Table of Contents
imgcvt - image format conversion for Dectris CBF images and mar images
into HDF5, TIFF, raw integer, Bruker sfrm, mrcfile
imgcvt [ -h
(--help) ] [ -a (--add) N ] [ -c (--cfg) configuration file ] [ -C (--compressor)
COMPRESSOR ] [ --data ] [ -o (--dir) OUTDIR ] [ -D (--deb=DEBUG) ] [ -g (--gui) ]
[ --gz (--gzip) ] [ -i (--infile) file ] [ --blz4 ] [ --lzf ] [ --cbf ] [ --h5 ] [ --int16
] [ --int32 ] [ --mrc ] [ --mrc1 ] [ --sfrm ] [ --tiff16 ] [ --tiff32 ] [ -S (--subdir)
] [ -f (--ffrm) FFRM ] [ -l (--lfrm) LFRM ] [ -k (--kfrm) KFRM ] [ -n (--nfrm) NFRM
] [ -F (--ff) ] [ -m (--master) ] [ -M (--pm) ] [ --mask FILE ] [ --raw [WxH][xBPP][+offset]
] [ -T (--tool) NAME ] [ -v (--verbose) ] [ -V (--VERSION) ] [ filename ]
imgcvt
is a console program with optional graphical user interface for converting
X-ray diffraction images into other formats (tiff, sfrm, hdf5, mar345, marccd,
raw integer, mrc). Other than most other diffraction images, HDF5 files
often consist of one or more data files that may contain a large number
of actual diffraction images and a "master" file that carries information
common to all data, typically the goniometer data and other parameters
that describe the experiment. Also the mrc format common in electron microscopy
as well as the tiff files may contain multiple images in one file. The program
imgcvt currently supports the following input formats:
- cbf (all sorts)
- sfrm
- tiff32 (32 bit data)
- tiff16 (16 bit data)
- mar345
- mar300
- marccd
- int16
- int32
- h5
- -a (--add) N
- Add N images up before writing into an output file.
- -c
(--cfg) FILE
- FILE is a configuration file for specifying header information
for output files, in particular for use with h5 and cbf files. See section
CONFIGURATION FILE for details
- -C (--compressor) COMPRESSOR
- HDF5 output only:
COMPRESSOR can be one of "blz4" (default), "lzf", "gzip" or "None". Data
conversion without compression is much faster but the resulting hdf5-files
will be about 50-90% larger than with "blz4" compression.
- -D--deb=DEBUG
- Hexadecimal
debug code
- --data
- HDF5 output only: create data files, mo master file. By
default, the program produces both data and master files.
- -F (--ff)
- HDF5 input
only: when given, a flatfield mask will be extracted from the input master
file - if it exists - and written out as TIFF file. The name of the output
file will be {rootname}_flatfield.bin
- -g, (--gui)
- Start the program with a
graphical user interface. The GUI allows for loading images and also modifying
header values. If no input file is given, the program automatically start
in GUI mode.
- --gz --gzip
- HDF5 output only: use gzip compression instead of
blz4.
- -i (--infile) FILE
- Optional input file parameter. The input file should
have the general form prefix_###.suffix, where ### (or more #) is a running
image number. You may either use the hashtag character or an actual numeric
value. Either way, the program converts the string into a template.
- -h (--help)
- Prints a summary of program command line options.
- --cbf
- Use cbf as output
format.
- --int16
- Use 16-bit integers as output format without header.
- --int32
- Use
32-bit integers as output format without header.
- --mrc
- Write all data of the
series into a single file in MRC format. Data are stored as 16-bit unsigned
integers with all values exceeding 16-bits set to 0.
- --mrc1
- For each input
file, write a separate file in MRC format, i.e. the output images only contain
data from a single image.
- --sfrm
- Use Bruker sfrm as output format for use
with APEX4.
- --tiff16
- Use 16-bit TIFF as output format.
- --tiff32
- Use 32-bit TIFF
as output format.
- -T (--tool) NAME
- Use tool NAME in computations
- -f (--ffrm) FFRM
- Starting frame of series.
- -l (--lfrm) LFRM
- Ending frame of series.
- -k (--kfrm)
KFRM
- When creating output images, start numbering with KFRM. By default,
the numbers of input files will be used.
- -n (--nfrm) NFRM
- HDF5 output only:
put up to NFRM images into each hdf5 data file.
- -m (--master)
- HDF5 output only:
when given, no data files will be produced but only a master file.
- -M (--pm)
- HDF5 input only: when given, a bad pixel mask will be extracted from the
input master file - if it exists - and written out as TIFF file. The name
of the output file will be {rootname}_mask.tif
- --mask
- HDF5 output only: when
given, no data files will be produced but only a master file.
- -o (--dir) OUTDIR
- The o/p=files will be written to OUTDIR when given. Otherwise, depending
on the chosen output format a subdirectory "tiff16", "tiff32", "sfrm",
"int16", "int32" or "h5" will be used. If the subdirectory does not exist,
it will be created.
- --raw=WxH[xBPP][+OFFSET]
- When processing raw images, the
program needs to know the pixels in x (W) and y (H) and the bytes per pixel
(BPP, defaults to 4). If the images have headers with a fixed length, you
need to provide the corresponding number of bytes as OFFSET.
- -S (--subdir)
- If specified, output files will be written in a subdirectory of the directory
where the input file comes from. The name of the subdirectory depends on
the output format. E.g.: if "sfrm" is the output format, a subdirectory sfrm
will be created.
- -T (--tool) NAME
- The program can also be used for special
purposes by calling tools. Currently, the following tools are implemented:
- mask - Creates a bad pixelmask. This expects a h5 master file as input and
a couple of tens to hundreds of empty image data. The tools writes a bad
pixel mask into a tif file called {rootname}_mask.tif that contains bad
pixels marked with value 16, good pixels are 0.
