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Making Data Tables from Vector Fields: avf2odt

The avf2odt program converts rectangularly meshed vector field files in any of the recognized formats (OVF, VIO) into the ODT 1.0 data table format. (Irregular meshes are not supported by this command. Note that any OVF file using the ``irregular'' meshtype is considered to be using an irregular mesh, even if the mesh nodes do in fact lie on a rectangular grid.)

Launching
The avf2odt launch command is:

tclsh oommf.tcl avf2odt [standard options] \
   [-average <space|plane|line|point|ball>] [-axis <x|y|z>] \
   [-ball_radius brad] [-defaultpos <0|1>] [-defaultvals <0|1>] \
   [-extravals flag] [-filesort method] [-headers <full|collapse|none>] \
   [-index label units valexpr] [-ipat pattern] [-normalize <0|1>] \
   [-numfmt fmt] [-onefile outfile] [-opatexp regexp] [-opatsub sub] \
   [-region xmin ymin zmin xmax ymax zmax] \
   [-rregion rxmin rymin rzmin rxmax rymax rzmax] \
   [-truncate <0|1>] [-v level] [-valfunc label units fcnexpr] \
   [infile ...]
where
-average <space|plane|line|point| ball>
Specify type of averaging. Selection of Space averaging results in the output of one data line (per input file) consisting of the average vx , vy and vz field values in the selected region (see -region option below). For example, in magnetization files, vx , vy and vz correspond to Mx , My and Mz . If plane or line is selected, then the output data table consists of multiple lines with 4 or 5 columns per line, respectively. The last 3 columns in both cases are the vx , vy and vz averaged over the specified axes-parallel affine subspace (i.e., plane or line). In the plane case, the first column specifies the averaging plane offset along the coordinate axis normal to the plane (see -axis option below). In the line case, the first 2 columns specify the offset of the averaging line in the coordinate plane perpendicular to the line. If the averaging type is point, then no averaging is done, and the output consists of lines of 6 column data, one line for each point in the selected region, where the first 3 columns are the point coordinates, and the last 3 are the vx , vy and vz values at the point. If the type is ball, then one line is output for each sample point for which a ball of radius brad (see -ball_radius option) centered about that point lies entirely inside the selected region. The output values consist of 6 columns: the ball center point location and the vx , vy and vz values averaged across the ball. As a special case, if the spatial extent of the selected region is two-dimensional (e.g., all the sample locations have the same z -coordinate), then the averaging region is taken to be a disk instead of a ball. Similarly, if the spatial extent of the selected region is one-dimensional, then the averaging region is reduced to a one-dimensional line segment. (Note: The output columns described above may be suppressed by the -defaultpos and -defaultvals options. Additional columns may be introduced by the -index and -valfunc options.) The default averaging type is space.
-axis <x|y|z>
For the -average plane and -average line averaging types, selects which subset of affine subspaces the averaging will be performed over. In the plane case, the -axis represents the normal direction to the planes, while for line it is the direction parallel to the lines. This parameter is ignored if -average is not either plane or line. Default value is x.
-ball_radius brad
This option is required if -average is ball, in which case brad specifies the radius of the averaging ball in problem units (e.g., meters). If -average is not ball, then this option is ignored.
-defaultpos <0|1>
By default, the output data columns are as described in the description of the -average option above. However, -defaultpos 0 may be used to omit the columns indicating the averaging position.
-defaultvals <0|1>
By default, the output data columns are as described in the description of the -average option above. However, -defaultvals 0 may be used to omit the columns containing the averaged vx , vy and vz values. In particular, this may be useful in conjunction with the -valfunc option.
-extravals <0|1>
Specify -extravals 1 to augment the output with columns for the average L1 norm $ \sum$$ \left(\vphantom{\vert v_x\vert + \vert v_y\vert + \vert v_z\vert}\right.$| vx| + | vy| + | vz|$ \left.\vphantom{\vert v_x\vert + \vert v_y\vert + \vert v_z\vert}\right)$/N , the normalized L2 norm $ \sqrt{{\sum v^2/N}}$ , the minimum component absolute value, and the maximum component absolute value.
-filesort method
Specifies the sorting order to apply to the input file list. This order is important when using the -onefile option, since it controls the order in which the rows from the various input files are concatenated. Method should be either the keyword ``none'', or else a valid option string for the Tcl command lsort, e.g., ``-ascii -decreasing''. Note that the lsort sort options all begin with a hyphen, ``-'', and that if you want to use multiple options they must be grouped as one element to filesort (by, for example, placing quotes around the list). The default value is ``-dictionary'' if the -ipat option is specified, or ``none'' otherwise.
-headers <full|collapse|none>
Determines the style of headers written to the output ODT file(s). The full style (default) provides the standard headers, as described in the ODT documentation. Specifying ``none'' produces raw data lines without any headers. The collapse style is used with multiple input files and the -onefile output option to concatenate output with no ODT header information between the segments.
-index label units valexpr
