mirror of https://github.com/Dioptas/Dioptas.git
150 lines
6.9 KiB
ReStructuredText
150 lines
6.9 KiB
ReStructuredText
.. sectnum::
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:start: 2
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Calibration Procedure
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=====================
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Make sure you are in the calibration mode, which should be selected on the left side of the window.
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Preparation
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~~~~~~~~~~~
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Load the calibration image by clicking the "*Load file*" button on the upper right side of the window.
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Now you can insert the starting values for the calibration in the menu on the right.
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The calibration procedure will estimate distance and center position of the x-ray, as well as detector rotation.
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For this procedure the wavelength and pixel width/height have to be defined based on the experimental setup and detector
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used.
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Please choose the correct calibrant from the Calibrant drop-down list.
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In case your calibrant is not available, your own calibrant can be added in the dioptas/calibrants folder as a text file
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containing a list of d-spacings, Dioptas will automatically have this calibrant available in the combobox after a
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restart.
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Different detector orientations can be accommodated by rotation or flipping the image.
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These image transformations will be applied to all subsequent loaded images in the calibration module and in the
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integration module.
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.. figure:: images/start_values.png
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:align: center
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:width: 300 px
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Start values for calibration
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Peak Picking
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~~~~~~~~~~~~
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In order for Dioptas to find the correct geometry it needs an initial guess for the position of some of the rings.
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This is done by selecting several peaks on each diffraction ring.
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The parameters for peak selection are given in the "*Peak Selection*" section on the right site of the calibration
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module, when "*Calibration Parameters*" is selected.
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.. figure:: images/peak_selection.png
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:align: center
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:width: 300 px
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Peak Selection Options
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By default automatic peak search is selected, which tries to automatically find peaks on a clicked ring.
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To search on the first ring please click on it with the left mouse button.
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In case it is very difficult to "hit" the ring with the mouse you can just zoom in by using the drag-zoom or mouse-wheel
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zoom.
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If the peak search was successful it should look like this:
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.. figure:: images/peak_selection2.png
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:align: center
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:width: 600 px
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LaB\ :sub:`6` \ 2D diffraction image with the first ring selected.
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If the automatic peak searching fails (when Dioptas fails to select other peaks on the first diffraction ring) there are
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several available options:
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* perform the automatic peak search on a different ring.
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- change the "*Current Ring Number*"
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- and select the a peak on this ring
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* choose "*single peak search*", which will search the highest intensity peak around the click position, whereby the
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size of the search area is defined byt the *search size*
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- then search one peak for one diffraction ring (the current peak number will automatically increase)
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- or deselect the automatic increase checkbox and click several spots on the first ring, or any ring you like (with
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the corresponding peak number selected)
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The Calibration and Refinement Process
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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After the peaks/ring(s) have been selected we can start the calibration procedure.
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This is done by clicking the "*Calibrate*" Button on the lower left of the interface.
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This will calculate the geometric parameters based on the current peak selection and then automatically refine the
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calibration parameters.
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After refinement Dioptas will automatically create a 360 degree cake image and an integrated pattern.
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When the procedure is finished it will jump to the "*Cake*" tab (top tab-bar above the image) and show the cake image.
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In this image you can easily check if the calibration was successful (by checking if the cake lines are straight).
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Additionally, the pattern is plotted with calculated calibrant positions in the "*Pattern*" Tab.
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All peak maxima should coincide with phase line positions.
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The resulting calibration parameters are shown by clicking the **pyFAI parameters** or **Fit2d Parameters** tabs in the
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right control panel.
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The current calibration parameters can be saved by clicking the **Save Calibration** button on the lower right of the
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user interface.
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To fast reuse the a calibration, the calibration can be reloaded by clicking **Load Calibration**.
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If the calibration failed, either the start values are wrong, the initial peak selection was faulty or the refinement
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parameters need to be adjusted.
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For a new peak selection, just click "clear all peaks" and start the the peak selection again, make sure that current
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peak number belongs to the corresponding clicked ring.
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The meaning of each of the refinement options are explained in the next section.
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Refinement Options
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__________________
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The refinement options are defined on the right control panel of the Calibration module, when "Calibration Parameters"
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is selected.
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.. figure:: images/refinement_options.png
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:align: center
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:width: 300 px
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Available options for calibration refinement
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There are several options available:
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- *automatic refinement:*
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Defines if Dioptas should search for peaks by itself after using the initially selected peaks.
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When this option is deselected only the selected peaks are used for calculating the detector calibration.
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- *use mask/transparent:*
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The refinement can be constraint to a certain image area by using a mask previously defined in the mask module.
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The image of the mask can be made transparent to be able to "look behind"
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- *Peaksearch algorithm:*
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The algorithm used for searching peaks on the ring.
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The standard algorithm is "Massif" although "Blob" detection may give better results in some cases.
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- *Delta 2th:*
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This is the +- search range used for automatic peak search for each ring.
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The center value depends on the values, estimated by the calibration procedure, so ultimately by the initial choice
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of predefined peaks (Peak selection)
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- *Intensity Min factor:*
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This factor determines how many times the peak intensity has to be higher than the mean value of the search area
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(within the delta 2th value) for each individual ring.
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The lower this value is the more peaks will be selected, however, also the likelihood of selecting wrong background
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peaks increase.
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The default value is 3, which is good for rather spotty patterns.
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If your calibration image has perfect diffraction rings, this value needs to be reduced to about 1-1.5.
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- *Intensity Max:*
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A threshold value which excludes all peaks above this value.
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The default value is 55000 which is good for 16 bit detectors.
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In case a detector with more levels is used this value needs to be adjusted.
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- *Number of rings:*
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The number of rings on which peaks are searched.
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This should be chosen based on the number of visible rings in the calibration image.
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For an optimal calibration all visible rings should be used.
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If the calibration/refinement fails you can in principle play with all parameters.
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However, the most common adjustments are the number of rings and the *Intensity Min factor*.
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