Frequently Asked Questions


Installation

File Types/File Opening

Images

Calibration/centering

Plots

Least-Squares Fits

Run-time errors

Your Questions Answered!

Installation

File Types

  • What kinds of data file can Datasqueeze read?
    Currently supported formats are: "ADSC_Quantum", "Binary-little-endian", "Binary-big-endian", "Brandeis_B4", "Bruker-Siemens", "Bruker-Nonius KCD", "CBF", "CrysAlis", "Ditabis IPC", "ESRF", "Fuji_IP", "Gatan DM3", "MAR_CCD", "MAR_IP (300)", "MAR_IP (345)"), "MAR_IP (PCK)", "Mercury", "Molecular Metrology", "Nonius DIP", "Rigaku_Raxis", "RaxisIV++" "Roper-Princeton", "SBIG", "Tiff", "XDR", "Unknown." The last one does its best to choose among the other available choices. It is also possible to read in Grayscale graphics images (PNG, GIF, JPG only)--this might be a way of reading in an image that is a Fourier transform of some real-space data, for example produced by a microscope or AFM. (Graphics images are not the preferred way of reading in data from x-ray detectors).
  • Datasqueeze does not read data files produced by my detector. What can I do?
    We anticipate adding more formats in the as the demand arises; contact us if there is a particular data format you would like to see added.
  • I saved my data as a GIF (or JPG or PNG) file. I can read it back with Datasqueeze, but the data are quite different. What is wrong?
    Graphics files are really intended only as a way of reading in non-xray data, for example produced as a Fourier transform of some optical image. A graphics file is not the same as the original data file. A typical data file is at least 1024x1024 pixels or larger, and has a depth of at least 16 bits (depending on the detector type). Graphics images are generally much smaller (so spatial resolution has been lost) and have much less dynamic range. Additionally, note that Datasqueeze expects grayscale images. It converts the image color to an intensity by adding the red, blue, and green components. If you start with a color image, this is almost certainly not how the data were encoded.
  • Can Datasqueeze read in graphics images that are not GIF, JPG, or PNG?
    Not right now--expansion of this feature will be driven by customer demand.
  • Datasqueeze returns an error when opening a file that I think is valid. What should I do?
    There are several possible origins for this problem:
    1. You may have selected the wrong file format. In the dialog window that opens, there is a drop-down box listing all the data file types that Datasqueeze knows about. This should be set to match the type of file you are opening. If you do not know the file type, select "Unkown".
    2. Your file may have been corrupted. This can happen, for example, if you use FTP or a similar protocol to transfer the file from one computer to another. When doing this, you should always using the "binary" option if it exists, rather than "Auto" or "Text." If you suspect that your file may be corrupted, try transferring it back to the original datataking computer and see if the original software that wrote it can read it.
    3. You may be looking at a graphical image of the file rather than the data file itself. With rare exceptions, a graphics image (jpeg, gif, etc.) has far less information content than the original data file, and in any case is in a different format. Look at the size--a typical x-ray data file is at least 1MB, and often much larger.
    4. If your problem is none of the above, it is possible that this is a data file format not currently recognized by Datasqueeze. Please contact support (support@datasqueezesoftware.com) with as much information as you can provide about the file you are trying to read.
  • My image plate data seem to consist mostly of zeros, even though I know that there is really structure there. What is wrong?
    The Fuji image plate data are recorded in logarithic form. When they are read back in, they are restored to linear form by exponention (i.e., Icalc = A x 10^(Imeas/I0)). Depending on the range of the data, it is possible that many or most of your data points are less than 1 (such as 0.01). Try multiplying the data by some large number such as 10000 when you open the file.

Images

  • Image is Completely Black or Completely White.
    Try playing with the Max, Min, and Contrast settings in the Image window. If this does not work, go to the Examine window and look at a few regions. If all of the pixels are zero, then something is seriously wrong-but this is unlikely.
  • What graphics formats are supported?
    The false color image can be saved to disk in the PNG, JPEG, TIFF, or BMP format.
  • What about GIF images?
    Sorry, there are copyright problems associated with the GIF format and we chose not to get ourselves in legal hot water.
    Yes! This feature was added to Datasqueeze 1.8.5.

Calibration/centering

  • What are x-center and y-center?
    In most diffraction applications, the primary beam is blocked by a beam stop. The beam center is the position at which the beam would have hit if it were not blocked. It will be at the center of any Bragg rings. Often this is close to the physical center of the detector, although sometimes it is near one edge of the detector. X-center and Y-center are the values of the pixels corresponding to the center of the diffraction pattern. So for example for a 1024 x 1024 pixel2 detector with the beam exactly in the center, X-center and Y-center would both be equal to 512.
  • What is the q-range?
    It is the value of q (= 4 pi sin(theta) / lambda) corresponding to the maximum horizontal range of the detector. This is set once for a particular data set to determine the relationship between the distance in pixels between a feature of interest and the origin and the q-value corresponding to that feature.
  • What is a Bruker standards file and how do I use it?
    You are supplied with a file called agbe.std, which is a text file containing powder diffraction information on Silver Behenate, a common calibration standard. If you have previously calibrated your detector with AgBe you can use this file with the Calibrate window to easily establish the center, q-range, etc., of your detector. If you have used some other calibration standard, you can easily use any text editor to create a standards file of your own, using agbe.std as a model. Note however that this is one place where the number format is not locale-dependent; the d-spacings should all use the American format. That is, a d-spacing that is a little over 45 Angstroms should be written as 45.3 rather than 45,3.
  • Diffraction patterns that should be circular look oval. What is wrong, and what can be done about it?
    This can come about in one of several ways. The most common is that your detector is not exactly perpendicular to the incident beam. It is also possible that the x- and y-directions have different gains, or equivalent that the pixels are not exactly square. All of these can be corrected by Datasqueeze. The Tilt/Azimuth combination on the Image and Calibrate windows correct for a detector that is tilted an arbitrary amount about an arbitrary axis relative to the central beam.
  • In my images, the beam center is near the bottom of the image. When I set the beam, the entire image is shifted up so that the actual beam center is now at the center of the screen. I can no longer see the upper edge of the image and setting the wedge-shaped region for the plot becomes guess work.
    This isactually something that you often want--for example, if you are looking at a small-angle diffractino pattern, you may wish to "zoom" in to the center. The default behavior is to force the image center to be at the beam center. If you don't like that, before resetting the beam center, in the Image panel, click the button that says "Image Center != Q Center". (This will deselect the button that says "Image Center = Q Center"). The whole image will now not be recentered when you change the beam center.
  • Datasqueeze Seems to Forget Settings When Opening a New File:
    In the File window, check the "Retain" box. This will keep beam center, angular range, etc., at their last set value.

