source: trunk/components/bf-ice/src/bio-formats.ice @ 5490

Revision 5490, 62.9 KB checked in by curtis, 10 years ago (diff)

Combine MetadataStore and MetadataRetrieve Ice interfaces into one IMetadata.

Line 
1//
2// bio-formats.ice
3//
4
5/*
6OME Bio-Formats package for reading and converting biological file formats.
7Copyright (C) 2005-2009 UW-Madison LOCI and Glencoe Software, Inc.
8
9This program is free software; you can redistribute it and/or modify
10it under the terms of the GNU General Public License as published by
11the Free Software Foundation; either version 2 of the License, or
12(at your option) any later version.
13
14This program is distributed in the hope that it will be useful,
15but WITHOUT ANY WARRANTY; without even the implied warranty of
16MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17GNU General Public License for more details.
18
19You should have received a copy of the GNU General Public License
20along with this program; if not, write to the Free Software
21Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
22*/
23
24/*-----------------------------------------------------------------------------
25 *
26 * THIS IS AUTOMATICALLY GENERATED CODE.  DO NOT MODIFY.
27 * Created by curtis via MetadataAutogen on Sep 21, 2009 3:33:03 PM CDT
28 *
29 *-----------------------------------------------------------------------------
30 */
31
32[["java:package:loci.ice"]]
33
34module formats {
35
36  sequence<byte> ByteSeq;
37  sequence<ByteSeq> ByteByteSeq;
38  sequence<short> ShortSeq;
39  sequence<ShortSeq> ShortShortSeq;
40  sequence<int> IntSeq;
41  sequence<string> StringSeq;
42
43  interface IMetadata;
44
45  interface IFormatReader {
46    void setId(string id);
47
48    //const int MUST_GROUP = 0;
49    //const int CAN_GROUP = 1;
50    //const int CANNOT_GROUP = 2;
51
52    bool isThisType(string name, bool open);
53    //bool isThisType2(ByteSeq block);
54    int getImageCount();
55    bool isRGB();
56    int getSizeX();
57    int getSizeY();
58    int getSizeZ();
59    int getSizeC();
60    int getSizeT();
61    int getPixelType();
62    int getEffectiveSizeC();
63    int getRGBChannelCount();
64    bool isIndexed();
65    bool isFalseColor();
66    ByteByteSeq get8BitLookupTable();
67    ShortShortSeq get16BitLookupTable();
68    IntSeq getChannelDimLengths();
69    StringSeq getChannelDimTypes();
70    int getThumbSizeX();
71    int getThumbSizeY();
72    bool isLittleEndian();
73    string getDimensionOrder();
74    bool isOrderCertain();
75    bool isInterleaved();
76    bool isInterleavedSubC(int subC);
77    //ByteSeq openBytes1(int no);
78    ByteSeq openBytes(int no, int x, int y, int width, int height);
79    //ByteSeq openBytes3(int no, ByteSeq buf);
80    //ByteSeq openBytes4(int no, ByteSeq buf,
81    //  int x, int y, int width, int height);
82    ByteSeq openThumbBytes(int no);
83    void closeFile(bool fileOnly);
84    string getFormat();
85    StringSeq getSuffixes();
86    void close();
87    int getSeriesCount();
88    void setSeries(int no);
89    int getSeries();
90    void setNormalized(bool normalize);
91    bool isNormalized();
92    void setMetadataCollected(bool collect);
93    bool isMetadataCollected();
94    void setOriginalMetadataPopulated(bool populate);
95    bool isOriginalMetadataPopulated();
96    void setGroupFiles(bool group);
97    bool isGroupFiles();
98    bool isMetadataComplete();
99    int fileGroupOption(string id);
100    StringSeq getUsedFiles();
101    string getCurrentFile();
102    int getIndex(int z, int c, int t);
103    IntSeq getZCTCoords(int index);
104    //Object getMetadataValue(string field);
105    //Hashtable getMetadata();
106    //CoreMetadata getCoreMetadata();
107    void setMetadataFiltered(bool filter);
108    bool isMetadataFiltered();
109    void setMetadataStore(IMetadata* store);
110    //IMetadata* getMetadataStore();
111    //Object getMetadataStoreRoot();
112    //IFormatReader[] getUnderlyingReaders();
113  };
114
115  interface IFormatWriter {
116    void setId(string id);
117    void close();
118    void saveBytes1(ByteSeq bytes, bool last);
119    void saveBytes2(ByteSeq bytes, int series, bool lastInSeries, bool last);
120    bool canDoStacks();
121    void setMetadataRetrieve(IMetadata* r);
122    IMetadata getMetadataRetrieve();
123    void setFramesPerSecond(int rate);
124    int getFramesPerSecond();
125    StringSeq getCompressionTypes();
126    IntSeq getPixelTypes();
127    bool isSupportedType(int type);
128    void setCompression(string compress);
129    bool isThisType(string name);
130    string getFormat();
131    StringSeq getSuffixes();
132  };
133
134  interface IMetadata {
135    // -- MetadataRetrieve methods --
136
137    string getOMEXML();
138
139    // - Entity counting -
140
141    int getChannelComponentCount(int imageIndex, int logicalChannelIndex);
142    int getDatasetCount();
143    int getDatasetRefCount(int imageIndex);
144    int getDetectorCount(int instrumentIndex);
145    int getDichroicCount(int instrumentIndex);
146    int getExperimentCount();
147    int getExperimenterCount();
148    int getExperimenterMembershipCount(int experimenterIndex);
149    int getFilterCount(int instrumentIndex);
150    int getFilterSetCount(int instrumentIndex);
151    int getGroupCount();
152    int getGroupRefCount(int experimenterIndex);
153    int getImageCount();
154    int getInstrumentCount();
155    int getLightSourceCount(int instrumentIndex);
156    int getLightSourceRefCount(int imageIndex, int microbeamManipulationIndex);
157    int getLogicalChannelCount(int imageIndex);
158    int getMicrobeamManipulationCount(int imageIndex);
159    int getMicrobeamManipulationRefCount(int experimentIndex);
160    int getOTFCount(int instrumentIndex);
161    int getObjectiveCount(int instrumentIndex);
162    int getPixelsCount(int imageIndex);
163    int getPlaneCount(int imageIndex, int pixelsIndex);
164    int getPlateCount();
165    int getPlateRefCount(int screenIndex);
166    int getProjectCount();
167    int getProjectRefCount(int datasetIndex);
168    int getROICount(int imageIndex);
169    int getROIRefCount(int imageIndex, int microbeamManipulationIndex);
170    int getReagentCount(int screenIndex);
171    int getRegionCount(int imageIndex);
172    int getRoiLinkCount(int imageIndex, int roiIndex);
173    int getScreenCount();
174    int getScreenAcquisitionCount(int screenIndex);
175    int getScreenRefCount(int plateIndex);
176    int getShapeCount(int imageIndex, int roiIndex);
177    int getTiffDataCount(int imageIndex, int pixelsIndex);
178    int getWellCount(int plateIndex);
179    int getWellSampleCount(int plateIndex, int wellIndex);
180    int getWellSampleRefCount(int screenIndex, int screenAcquisitionIndex);
181
182    // - Entity retrieval -
183
184    string getUUID();
185
186    // - Arc property retrieval -
187
188    string getArcType(int instrumentIndex, int lightSourceIndex);
189
190    // - ChannelComponent property retrieval -
191
192    string getChannelComponentColorDomain(int imageIndex, int logicalChannelIndex, int channelComponentIndex);
193    int getChannelComponentIndex(int imageIndex, int logicalChannelIndex, int channelComponentIndex);
194    string getChannelComponentPixels(int imageIndex, int logicalChannelIndex, int channelComponentIndex);
195
196    // - Circle property retrieval -
197
198    string getCircleCx(int imageIndex, int roiIndex, int shapeIndex);
199    string getCircleCy(int imageIndex, int roiIndex, int shapeIndex);
200    string getCircleID(int imageIndex, int roiIndex, int shapeIndex);
201    string getCircleR(int imageIndex, int roiIndex, int shapeIndex);
202    string getCircleTransform(int imageIndex, int roiIndex, int shapeIndex);
203
204    // - Contact property retrieval -
205
206    string getContactExperimenter(int groupIndex);
207
208    // - Dataset property retrieval -
209
210    string getDatasetDescription(int datasetIndex);
211    string getDatasetExperimenterRef(int datasetIndex);
212    string getDatasetGroupRef(int datasetIndex);
213    string getDatasetID(int datasetIndex);
214    bool getDatasetLocked(int datasetIndex);
215    string getDatasetName(int datasetIndex);
216
217    // - DatasetRef property retrieval -
218
219    string getDatasetRefID(int imageIndex, int datasetRefIndex);
220
221    // - Detector property retrieval -
222
223    float getDetectorAmplificationGain(int instrumentIndex, int detectorIndex);
224    float getDetectorGain(int instrumentIndex, int detectorIndex);
