source: trunk/loci/formats/auto/MetadataAutogenNodes.txt @ 3422

Revision 3422, 13.4 KB checked in by curtis, 13 years ago (diff)

Both 2007-06 and 2003 (FC) metadata implementations now compile,
though the list of method signatures is not yet comprehensive.

Line 
1#
2# MetadataAutogenNodes.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# Path key:
24# 1) Elements ending in plus (+) have maxOccurs > 1 and generate an index
25#    parameter to allow differentiation between them.
26# 2) Elements beginning with at (@) are not direct children of the previous
27#    element, but instead reference the parent via an ID reference.
28# 3) Elements beginning with at-bang (@!) also use a parent reference but
29#    the API is slightly different -- e.g., for a LightSource accessing its
30#    child Laser, the method is lightSource.getLaserListByLightSource() rather
31#    than lightSource.getLaserList().
32# 4) Overridden attributes ending in percent (%) indicate a type conflict
33#    that must be resolved by calling type conversion methods from the
34#    OMEXMLMetadata superclass.
35# 5) Attributes starting with small case indicate a method prefix other than
36#    "get" -- e.g., "isTunable" overrides default "getTunable" method name.
37
38[Image]
39an image in the metadata store with a particular index
40-
41Default: Image+
42String Name          the full name of the image
43String CreationDate  the creation date of the image
44*2003FC: Created
45String Description   the full description of the image
46
47[Experimenter]
48an experimenter in the metadata store with a particular index
49-
50Default: Experimenter+
512003FC: CA/Experimenter+
52String FirstName      the first name of the experimenter
53String LastName       the last name of the experimenter
54String Email          the e-mail address of the experimenter
55String Institution    the institution for which the experimenter belongs
56#CTR TODO - decide whether to include DataDirectory
57#String DataDirectory  the fully qualified path to the experimenter's data
58#CTR TODO - complexify
59#Object Group          the group to which the experimenter belongs
60
61[Group]
62a group in the metadata store with a particular index
63-
64Default: Group+
652003FC: CA/Group+
66String Name     the name of the group
67#CTR TODO - complexify
68#Object Leader   the leader of the group
69#CTR TODO - complexify
70#Object Contact  the contact for the group
71
72#CTR TODO - Instrument shouldn't have any attributes directly... right?
73#           so why are they in the 2003 FC CA schema...?
74#[Instrument]
75#an instrument in the metadata store with a particular index
76#-
77#Default: Instrument+
78#2003FC: CA/Instrument+
79#String Manufacturer  the name of the manufacturer
80#String Model         the model number of the instrument
81#String SerialNumber  the serial number of the instrument
82#String Type          the type of the instrument
83
84[Dimensions]
85a set of pixel dimensions in the metadata store with a particular index
86Unless both values are non-null, the MetadataStore should assume pixelSizeX equals pixelSizeY (i.e., should populate the null field with the other field's value).
87Default: Image+/Pixels+
882003FC: Image+/CA/Dimensions
89Float PhysicalSizeX    size of an individual pixel's X axis in microns
90*2003FC: PixelSizeX
91Float PhysicalSizeY    size of an individual pixel's Y axis in microns
92*2003FC: PixelSizeY
93Float PhysicalSizeZ    size of an individual pixel's Z axis in microns
94*2003FC: PixelSizeZ
95Float TimeIncrement    distance between adjacent time points in seconds
96*2003FC: PixelSizeT
97Integer WaveStart      starting wavelength in nanometers
98*2003FC: -
99Integer WaveIncrement  distance between adjacent wavelengths in nanometers
100*2003FC: PixelSizeC%
101
102[DisplayROI]
103a 5D bounding box region of interest and a set of display options in the metadata store with a particular index
104-
105Default: Image+/DisplayOptions/ROI+
1062003FC: Image+/CA/DisplayROI+
107Integer X0  the starting X coordinate
108Integer Y0  the starting Y coordinate
109Integer Z0  the starting Z coordinate
110Integer T0  the starting timepoint
111Integer X1  the ending X coordinate
112Integer Y1  the ending Y coordinate
113Integer Z1  the ending Z coordinate
114Integer T1  the ending timepoint
115#CTR TODO - complexify
116#Object DisplayOptions  the display options to attach to this region of interest
117
118[Pixels]
119a pixels set in the metadata store with a particular image and pixels index
120-
121Default: Image+/Pixels+
1222003FC: Image+/CA/Pixels+
123Integer SizeX          size of an individual plane or section's X axis (width)
124Integer SizeY          size of an individual plane of section's Y axis (height)
125Integer SizeZ          number of optical sections per channel, per timepoint (per stack)
126Integer SizeC          number of channels per timepoint
127Integer SizeT          number of timepoints
128String PixelType       the pixel type
129#CTR TODO - why not working?