Plots

  • Plot shows Few or No Data Points.
    Check the Plot Limits. Make sure that you actually expect to have data in that range. Make sure also that the Delta value is in a reasonable range--it should be somewhere between 1/10 and 1/100 of the total range of the independent variable.
  • When I go to make a plot it does not graph the full range that I selected.
    Check the "Delta" value (the increment corresponding to the spacing between points). If it is larger than the full range of the plot then you will only get 1 or 2 points. If it is much smaller than your plot might actually consist of thousands of points, and the program cuts off with a maximum number of points. You should typically set the "Delta" so that you have something like 100 points in your plot, but also so that the increment is not smaller than one pixel.
  • When I go to make a plot I get something crazy-looking that oscillates rapidly.
    See the previous question. If the "Delta" increment is smaller than one pixel then some points will have data associated with them and some will not.
  • The text file that is produced by saving plots seems to have a lot of blank lines (every other one).
    Did you transfer your file from one computer to another? These extra newline characters are sometimes inserted by ftp application (e.g. Fetch, WS_FTP) if it recognizes the file as being "text." Try telling the ftp that the file is "binary". This is a slower, but more reliable way, of transferring files.
    The problem arises because different operating sytems have different ideas of what constitutes a "new line." Datasqueeze inserts "\r\n", which seems to work on all the operating systems we have tried, but is sometimes translated by ftp applications into "\n\n".
  • Can we get better-looking plots suitable for publication?
    A program capable of producing publication-quality plots requires a substantial development effort, and there are many programs out there that already do a great job (Origin, Sigma-Plot, Excel, Kaleidagraph, IDL, C-Plot, to name just a few). You will do better to save your data as an ascii file and use professional tool designed for that purpose.
  • Peaks do not Appear at Expected Q-Values or Angles.
    This is almost certainly a calibration problem. You need to know enough about your detector to set several parameters. Go to the Calibrate window. First, you need to set Lambda (the wavelength). This is crucial! After that, you have several options:
    1. You can set the Q-range. This is, roughly speaking, the value of Q at one edge of the detector if the beamstop is in the center. You optimize it until peaks appear at the right position. See the manual entry on Calibration for more details.
    2. You can set 2theta-max. This accomplishes the same thing as setting Q-range, for those who are more comfortable using the language of angles than the language of momentum transfer.
    3. You can set both the sample-detector distance and the detector radius. (The radius should always be the same for a given detector, but the sample-detector distance may vary from one measurement to another).
  • Peaks are broadened or distorted.
    If plotted peaks appear broad or distorted even though the powder diffraction rings in the false color image are sharp, this is almost certainly a calibration problem. There are two obvious things to check:
    1. The beam center (X-center and Y-center in the Calibration window) may not be completely set. Note that the beam center is not in general exactly at the geometrical center of the beam stop. Use the "Circle" option in the Image window to see whether the powder diffraction rings are really centered. Or, make radial plots over limited ranges of Chi and verify that the peaks come at the same positions independent of Chi.
    2. It is also possible that the diffraction rings are not perfectly circular--see the discussion of Oval patterns above. You may need to change the Tilt in the Calibration window.
    3. I want to make a Qx-Qy plot through a fiber pattern that is somewhat tilted. Is there a way to do this?
      Yes, as of 2.0.7 there is a "Chi Offset" feature that allows you to change the definition of the orientation that we call the "equator".

Least-Squares Fits

  • Least Squares Fit Failed, Errors Generated
    This can have multiple causes, but the most likely are:
    1. Attempting to fit a parameter that actually has no effect on the model.
    2. Attempting to fit too many parameters at once
    3. Attempting to do a least squares fit to too few data points.
    If you suspect #1 or #2, click the Revert button, deselect one of the parameters that you fit, and try again. If the number of parameters is greater than or equal to the number of points, you will either need to redo the plot so as to increase the number of points, or decrease the number of fitting parameters.

Run-time errors

Feedback


Please report any bugs, anomalies, or requests for features to support@datasqueezesoftware.com. If you are reporting a bug, provide as much information as possible on exactly what you were doing when the bug surfaced, what platform you were using (e.g., PC running Windows ME), and the extent to which it is reproducible.

Last modified February 6, 2015
email: support@datasqueezesoftware.com