally{ | |
| 142 | if(b uffer != n ull){ | |
| 143 | try{ | |
| 144 | buffer.c lose(); | |
| 145 | } | |
| 146 | catch( Throwable T){ | |
| 147 | logger.e rror(this. getClass() .getName() +": Dicom Toolkit la yer: "+ | |
| 148 | "E xception t hrown whil e closing Text File "+textFile name+"."); | |
| 149 | } | |
| 150 | System .gc(); | |
| 151 | } | |
| 152 | } | |
| 153 | ||
| 154 | } | |
| 155 | /** | |
| 156 | * Inv oke method to create a DicomDa taSet base d on a Tex t data str eam. | |
| 157 | * | |
| 158 | * @pa ram textSt ream repre sents the stream of VistA Imag ing TXT da ta. | |
| 159 | * @re turn repre sents the encapsulat ed DicomDa taSet that is safe f or DicomGe neric Laye r. | |
| 160 | * @th rows TextF ileNotFoun dException | |
| 161 | * @th rows TextF ileExcepti on | |
| 162 | * @th rows TextF ileExtract ionExcepti on | |
| 163 | */ | |
| 164 | public IDicomDat aSet creat eDicomData Set(Buffer edReader b uffer, Ori ginalPixel DataInfo p ixelData) | |
| 165 | throws TextFileEx ception, T extFileExt ractionExc eption { | |
| 166 | ||
| 167 | lo gger.info( "... Dicom Toolkit L ayer: pars ing Text d ata into D icomDataSe t ..."); | |
| 168 | lo gger.debug ("... Star t Text Dat a Stream p arsing... "); | |
| 169 | th is.origina lPixelData = pixelDa ta; | |
| 170 | ||
| 171 | // Invoke par ser. | |
| 172 | th is.parseTe xtFile(buf fer, false ); | |
| 173 | ||
| 174 | pi xelData = this.origi nalPixelDa ta; | |
| 175 | // encapsulat e DicomDat aSet objec t. | |
| 176 | re turn (this .encapsula teDicomDat aSet()); | |
| 177 | } | |
| 178 | ||
| 179 | /** | |
| 180 | * Enc apsulates the DCF To olkit spec ific Dicom DataSet ob ject. | |
| 181 | * | |
| 182 | * @re turn repre sents the Generic Di comDataSet object. | |
| 183 | */ | |
| 184 | privat e IDicomDa taSet enca psulateDic omDataSet( ){ | |
| 185 | ||
| 186 | te stLogger.i nfo("... e ncapsulati ng DDS ... "); | |
| 187 | tr y{ | |
| 188 | //toolki tDDS = (ID icomDataSe t)SpringCo ntext.getC ontext().g etBean("Di comDataSet "); | |
| 189 | //to olkitDDS.s etDicomDat aSet(dicom DataSet); | |
| 190 | toolkitD DS = new D icomDataSe tImpl(dico mDataSet); | |
| 191 | } | |
| 192 | ca tch(Except ion e){ | |
| 193 | logger.e rror("Erro r: " + e.g etMessage( )); | |
| 194 | logger.e rror(this. getClass() .getName() +": Dicom Toolkit la yer: " + | |
| 195 | "Exception thrown wh ile encaps ulating Di com Datase t."); | |
| 196 | e.printS tackTrace( ); | |
| 197 | } | |
| 198 | re turn toolk itDDS; | |
| 199 | } | |
| 200 | ||
| 201 | /** | |
| 202 | * Inv oke method to extrac t HIS upda tes from a n open Tex t data str eam. | |
| 203 | * | |
| 204 | * @pa ram buffer represent s the stre am of Vist A Imaging TXT data. | |
| 205 | * @re turn HashM ap of DICO m tag-valu e pairs to be update d in DICOM DataSet. | |
| 206 | * @th rows TextF ileExtract ionExcepti on | |
| 207 | */ | |
| 208 | public HashMap<S tring, Str ing> getHi sUpdates(B ufferedRea der buffer ) | |
| 209 | throws TextFileEx ception, T extFileExt ractionExc eption { | |
| 210 | ||
| 211 | lo gger.info( "... Parsi ng text da ta HIS upd ate sectio n ..."); | |
| 212 | lo gger.debug ("... Cont inue Text Data parsi ng for Vis tA updates ... "); | |
| 213 | ||
| 214 | Ha shMap<Stri ng, String > hisChang es=null; | |
| 215 | hi sChanges = this.pars eHisUpdate s(buffer); | |
| 216 | tr y { | |
| 217 | buff er.close() ; | |
| 218 | } | |
| 219 | ca tch(IOExce ption io){ | |
| 220 | logger.e rror("Cann ot close T ext Stream Buffer.") ; | |
| 221 | throw ne w TextFile Extraction Exception( ); | |
| 222 | } | |
| 223 | re turn (hisC hanges); | |
| 224 | } | |
| 225 | ||
| 226 | /** | |
| 227 | * Inv oke method to extrac t HIS upda tes from a n open Tex t data str eam. | |
| 228 | * | |
| 229 | * @pa ram buffer represent s the stre am of Vist A Imaging TXT data. | |
| 230 | * @re turn HashM ap of DICO m tag-valu e pairs to be update d in DICOM DataSet. | |
| 231 | * @th rows TextF ileExtract ionExcepti on | |
| 232 | */ | |
| 233 | public HashMap<S tring, Str ing> extra ctHisUpdat esfromText Stream(Siz edInputStr eam sizedT extStream) | |
| 234 | throws TextFileEx ception, T extFileExt ractionExc eption { | |
| 235 | ||
| 236 | lo gger.info( "... Parsi ng text da ta HIS upd ate sectio n ..."); | |
| 237 | lo gger.debug ("... Star t parsing VistA upda tes... "); | |
| 238 | ||
| 239 | Ha shMap<Stri ng, String > hisChang es=null; | |
| 240 | Bu fferedRead er buffer = new Buff eredReader (new Input StreamRead er(sizedTe xtStream.g etInStream ())); | |
| 241 | ||
| 242 | hi sChanges = this.pars eHisUpdate s(buffer); | |
| 243 | tr y { | |
| 244 | buff er.close() ; | |
| 245 | } | |
| 246 | ca tch(IOExce ption io){ | |
| 247 | logger.e rror("Cann ot close T ext Stream Buffer.") ; | |
| 248 | throw ne w TextFile Extraction Exception( ); | |
| 249 | } | |
| 250 | re turn (hisC hanges); | |
| 251 | } | |
| 252 | ||
| 253 | /** | |
| 254 | * Par se the Tex t file. T he Text fi le is made up of two sections, "Data1" a nd | |
| 255 | * "DI COM Data". Both sec tions are read and d ecoded. | |
| 256 | * | |
| 257 | * @pa ram buffer represent s the Text file now in the for m of a Buf ferReader object. | |
| 258 | * @th rows TextF ileExcepti on | |
| 259 | * @th rows TextF ileExtract ionExcepti on | |
| 260 | */ | |
| 261 | privat e void par seTextFile (BufferedR eader buff er, boolea n doClose) throws Te xtFileExce ption, | |
