source: trunk/loci/formats/auto/entities.txt @ 3917

Revision 3917, 24.8 KB checked in by curtis, 12 years ago (diff)

A bunch of work on the loci.formats.meta autogenerator. Not finished yet.

Line 
1#
2# entities.txt
3#
4
5# LOCI Bio-Formats package for reading and converting biological file formats.
6# Copyright (C) 2005-@year@ Melissa Linkert, Curtis Rueden, Chris Allan,
7# Eric Kjellman and Brian Loranger.
8#
9# This program is free software; you can redistribute it and/or modify
10# it under the terms of the GNU Library General Public License as published by
11# the Free Software Foundation; either version 2 of the License, or
12# (at your option) any later version.
13#
14# This program is distributed in the hope that it will be useful,
15# but WITHOUT ANY WARRANTY; without even the implied warranty of
16# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
17# GNU Library General Public License for more details.
18#
19# You should have received a copy of the GNU Library General Public License
20# along with this program; if not, write to the Free Software
21# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
22
23# This file enumerates the metadata entity and property definitions for the
24# loci.formats.meta package, and loci.formats.ome.OMEXML*Metadata classes.
25
26# Path key and syntax notes:
27#
28# 1) Path elements ending in plus (+) have maxOccurs > 1 and generate an
29#    index parameter to allow differentiation between them.
30#
31# 2) Path elements beginning with at (@) are not direct children of the
32#    previous element, but instead reference the parent via an ID reference.
33#
34# 3) Path elements beginning with at-bang (@!) also use a parent reference but
35#    the API is slightly different -- e.g., for a LightSource accessing a
36#    child Laser, the method is lightSource.getLaserListByLightSource()
37#    rather than lightSource.getLaserList().
38
39### Entities for 5D Image information ###
40
41## Image ##
42
43[Image]
44countable = true
45path = Image+
46description = an image in the metadata store
47
48[Image ID]
49type = String
50getter = getNodeID
51setter = setNodeID
52description = TODO
53
54[Image Name]
55type = String
56description = the full name of the image
57
58[Image CreationDate]
59type = String
60description = the creation date of the image
61
62[Image CreationDate 2003FC]
63getter = getCreated
64setter = setCreated
65
66[Image Description]
67type = String
68description = the full description of the image
69
70## Pixels ##
71
72[Pixels]
73countable = true
74path = Image+/Pixels+
75description = A pixels set in the metadata store.
76
77[Pixels 2003FC]
78path = Image+/CA/Pixels+
79
80[Pixels ID]
81type = String
82getter = getNodeID
83setter = getNodeID
84description = TODO
85
86[Pixels SizeX]
87type = Integer
88description = The size of an individual plane or section's X axis (width).
89
90[Pixels SizeY]
91type = Integer
92description = The size of an individual plane or section's Y axis (height).
93
94[Pixels SizeZ]
95type = Integer
96description = number of optical sections per stack
97
98[Pixels SizeC]
99type = Integer
100description = number of channels per timepoint
101
102[Pixels SizeT]
103type = Integer
104description = number of timepoints
105
106[Pixels PixelType]
107type = String
108description = the pixel type
109
110[Pixels BigEndian]
111type = Boolean
112description = endianness of the pixels set
113
114[Pixels BigEndian 2003FC]
115getter = isBigEndian
116
117[Pixels DimensionOrder]
118type = String
119description = the dimension order of the pixels set
120
121## Dimensions ##
122
123[Dimensions]
124path = Image+/Pixels+
125description = a set of pixel dimensions in the metadata store \
126              with a particular index
127#notes = Unless both values are non-null, the MetadataStore should assume \
128#        physicalSizeX equals physicalSizeY (i.e., should populate the null \
129#        field with the other field's value).
130# TODO Does Bio-Formats still rely on the above requirement?
