Changes in Neuronvisio

0.9.1 – 1 October 2015

  • Fixed small formatting issue on the docs
  • Added pytables to the run dependences

0.9.0 – 24 September 2015

  • Created a conda package for Neuronvisio
  • Dropped paver for normal install via PyPi (Closed #57)

0.8.6 – 8 March 2013

  • we are using pip and requirements.txt to be able to install packages from DCVS
  • MacOs is now supported when we open the model, if not mosinit is present #56
  • Better explanation to the User if a model can’t be loaded. #55
  • Improved Install Docs for Mac. PR #53 and #54
  • Added 24 models available from ModelDB

0.8.5 – 6 Jul 2012

  • Closed #49
  • Text in the Animation is always formatted with 3 digits.
  • Added the ability to load a NeuroML (xml), a Hoc (.hoc) or a HDF file (.h5) with Neuronvisio format directly when the program is launched.

0.8.4 – 12 Jun 2012

  • Added new model to the ModelDBlist
  • updated the documentation
  • Added 3 new models to ModelDB

0.8.3 – 18 May 2012

  • Fixed paver minilib, missing from the tarball
  • Added one new model to the ModelDB.xml
  • Improved the documentation of several classes
  • Inserted the domain in the about (neuronvisio.org)

0.8.2 – 23 Apr 2012

  • Added two new model to ModelDB.xml
  • Introduced a new method to assign a color to more than one sections from the console
  • Added the apptools patched version as explicit dependency until it’s not released officially.

0.8.1 – 19 March 2012

  • Added new models on the ModelDB.xml
  • Closed #45
  • Easy function to export a video as a stack of screenshots
  • Updated the docs to work witht the latest pyqt
  • Geometry node in the HDF is directly a NeuroML string and not wrapped in a list

0.8.0 – 15 Feb 2012

  • New repo layout
  • Ported to Mayavi 4.1.1.dev
  • Closed #31
  • Reorganized controls method in alphabetical order.
  • Animation set true when simulation is launched.
  • Fixed a vectors handling if no values present.
  • Updated the doc for Mayavi 4.0.0
  • Load hoc or hdf with the same method
  • Added new models from ModelDB
  • User Interface improvement
  • Closed #37
  • Closed #32
  • Closed #34
  • Improved nrnvisio.py to integrate seamlessy with IPython session, or create a new one on the fly
  • Automatic handling of Mayavi installation through pip.

0.7.3 – 24 Nov 2011

  • Inserted how to configure ipython with the pylab and Q4Agg support in the doc
  • Selected section is now stored and used if the vector are created only for one sec
  • Inserted two new models on the ModelDb.xml. Fix #30.
  • Included the ModelDB.xml in the package

0.7.2 – 8 Nov 2011

  • Inserted modeldb in the pavement.

0.7.1 – 8 Nov 2011

  • fixed the name of the exectable on the setup file

0.7.0 – 3 Nov 2011

  • Added a new tab to have a ModelDb explorer inside Neuronvisio
  • Integrate the ability to download and extract a NEURON model from ModelDb
  • Ability to load the model directly from Neuronvisio
  • Used the logging python system through the package
  • Updated the docs to explain the ModelDb integration.

0.6.2 – 16 Jun 2011

  • New API to select sections directly from the commandline (controls.select_sections())
  • Animation Timeliner set up only if simulation has ran or be reloaded.

0.6.1 – 9 Jun 2011

  • Animation ported to the new infrastructure.
  • Updated the requirements with setuptools (needed for paver)
  • Animation timeline accept an arbitrary time and display it on the visio window.

0.6.0 – 10 May 2011

  • Added the function to plot a 3D plot to the manager (manager.plot3D)
  • Animation can will be enabled if any simulation is ran, either from the gui or the code.
  • Completely rewrote the visualization method. Now completely integrates in the mayavi pipelines, therefore axes and other modules/filters can be added at will
  • Now it’s faster. A lot faster
  • All the segments are plotted, not only the section. This is extremely helpful with geometrical reconstruct neurons and networks.
  • Updated the docs and the screenshots.

0.5.2 – 26 Jan 2011

  • Updated the version recall to GitPython 0.3.1 (used only if present!)
  • HocVector into NumpyArray for saving with swap in place, to reduce overhead
  • Restructured the package for an easier installation
  • Added the possibility to build documentation offline

0.5.1 - 23 Nov 2010

  • Fixed the picking of the cylinder. Possible to select a cylinder clicking anywhere.
  • Possibility to plot points instead of a lines
  • BaseREf class are discriminated through the group id and not any more on class base.

0.5.0 - 19 Jun 2010

  • Closed #16
  • Fixed some typos on the docs
  • Mechanisms are shown on the info tab
  • Refactored code for extensibility
  • Storage moved to a hdf file.
  • Extensibility to other kind of variables, not only vectors

0.4.4 - 1 Apr 2010

  • Fixed the name on the README
  • Treeview updated everytime a database is loaded.

0.4.3 - 2 Mar 2010

  • Info sections updated
  • Update the docs and website

0.4.2 - 18 Feb 2010

  • Added simulation saving abilities.
  • Updated the doc

0.4.1 - 28 Jan 2010

  • Closed #13
  • Introduced a tab to retrieve info on the section

0.4.0 - 19 Jan 2010

  • Remplemented using Mayavi2 and Qt4 for better performance and better usability.
  • Cleanup and refactoring of the code.
  • Closed #11, #12, #15

0.3.5 - 20 Nov 2009

  • Using sphinx for the doc
  • Using paver for deployment
  • python egg and easy install support
  • User manuel available in pdf format

0.3.4 - 15 Sep 2009

  • Changed the way the module is imported to allow other program to use the manager as a storing objects for results.

0.3.3 - 3 Sep 2009

  • Integrated the pylab interface using the GTK backend provided by pylab. It is possible to zoom and navigate the graph with the pylab tools.
  • It is now possible to decide in which figure to plot, using the current figure selector.

0.3.22 - 31 Jul 2009

  • Closed bug #10
  • Changed the name of the module from nrnVisio to nrnvisio to be python standard compliant.
  • Manager being transformed into a library (WIP)

0.3.21 - 20 Jul 2009

  • Better handling of the pick section routine
  • Changed the examples to use the create statement for hoc, to have a proper name of the section also in python.
  • Modified the GUI to handle a runtime change of a section. The model is redrawn completely, the zoom is conserved.

0.3.2 - 20 Jul 2009

Bug Release. Closed Bug #9

0.3.1 - 18 Jul 2009

Bug Release.

0.3.0 - 14 Jul 2009

New Features

  • Stop Button on the animation Control
  • Better handling on the timeline updating routine.

BUGFixes

  • Closed bug #8
  • Closed bug #3

0.2.0 - 6 Jul 2009

New Features

Some new features has been introduced:

  • User defined color. The user can now change the colors of the model for a better contrast.
  • Info tab. Reports the properties of the selected section.

BUGFixes

  • Closed bug #4
  • Closed bug #5
  • Closed bug #6

0.1.0 - 30 Jun 2009

Fist public release.

Features

  • 3D visualization of the model with the possibility to change it runtime
  • Creation of vectors to record any variable present in the section
  • Pylab integration to plot directly the result of the simulation
  • Explore of the timecourse of any variable among time using a color coded scale in the 3d representation
  • the GUI runs in its own thread so it’s possible to use the console to modify/interact with the model.