- direct[:N] - Computes the
direct beam coordinagtes from a series of images. The optional parameter
N specifies the search radius around the center coordinates as given in
the input file. Default for N is 8 pixels. See section DIRECT BEAM for more
details
- bkg - Computes a background table from a series of images. When working
with single crystal diffraction images This works better the more images
are contained within the series in order to remove diffraction spots. The
resulting background table is written out in TIFF format.
- peaks - Extract
diffraction spots from an image or a series of images. The diffraction
spots are written out as ASCII file into a file with extension .pks that
can be read by marIndex or other crystal indexing programs. It contains
spot coordinates, spot size, I/Sigma and number of pixels contributing
to the spot.
- -v (--verbose)
- Increases verbosity level for more program output.
- -V (--VERSION)
- Only show program version and exit.
- filename
- Any argument not
given with any of the keywords above will be treated as input file argument.
The graphical user interface should be self-explaining. Afer loading
an initial image, the header information is extracted and entered into
the corresponding fields. If you edit any of the header fields, modified
values will change the color. The values given here will end up in the HDF5-headers
unless they are overwritten by program initialization file (see below).
Please note, that the distance shown in the header file is given in mm
for sake of clarity. In the HDF5, the distance usually is given in meters.
The conversion will be done automatically.
The ELDICO electron
diffractometer does not have a beam stop, so the direct beam is visible
in diffraction images unless the beam hits solid parts of the sample holder.
The direct beam is the most accurate value for the origin of diffraction,
a parameter that is very important to be accurate in most data processing
programs. It is especially important to rely on it because in small molecule
sample there may not be sufficient reflections to refine the center coordinates
from. When using tool "direct", the conversion program takes the center
coordinates of the input file and looks in a radius of N pixels (N=8 by
default) for pixel values > 10000. For all selected pixels in a rectangular
area of NxN pixels around that given center, a center of gravity is computed.
When processing a series of images, in a first round only the average center
of all input images is computed and then applied to the converted images
in a second round. The search radius N can be modified by adding argument
:N to "direct" like in "direct:10".
The program automatically
determines wether a selected file is an implemented image format and loads
the file accordingly. The following image formats are implemented:
- cbf:
- Images in "CBF" format or miniCBF format (DECTRIS).
- mar345:
- Images in mar345
format. Usual extensions: .marXXXX where XXXX is 1200, 1600, 1800, 2000,
2300, 2400, 2560, 1536, 3000, 3072 or 3450
- marCCD:
- Images in marCCD format.
No standard extension
- h5:
- hdf5 files as produced by Dectris detectors (master
and data files)
- sfrm:
- Bruker sfrm formatted images
- tiff:
- TIFF files (8,
16, 32-bit integers, also floats)
- mrc:
- MRC files with one or more images.
When using HDF5 output, the program produces both master and
data files by default. The master file has no actual image data but only
information describing the experiment. The data files can be a single file
containing thousands of diffraction images. If you like, you may also produce
an data file for each single input file, which is less efficient. This
can be done by providing the input option "-nfrm" on the command line or
by setting the value for "# images/h5" in the GUI. By default, all images
found in a directory will go into one data file.
TIFF output comes in 2
flavours:
- 16-bit data (tiff16)
- 32-bit data (tiff32)
When using tiff16,
input data are truncated to 16-bits (65535). The file contains a plain array
of x*y 16 bit data. When using tiff32, x*y 32-bit values are written into
the file.
When using raw image output, a plain array of x*y 16-bit (int16)
or 32-bit (int32) data is generated. The output file comes without header.
When using sfrm output (default), images are written in Bruker 100 format.
When using mrc, input data are truncated to 16-bits (65535). The file contains
a plain array of x*y 16 bit data. One mrc file may contain multiple images.
A mrc-file containing multiple images can be used as input file. It will
produce as many output files as there are entries in the file.
The program reads a Windows type configuration file from the following
locations (in the order of precedence):
Following the convention of .ini-files on Windows,
the program reads configuration values from the section starting with line:
[imgcvt]
All further entries given here will go into the output master
file and values read from input image headers or those given in the GUI
will be ignored! Therefore, you should only provide parameters in the configuration
file that you would consider to be static. While you are allowed to give
goniometer parameters like "phi", it is not recommended to do that here.
Please see the section COMPLETE EXAMPLE, but refrain from using the goniometer
parameters.
[imgcvt]
wavelength=1.3477
detector_distance=120.0
bit_depth_readout=16
element="Cu"
wavelength=1.541789
beam_center_x=1150.0
beam_center_y=1150.0
frame_period=10.0
frame_time=10.0
bit_depth_readout=32
sensor_material="Silicon"
description="None"
detector_number="000-000"
sensor_thickness=0.00450
threshold_energy=4000
detector_distance=120.0
two_theta=0.0
two_theta_start=0.0
two_theta_end=0.0
two_theta_increment=0.0
two_theta_range_total=0.0
two_theta_range_average=0.0
kappa=0.0
kappa_start=0.0
kappa_end=0.0
kappa_increment=0.0
kappa_range_total=0.0
kappa_range_average=g
omega=0.0
omega_start=0.0
omega_end=0.0
omega_increment=0.0
omega_range_total=0.0
omega_range_average=0.0
chi=0.0
chi_start=0.0
chi_end=0.0
chi_increment=0.0
chi_range_total=0.0
chi_range_average=0.0
phi=0.0
phi_start=0.0
phi_end=0.0
phi_increment=0.0
phi_range_total=0.0
phi_range_average=0.0
marcvt
Claudio Klein, Marxperts GmbH, Norderstedt, Germany
© Copyright 2022 Marxperts GmbH, Norderstedt, Germany
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