225    string getDetectorID(int instrumentIndex, int detectorIndex);
226    string getDetectorManufacturer(int instrumentIndex, int detectorIndex);
227    string getDetectorModel(int instrumentIndex, int detectorIndex);
228    float getDetectorOffset(int instrumentIndex, int detectorIndex);
229    string getDetectorSerialNumber(int instrumentIndex, int detectorIndex);
230    string getDetectorType(int instrumentIndex, int detectorIndex);
231    float getDetectorVoltage(int instrumentIndex, int detectorIndex);
232    float getDetectorZoom(int instrumentIndex, int detectorIndex);
233
234    // - DetectorSettings property retrieval -
235
236    string getDetectorSettingsBinning(int imageIndex, int logicalChannelIndex);
237    string getDetectorSettingsDetector(int imageIndex, int logicalChannelIndex);
238    float getDetectorSettingsGain(int imageIndex, int logicalChannelIndex);
239    float getDetectorSettingsOffset(int imageIndex, int logicalChannelIndex);
240    float getDetectorSettingsReadOutRate(int imageIndex, int logicalChannelIndex);
241    float getDetectorSettingsVoltage(int imageIndex, int logicalChannelIndex);
242
243    // - Dichroic property retrieval -
244
245    string getDichroicID(int instrumentIndex, int dichroicIndex);
246    string getDichroicLotNumber(int instrumentIndex, int dichroicIndex);
247    string getDichroicManufacturer(int instrumentIndex, int dichroicIndex);
248    string getDichroicModel(int instrumentIndex, int dichroicIndex);
249
250    // - Dimensions property retrieval -
251
252    float getDimensionsPhysicalSizeX(int imageIndex, int pixelsIndex);
253    float getDimensionsPhysicalSizeY(int imageIndex, int pixelsIndex);
254    float getDimensionsPhysicalSizeZ(int imageIndex, int pixelsIndex);
255    float getDimensionsTimeIncrement(int imageIndex, int pixelsIndex);
256    int getDimensionsWaveIncrement(int imageIndex, int pixelsIndex);
257    int getDimensionsWaveStart(int imageIndex, int pixelsIndex);
258
259    // - DisplayOptions property retrieval -
260
261    string getDisplayOptionsDisplay(int imageIndex);
262    string getDisplayOptionsID(int imageIndex);
263    float getDisplayOptionsZoom(int imageIndex);
264
265    // - Ellipse property retrieval -
266
267    string getEllipseCx(int imageIndex, int roiIndex, int shapeIndex);
268    string getEllipseCy(int imageIndex, int roiIndex, int shapeIndex);
269    string getEllipseID(int imageIndex, int roiIndex, int shapeIndex);
270    string getEllipseRx(int imageIndex, int roiIndex, int shapeIndex);
271    string getEllipseRy(int imageIndex, int roiIndex, int shapeIndex);
272    string getEllipseTransform(int imageIndex, int roiIndex, int shapeIndex);
273
274    // - EmFilter property retrieval -
275
276    string getEmFilterLotNumber(int instrumentIndex, int filterIndex);
277    string getEmFilterManufacturer(int instrumentIndex, int filterIndex);
278    string getEmFilterModel(int instrumentIndex, int filterIndex);
279    string getEmFilterType(int instrumentIndex, int filterIndex);
280
281    // - ExFilter property retrieval -
282
283    string getExFilterLotNumber(int instrumentIndex, int filterIndex);
284    string getExFilterManufacturer(int instrumentIndex, int filterIndex);
285    string getExFilterModel(int instrumentIndex, int filterIndex);
286    string getExFilterType(int instrumentIndex, int filterIndex);
287
288    // - Experiment property retrieval -
289
290    string getExperimentDescription(int experimentIndex);
291    string getExperimentExperimenterRef(int experimentIndex);
292    string getExperimentID(int experimentIndex);
293    string getExperimentType(int experimentIndex);
294
295    // - Experimenter property retrieval -
296
297    string getExperimenterEmail(int experimenterIndex);
298    string getExperimenterFirstName(int experimenterIndex);
299    string getExperimenterID(int experimenterIndex);
300    string getExperimenterInstitution(int experimenterIndex);
301    string getExperimenterLastName(int experimenterIndex);
302    string getExperimenterOMEName(int experimenterIndex);
303
304    // - ExperimenterMembership property retrieval -
305
306    string getExperimenterMembershipGroup(int experimenterIndex, int groupRefIndex);
307
308    // - Filament property retrieval -
309
310    string getFilamentType(int instrumentIndex, int lightSourceIndex);
311
312    // - Filter property retrieval -
313
314    string getFilterFilterWheel(int instrumentIndex, int filterIndex);
315    string getFilterID(int instrumentIndex, int filterIndex);
316    string getFilterLotNumber(int instrumentIndex, int filterIndex);
317    string getFilterManufacturer(int instrumentIndex, int filterIndex);
318    string getFilterModel(int instrumentIndex, int filterIndex);
319    string getFilterType(int instrumentIndex, int filterIndex);
320
321    // - FilterSet property retrieval -
322
323    string getFilterSetDichroic(int instrumentIndex, int filterSetIndex);
324    string getFilterSetEmFilter(int instrumentIndex, int filterSetIndex);
325    string getFilterSetExFilter(int instrumentIndex, int filterSetIndex);
326    string getFilterSetID(int instrumentIndex, int filterSetIndex);
327    string getFilterSetLotNumber(int instrumentIndex, int filterSetIndex);
328    string getFilterSetManufacturer(int instrumentIndex, int filterSetIndex);
329    string getFilterSetModel(int instrumentIndex, int filterSetIndex);
330
331    // - Group property retrieval -
332
333    string getGroupID(int groupIndex);
334    string getGroupName(int groupIndex);
335
336    // - GroupRef property retrieval -
337
338
339    // - Image property retrieval -
340
341    string getImageAcquiredPixels(int imageIndex);
342    string getImageCreationDate(int imageIndex);
343    string getImageDefaultPixels(int imageIndex);
344    string getImageDescription(int imageIndex);
345    string getImageExperimentRef(int imageIndex);
346    string getImageExperimenterRef(int imageIndex);
347    string getImageGroupRef(int imageIndex);
348    string getImageID(int imageIndex);
349    string getImageInstrumentRef(int imageIndex);
350    string getImageName(int imageIndex);
351
352    // - ImagingEnvironment property retrieval -
353
354    float getImagingEnvironmentAirPressure(int imageIndex);
355    float getImagingEnvironmentCO2Percent(int imageIndex);
356    float getImagingEnvironmentHumidity(int imageIndex);
357    float getImagingEnvironmentTemperature(int imageIndex);
358
359    // - Instrument property retrieval -
360
361    string getInstrumentID(int instrumentIndex);
362
363    // - Laser property retrieval -
364
365    int getLaserFrequencyMultiplication(int instrumentIndex, int lightSourceIndex);
366    string getLaserLaserMedium(int instrumentIndex, int lightSourceIndex);
367    bool getLaserPockelCell(int instrumentIndex, int lightSourceIndex);
368    string getLaserPulse(int instrumentIndex, int lightSourceIndex);
369    bool getLaserRepetitionRate(int instrumentIndex, int lightSourceIndex);
370    bool getLaserTuneable(int instrumentIndex, int lightSourceIndex);
371    string getLaserType(int instrumentIndex, int lightSourceIndex);
372    int getLaserWavelength(int instrumentIndex, int lightSourceIndex);
373
374    // - LightSource property retrieval -
375
376    string getLightSourceID(int instrumentIndex, int lightSourceIndex);
377    string getLightSourceManufacturer(int instrumentIndex, int lightSourceIndex);
378    string getLightSourceModel(int instrumentIndex, int lightSourceIndex);
379    float getLightSourcePower(int instrumentIndex, int lightSourceIndex);
380    string getLightSourceSerialNumber(int instrumentIndex, int lightSourceIndex);
381
382    // - LightSourceRef property retrieval -
383
384    float getLightSourceRefAttenuation(int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
385    string getLightSourceRefLightSource(int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
386    int getLightSourceRefWavelength(int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
387
388    // - LightSourceSettings property retrieval -
389
390    float getLightSourceSettingsAttenuation(int imageIndex, int logicalChannelIndex);
391    string getLightSourceSettingsLightSource(int imageIndex, int logicalChannelIndex);
392    int getLightSourceSettingsWavelength(int imageIndex, int logicalChannelIndex);
393
394    // - Line property retrieval -
395
396    string getLineID(int imageIndex, int roiIndex, int shapeIndex);
397    string getLineTransform(int imageIndex, int roiIndex, int shapeIndex);
