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\" 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 HDF5 file. It sums the many individual intensities, Bragg peaks or pixel
locations in the HDF5 file, together to form a 1D powder histogram.
The output of powder_plot consists of a three line header followed by a tab
delimited list of 6 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 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 1/d value [units are inverse meters]
with: --min=<number> and --max=<number> The default value is to use the
entire detector setup in the .geom file (loaded with the -g flag).
You can also adjust the number of histogram bins with:
--bins=<intiger>
Scaling can be set to produce linearly, quadratically or cubicly spaced 1/d
values using: --spacing=<type> possible types are:
linear : linear (default)
wilson : even spacing in Wilson plots (quadratic)
volume : constant volume (cubic)
.SH DATA TYPE OPTIONS
Powder_plot can accept .stream, .hkl, or HDF5 files as input parameters. For
the stream many choices exist for assembling the powder these can be accessed
using the --data=<type> flag. Possible flags are:
reflection : uses peak positions 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 HDF5, excluding bad regions
Reflection differs from hkl or d as each crystal may index with a slightly
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 patterns that do not index.)
--no-d-scaling Use with .hkl files if you want to not scale the powder by d^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 symmetrical equivalent 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 HDF5 files from a list of HDF5 files. This
task is already accomplished with sum_stack. The output HDF5 file of sum_stack
can then be used as the input to powder_plot. This will produce the goal of
summing a list of HDF5 files into a powder. Also powder_plot can sum HDF5 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.
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