Task #2134 (closed)
Opened 9 years ago
Closed 9 years ago
Run Spider on server.
| Reported by: | wmoore | Owned by: | wmoore |
|---|---|---|---|
| Priority: | minor | Milestone: | OMERO-Beta4.2 |
| Component: | General | Version: | n.a. |
| Keywords: | n.a. | Cc: | |
| Resources: | n.a. | Referenced By: | n.a. |
| References: | n.a. | Remaining Time: | 0.0d |
| Sprint: | 2010-04-02 (6) |
Description (last modified by wmoore)
Script for running Spider Procedure Files (spf) on the server for image processing (generates new images).
- Create spf text file that takes 'input' and generates 'output' image. Name not important. See http://www.wadsworth.org/spider_doc/spider/docs/quickstart.html E.g.
RT input ; The input image rot001 ; The output image 60 ; Rotation angle (in degrees) IP rot001 ; Input image big001 ; Output image 150,150 ; New dimensions WI big001 ; Input image output ; Output image 75,75 ; Size of the window 1,75 ; Top left coordinates EN D
- In Insight, upload spf as attachment (E.g. attach to image)
- Look at file in 'Attachments' tab. Note File ID.
- Run script passing imageIds (or dataset Id) and Original file Id.
argMap = {"datasetId":omero.rtypes.rlong(6), # process all images in this dataset
"spfFileId":omero.rtypes.rlong(153), # using this file annotation
"newDatasetName": omero.rtypes.rstring("spider-results"), # optional: put results in new dataset
}
- Results are put back into server in new dataset.
Change History (8)
comment:1 Changed 9 years ago by wmoore
- Status changed from new to assigned
comment:2 Changed 9 years ago by wmoore
comment:3 Changed 9 years ago by wmoore
- Description modified (diff)
- Summary changed from Investigate SPIDER project file-system to Run Spider on server.
comment:4 Changed 9 years ago by wmoore
The above commits are the runSpiderProcedure.py script
comment:5 Changed 9 years ago by wmoore
comment:6 Changed 9 years ago by wmoore
- Description modified (diff)
comment:7 Changed 9 years ago by wmoore
- Description modified (diff)
comment:8 Changed 9 years ago by wmoore
- Remaining Time changed from 1 to 0
- Resolution set to fixed
- Status changed from assigned to closed
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r6635, r6633