source: trunk/loci/formats/auto/MetadataAutogenEntities.txt @ 3840

Revision 3840, 17.0 KB checked in by curtis, 12 years ago (diff)

Fix some problems with OME-XML metadata store logic.

Line 
1#
2# MetadataAutogenEntities.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# Add new metadata entity and property definitions to this file.
24
25# Path key and syntax notes:
26# 1) Entities ending in plus (+) have an associated counter method.
27# 2) Elements ending in plus (+) have maxOccurs > 1 and generate an index
28#    parameter to allow differentiation between them.
29# 3) Elements beginning with at (@) are not direct children of the previous
30#    element, but instead reference the parent via an ID reference.
31# 4) Elements beginning with at-bang (@!) also use a parent reference but
32#    the API is slightly different -- e.g., for a LightSource accessing a
33#    child Laser, the method is lightSource.getLaserListByLightSource()
34#    rather than lightSource.getLaserList().
35# 5) Overridden attributes ending in percent (%) indicate a type conflict
36#    that must be resolved by calling type conversion methods from the
37#    OMEXMLMetadata superclass.
38# 6) Attributes starting with small case indicate a method prefix other than
39#    "get" -- e.g., "isTunable" overrides default "getTunable" method name.
40
41
42### Entities for 5D Image information ###
43
44[Image+]
45an image in the metadata store with a particular index
46-
47Default: Image+
48String NodeID        TODO
49String Name          the full name of the image
50String CreationDate  the creation date of the image
51*2003FC: Created
52String Description   the full description of the image
53
54[Pixels+]
55a pixels set in the metadata store with a particular image and pixels index
56-
57Default: Image+/Pixels+
582003FC: Image+/CA/Pixels+
59String NodeID          TODO
60Integer SizeX          size of an individual plane or section's X axis (width)
61Integer SizeY          size of an individual plane of section's Y axis (height)
62Integer SizeZ          number of optical sections per stack
63Integer SizeC          number of channels per timepoint
64Integer SizeT          number of timepoints
65String PixelType       the pixel type
66Boolean BigEndian      if the pixels set is big endian or not
67*2003FC: isBigEndian
68String DimensionOrder  the dimension order of the pixels set
69
70[Dimensions]
71a set of pixel dimensions in the metadata store with a particular index
72Unless both values are non-null, the MetadataStore should assume physicalSizeX equals physicalSizeY (i.e., should populate the null field with the other field's value). # TODO Does Bio-Formats still rely on this requirement?
73Default: Image+/Pixels+
742003FC: Image+/CA/Dimensions
75Float PhysicalSizeX    size of an individual pixel's X axis in microns
76*2003FC: PixelSizeX
77Float PhysicalSizeY    size of an individual pixel's Y axis in microns
78*2003FC: PixelSizeY
79Float PhysicalSizeZ    size of an individual pixel's Z axis in microns
80*2003FC: PixelSizeZ
81Float TimeIncrement    distance between adjacent time points in seconds
82*2003FC: PixelSizeT
83Integer WaveStart      starting wavelength in nanometers
84*2003FC: -
85Integer WaveIncrement  distance between adjacent wavelengths in nanometers
86*2003FC: PixelSizeC%
87
88[ImagingEnvironment]
89the imaging environment for a particular image
90-
91Default: Image+/ImagingEnvironment
922003FC: Image+/CA/ImagingEnvironment
93Float Temperature  TODO
94Float AirPressure  TODO
95Float Humidity     TODO
96Float CO2Percent   TODO
97
98[Plane+]
99the plane information for a specific X-Y plane (section) within a particular pixels set
100-
101Default: Image+/Pixels+/Plane+
1022003FC: -
103Integer TheZ        the optical section index
104Integer TheC        the channel index
105Integer TheT        the timepoint
106
107[PlaneTiming]
108the timing information for a specific X-Y plane (section) within a particular pixels set
109-
110Default: Image+/Pixels+/Plane+/PlaneTiming
1112003FC: -
112Float DeltaT        the time in seconds since the beginning of the experiment
113Float ExposureTime  the exposure time in seconds
114
115[StagePosition]
116the stage position for a specific X-Y plane (section) within a particular pixels set
117-
118Default: Image+/Pixels+/Plane+/StagePosition
1192003FC: -
120Float PositionX  the X coordinate of the stage position
121Float PositionY  the Y coordinate of the stage position
