Camera Webpages

Automated Control and Robotics on 1230

Options for Automated Control
- SerialEM -- already installed, but does not fully work because of emulator issues, limited scriptability
- AutoEM -- software written for Digital Micrograph. Will need to be rewritten for JEOL. Currently do not have DM script control of microscope.
- Leginon -- software written for Tecnai. pyScope module will need to be rewritten for J1230.
- home - written software
serial port commands for JEOL1230
- jeol_1230_computer control manual
- jeol_1230_computer_toc.PDF: TOC for jeol1230 serial port commands

Currently connected through both COM1 (serial) and ethernet
Digital Micrograph currently using COM1
HaveTemServer20xx.exe emulator software, which allows emulation of TEMCON interface (J2100/J3200)
Settings required forTemServer20xx are inTemExtReg.exe program, as follows (note: program does not need to be run)
Settings in TemServer 20xx (visible when viewing Properties) are :

Digital Micrograph communicates with J1230 through serial port by default
Setup is as follows:
When emulator is running, can optionally use JEOL COM as microscope rather than JEOL 12n0
In either option, there is a test panel for testing Digital Micrograph's ability to control microscope

Testing of commands in Digital MicrographCommandWorking in J12n0 modeWorking in Temcon emulated mode Get beam energy yes yes Get camera length failed return 0 Get Illumination mode failed Get Image Optics mode yes Get mag yes no Set mag no no Get spot size failed no Set spot size failed no Get Brightness yes yes Set Brightness yes no Get Focus yes Change Focus yes Get Objective Stig yes Change Objective Stig yes Get Beam Shift yes Change Beam Shift yes Get Beam Tilt yes Change Beam Tilt yes Get C Stig yes Change C Stig yes Get Image Shift yes Change Image Shift yes

Will be using version 1.5 of Leginon
Done:
- InstalledNumExtension 1.1.0
- Installed pyscope 1.0.8 (THIS WILL NEED TO BE REPROGRAMMED FOR 1230)
- Installed sinedon -r39
- Installed pyami - r69
- Installed Imageviewer
- Installed Leginon - r5457
- Edited default.cfg to configure Leginon to communicate with proper database
- Edited sinedon.cfg configure Leginon to communicate with proper database
- Set up database and web server on outside linux box
- Communicates with camera, but complains about size. This has been fixed since version 1.6
Update -- we have updated to Leginon 1.6, modified by Minghui to add robot and j1230 communication (see below)
Apr 2010 -- installed packages on a test windows computer
- Python mysql database package is no longer available pre-compiled for windows. The working precompiled version is attached here for easy access
  - MySQL-python-1.2.2.win32-py2.5.exe
- In addition to packages listed on Leginon website, must install pywin32 package for serial port communication

Current configuration
- Tested commands in jeol_1230_computer control manual
- The initialization command is: serial.Serial(port='COM1', baudrate=9600, bytesize=8, parity='N', stopbits=1, xonxoff = 0, timeout=10, rtscts=0)
- Added jeol1230data.py, jeol1230mags.py, jeol1230cal.py, jeol1230lib.py, jeol1230.py in pyScope folder
- In jeol1230lib.py was added a defocus configuration file, called defocus.cfg in the pyScope folder. It saves the last defocus reset value. When leginon starts, it loads in the lasted save defocus values.
In order to access the serial port from within python, we are relying on the package pywin32-2.14.exe. This package must be installed on any Windows computer running the j1230 package *

Z-height adjustment is enabled for sq imaging on 09/01/2009. config_em.doc: The correct configuration can be checked here.
Updated Leginon to the 09/03/2009 svn, the following files are customized:
leginon\leginon.cfg
leginon\noderegistry\default.ncr
leginon\400mesh_x250_hole.mrc
leginon\robot3.py
pyScope\instruments.cfg
pyScope\jeol1230*.*
sinedon\sinedon.cfg
robot3 class in 2D screening application by application editor
File name system can be edited in targetmaker.py:
- Find the line containing "gridname=('prj%... ..."
Updated Leginon to the 09/28/09 svn.

In robot_parameters.py, find a section called "vacuum threshold values". Actual vacuum should be 10X of voltage values used in this file.
The robot3.py sets signals 1 and 6 to 1, asking for insertion and extraction; nysbc_robot.py sets and resets all of other signals; move_robot.py resets signals 1 and 6 back to 0.
Synchronized the leginon on robot computer with jeol1230 windows desktop. Now both are using the latest svn 09/04/2009, and the new robot3.py module by Minghui.

File down loadable in MS Word format Instruction_Robot.doc: Instruction_Robot.doc

Users will use irobot command as usually. No change for user operation is required.
The robot control software, irobot, saves its output to a file named by the system time in the format of YY-MM-DD_HH-MM-SS.txt (year-month-day_hour-minute-second) in the folder of /home/nysbc/robot_software/robot_control_programs/irobot_logs
Meanwhile, users will also get the output on the screen as usual in real time.
An additional log file with low level robot movement and communication information is also available in the folder of /home/nysbc/robot_software/robot_control_programs/spyfiles.
Both log files can be checked in case of trouble shooting.

from Kevin's mail (01/18/2011):

go_to_safe_cart2(self) is not called by anything and is probably left from testing; we could convince ourselves of it by doing a grep command on that string for all .py files and see that there is only one occurence of it.
extract_and_insert(self) is also a test routine not called by anything else so it is not needed.
Both of these commands can be commented out (add a note as to why with a date to the comment).

-- BillRice - 19 Oct 2007

: mysql-python windows binary installer