| 262 | TextFile Extraction Exception{ | |
| 263 | ||
| 264 | St ring textL ine = ""; | |
| 265 | te stLogger.i nfo("... P arsing tex t data top section . .."); | |
| 266 | tr y{ | |
| 267 | //Loop t hru the li nes until $$BEGIN DA TA1. | |
| 268 | //Ignore each line until $$B EGIN DATA1 | |
| 269 | do{ | |
| 270 | text Line = thi s.getNextT extLine(bu ffer); | |
| 271 | } while( !(textLine .equals("$ $BEGIN DAT A1"))); | |
| 272 | ||
| 273 | do{ | |
| 274 | text Line = thi s.getNextT extLine(bu ffer); | |
| 275 | //Ex tract only the PATIE NTS_XXX fi elds | |
| 276 | //Re place comm as with ca rats in Pa tient's Na me field | |
| 277 | //10 0507-WFP-R emoving al l IF state ments exce pt DCM_TO_ TGA_PARAME TERS. | |
| 278 | // Reason is the applic ation does not use t his inform ation. It serves | |
| 279 | // no purpose . But I'm leaving t he code in case I'm wrong. | |
| 280 | /* | |
| 281 | if(t extLine.st artsWith(" PATIENTS_N AME")){ | |
| 282 | String pat ientsName = textLine .substring (textLine. indexOf("= ")+1); | |
| 283 | } | |
| 284 | if(t extLine.st artsWith(" PATIENTS_I D")){ | |
| 285 | String pat ientsID = textLine.s ubstring(t extLine.in dexOf("=") +1); | |
| 286 | } | |
| 287 | if(t extLine.st artsWith(" PATIENTS_B IRTH_DATE" )){ | |
| 288 | String pat ientsBirth = textLin e.substrin g(textLine .indexOf(" =")+1); | |
| 289 | } | |
| 290 | if(t extLine.st artsWith(" PATIENTS_A GE")){ | |
| 291 | String pat ientsAge = textLine. substring( textLine.i ndexOf("=" )+1); | |
| 292 | } | |
| 293 | if(t extLine.st artsWith(" PATIENTS_S EX")){ | |
| 294 | String pat ientsSex = textLine. substring( textLine.i ndexOf("=" )+1); | |
| 295 | } | |
| 296 | if(t extLine.st artsWith(" ACCESSION_ NUMBER")){ | |
| 297 | String acc essionNumb er = textL ine.substr ing(textLi ne.indexOf ("=")+1); | |
| 298 | } | |
| 299 | */ | |
| 300 | if(t extLine.st artsWith(" DCM_TO_TGA _PARAMETER S")){ | |
| 301 | String dcm totgaParam eters = te xtLine.sub string(tex tLine.inde xOf("=")+1 ); | |
| 302 | this.origi nalPixelDa ta.setDcmt otgaParame ters(dcmto tgaParamet ers); | |
| 303 | } | |
| 304 | //Pl ace these PATIENTS_X XX fields into a tem p DicomDat aSet objec t. | |
| 305 | }while(! (textLine. equals("$$ END DATA1" ))); | |
| 306 | ||
| 307 | //Invoke parseDico mDataSecti on to pars e rest of file. | |
| 308 | this.par seDicomDat aSection(b uffer); | |
| 309 | if (doCl ose) | |
| 310 | buff er.close() ; | |
| 311 | } | |
| 312 | ca tch(IOExce ption io){ | |
| 313 | logger.e rror("Cann ot extract from Text File."); | |
| 314 | logger.e rror("Work ing on Lin e: " + tex tLine); | |
| 315 | throw ne w TextFile Extraction Exception( ); | |
| 316 | } | |
| 317 | } | |
| 318 | ||
| 319 | /** | |
| 320 | * Par se the "DI COM Data" section of the Text file. Thi s is the g runt of th e work | |
| 321 | * tha t needs to be done. | |
| 322 | * | |
| 323 | * @pa ram buffer represent s the Text file now in the for m of a Buf feredReade r object. | |
| 324 | * @th rows TextF ileExtract ionExcepti on | |
| 325 | */ | |
| 326 | privat e void par seDicomDat aSection(B ufferedRea der buffer ) | |
| 327 | throws T extFileExt ractionExc eption{ | |
| 328 | ||
| 329 | th is.dicomDa taSet = ne w DicomDat aSet(); | |
| 330 | St ring textD icomLine = ""; | |
| 331 | bo olean sequ enceFlag = false; | |
| 332 | Di comSQEleme nt sequenc eElement = null; | |
| 333 | te stLogger.i nfo("... P arsing tex t data Dic om DataSet section . .."); | |
| 334 | tr y{ | |
| 335 | //Mark B uffer. | |
| 336 | buffer.m ark(255); | |
| 337 | //Declar e lineArra y object. | |
| 338 | ArrayLis t<String> lineArray = new Arra yList<Stri ng>(); | |
| 339 | //Loop t hru the li nes until $BEGIN DIC OM DATA. | |
| 340 | //Ignore each line until $$B EGIN DICOM DATA. | |
| 341 | do{ | |
| 342 | text DicomLine = this.get NextTextLi ne(buffer) ; | |
| 343 | } while( !(textDico mLine.equa ls("$$BEGI N DICOM DA TA"))); | |
| 344 | ||
| 345 | textDico mLine = th is.getNext TextLine(b uffer); | |
| 346 | // testLogg er.debug(" Current Li ne: " + te xtDicomLin e); | |
| 347 | //Loop t hru each l ine until $$END DICO M DATA. | |
| 348 | while(!( textDicomL ine.equals ("$$END DI COM DATA") )){ | |
| 349 | //Ch eck for Od d Group. | |
| 350 | Stri ng checkGr oup = text DicomLine. substring( 0,4); | |
| 351 | //St ring check Element = textDicomL ine.substr ing(5,9); | |
| 352 | int i = Intege r.parseInt (checkGrou p, 16); | |
| 353 | if(t his.isGrou pToBeAdded (i)){ | |
| 354 | //If no Odd gr oup or Gro up 88, | |
| 355 | //Check if 9th chara cter in li ne is a "| ". | |
| 356 | if(!(textD icomLine.s ubstring(9 ,10).equal s("|"))){ | |
| 357 | //If no, | |
| 358 | //Add string to lineArray object. | |
| 359 | lineAr ray.add(te xtDicomLin e); | |
| 360 | //Set Sequence f lag. | |
| 361 | sequen ceFlag = t rue; | |
| 362 | } | |
| 363 | else{ | |
| 364 | //If yes, | |
| 365 | //Chec k if Seque nce flag i s set. | |
| 366 | if(seq uenceFlag) { | |
| 367 | //If y es, | |
| 368 | // Reset Mark Buffer. This allow s to pick up the ele ment after the | |
| 369 | // sequence again. | |
| 370 | bu ffer.reset (); | |
| 371 | // Invoke ext ractSequen ceData met hod and pa ss lineArr ay. | |
| 372 | se quenceElem ent = this .extractSe quenceData (lineArray ); | |
| 373 | // Add DicomS QElement o bject to d ds. | |