122Float PositionZ  the Z coordinate of the stage position
123
124
125### Entities for channel information for a particular Image ###
126
127[LogicalChannel+]
128a logical channel and physical channel in the metadata store for a particular pixels
129-
130Default: Image+/LogicalChannel+
1312003FC: Image+/CA/LogicalChannel+
132String NodeID                          TODO
133String Name                            the logical channel's name
134Integer SamplesPerPixel                TODO
135String IlluminationType                the illumination type
136Integer PinholeSize                    the size of the pinhole
137String PhotometricInterpretation       the photometric interpretation type
138String Mode                            the acquisition mode
139String ContrastMethod                  the constrast method name
140Integer ExWave                         the excitation wavelength
141*2003FC: ExcitationWavelength
142Integer EmWave                         the emission wavelength
143*2003FC: EmissionWavelength
144String Fluor                           the fluorescence type
145Float NdFilter                         the neutral-density filter value
146*2003FC: NDFilter
147Integer PockelCellSetting              TODO
148*2003FC: -
149
150[ChannelComponent+]
151a channel component describes how each channel in the pixel array relates to the logical channels
152-
153Default: Image+/LogicalChannel+/ChannelComponent+
1542003FC: Image+/CA/LogicalChannel+/@PixelChannelComponent+
155Integer Index       the index into the channel dimension of the 5-D pixel array
156String ColorDomain  which color channel this ChannelComponent belongs to (for example, 'R' for an 'RGB' PhotometricInterpretation)
157# FIXME xsd-fu needs to include get/setPixels methods in ChannelComponentNode
158#PixelsNode Pixels   the pixels to which this channel component corresponds
159
160[DisplayOptions]
161various display options for a particular pixels set
162-
163Default: Image+/DisplayOptions
1642003FC: Image+/CA/DisplayOptions
165String NodeID      TODO
166# FIXME xsd-fu needs to include get/setPixels methods in DisplayOptionsNode
167#PixelsNode Pixels  the pixels to which these display options correspond
168Float Zoom         zoom factor for use in the display (NOT THE LENS ZOOM)
169
170# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
171#[RedChannel]
172#information about the red channel for a particular image
173#-
174#Default: Image+/DisplayOptions/RedChannel
175## FIXME the 2003FC path below will cause compilation errors because RedChannel is not of type RedChannelNode, but DisplayChannelNode; need a notation to specify the distinction between node type and method getter name
176#2003FC: Image+/CA/DisplayOptions/RedChannel
177#Integer ChannelNumber  TODO
178#Float WhiteLevel       TODO
179#Float BlackLevel       TODO
180#Float Gamma            TODO
181
182# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
183#[RedChannelToggle]
184#visibility toggle for a particular image's red channel
185#-
186#Default: Image+/DisplayOptions/RedChannel
187#2003FC: Image+/CA/DisplayOptions
188## FIXME this attribute really is called "isOn"; needs to be addressed somehow
189#Boolean isOn  indicator for whether red channel is active in the display
190#*2003FC: isRedChannelOn
191
192# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
193#[GreenChannel]
194#information about the green channel for a particular image
195#-
196#Default: Image+/DisplayOptions/GreenChannel
197## FIXME the 2003FC path below will cause compilation errors because GreenChannel is not of type GreenChannelNode, but DisplayChannelNode; need a notation to specify the distinction between node type and method getter name
198#2003FC: Image+/CA/DisplayOptions/GreenChannel
199#Integer ChannelNumber  TODO
200#Float WhiteLevel       TODO
201#Float BlackLevel       TODO
202#Float Gamma            TODO
203
204# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
205#[GreenChannelToggle]
206#visibility toggle for a particular image's green channel
207#-
208#Default: Image+/DisplayOptions/GreenChannel
209#2003FC: Image+/CA/DisplayOptions
210## FIXME this attribute really is called "isOn"; needs to be addressed somehow
211#Boolean isOn  indicator for whether green channel is active in the display
212#*2003FC: isGreenChannelOn
213
214# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
215#[BlueChannel]
216#information about the blue channel for a particular image
217#-
218#Default: Image+/DisplayOptions/BlueChannel