398    string getLineX1(int imageIndex, int roiIndex, int shapeIndex);
399    string getLineX2(int imageIndex, int roiIndex, int shapeIndex);
400    string getLineY1(int imageIndex, int roiIndex, int shapeIndex);
401    string getLineY2(int imageIndex, int roiIndex, int shapeIndex);
402
403    // - LogicalChannel property retrieval -
404
405    string getLogicalChannelContrastMethod(int imageIndex, int logicalChannelIndex);
406    string getLogicalChannelDetector(int imageIndex, int logicalChannelIndex);
407    int getLogicalChannelEmWave(int imageIndex, int logicalChannelIndex);
408    int getLogicalChannelExWave(int imageIndex, int logicalChannelIndex);
409    string getLogicalChannelFilterSet(int imageIndex, int logicalChannelIndex);
410    string getLogicalChannelFluor(int imageIndex, int logicalChannelIndex);
411    string getLogicalChannelID(int imageIndex, int logicalChannelIndex);
412    string getLogicalChannelIlluminationType(int imageIndex, int logicalChannelIndex);
413    string getLogicalChannelLightSource(int imageIndex, int logicalChannelIndex);
414    string getLogicalChannelMode(int imageIndex, int logicalChannelIndex);
415    string getLogicalChannelName(int imageIndex, int logicalChannelIndex);
416    float getLogicalChannelNdFilter(int imageIndex, int logicalChannelIndex);
417    string getLogicalChannelOTF(int imageIndex, int logicalChannelIndex);
418    string getLogicalChannelPhotometricInterpretation(int imageIndex, int logicalChannelIndex);
419    float getLogicalChannelPinholeSize(int imageIndex, int logicalChannelIndex);
420    int getLogicalChannelPockelCellSetting(int imageIndex, int logicalChannelIndex);
421    int getLogicalChannelSamplesPerPixel(int imageIndex, int logicalChannelIndex);
422    string getLogicalChannelSecondaryEmissionFilter(int imageIndex, int logicalChannelIndex);
423    string getLogicalChannelSecondaryExcitationFilter(int imageIndex, int logicalChannelIndex);
424
425    // - Mask property retrieval -
426
427    string getMaskHeight(int imageIndex, int roiIndex, int shapeIndex);
428    string getMaskID(int imageIndex, int roiIndex, int shapeIndex);
429    string getMaskTransform(int imageIndex, int roiIndex, int shapeIndex);
430    string getMaskWidth(int imageIndex, int roiIndex, int shapeIndex);
431    string getMaskX(int imageIndex, int roiIndex, int shapeIndex);
432    string getMaskY(int imageIndex, int roiIndex, int shapeIndex);
433
434    // - MaskPixels property retrieval -
435
436    bool getMaskPixelsBigEndian(int imageIndex, int roiIndex, int shapeIndex);
437    string getMaskPixelsBinData(int imageIndex, int roiIndex, int shapeIndex);
438    string getMaskPixelsExtendedPixelType(int imageIndex, int roiIndex, int shapeIndex);
439    string getMaskPixelsID(int imageIndex, int roiIndex, int shapeIndex);
440    int getMaskPixelsSizeX(int imageIndex, int roiIndex, int shapeIndex);
441    int getMaskPixelsSizeY(int imageIndex, int roiIndex, int shapeIndex);
442
443    // - MicrobeamManipulation property retrieval -
444
445    string getMicrobeamManipulationExperimenterRef(int imageIndex, int microbeamManipulationIndex);
446    string getMicrobeamManipulationID(int imageIndex, int microbeamManipulationIndex);
447    string getMicrobeamManipulationType(int imageIndex, int microbeamManipulationIndex);
448
449    // - MicrobeamManipulationRef property retrieval -
450
451    string getMicrobeamManipulationRefID(int experimentIndex, int microbeamManipulationRefIndex);
452
453    // - Microscope property retrieval -
454
455    string getMicroscopeID(int instrumentIndex);
456    string getMicroscopeManufacturer(int instrumentIndex);
457    string getMicroscopeModel(int instrumentIndex);
458    string getMicroscopeSerialNumber(int instrumentIndex);
459    string getMicroscopeType(int instrumentIndex);
460
461    // - OTF property retrieval -
462
463    string getOTFBinaryFile(int instrumentIndex, int otfIndex);
464    string getOTFID(int instrumentIndex, int otfIndex);
465    string getOTFObjective(int instrumentIndex, int otfIndex);
466    bool getOTFOpticalAxisAveraged(int instrumentIndex, int otfIndex);
467    string getOTFPixelType(int instrumentIndex, int otfIndex);
468    int getOTFSizeX(int instrumentIndex, int otfIndex);
469    int getOTFSizeY(int instrumentIndex, int otfIndex);
470
471    // - Objective property retrieval -
472
473    float getObjectiveCalibratedMagnification(int instrumentIndex, int objectiveIndex);
474    string getObjectiveCorrection(int instrumentIndex, int objectiveIndex);
475    string getObjectiveID(int instrumentIndex, int objectiveIndex);
476    string getObjectiveImmersion(int instrumentIndex, int objectiveIndex);
477    bool getObjectiveIris(int instrumentIndex, int objectiveIndex);
478    float getObjectiveLensNA(int instrumentIndex, int objectiveIndex);
479    string getObjectiveManufacturer(int instrumentIndex, int objectiveIndex);
480    string getObjectiveModel(int instrumentIndex, int objectiveIndex);
481    int getObjectiveNominalMagnification(int instrumentIndex, int objectiveIndex);
482    string getObjectiveSerialNumber(int instrumentIndex, int objectiveIndex);
483    float getObjectiveWorkingDistance(int instrumentIndex, int objectiveIndex);
484
485    // - ObjectiveSettings property retrieval -
486
487    float getObjectiveSettingsCorrectionCollar(int imageIndex);
488    string getObjectiveSettingsMedium(int imageIndex);
489    string getObjectiveSettingsObjective(int imageIndex);
490    float getObjectiveSettingsRefractiveIndex(int imageIndex);
491
492    // - Path property retrieval -
493
494    string getPathD(int imageIndex, int roiIndex, int shapeIndex);
495    string getPathID(int imageIndex, int roiIndex, int shapeIndex);
496
497    // - Pixels property retrieval -
498
499    bool getPixelsBigEndian(int imageIndex, int pixelsIndex);
500    string getPixelsDimensionOrder(int imageIndex, int pixelsIndex);
501    string getPixelsID(int imageIndex, int pixelsIndex);
502    string getPixelsPixelType(int imageIndex, int pixelsIndex);
503    int getPixelsSizeC(int imageIndex, int pixelsIndex);
504    int getPixelsSizeT(int imageIndex, int pixelsIndex);
505    int getPixelsSizeX(int imageIndex, int pixelsIndex);
506    int getPixelsSizeY(int imageIndex, int pixelsIndex);
507    int getPixelsSizeZ(int imageIndex, int pixelsIndex);
508
509    // - Plane property retrieval -
510
511    string getPlaneHashSHA1(int imageIndex, int pixelsIndex, int planeIndex);
512    string getPlaneID(int imageIndex, int pixelsIndex, int planeIndex);
513    int getPlaneTheC(int imageIndex, int pixelsIndex, int planeIndex);
514    int getPlaneTheT(int imageIndex, int pixelsIndex, int planeIndex);
515    int getPlaneTheZ(int imageIndex, int pixelsIndex, int planeIndex);
516
517    // - PlaneTiming property retrieval -
518
519    float getPlaneTimingDeltaT(int imageIndex, int pixelsIndex, int planeIndex);
520    float getPlaneTimingExposureTime(int imageIndex, int pixelsIndex, int planeIndex);
521
522    // - Plate property retrieval -
523
524    string getPlateColumnNamingConvention(int plateIndex);
525    string getPlateDescription(int plateIndex);
526    string getPlateExternalIdentifier(int plateIndex);
527    string getPlateID(int plateIndex);
528    string getPlateName(int plateIndex);
529    string getPlateRowNamingConvention(int plateIndex);
530    string getPlateStatus(int plateIndex);
531    double getPlateWellOriginX(int plateIndex);
532    double getPlateWellOriginY(int plateIndex);
533
534    // - PlateRef property retrieval -
535
536    string getPlateRefID(int screenIndex, int plateRefIndex);
537    int getPlateRefSample(int screenIndex, int plateRefIndex);
538    string getPlateRefWell(int screenIndex, int plateRefIndex);
539
540    // - Point property retrieval -
541
542    string getPointCx(int imageIndex, int roiIndex, int shapeIndex);
543    string getPointCy(int imageIndex, int roiIndex, int shapeIndex);
544    string getPointID(int imageIndex, int roiIndex, int shapeIndex);
545    string getPointR(int imageIndex, int roiIndex, int shapeIndex);
546    string getPointTransform(int imageIndex, int roiIndex, int shapeIndex);
547
548    // - Polygon property retrieval -
549
550    string getPolygonID(int imageIndex, int roiIndex, int shapeIndex);
551    string getPolygonPoints(int imageIndex, int roiIndex, int shapeIndex);
552    string getPolygonTransform(int imageIndex, int roiIndex, int shapeIndex);
553
554    // - Polyline property retrieval -
555