| 374 | th is.dicomDa taSet.inse rt(sequenc eElement); | |
| 375 | // Clean line Array obje ct. | |
| 376 | li neArray.cl ear(); | |
| 377 | // Unset the Sequence f lag. | |
| 378 | se quenceFlag = false; | |
| 379 | } | |
| 380 | else{ | |
| 381 | //If n o, | |
| 382 | // Invoke ext ractDicomE lement met hod and pa ss the lin e. | |
| 383 | th is.extract DicomEleme nt(textDic omLine, th is.dicomDa taSet); | |
| 384 | } | |
| 385 | //End If f or "|" del imiter. | |
| 386 | } | |
| 387 | //En d If for O dd Group. | |
| 388 | } | |
| 389 | //Ma rk Buffer. | |
| 390 | buff er.mark(25 5); | |
| 391 | text DicomLine = this.get NextTextLi ne(buffer) ; | |
| 392 | // te stLogger.d ebug("Curr ent Line: " + textDi comLine); | |
| 393 | ||
| 394 | //End Lo op due to $$END DICO M DATA or EOF. | |
| 395 | } | |
| 396 | } | |
| 397 | ca tch(IOExce ption io){ | |
| 398 | logger.e rror(io.ge tMessage() ); | |
| 399 | logger.e rror(this. getClass() .getName() +": " + | |
| 400 | "Exception thrown wh ile readin g Text fil e's Dicom Data Secti on."); | |
| 401 | throw ne w TextFile Extraction Exception( "Failure t o read Dic omData Sec tion.", io ); | |
| 402 | } | |
| 403 | ca tch(Number FormatExce ption numb er){ | |
| 404 | logger.e rror(numbe r.getMessa ge()); | |
| 405 | logger.e rror(this. getClass() .getName() +": Workin g on Dicom Line: " + textDicom Line); | |
| 406 | throw ne w TextFile Extraction Exception( "Failure o n Number F ormat.", n umber); | |
| 407 | } | |
| 408 | ||
| 409 | th is.customT GAElementC leanup(); | |
| 410 | } | |
| 411 | ||
| 412 | /** | |
| 413 | * Rec ursive met hod to han dle the Se quences an d nested S equences i nside of t he "DICOM | |
| 414 | * Dat a" section . | |
| 415 | * | |
| 416 | * @pa ram lines represents the Array of Sequen ce lines i n the Text file. | |
| 417 | * @re turn repre sents the Sequence l ines conve rted into a single D icom Seque nce Elemen t. | |
| 418 | * @th rows TextF ileExtract ionExcepti on | |
| 419 | */ | |
| 420 | privat e DicomSQE lement ext ractSequen ceData(Arr ayList<Str ing> lines ) | |
| 421 | throws T extFileExt ractionExc eption{ | |
| 422 | ||
| 423 | Di comDataSet seqDDS = new DicomD ataSet(); | |
| 424 | Ar rayList<Di comDataSet > ddsArray List = new ArrayList <DicomData Set>(); | |
| 425 | // Create Dic omSQElemen t object. | |
| 426 | Di comSQEleme nt sequenc e = null; | |
| 427 | ||
| 428 | St ring eleme nt = new S tring(""); | |
| 429 | // Initialize seqDDS in dex to 0. | |
| 430 | in t ddsIndex = 0; | |
| 431 | // Create pre viouseSeqI tem. | |
| 432 | St ring previ ousSeqItem = ""; | |
| 433 | // Set Sequen ce flag to false. | |
| 434 | bo olean sequ enceFlag = false; | |
| 435 | // Declare se qArray obj ect. | |
| 436 | Ar rayList<St ring> seqA rray = new ArrayList <String>() ; | |
| 437 | tr y{ | |
| 438 | // Loop thru each line of lines a rray until null. Gr ab line in Loop. | |
| 439 | fo r(int x=0; x<lines.s ize(); x++ ){ | |
| 440 | ||
| 441 | //Split line into two substr ings using first per iod. | |
| 442 | String s eqLine = ( String)lin es.get(x); | |
| 443 | String s ubLines[] = seqLine. split("\\. ",2); | |
| 444 | //Assign first sub string to Tag. | |
| 445 | element = subLines [0]; | |
| 446 | //Split second sub string int o two sub- strings us ing first carat. | |
| 447 | String s ubSubLines [] = subLi nes[1].spl it("\\^",2 ); | |
| 448 | //Assign first sub -substring to seqIte m. | |
| 449 | String s eqItem = s ubSubLines [0]; | |
| 450 | //Assign second su b-substrin g to seqAr ray object . | |
| 451 | String e lementData = subSubL ines[1]; | |
| 452 | if(previ ousSeqItem .equals("" )){ | |
| 453 | //If yes , | |
| 454 | //In itialize p reviousSeq Item with seqItem. | |
| 455 | prev iousSeqIte m = seqIte m; | |
| 456 | } | |
| 457 | //Check if first s ub-substri ng matches seqItem. | |
| 458 | if(!(pre viousSeqIt em.equals( seqItem))) { | |
| 459 | //If no, | |
| 460 | ddsA rrayList.a dd(seqDDS) ; | |
| 461 | seqD DS = new D icomDataSe t(); | |
| 462 | prev iousSeqIte m = seqIte m; | |
| 463 | //End If | |
| 464 | } | |
| 465 | String c heckGroup = elementD ata.substr ing(0,4); | |
| 466 | int g = Integer.pa rseInt(che ckGroup, 1 6); | |
| 467 | if(this. isGroupToB eAdded(g)) { | |
| 468 | //Ch eck if 9th character is a "|". This mea ns another Sequence. | |
| 469 | //Th is if/else determine s if the l ine is ano ther seque nce. | |
| 470 | if(! (elementDa ta.substri ng(9,10).e quals("|") )){ | |
| 471 | //If no, | |
| 472 | //Add stri ng to seqA rray objec t. | |
| 473 | seqArray.a dd(element Data); | |
| 474 | //Set Sequ ence flag. | |
| 475 | sequenceFl ag = true; | |
| 476 | //If yes, | |
| 477 | } | |
| 478 | else { | |
| 479 | //Check if Sequence flag is se t. | |
| 480 | if(sequenc eFlag){ | |
| 481 | //If y es, | |
| 482 | //Decr ement line s array in dex. | |
| 483 | x--; | |
| 484 | //Re-i nvoke extr actSequenc eData meth od and pas s lineArra y. | |
| 485 | DicomS QElement s ubSequence = this.ex tractSeque nceData(se qArray); | |
| 486 | //add DicomSQEle ment objec t to dds. | |
| 487 | seqDDS .insert(su bSequence) ; | |
| 488 | //Unse t the Sequ ence flag. | |
| 489 | ||
| 490 | sequen ceFlag = f alse; | |
| 491 | } | |
| 492 | else{ | |
| 493 | //If n o, | |
| 494 | //Invo ke extract DicomEleme nt method and pass t he second substring and | |
| 495 | // an d temp Dic omDataSet object. | |
