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--- processing:phase_identification [2021/02/10 12:34] – smerkel
+++ processing:phase_identification [2023/03/16 15:04] (current) – smerkel
@@ Line 22: / Line 22: @@
 Some drawbacks
   * this is not a true powder diffraction pattern, peak broadening, in particular, is different,
-  * current easy-to-use versions do not sum intensities, but count the number of peaks for a given 2theta. The recovered //intensity// is proportional to the multiplicity, and not the structure factor. Diffraction intensities are messed up an can be used for structural refinements.
+  * pay attention to peak intensities
+    * older versions of ImageD11 created histograms of number of measured peaks -> intensity in the histogram should be proportional to the peak multiplicity
+    * new version have an option //weight_hist_intensities//. If this option is set to ''True'' or ''1'', histograms are weighted by the peak intensities. These should be closer to a true powder diffraction intensity, but also affected by very large grains in the sample.
 ===== Creating and exporting a 2theta histogram =====
@@ Line 30: / Line 32: @@
   * Transformation -> Plot tth histogram
-ImageD11 will ask for a number of bins (10000 is good) and you will get something like the screenshot below
+ImageD11 will ask for a number of bins (10000 is good) and you will get something like the screenshot below. New versions of ImageD11 (as of Feb 2021) have an option //weight_hist_intensities//. If this option is set to ''True'' or ''1'', histograms are weighted by the peak intensities. If this option is set to ''False'' or ''0'', histograms are based on the number of measured peaks.
 {{ :processing:2theta-histogram.png?direct&400 |}}
+Newer versions of ImageD11 (update February 2021) can then export this histogram using //Transformation → Export tth histogram //
+===== Phase identification and peak fitting =====
+You can use [[https://github.com/seto77/PDIndexer|PDIndexer]] to identify your phases and fit their unit cell parameters.
+To do so
+  * Remove the first line in the file (the header),
+  * Add a constant background to all intensity values. PDIndexer does not work if your diffraction intensities go to zero. This can be done in excel, for instance,
+  * Save the histogram with the new intensity values with an '.xy' extension,
+  * Open the XY file in PDIndexer.
+===== Loading the 2theta histogram in MAUD =====
+It can be useful to load the histogram in [[software:maud|MAUD]]. Remember, however, that this is not a true powder diffraction pattern,
+  * peak broadening, in particular, is different,
+  * pay attention to peak intensities
+    * older versions of ImageD11 created histograms of number of measured peaks -> intensity in the histogram should be proportional to the peak multiplicity
+    * new version have an option //weight_hist_intensities//. If this option is set to ''True'' or ''1'', histograms are weighted by the peak intensities. These should be closer to a true powder diffraction intensity, but also affected by very large grains in the sample.
+To convert the histogram, use ''timelessTthHistogram2Maud'' from the [[software:timelesstools|TIMEleSS tools]] (see details below). Simply provide the detector distance (in mm), the name of the histogram file, and the name of the new ESG file, and you are good to go.
+To load the data in MAUD
+  * Create a dataset with a simple diffraction instrument,
+    * no intensity calibration,
+    * flat image transmission, with the proper detector distance, no tilt, no beam center correction, nothing,
+    * Synchrotron source with the proper wavelength,
+    * Caglioti broadening, with asymmetry parameters set to 0,
+  * Load the ESG file
+It should work...
+Remember, intensities are messed up, but you will get your phases and cell parameters...
+{{ :processing:histogram-test-maud.png?direct&400 |}}
+===== timelessTthHistogram2Maud =====
+<code>
+timelessTthHistogram2Maud  -h
+usage: timelessTthHistogram2Maud -d distance histogram.dat data.esg
+Creates a MAUD ESG file from a text file with intensity vs. 2theta (in
+degrees). This is part of the TIMEleSS project http://timeless.texture.rocks
+positional arguments:
+  txtdata               Name of file with intensity vs. 2theta
+  output                Name of esg file
+optional arguments:
+  -h, --help            show this help message and exit
+  -d DISTANCE, --distance DISTANCE
+                        Detector distance (in mm, required)
+</code>