Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #3742 (accepted)

Opened 8 years ago

Last modified 3 years ago

Field Rotation Attribute

Reported by: ajpatterson Owned by: rleigh
Priority: minor Milestone: Unscheduled
Component: Specification Version: 4.4.8
Keywords: schema Cc: wmoore
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description (last modified by ajpatterson)

Moved from http://www.ome-xml.org/ticket/116

Request for "Field Rotation" attribute.
See Forums, Data Model > "OME schema parameters" topic

"Field rotation - the field of view/capture can be rotated to frame an image better or for consistency (e.g. always imaging a zebrafish with head to the left and tail to the right of the image with spine horizontal). Not particularly important to record for single images but useful for stitched images and tracking.

Field rotation is measured in degrees. The Leica LAS AF software (.lif files) include this, they refer to it as the scan field rotator and scan rotation is measured in degrees (-100 to +100)."

LIF file XML: (Rosier-Image007.xml)
Wonder if the rotation is always positive number, and rotation direction is either +/- 1? Need more examples.

<HardwareSetting>
  <FilterSetting>
    <FilterSettingRecord ObjectName="Scan Field Rotator MA4" ClassName="CRotator" 
        Attribute="Scan Rotation" Description="Scan Field Rotation" Data="0" Variant="77"
        VariantType="5" Unit="degrees">
    </FilterSettingRecord>
    <FilterSettingRecord ObjectName="Scan Field Rotator MA4" ClassName="CRotator" 
        Attribute="Rotation Direction" Description="Rotation Direction" Data="0" Variant="1" 
        VariantType="3">
    </FilterSettingRecord>

Change History (21)

comment:1 Changed 8 years ago by ajpatterson

  • Cc wmoore added

comment:2 Changed 8 years ago by ajpatterson

  • Description modified (diff)

Editing description just to allow for better printing in report.

comment:3 Changed 8 years ago by ajpatterson

  • Keywords schema added

comment:4 Changed 7 years ago by jburel

  • Milestone changed from Unscheduled to OMERO-Beta4.4

moving to 4.4 for consideration

comment:5 Changed 7 years ago by ajpatterson

  • Milestone changed from OMERO-Beta4.4 to Unscheduled

comment:6 Changed 6 years ago by ajpatterson

  • Component changed from Model to Specification
  • Owner set to ajpatterson

comment:7 Changed 6 years ago by ajpatterson

  • Milestone changed from Unscheduled to OMERO-5

comment:8 Changed 6 years ago by ajpatterson

  • Keywords xsd-2013-1 added

comment:9 Changed 6 years ago by ajpatterson

  • Status changed from new to accepted

comment:10 Changed 6 years ago by ajpatterson

Decision taken in meeting today with Jean-Marie & Roger to implement this as a general affine transform on image rather than just a rotation angle.

comment:11 Changed 6 years ago by wmoore

My only concern with this idea is that it's not at all clear to a user that they should store a rotation angle of N degrees (which is a scanner / scan setting) by calculating an affine transform. Especially since the affine transform may be used for a bunch of other stuff. Seems this is mixing acquisition metadata with visualisation / post-processing settings in a way that is not easily 'unmixed'.
I guess there's probably no harm in adding an affine transform, so that when viewed, the image appears as the user expects (I wonder if that's what the Leica software does??).
But do we have any plans to support affine transforms when viewing images in our clients? This would have to done server-side, right?
And I think you'd still want to know the acquisition settings too.

I wonder if it's still a requested feature for that user (from 4 years ago)? http://www.openmicroscopy.org/community/viewtopic.php?f=15&t=342

comment:12 Changed 6 years ago by ajpatterson

Roger raised the idea of allowing the storing of either a rotation, a scaling, or a matrix.

We decided that expanding the transform complex type and putting in the appropriate helper/access functions would be a separate problem.

comment:13 Changed 6 years ago by wmoore

The 'rotation, scaling or matrix' are still visualisation / processing attributes. E.g. this is an image that you've "stitched" together with other images and you want to record how to transform it into the stitched coordinates.
But this is different from recording the acquisition parameters.
E.g. If I'm looking at the acquisition parameters in the right-panel of the clients, so that I can set the microscope up in the same way again etc. This won't show up there.

comment:14 Changed 6 years ago by ajpatterson

  • Resolution set to fixed
  • Status changed from accepted to closed

comment:15 Changed 6 years ago by ajpatterson

  • Resolution fixed deleted
  • Status changed from closed to reopened

comment:16 Changed 6 years ago by mlinkert

Change reverted in https://github.com/openmicroscopy/bioformats/pull/467

Roger's documentation comment from that PR should be addressed when this work is completed.

comment:17 Changed 6 years ago by ajpatterson

  • Keywords xsd-2013-1 removed
  • Version set to 4.4.8

comment:18 Changed 4 years ago by ajpatterson

  • Owner changed from ajpatterson to rleigh
  • Status changed from reopened to accepted

comment:19 Changed 3 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:20 Changed 3 years ago by jamoore

Referencing ticket #10284 has changed sprint.

comment:21 Changed 3 years ago by jamoore

Referencing ticket #10284 has changed sprint.

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.82616 sec.)

We're Hiring!