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Leginon 3.5 Completed Features

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# Project Subject Updated
10953 Leginon Handle Talos 2.7 Flucam gui with extra button shifting beamstop control 10/26/2022 06:18 PM Actions

The auotit script is based on earlier version with 9 buttons before "screen insert". 2.7 added an extra one. We need to adjust for it.
9454 Leginon Change multitarget default to 4 10/19/2020 01:06 PM Actions

When using multi-focus targets, we always use 4 targets. Default is 1. This changes the default to 4, one less thing to change every time
9424 Leginon Falcon4 support that saves mrc stack as movie frames 10/19/2020 01:56 PM Actions

support through TEM Advanced Scripting. For Titan software version before 3.6 a patch is required from TFS. The current patch can only save the frame movies in mrc format.
9316 Leginon loop drift measurement and save to a file 10/19/2020 05:20 PM Actions

For testing purpose.
9288 Leginon function test for camera 10/19/2020 07:11 PM Actions

similar to scope_functions_test.py
9285 Leginon allow user to download tilts of a tomography series from web viewer. 08/06/2020 01:21 PM Actions

Easier than download the whole series and then read header.
9276 Leginon Accept all blobs as lattice points for targeting 10/19/2020 10:31 PM Actions

Gold foil blobs are good enough as lattice points without lattice fitting. This relieves the requirement of square hole pattern.
9267 Leginon add linear regression stats to holeicetoalslice.php 10/20/2020 02:25 PM Actions

Added linear regression calculations to this curve. stats appear at end of the "data" listing to be found more easily. Regression function added to inc/stats.inc to do this.
9188 Leginon reconnect to leginon-remote if remote server is down in the middle of a session 10/20/2020 10:02 PM Actions

If the connection is lost, leginon no longer check if tools are clicked in leginon-remote even if it is back up. This feature allow them to reconnect without closing the session
9132 Leginon use node order to block remote tool from being used when scope is busy on some other tasks 10/20/2020 10:09 PM Actions

For example, prevents two queues are submitted at the same time.
9108 Leginon return control to remote after terminating by local operator 10/20/2020 10:06 PM Actions

Local operator with leginon-remote staff status can remove remote access and take back control. When whatever task is finished, this feature allows them to give back the control to the user by setting the image again.
9105 Leginon add IMAGE_PEDESTRAL to smv diffraction files for DIALS 10/20/2020 10:07 PM Actions

Take median of minimum from images.
8801 Leginon record offset used in leginon to convert signed integer image format to smv 10/20/2020 10:22 PM Actions

Just as a record. Not used by DIAL or any program as we know. PEDESTRAL value is used in DIAL to apply offset in its import. We don't want to do that again. Therefore, PEDESTRAL will be assigned to 0
8776 Leginon option to reacquire image three times with some sleep time before pause 10/20/2020 10:21 PM Actions

This is added because there are recoverable error from instrument such as an non-blocking call. Use this only if opening column valve automatically is safe.
8758 Leginon set sesssion name prefix in a config file 10/20/2020 10:23 PM Actions

So that it is easier to tell session names apart if multiple database is present at the same institution.
8746 Leginon export/import image references 10/22/2020 07:37 PM Actions

Export into json files and mrc files. This can then import into a new database or to a back storage server in case of disaster recovery.
8697 Leginon use Django REST framework to exchange data between leginon and remote 10/20/2020 10:24 PM Actions

This is found while deploying these to production. We will have to write to different places and notify each other.
8622 Leginon calibrate camera movie saving delay 10/21/2020 02:27 PM Actions

to help better control continuous tilt timing
8621 Leginon calibrate stage tilt delay and rate 10/22/2020 07:30 PM Actions

To remove uncertainty in continuous tilt tilt angle per movie frame, this needs to be calibrated.
8620 Leginon set TEMAdvancedScripting version in fei.cfg 06/07/2021 12:41 PM Actions

Before Titan 1.15 and Talos 2.15 require different version requires difference type library calls from later ones
8492 Leginon overwrite k2 and k3 default frame flip from dmsem.cfg 10/28/2020 05:28 PM Actions

Since we could not predict the frame flip behavior in several installation sites, this feature allow them to set the frame flip pass to Appion directly if needed
8491 Leginon Allow user to set the length of idle timeout length in presets manager 10/28/2020 05:28 PM Actions

Without Queue Timeout tool, all timeout and valve closing is done by Presets Manager and there are cases, many lower-end scope where this might be better to be shorter than the default 30 minutes. This feature allows user to set it.
8490 Leginon get image data object mrc file shape and readability without reading the array 10/28/2020 06:46 PM Actions

This speeds up places where alll I want to know is these information to check if the data is available or is fake image like in early return fake image case.
8476 Leginon Show all target number on grid atlas 01/19/2020 01:32 PM Actions

So that it is easier to tell where the good square comes from without clicking
8404 Leginon allow environment variable replacement of path in leginon.cfg parsing 10/28/2020 07:05 PM Actions

SEMC starts to have more than one data storage system as we expand. We want to allow local staff with the same LDAP to collect to the different system depending on the leginon linux computer they log into.
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