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| author | Yaroslav Gevorkov <yaroslav.gevorkov@desy.de> | 2020-03-03 00:17:57 +0100 |
|---|---|---|
| committer | Thomas White <taw@physics.org> | 2020-03-04 10:02:08 +0100 |
| commit | ad0e55f5e1cd8fcf092d4883e16c9fe5608c428f (patch) | |
| tree | 5e79ed18426437f08b010dcdacc9af5c6ea90674 /doc | |
| parent | 9560b439213a51898d0c018ffc3e1fdc8bcaddbd (diff) | |
add option -pinkIndexer-max-refinement-disbalance
Diffstat (limited to 'doc')
| -rw-r--r-- | doc/man/indexamajig.1 | 3 |
1 files changed, 3 insertions, 0 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index 7bc71471..c9e156e3 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -448,6 +448,7 @@ These set low-level parameters for the XGANDALF indexing algorithm. .IP \fB--pinkIndexer-multi=\fIn\fR .IP \fB--pinkIndexer-thread-count=\fIn\fR .IP \fB--pinkIndexer-no-check-indexed=\fIn\fR +.IP \fB--pinkIndexer-max-refinement-disbalance=\fIn\fR .IP \fB--pinkIndexer-override-bandwidth=\fIn\fR .IP \fB--pinkIndexer-override-photon-energy=\fIn\fR .IP \fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR @@ -473,6 +474,8 @@ These set low-level parameters for the PinkIndexer indexing algorithm. .IP \fB--pinkIndexer-no-check-indexed\fR Leave the check whether a pattern is indexed completely to CrystFEL. Useful for monochromatic (since CrystFEL's prediction model is smarter than the one of pinkIndexer) or in combnation with --no-check-peaks for geometry optimization. This flag is meant to eventually disappear, when the full pink pipeline is implemented. .IP +\fB--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 parameters. +.IP \fB--pinkIndexer-override-bandwidth=\fIn\fR Overrides the bandwidth in (delta energy)/(mean energy) to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-photon-energy=\fIn\fR. Note: this option sets the borders for the spectrum, whereas the option in the geometry file sets the standard deviation for a Gaussian that fits the spectrum. Internally, the standard deviation is multiplied by 5 to compute the hard borders of the spectrum. I.e., photon_energy_bandwith = 0.005 in the geometry file equals --pinkIndexer-override-bandwidth=0.025. For monochromatic experiments usually --pinkIndexer-override-bandwidth=0.02 is sufficiently large. If in doubt, use --pinkIndexer-override-visible-energy-range. .IP \fB--pinkIndexer-override-photon-energy=\fIn\fR Overrides the mean energy in eV to use for indexing (which usually is defined in the geometry file). Should be used together with \fB--pinkIndexer-override-bandwidth=\fIn\fR |