130#Boolean isBigEndian    if the pixels set is big endian or not
131String DimensionOrder  the dimension order of the pixels set
132
133[StageLabel]
134a stage label in the metadata store with a particular index
135-
136Default: Image+/StageLabel
1372003FC: Image+/CA/StageLabel
138String Name  a name for the stage label
139Float X      x coordinate of the stage
140Float Y      y coordinate of the stage
141Float Z      z coordinate of the stage
142
143[LogicalChannel]
144a logical channel and physical channel in the metadata store for a particular pixels
145-
146Default: Image+/LogicalChannel+
1472003FC: Image+/CA/LogicalChannel+
148#CTR TODO - where has auxiliary light source gone...?
149#Integer AuxLightSource            the index of the auxiliary light source
150#Float AuxLightAttenuation         the auxiliary light source attenuation
151#String AuxTechnique               the auxiliary technique type
152#Integer AuxLightWavelength        the auxiliary light source wavelength
153String Name                       the logical channel's name
154Integer SamplesPerPixel           CTR TODO
155# CTR TODO - complexify
156#Integer SecondaryEmissionFilter  an index...
157# CTR TODO - complexify
158#Integer SecondaryExcitationFilter  an index...
159String IlluminationType           the illumination type
160Integer PinholeSize               the size of the pinhole
161String PhotometricInterpretation  the photometric interpretation type
162String Mode                       the acquisition mode
163String ContrastMethod             the constrast method name
164Integer ExWave                    the excitation wavelength
165*2003FC: ExcitationWavelength
166Integer EmWave                    the emission wavelength
167*2003FC: EmissionWavelength
168String Fluor                      the fluorescence type
169Float NdFilter                    the neutral-density filter value
170*2003FC: NDFilter
171Integer PockelCellSetting         CTR TODO
172*2003FC: -
173
174[ChannelLightSource]
175the light source associated with a particular logical channel
176-
177Default: Image+/LogicalChannel+/LightSourceRef
1782003FC: Image+/CA/LogicalChannel+
179#CTR TODO - complexify
180#Integer LightSource        the index of the primary light source
181Float Attenuation          the primary light source attenuation
182*2003FC: LightAttenuation
183Integer Wavelength         the primary light source wavelength
184*2003FC: LightWavelength
185
186#[ChannelOTF]
187#the optical transfer function associated with a particular logical channel
188#-
189#Default: Image+/LogicalChannel+/OTFRef
190#2003FC: x
191#CTR TODO - complexify
192#Integer OTF  the index of the OTF associated with this channel
193
194[ChannelDetector]
195the detector associated with a particular logical channel
196-
197Default: Image+/LogicalChannel+/DetectorRef
1982003FC: Image+/CA/LogicalChannel+
199#CTR TODO - complexify
200#Integer Detector         the index of the detector associated with this channel
201Float Offset             the detector offset
202*2003FC: DetectorOffset
203Float Gain               the detector gain
204*2003FC: DetectorGain
205
206# CTR TODO - finish/add this - LogicalChannel/FilterSetRef
207#[ChannelFilterSet]
208
209[PlaneInfo]
210the plane information for a particular X-Y plane (section) within a particular pixels set
211NOTE: The implementation of this method is optional as this is a transitional type. More information about the PlaneInfo type can be found <a href="http://cvs.openmicroscopy.org.uk/tiki/tiki-index.php?page=DataModelProposal#id119301">here</a>.
