FMB User Cheat Sheet

FMB beamline status page

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

Useful spec commands

Moving motors

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

we returns motor positions for all configured motors

umv motorname # moves motor to absolute position, e.g.: “umv samx 1” will move motor samx to position 1

umvr motorname # moves motor relative to current position, e.g.: “umvr samx 1” will move motor samx +1 from its current position

tw motorname # tweak motor position in steps of size #, e.g.: “tw samx 1” 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 letter to exit the dialog.

Upstream optics

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. u mkdir dir_name make a new directory in the working directory (example would make a folder called dir_name)
2. cd dir_name moves to new directory
3. For SAXS/WAXS: pil_setdir updates the Pilatus detector(s) with the working directory- need to run this every time directory is changed to update detector paths
4. newfile opens dialog to enter new filename and path for savingE data, applied to next scan

(move back up a level: cd ..)

Spec scans

tseries #snapshots #exposuretime(s)

dscan motorname #negative #positive #intervals #exposuretime(s) - spatial scan, dimensions relative to current position

e.g. dscan bedx -10 10 20 1

Would scan bedx from -10 to +10 mm relative to the current position, with 1 mm steps and 1 second exposure times

ascan motorname #start #end #intervals #exposuretime(s) - spatial scan, absolute dimensions

e.g. ascan bedx 200 220 20 1

Would scan bedx from motor positions 200 to 220, with 1 mm steps and 1 second exposure times

plotselect choose what variable to show in the yellow spec plot

Pilatus area detector macros

Example 1: one detector with internal triggering (the 300K as “PIL5”)

Command	Action
pil_setup PIL5	Sets up the detector with EPICS prefix “PIL5” as Pilatus number “0”, to save images to the current directory on CHESS_DAQ.
pil_settrig “Internal”	Selects Internal trigger mode use when taking snapshots within scans. NOTE: this has no effect on the TriggerMode EPICS PV until a scan is performed.
pil_on	Turns all detectors (in this case, only PIL5) “on”, such that a spec scan will trigger one snapshot per scan point.
pil_movie 10 .1	Immediately take 10 images, 0.1-second each. (no metadata).
tseries 5 .5	Perform a five-point time series, taking a half-second snapshot at each point. Images will have the format: <specfile_PIL5_SCAN#_POINT#>
dscan samx 0 5 1	Perform a single motor scan, taking a 1-second snapshot at each point. Images have the same format as above.
mesh samx 0 1 samz 0 1 1	Perform a 2D, 2-motor scan, taking 1 second snapshots at each. point. Images will have the format: <specfile_PIL5_SCAN#_ROW#_POINT#>
pil_off	Turn off snapshot acquisition.
pil_unsetup all	Erase SPEC’s knowledge of PILATUS detectors and associated macros. (This amounts to erasing the associative array “PIL”)

Example 2: two detectors and external triggering ( “PIL5” and “PIL9”)

Command	Action
pil_setup PIL5 0 PIL5 or pil_setup PIL5 PIL5	Sets up the detector with EPICS prefix “PIL5” as Pilatus number “0”, to save images to the “PIL5” subdirectory of the current directory on CHESS_DAQ.
pil_setup PIL9 1 PIL9	As above, but sets up the detector “PIL9” as Pilatus number “1”, to save images to the “PIL9” subdirectory
pil_settrig “Mult. Trigger”	Selects Multi trigger mode on both detectors when taking snapshots within scans. This implies that there is digital output / hardware trigger hooked into both detectors, that will go “high” for each point in any scan.
pil_on 0 1 or pil_on	Enable in-scan snapshots for both detectors.
“tseries”, “dscan”, and “mesh”	Perform scans as in Example 1. Images will have the format <specfile_PIL#_SCAN#_POINT#> or <specfile_PIL#_SCAN#_ROW#_POINT#> for 1D or 2D scans, respectively.
pil_off 0	Turn off detector 0, such that only PIL9 will take images.

Example 3: three detectors in fly mode ( “PIL5”, “PIL9” and “PIL6”)

In addition to “multi_pilatus_v4.mac”, this functionality requires “flyscan_v4.mac”

Command	Action
pil_setup PIL5	Sets up the detector with EPICS prefix “PIL5” (the 300K) as Pilatus number “0”, to save images to the current CHESS_DAQ directory.
pil_setup PIL9 1	As above, but sets up the detector “PIL9” (a 200K) as Pilatus number “1”.
pil_setup PIL6 2	As above, but sets up the detector “PIL6” (a 100K) as Pilatus number “2”.
pil_settrig “Mult. Trigger”	Selects Multi trigger mode on both detectors when taking snapshots within scans. For fly scanning (below), this requires that the USBCTR device is setup as described in flyscan_v4.mac, with step signal from the MDCP going into it, and the “CLK1” output going to the detectors. Also: a digital I/O output (see FLY_TRIGCHAN in id3b_NI_DIO.mac ~/Macros) goes to the USBCTR.
pil_on 0 1 2 or pil_on	Enable in-scan snapshots for all detectors.
flysetup	Set up the fly mode fast and slow motors, and verify USBCTR setup.
flyscan 10 .5 100	Scan the fast flymode motor 10 mm, taking 0.1 second. images every 0.5 mm (20 images). Images have the format <specfile_PIL#_SCAN#_POINT#>.
flymesh 10 .1 2 .1 50	Perform a 10 mm x 2 mm 2D flymode map, with 0.1 mm pitch and 50 miliseconds per point (100 x 20 point map). Images have the format <specfile_PIL#_SCAN#_ROW#_POINT#>.

See SOP (last update: August 31 2020)

SOP-DET-NNN-v3.docx

Querying/setting motor parameters

To query motor velocity (pulses/sec):

p motor_par(motorname, “velocity”)

To query pulses/mm

p motor_par(motorname, “step_size”)

To change velocity:

motor_par(motorname, “velocity”, newvalue)

e.g.: p motor_par(bedx, “velocity”, 40000)

Station computer links/procedures

Camera views and ion chamber medms

In-hutch PTZ camera by hutch door/on south wall (original StanCam): http://192.168.182.44/

In-hutch PTZ camera (upstream wall): http://192.168.182.81/

3B 4-channel Video encoder: http://192.168.182.43

Cave cameras: from terminal, run “vimba”

To restart preamp gui: show_amps

Defining macros

edit a file, “my_macros.mac” (or other filname) in specuser/Macros directory

in SPEC:

SPEC> udo my_macros.mac

check that it was read:

SPEC> prdef <macro_name>

Open ion chamber viewer

cd bin

./counter_display

Data analysis- useful information

File paths

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

Analysis area: /nfs/chess/aux/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)

Open a terminal window.

Set python path if needed:

> export PATH="/nfs/chess/opt/anaconda3_ls/bin:$PATH"

Start the GUI:

> pyFAI-calib2

Documention for the GUI is here: pyFAI-calib2

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)

See Remote Access to FMB Station Computer

Computing cluster (X2Go)

See Installing X2Go and X2Go Startup

Transferring files

See SFTP-SCP access or Globus

Other useful links

See FMBUseful Links

-- LouisaSmieska - 11 Sep 2020