| 496 | this.e xtractDico mElement(e lementData , seqDDS); | |
| 497 | //End If for Seq uence flag . | |
| 498 | } | |
| 499 | //End If f or "|" del imiter. | |
| 500 | } | |
| 501 | //En d If for G roup Check | |
| 502 | } | |
| 503 | //Increm ent lines array inde x. | |
| 504 | // Loop thru lines arra y is compl ete. | |
| 505 | } | |
| 506 | // Check if S equence fl ag is set. | |
| 507 | if (sequenceF lag){ | |
| 508 | // If yes, | |
| 509 | //Re-inv oke extrac tSequenceD ata method and pass lineArray. | |
| 510 | DicomSQE lement sub Sequence = this.extr actSequenc eData(seqA rray); | |
| 511 | //add Di comSQEleme nt object to dds. | |
| 512 | seqDDS.i nsert(subS equence); | |
| 513 | //Unset the Sequen ce flag. | |
| 514 | sequence Flag = fal se; | |
| 515 | } | |
| 516 | dd sArrayList .add(seqDD S); | |
| 517 | dd sIndex = d dsArrayLis t.size(); | |
| 518 | Di comDataSet ddsSeqIte ms[] = new DicomData Set[ddsInd ex]; | |
| 519 | fo r(int y=0; y<ddsInde x; y++){ | |
| 520 | ddsSeqIte ms[y] = dd sArrayList .get(y); | |
| 521 | } | |
| 522 | At tributeTag tag = new Attribute Tag(elemen t); | |
| 523 | se quence = n ew DicomSQ Element(ta g, ddsSeqI tems); | |
| 524 | } | |
| 525 | ca tch(DCSExc eption dcs ){ | |
| 526 | logger.e rror(dcs.g etMessage( )); | |
| 527 | logger.e rror(this. getClass() .getName() +": " + | |
| 528 | "Exception thrown wh ile extrac ting Seque nce Data." ); | |
| 529 | throw ne w TextFile Extraction Exception( "Failure t o extract Sequence." , dcs); | |
| 530 | } | |
| 531 | re turn seque nce; | |
| 532 | } | |
| 533 | ||
| 534 | /** | |
| 535 | * Ext racts a si ngle parse d line, in dependent of any seq uences, an d converts it to a D ICOM | |
| 536 | * Ele ment and s tores the DICOM Elme nt into th e desired DCF Toolki t specific | |
| 537 | * Dic omDataSet. | |
| 538 | * | |
| 539 | * @pa ram line r epresents the parsed line from the Text file. | |
| 540 | * @pa ram dds re presents t he DCF Too lkit speci fic DicomD ataSet obj ect. | |
| 541 | * @th rows TextF ileExtract ionExcepti on | |
| 542 | */ | |
| 543 | privat e void ext ractDicomE lement(Str ing line, DicomDataS et dds) | |
| 544 | throws T extFileExt ractionExc eption{ | |
| 545 | // Setup the ^ parser. | |
| 546 | St ring split CaratPatte rn = "\\^" ; | |
| 547 | Pa ttern pInf o = Patter n.compile( splitCarat Pattern); | |
| 548 | // Setup the | parser. | |
| 549 | St ring split PipePatter n = "\\|"; | |
| 550 | Pa ttern pFie lds = Patt ern.compil e(splitPip ePattern); | |
| 551 | // Setup the , parser. | |
| 552 | St ring split CommaPatte rn = ","; | |
| 553 | Pa ttern pTag = Pattern .compile(s plitCommaP attern); | |
| 554 | ||
| 555 | St ring field s[] = new String[4]; | |
| 556 | fi elds = pFi elds.split (line); | |
| 557 | // Parse the basic data . | |
| 558 | // Set the Ta g variable . | |
| 559 | St ring tag = fields[0] ; | |
| 560 | ||
| 561 | St ring eleme ntInfo = f ields[1]; | |
| 562 | sh ort elemen tVR = ' '; | |
| 563 | ||
| 564 | tr y{ | |
| 565 | Attribut eTag aTag = new Attr ibuteTag(t ag); | |
| 566 | ||
| 567 | //Get th e VR. | |
| 568 | if(eleme ntInfo.cha rAt(elemen tInfo.leng th()-3) == '^'){ | |
| 569 | Stri ng subElem entInfo[] = new Stri ng[2]; | |
| 570 | subE lementInfo = pInfo.s plit(line) ; | |
| 571 | elem entVR = Di comDataDic tionary.ge tVR(subEle mentInfo[1 ]); | |
| 572 | orig inalPixelD ata.setVal ueRepresen tationInTe xtFile(tru e); | |
| 573 | } | |
| 574 | else{ | |
| 575 | elem entVR = Di comDataDic tionary.ge tElementVR (aTag); | |
| 576 | orig inalPixelD ata.setVal ueRepresen tationInTe xtFile(fal se); | |
| 577 | } | |
| 578 | ||
| 579 | String m ultiplicit y; | |
| 580 | //This I F makes su re the VM, ML values exist. | |
| 581 | if(field s.length > 2){ | |
| 582 | mult iplicity = fields[2] ; | |
| 583 | //Th is IF make s sure the re is a co mma delimi ter. | |
| 584 | if(m ultiplicit y.indexOf( ",") >= 0) { | |
| 585 | String val ue; | |
| 586 | if(fields. length < 4 ){ | |
| 587 | value = ""; | |
| 588 | } | |
| 589 | else{ | |
| 590 | value = fields[3 ]; | |
| 591 | if(val ue.equals( "<unknown> ")){ | |
| 592 | va lue = ""; | |
| 593 | } | |
| 594 | } | |
| 595 | String mul tiple[] = multiplici ty.split(" ,"); | |
| 596 | //Assign t he VM to a temp fiel d. |VM,ML| | |
| 597 | int vm = I nteger.par seInt(mult iple[0]); | |
| 598 | //Assign t he ML to a temp fiel d. |VM,ML| | |
| 599 | int ml = I nteger.par seInt(mult iple[1]); | |
| 600 | //100407-W FP-Discove red DCF do es not han dle VR=OF. Adding I F | |
| 601 | // statem ent to ign ore any te xt lines w ith this V R value. | |
| 602 | if(element VR == Dico mDataDicti onary.getV R("OF")){ | |
| 603 | return ; | |
| 604 | } | |
| 605 | //If VM is greater t han 1. | |
| 606 | if(vm > 1) { | |
| 607 | ||
| 608 | if(ele mentVR == DicomDataD ictionary. getVR("OB" )){ | |
| 609 | Di comOBEleme nt element ; | |
| 610 | by te[] dataA rray = nul l; | |
| 611 | // If element already e xist, then pull the data and a dd new val ue. | |
| 612 | if (dds.conta insElement (aTag)){ | |
| 613 | //Extrac t element from dds. | |
| 614 | element = (DicomOB Element)dd s.findElem ent(aTag); | |
| 615 | //Extrac t the exis ting data from the e lement | |
| 616 | ByteBuff er dataBuf fer = elem ent.getBuf fer(); | |
| 617 | dataBuff er.get(dat aArray); | |
| 618 | } | |
| 619 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 620 | // truncati on of data . | |
