Task #1266
open
Create download particle data file base on each stack creation
Added by Eric Hou over 13 years ago.
Updated almost 13 years ago.
Description
Create download particle data file base on each stack creation
Related issues
1 (1 open — 0 closed)
- Status changed from Assigned to Closed
This is in the Appion pipeline now, user can download it via the web page.
- Category set to Web interface
- Status changed from Closed to Assigned
- Assignee changed from Eric Hou to Lauren Fisher
Lauren,
I came across this after two requests for particle coordinates from a stack and noticed that what Eric wrote is outputing
particleId, mean, stdev, skew. kurtosis, edgemean, edgestdev, centermean, centerstdev, min, max
but not coordinates and image where the particle is from. I would have thought the latter two are more useful than the rest for a user. Bridget suggested that I double check with you to see if the current set of stuff it is outputting is based on a request from some external people. Otherwise, I might change the output to give coordinates and images instead.
There is a download function for the particle coordinates and the image it came from, but that is linked to the particle picking run not the stack. The way I've been doing it for outside users who request this data is to download three files: the stack particle data, the particle coordinates data, and the ctf data. I then have a script which searches and extracts what I consider to be the important information (i.e. particle no., image name, coordinates, defocus value, etc.) for each particle in the stack and compile it into a single file, which ends up looking like this:
No Part_No Image_Name Image_No X_coord Y_coord Defocus1 Defocus2 Angle_Astig Confidence
0 27004614 09apr14b_a_00014gr_00001sq_v01_00002hl_00003en 969340 3092 1412 -7.7172e-7 -7.0448e-7 2.9037e+1 0.9216
1 27004613 09apr14b_a_00014gr_00001sq_v01_00002hl_00003en 969340 1000 1624 -7.7172e-7 -7.0448e-7 2.9037e+1 0.9216
The only issue I have is that all of these download functions are not available on myami, only betamyami, so outside users still require someone in-house to download the data for them.
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