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Task #1266

open

Create download particle data file base on each stack creation

Added by Eric Hou about 13 years ago. Updated over 12 years ago.

Status:
Assigned
Priority:
High
Assignee:
Lauren Fisher
Category:
Web interface
Target version:
-
Start date:
04/15/2011
Due date:
% Done:

0%

Estimated time:

Description

Create download particle data file base on each stack creation

Related issues 1 (1 open — 0 closed)

Related to Appion - Feature #1519: allow download of particle coordinates from a particular stackNew01/13/2012

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 #1

Updated by Eric Hou about 13 years ago

  • Status changed from Assigned to Closed

This is in the Appion pipeline now, user can download it via the web page.

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 #2

Updated by Anchi Cheng over 12 years ago

  • 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.

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 #3

Updated by Lauren Fisher over 12 years ago

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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