Getting started with CSS and Bluesky
The primary user interface for new users, this screen provides basic tools for visualizing samples and surveying them in preparation for scanning, which is accomplished through the Bluesky interface described below.
TOP LEFT
A "visible light microscope" (VLM) live image with the approximate x-ray location marked with a cross. Note that the x-ray beam is more than 30 times smaller than a single pixel in this image. The full field of view is about 2 mm x 2 mm. Use this image for rough alignment and to check the limits on the XRF scans that you wish to perform. The VLM image must be in focus in order to assure that the x-ray beam position is known.
BOTTOM LEFT
The energy spectrum of the x-rays detected from the interaction of the x-ray beam and the sample at this position. The silicon drift detector (SDD) is comprised of three individual detectors, shown here in red, green, and blue. The light colored green and blue boxes above this read out allow for some control of the detector outside of a scan. In the green box, one can trigger the detector to get a continuous readout while manually scanning the sample, usually searching for an interesting portion of the sample to investigate. The blue box is used to control the regions of interest (ROIs) that we use for real time feedback during a scan. The values here are in units of "channel" where one channel on the SDD is 10 eV. Set the ROI in a 200 eV window around the emission line of the element of interest.
TOP CENTER
Detector and motor controls are located here. In the purple box to the left, one can change the VLM parameters. These have no effect on either an XRF or XANES scan. The sample motion is controlled by the parameters in the blue box: X and Y are the directions perpendicular to the beam and Z brings the sample into and out of the focus of the VLM; the buttons summon windows for specifying scan parameters, if they are not already open. The brown box may be used to tweak the beam trajectory, but this is not normally needed. The light gray box contains the readback from the ion chamber and the transmission diode. If these stop updating outside of a scan use the reset and trigger buttons to reinitialize them.
TOP RIGHT
These are controls related to the very first optical elements of the beamline. On the far right is the control for the three beamline shutters, of which one normally only controls 'B'. Green indicates that these are open and red, closed. The current value for the ring current is shown at the bottom for informational purposes. The filters are not normally needed and should be out. The energy displayed corresponds to the Bragg angle of the monochromator. The top-left group of controls relates to the undulator gap, which will only be used if the beamline must be "detuned," a situation that is restricted to the case where a sample contains a very high concentration of a high-Z element.
CENTER RIGHT
The gray buttons invoke more detailed information on the devices named on the button. The pink box allows the "rephasing" and homing of the X and Y stages, which is necessary if they begin to behave unreliably. The order for using these should be as follows: "Phase motors", home Y, move Y to 2 mm, home X.
BOTTOM RIGHT
The only motor that should be touched here is the 'SDD X' stage which controls the distance between the sample and the fluorescence detector. Be very careful when moving this motor as collisions with your sample may be possible and would result in very bad things!
Accessible from the Home screen through the "XRF Scans" button:
Enter the parameters for your scans here. Each "checked" scan will run after the Bluesky command is invoked. The scans will run in order and higher numbered scans may be queued by checking them while earlier scans are running.
Accessible from the Home screen through the "XANES Scans" button:
Enter the parameters for your scans here. Each "checked" scan will run after the Bluesky command is invoked. The scans will run in order and higher numbered scans may be queued by checking them while earlier scans are running. Make sure that the calculated parameters, especially the number of points is reasonable!
Bluesky is a command-line-based user interface that we use to control our scans. Scans will automatically pause when the x-ray beam becomes unavailable. Basic usage can be seen above and on the FAQ page. A history of all commands typed is maintained and can be accessed by using the 'up' arrow. Command line completion can be accessed using the 'tab' key. Typing a partial command followed by a '?' will provide help:
BlueSky@SRX [1]: RE(hfxanes_ioc?
X-RAY ENERGY
You may change the x-ray photon energy:
BlueSky@SRX [2]: energy.move(7.2)
BlueSky@SRX [3]: energy.move(12000)
BlueSky@SRX [4]: peakup_dcm()
where the photon energy may be specified in either eV or keV. When changing the energy by more than a few hundred eV, it is best practice to issue the 'peakup_dcm()' command, which automatically checks the trajectory of the x-rays coming into the D Hutch(This command will open the shutter and leave it open, so it is helpful to change the energy when looking at a non-radiation-sensitve portion of your sample.).
SETTING ENERGY ROIS
ROIs for the SDD may be set in the GUI as described above or on the command line:
BlueSky@SRX [1]: setroi(2,'Zn','ka1')
ROI2 set for Zn-ka1 edge.
if no edge is specified, the highest energy edge accessible at the current energy is selected:
BlueSky@SRX [1]: energy.move(7300)
BlueSky@SRX [1]: setroi(1,'Fe')
ROI1 set for Fe-ka1 edge.
SCANNING
Scans are accomplished by passing a helper function to the "Run Engine":
BlueSky@SRX [5]: RE(hf2dxrf(xstart=25, xnumstep=10, xstepsize=0.001, ystart=20, ynumstep=10,ystepsize=0.001, acqtime=1., numrois=2, shutter=True, align=False))
will perform 2D x-ray fluorescence mapping scan starting at X,Y=25.,20. with 121 points at 1 micron stepsize and 1 second dwell time per point. 'numrois' refers to the ROIs defined for the SDD as described above and indicates that one wishes to see the first two ROIs while the scan is progressing (All data will be saved and a more complete analysis, which does not rely upon these predetermined ROIs, can be done offline using pyxrf.) The 'shutter' keyword instructs the Run Engine to open and close the shutter before and after the scan. The 'align' keyword instructs the Run Engine to check the beam trajectory before the scan begins, which is especially useful when collecting an 'energy stack,' a collection of images of the same region on the sample with different incident photon energy (Note that the alignment will be performed with beam on the sample, which may be important if this is sensitive to radiation.).
Here is an example of a XANES scan:
BlueSky@SRX [6]: FeK = 7112.
BlueSky@SRX [7]: RE(xanes_plan(erange=[FeK-80, FeK-20, FeK+30, 7300], estep=[3,0.75,2], acqtime=1., roinum=2, samplename='My iron-containing sample', filename='Fe_smple_2sa3'))
which simply passes the energy intervals that are to be scanned and their respective step sizes to the Run Engine. Here, the 'roinum' keyword is important and the user must ensure that ROI referenced is properly selected for the SDD as described above. Unlike the XRF scans, a XANES scan will automatically produce a text file that is ready to be loaded into Athena, so the 'filename' keyword should be meaningful and the 'samplename' keyword will be added as metadata to the text file.