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Diffstat (limited to 'doc/man/indexamajig.1.md')
| -rw-r--r-- | doc/man/indexamajig.1.md | 54 |
1 files changed, 29 insertions, 25 deletions
diff --git a/doc/man/indexamajig.1.md b/doc/man/indexamajig.1.md index 0d02b16b..605782bd 100644 --- a/doc/man/indexamajig.1.md +++ b/doc/man/indexamajig.1.md @@ -633,47 +633,50 @@ INDEXING OPTIONS : The rotation matrix trace tolerance in degrees. Default 3. **--felix-domega=n** -: Low-level parameter for the Felix indexing algorithm. +: Degree range of omega (moscaicity) to consider. Default 2. **--felix-fraction-max-visits=n** -: Low-level parameter for the Felix indexing algorithm. +: Cutoff for minimum fraction of the max visits. Default: 0.75. **--felix-max-internal-angle=n** -: Low-level parameter for the Felix indexing algorithm. +: Cutoff for maximum internal angle between observed spots and predicted spots. +: Default: 0.25. **--felix-max-uniqueness=n** -: Low-level parameter for the Felix indexing algorithm. +: Cutoff for maximum fraction of found spots which can belong to other crystallites. +: Default: 0.5. **--felix-min-completeness=n** -: Low-level parameter for the Felix indexing algorithm. +: Cutoff for minimum fraction of projected spots found in the pattern. +: Default: 0.001. **--felix-min-visits=n** -: Low-level parameter for the Felix indexing algorithm. +: Cutoff for minimum number of voxel visits. Default: 15. **--felix-num-voxels=n** -: Low-level parameter for the Felix indexing algorithm. +: Number of voxels for Rodrigues space search Default: 100. **--felix-sigma=n** -: Low-level parameter for the Felix indexing algorithm. +: The sigma of the 2theta, eta and omega angles. Default: 0.2. **--felix-tthrange-max=n** -: Low-level parameter for the Felix indexing algorithm. +: Maximum 2theta to consider for indexing (degrees). Default: 30. **--felix-tthrange-min=n** -: Low-level parameter for the Felix indexing algorithm. +: Minimum 2theta to consider for indexing (degrees). Default: 0. **--xgandalf-sampling-pitch=n** : Selects how dense the reciprocal space is sampled. [0-4]: extremelyLoose to -: extremelyDense. [5-7]: standardWithSeondaryMillerIndices to -: extremelyDenseWithSeondaryMillerIndices. Default is 6 -: (denseWithSeondaryMillerIndices). +: extremelyDense. [5-7]: standardWithSecondaryMillerIndices to +: extremelyDenseWithSecondaryMillerIndices. Default: 6 +: (denseWithSecondaryMillerIndices). **--xgandalf-grad-desc-iterations** : Selects how many gradient descent iterations are performed. [0-5]: veryFew to -: extremelyMany. Default is 4 (manyMany). +: extremelyMany. Default: 4 (manyMany). **--xgandalf-tolerance** -: relative tolerance of the lattice vectors. Default is 0.02. +: relative tolerance of the lattice vectors. Default: 0.02. **--xgandalf-no-deviation-from-provided-cell** : If a prior unit cell was provided, and this flag is set, the found unit cell @@ -682,14 +685,14 @@ INDEXING OPTIONS **--xgandalf-min-lattice-vector-length** **--xgandalf-min-lattice-vector-length** : Minimum and maximum possible lattice vector lengths (unit is A). Used for : fitting without prior lattice as starting point for gradient descent, so the -: final minimum lattice vector length can be smaller/highier as min/max. Note: +: final minimum lattice vector length can be smaller/bigger than min/max. Note: : This is valid for the uncentered cell, i.e. the P-cell! Default is 30A and 250A : respectively. **--xgandalf-max-peaks** : Maximum number of peaks used for indexing. For refinement all peaks are used. : Peaks are selected by increasing radius. Limits the maximum execution time for -: Patterns with a huge amount of peaks - either real ones or false positives. +: patterns with a huge amount of peaks - either real ones or false positives. : Default is 250. **--xgandalf-fast-execution** @@ -697,27 +700,28 @@ INDEXING OPTIONS **--pinkIndexer-considered-peaks-count** : Selects how many peaks are considered for indexing. [0-4] (veryFew to -: manyMany). Default is 4 (manyMany). +: manyMany). Default: 4 (manyMany). **--pinkIndexer-angle-resolution** : Selects how dense the orientation angles of the sample lattice are sampled. -: [0-4] (extremelyLoose to extremelyDense). Default is 2 (normal). +: [0-4] (extremelyLoose to extremelyDense). Default: 2 (normal). **--pinkIndexer-refinement-type** : Selects the refinement type. 0 = none, 1 = fixedLatticeParameters, 2 = : variableLatticeParameters, 3 = firstFixedThenVariableLatticeParameters, 4 = : firstFixedThenVariableLatticeParametersMultiSeed, 5 = -: firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed. +: firstFixedThenVariableLatticeParametersCenterAdjustmentMultiSeed. Default: 1 +: (fixedLatticeParameters). **--pinkIndexer-tolerance** : Selects the tolerance of the pinkIndexer (relative tolerance of the lattice -: vectors). Default is 0.06. For bad geometrys or cell parameters use a high +: vectors). For bad geometries or cell parameters use a high : tolerance. For a well known geometry and cell use a small tolerance. Only : important for refinement and indexed/not indexed identificaton. Too small : tolerance will lead to refining to only a fraction of the peaks and possibly : discarding of correctly indexed images. Too high tolerance will lead to bad -: Fitting in presence of multiples or noise and can mark wrongly-indexed patterns -: as indexed. +: fitting in presence of multiples or noise and can mark wrongly-indexed patterns +: as indexed. Default: 0.06. **--pinkIndexer-reflection-radius** : Sets radius of the reflections in reciprocal space in 1/A. Default is 2%% of a* @@ -726,14 +730,14 @@ INDEXING OPTIONS **--pinkIndexer-max-resolution-for-indexing** : Sets the maximum resolution in 1/A used for indexing. Peaks at high resolution -: Don't add much information, but they add a lot of computation time. Default is +: don't add much information, but they add a lot of computation time. Default is : infinity. Does not influence the refinement. **--pinkIndexer-max-refinement-disbalance** : Indexing solutions are dismissed if the refinement refined very well to one : side of the detector and very badly to the other side. Allowed values range : from 0 (no disbalance) to 2 (extreme disbalance), default 0.4. Disbalance after -: Refinement usually appears for bad geometries or bad prior unit cell +: refinement usually appears for bad geometries or bad prior unit cell : parameters. **--asdf-fast** |