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ome / omero-figure

An OMERO.web app for creating Figures from images in OMERO
http://figure.openmicroscopy.org
GNU Affero General Public License v3.0
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Add Dataset_ID param to export script #296

Closed will-moore closed 5 years ago

will-moore commented 6 years ago

When exporting a Figure as a new Image in OMERO, this allows us to choose a Dataset to add the new Image to (instead of using the same Dataset that images in the figure are in). This isn't supported in the UI yet.

To test:

cc @jstitlow

jstitlow commented 6 years ago

Putting them in the image source dataset. Where should the dataset ID be entered?

On Tue, Jun 5, 2018 at 9:50 PM, Will Moore notifications@github.com wrote:

When exporting a Figure as a new Image in OMERO, this allows us to choose a Dataset to add the new Image to (instead of using the same Dataset that images in the figure are in). This isn't supported in the UI yet.

To test:

  • This can be tested in the Script menu...
  • Open a Figure to export and File -> Export as JSON.
  • Select All and Copy the JSON.
  • Go to webclient, Run Script -> Figure scripts -> Figure to Pdf
    • Paste the JSON in first field
    • Select Export Option: "OMERO"
    • Enter a Dataset ID
    • Enter a URL in Webclient URI: e.g.http://localhost
  • Run Script.

Figure should be exported as new Image in the Dataset specified.

cc @jstitlow https://github.com/jstitlow

You can view, comment on, or merge this pull request online at:

https://github.com/ome/omero-figure/pull/296 Commit Summary

  • Add Dataset_ID param to export script

File Changes

Patch Links:

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ome/omero-figure/pull/296, or mute the thread https://github.com/notifications/unsubscribe-auth/AFjBBgyKtxwLWfIb3qPcw8kjqCkPX6sxks5t5u8fgaJpZM4UbiOQ .

jstitlow commented 6 years ago

Of course, it isn't added yet. Sorry.

On Tue, Jun 5, 2018 at 9:50 PM, Will Moore notifications@github.com wrote:

When exporting a Figure as a new Image in OMERO, this allows us to choose a Dataset to add the new Image to (instead of using the same Dataset that images in the figure are in). This isn't supported in the UI yet.

To test:

  • This can be tested in the Script menu...
  • Open a Figure to export and File -> Export as JSON.
  • Select All and Copy the JSON.
  • Go to webclient, Run Script -> Figure scripts -> Figure to Pdf
    • Paste the JSON in first field
    • Select Export Option: "OMERO"
    • Enter a Dataset ID
    • Enter a URL in Webclient URI: e.g.http://localhost
  • Run Script.

Figure should be exported as new Image in the Dataset specified.

cc @jstitlow https://github.com/jstitlow

You can view, comment on, or merge this pull request online at:

https://github.com/ome/omero-figure/pull/296 Commit Summary

  • Add Dataset_ID param to export script

File Changes

Patch Links:

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ome/omero-figure/pull/296, or mute the thread https://github.com/notifications/unsubscribe-auth/AFjBBgyKtxwLWfIb3qPcw8kjqCkPX6sxks5t5u8fgaJpZM4UbiOQ .

will-moore commented 5 years ago

@jstitlow Apologies for dropping this... Is this feature still useful to you?

jstitlow commented 5 years ago

Yes, but this function will mostly be used for programmatic export in our application. Is it already possible to assign a dataset ID when exporting figures from a Python script?

Defaulting to the dataset ID of the first image is the ideal default behavior for Figure export.

Thanks, j

On Sep 24, 2018 05:24, "Will Moore" notifications@github.com wrote:

@jstitlow https://github.com/jstitlow Apologies for dropping this... Is this feature still useful to you?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ome/omero-figure/pull/296#issuecomment-423918427, or mute the thread https://github.com/notifications/unsubscribe-auth/AFjBBtNvnSPy_SpY4HiX7yf4MVkmsb5kks5ueKTXgaJpZM4UbiOQ .

will-moore commented 5 years ago

@jstitlow Currently there's no support in the released script for specifying a Dataset_ID as a script parameter. The current behaviour is to use the Dataset of the first Image in the figure, and this remains the default in this PR if no Dataset_ID is specified.