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authorThomas White <taw@physics.org>2011-08-03 16:58:44 +0200
committerThomas White <taw@physics.org>2012-02-22 15:27:35 +0100
commite23381049dcdbd2c3f1f39276adb3c466d646868 (patch)
treeec590ec6908f15f4a1949b3781278ff463d0cdd5 /doc/man
parent9b57e5e44a0f6d47db318285c58f0f0b5ca9e36f (diff)
Fussiness
Diffstat (limited to 'doc/man')
-rw-r--r--doc/man/powder_plot.137
1 files changed, 18 insertions, 19 deletions
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=<number> and --q_max=<number> 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=<number> and --q_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:
@@ -59,15 +58,15 @@ values using: --spacing=<type> 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=<type> 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.