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Diffstat (limited to 'doc/man/indexamajig.1')
| -rw-r--r-- | doc/man/indexamajig.1 | 42 |
1 files changed, 15 insertions, 27 deletions
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1 index e400c211..6dffdffd 100644 --- a/doc/man/indexamajig.1 +++ b/doc/man/indexamajig.1 @@ -41,11 +41,7 @@ Indexamajig requires an input file with a list of diffraction patterns ("events" .SH PEAK DETECTION -You can control the peak detection on the command line. Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR. There are three possibilities for "method" here. \fB--peaks=hdf5\fR will take the peak locations from the HDF5 file. It expects a two dimensional array, by default at /processing/hitfinder/peakinfo, whose size in the first dimension equals the number of peaks and whose size in the second dimension is three. The first two columns contain the fast scan and slow scan coordinates, the third contains the intensity. However, the intensity will be ignored since the pattern will always be re-integrated using the unit cell provided by the indexer on the basis of the peaks. You can tell indexamajig where to find this table inside each HDF5 file using \fB--hdf5-peaks=\fR\fIpath\fR. - -\fB--peaks=cxi\fR works similarly to this, but expects four separate HDF5 datasets beneath \fIpath\fR, \fBnPeaks\fR, \fBpeakXPosRaw\fR, \fBpeakYPosRaw\fR and \fBpeakTotalIntensity\fR. See the specification for the CXI file format at http://www.cxidb.org/ for more details. - -CrystFEL considers all peak locations to be distances from the corner of the detector panel, in pixel units, consistent with its description of detector geometry (see 'man crystfel_geometry'). The software which generates the HDF5 or CXI files, including Cheetah, may instead consider the peak locations to be pixel indices in the data array. Therefore, the peak coordinates from \fB--peaks=cxi\fR or \fB--peaks=hdf5\fR will by default have 0.5 added to them. Use \fB--no-half-pixel-shift\fR if this isn't what you want. +You can control the peak detection on the command line. Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR. \fB--peaks=hdf5\fR or \fB--peaks=cxi\fR will take the peak locations from the input file. See the documentation for \fBpeak_list\fR and \fBpeak_list_type\fR in crystfel_geometry(5) for details. If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000). You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-squared-gradient\fR. The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units. Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below). They will also be rejected if the peak is closer than twice the inner integration radius from another peak. @@ -147,7 +143,7 @@ Center the peak boxes iteratively on the actual peak locations. The opposite is .IP \fB-sat\fR .PD -Normally, reflections which contain one or more pixels above max_adu (defined in the detector geometry file) will not be integrated and written to the stream. Using this option skips this check, and allows saturated reflections to be passed to the later merging stages. This is not usually a good idea, but might be your only choice if there are many saturated reflections. The opposite is \fB-nosat\fR, which is the default for all integration methods. +Normally, reflections which contain one or more pixels above max_adu (defined in the detector geometry file) will not be integrated and written to the stream. Using this option skips this check, and allows saturated reflections to be passed to the later merging stages. The opposite is \fB-nosat\fR, which is the default for all integration methods. However, note that the saturation check will only be done if max_adu is set in the geometry file. Usually, it's better to exclude saturated reflections at the merging stage. The the documentation for max_adu in crystfel_geometry(5). .IP \fB-grad\fR .PD @@ -194,7 +190,7 @@ Prefix the filenames from the input file with \fIprefix\fR. If \fB--basename\fR .PD 0 .IP "\fB-j\fR \fIn\fR" .PD -Run \fIn\fR analyses in parallel. Default: 1. +Run \fIn\fR analyses in parallel. Default: 1. See also \fB--max-indexer-threads\fR. .PD 0 .IP \fB--no-check-prefix\fR @@ -389,6 +385,16 @@ Skip the prediction refinement step. Usually this will decrease the quality of Check that most of the peaks can be accounted for by the indexing solution. This usually increases the quality of the indexing solutions, but prevents "subtract and retry" multi-lattice indexing from working well. .PD 0 +.IP \fB--wavelength-estimate=\fIm\fR +.PD +Some indexing algorithms need to know the wavelength of the incident radiation in advance, e.g. to prepare an internal look-up table. However, if the wavelength is taken from image headers, then the wavelength is not available at start-up. In this case, you will be prompted to add this option to give an approximate wavelength, in metres. A warning will be generated if the actual wavelength differs from this value by more than 10%. + +.PD 0 +.IP \fB--max-indexer-threads=\fIn\fR +.PD +Some indexing algorithms (e.g. pinkIndexer) can use multiple threads for faster calculations. This is in addition to the frame-based parallelism already available in indexamajig (see \fB-j\fR). This option sets the maximum number of threads that each indexing engine is allowed to use. Default: 1. + +.PD 0 .IP \fB--taketwo-member-threshold=\fIn\fR .IP \fB--taketwo-len-tolerance=\fIn\fR .IP \fB--taketwo-angle-tolerance=\fIn\fR @@ -445,13 +451,7 @@ These set low-level parameters for the XGANDALF indexing algorithm. .IP \fB--pinkIndexer-tolerance=\fIn\fR .IP \fB--pinkIndexer-reflection-radius=\fIn\fR .IP \fB--pinkIndexer-max-resolution-for-indexing=\fIn\fR -.IP \fB--pinkIndexer-multi\fR -.IP \fB--pinkIndexer-thread-count=\fIn\fR -.IP \fB--pinkIndexer-no-check-indexed\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 .PD These set low-level parameters for the PinkIndexer indexing algorithm. @@ -466,21 +466,9 @@ These set low-level parameters for the PinkIndexer indexing algorithm. .IP \fB--pinkIndexer-reflection-radius\fR sets radius of the reflections in reciprocal space in 1/A. Default is 2%% of a* (which works quiet well for X-rays). Should be chosen much bigger for electrons (~0.002). .IP -\fB--pinkIndexer-max-resolution-for-indexing\fR sets the maximum resolition 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 infinity. Does not influence the refinement. -.IP -\fB--pinkIndexer-multi\fR Use pinkIndexers own multi indexing. Should be combined with the --no-multi flag. -.IP -\fB--pinkIndexer-thread-count\fR sets the thread count for internal parallelization. Default is 1. Very useful for small datasets (e.g. for screening). Internal parallelization does not significantly increase the amount of RAM needed, whereas CrystFEL's parallelization does. For HPCs typically a mixture of both parallelizations leads to best results. -.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 +\fB--pinkIndexer-max-resolution-for-indexing\fR 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 infinity. Does not influence the refinement. .IP -\fB--pinkIndexer-override-visible-energy-range=\fImin-max\fR Overrides photon energy and bandwidth according to a range of energies that have high enough intensity to produce visible Bragg spots on the detector. min and max range borders are separated by a minus sign (no whitespace). +\fB--pinkIndexer-max-refinement-disbalance\fR 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. .SH INTEGRATION OPTIONS .PD 0 |