556    string getPolylineID(int imageIndex, int roiIndex, int shapeIndex);
557    string getPolylinePoints(int imageIndex, int roiIndex, int shapeIndex);
558    string getPolylineTransform(int imageIndex, int roiIndex, int shapeIndex);
559
560    // - Project property retrieval -
561
562    string getProjectDescription(int projectIndex);
563    string getProjectExperimenterRef(int projectIndex);
564    string getProjectGroupRef(int projectIndex);
565    string getProjectID(int projectIndex);
566    string getProjectName(int projectIndex);
567
568    // - ProjectRef property retrieval -
569
570    string getProjectRefID(int datasetIndex, int projectRefIndex);
571
572    // - Pump property retrieval -
573
574    string getPumpLightSource(int instrumentIndex, int lightSourceIndex);
575
576    // - ROI property retrieval -
577
578    string getROIID(int imageIndex, int roiIndex);
579    int getROIT0(int imageIndex, int roiIndex);
580    int getROIT1(int imageIndex, int roiIndex);
581    int getROIX0(int imageIndex, int roiIndex);
582    int getROIX1(int imageIndex, int roiIndex);
583    int getROIY0(int imageIndex, int roiIndex);
584    int getROIY1(int imageIndex, int roiIndex);
585    int getROIZ0(int imageIndex, int roiIndex);
586    int getROIZ1(int imageIndex, int roiIndex);
587
588    // - ROIRef property retrieval -
589
590    string getROIRefID(int imageIndex, int microbeamManipulationIndex, int roiRefIndex);
591
592    // - Reagent property retrieval -
593
594    string getReagentDescription(int screenIndex, int reagentIndex);
595    string getReagentID(int screenIndex, int reagentIndex);
596    string getReagentName(int screenIndex, int reagentIndex);
597    string getReagentReagentIdentifier(int screenIndex, int reagentIndex);
598
599    // - Rect property retrieval -
600
601    string getRectHeight(int imageIndex, int roiIndex, int shapeIndex);
602    string getRectID(int imageIndex, int roiIndex, int shapeIndex);
603    string getRectTransform(int imageIndex, int roiIndex, int shapeIndex);
604    string getRectWidth(int imageIndex, int roiIndex, int shapeIndex);
605    string getRectX(int imageIndex, int roiIndex, int shapeIndex);
606    string getRectY(int imageIndex, int roiIndex, int shapeIndex);
607
608    // - Region property retrieval -
609
610    string getRegionID(int imageIndex, int regionIndex);
611    string getRegionName(int imageIndex, int regionIndex);
612    string getRegionTag(int imageIndex, int regionIndex);
613
614    // - RoiLink property retrieval -
615
616    string getRoiLinkDirection(int imageIndex, int roiIndex, int roiLinkIndex);
617    string getRoiLinkName(int imageIndex, int roiIndex, int roiLinkIndex);
618    string getRoiLinkRef(int imageIndex, int roiIndex, int roiLinkIndex);
619
620    // - Screen property retrieval -
621
622    string getScreenDescription(int screenIndex);
623    string getScreenExtern(int screenIndex);
624    string getScreenID(int screenIndex);
625    string getScreenName(int screenIndex);
626    string getScreenProtocolDescription(int screenIndex);
627    string getScreenProtocolIdentifier(int screenIndex);
628    string getScreenReagentSetDescription(int screenIndex);
629    string getScreenReagentSetIdentifier(int screenIndex);
630    string getScreenType(int screenIndex);
631
632    // - ScreenAcquisition property retrieval -
633
634    string getScreenAcquisitionEndTime(int screenIndex, int screenAcquisitionIndex);
635    string getScreenAcquisitionID(int screenIndex, int screenAcquisitionIndex);
636    string getScreenAcquisitionStartTime(int screenIndex, int screenAcquisitionIndex);
637
638    // - ScreenRef property retrieval -
639
640    string getScreenRefID(int plateIndex, int screenRefIndex);
641
642    // - Shape property retrieval -
643
644    string getShapeBaselineShift(int imageIndex, int roiIndex, int shapeIndex);
645    string getShapeDirection(int imageIndex, int roiIndex, int shapeIndex);
646    string getShapeFillColor(int imageIndex, int roiIndex, int shapeIndex);
647    string getShapeFillOpacity(int imageIndex, int roiIndex, int shapeIndex);
648    string getShapeFillRule(int imageIndex, int roiIndex, int shapeIndex);
649    string getShapeFontFamily(int imageIndex, int roiIndex, int shapeIndex);
650    int getShapeFontSize(int imageIndex, int roiIndex, int shapeIndex);
651    string getShapeFontStretch(int imageIndex, int roiIndex, int shapeIndex);
652    string getShapeFontStyle(int imageIndex, int roiIndex, int shapeIndex);
653    string getShapeFontVariant(int imageIndex, int roiIndex, int shapeIndex);
654    string getShapeFontWeight(int imageIndex, int roiIndex, int shapeIndex);
655    string getShapeG(int imageIndex, int roiIndex, int shapeIndex);
656    int getShapeGlyphOrientationVertical(int imageIndex, int roiIndex, int shapeIndex);
657    string getShapeID(int imageIndex, int roiIndex, int shapeIndex);
658    bool getShapeLocked(int imageIndex, int roiIndex, int shapeIndex);
659    string getShapeStrokeAttribute(int imageIndex, int roiIndex, int shapeIndex);
660    string getShapeStrokeColor(int imageIndex, int roiIndex, int shapeIndex);
661    string getShapeStrokeDashArray(int imageIndex, int roiIndex, int shapeIndex);
662    string getShapeStrokeLineCap(int imageIndex, int roiIndex, int shapeIndex);
663    string getShapeStrokeLineJoin(int imageIndex, int roiIndex, int shapeIndex);
664    int getShapeStrokeMiterLimit(int imageIndex, int roiIndex, int shapeIndex);
665    float getShapeStrokeOpacity(int imageIndex, int roiIndex, int shapeIndex);
666    int getShapeStrokeWidth(int imageIndex, int roiIndex, int shapeIndex);
667    string getShapeText(int imageIndex, int roiIndex, int shapeIndex);
668    string getShapeTextAnchor(int imageIndex, int roiIndex, int shapeIndex);
669    string getShapeTextDecoration(int imageIndex, int roiIndex, int shapeIndex);
670    string getShapeTextFill(int imageIndex, int roiIndex, int shapeIndex);
671    string getShapeTextStroke(int imageIndex, int roiIndex, int shapeIndex);
672    int getShapeTheT(int imageIndex, int roiIndex, int shapeIndex);
673    int getShapeTheZ(int imageIndex, int roiIndex, int shapeIndex);
674    string getShapeVectorEffect(int imageIndex, int roiIndex, int shapeIndex);
675    bool getShapeVisibility(int imageIndex, int roiIndex, int shapeIndex);
676    string getShapeWritingMode(int imageIndex, int roiIndex, int shapeIndex);
677
678    // - StageLabel property retrieval -
679
680    string getStageLabelName(int imageIndex);
681    float getStageLabelX(int imageIndex);
682    float getStageLabelY(int imageIndex);
683    float getStageLabelZ(int imageIndex);
684
685    // - StagePosition property retrieval -
686
687    float getStagePositionPositionX(int imageIndex, int pixelsIndex, int planeIndex);
688    float getStagePositionPositionY(int imageIndex, int pixelsIndex, int planeIndex);
689    float getStagePositionPositionZ(int imageIndex, int pixelsIndex, int planeIndex);
690
691    // - Thumbnail property retrieval -
692
693    string getThumbnailHref(int imageIndex);
694    string getThumbnailID(int imageIndex);
695    string getThumbnailMIMEtype(int imageIndex);
696
697    // - TiffData property retrieval -
698
699    string getTiffDataFileName(int imageIndex, int pixelsIndex, int tiffDataIndex);
700    int getTiffDataFirstC(int imageIndex, int pixelsIndex, int tiffDataIndex);
701    int getTiffDataFirstT(int imageIndex, int pixelsIndex, int tiffDataIndex);
702    int getTiffDataFirstZ(int imageIndex, int pixelsIndex, int tiffDataIndex);
703    int getTiffDataIFD(int imageIndex, int pixelsIndex, int tiffDataIndex);
704    int getTiffDataNumPlanes(int imageIndex, int pixelsIndex, int tiffDataIndex);
705    string getTiffDataUUID(int imageIndex, int pixelsIndex, int tiffDataIndex);
706
707    // - TransmittanceRange property retrieval -
708
709    int getTransmittanceRangeCutIn(int instrumentIndex, int filterIndex);
710    int getTransmittanceRangeCutInTolerance(int instrumentIndex, int filterIndex);
711    int getTransmittanceRangeCutOut(int instrumentIndex, int filterIndex);
712    int getTransmittanceRangeCutOutTolerance(int instrumentIndex, int filterIndex);
713    int getTransmittanceRangeTransmittance(int instrumentIndex, int filterIndex);
714
715    // - Well property retrieval -
716
717    int getWellColumn(int plateIndex, int wellIndex);
718    string getWellExternalDescription(int plateIndex, int wellIndex);
719    string getWellExternalIdentifier(int plateIndex, int wellIndex);
720    string getWellID(int plateIndex, int wellIndex);
