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diff --git a/doc/man/powder_plot.1 b/doc/man/powder_plot.1 new file mode 100644 index 00000000..48899114 --- /dev/null +++ b/doc/man/powder_plot.1 @@ -0,0 +1,106 @@ +.\" +.\" powder_plot man page +.\" +.\" (c) 2011 Andrew Aquila <andrew.aquila@cfel.de> +.\" (c) 2009-2011 Thomas White <taw@physics.org> +.\" +.\" Part of CrystFEL - crystallography with a FEL +.\" + +.TH POWDER\_PLOT 1 +.SH NAME +powder\_plot \- 1D powder pattern generating program +.SH SYNOPSIS +.PP +.B powder\_plot +-i mypatterns.stream -o mydata.dat [options] + +.SH DESCRIPTION + +This program takes as input the data stream from "indexamajig" or an hkl file, +or an h5 file. It sums the many individual intensities, Bragg peaks or pixel +location in the h5 file, together to form a 1D powder histogram which is +useful for crystallography. + +The output of powder_plot consists of a 2 line header followed by a tab +delimitated list of 6 values: + +q of the histogram bin +the total number of peaks (N) +the total intensity in the N peaks +the mean intensity of the N peaks +the 1 sigma (standard deviation) of the distribution +the 1 sigma (standard deviation) of the mean of the data + +Please note that the sigma of the mean is not the sigma of the distribution, +however they are related by the sqrt(N). + +Typical usage is of the form: + +$ powder_plot -i mypatterns.stream -o mydata.dat [options] + +The options include added geometry, beam, pdb files or symmetry elements. The +program will prompt you as needed depending on the file type and data types +selected. + +.SH HISTOGRAM OPTIONS + +You can choose to set the min and maximum q value [units are inverse meters] +with: +--q_min=<number> +and +--q_max=<number> +The default value is to use the entire detector setup in the .geom file +(loaded wiht the -g flag). + +You can also adjust the number of histogram bins wiht: +--bins=<intiger> + +Scaling can be set to produce linearly, quadratically or cubicly spaced q +values using: + --spacing=<type> possible types are: + linear : linear (default) + q2 : even spacing in Wilson plots (quadratic) + volume : constant volume (cubic) + +.SH DATA TYPE OPTIONS + +Powder_plot can accept .stream, .hkl, or .h5 files as input parameters. For +the stream many choices exist for assembling the powder these can be accesed +using the --data=<type> flag. Possible flags are: + reflection : uses peak positons from indexed reflection + hkl : uses the hkl list from indexed reflections (requires pdb + file) + d : uses the 1/d list from indexed reflections (default) + peaks : uses all peaks found from peak search + h5 : all points in h5, excluding bad regions + +Reflection differs from hkl or d as each crystal may index with a sligtly +different unit cell size. The peaks option uses the peak lists and includes +and peaks (regardless if they indexed). + +A few other implemented flags to give better control are: +--no-sat-corr Don't correct values of saturated peaks using a table included + in the HDF5 file. +--only-indexed Use with -data=peaks or h5 if you want to use the peak list of + only indexed patterns. (Useful for seeing changes from paterns + that do not index.) +--no-q-scaling Use with .hkl files if you want to not scale the powder by 1/q^2 +--ring-corr Use if you want to scale the powder plot to correct for the + fractional area sampled of the powder ring. (Useful for + detectors with gaps.) +--use-redundancy Use with .hkl files if you want to use the number of + measurements and not the number of symetrical equivelent + reflections as the number of time a reflection occurs + in the powder + +.SH NOTE ON SUMMING H5 FILES + +Powder_plot does not sum a stack of h5 files from a list of h5 files. This +task is already accomplished with sum_stack. The output h5 file of sum_stack +can then be used as the input to powder_plot. This will produce the goal of +summing a list of h5 files into a powder. Also powder_plot , can sum h5 files +if they are located in a .stream file. This is useful with the --only-indexed, +to compare the powder from all the data to the power from only indexed patterns. + + |