| 621 | Lo ng nuValue = new Lon g(value); | |
| 622 | // Add nuValu e to exist ing data. | |
| 623 | by te[] nuArr ay = this. addElement ToByteArra y(dataArra y, nuValue ); | |
| 624 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 625 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 626 | // overwrit es the ori ginal elem ent. | |
| 627 | Di comOBEleme nt updated Element = new DicomO BElement(a Tag, nuArr ay); | |
| 628 | dd s.insert(u pdatedElem ent); | |
| 629 | } | |
| 630 | else i f(elementV R == Dicom DataDictio nary.getVR ("US")){ | |
| 631 | Di comUSEleme nt element ; | |
| 632 | in t[] dataAr ray = null ; | |
| 633 | // If element already e xist, then pull the data and a dd new val ue. | |
| 634 | if (dds.conta insElement (aTag)){ | |
| 635 | //Extrac t element from dds. | |
| 636 | element = (DicomUS Element)dd s.findElem ent(aTag); | |
| 637 | //Extrac t the exis ting data from the e lement | |
| 638 | dataArra y = elemen t.getUSDat a(); | |
| 639 | } | |
| 640 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 641 | // truncati on of data . | |
| 642 | Lo ng nuValue = new Lon g(value); | |
| 643 | // Add nuValu e to exist ing data. | |
| 644 | in t[] nuArra y = this.a ddElementT oIntArray( dataArray, nuValue); | |
| 645 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 646 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 647 | // overwrit es the ori ginal elem ent. | |
| 648 | Di comUSEleme nt updated Element = new DicomU SElement(a Tag, nuArr ay); | |
| 649 | dd s.insert(u pdatedElem ent); | |
| 650 | } | |
| 651 | else i f(elementV R == Dicom DataDictio nary.getVR ("SL")){ | |
| 652 | Di comSLEleme nt element ; | |
| 653 | in t[] dataAr ray = null ; | |
| 654 | // If element already e xist, then pull the data and a dd new val ue. | |
| 655 | if (dds.conta insElement (aTag)){ | |
| 656 | //Extrac t element from dds. | |
| 657 | element = (DicomSL Element)dd s.findElem ent(aTag); | |
| 658 | //Extrac t the exis ting data from the e lement | |
| 659 | dataArra y = elemen t.getSLDat a(); | |
| 660 | } | |
| 661 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 662 | // truncati on of data . | |
| 663 | Lo ng nuValue = new Lon g(value); | |
| 664 | // Add nuValu e to exist ing data. | |
| 665 | in t[] nuArra y = this.a ddElementT oIntArray( dataArray, nuValue); | |
| 666 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 667 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 668 | // overwrit es the ori ginal elem ent. | |
| 669 | Di comSLEleme nt updated Element = new DicomS LElement(a Tag, nuArr ay); | |
| 670 | dd s.insert(u pdatedElem ent); | |
| 671 | } | |
| 672 | else i f(elementV R == Dicom DataDictio nary.getVR ("OW")){ | |
| 673 | Di comOWEleme nt element ; | |
| 674 | sh ort[] data Array = nu ll; | |
| 675 | // If element already e xist, then pull the data and a dd new val ue. | |
| 676 | if (dds.conta insElement (aTag)){ | |
| 677 | //Extrac t element from dds. | |
| 678 | element = (DicomOW Element)dd s.findElem ent(aTag); | |
| 679 | //Extrac t the exis ting data from the e lement | |
| 680 | ShortBuf fer dataBu ffer = (Sh ortBuffer) element.ge tValue(); // 3.2.2c getShortBu ffer(); | |
| 681 | dataBuff er.get(dat aArray); | |
| 682 | } | |
| 683 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 684 | // truncati on of data . | |
| 685 | Lo ng nuValue = new Lon g(value); | |
| 686 | // Add nuValu e to exist ing data. | |
| 687 | sh ort[] nuAr ray = this .addElemen tToShortAr ray(dataAr ray, nuVal ue); | |
| 688 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 689 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 690 | // overwrit es the ori ginal elem ent. | |
| 691 | Di comOWEleme nt updated Element = new DicomO WElement(a Tag, nuArr ay); | |
| 692 | dd s.insert(u pdatedElem ent); | |
| 693 | } | |
| 694 | else i f(elementV R == Dicom DataDictio nary.getVR ("SS")){ | |
| 695 | Di comSSEleme nt element ; | |
| 696 | sh ort[] data Array = nu ll; | |
| 697 | // If element already e xist, then pull the data and a dd new val ue. | |
| 698 | if (dds.conta insElement (aTag)){ | |
| 699 | //Extrac t element from dds. | |
| 700 | element = (DicomSS Element)dd s.findElem ent(aTag); | |
| 701 | //Extrac t the exis ting data from the e lement | |
| 702 | dataArra y = elemen t.getSSDat a(); | |
| 703 | } | |
| 704 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 705 | // truncati on of data . | |
| 706 | Lo ng nuValue = new Lon g(value); | |
| 707 | // Add nuValu e to exist ing data. | |
| 708 | sh ort[] nuAr ray = this .addElemen tToShortAr ray(dataAr ray, nuVal ue); | |
| 709 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 710 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 711 | // overwrit es the ori ginal elem ent. | |
| 712 | Di comSSEleme nt updated Element = new DicomS SElement(a Tag, nuArr ay); | |
| 713 | dd s.insert(u pdatedElem ent); | |
| 714 | } | |
| 715 | else i f(elementV R == Dicom DataDictio nary.getVR ("UL")){ | |
| 716 | Di comULEleme nt element ; | |
| 717 | in t[] dataAr ray = null ; | |
| 718 | // If element already e xist, then pull the data and a dd new val ue. | |
| 719 | if (dds.conta insElement (aTag)){ | |
| 720 | //Extrac t element from dds. | |
| 721 | element = (DicomUL Element)dd s.findElem ent(aTag); | |
| 722 | //Extrac t the exis ting data from the e lement | |