131
132[Dimensions 2003FC]
133path = Image+/CA/Dimensions
134
135[Dimensions PhysicalSizeX]
136type = Float
137description = the size of an individual pixel's X axis in microns
138
139[Dimensions PhysicalSizeX 2003FC]
140getter = getPixelSizeX
141setter = setPixelSizeX
142
143[Dimensions PhysicalSizeY]
144type = Float
145description = the size of an individual pixel's Y axis in microns
146
147[Dimensions PhysicalSizeY 2003FC]
148getter = getPixelSizeY
149setter = setPixelSizeY
150
151[Dimensions PhysicalSizeZ]
152type = Float
153description = the size of an individual pixel's Z axis in microns
154
155[Dimensions PhysicalSizeZ 2003FC]
156getter = getPixelSizeZ
157setter = setPixelSizeZ
158
159[Dimensions TimeIncrement]
160type = Float
161description = the distance between adjacent time points in seconds
162
163[Dimensions TimeIncrement 2003FC]
164getter = getPixelSizeT
165setter = setPixelSizeT
166
167[Dimensions WaveStart]
168type = Integer
169description = the starting wavelength in nanometers
170
171[Dimensions WaveStart 2003FC]
172path = -
173
174[Dimensions WaveIncrement]
175type = Integer
176description = the distance between adjacent wavelengths in nanometers
177
178[Dimensions WaveIncrement 2003FC]
179type = Float
180getter = getPixelSizeC
181setter = setPixelSizeC
182
183## ImagingEnvironment ##
184
185[ImagingEnvironment]
186path = Image+/ImagingEnvironment
187description = the imaging environment for a particular image
188
189[ImagingEnvironment 2003FC]
190path = Image+/CA/ImagingEnvironment
191
192[ImagingEnvironment Temperature]
193type = Float
194description = TODO
195
196[ImagingEnvironment AirPressure]
197type = Float
198description = TODO
199
200[ImagingEnvironment Humidity]
201type = Float
202description = TODO
203
204[ImagingEnvironment CO2Percent]
205type = Float
206description = TODO
207
208## Plane ##
209
210[Plane]
211countable = true
212path = Image+/Pixels+/Plane+
213description = the plane information for a specific X-Y plane (section) \
214              within a particular pixels set
215
216[Plane 2003FC]
217path = -
218
219[Plane TheZ]
220type = Integer
221description = the optical section index
222
223[Plane TheC]
224type = Integer
225description = the channel index
226
227[Plane TheT]
228type = Integer
229description = the timepoint
230
231## PlaneTiming ##
232
233[PlaneTiming]
234path = Image+/Pixels+/Plane+/PlaneTiming
235description = the timing information for a specific X-Y plane (section) \
236              within a particular pixels set
237
238[PlaneTiming 2003FC]
239path = -
240
241[PlaneTiming DeltaT]
242type = Float
243description = the time in seconds since the beginning of the experiment
244
245[PlaneTiming ExposureTime]
246type = Float
247description = the exposure time in seconds
248
249## StagePosition ##
250
251[StagePosition]
252path = Image+/Pixels+/Plane+/StagePosition
253description = the stage position for a specific X-Y plane (section) \
254              within a particular pixels set
255
256[StagePosition 2003FC]
257path = -
258
259[StagePosition PositionX]
260type = Float
261description = the X coordinate of the stage position
262
263[StagePosition PositionY]
264type = Float
265description = the Y coordinate of the stage position
266
267[StagePosition PositionZ]
268type = Float
269description = the Z coordinate of the stage position
270
271### Entities for channel information for a particular Image ###
272
273## LogicalChannel ##
274
275[LogicalChannel]
276countable = true
277path = Image+/LogicalChannel+
278description = a logical channel and physical channel in the metadata store \
279              for a particular pixels set
280
281[LogicalChannel 2003FC]
282path = Image+/CA/LogicalChannel+
283
284[LogicalChannel ID]
285type = String
286getter = getNodeID
287setter = setNodeID
288description = TODO
289
290[LogicalChannel Name]
291type = String
292description = the logical channel's name
293
294[LogicalChannel SamplesPerPixel]
295type = Integer
296description = TODO
297
298[LogicalChannel IlluminationType]
299type = String
300description = the illumination type
301
302[LogicalChannel PinholeSize]
303type = Integer
304description = the size of the pinhole
305
306[LogicalChannel PhotometricInterpretation]
307type = String
308description = the photometric interpretation type
309
310[LogicalChannel Mode]
