source: trunk/loci/formats/auto/MetadataAutogenEntities.txt @ 3481

Revision 3481, 13.4 KB checked in by curtis, 12 years ago (diff)

Use Velocity template engine for metadata logic autogenerator.

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# Add new metadata entity and property definitions to this file.
24
25# Path key:
26# 1) Elements ending in plus (+) have maxOccurs > 1 and generate an index
27#    parameter to allow differentiation between them.
28# 2) Elements beginning with at (@) are not direct children of the previous
29#    element, but instead reference the parent via an ID reference.
30# 3) Elements beginning with at-bang (@!) also use a parent reference but
31#    the API is slightly different -- e.g., for a LightSource accessing a
32#    child Laser, the method is lightSource.getLaserListByLightSource()
33#    rather than lightSource.getLaserList().
34# 4) Overridden attributes ending in percent (%) indicate a type conflict
35#    that must be resolved by calling type conversion methods from the
36#    OMEXMLMetadata superclass.
37# 5) Attributes starting with small case indicate a method prefix other than
38#    "get" -- e.g., "isTunable" overrides default "getTunable" method name.
39
40[Image]
41an image in the metadata store with a particular index
42-
43Default: Image+
44String Name          the full name of the image
45String CreationDate  the creation date of the image
46*2003FC: Created
47String Description   the full description of the image
48
49[Experimenter]
50an experimenter in the metadata store with a particular index
51-
52Default: Experimenter+
532003FC: CA/Experimenter+
54String FirstName      the first name of the experimenter
55String LastName       the last name of the experimenter
56String Email          the e-mail address of the experimenter
57String Institution    the institution to which the experimenter belongs
58String DataDirectory  the fully qualified path to the experimenter's data
59*200706: -
60#CTR TODO - complexify
61#GroupIndex Group      the group to which the experimenter belongs
62
63[Group]
64a group in the metadata store with a particular index
65-
66Default: Group+
672003FC: CA/Group+
68String Name                the name of the group
69#CTR START HERE
70#ExperimenterIndex Leader   the leader of the group
71#ExperimenterIndex Contact  the contact for the group
72
73#CTR TODO - Instrument shouldn't have any attributes directly... right?
74#           so why are they in the 2003 FC CA schema...?
75#[Instrument]
76#an instrument in the metadata store with a particular index
77#-
78#Default: Instrument+
79#2003FC: CA/Instrument+
80#String Manufacturer  the name of the manufacturer
81#String Model         the model number of the instrument
82#String SerialNumber  the serial number of the instrument
83#String Type          the type of the instrument
84
85[Dimensions]
86a set of pixel dimensions in the metadata store with a particular index
87Unless 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).
88Default: Image+/Pixels+
892003FC: Image+/CA/Dimensions
90Float PhysicalSizeX    size of an individual pixel's X axis in microns
91*2003FC: PixelSizeX
92Float PhysicalSizeY    size of an individual pixel's Y axis in microns
93*2003FC: PixelSizeY
94Float PhysicalSizeZ    size of an individual pixel's Z axis in microns
95*2003FC: PixelSizeZ
96Float TimeIncrement    distance between adjacent time points in seconds
97*2003FC: PixelSizeT
98Integer WaveStart      starting wavelength in nanometers
99*2003FC: -
100Integer WaveIncrement  distance between adjacent wavelengths in nanometers
101*2003FC: PixelSizeC%
102
103[DisplayROI]
104a 5D bounding box region of interest and a set of display options in the metadata store with a particular index
105-
106Default: Image+/DisplayOptions/ROI+
1072003FC: Image+/CA/DisplayROI+
108Integer X0                          the starting X coordinate
109Integer Y0                          the starting Y coordinate
110Integer Z0                          the starting Z coordinate
111Integer T0                          the starting timepoint
112Integer X1                          the ending X coordinate
113Integer Y1                          the ending Y coordinate
114Integer Z1                          the ending Z coordinate
115Integer T1                          the ending timepoint
116#CTR TODO - complexify
117#DisplayOptionsIndex DisplayOptions  the display options to attach to this region of interest
118
119[Pixels]
120a pixels set in the metadata store with a particular image and pixels index
121-
122Default: Image+/Pixels+
1232003FC: Image+/CA/Pixels+
124Integer SizeX          size of an individual plane or section's X axis (width)
125Integer SizeY          size of an individual plane of section's Y axis (height)
126Integer SizeZ          number of optical sections per stack
127Integer SizeC          number of channels per timepoint
128Integer SizeT          number of timepoints
129String PixelType       the pixel type
130Boolean BigEndian      if the pixels set is big endian or not
131*2003FC: isBigEndian
132String DimensionOrder  the dimension order of the pixels set
133
134[StageLabel]
135a stage label in the metadata store with a particular index
136-
137Default: Image+/StageLabel
1382003FC: Image+/CA/StageLabel
139String Name  a name for the stage label
140Float X      x coordinate of the stage
141Float Y      y coordinate of the stage
142Float Z      z coordinate of the stage
143
144[LogicalChannel]
145a logical channel and physical channel in the metadata store for a particular pixels
146-
147Default: Image+/LogicalChannel+
1482003FC: Image+/CA/LogicalChannel+
149#CTR TODO - where has auxiliary light source gone...?