| 723 | dataArra y = elemen t.getULDat a(); | |
| 724 | } | |
| 725 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 726 | // truncati on of data . | |
| 727 | Lo ng nuValue = new Lon g(value); | |
| 728 | // Add nuValu e to exist ing data. | |
| 729 | in t[] nuArra y = this.a ddElementT oIntArray( dataArray, nuValue); | |
| 730 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 731 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 732 | // overwrit es the ori ginal elem ent. | |
| 733 | Di comULEleme nt updated Element = new DicomU LElement(a Tag, nuArr ay); | |
| 734 | dd s.insert(u pdatedElem ent); | |
| 735 | } | |
| 736 | else i f(elementV R == Dicom DataDictio nary.getVR ("FL")){ | |
| 737 | DicomFLE lement ele ment; | |
| 738 | fl oat[] data Array = nu ll; | |
| 739 | // If element already e xist, then pull the data and a dd new val ue. | |
| 740 | if (dds.conta insElement (aTag)){ | |
| 741 | //Extrac t element from dds. | |
| 742 | element = (DicomFL Element)dd s.findElem ent(aTag); | |
| 743 | //Extrac t the exis ting data from the e lement | |
| 744 | dataArra y = elemen t.getFLDat a(); | |
| 745 | } | |
| 746 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 747 | // truncati on of data . | |
| 748 | fl oat nuValu e = new Fl oat(value) ; | |
| 749 | // Add nuValu e to exist ing data. | |
| 750 | fl oat[] nuAr ray = this .addElemen tToFloatAr ray(dataAr ray, nuVal ue); | |
| 751 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 752 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 753 | // overwrit es the ori ginal elem ent. | |
| 754 | Di comFLEleme nt updated Element = new DicomF LElement(a Tag, nuArr ay); | |
| 755 | dd s.insert(u pdatedElem ent); | |
| 756 | } | |
| 757 | else i f(elementV R == Dicom DataDictio nary.getVR ("FD")){ | |
| 758 | DicomFDE lement ele ment; | |
| 759 | do uble[] dat aArray = n ull; | |
| 760 | // If element already e xist, then pull the data and a dd new val ue. | |
| 761 | if (dds.conta insElement (aTag)){ | |
| 762 | //Extrac t element from dds. | |
| 763 | element = (DicomFD Element)dd s.findElem ent(aTag); | |
| 764 | //Extrac t the exis ting data from the e lement | |
| 765 | dataArra y = elemen t.getFDDat a(); | |
| 766 | } | |
| 767 | // Assign val ue to nuVa lue. It u ses Long p rimitive t o make sur e there is no | |
| 768 | // truncati on of data . | |
| 769 | do uble nuVal ue = new D ouble(valu e); | |
| 770 | // Add nuValu e to exist ing data. | |
| 771 | do uble[] nuA rray = thi s.addEleme ntToDouble Array(data Array, nuV alue); | |
| 772 | // You cannot just add the nuArra y to the e xisting el ement in t he dds. | |
| 773 | // Must cre ate a new element an d insert i t into the dds. Thi s automati cally | |
| 774 | // overwrit es the ori ginal elem ent. | |
| 775 | Di comFDEleme nt updated Element = new DicomF DElement(a Tag, nuArr ay); | |
| 776 | dd s.insert(u pdatedElem ent); | |
| 777 | } | |
| 778 | else{ | |
| 779 | // at th is point i t is assum ed value V R is of ch ar string, not binar y! | |
| 780 | St ring curre ntValue = ""; | |
| 781 | if (dds.conta insElement (aTag)){ | |
| 782 | // Extra ct element from dds -- Must re trieve eac h individu al value t his way | |
| 783 | // as th e VM is gr eater than 1. -- The n concaten ate togeth er again. | |
| 784 | DicomEle ment eleme nt = dds.f indElement (aTag); | |
| 785 | for(int i=0; i<ele ment.vm(); i++){ | |
| 786 | curr entValue = currentVa lue.concat (element.g etStringVa lue(i)); | |
| 787 | if(i < element .vm()-1){ | |
| 788 | currentVal ue = curre ntValue.co ncat("\\") ; | |
| 789 | } | |
| 790 | } | |
| 791 | } | |
| 792 | el se{ | |
| 793 | currentV alue = nul l; | |
| 794 | } | |
| 795 | ||
| 796 | // then Appen d a "\\" a nd the Val ue variabl e to this Tag. | |
| 797 | Di comElement updatedEl ement = Di comElement Factory.in stance().c reateEleme nt(aTag, | |
| 798 | (cur rentValue+ "\\"+value )); | |
| 799 | dd s.insert(u pdatedElem ent); | |
| 800 | } | |
| 801 | } | |
| 802 | //If ML is greater t han 1. | |
| 803 | else if(ml > 1){ | |
| 804 | //then extract t his Tag fr om the dds . | |
| 805 | String currentVa lue; | |
| 806 | if(dds .containsE lement(aTa g)){ | |
| 807 | cu rrentValue = dds.get ElementStr ingValue(a Tag); | |
| 808 | } | |
| 809 | else{ | |
| 810 | cu rrentValue = null; | |
| 811 | } | |
| 812 | //then Append th e Value va riable to this Tag. | |
| 813 | if(aTa g.group() != 0x7FE0) { | |
| 814 | Di comElement updatedEl ement = Di comElement Factory.in stance().c reateEleme nt(aTag, | |
| 815 | (cur rentValue+ value)); | |
| 816 | dd s.insert(u pdatedElem ent); | |
| 817 | } | |
| 818 | if(aTa g.group() == 0x7FE0) { | |
| 819 | if (ml == 2){ | |
| 820 | String p arsedValue s[] = valu e.split("= "); | |
| 821 | String l engthValue = parsedV alues[1]; | |
| 822 | String p arsedLengt h[] = leng thValue.sp lit(" "); | |
| 823 | String p ixelDataLe ngth = par sedLength[ 0].trim(); | |
| 824 | Long len gthLong = new Long(p ixelDataLe ngth); | |
| 825 | this.ori ginalPixel Data.setOr iginalLeng th(lengthL ong.longVa lue()); | |
| 826 | } | |
| 827 | if (ml == 3){ | |
| 828 | String p arsedValue s[] = valu e.split("= "); | |
| 829 | String l engthValue = parsedV alues[1]; | |
| 830 | String p arsedOffse t[] = leng thValue.sp lit(" "); | |
| 831 | String p ixelDataOf fset = par sedOffset[ 0].trim(); | |
