FMB User Cheat Sheet

FMB beamline status page

http://new-status.chess.cornell.edu/id3b

CESR status page

https://cesrwww.lepp.cornell.edu/docs/statpanel/fullscore_auto.html

Useful spec commands

Moving motors and querying motor positions

wm motorname returns motor positions for given motor, e.g.: wm samx

we returns motor positions for all configured motors.

umv motorname absolute_position moves motor to absolute position, e.g.: umv samx 1.5 will move motor samx to position 1.5.

umvr motorname rel_position moves motor relative to current position, e.g.: umvr samx -1.25 will move motor samx -1.25 from its current position.

tw motorname step_size tweaks motor position in steps of step_size, e.g.: tw samx 0.5 will open a dialog where you are asked to enter the sign (direction) of steps, and then pressing enter/return will allow you to take multiple steps of that size in a row. Type any letters to exit the dialog.

• When using tw command, specify the step size as magnitude (i.e. absolute value) without any sign, even if you want to tweak in the negative direciton. You will be asked to enter the sign afterward. (i.e. it is recommended you do not run tw samx -1. Instead, run tw samx 1, and when prompted to indicate the direction, type -)

Which direction is lab x, y and z? Which direction is positive for each?

+x: transverse to the beam, away from the hutch doors

+y: direction of the beam

+z: upward

Shutter, attenuator, and slits

opens - open upstream shutter.

closes - close upstream shutter.

umv att 0 - move attenuator completely out of the beam; att -1 fluorescent screen; att 12 significant attenuation

wg s1 - print positions for upstream hutch slits (define beam size with s1h and s1v).

wg s2 - print positions for downstream hutch slits (guard slits).

• Can move s1h, s1v, s2h, and s2v, with umv commands; units are mm.

Organizing data (making folders, changing directories)

1. newdir dir_name make a new directory in the user's raw BTR directory, and makes it the working directory (i.e. newdir would make a folder called dir_name in the current user's BTR directory in DAQ and make it the working directory)
   • This replaces what used to be a two-step process of u mkdir dir_name, followed by cd dir_name.
   • Running newdir without any argument will prompt for the name of the directory you wish to create.
   • newdir can be run regardless of what the current working directory is. It will create the directory in the current user's BTR directory in DAQ and make it the working directory.
   • TIP: If you happen to restart spec (not a fresh start), running newdir and taking the default argument will ensure that you are back to the working directory you were at before the restart.
2. Update detector path to the current directory - need to run this every time directories are changed.
   1. For SAXS/WAXS, pil_setdir updates the Pilatus detector(s).
   2. For radiography/tomography, andor_setdir updates the Andor detector.
   3. For XRF, xps_setdir updates the xpress3 paths.
   4. For the Eiger, eig_setdir updates the detector paths.
3. newfile opens dialog to enter new filename and path for saving data, applied to next scan.

SPEC scans

tseries: series of snapshots

• Usage: tseries number_of_snapshots exposure_time(s)
• e.g. tseries 10 1
  • will take 10 snapshots with 1 second exposures

loopscan: series of snapshots with a wait in between

• Usage: loopscan number_of_snapshots exposure_time(s) sleep_time(s)
• e.g. loopscan 10 1 5
  • will take 10 snapshots with 1 second exposures and wait 5 seconds between each exposure

dscan: snapshots while moving a motor step-wise (not flyscanning)- relative positions

• Usage: dscan motorname start end intervals exposure_time(s)
• Positions are relative to current position
• At the end of the scan, the motor will return to the position it was at when the scan command was executed.
• e.g. dscan bedx -10 10 20 1
  • Will scan the motor bedx from -10 to +10 mm relative to the current position, with 1 mm steps and 1 second exposure times
    • If the current position of motor bedx is 30, it will be scanned from 20 to 40. At the end of the scan, motor bedx will return to 30.

ascan: snapshots while moving a motor step-wise (not flyscanning)- absolute positions

• Usage: ascan motorname start end intervals exposure_time(s)
• Positions are absolute, not relative to current position when the command is issued
• e.g. ascan bedx 200 220 20 1
  • Will scan bedx from motor positions 200 to 220, with 1 mm steps and 1 second exposure times, regardless of where motors are when the command is issued.
  • The motor does not reutrn. It will remain at the final position (in this example, at 220) at the end of the scan.

plotselect: choose what variable to show in the yellow spec plot

Pilatus area detector macros

List of important commands

• pil_setup PILX #: sets up the detector with prefix (e.g. pil_setup PIL5 0).
  • Typical for simultaneous SAXS/WAXS: PIL5 = 0, PIL9 = 1, PIL11 = 2.
• pil_on|off: turns all configured detectors on|off.
  • pil_on # - turn on just one configured detector (e.g. pil_on 0 turns on the 0th configured detector).
• pil_von|voff: turns live view (video mode) on|off.
  • ImageJ plugin can only handle this for one detector at a time, so if you have multiples configured, make sure only one is on before running pil_von.
  • video mode must be off before starting captures or any scans.
• pil_setdir: sets all the pilatus paths to the current working directory.
• pil_settrig: choose trigger mode for configured detectors.
  • use "Internal" for single snapshots (for tseries or dscans).
    • Alternatively, pil_setint sets trigger mode as Internal.
  • use "Mult. Trigger" for external trigger (for flyscan).
    • Alternatively, pil_setex sets trigger mode as Mult. Trigger.