150#Integer AuxLightSource            the index of the auxiliary light source
151#Float AuxLightAttenuation         the auxiliary light source attenuation
152#String AuxTechnique               the auxiliary technique type
153#Integer AuxLightWavelength        the auxiliary light source wavelength
154String Name                            the logical channel's name
155Integer SamplesPerPixel                CTR TODO
156# CTR TODO - complexify
157#FilterIndex SecondaryEmissionFilter    CTR TODO
158# CTR TODO - complexify
159#FilterIndex SecondaryExcitationFilter  CTR TODO
160String IlluminationType                the illumination type
161Integer PinholeSize                    the size of the pinhole
162String PhotometricInterpretation       the photometric interpretation type
163String Mode                            the acquisition mode
164String ContrastMethod                  the constrast method name
165Integer ExWave                         the excitation wavelength
166*2003FC: ExcitationWavelength
167Integer EmWave                         the emission wavelength
168*2003FC: EmissionWavelength
169String Fluor                           the fluorescence type
170Float NdFilter                         the neutral-density filter value
171*2003FC: NDFilter
172Integer PockelCellSetting              CTR TODO
173*2003FC: -
174
175[LightSourceSettings]
176the light source associated with a particular logical channel
177-
178Default: Image+/LogicalChannel+/LightSourceRef
1792003FC: Image+/CA/LogicalChannel+
180#CTR TODO - complexify
181#LightSourceIndex ID  the index of the primary light source
182*2003FC: LightSource
183Float Attenuation    the primary light source attenuation
184*2003FC: LightAttenuation
185Integer Wavelength   the primary light source wavelength
186*2003FC: LightWavelength
187
188#[OTFSettings]
189#the optical transfer function associated with a particular logical channel
190#-
191#Default: Image+/LogicalChannel+/OTFRef
192#2003FC: x
193#CTR TODO - complexify
194#OTFIndex OTF  the index of the OTF associated with this channel
195
196[DetectorSettings]
197the detector associated with a particular logical channel
198-
199Default: Image+/LogicalChannel+/DetectorRef
2002003FC: Image+/CA/LogicalChannel+
201#CTR TODO - complexify
202#DetectorIndex Detector  the index of the detector associated with this channel
203Float Offset            the detector offset
204*2003FC: DetectorOffset
205Float Gain              the detector gain
206*2003FC: DetectorGain
207
208# CTR TODO - finish/add this - LogicalChannel/FilterSetRef
209#[ChannelFilterSet]
210
211[Plane]
212the plane information for a specific X-Y plane (section) within a particular pixels set
213-
214Default: Image+/Pixels+/Plane+
2152003FC: -
216Integer TheZ        the optical section index
217Integer TheC        the channel index
218Integer TheT        the timepoint
219
220[PlaneTiming]
221the timing information for a specific X-Y plane (section) within a particular pixels set
222-
223Default: Image+/Pixels+/Plane+/PlaneTiming
2242003FC: -
225Float DeltaT        the time in seconds since the beginning of the experiment
226Float ExposureTime  the exposure time in seconds
227
228[StagePosition]
229the stage position for a specific X-Y plane (section) within a particular pixels set
230-
231Default: Image+/Pixels+/Plane+/StagePosition
2322003FC: -
233Float PositionX  the X coordinate of the stage position
234Float PositionY  the Y coordinate of the stage position
235Float PositionZ  the Z coordinate of the stage position
236
237[ImagingEnvironment]
238the imaging environment for a particular image
239-
240Default: Image+/ImagingEnvironment
2412003FC: Image+/CA/ImagingEnvironment
242Float Temperature  CTR TODO
243Float AirPressure  CTR TODO
244Float Humidity     CTR TODO
245Float CO2Percent   CTR TODO
246
247#TODO figure out how to solve problem with multiple subtypes of ChannelSpecType
248#[DisplayChannel]
249#information about the specified channel for a particular image
250#-
251#Default: ChannelSpecType
252#2003FC: Image+/CA/DisplayChannel+
253#Integer ChannelNumber  CTR TODO
254#Double BlackLevel      CTR TODO
