NAME#

stemview - viewer for STEM images produced by ELDICO system

SYNOPSIS#

stemview [ -h (--help) ] [ -D (--debug) code ] [ -d (--dir) DIRECTORY ] [ -f (--file) FILE ] [ -H (--host) HOSTNAME ] [ -x (--nx) NX ] [ -y (--ny) NY ] [ -p (--port) PORT ] [ -v (--verbose) ] [ -V (--VERSION) ] [ directory | file ]

DESCRIPTION#

stemview is a stand-alone viewer for STEM data produced by the ELDICO system.

OPTIONS#

-d (--dir) DIRECTORY: Directory to look for STEM raw data. The program allows for easily loading all data files from that directory py using the Previous/Next feature. Default: working directory
-f (--file) FILE: Directly loads FILE into the viewing area. Also extracts directory name from the file path.
-h (--help): Prints a summary of program command line options.
-m (--map): Load MAP*tiff images from a directory as produced by the mapping tool in eldix and show grid, mesh, particles and corrsponding diffraction image as tiles.
-x (--nx) NX: Horizontal dimension of images. By default, images are supposed to be square and the x,y dimensions are calculated from the square root of the number of elements. If that is not true, you have to provide x and y dimensions explicetely. Default: square root of number of elements in file
-y (--ny) NY: Vertical dimension of images. See -x NX.
-H (-E, --host) HOSTNAME: Instead of loading data from file, connect to the E-beam system and directly obtain STEM images from here. You need to specify the HOSTNAME and PORTNAME to establish a TCP/IP-connection Default: none
-p (--port) PORT: Port number of TCP/IP-connection. See HOSTNAME. Default: 4944
-v (--verbose): Increases verbosity level for more program output.
-V (--VERSION): Only show program version and exit.
-w (--write): Write out compressed data after transfer to file \"test.lz4\" or \"test.bslz4\". Default: ignore
directory | file: The program loads raw STEM data from \"directory\" or directly loads the given file.

Interacting with E-beam system#

If a hostname (and port number) is supplied, the program will try to talk directly to the E-beam system. The only thing it will do, though, is to send commands to capture a STEM image and retrieve the data from the system. It will not allow to do any other type of control. The E-beam system must already be in STEM mode and the detector(s) must be put in place. If a connection is available, the File menu of the program offers option \"New\". When pushed, a window pops up that allows for entering the scan range (min. to max in x and y), the number of scan rows and columns (dimensions in y and x) as well as the gain, brightness, and contrast. After pushing the \"Go\" button, the command is executed and the E-beam system returns a 2D-array of values that is being displayed and written to disk (as file YYYY-MM-DD--HH.MM.SS-[detector].report, where [detector] is either one of \"bf\" (\"bright field\", df1 (\"dark field 1\") or df2.

Mapping mode#

When called with option --map, the program reads all files starting with string MAP from the given directory. In mapping mode, program eldix produces tiff files named MAPiiii.[GRID].MESHj.[PARTk].FOV_m.tiff where iiii is a 4-digit number, j is the mesh number as detected in a STEM of the grid and k is a particle numer as detected in the STEM of the mesh. m denotes the field of view in microns. Typical files names are thus: MAP0001.GRID.FOV_400.tiff, MAP0002.MESH1.FOV_75.tiff and MAP0003.MESH1.PART1.FOV_10.tiff. If the mapping also includes diffraction images, they are not tiff files but png files and named like MAP0003.MESH1.PART1.FOV_10.png. When program stemview finds series of these files in a directory, they pictures will be assembled together in a 2x2 tile with the overview of the grip in the upper left corner, the mesh in the upper right corner, the particle in the lower right corner and optionally the corresponding diffractio image in the lower right corner. By clicking the left mouse button in the grid area, a new mesh can be selected. Selectable meshes (i.e. those for which STEM images exist in the given directory) are drawn in green, the one that is currently loaded is marked in yellow. Likewise, in the mesh in the upper right quadrant green numbers indicate available particles and the yellow one is currently shown. When selecting other particles or meshes, the image area is redrawn with the selected meshes and/or particle. Thus it is easily possible to evaluate a series of images.

INPUT FILES#

Data files with x*y elements as floating point numbers.

CONFIGURATION FILE#

The program reads configuration files from the following locations in the given order (in parenthesis: Windows)

current_working_directory/eldix.cfg (eldix.ini)
\$HOME/.eldix.cfg (%HOME%\eldix.ini)
\$HOME/.local/share/ELDICO/eldix.cfg (%APPDATA%\ELDICO\eldix.ini)
/usr/local/ELDICO/eldix.cfg (%PROGRAMDATA%\ELDICO\eldix.ini)

Entries given in the next available file will override all previous entries. This allows for mixing entries that can be changed by the user with entries set by a system administrator.

AUTHOR#

Claudio Klein, MarXperts GmbH, Norderstedt, Germany.

COPYRIGHT#

ADDRESS#

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MarXperts GmbH Phone: +49 - (40) - 529 884-0 Werkstr. 3 FAX: +49 - (40) - 529 884-20 D-22844 Norderstedt - GERMANY info\@marxperts.com www.marxperts.com _