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diff --git a/doc/man/powder_plot.1 b/doc/man/powder_plot.1 deleted file mode 100644 index 6dac163f..00000000 --- a/doc/man/powder_plot.1 +++ /dev/null @@ -1,159 +0,0 @@ -.\" powder_plot man page -.\" -.\" Copyright © 2012 Andrew Aquila <andrew.aquila@cfel.de> -.\" Copyright © 2012 Thomas White <taw@physics.org> -.\" -.\" Part of CrystFEL - crystallography with a FEL -.\" - -.TH POWDER_PLOT 1 -.SH NAME -powder_plot \- generate 1D powder patterns -.SH SYNOPSIS -.PP -.B powder_plot -\fB-i\fR \fIinput.hkl\fR | \fB-i\fR \fIinput.h5\fR | \fB-i\fR \fIinput.stream\fR -\fB-o\fR \fIoutput.dat\fR -[\fB--min=\fR\fI1/d\fR \fB--max=\fR\fI1/d\fR] -[\fIoptions\fR\] \fB...\fR - -.PP -.BR powder_plot -\fB-i\fR \fIfile.hkl\fR [\fIoptions\fR\] \fB...\fR [\fB--use-redundancy\fR] [\fB--no-d-scaling\fR] - -.PP -.BR powder_plot -\fB-i\fR \fIfile.h5\fR [\fIoptions\fR\] \fB...\fR -\fB-g\fR \fIgeometry.geom\fR -\fB-b\fR \fIbeam.beam\fR [\fB--no-sat-corr\fR] [\fB--ring-corr\fR] - -.PP -.BR powder_plot -\fB-i\fR \fIfile.stream\fR [\fIoptions\fR\] \fB...\fR --data=\fItype\fR -[-g \fIgeometry.geom\fR] [-b \fIbeam.beam\fR] [\fB--no-sat-corr\fR] [\fB--only-indexed\fR] -[\fB--use-redundancy\fR] [\fB--ring-corr\fR] [\fB--no-d-scaling\fR] - -.PP -.BR powder_plot -\fB--help\fR - -.SH DESCRIPTION - -powder_plot calculates one dimensional powder traces by summing many individual intensities, Bragg peaks or pixels. Its input can come from a CrystFEL stream (such as that written by "indexamajig"), an reflection list in CrystFEL format (".hkl" format), or an HDF5 file. - -The output of powder_plot consists of a three line header followed by a tab-delimited list of six values: - - 1/d of the histogram bin, where d is the Bragg law d spacing in meters - the total number of peaks (N) - the total intensity in the N peaks - the mean intensity of the N peaks - the standard deviation of the distribution - the standard deviation of the mean of the data - -The sigma of the mean is not the same as the sigma of the intensities -themselves. The former quantity measures how accurately the mean intensity has -been determined, whereas the latter quantity measures the spread of the -intensities. - -.SH DATA TYPE OPTIONS WHEN READING FROM A STREAM - -When taking input from stream, the d-spacing for a particular intensity can be -generated in a variety of different ways. You can choose which one with -\fB--data=\fR\fItype\fR. Possibilities for \fItype\fR are: -.RS -.IP \fBreflection\fR -.PD -Use peak positions from indexed reflections -.IP \fBhkl\fR -.PD -Use the Miller indices from indexed reflections, combined with a unit cell from PDB file provided with -p. -.IP \fBpeaks\fR -.PD -Use peak positions from peak search -.IP \fBh5\fR -.PD -Use all pixels in the HDF5 file, excluding bad regions -.RE -.PP -The default is \fB--data=hkl\fR. - - -.SH HISTOGRAM OPTIONS - -You can set the mininum and maximum 1/d values, in units of inverse meters, -with the options \fB-min=\fR\fIn\fR and \fB--max=\fR\fIn\fR. -When taking input from peak positions, The default behaviour is to use the entire detector extent from the geometry description file, which you with the \fB-g\fR flag. - -You can also adjust the number of histogram bins with the option --bins=<n>, -where n is an integer. - -Scaling can be set to produce linearly, quadratically or cubically spaced 1/d -values using \fB--spacing=\fR\fItype\fR. Possibilities for \fItype\fR are: -.RS -.IP \fBlinear\fR -.PD -The resolution shells will have equal widths in terms of 1/d. -.IP \fBwilson\fR -.PD -The resolution shells will be quadratically spaced, giving even spacing in a plot against 1/d^2 (a Wilson plot). -.IP \fBvolume\fR -.PD -The resolution shells will all have equal volumes in reciprocal space. -.RE -.PP -The default is \fB--spacing=linear\fR. - -.SH OPTIONS FOR MORE CONTROL - -.B -.IP --no-sat-corr -Don't correct values of saturated peaks using the table included in the HDF5 file. -See the help for indexamajig for more information. - -.B -.IP --only-indexed -Use with --data=peaks or h5 if you want to use the peak list of only indexed patterns. -This is useful for finding differences between patterns which could be indexed and -those which could not. - -.B -.IP --no-d-scaling -Do not scale the intensities in the powder plot by d^2. This should be used when -creating a powder plot from a reflection list. - -.B -.IP --ring-corr -Do not correct for the fractional area sampled of the powder ring. This might be -useful for detectors with gaps. - -.B -.IP --use-redundancy -Divide intensities by the number of measurements (the redundancy column in the -reflection list), and not the number of symmetrical equivalent reflections as the -number of times a reflection occurs in the powder. - -.SH AUTHOR -This page was written by Andrew Aquila and Thomas White. - -.SH REPORTING BUGS -Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>. - -.SH COPYRIGHT AND DISCLAIMER -Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. -.PD -.P -powder_plot, and this manual, are part of CrystFEL. -.P -CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. -.P -CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. -.P -You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. - -.SH SEE ALSO -.BR crystfel (7), -.BR indexamajig (1), -.BR process_hkl (1), -.BR check_hkl (1), -.BR crystfel_geometry (5), -.BR render_hkl (1) . |