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IM2DAT manual

im2dat

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© ATSAS Team, 2003-2020

Table of Contents

Manual

The following sections shortly describe how to run IM2DAT from the command-line on any of the supported platforms, details the required input and output files.

Introduction

IM2DAT radially (or azimuthally) averages a two-dimensional input image in TIFF, CBF or EDF format to a one-dimensional scattering pattern. Besides the input image the user may provide:

  • a text file in "key: value" format that will be appended as a footer to the final output.
  • a detector or beam-stop mask to mask out certain pixels or areas
  • an axis file prepared by AXIS based on an experimental standard, or IMSIM for simulated data

In addition the beam-center position in x/y image coordinates is required.

Additional options that modify the behaviour of IM2DAT are described below.

Running im2dat

Usage:

$ im2dat [OPTIONS] <IMAGE> [HEADER]

OPTIONS known by IM2DAT are described in next section, the required and optional arguments are described in the section on input files.

Command-Line Arguments and Options

IM2DAT accepts the following command line arguments:

ArgumentDescription
IMAGE Required: a two-dimensional image in TIFF, CBF or EDF formats.
HEADER Optional: may contain "key: value" pairs that are included verbatim in the footer of the final data output file.1

IM2DAT accepts the following command line options:

Short OptionLong OptionDescription
--flatfield=<FILE> Flatfield image (default: none)
--beamstop-mask=<FILE> Beamstop mask file (default: none)2
--shield-mask=<FILE> Shield mask for MAR345 (default: none)
--axis-data=<FILE> Angular axis data file derived from standard measurement (default: none)3
--response-data=<FILE> Detector response data (default: none)
-x --beam-center-x=<ARG> Pixel x-coordinate of the beam center in image coordinates (default: 0.0)
-y --beam-center-y=<ARG> Pixel y-coordinate of the beam center in image coordinates (default: 0.0)
--unit-time=<ARG> Unit time for standardization in seconds (default: 1)
--maxpoints=<ARG> Maximum number of data points in output (default: all)
--angular-unit=<ARG> Character string describing the angular units, e.g. '1/nm' (default: undefined)4
--frame=<ARG> Frame number in image file (default: 1)5
--median-filter=<y|n> Whether or not to apply a median filter (default: yes)6
-o --output=<FILE> Radially averaged output file (default: stdout)
-v --version Print version information and exit.
-h --help Print a summary of arguments and options and exit.

1 Some keywords are parsed and used to format the output file, in particular: Description, Code, Concentration, Exposure time, Transmitted Beam

2 Generated by external software or IMSIM for simulated data, in any of the supported image formats or FIT2D mask .msk format.

3 See AXIS for experimental and IMSIM for simulated data on how to obtain axis data files.

4 May be any string, if defined it will be added as key-value-pair to the footer of the output file.

5 Only applicable to image file formats that support multiple data frames in a single image file.

6 Median filter discards outliers of the expected Poisson distribution (recommended).

Runtime Output

There is no output of IM2DAT at run-time. For data output see output files.

im2dat Input Files

IM2DAT requires the image to work radially average and has a number of additional, but optional, input files:

  • a text file in "key: value" format that will be appended as a footer to the final output.
  • a detector or beam-stop mask to mask out certain pixels or areas
  • an axis file prepared by AXIS based on an experimental standard, or IMSIM for simulated data

im2dat Output Files

If the output option is given, the radially averaged data is written to the specified location, existing files will be overwritten without further notice. Otherwise the data is written to standard output.

Example

See the manual of IMSIM for a fully worked example on the usage of IMSIM and IM2DAT. Everything shown there for simulated data also applies to experimental data.


  Last modified: January 7, 2020

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