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Adrian Quintana edited this page Dec 11, 2017 · 1 revision

convert_data2descr

Purpose

convert_data2descr application is intended to convert a set of coordinate values into spheres with a determined radius in an Xmipp phantom volume. This is specially useful for visualizing 3D data as a "spheres" with any of the Spider visualization systems. e.g.: Web, xv, Amira, etc.

The input data to this program is a text file with the following format:


3 1000
12 34 54
-12 45 76
...
32 45 76

The first line indicates the dimension of the vectors (in this case 3) and the number of vectors (in this case 1000). The rest of the lines are the coordinates vectors. Each line is a vector and each column is a vectors' component. In case the data file is composed by vectors of more than 3 dimension, then only the first three components will be taken into account. If the radius parameter is ommited, then the phantom description file will be filled with aXXX character string in the position of the radius value. This is useful for manually trying different radius for the phantom (using the replace option in any text editor application)

Usage


$ convert_data2descr ...

Parameters

  • `` The input data file
  • `` The output file name. This file name is the Phantom Description File, that can be used with Create_phantom application
  • `` Indicates the radius of each sphere to be generated.
  • `` X dimension of the generated phantom image. Default:60
  • `` Y dimension of the generated phantom image. Default:dimX
  • `` Z dimension of the generated phantom image. Default:dimX
  • `` Offset applied to each atom in the X axis. Default:0
  • `` Offset applied to each atom in the Y axis: Default:offX
  • `` Offset applied to each atom in the Z axis: Default:offX

Examples and notes


$ convert_data2descr -iname results.dat -oname results.pht -radius 2

In this example, theresults.dat file will be converted into a phantom description file and the results is saved inresults.pht

If the input file is the following:


4 4
12 54 56 0.3
15 65 98 0.9
9 65 14 0.1
98 32 19 0.0

The output file will be:


60 60 60 0
sph = 1 12.000 54.000 56.000 1.000
sph = 1 15.000 65.000 98.000 1.000
sph = 1 9.000 65.000 14.000 1.000
sph = 1 98.000 32.000 19.000 1.000

Note that only the first three components were used for generating the Phantom file. This phantom description file can be later converted into a Spider volume by using the following command:


$ phantom_create -i results.pht -o results.spi

result.spi is a 60x60x60 SPIDER volume.

--Main.AlfredoSolano - 26 Jan 2007

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