Metadata-Version: 1.1
Name: swc2vtk
Version: 1.0.1
Summary: SWC to VTK converter for visualize multi-compartment neurons and neural circuit simulations
Home-page: https://github.com/DaisukeMiyamoto/swc2vtk
Author: nebula
Author-email: miyamoto@brain.imi.i.u-tokyo.ac.jp
License: UNKNOWN
Description: swc2vtk
        =======
        
        |travisci| |Coverage Status| |python-2.7,3.3,3.4-blue| |license|
        |paraview| |NEURON|
        
        | SWC to VTK converter for visualizing neurons and neural circuit
          simulations in ParaView.
        | This software helps making easy and beautiful visualization of large
          scale multi-compartmental neuron simulation with highly parallelized
          environments.
        
        Dependency
        ----------
        
        -  tqdm
        -  numpy
        -  [STRIKEOUT:PyVTK]
        
        Install
        -------
        
        -  $ pip install swc2vtk
        
        Usage
        -----
        
        Basic way to generate VTK file from one SWC file
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
            vtkgen.write_vtk('simple.vtk')
        
        generate a VTK file from multiple SWC files
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
            vtkgen.add_swc('simple1.swc')
            vtkgen.add_swc('simple2.swc')
            vtkgen.write_vtk('combined.vtk')
        
        generate a VTK file from SWC file with simulation data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
            vtkgen.add_datafile('result.dat')
            vtkgen.write_vtk('simple.vtk')
        
        -  | data example
           | each rows correspondence to SWC compartments
        
           ::
        
               -65.0
               -65.0
               -65.0
               -65.0
        
        generate VTK files from SWC file with sequential simulation data
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
        
            vtkgen.add_datafile('result1.dat')
            vtkgen.write_vtk('simple1.vtk')
        
            vtkgen.clear_datafile()
            vtkgen.add_datafile('result2.dat')
            vtkgen.write_vtk('simple2.vtk')
        
            vtkgen.clear_datafile()
            vtkgen.add_datafile('result3.dat')
            vtkgen.write_vtk('simple3.vtk')
        
        generate VTK file for volume rendering
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
            vtkgen.write_volume_vtk('volume.vtk')
        
        Settings
        --------
        
        Visualization Quality
        ~~~~~~~~~~~~~~~~~~~~~
        
        -  ``Draw Mode`` change SWC compartment drawing method. Largeer number
           is better.
        -  ``0``: simple cylinder
        -  ``1``: one cylinder with variable top surface
        -  ``2``: one cylinder with three cell mode
        -  ``3``: one cylinder with a hemisphere
        
        .. code:: python
        
            from swc2vtk.vtkgenerator import VtkGenerator
            vtkgen = VtkGenerator()
            vtkgen.add_swc('simple.swc')
            vtkgen.set_draw_mode(4)
            vtkgen.write_vtk('simple.vtk')
        
        -  ``Division Number``
        
           .. code:: python
        
               from swc2vtk.vtkgenerator import VtkGenerator
               vtkgen = VtkGenerator()
               vtkgen.add_swc('simple.swc')
               vtkgen.set_division_number(20)
               vtkgen.write_vtk('simple.vtk')
        
        adjust compartment diameter
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        -  ``normalize_diam``
        
        Output Examples
        ---------------
        
        Single Neuron Morphology
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. figure:: https://github.com/DaisukeMiyamoto/swc2vtk/releases/download/v0.01/singleneuron_small.png
           :alt: single
        
           single
        
        -  `high resolution
           version <https://github.com/DaisukeMiyamoto/swc2vtk/releases/download/v0.01/singleneuron.png>`__
        
        Coloring Multiple SWC Files
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. figure:: https://github.com/DaisukeMiyamoto/swc2vtk/releases/download/v0.01/standardbrain_small20170110.png
           :alt: Coloring
        
           Coloring
        
        Single Neuron Simulation
        ~~~~~~~~~~~~~~~~~~~~~~~~
        
        Neural Circuit Simulation
        ~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Volume Rendering
        ~~~~~~~~~~~~~~~~
        
        References
        ----------
        
        -  SWC format: http://research.mssm.edu/cnic/swc.html
        -  http://www.paraview.org/
        -  http://www.vtk.org/
        
        .. |travisci| image:: https://travis-ci.org/DaisukeMiyamoto/swc2vtk.svg?branch=master
        .. |Coverage Status| image:: https://coveralls.io/repos/github/DaisukeMiyamoto/swc2vtk/badge.svg?branch=master
           :target: https://coveralls.io/github/DaisukeMiyamoto/swc2vtk?branch=master
        .. |python-2.7,3.3,3.4-blue| image:: https://img.shields.io/badge/python-2.7,3.3,3.4-blue.svg
        .. |license| image:: https://img.shields.io/badge/license-apache-blue.svg
        .. |paraview| image:: https://img.shields.io/badge/Paraview-5.2-green.svg
        .. |NEURON| image:: https://img.shields.io/badge/NEURON-7.4-green.svg
        
        
Keywords: neuron,simulation,visualization,paraview,vtk
Platform: UNKNOWN
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