311type = String
312description = the acquisition mode
313
314[LogicalChannel ContrastMethod]
315type = String
316description = the constrast method name
317
318[LogicalChannel ExWave]
319type = Integer
320description = the excitation wavelength
321
322[LogicalChannel ExWave 2003FC]
323getter = getExcitationWavelength
324setter = setExcitationWavelength
325
326[LogicalChannel EmWave]
327type = Integer
328description = the emission wavelength
329
330[LogicalChannel EmWave 2003FC]
331getter = getEmissionWavelength
332setter = setEmissionWavelength
333
334[LogicalChannel Fluor]
335type = String
336description = the fluorescence type
337
338[LogicalChannel NdFilter]
339type = Float
340description = the neutral-density filter value
341
342[LogicalChannel NdFilter 2003FC]
343getter = getNDFilter
344setter = setNDFilter
345
346[LogicalChannel PockelCellSetting]
347type = Integer
348description = TODO
349
350[LogicalChannel PockelCellSetting 2003FC]
351path = -
352
353## ChannelComponent ##
354
355[ChannelComponent]
356countable = true
357path = Image+/LogicalChannel+/ChannelComponent+
358description = a channel component describes how each channel \
359              in the pixel array relates to the logical channels
360
361[ChannelComponent 2003FC]
362path = Image+/CA/LogicalChannel+/@PixelChannelComponent+
363
364[ChannelComponent Index]
365type = Integer
366description = the index into the channel dimension of the 5-D pixel array
367
368[ChannelComponent ColorDomain]
369type = String
370description = which color channel this ChannelComponent belongs to \
371              (for example, 'R' for an 'RGB' PhotometricInterpretation)
372
373# FIXME xsd-fu needs to include get/setPixels methods in ChannelComponentNode?
374#[ChannelComponent Pixels]
375#type = String
376#description = the pixels to which this channel component corresponds
377
378## DisplayOptions ##
379
380[DisplayOptions]
381path = Image+/DisplayOptions
382description = various display options for a particular pixels set
383
384[DisplayOptions 2003FC]
385path = Image+/CA/DisplayOptions
386
387[DisplayOptions ID]
388type = String
389getter = getNodeID
390setter = setNodeID
391description = TODO
392
393# FIXME xsd-fu needs to include get/setPixels methods in DisplayOptionsNode
394#[DisplayOptions Pixels]
395#type = String
396#description = the pixels to which these display options correspond
397
398[DisplayOptions Zoom]
399type = Float
400description = zoom factor for use in the display (NOT THE LENS ZOOM)
401
402## RedChannel ##
403
404# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
405#[RedChannel]
406#path = Image+/DisplayOptions/RedChannel
407#description = information about the red channel for a particular image
408#
409# FIXME the 2003FC path below will cause compilation errors because RedChannel
410# is not of type RedChannelNode, but DisplayChannelNode; need a notation to
411# specify the distinction between node type and method getter name
412#[RedChannel 2003FC]
413#path = Image+/CA/DisplayOptions/RedChannel
414#
415#[RedChannel ChannelNumber]
416#type = Integer
417#description = TODO
418#
419#[RedChannel WhiteLevel]
420#type = Float
421#description = TODO
422#
423#[RedChannel BlackLevel]
424#type = Float
425#description = TODO
426#
427#[RedChannel Gamma]
428#type = Float
429#description = TODO
430
431## RedChannelToggle ##
432
433# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
434#[RedChannelToggle]
435#description = visibility toggle for a particular image's red channel
436#path = Image+/DisplayOptions/RedChannel
437#
438#[RedChannelToggle 2003FC]
439#path = Image+/CA/DisplayOptions
440#
441#[RedChannelToggle Enabled]
442#type = Boolean
443#getter = getisOn
444#setter = setisOn
445#description = indicator for whether red channel is active in the display
446#
447#[RedChannelToggle Enabled 2003FC
448#getter = isRedChannelOn
449#setter = setRedChannelOn
450
451## GreenChannel ##
452
453# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
454#[GreenChannel]
455#path = Image+/DisplayOptions/GreenChannel
456#description = information about the green channel for a particular image
457#
458# FIXME the 2003FC path below will cause compilation errors because GreenChannel
459# is not of type GreenChannelNode, but DisplayChannelNode; need a notation to
