source: trunk/loci/formats/auto/MetadataAutogenNodes.txt @ 3385

Revision 3385, 10.8 KB checked in by curtis, 13 years ago (diff)

Allow multiple Plane elements per Pixels.

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[Image]
24an image in the metadata store with a particular index
25-
26200706: Image+
272003FC: Image+
28String Name          the full name of the image
29String CreationDate  the creation date of the image
30String Description   the full description of the image
31
32[Experimenter]
33an experimenter in the metadata store with a particular index
34-
35200706: Experimenter+
362003FC: CA/Experimenter+
37String FirstName      the first name of the experimenter
38String LastName       the last name of the experimenter
39String Email          the e-mail address of the experimenter
40String Institution    the institution for which the experimenter belongs
41String DataDirectory  the fully qualified path to the experimenter's data
42Object Group          the group to which the experimenter belongs
43
44[Group]
45a group in the metadata store with a particular index
46-
47200706: Group+
482003FC: CA/Group+
49String Name     the name of the group
50Object Leader   the leader of the group
51Object Contact  the contact for the group
52
53[Instrument]
54an instrument in the metadata store with a particular index
55-
56200706: Instrument+
572003FC: CA/Instrument+
58String Manufacturer  the name of the manufacturer
59String Model         the model number of the instrument
60String SerialNumber  the serial number of the instrument
61String Type          the type of the instrument
62
63[Dimensions]
64a set of pixel dimensions in the metadata store with a particular index
65Unless 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).
66200706: Image+
672003FC: Image+/CA/Dimensions
68Float PhysicalSizeX  size of an individual pixel's X axis in microns
69*2003FC: PixelSizeX
70Float PhysicalSizeY  size of an individual pixel's Y axis in microns
71*2003FC: PixelSizeY
72Float PhysicalSizeZ  size of an individual pixel's Z axis in microns
73*2003FC: PixelSizeZ
74Float TimeIncrement  distance between adjacent time points in seconds
75*2003FC: PixelSizeT
76Integer WaveStart    starting wavelength in nanometers
77*2003FC: -
78Float WaveIncrement  distance between adjacent wavelengths in nanometers
79*2003FC: PixelSizeC
80
81[DisplayROI]
82a 5D bounding box region of interest and a set of display options in the metadata store with a particular index
83-
84200706: Image+/ROI
852003FC: Image+/CA/DisplayROI
86Integer X0             the starting X coordinate
87Integer Y0             the starting Y coordinate
88Integer Z0             the starting Z coordinate
89Integer T0             the starting timepoint
90Integer X1             the ending X coordinate
91Integer Y1             the ending Y coordinate
92Integer Z1             the ending Z coordinate
93Integer T1             the ending timepoint
94Object DisplayOptions  the display options to attach to this region of interest
95
96[Pixels]
97a pixels set in the metadata store with a particular image and pixels index
98-
99200706: Image+/Pixels+
1002003FC: Image+/CA/Pixels+
101Integer SizeX          size of an individual plane or section's X axis (width)
102Integer SizeY          size of an individual plane of section's Y axis (height)
103Integer SizeZ          number of optical sections per channel, per timepoint (per stack)
104Integer SizeC          number of channels per timepoint
105Integer SizeT          number of timepoints
106String PixelType       the pixel type
107Boolean BigEndian      if the pixels set is big endian or not
108String DimensionOrder  the dimension order of the pixels set
109
110[StageLabel]
111a stage label in the metadata store with a particular index
112200706: Image+/StageLabel+
1132003FC: Image+/CA/StageLabel+
114String Name  a name for the stage label
115Float X      x coordinate of the stage
116Float Y      y coordinate of the stage
117Float Z      z coordinate of the stage
118
119[LogicalChannel]
120a logical channel and physical channel in the metadata store for a particular pixels
121-
122200706: Image+/LogicalChannel+
1232003FC: Image+/CA/LogicalChannel+
124String Name                       the logical channel's name
125Integer SamplesPerPixel           CTR TODO
126Integer Filter                    index of the filter associated with this channel
127Integer LightSource               index of the primary light source
128Float LightAttenuation            the primary light source attenuation
129Integer LightWavelength           the primary light source wavelength
130Integer OTF                       the index of the OTF associated with this channel
131Integer Detector                  the index of the detector associated with this channel
132Float DetectorOffset              the detector offset
133Float DetectorGain                the detector gain
134String IlluminationType           the illumination type
135Integer PinholeSize               the size of the pinhole
136String PhotometricInterpretation  the photometric interpretation type
137String Mode                       the acquisition mode
138String ContrastMethod             the constrast method name
139Integer AuxLightSource            index of the auxiliary light source
140Float AuxLightAttenuation         the auxiliary light source attenuation
141String AuxTechnique               the auxiliary technique type
