Name

Synopsis

Description

• cbf (all sorts)
• sfrm
• tiff32 (32 bit data)
• tiff16 (16 bit data)
• mar345
• mar300
• marccd
• int16
• int32
• h5
  

Options

-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

--colors MIN MAX

PNG output only: when converting diffraction data into graphics formats, pixel values will be assigned to a color (grays). All pixels <= MIN will be painted in white, all pixels >= MAX will be painted black and 255 grays will be distributed inbetween MIN and MAX. By default, the program obtains suitable thresholds from a histogram, so there should normally not be a need to specify the color thresholds explicitely.

-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.

--png

Convert diffraction images into PNG graphics formats. Please note, that graphics formats cannot be converted back into diffraction data without significant loss of information.

--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.

GUI

Direct Beam

Input Files

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.

Output Files

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.

When using png, input data are converted into 255 grayscales. The program tries to distribute the colors based on a pixel intensity histogram. With option --colors it is possible, however, to assign specific values to the color thresholds.

Configuration File

• ./imgcvt.cfg
• $HOME/.imgcvt.cfg
• $HOME/.mar.cfg
• /usr/local/mar/imgcvt.cfg

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.

COMPLETE EXAMPLE for imgcvt.cfg

[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

See Also

Author

Copyright

Address

Table of Contents

• Name
• Synopsis
• Description
• Options
• GUI
• Direct Beam
• Input Files
• Output Files
• Configuration File
• COMPLETE EXAMPLE for imgcvt.cfg
• See Also
• Author
• Copyright
• Address