source: trunk/loci/formats/auto/MetadataAutogenEntities.txt @ 3616

Revision 3616, 16.6 KB checked in by curtis, 12 years ago (diff)

Some work on DisplayOptions and ChannelComponent.

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 Name          the full name of the image
49String CreationDate  the creation date of the image
50*2003FC: Created
51String Description   the full description of the image
52
53[Pixels+]
54a pixels set in the metadata store with a particular image and pixels index
55-
56Default: Image+/Pixels+
572003FC: Image+/CA/Pixels+
58Integer SizeX          size of an individual plane or section's X axis (width)
59Integer SizeY          size of an individual plane of section's Y axis (height)
60Integer SizeZ          number of optical sections per stack
61Integer SizeC          number of channels per timepoint
62Integer SizeT          number of timepoints
63String PixelType       the pixel type
64Boolean BigEndian      if the pixels set is big endian or not
65*2003FC: isBigEndian
66String DimensionOrder  the dimension order of the pixels set
67
68[Dimensions]
69a set of pixel dimensions in the metadata store with a particular index
70Unless 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?
71Default: Image+/Pixels+
722003FC: Image+/CA/Dimensions
73Float PhysicalSizeX    size of an individual pixel's X axis in microns
74*2003FC: PixelSizeX
75Float PhysicalSizeY    size of an individual pixel's Y axis in microns
76*2003FC: PixelSizeY
77Float PhysicalSizeZ    size of an individual pixel's Z axis in microns
78*2003FC: PixelSizeZ
79Float TimeIncrement    distance between adjacent time points in seconds
80*2003FC: PixelSizeT
81Integer WaveStart      starting wavelength in nanometers
82*2003FC: -
83Integer WaveIncrement  distance between adjacent wavelengths in nanometers
84*2003FC: PixelSizeC%
85
86[ImagingEnvironment]
87the imaging environment for a particular image
88-
89Default: Image+/ImagingEnvironment
902003FC: Image+/CA/ImagingEnvironment
91Float Temperature  TODO
92Float AirPressure  TODO
93Float Humidity     TODO
94Float CO2Percent   TODO
95
96[Plane+]
97the plane information for a specific X-Y plane (section) within a particular pixels set
98-
99Default: Image+/Pixels+/Plane+
1002003FC: -
101Integer TheZ        the optical section index
102Integer TheC        the channel index
103Integer TheT        the timepoint
104
105[PlaneTiming]
106the timing information for a specific X-Y plane (section) within a particular pixels set
107-
108Default: Image+/Pixels+/Plane+/PlaneTiming
1092003FC: -
110Float DeltaT        the time in seconds since the beginning of the experiment
111Float ExposureTime  the exposure time in seconds
112
113[StagePosition]
114the stage position for a specific X-Y plane (section) within a particular pixels set
115-
116Default: Image+/Pixels+/Plane+/StagePosition
1172003FC: -
118Float PositionX  the X coordinate of the stage position
119Float PositionY  the Y coordinate of the stage position
120Float PositionZ  the Z coordinate of the stage position
121
122
123### Entities for channel information for a particular Image ###
124
125[LogicalChannel+]
126a logical channel and physical channel in the metadata store for a particular pixels
127-
128Default: Image+/LogicalChannel+
1292003FC: Image+/CA/LogicalChannel+
130String Name                            the logical channel's name
131Integer SamplesPerPixel                TODO
132String IlluminationType                the illumination type
133Integer PinholeSize                    the size of the pinhole
134String PhotometricInterpretation       the photometric interpretation type
135String Mode                            the acquisition mode
136String ContrastMethod                  the constrast method name
137Integer ExWave                         the excitation wavelength
138*2003FC: ExcitationWavelength
