.TH mia\-3deval\-transformquantity 1 "v2.4.7"  "USER COMMANDS"
.SH NAME
mia\-3deval\-transformquantity
\- Evaluate derivative of a transformation
.SH SYNOPSIS
.B  mia\-3deval\-transformquantity \-o <out\-file> \-t <transformation> [options]
.SH DESCRIPTION
.B mia\-3deval\-transformquantity
Get derivative a transformation obtained by by using image registration for any given positions in 3D. The position data is given in CSV format:
   id;time;x;y;z;reserved
The output data will be stored in a binary file with an ascii header describing the data. An example header is given below:

MIA
tensorfield {
  dim=3          #number of dimensions of the data
  components=13  #number of components per element
  component_description=vector3,scalar,matrix3x3 #interpretation of components 
  elements=20    #number of elements in file
  interpretation=strain #interpretation of elements (strain|derivative)
  style=sparse   #storage style (sparse|grid) 
  repn=float32   #representation of values 
  size=1000 1000 200 #grid size of the transformation
  endian=low     #endianess of binary data (low|big) 
}

This example header has to be interpreted like follows: three-dimensional data, each entry consists of 13 values the values etry consists of a 3D vector, a scalar, and a 3x3 matrix (saved in row-major format).The data records represent strain tensors, and only a sparse set of points is given. The values are given as single floating point (32 bit). The original transformation field corresponds to images of 1000x1000x200 voxels and the binary data is stored in low endian format.
.SH OPTIONS
.SS 
File-IO
.RS
.IP "\-i \-\-in-file=(input); string"
input point set, if this parameter is given a sparse evaluation of the quantity will be done, otherwise the quantity is evaluated for each grid point of the transformation range.

.IP "\-o \-\-out-file=(required, output); string"
output strains file, for a format description see above.

.IP "\-t \-\-transformation=(required, input); io"
transformation of which the quantity will be evaluated.
 For supported file types see PLUGINS:3dtransform/io
.RE
.SS 
Parameters
.RS
.IP "\-q \-\-quantity=strain"
Specify the quantity to be evaluated at the given points

.RS 10
.I
derivative
\(hy Evaluate the transformation derivative at the given points
.RE
.RS 10
.I
strain
\(hy Evaluate the strain tensor at the given points
.RE
.RE
.SS Help & Info
.RS
.IP "\-V \-\-verbose=warning"
verbosity of output, print messages of given level and higher priorities. Supported priorities starting at lowest level are:

.RS 10
.I
trace
\(hy Function call trace
.RE
.RS 10
.I
debug
\(hy Debug output
.RE
.RS 10
.I
info
\(hy Low level messages
.RE
.RS 10
.I
message
\(hy Normal messages
.RE
.RS 10
.I
warning
\(hy Warnings
.RE
.RS 10
.I
fail
\(hy Report test failures
.RE
.RS 10
.I
error
\(hy Report errors
.RE
.RS 10
.I
fatal
\(hy Report only fatal errors
.RE
.IP "   \-\-copyright"
print copyright information

.IP "\-h \-\-help"
print this help

.IP "\-? \-\-usage"
print a short help

.IP "   \-\-version"
print the version number and exit

.RE
.SS Processing
.RS
.IP "   \-\-threads=\-1"
Maxiumum number of threads to use for processing,This number should be lower or equal to the number of logical processor cores in the machine. (\-1: automatic estimation).

.RE
.SH PLUGINS: 3dtransform/io
.TP 10
.B bbs
Binary (non-portable) serialized IO of 3D transformations
.P
.RS 14
Recognized file extensions:  .bbs
.RE
 
.TP 10
.B datapool
Virtual IO to and from the internal data pool
.P
.RS 14
Recognized file extensions:  .@
.RE
 
.TP 10
.B vista
Vista storage of 3D transformations
.P
.RS 14
Recognized file extensions:  .v, .v3dt
.RE
 
.TP 10
.B xml
XML serialized IO of 3D transformations
.P
.RS 14
Recognized file extensions:  .x3dt
.RE
 
.SH EXAMPLE
Derivative of the transformation change.v3df for each  point given in input.csv are evaluated and written to output.s.
.HP
mia\-3deval\-transformquantity \-i input.csv \-o output.s \-\-transformation change.v3df
.SH AUTHOR(s)
Gert Wollny
.SH COPYRIGHT
This software is Copyright (c) 1999\(hy2015 Leipzig, Germany and Madrid, Spain.
It comes  with  ABSOLUTELY  NO WARRANTY  and  you  may redistribute it under the terms of the GNU 
GENERAL PUBLIC LICENSE Version 3 (or later). For more 
information run the program with the option '\-\-copyright'.