| 832 | Integer offsetInt = new Inte ger(pixelD ataOffset) ; | |
| 833 | this.ori ginalPixel Data.setOr iginalOffs et(offsetI nt.intValu e()); | |
| 834 | } | |
| 835 | } | |
| 836 | } | |
| 837 | else{ | |
| 838 | //FUTU RE The if sequence w orks. But I like to find a mo re efficie nt way. | |
| 839 | //Attr ibuteTag a Tag = new AttributeT ag(tag); | |
| 840 | if((aT ag.element () == 0) | | (aTag.el ement() == 1)){ | |
| 841 | if (aTag.grou p() <= 2){ | |
| 842 | DicomEle ment nuEle ment = Dic omElementF actory.ins tance().cr eateElemen t(aTag, | |
| 843 | value); | |
| 844 | dds.inse rt(nuEleme nt); | |
| 845 | } | |
| 846 | } | |
| 847 | else{ | |
| 848 | if (aTag.grou p() != 0x7 FE0){ | |
| 849 | DicomEle ment nuEle ment = Dic omElementF actory.ins tance().cr eateElemen t(aTag, | |
| 850 | value); | |
| 851 | dds.inse rt(nuEleme nt); | |
| 852 | } | |
| 853 | if ((aTag.gro up() == 0x 7FE0) && ( aTag.eleme nt() == 0x 0010)) { | |
| 854 | char isC arat = fie lds[1].cha rAt((field s[1].lengt h())-3); | |
| 855 | if(isCar at == '^') { | |
| 856 | Stri ng desc_vr Field = fi elds[1]; | |
| 857 | Stri ng desc_vr [] = desc_ vrField.sp lit("\\^") ; | |
| 858 | Stri ng textfil eVR = desc _vr[1]; | |
| 859 | orig inalPixelD ata.setOri ginalVR(Di comDataDic tionary.ge tVR(textfi leVR)); | |
| 860 | } | |
| 861 | else{ | |
| 862 | shor t bitsAllo cated = (s hort)dds.g etElementI ntValue(DC M.E_BITS_A LLOCATED); | |
| 863 | this .originalP ixelData.s etBitsAllo cated(bits Allocated) ; | |
| 864 | } | |
| 865 | } | |
| 866 | } | |
| 867 | } | |
| 868 | //End If f or VM/VL. | |
| 869 | } | |
| 870 | } | |
| 871 | else if (fields.le ngth == 2) { | |
| 872 | shor t vr = Dic omDataDict ionary.get ElementVR( aTag); | |
| 873 | if(D icomDataDi ctionary.g etVRString (vr).equal s("SQ")){ | |
| 874 | DicomSQEle ment nuEle ment = new DicomSQEl ement( aTa g, (DicomD ataSet[])n ull ); | |
| 875 | dds.insert (nuElement ); | |
| 876 | } | |
| 877 | } | |
| 878 | } | |
| 879 | ca tch(DCSExc eption dcs ){ | |
| 880 | logger.e rror(dcs.g etMessage( )); | |
| 881 | logger.e rror(this. getClass() .getName() +": " + | |
| 882 | "Exception thrown wh ile extrac ting Dicom Element." ); | |
| 883 | throw ne w TextFile Extraction Exception( "Failure t o extract Dicom Elem ent.", dcs ); | |
| 884 | } | |
| 885 | } | |
| 886 | ||
| 887 | /** | |
| 888 | * Par se the Tex t file HIS Update se ction. Th e Text fil e is made up of thre e sections , | |
| 889 | * "Da ta1", "DIC OM Data" a nd option ally "HIS UPDATE". Here only the HIS UP DATE secti on | |
| 890 | * is read and d ecoded. | |
| 891 | * | |
| 892 | * @pa ram buffer represent s the Text file now in the for m of a Buf ferReader object. | |
| 893 | * @th rows TextF ileExtract ionExcepti on | |
| 894 | */ | |
| 895 | //WFP- This does not appear to be cor rect. The re is no s uch sectio n in the . txt file. | |
| 896 | // Wi ll address later whe n I have t ime. | |
| 897 | privat e HashMap< String, St ring> pars eHisUpdate s(Buffered Reader buf fer) | |
| 898 | th rows TextF ileExtract ionExcepti on { | |
| 899 | ||
| 900 | St ring textL ine = ""; | |
| 901 | Ha shMap<Stri ng, String > hisUpdat es=null; | |
| 902 | // te stLogger.i nfo("... P arsing tex t data upd ate sectio n ..."); | |
| 903 | tr y { // par se line fo r initial "gggg,eeee " or "gggg ,eeee gggg ,eeee" tag s | |
| 904 | do { | |
| 905 | t extLine = this.getNe xtTextLine (buffer); | |
| 906 | } wh ile(!(text Line.start sWith("$$B EGIN HIS U PDATE"))); | |
| 907 | } | |
| 908 | catch(Te xtFileExtr actionExce ption tfee ) { // cat ch all | |
| 909 | logg er.info("W arning: NO HIS Updat e section in text da ta !!!"); | |
| 910 | logg er.debug(" Warning: o bsolete TX T format N O VistA up dates !!! "); | |
| 911 | retu rn hisUpda tes; | |
| 912 | } | |
| 913 | te xtLine = t his.getNex tTextLine( buffer); / / skip to first HIS update lin e | |
| 914 | hi sUpdates=n ew HashMap <String, S tring>(); | |
| 915 | ||
| 916 | wh ile(!(text Line.start sWith("$$E ND HIS UPD ATE"))) { | |
| 917 | try { // parse line for initi al "gggg,e eee" or "g ggg,eeee g ggg,eeee" tags | |
| 918 | / / and endi ng text va lue | |
| 919 | S tring spli tPipePatte rn = "\\|" ; | |
| 920 | P attern pFi elds = Pat tern.compi le(splitPi pePattern) ; | |
| 921 | S tring fiel ds[] = new String[4] ; | |
| 922 | f ields = pF ields.spli t(textLine ); | |
| 923 | i f ( ((fiel ds[0].leng th()==9) | | (fields[ 0].length( )==18)) && | |
| 924 | (fiel ds[3].leng th()>0)) { | |
| 925 | // place tag( s)-value p airs to Ha shMap | |
| 926 | his Updates.pu t(fields[0 ], fields[ 3]); | |
| 927 | } | |
| 928 | } | |
| 929 | catch(Thr owable t) { // catch all | |
| 930 | } | |
| 931 | textLine = this.get NextTextLi ne(buffer) ; | |
| 932 | } // end wil e | |
| 933 | lo gger.debug ("Number o f HIS Upda tes: "+his Updates.si ze()); | |
| 934 | if (hisUpdat es.isEmpty ()) | |
| 935 | retu rn null; | |
| 936 | el se | |
| 937 | retu rn hisUpda tes; | |
| 938 | } | |
| 939 | ||
| 940 | /** | |
| 941 | * Rea ds next li ne from th e Text fil e, which i s now in t he form of BufferedR eader | |
| 942 | * obj ect. This method ch ecks for E OF, nulls, and blank lines. T his is pri marily in | |
| 943 | * cas e the Text file was not proper ly formatt ed or corr upted. If the line is valid, | |
| 944 | * the line is r eturned. | |
| 945 | * | |
