Leginon

h1. General operation problems

* [[General operation problems#Leginon_main_window_has_frozen|Leginon has frozen]]

* [[General operation problems#Leginon_has_crashed|Leginon has crached]]

* [[General operation problems#Leginon_has_crashed|Python process window does not close after Leginon or Client GUI is closed]]

* [[General operation problems#Data_collection_does_not_resume_after_restarting_Leginon|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>

h2. 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.

h2. 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.

h2. 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.

h2. 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.

h2. 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.

h2. 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).

h2. 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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[[Pausing and Aborting during data collection|< Pausing and Aborting during data collection]] | [[Hardware Troubles|Hardware Troubles >]]

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