Actions
Feature #15719
openAdd ability to download image shifts as XML file
Start date:
11/28/2023
Due date:
% Done:
0%
Estimated time:
Deliverable:
Description
- Cryosparc 4.4+ allows import of microscope image shift data from EPU-formatted XML files
- This update to the web site allows the same data to be downloaded from Leginon
- Download link is under the Image Shift area in the Summary page (summary_full or summary_links)
- It automatically makes an xml file for each high magnification micrograph then zips them into a downloaded archive called SessionName.zip
- intermediate xml files are deleted automatically, zip files currently stay
- uses /tmp as the working directory, unless TEMP_DIR is defined in the config.php file, in which case $TEMP_DIR is used as the working directory
- needs php-pecl-zip package to create zip archive (may or may not be installed already on server)
- uses php SimpleXML package to create xml files, likely already installed and enabled
- zip archive does not contain a folder, so it's best to unzip into a fresh folder to avoid polluting your filesystem
- example filename: 23nov22b_p2b6g3_9160A1_00033sq_v01_00014hl_00006esn-a-DW.xml
- If matching to appion-created DW files, truncating the final 4 characters of the image and the mrc file will make them match
- for movies aligned in cryosparc, you likely need to truncate the final 9 characters of the xml file to match
Updated by Anchi Cheng 5 months ago
- Status changed from New to In Test
tested download. Created XML files as designed. merged to trunk.
Updated by Anchi Cheng 5 months ago
- Assignee set to cesar mena
Cesar, please check if something needs to be added in autoinstaller for php-pecl-zip support.
Updated by William Rice 4 months ago
Minor change. Changed filenames to remove reference to aligned+DW images. Now just does the raw presets collected. Otherwise there is an issue if more than one alignment run is done and the first run was not completed. This way, all collected data will be downloaded.
Example filename is now 23nov22b_p2b6g3_9160A1_00033sq_v01_00014hl_00006esn.xml
Updated by cesar mena 4 months ago
Update: no change was needed on our end for this feature. php zip support is standard on Debian.
Anchi, will you merge these latest set of changes from Bill onto beta? We're 2 weeks from a release.
Thanks.
Actions