| 946 | * @pa ram in rep resents th e Buffered Reader obj ect. | |
| 947 | * @re turn repre sents the next line read from the Buffer edReader o bject. | |
| 948 | * @th rows TextF ileExtract ionExcepti on | |
| 949 | */ | |
| 950 | privat e String g etNextText Line(Buffe redReader in) throws TextFileE xtractionE xception{ | |
| 951 | St ring line = null; | |
| 952 | tr y{ | |
| 953 | do{ | |
| 954 | if(( line = in. readLine() ) == null) { | |
| 955 | throw new TextFileEx tractionEx ception(); | |
| 956 | } | |
| 957 | }while(l ine.equals ("")); | |
| 958 | } | |
| 959 | ca tch(IOExce ption io){ | |
| 960 | logger.e rror(io.ge tMessage() ); | |
| 961 | logger.e rror(this. getClass() .getName() +": " + | |
| 962 | "Exception thrown wh ile gettin g next lin e from Tex t Line."); | |
| 963 | throw ne w TextFile Extraction Exception( "Failure t o get next line.", i o); | |
| 964 | } | |
| 965 | re turn line; | |
| 966 | } | |
| 967 | ||
| 968 | privat e boolean isGroupToB eAdded(int Group){ | |
| 969 | bo olean addG roup = tru e; | |
| 970 | ||
| 971 | // Do not all ow Odd Gro ups | |
| 972 | if ((Group % 2) != 0){ | |
| 973 | addGroup = false; | |
| 974 | } | |
| 975 | ||
| 976 | // Do not all ow Icon Im age Sequen ces | |
| 977 | if (Group == 0x0088){ | |
| 978 | addGroup = false; | |
| 979 | } | |
| 980 | ||
| 981 | // Need to re move Group 0002 elem ents. Fou nd bug of sending Gr oup 0002 e lements | |
| 982 | // to CSTor e SCP devi ce. This is not val id. I str ongly beli eve to add it here. I do | |
| 983 | // not thin k any code between h ere and th e sending uses this group. Bu t I could be | |
| 984 | // wrong. | |
| 985 | if (Group == 0x0002){ | |
| 986 | addGroup = false; | |
| 987 | } | |
| 988 | ||
| 989 | re turn addGr oup; | |
| 990 | } | |
| 991 | ||
| 992 | privat e void cus tomTGAElem entCleanup (){ | |
| 993 | tr y{ | |
| 994 | if(t his.dicomD ataSet.con tainsEleme nt(new Att ributeTag( "0008,0008 "))){ | |
| 995 | DicomC SElement o bjectType = (DicomCS Element)th is.dicomDa taSet.find Element(ne w Attribut eTag("0008 ,0008")); | |
| 996 | String [] values = objectTy pe.getStri ngData(); | |
| 997 | ArrayL ist<String > nuValueA rray = new ArrayList <String>(v alues.leng th); | |
| 998 | for(in t i=0; i<v alues.leng th; i++){ | |
| 999 | nuValueArr ay.add(val ues[i]); | |
| 1000 | } | |
| 1001 | while( nuValueArr ay.contain s("")){ | |
| 1002 | nuValueA rray.remov e(""); | |
| 1003 | } | |
| 1004 | nuValu eArray.tri mToSize(); | |
| 1005 | ||
| 1006 | String [] nuValue s = new St ring[nuVal ueArray.si ze()]; | |
| 1007 | Iterat or<String> iter = nu ValueArray .iterator( ); | |
| 1008 | int j = 0; | |
| 1009 | while( iter.hasNe xt()){ | |
| 1010 | nuValues [j] = iter .next(); | |
| 1011 | j++; | |
| 1012 | } | |
| 1013 | DicomC SElement n uObjectTyp e = new Di comCSEleme nt(new Att ributeTag( "0008,0008 "), | |
| 1014 | nu Values); | |
| 1015 | this.d icomDataSe t.insert(n uObjectTyp e); | |
| 1016 | } | |
| 1017 | } | |
| 1018 | ca tch(DCSExc eption dcs X){ | |
| 1019 | //do nothing | |
| 1020 | } | |
| 1021 | ||
| 1022 | } | |
| 1023 | ||
| 1024 | privat e byte[] a ddElementT oByteArray (byte[] ol dArray, Lo ng nuValue ){ | |
| 1025 | ||
| 1026 | if (oldArray == null){ | |
| 1027 | oldArray = new byt e[0]; | |
| 1028 | } | |
| 1029 | in t length = oldArray. length; | |
| 1030 | in t index = length+1; | |
| 1031 | by te nuArray [] = new b yte[index] ; | |
| 1032 | Sy stem.array copy(oldAr ray, 0, nu Array, 0, length); | |
| 1033 | nu Array[inde x-1] = nuV alue.byteV alue(); | |
| 1034 | re turn nuArr ay; | |
| 1035 | } | |
| 1036 | ||
| 1037 | privat e short[] addElement ToShortArr ay(short[] oldArray, Long nuVa lue){ | |
| 1038 | ||
| 1039 | int leng th = oldAr ray.length ; | |
| 1040 | int inde x = length +1; | |
| 1041 | short nu Array[] = new short[ index]; | |
| 1042 | System.a rraycopy(o ldArray, 0 , nuArray, 0, length ); | |
| 1043 | nuArray[ index-1] = nuValue.s hortValue( ); | |
| 1044 | return n uArray; | |
| 1045 | } | |
| 1046 | ||
| 1047 | privat e int[] ad dElementTo IntArray(i nt[] oldAr ray, Long nuValue){ | |
| 1048 | ||
| 1049 | int leng th = oldAr ray.length ; | |
| 1050 | int inde x = length +1; | |
| 1051 | int nuAr ray[] = ne w int[inde x]; | |
| 1052 | System.a rraycopy(o ldArray, 0 , nuArray, 0, length ); | |
| 1053 | nuArray[ index-1] = nuValue.i ntValue(); | |
| 1054 | return n uArray; | |
| 1055 | } | |
| 1056 | ||
| 1057 | privat e float[] addElement ToFloatArr ay(float[] oldArray, Float nuV alue){ | |
| 1058 | ||
| 1059 | int leng th = oldAr ray.length ; | |
| 1060 | int inde x = length +1; | |
| 1061 | float nu Array[] = new float[ index]; | |
| 1062 | System.a rraycopy(o ldArray, 0 , nuArray, 0, length ); | |
| 1063 | nuArray[ index-1] = nuValue.f loatValue( ); | |
| 1064 | return n uArray; | |
| 1065 | } | |
| 1066 | ||
| 1067 | privat e double[] addElemen tToDoubleA rray(doubl e[] oldArr ay, Double nuValue){ | |
| 1068 | ||
| 1069 | int leng th = oldAr ray.length ; | |
| 1070 | int inde x = length +1; | |
| 1071 | double n uArray[] = new doubl e[index]; | |
| 1072 | System.a rraycopy(o ldArray, 0 , nuArray, 0, length ); | |
| 1073 | nuArray[ index-1] = nuValue.d oubleValue (); | |
| 1074 | return n uArray; | |
| 1075 | } | |
| 1076 | } |
Araxis Merge (but not the data content of this report) is Copyright © 1993-2016 Araxis Ltd (www.araxis.com). All rights reserved.