139Integer EmWave                         the emission wavelength
140*2003FC: EmissionWavelength
141String Fluor                           the fluorescence type
142Float NdFilter                         the neutral-density filter value
143*2003FC: NDFilter
144Integer PockelCellSetting              TODO
145*2003FC: -
146
147[ChannelComponent+]
148a channel component describes how each channel in the pixel array relates to the logical channels
149-
150Default: Image+/LogicalChannel+/ChannelComponent+
1512003FC: Image+/CA/LogicalChannel+/@PixelChannelComponent+
152Integer Index       the index into the channel dimension of the 5-D pixel array
153String ColorDomain  which color channel this ChannelComponent belongs to (for example, 'R' for an 'RGB' PhotometricInterpretation)
154# FIXME xsd-fu needs to include get/setPixels methods in ChannelComponentNode
155#PixelsNode Pixels   the pixels to which this channel component corresponds
156
157[DisplayOptions]
158various display options for a particular pixels set
159-
160Default: Image+/DisplayOptions
1612003FC: Image+/CA/DisplayOptions
162# FIXME xsd-fu needs to include get/setPixels methods in DisplayOptionsNode
163#PixelsNode Pixels  the pixels to which these display options correspond
164Float Zoom         zoom factor for use in the display (NOT THE LENS ZOOM)
165
166# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
167#[RedChannel]
168#information about the red channel for a particular image
169#-
170#Default: Image+/DisplayOptions/RedChannel
171## 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
172#2003FC: Image+/CA/DisplayOptions/RedChannel
173#Integer ChannelNumber  TODO
174#Float WhiteLevel       TODO
175#Float BlackLevel       TODO
176#Float Gamma            TODO
177
178# FIXME xsd-fu needs to include RedChannelNode (extension of ChannelSpecNode)
179#[RedChannelToggle]
180#visibility toggle for a particular image's red channel
181#-
182#Default: Image+/DisplayOptions/RedChannel
183#2003FC: Image+/CA/DisplayOptions
184## FIXME this attribute really is called "isOn"; needs to be addressed somehow
185#Boolean isOn  indicator for whether red channel is active in the display
186#*2003FC: isRedChannelOn
187
188# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
189#[GreenChannel]
190#information about the green channel for a particular image
191#-
192#Default: Image+/DisplayOptions/GreenChannel
193## 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
194#2003FC: Image+/CA/DisplayOptions/GreenChannel
195#Integer ChannelNumber  TODO
196#Float WhiteLevel       TODO
197#Float BlackLevel       TODO
198#Float Gamma            TODO
199
200# FIXME xsd-fu needs to include GreenChannelNode (extension of ChannelSpecNode)
201#[GreenChannelToggle]
202#visibility toggle for a particular image's green channel
203#-
204#Default: Image+/DisplayOptions/GreenChannel
205#2003FC: Image+/CA/DisplayOptions
206## FIXME this attribute really is called "isOn"; needs to be addressed somehow
207#Boolean isOn  indicator for whether green channel is active in the display
208#*2003FC: isGreenChannelOn
209
210# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
211#[BlueChannel]
212#information about the blue channel for a particular image
213#-
214#Default: Image+/DisplayOptions/BlueChannel
215## 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
216#2003FC: Image+/CA/DisplayOptions/BlueChannel
217#Integer ChannelNumber  TODO
218#Float WhiteLevel       TODO
219#Float BlackLevel       TODO
220#Float Gamma            TODO
221
222# FIXME xsd-fu needs to include BlueChannelNode (extension of ChannelSpecNode)
223#[BlueChannelToggle]
224#visibility toggle for a particular image's blue channel
225#-
226#Default: Image+/DisplayOptions/BlueChannel
227#2003FC: Image+/CA/DisplayOptions
228## FIXME this attribute really is called "isOn"; needs to be addressed somehow
229#Boolean isOn  indicator for whether blue channel is active in the display
