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Centering and calibration
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. _s3p1:
The next step is to set the beam center, x-ray wavelength, and sample to detector distance.
Before this can be done, you have to set the image and file header type in the Options window.
The best way to find the beam center and sample to detector distance is using the automated
method in RAW. This tutorial assumes you have just done :ref:`Part 1 <s3p3>`.
If not, open RAW as in Step 1 and set your data folder as in Step 8 of :ref:`Part 1 <s3p3>`.
A video version of this tutorial is available:
.. raw:: html
<style>.embed-container { position: relative; padding-bottom: 56.25%; height: 0; overflow: hidden; max-width: 100%; } .embed-container iframe, .embed-container object, .embed-container embed { position: absolute; top: 0; left: 0; width: 100%; height: 100%; }</style><div class='embed-container'><iframe src='https://www.youtube.com/embed/v7-CROk8oqM' frameborder='0' allowfullscreen></iframe></div>
The written version of the tutorial follows.
#. We will use silver behenate to calibrate the sample to detector distance,
the beam center on the detector, and the detector rotation. Show the silver
behenate image by selecting the **agbe_008_0001.tif** file and clicking
the show image button at the bottom of the File Control panel.
|calibration_image_png|
#. In the Image Plot Panel that is now showing, click on the Image Display Settings
button (looks like vertical slider bars) at the bottom of the screen.
#. In the window that appears, set the scale to logarithmic and and click “OK”.
|calibration_logscale_png|
#. Open the Centering/Calibration panel by going to the Tools menu and selecting
“Centering/Calibration”.
|calibraiton_auto_panel_png|
#. In the Centering/Calibration panel set the Energy to 12.0 keV. Verify that the
Detector Pixel Size is 172.0 x 172.0 micron. Verify that the Detector is set to
"pilatus_1m". Verify that the standard is set to AgBh.
* *Note:* The x-ray energy/wavelength is a previously measured value.
* *Note:* If you set the detector properly in the radially averaging
options panel the detector and detector pixel size values will
fill in automatically (if the detector is not Other).
|calibration_parameters_png|
#. The goal of centering and calibration is to find a beam center position, sample
to detector distance, and detector rotation that causes the calculated
Silver Behenate ring pattern to match up with the rings on the image.
* *Note:* The beamstop is the blue/green bar extending out from the top
right edge of the detector
#. Click the “Start” button in the “Automatic Centering/Calibration” panel.
#. Make sure the “Ring #” is set to 0. Click on a point with strong intensity in
the Silver Behenate ring nearest the beamstop.
* *Note:* For some experimental setups, one or more of the largest d-spacing
rings may not be visible on the detector. In this case, you need to figure
out what the first visible ring on the detector is, and set the ring number
to that. So, if the third ring was the first one on the detector, the Ring #
would be set to 2 (the ring number is zero index, so 0 corresponds to the first
ring, 1 to the second ring, and so on).
|calibraiton_centering_1_png|
#. The peak intensity points in that ring will be automatically found, and labeled with
tan-ish dots.
* *Tip:* If it didn’t find very many points, try clicking again on another
part of the ring, and it will add more points to your selection.
#. If needed, click on the other portions of the same ring that are on different detector
panels to find out the rest of the points in this calibration ring.
* *Note:* The autofind algorithm will only find peaks in contiguous
regions. However, masked regions don't count, so if you've masked the
panel gaps before calibration it should find points in all of the panels.
* *Tip:* Due to the color map selected, the points may be hard to see. Try changing
to the heat map or grayscale to see the selected points,.
|calibraiton_centering_2_png|
#. Change the “Ring #” to 1.
|calibraiton_ring_number_png|
#. Click on a peak intensity point of the second visible ring. Do this for all
the sections of this ring in different detector modules.
#. Change the “Ring #” to 2. Click on a peak intensity point of the third visible
ring. Points will be shown with green dots.
#. Click the “Done” button in the “Automatic Centering/Calibration” panel.
|calibraiton_centering_3_png|
#. The beam position, sample to detector distance, and detector tilt angles will
be calculated and filled in. Calculated rings will display on the plot as
dashed red lines, based on the parameters found in the fit. The beam center
is displayed as a red dot on the image. You can verify the validity of the
fit based on how these calculated values match up with what is shown on the image.
* *Note:* Calculated rings are displayed without detector tilt angles, so if the detector
is significantly off beam normal the calculated rings will not match up with the
measured rings.
* *Note:* Image tilt plane rotation is an odd value. It represents motions of
both X and Y around the Z axis of the detector. As such, it can take on
large values (such as -131) for very small detector angles, which is just
representing motion in both axes. In this case, all three detector angles are
~0.7 degrees or less.
|calibraiton_centering_4_png|
#. If necessary (such as if the autocentering routine fails), all of the calibration
values can be adjusted manually. The beam center can either be typed into the
appropriate boxes, or the red arrows can be used to nudge it by "Steps" pixels
in any direction. The crosshairs can be used to pick the beam center position by
hand, good for getting a rough alignment. The other parameters can be
typed into their appropriate boxes. Manual centering is an iterative process:
#. Enter rough values based on observation, measurement of actual sample
detector distance.
#. Use arrows to move beam center until you match up with the first ring.
#. Adjust the distance until you match up with the second ring.
#. Repeat the last two steps as necessary until you converge on a solution.
#. Click the OK button in the Centering/Calibration panel to save your settings and
exit the panel.
.. |calibration_image_png| image:: images/calibration_image.png
:target: ../_images/calibration_image.png
.. |calibration_logscale_png| image:: images/calibration_logscale.png
:target: ../_images/calibration_logscale.png
.. |calibraiton_auto_panel_png| image:: images/calibration_auto_panel.png
:target: ../_images/calibration_auto_panel.png
.. |calibration_parameters_png| image:: images/calibration_parameters.png
:width: 400 px
:target: ../_images/calibration_parameters.png\
.. |calibraiton_centering_1_png| image:: images/calibration_centering_1.png
:target: ../_images/calibration_centering_1.png
.. |calibraiton_centering_2_png| image:: images/calibration_centering_2.png
:target: ../_images/calibration_centering_2.png
.. |calibraiton_centering_3_png| image:: images/calibration_centering_3.png
:target: ../_images/calibration_centering_3.png
.. |calibraiton_centering_4_png| image:: images/calibration_centering_4.png
:target: ../_images/calibration_centering_4.png
.. |calibraiton_ring_number_png| image:: images/calibration_ring_number.png
:width: 400 px
:target: ../_images/calibration_ring_number.png
|