219## FIXME the 2003FC path below will cause compilation errors because BlueChannel is not of type BlueChannelNode, but DisplayChannelNode; need a notation to specify the distinction between node type and method getter name
220#2003FC: Image+/CA/DisplayOptions/BlueChannel
221#Integer ChannelNumber  TODO
222#Float WhiteLevel       TODO
223#Float BlackLevel       TODO
224#Float Gamma            TODO
225
226# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
227#[BlueChannelToggle]
228#visibility toggle for a particular image's blue channel
229#-
230#Default: Image+/DisplayOptions/BlueChannel
231#2003FC: Image+/CA/DisplayOptions
232## FIXME this attribute really is called "isOn"; needs to be addressed somehow
233#Boolean isOn  indicator for whether blue channel is active in the display
234#*2003FC: isBlueChannelOn
235
236# FIXME xsd-fu needs to include GreyChannelNode
237#[GreyChannel]
238#information about the grey channel for a particular image
239#-
240#Default: Image+/DisplayOptions/GreyChannel
241## FIXME the 2003FC path below will cause compilation errors because GreyChannel is not of type GreyChannelNode, but DisplayChannelNode; need a notation to specify the distinction between node type and method getter name
242#2003FC: Image+/CA/DisplayOptions/GreyChannel
243#Integer ChannelNumber  TODO
244#Float WhiteLevel       TODO
245#Float BlackLevel       TODO
246#Float Gamma            TODO
247
248# FIXME xsd-fu needs to include GreyChannelNode
249#[GreyChannelMap]
250#color map setting for a particular image's grey channel
251#-
252#Default: Image+/DisplayOptions/GreyChannel
253#2003FC: Image+/CA/DisplayOptions
254#String ColorMap     TODO
255## FIXME need to implement this conversion method in OMEXMLNode
256#*2003FC: isDisplayRGB%
257
258[DisplayOptionsProjection]
259maximum intensity projection-related display options for a particular pixels set
260-
261Default: Image+/DisplayOptions/Projection
2622003FC: Image+/CA/DisplayOptions
263Integer ZStart  the first focal plane to include in the maximum intensity projection
264Integer ZStop   the last focal plane to include in the maximum intensity projection
265
266[DisplayOptionsTime]
267time range-related display options for a particular pixels set
268-
269Default: Image+/DisplayOptions/Time
2702003FC: Image+/CA/DisplayOptions
271Integer TStart  the first time point to include in the animation
272Integer TStop   the last time point to include in the animation
273
274[ROI+]
275a 5D bounding box region of interest in the metadata store with a particular index
276-
277Default: Image+/DisplayOptions/ROI+
2782003FC: Image+/CA/DisplayOptions/@DisplayROI+
279String NodeID  TODO
280Integer X0     the starting X coordinate
281Integer Y0     the starting Y coordinate
282Integer X1     the ending X coordinate
283Integer Y1     the ending Y coordinate
284Integer Z0     the starting Z coordinate
285Integer Z1     the ending Z coordinate
286Integer T0     the starting timepoint
287Integer T1     the ending timepoint
288
289
290### Entities for Instrument settings for a particular Image ###
291
292[DetectorSettings]
293the detector associated with a particular logical channel
294-
295Default: Image+/LogicalChannel+/DetectorRef
2962003FC: Image+/CA/LogicalChannel+
297DetectorNode Detector   the detector associated with this channel
298Float Offset            the detector offset
299*2003FC: DetectorOffset
300Float Gain              the detector gain
301*2003FC: DetectorGain
302
303[LightSourceSettings]
304the light source associated with a particular logical channel
305-
306Default: Image+/LogicalChannel+/LightSourceRef
3072003FC: Image+/CA/LogicalChannel+
308LightSourceNode LightSource  the primary light source
309Float Attenuation            the primary light source attenuation
310*2003FC: LightAttenuation
311Integer Wavelength           the primary light source wavelength
312*2003FC: LightWavelength
313
314
315### Entities for other Image-specific information ###
316
317[StageLabel]
318a stage label in the metadata store with a particular index
319-
320Default: Image+/StageLabel
3212003FC: Image+/CA/StageLabel
322String Name  a name for the stage label
323Float X      x coordinate of the stage
324Float Y      y coordinate of the stage
325Float Z      z coordinate of the stage
326
327
328### Entities for Instrument hardware -- these DO NOT vary by Image ###
329
330[Instrument+]
331an instrument in the metadata store with a particular index
332-