230#*2003FC: isBlueChannelOn
231
232# FIXME xsd-fu needs to include GreyChannelNode
233#[GreyChannel]
234#information about the grey channel for a particular image
235#-
236#Default: Image+/DisplayOptions/GreyChannel
237## 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
238#2003FC: Image+/CA/DisplayOptions/GreyChannel
239#Integer ChannelNumber  TODO
240#Float WhiteLevel       TODO
241#Float BlackLevel       TODO
242#Float Gamma            TODO
243
244# FIXME xsd-fu needs to include GreyChannelNode
245#[GreyChannelMap]
246#color map setting for a particular image's grey channel
247#-
248#Default: Image+/DisplayOptions/GreyChannel
249#2003FC: Image+/CA/DisplayOptions
250#String ColorMap     TODO
251## FIXME need to implement this conversion method in OMEXMLNode
252#*2003FC: isDisplayRGB%
253
254[DisplayOptionsProjection]
255maximum intensity projection-related display options for a particular pixels set
256-
257Default: Image+/DisplayOptions/Projection
2582003FC: Image+/CA/DisplayOptions
259Integer ZStart  the first focal plane to include in the maximum intensity projection
260Integer ZStop   the last focal plane to include in the maximum intensity projection
261
262[DisplayOptionsTime]
263time range-related display options for a particular pixels set
264-
265Default: Image+/DisplayOptions/Time
2662003FC: Image+/CA/DisplayOptions
267Integer TStart  the first time point to include in the animation
268Integer TStop   the last time point to include in the animation
269
270[ROI+]
271a 5D bounding box region of interest in the metadata store with a particular index
272-
273Default: Image+/DisplayOptions/ROI+
2742003FC: Image+/CA/DisplayOptions/@DisplayROI+
275Integer X0  the starting X coordinate
276Integer Y0  the starting Y coordinate
277Integer X1  the ending X coordinate
278Integer Y1  the ending Y coordinate
279Integer Z0  the starting Z coordinate
280Integer Z1  the ending Z coordinate
281Integer T0  the starting timepoint
282Integer T1  the ending timepoint
283
284
285### Entities for Instrument settings for a particular Image ###
286
287[DetectorSettings]
288the detector associated with a particular logical channel
289-
290Default: Image+/LogicalChannel+/DetectorRef
2912003FC: Image+/CA/LogicalChannel+
292DetectorNode Detector   the detector associated with this channel
293Float Offset            the detector offset
294*2003FC: DetectorOffset
295Float Gain              the detector gain
296*2003FC: DetectorGain
297
298[LightSourceSettings]
299the light source associated with a particular logical channel
300-
301Default: Image+/LogicalChannel+/LightSourceRef
3022003FC: Image+/CA/LogicalChannel+
303LightSourceNode LightSource  the primary light source
304Float Attenuation            the primary light source attenuation
305*2003FC: LightAttenuation
306Integer Wavelength           the primary light source wavelength
307*2003FC: LightWavelength
308
309
310### Entities for other Image-specific information ###
311
312[StageLabel]
313a stage label in the metadata store with a particular index
314-
315Default: Image+/StageLabel
3162003FC: Image+/CA/StageLabel
317String Name  a name for the stage label
318Float X      x coordinate of the stage
319Float Y      y coordinate of the stage
320Float Z      z coordinate of the stage
321
322
323### Entities for Instrument hardware -- these DO NOT vary by Image ###
324
325[Instrument+]
326an instrument in the metadata store with a particular index
327-
328Default: Instrument+
3292003FC: CA/Instrument+
330
331[LightSource+]
332a light source for a particular instrument
333-
334Default: Instrument+/LightSource+
3352003FC: CA/Instrument+/@LightSource+
336String Manufacturer  TODO
337String Model         TODO
338String SerialNumber  TODO
339
340[Laser]
341a laser for a particular instrument
342-
343Default: Instrument+/LightSource+/Laser
