Task #10648 (new)
Opened 11 years ago
Last modified 8 years ago
Command-line processing via Scripts Example
| Reported by: | wmoore | Owned by: | wmoore |
|---|---|---|---|
| Priority: | major | Milestone: | Unscheduled |
| Component: | Scripting | Version: | n.a. |
| Keywords: | n.a. | Cc: | rleigh |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | n.a. |
| Sprint: | n.a. |
Description
Need to provide an up-to-date example of processing via command line called from Scripting service". We could use ImageJ as an example, since we know this is useful.
See: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=4650
And: https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=3082
Ideally this would take a Tiff stack (or a single Tiff) and generate a processed Tiff stack (or single Tiff).
Most of what we need is in this example (we write a macro and pass it to ImageJ along with a tiff stack), https://github.com/will-moore/weblabs/blob/master/views.py#L74 except that it is in the web framework and it only generates a jpeg output (not suitable to upload back to OMERO as a new image).
First task is to identify a suitable macro / process to call on the command line from ImageJ, otherwise I'll just go with the example we have and upload jpegs as new images.
Change History (1)
comment:1 Changed 8 years ago by jamoore
- Milestone changed from 5.x to Unscheduled