142Integer AuxLightWavelength        the auxiliary light source wavelength
143Integer EmWave                    the emission wavelength
144Integer ExWave                    the excitation wavelength
145String Fluor                      the fluorescence type
146Float NdFilter                    the neutral-density filter value
147
148[PlaneInfo]
149the plane information for a particular X-Y plane (section) within a particular pixels set
150NOTE: 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>.
151200706: Image+/Pixels+/Plane+
1522003FC: Image+/Pixels+/Plane+/-
153Integer TheZ        the optical section index
154Integer TheC        the channel index
155Integer TheT        the timepoint
156Float Timestamp     the time of acquisition in seconds of the plane (section) with zero being the start of acquisition
157Float ExposureTime  exposureTime exposure time in seconds.
158
159[ImagingEnvironment]
160the imaging environment for a particular image
161-
162200706: Image+/ImagingEnvironment
1632003FC: Image+/CA/ImagingEnvironment
164Float Temperature  CTR TODO
165Float AirPressure  CTR TODO
166Float Humidity     CTR TODO
167Float Co2Percent   CTR TODO
168
169#TODO figure out how to solve problem with multiple subtypes of ChannelSpecType
170#[DisplayChannel]
171#information about the specified channel for a particular image
172#-
173#200706: ChannelSpecType
174#2003FC: Image+/CA/DisplayChannel+
175#Integer ChannelNumber  CTR TODO
176#Double BlackLevel      CTR TODO
177#Double WhiteLevel      CTR TODO
178#Float Gamma            CTR TODO
179
180[DisplayOptions]
181various display options for a particular pixels set
182-
183200706: Image+/DisplayOptions
1842003FC: Image+/CA/DisplayOptions
185Float Zoom              CTR TODO
186Boolean RedChannelOn    CTR TODO
187Boolean GreenChannelOn  CTR TODO
188Boolean BlueChannelOn   CTR TODO
189Boolean DisplayRGB      CTR TODO
190String ColorMap         CTR TODO
191Integer ZStart          CTR TODO
192Integer ZStop           CTR TODO
193Integer TStart          CTR TODO
194Integer TStop           CTR TODO
195
196[LightSource]
197a light source for a particular instrument
198-
199200706: Instrument+/LightSource+
2002003FC: CA/Instrument+/@LightSource+
201String Manufacturer  CTR TODO
202String Model         CTR TODO
203String SerialNumber  CTR TODO
204
205[Laser]
206a laser for a particular instrument
207-
208200706: Instrument+/LightSource+/Laser
2092003FC: CA/Instrument+/@LightSource+/@Laser
210String Type               CTR TODO
211String Medium             CTR TODO
212Integer Wavelength        CTR TODO
213Boolean FrequencyDoubled  CTR TODO
214Boolean Tunable           CTR TODO
215String Pulse              CTR TODO
216Float Power               CTR TODO
217
218[Filament]
219a filament for a particular instrument
220-
221200706: Instrument+/LightSource+/Filament
2222003FC: CA/Instrument+/@LightSource+/@Filament
223String Type  CTR TODO
224Float Power  CTR TODO
225
226[Arc]
227an arc for a particular instrument
228-
229200706: Instrument+/LightSource+/Arc
2302003FC: CA/Instrument+/@LightSource+/@Arc
231String Type  CTR TODO
232Float Power  CTR TODO
233
234[Detector]
235a detector for a particular instrument
236-
237200706: Instrument+/Detector+
2382003FC: CA/Instrument+/@Detector+
239String Manufacturer  CTR TODO
240String Model         CTR TODO
241String SerialNumber  CTR TODO
242String Type          CTR TODO
243Float Gain           CTR TODO
244Float Voltage        CTR TODO
245Float Offset         CTR TODO
246
247[Objective]
248an objective for a particular instrument
249-
250200706: Instrument+/Objective+
2512003FC: CA/Instrument+/@Objective+
252String Manufacturer  CTR TODO
253String Model         CTR TODO
254String SerialNumber  CTR TODO
255Float LensNA         CTR TODO
256Float Magnification  CTR TODO
257
258#TODO figure out how to reconcile the two filter models
259#[ExcitationFilter]
260#an excitation filter for a particular instrument
261#-
262#200706: ?
263#2003FC: CA/ExcitationFilter+
264#String Manufacturer  CTR TODO
265#String Model         CTR TODO
266#String LotNumber     CTR TODO
267#String Type          CTR TODO
268
269#TODO figure out how to reconcile the two filter models
270#[Dichroic]
271#a dichroic for a particular instrument
272#-
273#200706: ?
274#2003FC: CA/Dichroic+
275#String Manufacturer  CTR TODO
276#String Model         CTR TODO
277#String LotNumber     CTR TODO
278#
279#TODO figure out how to reconcile the two filter models
280#[EmissionFilter]
281#an emission filter for a particular instrument
282#-
283#200706: ?
284#2003FC: CA/EmissionFilter+
285#String Manufacturer  CTR TODO
286#String Model         CTR TODO
287#String LotNumber     CTR TODO
288#String Type          CTR TODO
289#
290#TODO figure out how to reconcile the two filter models
291#[FilterSet]
292#a filter set for a particular instrument
293#-
294#200706: ?
295#2003FC: CA/FilterSet+
296#String Manufacturer  CTR TODO
297#String Model         CTR TODO
298#String LotNumber     CTR TODO
299
300[OTF]
301an optical transfer function for a particular instrument
302-
303200706: Instrument+/OTF+
3042003FC: CA/Instrument+/@OTF+
305Integer SizeX                CTR TODO
306Integer SizeY                CTR TODO
307String PixelType             CTR TODO
308String Path                  CTR TODO
309*200706: -
310Boolean OpticalAxisAveraged  CTR TODO
311*2003FC: OpticalAxisAverage
312
313[-]
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