General operation problems¶

• Leginon has frozen

• Leginon has crached

• Python process window does not close after Leginon or Client GUI is closed

• Leginon does not resume data collection after restart

• <link linkend="badinput">Parameter used does not follow the input</link>

• <link linkend="settingapply">Changing parameters in setting window does not change node
  image display</link>

• <link linkend="settingapply">Create atlas in different dimension seems not to
  function</link>

• <link linkend="settingapply">Error in starting MSI application with error regarding
  reference data can not be found</link>

• <link linkend="no_mag_list">Magnification List does not show up properly (See
  Installation Trouble Shoot)</link>

Leginon main window has frozen¶

Commonly Why: You have a setting window open somewhere. The main window can not do
anything if there is a subwindow open.

Solution:

Find the setting window on your desktop and close it.

Other reason: Run out of memory or other hardware/software/network problems.

Solution:

• If the freeze is reproducable, record and report the circumstance when this
  happens to those in charge with Bugzilla-
• Leginon core - pulokas@scripps.edu

• database and image viewer - dfellman@scripps.edu

• documentation - acheng@scripps.edu

• Kill frozen Leginon window by one of the following. Try the gentler ones listed
  at front first. Check to see if any Leginon related process is running by Unix command

ps. If there are left-over python processes, try the next more aggresive

one.

• close the window

• main>ctrl-c

• main>xkill

A cursor in the shape of a skeleton will show up. Point it to the window you
want to kill and click on it)

• main>killall -9 python

This kills all processes with name containing python. Therefore, it may kill
other process you run in the background!

• scope> kill and restart Leginon Client if desired.

• Close the python window. The Leginon window will close automatically this
  way.

• If several restart of leginon is needed, Leginon Client is more likely to
  behave badly without its own restart.

• main> restart Leginon by 'start-leginon.py'

• Leginon Setup Wizard> Select user and returning sesson and "Start" the
  program.

• Leginon/Application> select the application used to run. Select the scope and
  the main launcher, and then launch the application.

• If a simple application such as "Manual" is used, just
  continue what you were doing.

• If "MSI" or "Multiscale Tomography" application is used and Leginon did not crash
  during queue processing, do the following to continue:

• Leginon/Square Targeting/Toolbar/Tiles> select the current mosaic from
  the pull-down list by checking the ID and label, and then "Load" it.

• Leginon/Square Targeting/Toolbar> "Submit" the target list that is
  loaded with the atlas. Leginon will check the status of the target acquisition
  and processing and pick it up from where it was left off.

• If "MSI" or "Multiscale Tomography" application is used and Leginon crash during
  queue processing, do the following at the node where the targets from its queue you
  wish to continue process.

Leginon/XXX Targeting/Toolbar> click on the "Submit the queued target".

Still not working: Check for hardware and network problems.

Leginon has crashed¶

Commonly Why: You have click too many places and make changes so fast that leginon can
not follow it.

Solution:

Slow down, especially in preset manager.

Other reason: Run out of memory or other hardware/software/network problems.

Solution:

• If the crash is reproducable, record and report the circumstance when this
  happens to those in charge with Bugzilla-
• Leginon core - pulokas@scripps.edu

• database and image viewer - dfellman@scripps.edu

• documentation - acheng@scripps.edu

• Check to see if any Leginon related process is running by Unix command >ps. If
  there are left-over python processes, try the next more aggresive one.

• main>ctrl-c

• main>killall -9 python

This kills all processes with name containing python. Therefore, it may kill
other process you run in the background!

• scope> kill and restart Leginon Client if desired.

• Close the python window. The Leginon window will close automatically this
  way.

• If several restart of leginon is needed, Leginon Client is more likely to
  behave badly without its own restart.

• main> restart Leginon by 'start-leginon.py'

• Leginon Setup Wizard> Select user and returning sesson and "Start" the
  program.

• Leginon/Application> select the application used to run. Select the scope and
  the main launcher, and then launch the application.

• If a simple application such as "Manual" is used, just continue what you were
  doing.

• If "MSI" or "Multiscale Tomography" application is used and Leginon did not crash
  during queue processing, do the following to continue:

• Leginon/Square Targeting/Toolbar/Tiles> select the current mosaic from
  the pull-down list by checking the ID and label, and then "Load" it.

