From e23381049dcdbd2c3f1f39276adb3c466d646868 Mon Sep 17 00:00:00 2001 From: Thomas White Date: Wed, 3 Aug 2011 16:58:44 +0200 Subject: Fussiness --- doc/man/powder_plot.1 | 37 ++++++++++++++++++------------------- 1 file changed, 18 insertions(+), 19 deletions(-) (limited to 'doc') diff --git a/doc/man/powder_plot.1 b/doc/man/powder_plot.1 index a28a7459..45f10eca 100644 --- a/doc/man/powder_plot.1 +++ b/doc/man/powder_plot.1 @@ -17,35 +17,34 @@ powder\_plot \- 1D powder pattern generating program .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. +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 2 line header followed by a tab -delimitated list of 6 values: +The output of powder_plot consists of a two line header followed by a tab +delimited list of 6 values: q of the histogram bin the total number of peaks (N) - the total intensity in the N peaks + 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, +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 +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. +selected. .SH HISTOGRAM OPTIONS -You can choose to set the min and maximum q value [units are inverse meters] -with: --q_min= and --q_max= The default value is to use the +You can choose to set the min and maximum q value [units are inverse meters] +with: --q_min= and --q_max= 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: @@ -59,15 +58,15 @@ values using: --spacing= possible types are: .SH DATA TYPE OPTIONS -Powder_plot can accept .stream, .hkl, or .h5 files as input parameters. For +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= flag. Possible flags are: - reflection : uses peak positions from indexed reflection - hkl : uses the hkl list from indexed reflections (requires pdb + 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 h5, excluding bad regions + 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 @@ -82,9 +81,9 @@ A few other implemented flags to give better control are: .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 +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 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, +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. -- cgit v1.2.3