Kick powder_plot out (to crystfel-programs)

1 files changed, 0 insertions, 159 deletions

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) .