.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.48.5.
.TH SPARSIFY-BRAGG "1" "November 2021" "sparsify-Bragg 0.20.0" "User Commands"
.SH NAME
sparsify-Bragg \- Sparsify 2D single crystall diffraction images by separating Bragg peaks from background signal.

Positive outlier pixels (i.e. Bragg peaks) are all recorded as they are without destruction. 
Peaks are not integrated.

Background is calculated by an iterative sigma-clipping in the polar space. 
The number of iteration, the clipping value and the number of radial bins could be adjusted.

This program requires OpenCL. The device needs be properly selected.
.SH DESCRIPTION
usage: spasify\-Bragg [\-h] [\-V] [\-v] [\-\-debug] [\-o OUTPUT] [\-\-save\-source]
.TP
[\-b BEAMLINE] [\-p PONI] [\-m MASK] [\-\-dummy DUMMY]
[\-\-delta\-dummy DELTA_DUMMY]
[\-\-radial\-range RADIAL_RANGE RADIAL_RANGE] [\-\-bins BINS]
[\-\-cycle CYCLE] [\-\-cutoff\-clip CUTOFF_CLIP]
[\-\-cutoff\-pick CUTOFF_PICK] [\-\-error\-model ERROR_MODEL]
[\-\-noise NOISE] [\-\-device DEVICE DEVICE]
[\-\-device\-type DEVICE_TYPE]
[IMAGE ...]
.PP
Sparsify 2D single crystall diffraction images by separating Bragg peaks from
background signal. Positive outlier pixels (i.e. Bragg peaks) are all recorded
as they are without destruction. Peaks are not integrated. Background is
calculated by an iterative sigma\-clipping in the polar space. The number of
iteration, the clipping value and the number of radial bins could be adjusted.
This program requires OpenCL. The device needs be properly selected.
.SS "positional arguments:"
.TP
IMAGE
File with input images. All frames will be
concatenated in a single HDF5 file.
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-V\fR, \fB\-\-version\fR
output version and exit
.TP
\fB\-v\fR, \fB\-\-verbose\fR
show information for each frame
.TP
\fB\-\-debug\fR
show debug information
.SS "main arguments:"
.TP
\fB\-o\fR OUTPUT, \fB\-\-output\fR OUTPUT
Output filename
.TP
\fB\-\-save\-source\fR
save the path for all source files
.SS "Experimental setup options:"
.TP
\fB\-b\fR BEAMLINE, \fB\-\-beamline\fR BEAMLINE
Name of the instument (for the HDF5 NXinstrument)
.TP
\fB\-p\fR PONI, \fB\-\-poni\fR PONI
geometry description file
.TP
\fB\-m\fR MASK, \fB\-\-mask\fR MASK
mask to be used for invalid pixels
.TP
\fB\-\-dummy\fR DUMMY
value of dynamically masked pixels
.TP
\fB\-\-delta\-dummy\fR DELTA_DUMMY
precision for dummy value
.TP
\fB\-\-radial\-range\fR RADIAL_RANGE RADIAL_RANGE
radial range as a 2\-tuple of number of pixels, by
default all available range
.SS "Sigma-clipping options:"
.TP
\fB\-\-bins\fR BINS
Number of radial bins to consider
.TP
\fB\-\-cycle\fR CYCLE
precision for dummy value
.TP
\fB\-\-cutoff\-clip\fR CUTOFF_CLIP
Threshold to be used when performing the sigmaclipping
.TP
\fB\-\-cutoff\-pick\fR CUTOFF_PICK
Threshold to be used when picking the pixels to be
saved
.TP
\fB\-\-error\-model\fR ERROR_MODEL
Statistical model for the signal error, may be
`poisson`(default) or `azimuthal` (slower)
.TP
\fB\-\-noise\fR NOISE
Noise level: n\-sigma cannot be smaller than this value
.SS "Opencl setup options:"
.TP
\fB\-\-device\fR DEVICE DEVICE
definition of thee platform and device identifyer: 2
integers. Use `clinfo` to get a description of your
system
.TP
\fB\-\-device\-type\fR DEVICE_TYPE
device type like `cpu` or `gpu` or `acc`. Can help to
select the proper device.
.PP
Current status of the program: status