460# specify the distinction between node type and method getter name
461#[GreenChannel 2003FC]
462#path = Image+/CA/DisplayOptions/GreenChannel
463#
464#[GreenChannel ChannelNumber]
465#type = Integer
466#description = TODO
467#
468#[GreenChannel WhiteLevel]
469#type = Float
470#description = TODO
471#
472#[GreenChannel BlackLevel]
473#type = Float
474#description = TODO
475#
476#[GreenChannel Gamma]
477#type = Float
478#description = TODO
479
480## GreenChannelToggle ##
481
482# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
483#[GreenChannelToggle]
484#description = visibility toggle for a particular image's green channel
485#path = Image+/DisplayOptions/GreenChannel
486#
487#[GreenChannelToggle 2003FC]
488#path = Image+/CA/DisplayOptions
489#
490#[GreenChannelToggle Enabled]
491#type = Boolean
492#getter = getisOn
493#setter = setisOn
494#description = indicator for whether Green channel is active in the display
495#
496#[GreenChannelToggle Enabled 2003FC
497#getter = isGreenChannelOn
498#setter = setGreenChannelOn
499
500## BlueChannel ##
501
502# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
503#[BlueChannel]
504#path = Image+/DisplayOptions/BlueChannel
505#description = information about the blue channel for a particular image
506#
507# FIXME the 2003FC path below will cause compilation errors because BlueChannel
508# is not of type BlueChannelNode, but DisplayChannelNode; need a notation to
509# specify the distinction between node type and method getter name
510#[BlueChannel 2003FC]
511#path = Image+/CA/DisplayOptions/BlueChannel
512#
513#[BlueChannel ChannelNumber]
514#type = Integer
515#description = TODO
516#
517#[BlueChannel WhiteLevel]
518#type = Float
519#description = TODO
520#
521#[BlueChannel BlackLevel]
522#type = Float
523#description = TODO
524#
525#[BlueChannel Gamma]
526#type = Float
527#description = TODO
528
529## BlueChannelToggle ##
530
531# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
532#[BlueChannelToggle]
533#description = visibility toggle for a particular image's blue channel
534#path = Image+/DisplayOptions/BlueChannel
535#
536#[BlueChannelToggle 2003FC]
537#path = Image+/CA/DisplayOptions
538#
539#[BlueChannelToggle Enabled]
540#type = Boolean
541#getter = getisOn
542#setter = setisOn
543#description = indicator for whether red channel is active in the display
544#
545#[BlueChannelToggle Enabled 2003FC
546#getter = isBlueChannelOn
547#setter = setBlueChannelOn
548
549## GreyChannel ##
550
551# FIXME xsd-fu needs to include GreyChannelNode
552#[GreyChannel]
553#path = Image+/DisplayOptions/GreyChannel
554#description = information about the grey channel for a particular image
555#
556# FIXME the 2003FC path below will cause compilation errors because
557# GreyChannel is not of type GreyChannelNode, but DisplayChannelNode; need a
558# notation to specify the distinction between node type and method getter name
559#[GreyChannel 2003FC]
560#path = Image+/CA/DisplayOptions/GreyChannel
561#
562#[GreyChannel ChannelNumber]
563#type = Integer
564#description = TODO
565#
566#[GreyChannel WhiteLevel]
567#type = Float
568#description = TODO
569#
570#[GreyChannel BlackLevel]
571#type = Float
572#description = TODO
573#
574#[GreyChannel Gamma]
575#type = Float
576#description = TODO
577
578## GreyChannelMap ##
579
580# FIXME xsd-fu needs to include GreyChannelNode
581#[GreyChannelMap]
582#path = Image+/DisplayOptions/GreyChannel
583#description = color map setting for a particular image's grey channel
584#
585#[GreyChannelMap 2003FC]
586#path = Image+/CA/DisplayOptions
587#
588#[GreyChannelMap ColorMap]
589#type = String
590#description = TODO
591#
592# FIXME need to implement this conversion method in OMEXMLNode
593#[GreyChannelMap ColorMap 2003FC]
594#type = Boolean
595#getter = isDisplayRGB
596#setter = setDisplayRGB
597
598## DisplayOptionsProjection ##
599
600[DisplayOptionsProjection]
601path = Image+/DisplayOptions/Projection
602description = maximum intensity projection-related display options \
603              for a particular image
604
605[DisplayOptionsProjection 2003FC]
606path = Image+/CA/DisplayOptions
607
608[DisplayOptionsProjection ZStart]
609type = Integer
610description = the first focal plane to include \
611              in the maximum intensity projection
612
613[DisplayOptionsProjection ZStop]
614type = Integer
