File hdf52smv.1 of Package crystfel-extra

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File hdf52smv.1 of Package crystfel-extra

.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH HDF52SMV "1" "October 2013" "hdf52smv 0.0.1" "User Commands"
.SH NAME
hdf52smv \- a CrystFEL program to convert hdf5 diffraction images to img format
.SH DESCRIPTION
Syntax: hdf52smv/hdf52smv [options]
.PP
Convert .hdf5 diffraction images to .img.
.TP
\fB\-h\fR, \fB\-\-help\fR
Display the help message.
.TP
\fB\-i\fR, \fB\-\-input=\fR<filename>
Specify file containing list of images to process.
\&'\-' means stdin, which is the default.
Output files (.img) will be written to the same
directory as the hdf5's. The option to put all
files to a specified dir will be added later.
.TP
\fB\-\-basename\fR
Remove the directory parts of the filenames.
.TP
\fB\-x\fR, \fB\-\-prefix=\fR<p>
Prefix filenames from input file with <p>.
.TP
\fB\-g\fR, \fB\-\-geometry=\fR<file>
Get detector distance from geometry file.
.TP
\fB\-m\fR, \fB\-\-pixelmap=\fR<file>
Get pixelmap for 2D assembly.
.TP
\fB\-b\fR, \fB\-\-beam=\fR<file>
Get beam parameters from file (provides nominal
wavelength value if no per\-shot value is found in
the HDF5 files).
.TP
\fB\-e\fR, \fB\-\-image=\fR<element>
Use this image from the HDF5 file.
Example: \fI/data/data0\fP.
Default: The first one found.
.TP
\fB\-\-offset=\fR<n>
Make pixels have positive values only (add constant
value to all pixels based on minimum valued pixel)
and set <n> as ADCOFFSET. Must use this for (e.g.)
.IP
MOSFLM if there are negative intensities.
.TP
\fB\-\-no\-sat\-corr\fR
Don't correct values of saturated peaks using a
table included in the HDF5 file.
.TP
\fB\-\-no\-check\-prefix\fR
Don't attempt to correct the \fB\-\-prefix\fR.
.TP
\fB\-j\fR <n>
Run <n> conversions in parallel.  Default 1.
.PP
You can tune the CPU affinities for enhanced performance on NUMA machines:
.TP
\fB\-\-cpus=\fR<n>
Specify number of CPUs.  This is NOT the same as
giving the number of analyses to run in parallel.
.TP
\fB\-\-cpugroup=\fR<n>
Batch threads in groups of this size.
.TP
\fB\-\-cpuoffset=\fR<n>
Start using CPUs at this group number.

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