721    string getWellReagent(int plateIndex, int wellIndex);
722    int getWellRow(int plateIndex, int wellIndex);
723    string getWellType(int plateIndex, int wellIndex);
724
725    // - WellSample property retrieval -
726
727    string getWellSampleID(int plateIndex, int wellIndex, int wellSampleIndex);
728    string getWellSampleImageRef(int plateIndex, int wellIndex, int wellSampleIndex);
729    int getWellSampleIndex(int plateIndex, int wellIndex, int wellSampleIndex);
730    float getWellSamplePosX(int plateIndex, int wellIndex, int wellSampleIndex);
731    float getWellSamplePosY(int plateIndex, int wellIndex, int wellSampleIndex);
732    int getWellSampleTimepoint(int plateIndex, int wellIndex, int wellSampleIndex);
733
734    // - WellSampleRef property retrieval -
735
736    string getWellSampleRefID(int screenIndex, int screenAcquisitionIndex, int wellSampleRefIndex);
737
738    // -- MetadataStore methods --
739
740    void createRoot();
741    //void setRoot(Object root);
742    //Object getRoot();
743
744    // - Entity storage -
745
746    void setUUID(string uuid);
747
748    // - Arc property storage -
749    void setArcType(string type, int instrumentIndex, int lightSourceIndex);
750
751    // - ChannelComponent property storage -
752    void setChannelComponentColorDomain(string colorDomain, int imageIndex, int logicalChannelIndex, int channelComponentIndex);
753    void setChannelComponentIndex(int index, int imageIndex, int logicalChannelIndex, int channelComponentIndex);
754    void setChannelComponentPixels(string pixels, int imageIndex, int logicalChannelIndex, int channelComponentIndex);
755
756    // - Circle property storage -
757    void setCircleCx(string cx, int imageIndex, int roiIndex, int shapeIndex);
758    void setCircleCy(string cy, int imageIndex, int roiIndex, int shapeIndex);
759    void setCircleID(string id, int imageIndex, int roiIndex, int shapeIndex);
760    void setCircleR(string r, int imageIndex, int roiIndex, int shapeIndex);
761    void setCircleTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
762
763    // - Contact property storage -
764    void setContactExperimenter(string experimenter, int groupIndex);
765
766    // - Dataset property storage -
767    void setDatasetDescription(string description, int datasetIndex);
768    void setDatasetExperimenterRef(string experimenterRef, int datasetIndex);
769    void setDatasetGroupRef(string groupRef, int datasetIndex);
770    void setDatasetID(string id, int datasetIndex);
771    void setDatasetLocked(bool locked, int datasetIndex);
772    void setDatasetName(string name, int datasetIndex);
773
774    // - DatasetRef property storage -
775    void setDatasetRefID(string id, int imageIndex, int datasetRefIndex);
776
777    // - Detector property storage -
778    void setDetectorAmplificationGain(float amplificationGain, int instrumentIndex, int detectorIndex);
779    void setDetectorGain(float gain, int instrumentIndex, int detectorIndex);
780    void setDetectorID(string id, int instrumentIndex, int detectorIndex);
781    void setDetectorManufacturer(string manufacturer, int instrumentIndex, int detectorIndex);
782    void setDetectorModel(string model, int instrumentIndex, int detectorIndex);
783    void setDetectorOffset(float offset, int instrumentIndex, int detectorIndex);
784    void setDetectorSerialNumber(string serialNumber, int instrumentIndex, int detectorIndex);
785    void setDetectorType(string type, int instrumentIndex, int detectorIndex);
786    void setDetectorVoltage(float voltage, int instrumentIndex, int detectorIndex);
787    void setDetectorZoom(float zoom, int instrumentIndex, int detectorIndex);
788
789    // - DetectorSettings property storage -
790    void setDetectorSettingsBinning(string binning, int imageIndex, int logicalChannelIndex);
791    void setDetectorSettingsDetector(string detector, int imageIndex, int logicalChannelIndex);
792    void setDetectorSettingsGain(float gain, int imageIndex, int logicalChannelIndex);
793    void setDetectorSettingsOffset(float offset, int imageIndex, int logicalChannelIndex);
794    void setDetectorSettingsReadOutRate(float readOutRate, int imageIndex, int logicalChannelIndex);
795    void setDetectorSettingsVoltage(float voltage, int imageIndex, int logicalChannelIndex);
796
797    // - Dichroic property storage -
798    void setDichroicID(string id, int instrumentIndex, int dichroicIndex);
799    void setDichroicLotNumber(string lotNumber, int instrumentIndex, int dichroicIndex);
800    void setDichroicManufacturer(string manufacturer, int instrumentIndex, int dichroicIndex);
801    void setDichroicModel(string model, int instrumentIndex, int dichroicIndex);
802
803    // - Dimensions property storage -
804    void setDimensionsPhysicalSizeX(float physicalSizeX, int imageIndex, int pixelsIndex);
805    void setDimensionsPhysicalSizeY(float physicalSizeY, int imageIndex, int pixelsIndex);
806    void setDimensionsPhysicalSizeZ(float physicalSizeZ, int imageIndex, int pixelsIndex);
807    void setDimensionsTimeIncrement(float timeIncrement, int imageIndex, int pixelsIndex);
808    void setDimensionsWaveIncrement(int waveIncrement, int imageIndex, int pixelsIndex);
809    void setDimensionsWaveStart(int waveStart, int imageIndex, int pixelsIndex);
810
811    // - DisplayOptions property storage -
812    void setDisplayOptionsDisplay(string display, int imageIndex);
813    void setDisplayOptionsID(string id, int imageIndex);
814    void setDisplayOptionsZoom(float zoom, int imageIndex);
815
816    // - Ellipse property storage -
817    void setEllipseCx(string cx, int imageIndex, int roiIndex, int shapeIndex);
818    void setEllipseCy(string cy, int imageIndex, int roiIndex, int shapeIndex);
819    void setEllipseID(string id, int imageIndex, int roiIndex, int shapeIndex);
820    void setEllipseRx(string rx, int imageIndex, int roiIndex, int shapeIndex);
821    void setEllipseRy(string ry, int imageIndex, int roiIndex, int shapeIndex);
822    void setEllipseTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
823
824    // - EmFilter property storage -
825    void setEmFilterLotNumber(string lotNumber, int instrumentIndex, int filterIndex);
826    void setEmFilterManufacturer(string manufacturer, int instrumentIndex, int filterIndex);
827    void setEmFilterModel(string model, int instrumentIndex, int filterIndex);
828    void setEmFilterType(string type, int instrumentIndex, int filterIndex);
829
830    // - ExFilter property storage -
831    void setExFilterLotNumber(string lotNumber, int instrumentIndex, int filterIndex);
832    void setExFilterManufacturer(string manufacturer, int instrumentIndex, int filterIndex);
833    void setExFilterModel(string model, int instrumentIndex, int filterIndex);
834    void setExFilterType(string type, int instrumentIndex, int filterIndex);
835
836    // - Experiment property storage -
837    void setExperimentDescription(string description, int experimentIndex);
838    void setExperimentExperimenterRef(string experimenterRef, int experimentIndex);
839    void setExperimentID(string id, int experimentIndex);
840    void setExperimentType(string type, int experimentIndex);
841
842    // - Experimenter property storage -
843    void setExperimenterEmail(string email, int experimenterIndex);
844    void setExperimenterFirstName(string firstName, int experimenterIndex);
845    void setExperimenterID(string id, int experimenterIndex);
846    void setExperimenterInstitution(string institution, int experimenterIndex);
847    void setExperimenterLastName(string lastName, int experimenterIndex);
848    void setExperimenterOMEName(string omeName, int experimenterIndex);
849
850    // - ExperimenterMembership property storage -
851    void setExperimenterMembershipGroup(string group, int experimenterIndex, int groupRefIndex);
852
853    // - Filament property storage -
854    void setFilamentType(string type, int instrumentIndex, int lightSourceIndex);
855
856    // - Filter property storage -
857    void setFilterFilterWheel(string filterWheel, int instrumentIndex, int filterIndex);
858    void setFilterID(string id, int instrumentIndex, int filterIndex);
859    void setFilterLotNumber(string lotNumber, int instrumentIndex, int filterIndex);
860    void setFilterManufacturer(string manufacturer, int instrumentIndex, int filterIndex);
861    void setFilterModel(string model, int instrumentIndex, int filterIndex);
862    void setFilterType(string type, int instrumentIndex, int filterIndex);
