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--- processing:advanced_indexing_with_grainspotter [2023/12/07 08:44] – smerkel
+++ processing:advanced_indexing_with_grainspotter [2023/12/09 23:30] (current) – ↷ Links adapted because of a move operation smerkel
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 ====== Advanced GrainSpotter indexing: indexing loops ======
-In the previous section, we described how to perform [[processing:indexing_with_grainspotter|grain indexing with GrainSpotter]]. After some time, you might realize that you are not satisfied with the results and need more advanced tuning of the process.
-Below is an example on how to proceed to improve your indexing. It includes several steps
-  - Check your expected crystal structures, the corresponding peaks, and your g-vectors input,
-  - Run loops of GrainSpotter indexings,
-  - Optimize results for your fitted grains with FitAllB.
-===== Crystal structure =====
-As this point, you probably [[processing:compute_gvectors|computed your list of G-vectors]] with [[software:imaged11|ImageD11]]. The first line of the [[fileformat:gve|G-vectors file]] contains the unit cell parameters and lattice centering (one of P,A,B,C,I,F) and, below, you can find list of computed theoretical g-vectors for the expected unit cell.
-This list is generated with crude calculations that do not know anything about atom types of positions in your structure. Chances are that many of those theoretical g-vectors do not exist for your structure or have a very low intensity.
-At this point, you can use other softwares, such as [[software:vesta|VESTA]] to generate a list of the expected peaks as well as their relative intensities. You can then check your computed theoretical g-vectors in the [[fileformat:gve|G-vectors file]] and remove peaks that do not exist or with a low intensity.
-===== GrainSpotter indexing loop =====
 You probably noticed that, after some time, GrainSpotter does not find any new grains. At this point, you should
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   * [[processing:grainspotter-merge|merge the GrainSpotter output files]] into one.
-This process can be combined into advanced indexing loops. Attached is an example of custom [[restricted:GS_loop_olivine|loop for olivine]] (//restricted access to team members//) that will run a series of 25 GrainSpotter indexing with various tolerances.
+This process can be combined into advanced indexing loops with a bash script:
+  * Here is a first example of custom [[examples:gs_loop_olivine|loop for olivine]] that will run a series of 25 GrainSpotter indexing with increasing tolerances in 2θ, η, and ω.
+  * We also include a second example, based on a [[examples:gs_loop_ppv|NaCoF3 post-perovskite indexing]]. This second version of the loop is more advanced. You can have multiple indexings running in parallel on a multi-core machine. Some unnecessary output files have also been removed.
-There a second example, based on a [[restricted:GS_loop_pPv|NaCoF3 post-perovskite indexing]] (//restricted access to team members//). This second version of the loop is more advanced. You can have multiple indexings running in parallel on a multi-core machine. Some unnecessary output files have also been removed.
+Spend time to study the content of these loops to adjust their parameters to your needs. If you have made it so far in the manual, it should be within your reach.
 At the end, you will want to analyze and understand the reliability of your final indexings. [[evaluation:plotting-grain-orientations|Plotting grain orientations]] and comparing the indexings is a good start.
-===== Optimize results for your fitted grains with FitAllB =====
+Next, step: [[processing:complex-multi-phase|Indexing a complex dataset with many phases]]...
-Next step...