Adds an input file based index column to the output, where label is the column header, units is a string displayed as the column units header, and valexpr is a Tcl expr expression that may include the special variables $i, $f1, $f2, ..., $d1, $d2, ...; here $i is the 0-based index of the file in the list of input files, $f1 is the first number appearing in the input filename, $f2 is the second number appearing in the input filename, $d1 is the first number appearing in the ``Desc'' fields in the header of the input file, etc. For example, if there are two input files named foo-100.ovf and and foo-101.ovf, then setting valexpr to abs($f1)+1 would yield a column with the value 101 for all lines coming from foo-100.ovf, and the value 102 for all lines coming from foo-101.ovf. (We use the Tcl expr function abs because the leading hyphen in foo-100.ovf gets interpreted as a minus sign, so $f1 is extracted as -100.) On Unix systems, the valexpr string should be surrounding by single quotes in order to forestall interpolation of the special variables by the shell. On Windows, the valexpr string should be surrounded by double quotes as usual to protect embedded spaces. Multiple instances of the -index option on the command line will result in multiple columns in the output file, in the order specified. The index columns, if any, will be the first columns in the output file.
-ipat pattern
Specify input files using a pattern with ``glob-style'' wildcards. Especially useful in DOS. Files must meet the infile requirements (see below).
-normalize <0|1>
If 1, then the default averaged output values vx , vy and vz are divided by the maximum magnitude that would occur if all the vectors in the averaging manifold are aligned. (In particular, the maximum magnitude of the output vector is 1.) This option should be used carefully because the normalization is done independently for each output row. For -normalize 0 (the default), averaged output values are in file units.
-numfmt fmt
C-style output format for numeric data in the body of the output table. Default value is ``%- #20.15g''.
-onefile outfile
Generally a avf2odt writes its output to a collection of files with names generated using the -opatexp and -opatsub specifications. This option overrides that behavior and sends all output to one place. If outfile is ``-'', then the output is sent to standard output, otherwise outfile is the name of the output file.
-opatexp regexp
Specify the ``regular expression'' applied to input filenames to determine portion to be replaced in generation of output filenames. The default regular expression is: (\.[^.]?[^.]?[^.]?$|$)
-opatsub sub
The string with which to replace the portion of input filenames matched by the -opatexp regexp during output filename generation. The default is .odt.
-region xmin ymin zmin xmax ymax zmax
Axes-parallel rectangular box denoting region in the vector field file over which data is to be collected. The locations are in problem units (typically meters). A single hyphen, ``-'', may be specified for any of the box corner coordinates, in which case the corresponding extremal value from the input file is used. Optional; the default, -region - - - - - -, selects the entire input file.
-rregion rxmin rymin rzmin rxmax rymax rzmax
This option is the same as -region, except that the locations are specified in relative units, between 0 and 1.
-truncate <0|1>
When opening an existing file for output, the new output can either be appended to the file (-truncate 0), or else the existing data can be discarded (-truncate 1). The default is -truncate 0.
-v level
Verbosity (informational message) level, with 0 generating only error messages, and larger numbers generating additional information. The level value is an integer, defaulting to 1.
-valfunc label units fcnexpr
Similar to the -index option, -valfunc adds an additional column to the output with label and units as the column header, and fcnexpr is a Tcl expr expression that may include special variables. Here, however, the allowed special variables are $x, $y, $z, $r, $vx, $vy, $vz, $vmag, where $x, $y, $z, and $r are sample location and magnitude, respectively ( r = $ \sqrt{{x^2+y^2+z^2}}$ ), and $vx, $vy, $vz and $vmag are vector component values and magnitude. The output is the value of fcnexpr averaged across the manifold selected by the -average option. A couple of examples are
   -valfunc Ms   A/m '$vmag'
   -valfunc M110 A/m '($vx+$vy)/sqrt(2.)'
As with the valexpr string for -index, the fcnexpr string should be surrounding by single quotes on Unix in order to forestall interpolation of the special variables by the shell. On Windows, the fcnexpr string should be surrounded by double quotes as usual to protect embedded spaces. The output value is not affected by the -normalize option. Multiple instances of the -valfunc option on the command line will result in multiple columns in the output file, in the order specified. These additional columns will be append to the right of all other columns in the output file.
infile ...
Input file list. Files must be one of the recognized formats, OVF 1.0 or VIO, in a rectangular mesh subformat.

The file specification options require some explanation. Input files may be specified either by an explicit list (infile ...), or by giving a wildcard pattern, e.g., -ipat *.omf, which is expanded in the usual way by avf2odt (using the Tcl command glob). Unix shells (sh, csh, etc.) automatically expand wildcards before handing control over to the invoked application, so the -ipat option is not usually needed--although it is useful in case of a ``command-line too long'' error. DOS does not do this expansion, so you must use -ipat to get wildcard expansion in Windows. The resulting file list is sorted based on the -filesort specification as described above.

If -onefile is not requested, then as each input file is processed, a name for the corresponding output file is produced from the input filename by rules determined by handing the -opatexp and -opatsub expressions to the Tcl regsub command. Refer to the Tcl regsub documentation for details, but essentially whatever portion of the input filename is matched by the -opatexp expression is removed and replaced by the -opatsub string. The default -opatexp expression matches against any filename extension of up to 3 characters, and the default -opatsub string replaces this with the extension .odt.


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OOMMF Documentation Team
September 30, 2019