255#Double WhiteLevel      CTR TODO
256#Float Gamma            CTR TODO
257
258[DisplayOptions]
259various display options for a particular pixels set
260-
261Default: Image+/DisplayOptions
2622003FC: Image+/CA/DisplayOptions
263Float Zoom                CTR TODO
264#TODO need to split this into separate blocks for each of R, G, B & maybe gray
265#Boolean isRedChannelOn    CTR TODO
266#Boolean isGreenChannelOn  CTR TODO
267#Boolean isBlueChannelOn   CTR TODO
268#Boolean isDisplayRGB      CTR TODO
269#String ColorMap           CTR TODO
270#Integer ZStart            CTR TODO
271#Integer ZStop             CTR TODO
272#Integer TStart            CTR TODO
273#Integer TStop             CTR TODO
274
275[LightSource]
276a light source for a particular instrument
277-
278Default: Instrument+/LightSource+
2792003FC: CA/Instrument+/@LightSource+
280String Manufacturer  CTR TODO
281String Model         CTR TODO
282String SerialNumber  CTR TODO
283
284[Laser]
285a laser for a particular instrument
286-
287Default: Instrument+/LightSource+/Laser
2882003FC: CA/Instrument+/@LightSource+/@!Laser
289String Type                      CTR TODO
290String LaserMedium               CTR TODO
291*2003FC: Medium
292Integer Wavelength               CTR TODO
293Integer FrequencyMultiplication  CTR TODO
294*2003FC: isFrequencyDoubled%
295Boolean Tuneable                 CTR TODO
296*2003FC: isTunable
297String Pulse                     CTR TODO
298Float Power                      CTR TODO
299*200706: -
300
301[Filament]
302a filament for a particular instrument
303-
304Default: Instrument+/LightSource+/Filament
3052003FC: CA/Instrument+/@LightSource+/@Filament
306String Type  CTR TODO
307Float Power  CTR TODO
308
309[Arc]
310an arc for a particular instrument
311-
312Default: Instrument+/LightSource+/Arc
3132003FC: CA/Instrument+/@LightSource+/@Arc
314String Type  CTR TODO
315Float Power  CTR TODO
316
317[Detector]
318a detector for a particular instrument
319-
320Default: Instrument+/Detector+
3212003FC: CA/Instrument+/@Detector+
322String Manufacturer  CTR TODO
323String Model         CTR TODO
324String SerialNumber  CTR TODO
325String Type          CTR TODO
326Float Gain           CTR TODO
327Float Voltage        CTR TODO
328Float Offset         CTR TODO
329
330[Objective]
331an objective for a particular instrument
332-
333Default: Instrument+/Objective+
3342003FC: CA/Instrument+/@Objective+
335String Manufacturer            CTR TODO
336String Model                   CTR TODO
337String SerialNumber            CTR TODO
338Float LensNA                   CTR TODO
339Integer NominalMagnification   CTR TODO
340*2003FC: -
341Float CalibratedMagnification  CTR TODO
342*2003FC: Magnification
343
344#TODO figure out how to reconcile the two filter models
345#[ExcitationFilter]
346#an excitation filter for a particular instrument
347#-
348#Default: ?
349#2003FC: CA/ExcitationFilter+
350#String Manufacturer  CTR TODO
351#String Model         CTR TODO
352#String LotNumber     CTR TODO
353#String Type          CTR TODO
354
355#[Dichroic]
356#a dichroic for a particular instrument
357#-
358#Default: ?
359#2003FC: CA/Dichroic+
360#String Manufacturer  CTR TODO
361#String Model         CTR TODO
362#String LotNumber     CTR TODO
363#
364#[EmissionFilter]
365#an emission filter for a particular instrument
366#-
367#Default: ?
368#2003FC: CA/EmissionFilter+
369#String Manufacturer  CTR TODO
370#String Model         CTR TODO
371#String LotNumber     CTR TODO
372#String Type          CTR TODO
373#
374#[FilterSet]
375#a filter set for a particular instrument
376#-
377#Default: ?
378#2003FC: CA/FilterSet+
379#String Manufacturer  CTR TODO
380#String Model         CTR TODO
381#String LotNumber     CTR TODO
382
383[OTF]
384an optical transfer function for a particular instrument
385-
386Default: Instrument+/OTF+
3872003FC: CA/Instrument+/@OTF+
388Integer SizeX                CTR TODO
389Integer SizeY                CTR TODO
390String PixelType             CTR TODO
391String Path                  CTR TODO
392*200706: -
393Boolean OpticalAxisAveraged  CTR TODO
394*2003FC: isOpticalAxisAverage
395
396[-]
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