333Default: Instrument+
3342003FC: CA/Instrument+
335String NodeID  TODO
336
337[LightSource+]
338a light source for a particular instrument
339-
340Default: Instrument+/LightSource+
3412003FC: CA/Instrument+/@LightSource+
342String NodeID        TODO
343String Manufacturer  TODO
344String Model         TODO
345String SerialNumber  TODO
346
347[Laser]
348a laser for a particular instrument
349-
350Default: Instrument+/LightSource+/Laser
3512003FC: CA/Instrument+/@LightSource+/@!Laser
352String Type                      TODO
353String LaserMedium               TODO
354*2003FC: Medium
355Integer Wavelength               TODO
356Integer FrequencyMultiplication  TODO
357*2003FC: isFrequencyDoubled%
358Boolean Tuneable                 TODO
359*2003FC: isTunable
360String Pulse                     TODO
361#Float Power                      TODO
362#*200706: -
363
364[Filament]
365a filament for a particular instrument
366-
367Default: Instrument+/LightSource+/Filament
3682003FC: CA/Instrument+/@LightSource+/@Filament
369String Type  TODO
370Float Power  TODO
371
372[Arc]
373an arc for a particular instrument
374-
375Default: Instrument+/LightSource+/Arc
3762003FC: CA/Instrument+/@LightSource+/@Arc
377String Type  TODO
378Float Power  TODO
379
380[Detector+]
381a detector for a particular instrument
382-
383Default: Instrument+/Detector+
3842003FC: CA/Instrument+/@Detector+
385String NodeID        TODO
386String Manufacturer  TODO
387String Model         TODO
388String SerialNumber  TODO
389String Type          TODO
390Float Gain           TODO
391Float Voltage        TODO
392Float Offset         TODO
393
394[Objective+]
395an objective for a particular instrument
396-
397Default: Instrument+/Objective+
3982003FC: CA/Instrument+/@Objective+
399String NodeID                  TODO
400String Manufacturer            TODO
401String Model                   TODO
402String SerialNumber            TODO
403String Correction              TODO
404*2003FC: -
405String Immersion               TODO
406*2003FC: -
407Float LensNA                   TODO
408Integer NominalMagnification   TODO
409*2003FC: -
410Float CalibratedMagnification  TODO
411*2003FC: Magnification
412Float WorkingDistance          TODO
413*2003FC: -
414
415#TODO figure out how to reconcile the two filter models
416
417#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
418#http://ome-xml.org/wiki/FilterAndFilterSet
419
420#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
421#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
422
423#[ExcitationFilter]
424#an excitation filter for a particular instrument
425#-
426#Default: ?
427#2003FC: CA/ExcitationFilter+
428#String Manufacturer  TODO
429#String Model         TODO
430#String LotNumber     TODO
431#String Type          TODO
432
433#[Dichroic]
434#a dichroic for a particular instrument
435#-
436#Default: ?
437#2003FC: CA/Dichroic+
438#String Manufacturer  TODO
439#String Model         TODO
440#String LotNumber     TODO
441
442#[EmissionFilter]
443#an emission filter for a particular instrument
444#-
445#Default: ?
446#2003FC: CA/EmissionFilter+
447#String Manufacturer  TODO
448#String Model         TODO
449#String LotNumber     TODO
450#String Type          TODO
451
452#[FilterSet]
453#a filter set for a particular instrument
454#-
455#Default: ?
456#2003FC: CA/FilterSet+
457#String Manufacturer  TODO
458#String Model         TODO
459#String LotNumber     TODO
460
461[OTF+]
462an optical transfer function for a particular instrument
463-
464Default: Instrument+/OTF+
4652003FC: CA/Instrument+/@OTF+
466String NodeID                TODO
467Integer SizeX                TODO
468Integer SizeY                TODO
469String PixelType             TODO
470#String Path                  TODO
471#*200706: -
472Boolean OpticalAxisAveraged  TODO
473*2003FC: isOpticalAxisAverage
474
475
476### Entities for Experimenter details ###
477
478[Experimenter+]
479an experimenter in the metadata store with a particular index
480-
481Default: Experimenter+
4822003FC: CA/Experimenter+
483String NodeID         TODO
484String FirstName      the first name of the experimenter
485String LastName       the last name of the experimenter
486String Email          the e-mail address of the experimenter
487String Institution    the institution to which the experimenter belongs
488#String DataDirectory  the fully qualified path to the experimenter's data
489#*200706: -
490
491[-]
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