TIMEleSS Multigrain Wiki

User Tools

Site Tools

Trace:
processing:indexing_with_imaged11

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revisionPrevious revision
Next revision		Previous revision
processing:indexing_with_imaged11 [2019/07/05 14:05] – [First evaluation] matthiasprocessing:indexing_with_imaged11 [2019/07/08 17:19] (current) – [Using only the best rings] matthias
Line 17: Line 17:
   * Go into the menu item of ImageD11, click on ''Indexing'' and ''Load g-vectors'' and select your //.gve// file   * Go into the menu item of ImageD11, click on ''Indexing'' and ''Load g-vectors'' and select your //.gve// file
   * Use ''Indexing'' and ''Assign peaks to powder rings''. The result of this computation will appear in the command line. It shows all theoretical peaks for your unit cell (for the phase defined in ''transformation'' > ''parameters'') as well as the number of measured g-vectors assigned to each theoretical peaks.    * Use ''Indexing'' and ''Assign peaks to powder rings''. The result of this computation will appear in the command line. It shows all theoretical peaks for your unit cell (for the phase defined in ''transformation'' > ''parameters'') as well as the number of measured g-vectors assigned to each theoretical peaks. 
- +  * Select a pair of 2 peaks in this list: Good peaks for indexing have a low multiplicity and lots of assigned g-vectors. Use the menu item ''Indexing'', ''Edit parameters'' and enter the index of these rings as //ring_1// and //ring_2//. Press ''OK'' to close the parameter window. 
-Select a pair of 2 peaks in this list: Good peaks for indexing have a low multiplicity and lots of assigned g-vectors. Use the menu item ''Indexing'', ''Edit parameters'' and enter the index of these rings as //ring_1// and //ring_2//. Press ''OK'' to close the parameter window. +  * Click ''Indexing'' and ''Generate trial orientation'', followed by ''Indexing'' ''Score trial orientation''. At the end the number of grains indexed is shown in the command line. 
- +  * From here you need to save the //.ubi// file (a file with a list of UBi matrices for indexed grains) with ''Indexing'' and ''Save UBI matrices''.
-Click ''Indexing'' and ''Generate trial orientation'', followed by ''Indexing'' ''Score trial orientation''. At the end the number of grains indexed is shown in the command line. +
- +
-From here you need to save the //.ubi// file (a file with a list of UBi matrices for indexed grains) with ''Indexing'' and ''Save UBI matrices''.+
  
 In a second stage, you can use a command like In a second stage, you can use a command like
Line 42: Line 39:
 ===== Automatization of this indexing process ===== ===== Automatization of this indexing process =====
  
- you can copy the commands in a batch file like the idx_0.py we made. +You can copy the commands in a bash file like the idx_0.py we made. 
-In that script, you need to load your gve file (from ImageD11), your parameters file (from ImageD11) and your peaks file (from peaksearch). Don't forget to specify the name of the ouput file. In the line myindexer.parameterobject.set_parameters, you can set the indexing parameters (mainly minpks and hkl_tol). To specify  the rings you want to use for the indexation, copy the list of peaks from Assign peaks to powder rings in the bloc below rings = [] and enter in that rings = [] list the index of the rings you want to use.+In that script, you need to load your //.gve// file (from ImageD11), your parameters file (from ImageD11) and your peaks file (from peaksearch). Don't forget to specify the name of the output file. In the line myindexer.parameterobject.set_parameters, you can set the indexing parameters (mainly minpks and hkl_tol). To specify  the rings you want to use for the indexing, copy the list of peaks you obtained from ''Assign peaks to powder rings'' in the block below rings = [] and enter in that rings = [] list the index of the rings you want to use.
 This script will pair every ring with all the other to index the peaks in grains.  This script will pair every ring with all the other to index the peaks in grains. 
 At the end, it will give you the number of grains it found. Once it is finish, the indexed grains are stored in a ubi file and you can get back the not indexed grains to run idx.py again with more generous parameters and try to found more grains with the left peaks. At the end, it will give you the number of grains it found. Once it is finish, the indexed grains are stored in a ubi file and you can get back the not indexed grains to run idx.py again with more generous parameters and try to found more grains with the left peaks.
Line 131: Line 128:
  
 The idea of this script is to index one phase after another and be able to remove the peaks of the grains indexed. This will avoid reusing already indexed peaks and make the indexing of the weaker phases easier. The idea of this script is to index one phase after another and be able to remove the peaks of the grains indexed. This will avoid reusing already indexed peaks and make the indexing of the weaker phases easier.
 +
 +{{:processing:ringselect_before.png?500|Peaks opened in ImageD11 before ringselect treatment}}
 +{{:processing:ringselect_after.png?500|Peaks opened in ImageD11 after removal of everything except the desired phase (marked by the red ticks)}}
processing/indexing_with_imaged11.1562328316.txt.gz · Last modified: by matthias