• Leginon/Square Targeting/Toolbar> "Submit" the target list that is
  loaded with the atlas. Leginon will check the status of the target acquisition
  and processing and pick it up from where it was left off.

• If "MSI" or "MSI-Tomography" application is used and Leginon crash during queue
  processing, do the following at the node where the targets from its queue you wish to
  continue process.

Leginon/XXX Targeting/Toolbar> click on the "Submit the queued target".

Still not working: Check for hardware and network problems.

Python window does not close on Windows after Leginon
GUI window is closed¶

Why: Python process controls Leginon GUI window. On Windows, Python process is
considered broken without Leginon GUI.

• Always close the python process window to exit both Leginon GUI and the python
  process.

Data collection does not resume after restarting Leginon¶

Commonly Why:

For applications that process targets on grid atlas such as MSI and "Multiscale
Tomography", resuming data collection depends on whether "queuing" option is used and if
there are still targets left in the queues.

• If "queuing" is not used, resume data collection in Square Targeting by reloading
  the atlas and resubmit the unprocessed targets (green) will resume the data collection
  at where it left off.

• Leginon/Square Targeting/Toolbar/Tiles> select the current mosaic from the
  pull-down list by checking the ID and label, and then "Load" it.

• Leginon/Square Targeting/Toolbar> "Submit" the target list that is loaded
  with the atlas. Leginon will check the status of the target acquisition and
  processing and pick it up from where it was left off.

• Leginon/Square Targeting/Toolbar> If all targets are done, select new ones
  on the atlas for more data collection.

• If "queuing" is used, data collection should be resumed at the targeting node it
  left off. If unsure where it has been interrupted, follow this safe instruction to
  process the high level queued targets first:

• Resume at Exposure (or Tomography) Targeting. If there is no unprocessed
  targets, no data will be collected.

• Leginon/Exposure Targeting/Toolbar> click on the "Submit the queued
  target".

• When all queued targets at higher level are done, resume at Hole (or
  Subsquare) Targeting.

• Leginon/Hole Targeting/Toolbar> click on the "Submit the queued
  target".

• Resume at Square Targeting when queued targets at hole targeting are
  processed.

• Leginon/Square Targeting/Toolbar/Tiles> select the current mosaic from
  the pull-down list by checking the ID and label, and then "Load" it.

• Leginon/Square Targeting/Toolbar> "Submit" the target list that is
  loaded with the atlas. Leginon will check the status of the target acquisition
  and processing and pick it up from where it was left off.

• None of the above will resume data collection if all targets are done or
  abort by the user. Select new ones on the atlas for more data collection.

Acquired image or program parameters do not behave in the same
way as the input¶

Commonly Why: An invalid input is entered such as an invalid camera setting, text in
place of an inumber.

• For camera setting: Leginon/Presets Manager> Send the suspected preset to
  scope and check the actual values in scope/Instrument/Camera> with a
  refresh.

• For all other inputs: Check by reenter the value and hit "Enter" on the keyboard.
  The cursor will return to the front of the number and the entry box no longer
  highlighted if it is valid.

• Preset Manager> Select another preset to refresh the parameter list and then
  select the problematic preset and check its current saved parameter.

Parameters in setting windows do not apply to the node image
display¶

<title>Why:</title>

• The display panel is set to output other than the direct result of the
  setting.

• The function needs to be excuted to its input in the setting window. Use "Test"
  button to do this.

• if still not working, "Apply" the parameters before "Test" or "Create" (in Suqare
  Targeting Node).

Fail to load a node in an new application with
DataAccessError¶

<title>Why:</title>

• A bug in default setting loading causes some JAHCFinder or HoleFinder nodes with
  bad reference to LowPassFilterSettings.

You may want to get help from the most experienced user at your institute to do
these:

• Start Leginon as "administrator".

• Identify the node name that failed to load in the application.

• Start the same application.

• If you get the same problem, the database entry will need modification, get help
  from Leginon team to do this if you don't know how.

• If the application is loaded normally, select the problematic node.

• If the node belongs to JAHCFinder Class, open the settings for Template. Change
  LowPassFilter Sigma to a different value, apply the change and then change it back
  before exist with OK. This will create a new and valid data reference to the node's
  settings.

• If the node belongs to HoleFinder Class, open the settings for Edge and for
  Template. Repeat the same sequence as above.

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