Appion

r18300 contains changes for this feature.

Note: this works only with mrc stack input for now and does not work with defocal pair since that uses a different script.

Usage:

1. point the image directory for upload (--dir) to the directory containing the stack files (extension mrc).
2. If needed, also assign --norm and --dark to the reference image.

The results:

The program recognize that that mrc files are image stack by checking its header.

1. The frames will be copied to a parallel directory to the leginon session. For example, if the session is going to be uploaded to /data/leginon/14may29/rawdata, the frames.mrc will be saved at the same time to /data/frames/14may29/rawdata.

2. The frames will be summed up to make the image show up in the web image viewer. If norm/dark are assigned, it is assumed that the frames are not gain/dark corrected, and such correction will be applied to the summed image before uploading.

3. norm/dark images must be at the same dimension and orientation as the frames to be uploaded. If you have acquired the movies with a rotation and/or flip applied at the camera, chances are that the frames are not transformed but the norm/dark images are. You should check and transform them in advance. In addition, if dark is assigned and is non-zero, it is assumed that it is that of one frame exposure and that dark correction is dominated by dark current.

There is no gui for --norm and --dark assignment in myamiweb, yet. You will need to add them at the end of the command line you construct.

For example:

imageloader.py --projectid=5 --session=14may28y --cs=2 --dir=/data/my_upload_area --filetype=mrc --apix=1.21 --binx=1 --biny=1 --df=-2.0 --mag=29000 --kv=200 --description='test rectangular upload' --jobtype=uploadimage --norm=/my_ref_dir/14may28h_28155213_03_3838x3710_norm_0.mrc

Amber, if you have a chance to add --dark --norm assignment (textbox would be fine) to the myamiweb upload page, please do so after code review my changes.

Tom, if your people need to use it and o.k. with without gui for --norm --dark assignment, this is ready for you to test.