Sample Session
This section leads you through some of the actions you might take in a typical data analysis section.
Setting Calibration Parameters
We begin by opening a calibrating the detector parameters.
- Double-click the Datasqueeze icon to start the program.
- In the File panel verify that the number of files is set to 1
and "Calibration Parameter Source" is set to "File. " Verify also that
for the top set of boxes "Add " is set to 0, "Mult " is set to
1, and "Im. # " is set to -1.
- Use the Browse button to go to the "samples " folder that was
created when you installed the program. This will probably be in
C:\Program Files\samples\samples on Windows, /usr/src/datasqueeze_files/samples on Linux,
or Macintosh HD/Applications/datasqueeze_files/samples on a Macintosh.
- Set the data type to "Bruker-Siemens".
- Select the file called agbe.std by selecting it and clicking on Open. The open file dialog box should close.
- Click on Open Files. Oops! This wasn't a data file.
The file dialog box is highlighted in red and you got an error message.
- Try again, this time opening the file called agbe_calib.unw.
After clicking "Open Files " you should see a black screen with a
bright central ring, an X that is somewhat off center, and a bright ring.
- Go to the Calibrate Panel and click Run Least Squares Calibration Wizard.
- The first window asks you what the instrumental mode is. In this case, the beam zero
lands at approximately the center of the detector, so we select "Small-angle mode"
and then click Next.
- A new window opens which asks you to set the correct
wavelength. For the file in question this should be
Cu K-alpha wavelength, 1.54184. If it is not, type the
correct number in the box. Then click Next.
- The next window asks us to set the pixel size or detector dimensions.
Since we are not sure of these values for our detector, we follow instructions and
leave them as they are. Click Next.
- Now we set the number of Bragg rings, which is three for this particular file.
Set the drop-down box to 3 and click Next.
- The parameters are indeed in a standard calibration file. Set the "Yes " check box and click Next.
- In the dialog box that opens, select agbe.std.
This sample file is silver behenate, a lamellar material with a d-spacing of 58.3 angstroms.
- The next window displays the Q, 2-theta value, and d-spacing for the rings we chose.
If we had not read in the agbe.std file, we could have entered any of these by hand. Click Next.
- We are now asked to set the estimated position of the beam center.
Drag the blue dot in the false color image until it is approximately in the
center of black dot in the middle of the image. In the boxes, X and Y should be
approximately 547 and 530. Then click Next.
- We now need to tell Datasqueeze where the first ring is that we will use for calibration.
Drag the outer blue dot so it is just outside the innermost data circle.
Drag the inner blue dot so it is just inside that circle, and click Next.
Repeat for the second and third rings.
- We now get a window asking us to verify the starting parameters. Click Next.
- Datasqueeze will now do a series of least squares fits to determine the optimum
detector parameters. This may take several minutes depending on the speed of your computer.
- When the calibration is finished, the results should appear in the white box.
You should get something like: X Center set to 539.462, Y Center set to 523.801,
Q-Range set to 0.39784, Tilt set to 4.56488 and Tilt Azimuth set to -32.299. The
X Center and Y Center define the center of the diffraction pattern (not necessarily
exactly where your beam stop is). In this file they are close to the geometric
center of the image. The Q-range is a measure of the angular scale of your instrument.
The Tilt reflects the fact that, either due to electronic anisotropies or detector misorientation,
your patterns might not be exactly circular. On the false color image, in addition to the data,
you will see black-and-white dashed circles; verify that one of those circles is in fact directly
on top of the Bragg ring.
- If you are happy with these results (we are) Click Next.
You could also click Restore to revert to former calibration values or Back to back up one or more steps.
- We are now asked if we want to save these d-spacings.
Since we already read the data in from a calibration file, the answer is
probably "no " but if we had typed them in by hand this would be our chance to
create our own calibration file. Click Next.
- We are now asked if we wish to save these calibration parameters in a file.
If we check Yes then we will create a file with information on the current session,
which we could use to avoid repeating the calibration process in a future session. Click Yes and Finish.
Look at some real data
Now let's look at a real data file.
- Go back to the In the File panel. As before, select
(with the Browse button) and open (with the Open Files button)
the file called sample.unw.
You should observe multiple rings.
- In the Image Panel, highlight the text in the Maximum for False Color box,
set it to 5, and hit a carriage return. The inner rings become more distinct while the outer rings become darker.
- Click on Logarithmic to see what that does, then go back to Linear.
- This is a nice image; we might want to publish it. Go to the FILE Menu and select Save False Color Image.
- The file chooser dialog box opens.
Use the directory scroll button near the top to choose a better folder, maybe your home directory
(on Linux) or the desktop (on Mac or Windows) so that you can find this thing to delete it later.
- Let's save it as a JPEG file--verify that the drag- down menu to the left is set correctly.
- In the Name box type tmp.jpg. Click on the Save button.
- Let's examine a region of the plot more closely. Go to the Examine Panel and click the Start button.
- An X with a blue center appears near the center of the main image.
- Click on the X and drag it to see a pixel-by-pixel blow-up of different regions of the image.
- Now Click Done.
- Go to the Plot Panel. Let's do a Q/Chi plot that emphasizes the top part of the pattern.
With the drop-down menu, select Plot versus Q / Sum or average over Chi
(it is the default, so it is quite likely already selected).
- Click on the Start button for Set Plot Limits. Either by dragging the blue dots,
or by entering directly in the relevant boxes, set up a region that covers all but the innermost
ring. We found that Qmin=0.15, Qmax=0.37, Chimin=10, Chimax=170 worked well.
- We also need to set Delta. Let's try Q-Delta = 0.002
- Set the Integrate button to Average.
- Let's see what this looks like. Click Make/Update Plot. You should see one weak peak and
two strong peaks in the Line Plot Image Window.
- Select the plot cursor (it should turn from blue to red) and drag it over to the top of
the strongest peak. The readout in the upper right-hand corner of the Line Plot Image Window
tells us that this peak is located at Q=0.2402 and has an intensity of 6.2.
- Set the Integrate button to Sum and click again on Make Plot. Notice that the higher-Q peak
got stronger, relatively speaking.
- Let's save these data. Go to the FILE Menu and select Save Plot Data as ASCII File.
Choose the Comma button for Set Separator. Enter the name as "test.txt".
- Temporarily leave the program and use your favorite text editor to look at the file
you got: two columns of ASCII numerical data separated by commas.
- Let's find out some statistics on this dataset. Select Statistics in the View menu.
Average, maximum, and minimum counts are calculated for the dataset as a whole and
also for the region selected for plotting, and the number of counts in
each of 20 different bins are calculated. If we wanted to know more we could
reset the number of bins and the bin ranges and recalculate all of this in more detail.
- Let's make a souvenir printout. Select Print in the File menu.
- Just for fun, change the X and Y Axes from Linear to Log and click the
Make Plot. The plot should look quite different--the weak peaks are emphasized
much more in this plot.
This concludes the tour of the program. You have used most of the features,
and the ones that you have not (such as Zoom) are pretty obvious. Have fun analyzing data!
Last modified February 6, 2015
email:
support@datasqueezesoftware.com
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