3442003FC: CA/Instrument+/@LightSource+/@!Laser
345String Type                      TODO
346String LaserMedium               TODO
347*2003FC: Medium
348Integer Wavelength               TODO
349Integer FrequencyMultiplication  TODO
350*2003FC: isFrequencyDoubled%
351Boolean Tuneable                 TODO
352*2003FC: isTunable
353String Pulse                     TODO
354Float Power                      TODO
355*200706: -
356
357[Filament]
358a filament for a particular instrument
359-
360Default: Instrument+/LightSource+/Filament
3612003FC: CA/Instrument+/@LightSource+/@Filament
362String Type  TODO
363Float Power  TODO
364
365[Arc]
366an arc for a particular instrument
367-
368Default: Instrument+/LightSource+/Arc
3692003FC: CA/Instrument+/@LightSource+/@Arc
370String Type  TODO
371Float Power  TODO
372
373[Detector+]
374a detector for a particular instrument
375-
376Default: Instrument+/Detector+
3772003FC: CA/Instrument+/@Detector+
378String Manufacturer  TODO
379String Model         TODO
380String SerialNumber  TODO
381String Type          TODO
382Float Gain           TODO
383Float Voltage        TODO
384Float Offset         TODO
385
386[Objective+]
387an objective for a particular instrument
388-
389Default: Instrument+/Objective+
3902003FC: CA/Instrument+/@Objective+
391String Manufacturer            TODO
392String Model                   TODO
393String SerialNumber            TODO
394String Correction              TODO
395*2003FC: -
396String Immersion               TODO
397*2003FC: -
398Float LensNA                   TODO
399Integer NominalMagnification   TODO
400*2003FC: -
401Float CalibratedMagnification  TODO
402*2003FC: Magnification
403Float WorkingDistance          TODO
404*2003FC: -
405
406#TODO figure out how to reconcile the two filter models
407
408#http://www.openmicroscopy.org/Schemas/OME/2007-06/ome.xsd
409#http://ome-xml.org/wiki/FilterAndFilterSet
410
411#http://www.openmicroscopy.org/XMLschemas/OME/FC/ome.xsd
412#http://openmicroscopy.org/api/xml/OME/ome-instrument.html
413
414#[ExcitationFilter]
415#an excitation filter for a particular instrument
416#-
417#Default: ?
418#2003FC: CA/ExcitationFilter+
419#String Manufacturer  TODO
420#String Model         TODO
421#String LotNumber     TODO
422#String Type          TODO
423
424#[Dichroic]
425#a dichroic for a particular instrument
426#-
427#Default: ?
428#2003FC: CA/Dichroic+
429#String Manufacturer  TODO
430#String Model         TODO
431#String LotNumber     TODO
432
433#[EmissionFilter]
434#an emission filter for a particular instrument
435#-
436#Default: ?
437#2003FC: CA/EmissionFilter+
438#String Manufacturer  TODO
439#String Model         TODO
440#String LotNumber     TODO
441#String Type          TODO
442
443#[FilterSet]
444#a filter set for a particular instrument
445#-
446#Default: ?
447#2003FC: CA/FilterSet+
448#String Manufacturer  TODO
449#String Model         TODO
450#String LotNumber     TODO
451
452[OTF+]
453an optical transfer function for a particular instrument
454-
455Default: Instrument+/OTF+
4562003FC: CA/Instrument+/@OTF+
457Integer SizeX                TODO
458Integer SizeY                TODO
459String PixelType             TODO
460String Path                  TODO
461*200706: -
462Boolean OpticalAxisAveraged  TODO
463*2003FC: isOpticalAxisAverage
464
465
466### Entities for Experimenter details ###
467
468[Experimenter+]
469an experimenter in the metadata store with a particular index
470-
471Default: Experimenter+
4722003FC: CA/Experimenter+
473String FirstName      the first name of the experimenter
474String LastName       the last name of the experimenter
475String Email          the e-mail address of the experimenter
476String Institution    the institution to which the experimenter belongs
477String DataDirectory  the fully qualified path to the experimenter's data
478*200706: -
479
480[-]
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