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Task #3682 (accepted)

Opened 8 years ago

Last modified 3 years ago

Detector - Changing to a new complex entity (similar to LightSource)

Reported by: jburel Owned by: jburel
Priority: minor Milestone: Unscheduled
Component: Specification Version: n.a.
Keywords: schema Cc: wmoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Moved from http://www.ome-xml.org/ticket/50

Evolution of the Detector element: being more specific i.e. PMT, CCD etc.

The detector element at the moment is a single unit that tries to work for any form of detector. The complexity of detectors available has outgrown this simplistic representation.

Proposal 1

We propose to introduce elements for each different type of detector housed within an abstract Detector elements. We have already used this approach to model light sources (arc, laser, filament, LED).

Detector will be changed to a new Detector element derived from ManufacturerSpec but with no attributes of its own. It will be marked as abstract-proprietary using an xsd:appinfo node. This will allow the code generation to identify it correctly.

Detector will have a choice of two child nodes OME:PMT and OME:CCD. These each contain only attributes specific to the type.

The DetectorSettings element within channel will also be updated. It will now just have and ID attribute but will have a choice of two child elements CCDSettings and PMTSettings. These work in the same way but each only has attributes appropriate for the matching detector type.

Old example
<Detector ID="Detector:0" Type="CCD" Manufacturer="OME Detectors"
    Model="Standard CCD Mk2"/>
...
<Channel Color="4294967295" ID="Channel:0:1">
	<DetectorSettings ID="Detector:0" 
	    Binning="2x2" Gain="1.2" Offset="0.7" 
	    ReadOutRate="3200" Voltage="120"/>
	...
</Channel>
New CCD example
<Detector ID="Detector:0" Manufacturer="OME Detectors" 
    Model="Standard CCD Mk2">
    <CCD 
        Type="IntensifiedCCD" CCDArchitectureType="FrameTransfer"
        PixelArrayX="1344" PixelArrayY="1024" 
        PixelSizeX="6.45" PixelSizeX="6.45"/>
</Detector>
...
<Channel Color="4294967295" ID="Channel:0:1">
	<DetectorSettings ID="Detector:0">
	    <CCDSettings 
	        Binning="2x2" EMGain="1.2"
	        Temperature="-30"/>
	</Detector>
	...
</Channel>
New PMT example
<Detector ID="Detector:0" Manufacturer="OME Detectors" 
    Model="Standard PMT Mk2">
    <PMT/>
</Detector>
...
<Channel Color="4294967295" ID="Channel:0:1">
	<DetectorSettings ID="Detector:0">
	    <PMTSettings 
	        PinholeSize="4.8" Voltage="1200" Zoom="1.5" 
	        AmplificationGain="3.14"
	        AverageNumber="2x2" SampelingSpeed="2"
	        AverageScanMode="Line"/>
	</Detector>
	...
</Channel>

We have included many attributes of each detector that could be included in the exiting schema, but perhaps we do not want all of them.

Some questions: Detector settings. Do we want a "CCD settings" and a "PMT settings", each with a DetectorID. Do we want to have a CCD ID and a PMT ID (so that you can't have a CCD settings that references a PMT detector - for example).

Further comment from the Forums: OME Data Model > OME schema parameters: Averaging and Accumulation can be performed independently to either average the values of a pixel over multiple scans, or sum the pixels from multiple scans. Averaging and Accumulation can both be performed by line or frame, there is a number of iterations associated with the parameter, e.g. Line average x 4. Both can be used at the same time, but one must be frame and the other line, it does not matter whether it is line accumulation or frame, just cannot have line averaging and line accumulation, but you can have line averaging and frame averaging at the same time and line accumulation and frame accumulation at the same time.

Change History (14)

comment:1 Changed 8 years ago by ajpatterson

  • Cc wmoore ajpatterson added

comment:2 Changed 8 years ago by jburel

Meeting: 05/04/11
Attendance: J-M, Andrew, Will

First step will be to indicate in the description

  • which attributes should be filled depending on the detector selected.
  • Format the documentation in a way that we can easily find relevant information e.g. EM#gain.
  • Indicate a range if required depending on the detector used.

comment:3 Changed 8 years ago by ajpatterson

  • Owner set to ajpatterson
  • Status changed from new to accepted

comment:4 Changed 8 years ago by Andrew J Patterson <ajpatterson@…>

(In [de9920a989af4061945f7683ace8d395cf125aff/ome.git] on branch develop) Adding used section to Detector docs see #3682

comment:5 Changed 8 years ago by ajpatterson

  • Component changed from Model to Specification

comment:6 Changed 8 years ago by ajpatterson

  • Keywords schema added

comment:7 Changed 6 years ago by ajpatterson

Referencing ticket #10284 has changed sprint.

comment:8 Changed 6 years ago by ajpatterson

  • Milestone changed from Unscheduled to OMERO-5

comment:9 Changed 6 years ago by ajpatterson

Be sure to include a Spectral Detector see #7355 for information.

comment:10 Changed 4 years ago by ajpatterson

  • Cc ajpatterson removed
  • Owner changed from ajpatterson to jburel
  • Version set to 5.0.8

comment:11 Changed 4 years ago by ajpatterson

  • Version 5.0.8 deleted

comment:12 Changed 3 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:13 Changed 3 years ago by jamoore

Referencing ticket #10284 has changed sprint.

comment:14 Changed 3 years ago by jamoore

Referencing ticket #10284 has changed sprint.

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