863
864    // - FilterSet property storage -
865    void setFilterSetDichroic(string dichroic, int instrumentIndex, int filterSetIndex);
866    void setFilterSetEmFilter(string emFilter, int instrumentIndex, int filterSetIndex);
867    void setFilterSetExFilter(string exFilter, int instrumentIndex, int filterSetIndex);
868    void setFilterSetID(string id, int instrumentIndex, int filterSetIndex);
869    void setFilterSetLotNumber(string lotNumber, int instrumentIndex, int filterSetIndex);
870    void setFilterSetManufacturer(string manufacturer, int instrumentIndex, int filterSetIndex);
871    void setFilterSetModel(string model, int instrumentIndex, int filterSetIndex);
872
873    // - Group property storage -
874    void setGroupID(string id, int groupIndex);
875    void setGroupName(string name, int groupIndex);
876
877    // - GroupRef property storage -
878
879    // - Image property storage -
880    void setImageAcquiredPixels(string acquiredPixels, int imageIndex);
881    void setImageCreationDate(string creationDate, int imageIndex);
882    void setImageDefaultPixels(string defaultPixels, int imageIndex);
883    void setImageDescription(string description, int imageIndex);
884    void setImageExperimentRef(string experimentRef, int imageIndex);
885    void setImageExperimenterRef(string experimenterRef, int imageIndex);
886    void setImageGroupRef(string groupRef, int imageIndex);
887    void setImageID(string id, int imageIndex);
888    void setImageInstrumentRef(string instrumentRef, int imageIndex);
889    void setImageName(string name, int imageIndex);
890
891    // - ImagingEnvironment property storage -
892    void setImagingEnvironmentAirPressure(float airPressure, int imageIndex);
893    void setImagingEnvironmentCO2Percent(float cO2Percent, int imageIndex);
894    void setImagingEnvironmentHumidity(float humidity, int imageIndex);
895    void setImagingEnvironmentTemperature(float temperature, int imageIndex);
896
897    // - Instrument property storage -
898    void setInstrumentID(string id, int instrumentIndex);
899
900    // - Laser property storage -
901    void setLaserFrequencyMultiplication(int frequencyMultiplication, int instrumentIndex, int lightSourceIndex);
902    void setLaserLaserMedium(string laserMedium, int instrumentIndex, int lightSourceIndex);
903    void setLaserPockelCell(bool pockelCell, int instrumentIndex, int lightSourceIndex);
904    void setLaserPulse(string pulse, int instrumentIndex, int lightSourceIndex);
905    void setLaserRepetitionRate(bool repetitionRate, int instrumentIndex, int lightSourceIndex);
906    void setLaserTuneable(bool tuneable, int instrumentIndex, int lightSourceIndex);
907    void setLaserType(string type, int instrumentIndex, int lightSourceIndex);
908    void setLaserWavelength(int wavelength, int instrumentIndex, int lightSourceIndex);
909
910    // - LightSource property storage -
911    void setLightSourceID(string id, int instrumentIndex, int lightSourceIndex);
912    void setLightSourceManufacturer(string manufacturer, int instrumentIndex, int lightSourceIndex);
913    void setLightSourceModel(string model, int instrumentIndex, int lightSourceIndex);
914    void setLightSourcePower(float power, int instrumentIndex, int lightSourceIndex);
915    void setLightSourceSerialNumber(string serialNumber, int instrumentIndex, int lightSourceIndex);
916
917    // - LightSourceRef property storage -
918    void setLightSourceRefAttenuation(float attenuation, int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
919    void setLightSourceRefLightSource(string lightSource, int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
920    void setLightSourceRefWavelength(int wavelength, int imageIndex, int microbeamManipulationIndex, int lightSourceRefIndex);
921
922    // - LightSourceSettings property storage -
923    void setLightSourceSettingsAttenuation(float attenuation, int imageIndex, int logicalChannelIndex);
924    void setLightSourceSettingsLightSource(string lightSource, int imageIndex, int logicalChannelIndex);
925    void setLightSourceSettingsWavelength(int wavelength, int imageIndex, int logicalChannelIndex);
926
927    // - Line property storage -
928    void setLineID(string id, int imageIndex, int roiIndex, int shapeIndex);
929    void setLineTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
930    void setLineX1(string x1, int imageIndex, int roiIndex, int shapeIndex);
931    void setLineX2(string x2, int imageIndex, int roiIndex, int shapeIndex);
932    void setLineY1(string y1, int imageIndex, int roiIndex, int shapeIndex);
933    void setLineY2(string y2, int imageIndex, int roiIndex, int shapeIndex);
934
935    // - LogicalChannel property storage -
936    void setLogicalChannelContrastMethod(string contrastMethod, int imageIndex, int logicalChannelIndex);
937    void setLogicalChannelDetector(string detector, int imageIndex, int logicalChannelIndex);
938    void setLogicalChannelEmWave(int emWave, int imageIndex, int logicalChannelIndex);
939    void setLogicalChannelExWave(int exWave, int imageIndex, int logicalChannelIndex);
940    void setLogicalChannelFilterSet(string filterSet, int imageIndex, int logicalChannelIndex);
941    void setLogicalChannelFluor(string fluor, int imageIndex, int logicalChannelIndex);
942    void setLogicalChannelID(string id, int imageIndex, int logicalChannelIndex);
943    void setLogicalChannelIlluminationType(string illuminationType, int imageIndex, int logicalChannelIndex);
944    void setLogicalChannelLightSource(string lightSource, int imageIndex, int logicalChannelIndex);
945    void setLogicalChannelMode(string mode, int imageIndex, int logicalChannelIndex);
946    void setLogicalChannelName(string name, int imageIndex, int logicalChannelIndex);
947    void setLogicalChannelNdFilter(float ndFilter, int imageIndex, int logicalChannelIndex);
948    void setLogicalChannelOTF(string otf, int imageIndex, int logicalChannelIndex);
949    void setLogicalChannelPhotometricInterpretation(string photometricInterpretation, int imageIndex, int logicalChannelIndex);
950    void setLogicalChannelPinholeSize(float pinholeSize, int imageIndex, int logicalChannelIndex);
951    void setLogicalChannelPockelCellSetting(int pockelCellSetting, int imageIndex, int logicalChannelIndex);
952    void setLogicalChannelSamplesPerPixel(int samplesPerPixel, int imageIndex, int logicalChannelIndex);
953    void setLogicalChannelSecondaryEmissionFilter(string secondaryEmissionFilter, int imageIndex, int logicalChannelIndex);
954    void setLogicalChannelSecondaryExcitationFilter(string secondaryExcitationFilter, int imageIndex, int logicalChannelIndex);
955
956    // - Mask property storage -
957    void setMaskHeight(string height, int imageIndex, int roiIndex, int shapeIndex);
958    void setMaskID(string id, int imageIndex, int roiIndex, int shapeIndex);
959    void setMaskTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
960    void setMaskWidth(string width, int imageIndex, int roiIndex, int shapeIndex);
961    void setMaskX(string x, int imageIndex, int roiIndex, int shapeIndex);
962    void setMaskY(string y, int imageIndex, int roiIndex, int shapeIndex);
963
964    // - MaskPixels property storage -
965    void setMaskPixelsBigEndian(bool bigEndian, int imageIndex, int roiIndex, int shapeIndex);
966    void setMaskPixelsBinData(string binData, int imageIndex, int roiIndex, int shapeIndex);
967    void setMaskPixelsExtendedPixelType(string extendedPixelType, int imageIndex, int roiIndex, int shapeIndex);
968    void setMaskPixelsID(string id, int imageIndex, int roiIndex, int shapeIndex);
969    void setMaskPixelsSizeX(int sizeX, int imageIndex, int roiIndex, int shapeIndex);
970    void setMaskPixelsSizeY(int sizeY, int imageIndex, int roiIndex, int shapeIndex);
971
972    // - MicrobeamManipulation property storage -
973    void setMicrobeamManipulationExperimenterRef(string experimenterRef, int imageIndex, int microbeamManipulationIndex);
974    void setMicrobeamManipulationID(string id, int imageIndex, int microbeamManipulationIndex);
975    void setMicrobeamManipulationType(string type, int imageIndex, int microbeamManipulationIndex);
976
977    // - MicrobeamManipulationRef property storage -
978    void setMicrobeamManipulationRefID(string id, int experimentIndex, int microbeamManipulationRefIndex);
979
980    // - Microscope property storage -
981    void setMicroscopeID(string id, int instrumentIndex);