615description = the last focal plane to include \
616              in the maximum intensity projection
617
618## DisplayOptionsTime ##
619
620[DisplayOptionsTime]
621path = Image+/DisplayOptions/Time
622description = time range-related display options for a particular image
623
624[DisplayOptionsTime 2003FC]
625path = Image+/CA/DisplayOptions
626
627[DisplayOptionsTime TStart]
628type = Integer
629description = the first time point to include in the animation
630
631[DisplayOptionsTime TStop]
632type = Integer
633description = the last time point to include in the animation
634
635## ROI ##
636
637[ROI]
638countable = true
639path = Image+/DisplayOptions/ROI+
640description = a 5D bounding box region of interest in the metadata store \
641              with a particular index
642
643[ROI 2003FC]
644path = Image+/CA/DisplayOptions/@DisplayROI+
645
646[ROI ID]
647type = String
648getter = getNodeID
649setter = setNodeID
650description = TODO
651
652[ROI X0]
653type = Integer
654description = the starting X coordinate
655
656[ROI Y0]
657type = Integer
658description = the starting Y coordinate
659
660[ROI X1]
661type = Integer
662description = the ending X coordinate
663
664[ROI Y1]
665type = Integer
666description = the ending Y coordinate
667
668[ROI Z0]
669type = Integer
670description = the starting Z coordinate
671
672[ROI Z1]
673type = Integer
674description = the ending Z coordinate
675
676[ROI T0]
677type = Integer
678description = the starting timepoint
679
680[ROI T1]
681type = Integer
682description = the ending timepoint
683
684### Entities for Instrument settings for a particular Image ###
685
686## DetectorSettings ##
687
688[DetectorSettings]
689path = Image+/LogicalChannel+/DetectorRef
690description = the detector associated with a particular logical channel
691
692[DetectorSettings 2003FC]
693path = Image+/CA/LogicalChannel+
694
695[DetectorSettings Detector]
696type = String
697# TODO
698description = the detector associated with this channel
699
700[DetectorSettings Offset]
701type = Float
702description = the detector offset
703
704[DetectorSettings Offset 2003FC]
705getter = getDetectorOffset
706setter = setDetectorOffset
707
708[DetectorSettings Gain]
709type = Float
710description = the detector gain
711
712[DetectorSettings Gain 2003FC]
713getter = getDetectorGain
714setter = setDetectorGain
715
716## LightSourceSettings ##
717
718[LightSourceSettings]
719path = Image+/LogicalChannel+/LightSourceRef
720description = the light source associated with a particular logical channel
721
722[LightSourceSettings 2003FC]
723path = Image+/CA/LogicalChannel+
724
725[LightSourceSettings LightSource]
726type = String
727# TODO
728description = the primary light source
729
730[LightSourceSettings Attenuation]
731type = Float
732description = the primary light source attenuation
733
734[LightSourceSettings Attenuation 2003FC]
735getter = getLightAttenuation
736setter = setLightAttenuation
737
738[LightSourceSettings Wavelength]
739type = Integer
740description = the primary light source wavelength
741
742[LightSourceSettings Wavelength 2003FC]
743getter = getLightWavelength
744setter = setLightWavelength
745
746### Entities for other Image-specific information ###
747
748## StageLabel ##
749
750[StageLabel]
751path = Image+/StageLabel
752description = a stage label in the metadata store with a particular index
753
754[StageLabel 2003FC]
755path = Image+/CA/StageLabel
756
757[StageLabel Name]
758type = String
759description = a name for the stage label
760
761[StageLabel X]
762type = Float
763description = the x coordinate of the stage
764
765[StageLabel Y]
766type = Float
767description = the y coordinate of the stage
768
769[StageLabel Z]
770type = Float
771description = the z coordinate of the stage
772
773### Entities for Instrument hardware -- these DO NOT vary by Image ###
774
775## Instrument ##
776
777[Instrument]
778countable = true
779path = Instrument+
780description = an instrument in the metadata store with a particular index
781
782[Instrument 2003FC]
783path = CA/Instrument+
784
785[Instrument ID]
786type = String
787getter = getNodeID
788setter = setNodeID
789description = TODO
790
791## LightSource ##
792
793[LightSource]
794countable = true
795path = Instrument+/LightSource+
796description = a light source for a particular instrument