Examples of usage with multiple detectors

See: PilatusExamples

Andor area detector macros

List of important commands

• andor_setup ANDOR#: sets up the detector with prefix.
  • Typical e.g. andor_setup ANDOR2.
• andor_on|off:turns andor detector capture on|off
• andor_von|voff: turns live view (video mode) on|off.
  • video mode must be off before starting captures or any scans
• andor_setdir: sets the andor save paths to the current working directory.
• andor_settrig: choose trigger mode.
  • use "Internal" for tseries, loopscans, etc.
  • use "External Start" for tomography movies with the air bearing rotation stage
• andor_setformat: save as .tiff or .hdf5
  • either: andor_setformat "TIFF1" or andor_setformat "HDF1".
  • saving to hdf5 is necessary for fast framing rates

Querying/setting motor parameters

• p motor_par(motorname, “velocity”): to query motor velocity (pulses/sec)
• p motor_parmotor_par(motorname, “step_size”): to query pulses/mm
• motor_par(motorname, “velocity”, newvalue): to change velocity, e.g. motor_par(bedx, “velocity”, 40000)

Station computer links/procedures

Camera views

In-hutch microscope (Mako G-234C)

• To view images:
  • On a terminqal window, run ImageJ to launch ImageJ.
  • From the toolbar: Plugins > EPICS_areaDetector > EPICS AD Viewer to open the EPICS_ADViewer_Plugin window
  • In the field labelled ‘PVPrefix’ enter the value ID3B:image1:. Note the colon at the end.
  • Click on the Start button to open the image view window and start acquisition.
  • On a terminal window, run sample_view_controls to launch the MEDM cursor control screen.
• Launching IOC and more information (internal document -- staff access only)

In-hutch PTZ camera by hutch door/on south wall (original)

http://192.168.182.44 (requires login -- staff access only)

In-hutch PTZ camera (upstream wall)

http://192.168.182.81 (requires login -- staff access only)

3B 4-channel Video encoder

http://192.168.182.43 (requires login -- staff access only)

Cave cameras

from terminal, run vimba

Preamp gui

To restart preamp gui, from terminal, run show_amps.

Open counter/ion chamber viewer

From terminal, run conter_display.

Open beam position and station status viewers

• To start a viewer for beam positions, CESR correction, CESR and CHESS enables, beam current and time to next topoff: beam_positions
• To start a viewer for status lines stops and station stops: station_status

Defining macros

1. Edit the .mac file containing definitions for macros (e.g. my_macros.mac). This is saved in ~/Macros on the station computer. User-specific .mac files are often located in ~/Macros/User_Macros.
2. In SPEC, run udo my_macros.mac to read in your .mac file.
   • If your .mac file is in User_Macros, run udo User_Macros/my_macros.mac
3. Verify that your .mac file was read in successfully.
   • On SPEC, run prdef your_function_in_mac_file to see if the definition for that function displays correctly.

Data analysis- useful information

Group Permissions and Setting Your Default Group

When using shared directories or NoteBooks for data analysis, it is often convenient to permit group members to edit each others analysis files. This can be accomplished using two steps:

1. Setting the default permissions on files you create to "group writable" by issuing the command "umask 0002" or placing that command inside the file called ".bashrc" in your home directory.
2. Making sure all group members set your default group to the same group, e.g. "chess3buser" or your btr-specific group. This can be done using the group management utillity, found here.

File paths

Raw data: /nfs/chess/raw/current/id3b/YOUR-PROJECT-ID

Analysis area: /nfs/chess/aux/reduced_data/cycles/current/id3b/YOUR-PROJECT-ID

Note, instead of "current" you can also use the run cycle, e.g. "2020-3" (this is necessary for returning to data after a run is over)

Analysis area always stays accessible. Raw data is archived after two cycles. To request raw data be restored to disk, submit a service request: https://wiki.classe.cornell.edu/Computing/ServiceRequest

Calibrating SAXS/WAXS detectors with pyFAI GUI (generating .poni files)

Refer to CHESS-specific documentation. Use the pyFAI-calib2 GUI to generate a .poni file for each of the area detectors used in your experiment. Save the .poni files in your aux area.

Remote access

Station computer (NoMachine) and lnx201

• CHESS Remote Access User Guide
• (Deprecated) Remote access with NoMachine

CLASSE IT documentation for NoMachine can be found here.

Transferring files

See SFTP / SCP file access or Globus

Other useful links

Virtual tour

A 3D Virtual tour of the MSN-C user area, including inside FMB and SMB (screenshot shown above) is located here.

InstantPlot Documentation

• InstantPlot

Rough flyscan time estimator

• Online estimation tool
• ScanTimeEstimator.xlsx

CHESS ion chamber flux calculator

• Flux calculator

X-ray attenuation calculators

• X-Ray attenuation length

Running Jupyter notebooks on the CLASSE cluster

• CLASSE JupyterHub
• (Obsolete) Accessing Jupyter prior to JupyterHub

CLASSE Git area

• CLASSE gitlab

If you are a contributor to InstantPlot, please use gitlabs for issue reporting.

-- LouisaSmieska - 11 May 2022