982    void setMicroscopeManufacturer(string manufacturer, int instrumentIndex);
983    void setMicroscopeModel(string model, int instrumentIndex);
984    void setMicroscopeSerialNumber(string serialNumber, int instrumentIndex);
985    void setMicroscopeType(string type, int instrumentIndex);
986
987    // - OTF property storage -
988    void setOTFBinaryFile(string binaryFile, int instrumentIndex, int otfIndex);
989    void setOTFID(string id, int instrumentIndex, int otfIndex);
990    void setOTFObjective(string objective, int instrumentIndex, int otfIndex);
991    void setOTFOpticalAxisAveraged(bool opticalAxisAveraged, int instrumentIndex, int otfIndex);
992    void setOTFPixelType(string pixelType, int instrumentIndex, int otfIndex);
993    void setOTFSizeX(int sizeX, int instrumentIndex, int otfIndex);
994    void setOTFSizeY(int sizeY, int instrumentIndex, int otfIndex);
995
996    // - Objective property storage -
997    void setObjectiveCalibratedMagnification(float calibratedMagnification, int instrumentIndex, int objectiveIndex);
998    void setObjectiveCorrection(string correction, int instrumentIndex, int objectiveIndex);
999    void setObjectiveID(string id, int instrumentIndex, int objectiveIndex);
1000    void setObjectiveImmersion(string immersion, int instrumentIndex, int objectiveIndex);
1001    void setObjectiveIris(bool iris, int instrumentIndex, int objectiveIndex);
1002    void setObjectiveLensNA(float lensNA, int instrumentIndex, int objectiveIndex);
1003    void setObjectiveManufacturer(string manufacturer, int instrumentIndex, int objectiveIndex);
1004    void setObjectiveModel(string model, int instrumentIndex, int objectiveIndex);
1005    void setObjectiveNominalMagnification(int nominalMagnification, int instrumentIndex, int objectiveIndex);
1006    void setObjectiveSerialNumber(string serialNumber, int instrumentIndex, int objectiveIndex);
1007    void setObjectiveWorkingDistance(float workingDistance, int instrumentIndex, int objectiveIndex);
1008
1009    // - ObjectiveSettings property storage -
1010    void setObjectiveSettingsCorrectionCollar(float correctionCollar, int imageIndex);
1011    void setObjectiveSettingsMedium(string medium, int imageIndex);
1012    void setObjectiveSettingsObjective(string objective, int imageIndex);
1013    void setObjectiveSettingsRefractiveIndex(float refractiveIndex, int imageIndex);
1014
1015    // - Path property storage -
1016    void setPathD(string d, int imageIndex, int roiIndex, int shapeIndex);
1017    void setPathID(string id, int imageIndex, int roiIndex, int shapeIndex);
1018
1019    // - Pixels property storage -
1020    void setPixelsBigEndian(bool bigEndian, int imageIndex, int pixelsIndex);
1021    void setPixelsDimensionOrder(string dimensionOrder, int imageIndex, int pixelsIndex);
1022    void setPixelsID(string id, int imageIndex, int pixelsIndex);
1023    void setPixelsPixelType(string pixelType, int imageIndex, int pixelsIndex);
1024    void setPixelsSizeC(int sizeC, int imageIndex, int pixelsIndex);
1025    void setPixelsSizeT(int sizeT, int imageIndex, int pixelsIndex);
1026    void setPixelsSizeX(int sizeX, int imageIndex, int pixelsIndex);
1027    void setPixelsSizeY(int sizeY, int imageIndex, int pixelsIndex);
1028    void setPixelsSizeZ(int sizeZ, int imageIndex, int pixelsIndex);
1029
1030    // - Plane property storage -
1031    void setPlaneHashSHA1(string hashSHA1, int imageIndex, int pixelsIndex, int planeIndex);
1032    void setPlaneID(string id, int imageIndex, int pixelsIndex, int planeIndex);
1033    void setPlaneTheC(int theC, int imageIndex, int pixelsIndex, int planeIndex);
1034    void setPlaneTheT(int theT, int imageIndex, int pixelsIndex, int planeIndex);
1035    void setPlaneTheZ(int theZ, int imageIndex, int pixelsIndex, int planeIndex);
1036
1037    // - PlaneTiming property storage -
1038    void setPlaneTimingDeltaT(float deltaT, int imageIndex, int pixelsIndex, int planeIndex);
1039    void setPlaneTimingExposureTime(float exposureTime, int imageIndex, int pixelsIndex, int planeIndex);
1040
1041    // - Plate property storage -
1042    void setPlateColumnNamingConvention(string columnNamingConvention, int plateIndex);
1043    void setPlateDescription(string description, int plateIndex);
1044    void setPlateExternalIdentifier(string externalIdentifier, int plateIndex);
1045    void setPlateID(string id, int plateIndex);
1046    void setPlateName(string name, int plateIndex);
1047    void setPlateRowNamingConvention(string rowNamingConvention, int plateIndex);
1048    void setPlateStatus(string status, int plateIndex);
1049    void setPlateWellOriginX(double wellOriginX, int plateIndex);
1050    void setPlateWellOriginY(double wellOriginY, int plateIndex);
1051
1052    // - PlateRef property storage -
1053    void setPlateRefID(string id, int screenIndex, int plateRefIndex);
1054    void setPlateRefSample(int sample, int screenIndex, int plateRefIndex);
1055    void setPlateRefWell(string well, int screenIndex, int plateRefIndex);
1056
1057    // - Point property storage -
1058    void setPointCx(string cx, int imageIndex, int roiIndex, int shapeIndex);
1059    void setPointCy(string cy, int imageIndex, int roiIndex, int shapeIndex);
1060    void setPointID(string id, int imageIndex, int roiIndex, int shapeIndex);
1061    void setPointR(string r, int imageIndex, int roiIndex, int shapeIndex);
1062    void setPointTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
1063
1064    // - Polygon property storage -
1065    void setPolygonID(string id, int imageIndex, int roiIndex, int shapeIndex);
1066    void setPolygonPoints(string points, int imageIndex, int roiIndex, int shapeIndex);
1067    void setPolygonTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
1068
1069    // - Polyline property storage -
1070    void setPolylineID(string id, int imageIndex, int roiIndex, int shapeIndex);
1071    void setPolylinePoints(string points, int imageIndex, int roiIndex, int shapeIndex);
1072    void setPolylineTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
1073
1074    // - Project property storage -
1075    void setProjectDescription(string description, int projectIndex);
1076    void setProjectExperimenterRef(string experimenterRef, int projectIndex);
1077    void setProjectGroupRef(string groupRef, int projectIndex);
1078    void setProjectID(string id, int projectIndex);
1079    void setProjectName(string name, int projectIndex);
1080
1081    // - ProjectRef property storage -
1082    void setProjectRefID(string id, int datasetIndex, int projectRefIndex);
1083
1084    // - Pump property storage -
1085    void setPumpLightSource(string lightSource, int instrumentIndex, int lightSourceIndex);
1086
1087    // - ROI property storage -
1088    void setROIID(string id, int imageIndex, int roiIndex);
1089    void setROIT0(int t0, int imageIndex, int roiIndex);
1090    void setROIT1(int t1, int imageIndex, int roiIndex);
1091    void setROIX0(int x0, int imageIndex, int roiIndex);
1092    void setROIX1(int x1, int imageIndex, int roiIndex);
1093    void setROIY0(int y0, int imageIndex, int roiIndex);
1094    void setROIY1(int y1, int imageIndex, int roiIndex);
1095    void setROIZ0(int z0, int imageIndex, int roiIndex);
1096    void setROIZ1(int z1, int imageIndex, int roiIndex);
1097
1098    // - ROIRef property storage -
1099    void setROIRefID(string id, int imageIndex, int microbeamManipulationIndex, int roiRefIndex);
1100
1101    // - Reagent property storage -
1102    void setReagentDescription(string description, int screenIndex, int reagentIndex);
1103    void setReagentID(string id, int screenIndex, int reagentIndex);
1104    void setReagentName(string name, int screenIndex, int reagentIndex);
1105    void setReagentReagentIdentifier(string reagentIdentifier, int screenIndex, int reagentIndex);
1106
1107    // - Rect property storage -
1108    void setRectHeight(string height, int imageIndex, int roiIndex, int shapeIndex);
1109    void setRectID(string id, int imageIndex, int roiIndex, int shapeIndex);
1110    void setRectTransform(string transform, int imageIndex, int roiIndex, int shapeIndex);
1111    void setRectWidth(string width, int imageIndex, int roiIndex, int shapeIndex);
1112    void setRectX(string x, int imageIndex, int roiIndex, int shapeIndex);
1113    void setRectY(string y, int imageIndex, int roiIndex, int shapeIndex);
1114
1115    // - Region property storage -
1116    void setRegionID(string id, int imageIndex, int regionIndex);