797
798[LightSource 2003FC]
799path = CA/Instrument+/@LightSource+
800
801[LightSource ID]
802type = String
803getter = getNodeID
804setter = setNodeID
805description = TODO
806
807[LightSource Manufacturer]
808type = String
809description = TODO
810
811[LightSource Model]
812type = String
813description = TODO
814
815[LightSource SerialNumber]
816type = String
817description = TODO
818
819## Laser ##
820
821[Laser]
822path = Instrument+/LightSource+/Laser
823description = a laser for a particular instrument
824
825[Laser 2003FC]
826path = CA/Instrument+/@LightSource+/@!Laser
827
828[Laser Type]
829type = String
830description = TODO
831
832[Laser LaserMedium]
833type = String
834description = TODO
835
836[Laser LaserMedium 2003FC]
837getter = getMedium
838setter = setMedium
839
840[Laser Wavelength]
841type = Integer
842description = TODO
843
844[Laser FrequencyMultiplication]
845type = Integer
846description = TODO
847
848[Laser FrequencyMultiplication 2003FC]
849type = Boolean
850getter = isFrequencyDoubled
851setter = setFrequencyDoubled
852
853[Laser Tuneable]
854type = Boolean
855description = TODO
856
857[Laser Tuneable 2003FC]
858getter = isTunable
859setter = setTunable
860
861[Laser Pulse]
862type = String
863description = TODO
864
865## Filament ##
866
867[Filament]
868path = Instrument+/LightSource+/Filament
869description = a filament for a particular instrument
870
871[Filament 2003FC]
872path = CA/Instrument+/@LightSource+/@Filament
873
874[Filament Type]
875type = String
876description = TODO
877
878[Filament Power]
879type = Float
880description = TODO
881
882## Arc ##
883
884[Arc]
885path = Instrument+/LightSource+/Arc
886description = an arc for a particular instrument
887
888[Arc 2003FC]
889path = CA/Instrument+/@LightSource+/@Arc
890
891[Arc Type]
892type = String
893description = TODO
894
895[Arc Power]
896type = Float
897description = TODO
898
899## Detector ##
900
901[Detector]
902countable = true
903path = Instrument+/Detector+
904description = a detector for a particular instrument
905
906[Detector 2003FC]
907path = CA/Instrument+/@Detector+
908
909[Detector ID]
910type = String
911getter = getNodeID
912setter = setNodeID
913description = TODO
914
915[Detector Manufacturer]
916type = String
917description = TODO
918
919[Detector Model]
920type = String
921description = TODO
922
923[Detector SerialNumber]
924type = String
925description = TODO
926
927[Detector Type]
928type = String
929description = TODO
930
931[Detector Gain]
932type = Float
933description = TODO
934
935[Detector Voltage]
936type = Float
937description = TODO
938
939[Detector Offset]
940type = Float
941description = TODO
942
943## Objective ##
944
945[Objective]
946countable = true
947path = Instrument+/Objective+
948description = an objective for a particular instrument
949
950[Objective 2003FC]
951path = CA/Instrument+/@Objective+
952
953[Objective ID]
954type = String
955getter = getNodeID
956setter = setNodeID
957description = TODO
958
959[Objective Manufacturer]
960type = String
961description = TODO
962
963[Objective Model]
964type = String
965description = TODO
966
967[Objective SerialNumber]
968type = String
969description = TODO
970
971[Objective Correction]
972type = String
973description = TODO
974
975[Objective Correction 2003FC]
976path = -
977
978[Objective Immersion]
979type = String
980description = TODO
981
982[Objective Immersion 2003FC]
983path = -
984
985[Objective LensNA]
986type = Float
987description = TODO
988
989[Objective NominalMagnification]
990type = Integer
991description = TODO
992
993[Objective NominalMagnification 2003FC]
994path = -
995
996[Objective CalibratedMagnification]
997type = Float
998description = TODO
999
1000[Objective CalibratedMagnification 2003FC]
1001getter = getMagnification
1002setter = setMagnification
1003
1004[Objective WorkingDistance]
1005type = Float
1006description = TODO
1007
1008[Objective WorkingDistance 2003FC]
1009path = -
1010
1011#TODO figure out how to reconcile the two filter models
1012
1013#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
1014#http://ome-xml.org/wiki/FilterAndFilterSet
1015
1016#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
1017#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
1018
1019## ExcitationFilter ##
1020
1021#[ExcitationFilter]
1022#path = ?