212Default: Image+/Pixels+/Plane+
2132003FC: -
214Integer TheZ        the optical section index
215Integer TheC        the channel index
216Integer TheT        the timepoint
217
218[PlaneTiming]
219the timing information for a particular X-Y plane (section) within a particular pixels set
220-
221Default: Image+/Pixels+/Plane+/PlaneTiming
2222003FC: -
223Float DeltaT        the time in seconds since the beginning of the experiment
224Float ExposureTime  the exposure time in seconds
225
226[StagePosition]
227the stage position for a particular X-Y plane (section) within a particular pixels set
228-
229Default: Image+/Pixels+/Plane+/StagePosition
2302003FC: -
231Float PositionX  the X coordinate of the stage position
232Float PositionY  the Y coordinate of the stage position
233Float PositionZ  the Z coordinate of the stage position
234
235
236[ImagingEnvironment]
237the imaging environment for a particular image
238-
239Default: Image+/ImagingEnvironment
2402003FC: Image+/CA/ImagingEnvironment
241Float Temperature  CTR TODO
242Float AirPressure  CTR TODO
243Float Humidity     CTR TODO
244Float CO2Percent   CTR TODO
245
246#TODO figure out how to solve problem with multiple subtypes of ChannelSpecType
247#[DisplayChannel]
248#information about the specified channel for a particular image
249#-
250#Default: ChannelSpecType
251#2003FC: Image+/CA/DisplayChannel+
252#Integer ChannelNumber  CTR TODO
253#Double BlackLevel      CTR TODO
254#Double WhiteLevel      CTR TODO
255#Float Gamma            CTR TODO
256
257[DisplayOptions]
258various display options for a particular pixels set
259-
260Default: Image+/DisplayOptions
2612003FC: Image+/CA/DisplayOptions
262Float Zoom                CTR TODO
263#TODO need to split this into separate blocks for each of R, G, B & maybe gray
264#Boolean isRedChannelOn    CTR TODO
265#Boolean isGreenChannelOn  CTR TODO
266#Boolean isBlueChannelOn   CTR TODO
267#Boolean isDisplayRGB      CTR TODO
268#String ColorMap           CTR TODO
269#Integer ZStart            CTR TODO
270#Integer ZStop             CTR TODO
271#Integer TStart            CTR TODO
272#Integer TStop             CTR TODO
273
274[LightSource]
275a light source for a particular instrument
276-
277Default: Instrument+/LightSource+
2782003FC: CA/Instrument+/@LightSource+
279String Manufacturer  CTR TODO
280String Model         CTR TODO
281String SerialNumber  CTR TODO
282
283[Laser]
284a laser for a particular instrument
285-
286Default: Instrument+/LightSource+/Laser
2872003FC: CA/Instrument+/@LightSource+/@!Laser
288String Type                      CTR TODO
289String LaserMedium               CTR TODO
290*2003FC: Medium
291Integer Wavelength               CTR TODO
292Integer FrequencyMultiplication  CTR TODO
293*2003FC: isFrequencyDoubled%
294Boolean Tuneable                 CTR TODO
295*2003FC: isTunable
296String Pulse                     CTR TODO
297Float Power                      CTR TODO
298*200706: -
299
300[Filament]
301a filament for a particular instrument
302-
303Default: Instrument+/LightSource+/Filament
3042003FC: CA/Instrument+/@LightSource+/@Filament
305String Type  CTR TODO
306Float Power  CTR TODO
307
308[Arc]
309an arc for a particular instrument
310-
311Default: Instrument+/LightSource+/Arc
3122003FC: CA/Instrument+/@LightSource+/@Arc
313String Type  CTR TODO
314Float Power  CTR TODO
315
316[Detector]
317a detector for a particular instrument
318-
319Default: Instrument+/Detector+
3202003FC: CA/Instrument+/@Detector+
321String Manufacturer  CTR TODO
322String Model         CTR TODO
323String SerialNumber  CTR TODO
324String Type          CTR TODO
325Float Gain           CTR TODO
326Float Voltage        CTR TODO
327Float Offset         CTR TODO
328
329[Objective]
330an objective for a particular instrument
331-
332Default: Instrument+/Objective+
3332003FC: CA/Instrument+/@Objective+
334String Manufacturer            CTR TODO
335String Model                   CTR TODO
336String SerialNumber            CTR TODO
337Float LensNA                   CTR TODO
338Integer NominalMagnification   CTR TODO
339*2003FC: -
340Float CalibratedMagnification  CTR TODO
341*2003FC: Magnification
342
343#TODO figure out how to reconcile the two filter models
344#[ExcitationFilter]
345#an excitation filter for a particular instrument
346#-
347#Default: ?
348#2003FC: CA/ExcitationFilter+
349#String Manufacturer  CTR TODO
350#String Model         CTR TODO
351#String LotNumber     CTR TODO
352#String Type          CTR TODO
353
354#[Dichroic]
355#a dichroic for a particular instrument
356#-
357#Default: ?
358#2003FC: CA/Dichroic+
359#String Manufacturer  CTR TODO
360#String Model         CTR TODO
361#String LotNumber     CTR TODO
362#
363#[EmissionFilter]
364#an emission filter for a particular instrument
365#-
366#Default: ?
367#2003FC: CA/EmissionFilter+
368#String Manufacturer  CTR TODO
369#String Model         CTR TODO
370#String LotNumber     CTR TODO
371#String Type          CTR TODO
372#
373#[FilterSet]
374#a filter set for a particular instrument
375#-
376#Default: ?
377#2003FC: CA/FilterSet+
378#String Manufacturer  CTR TODO
379#String Model         CTR TODO
380#String LotNumber     CTR TODO
381
382[OTF]
383an optical transfer function for a particular instrument
384-
385Default: Instrument+/OTF+
3862003FC: CA/Instrument+/@OTF+
387Integer SizeX                CTR TODO
388Integer SizeY                CTR TODO
389String PixelType             CTR TODO
390String Path                  CTR TODO
391*200706: -
392Boolean OpticalAxisAveraged  CTR TODO
393*2003FC: isOpticalAxisAverage
394
395[-]
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