1117    void setRegionName(string name, int imageIndex, int regionIndex);
1118    void setRegionTag(string tag, int imageIndex, int regionIndex);
1119
1120    // - RoiLink property storage -
1121    void setRoiLinkDirection(string direction, int imageIndex, int roiIndex, int roiLinkIndex);
1122    void setRoiLinkName(string name, int imageIndex, int roiIndex, int roiLinkIndex);
1123    void setRoiLinkRef(string ref, int imageIndex, int roiIndex, int roiLinkIndex);
1124
1125    // - Screen property storage -
1126    void setScreenDescription(string description, int screenIndex);
1127    void setScreenExtern(string extern, int screenIndex);
1128    void setScreenID(string id, int screenIndex);
1129    void setScreenName(string name, int screenIndex);
1130    void setScreenProtocolDescription(string protocolDescription, int screenIndex);
1131    void setScreenProtocolIdentifier(string protocolIdentifier, int screenIndex);
1132    void setScreenReagentSetDescription(string reagentSetDescription, int screenIndex);
1133    void setScreenReagentSetIdentifier(string reagentSetIdentifier, int screenIndex);
1134    void setScreenType(string type, int screenIndex);
1135
1136    // - ScreenAcquisition property storage -
1137    void setScreenAcquisitionEndTime(string endTime, int screenIndex, int screenAcquisitionIndex);
1138    void setScreenAcquisitionID(string id, int screenIndex, int screenAcquisitionIndex);
1139    void setScreenAcquisitionStartTime(string startTime, int screenIndex, int screenAcquisitionIndex);
1140
1141    // - ScreenRef property storage -
1142    void setScreenRefID(string id, int plateIndex, int screenRefIndex);
1143
1144    // - Shape property storage -
1145    void setShapeBaselineShift(string baselineShift, int imageIndex, int roiIndex, int shapeIndex);
1146    void setShapeDirection(string direction, int imageIndex, int roiIndex, int shapeIndex);
1147    void setShapeFillColor(string fillColor, int imageIndex, int roiIndex, int shapeIndex);
1148    void setShapeFillOpacity(string fillOpacity, int imageIndex, int roiIndex, int shapeIndex);
1149    void setShapeFillRule(string fillRule, int imageIndex, int roiIndex, int shapeIndex);
1150    void setShapeFontFamily(string fontFamily, int imageIndex, int roiIndex, int shapeIndex);
1151    void setShapeFontSize(int fontSize, int imageIndex, int roiIndex, int shapeIndex);
1152    void setShapeFontStretch(string fontStretch, int imageIndex, int roiIndex, int shapeIndex);
1153    void setShapeFontStyle(string fontStyle, int imageIndex, int roiIndex, int shapeIndex);
1154    void setShapeFontVariant(string fontVariant, int imageIndex, int roiIndex, int shapeIndex);
1155    void setShapeFontWeight(string fontWeight, int imageIndex, int roiIndex, int shapeIndex);
1156    void setShapeG(string g, int imageIndex, int roiIndex, int shapeIndex);
1157    void setShapeGlyphOrientationVertical(int glyphOrientationVertical, int imageIndex, int roiIndex, int shapeIndex);
1158    void setShapeID(string id, int imageIndex, int roiIndex, int shapeIndex);
1159    void setShapeLocked(bool locked, int imageIndex, int roiIndex, int shapeIndex);
1160    void setShapeStrokeAttribute(string strokeAttribute, int imageIndex, int roiIndex, int shapeIndex);
1161    void setShapeStrokeColor(string strokeColor, int imageIndex, int roiIndex, int shapeIndex);
1162    void setShapeStrokeDashArray(string strokeDashArray, int imageIndex, int roiIndex, int shapeIndex);
1163    void setShapeStrokeLineCap(string strokeLineCap, int imageIndex, int roiIndex, int shapeIndex);
1164    void setShapeStrokeLineJoin(string strokeLineJoin, int imageIndex, int roiIndex, int shapeIndex);
1165    void setShapeStrokeMiterLimit(int strokeMiterLimit, int imageIndex, int roiIndex, int shapeIndex);
1166    void setShapeStrokeOpacity(float strokeOpacity, int imageIndex, int roiIndex, int shapeIndex);
1167    void setShapeStrokeWidth(int strokeWidth, int imageIndex, int roiIndex, int shapeIndex);
1168    void setShapeText(string text, int imageIndex, int roiIndex, int shapeIndex);
1169    void setShapeTextAnchor(string textAnchor, int imageIndex, int roiIndex, int shapeIndex);
1170    void setShapeTextDecoration(string textDecoration, int imageIndex, int roiIndex, int shapeIndex);
1171    void setShapeTextFill(string textFill, int imageIndex, int roiIndex, int shapeIndex);
1172    void setShapeTextStroke(string textStroke, int imageIndex, int roiIndex, int shapeIndex);
1173    void setShapeTheT(int theT, int imageIndex, int roiIndex, int shapeIndex);
1174    void setShapeTheZ(int theZ, int imageIndex, int roiIndex, int shapeIndex);
1175    void setShapeVectorEffect(string vectorEffect, int imageIndex, int roiIndex, int shapeIndex);
1176    void setShapeVisibility(bool visibility, int imageIndex, int roiIndex, int shapeIndex);
1177    void setShapeWritingMode(string writingMode, int imageIndex, int roiIndex, int shapeIndex);
1178
1179    // - StageLabel property storage -
1180    void setStageLabelName(string name, int imageIndex);
1181    void setStageLabelX(float x, int imageIndex);
1182    void setStageLabelY(float y, int imageIndex);
1183    void setStageLabelZ(float z, int imageIndex);
1184
1185    // - StagePosition property storage -
1186    void setStagePositionPositionX(float positionX, int imageIndex, int pixelsIndex, int planeIndex);
1187    void setStagePositionPositionY(float positionY, int imageIndex, int pixelsIndex, int planeIndex);
1188    void setStagePositionPositionZ(float positionZ, int imageIndex, int pixelsIndex, int planeIndex);
1189
1190    // - Thumbnail property storage -
1191    void setThumbnailHref(string href, int imageIndex);
1192    void setThumbnailID(string id, int imageIndex);
1193    void setThumbnailMIMEtype(string mimEtype, int imageIndex);
1194
1195    // - TiffData property storage -
1196    void setTiffDataFileName(string fileName, int imageIndex, int pixelsIndex, int tiffDataIndex);
1197    void setTiffDataFirstC(int firstC, int imageIndex, int pixelsIndex, int tiffDataIndex);
1198    void setTiffDataFirstT(int firstT, int imageIndex, int pixelsIndex, int tiffDataIndex);
1199    void setTiffDataFirstZ(int firstZ, int imageIndex, int pixelsIndex, int tiffDataIndex);
1200    void setTiffDataIFD(int ifd, int imageIndex, int pixelsIndex, int tiffDataIndex);
1201    void setTiffDataNumPlanes(int numPlanes, int imageIndex, int pixelsIndex, int tiffDataIndex);
1202    void setTiffDataUUID(string uuid, int imageIndex, int pixelsIndex, int tiffDataIndex);
1203
1204    // - TransmittanceRange property storage -
1205    void setTransmittanceRangeCutIn(int cutIn, int instrumentIndex, int filterIndex);
1206    void setTransmittanceRangeCutInTolerance(int cutInTolerance, int instrumentIndex, int filterIndex);
1207    void setTransmittanceRangeCutOut(int cutOut, int instrumentIndex, int filterIndex);
1208    void setTransmittanceRangeCutOutTolerance(int cutOutTolerance, int instrumentIndex, int filterIndex);
1209    void setTransmittanceRangeTransmittance(int transmittance, int instrumentIndex, int filterIndex);
1210
1211    // - Well property storage -
1212    void setWellColumn(int column, int plateIndex, int wellIndex);
1213    void setWellExternalDescription(string externalDescription, int plateIndex, int wellIndex);
1214    void setWellExternalIdentifier(string externalIdentifier, int plateIndex, int wellIndex);
1215    void setWellID(string id, int plateIndex, int wellIndex);
1216    void setWellReagent(string reagent, int plateIndex, int wellIndex);
1217    void setWellRow(int row, int plateIndex, int wellIndex);
1218    void setWellType(string type, int plateIndex, int wellIndex);
1219
1220    // - WellSample property storage -
1221    void setWellSampleID(string id, int plateIndex, int wellIndex, int wellSampleIndex);
1222    void setWellSampleImageRef(string imageRef, int plateIndex, int wellIndex, int wellSampleIndex);
1223    void setWellSampleIndex(int index, int plateIndex, int wellIndex, int wellSampleIndex);
1224    void setWellSamplePosX(float posX, int plateIndex, int wellIndex, int wellSampleIndex);
1225    void setWellSamplePosY(float posY, int plateIndex, int wellIndex, int wellSampleIndex);
1226    void setWellSampleTimepoint(int timepoint, int plateIndex, int wellIndex, int wellSampleIndex);
1227
1228    // - WellSampleRef property storage -
1229    void setWellSampleRefID(string id, int screenIndex, int screenAcquisitionIndex, int wellSampleRefIndex);
1230  };
1231};
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