1023#description = an excitation filter for a particular instrument
1024#
1025#[ExcitationFilter 2003FC]
1026#path = CA/ExcitationFilter+
1027#
1028#[ExcitationFilter Manufacturer]
1029#type = String
1030#description = TODO
1031#
1032#[ExcitationFilter Model]
1033#type = String
1034#description = TODO
1035#
1036#[ExcitationFilter LotNumber]
1037#type = String
1038#description = TODO
1039#
1040#[ExcitationFilter Type]
1041#type = String
1042#description = TODO
1043
1044## Dichroic ##
1045
1046#[Dichroic]
1047#path = ?
1048#description = a dichroic for a particular instrument
1049#
1050#[Dichroic 2003FC]
1051#path = CA/Dichroic+
1052#
1053#[Dichroic Manufacturer]
1054#type = String
1055#description = TODO
1056#
1057#[Dichroic Model]
1058#type = String
1059#description = TODO
1060#
1061#[Dichroic LotNumber]
1062#type = String
1063#description = TODO
1064
1065## EmissionFilter ##
1066
1067#[EmissionFilter]
1068#path = ?
1069#description = an emission filter for a particular instrument
1070#
1071#[EmissionFilter 2003FC]
1072#path = CA/EmissionFilter+
1073#
1074#[EmissionFilter Manufacturer]
1075#type = String
1076#description = TODO
1077#
1078#[EmissionFilter Model]
1079#type = String
1080#description = TODO
1081#
1082#[EmissionFilter LotNumber]
1083#type = String
1084#description = TODO
1085#
1086#[EmissionFilter Type]
1087#type = String
1088#description = TODO
1089
1090## FilterSet ##
1091
1092#[FilterSet]
1093#path = ?
1094#description = a filter set for a particular instrument
1095#
1096#[FilterSet 2003FC]
1097#path = CA/FilterSet+
1098#
1099#[FilterSet Manufacturer]
1100#type = String
1101#description = TODO
1102#
1103#[FilterSet Model]
1104#type = String
1105#description = TODO
1106#
1107#[FilterSet LotNumber]
1108#type = String
1109#description = TODO
1110
1111## OTF ##
1112
1113[OTF]
1114countable = true
1115path = Instrument+/OTF+
1116description = an optical transfer function for a particular instrument
1117
1118[OTF 2003FC]
1119path = CA/Instrument+/@OTF+
1120
1121[OTF ID]
1122type = String
1123getter = getNodeID
1124setter = setNodeID
1125description = TODO
1126
1127[OTF SizeX]
1128type = Integer
1129description = TODO
1130
1131[OTF SizeY]
1132type = Integer
1133description = TODO
1134
1135[OTF PixelType]
1136type = String
1137description = TODO
1138
1139[OTF OpticalAxisAveraged]
1140type = Boolean
1141description = TODO
1142
1143[OTF OpticalAxisAveraged 2003FC]
1144getter = isOpticalAxisAverage
1145setter = setOpticalAxisAverage
1146
1147### Entities for Experimenter details ###
1148
1149## Experimenter ##
1150
1151[Experimenter]
1152countable = true
1153path = Experimenter+
1154description = an experimenter in the metadata store with a particular index
1155
1156[Experimenter 2003FC]
1157path = CA/Experimenter+
1158
1159[Experimenter ID]
1160type = String
1161getter = getNodeID
1162setter = setNodeID
1163description = TODO
1164
1165[Experimenter FirstName]
1166type = String
1167description = the first name of the experimenter
1168
1169[Experimenter LastName]
1170type = String
1171description = the last name of the experimenter
1172
1173[Experimenter Email]
1174type = String
1175description = the e-mail address of the experimenter
1176
1177[Experimenter Institution]
1178type = String
1179description = the institution to which the experimenter belongs
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