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
Actions