[Pybrainsim-activity] SF.net SVN: pybrainsim:[2] trunk/src

[<rg...@us...>]

Revision: 2
          http://pybrainsim.svn.sourceforge.net/pybrainsim/?rev=2&view=rev
Author:   rgoj
Date:     2009-07-16 19:38:35 +0000 (Thu, 16 Jul 2009)

Log Message:
-----------
Initial import of classes:
* Head, with the following functionality
    ** setting the sampling frequency
    ** a list of generators
    ** running a simulation by looping through all the generators
* Generator, with the following functionality
    ** producing output, when asked for, the output now is only an incremented integer

Initial import of the PyBrainSim.py script, which is now a demo of the above functionalites.

Initial import of the license - the GNU GPL in the file COPYING.

Added Paths:
-----------
    trunk/src/COPYING
    trunk/src/Generator.py
    trunk/src/Head.py
    trunk/src/PyBrainSim.py
    trunk/src/svn-commit.2.tmp
    trunk/src/svn-commit.tmp

Added: trunk/src/COPYING
===================================================================
--- trunk/src/COPYING	                        (rev 0)
+++ trunk/src/COPYING	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
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+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

Added: trunk/src/Generator.py
===================================================================
--- trunk/src/Generator.py	                        (rev 0)
+++ trunk/src/Generator.py	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,31 @@
+# PyBrainSim
+# Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyBrainSim is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PyBrainSim.  If not, see <http://www.gnu.org/licenses/>.
+
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+The Generator class serves as a starting point for creating complex classes simulation populations of neurons. Although currently all it does is adding integers.
+"""
+
+class Generator:
+    def __init__(self):
+        self.output = 0
+
+    def runGenerator(self):
+        self.output = self.output + 1
+        return self.output

Added: trunk/src/Head.py
===================================================================
--- trunk/src/Head.py	                        (rev 0)
+++ trunk/src/Head.py	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,47 @@
+# PyBrainSim
+# Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyBrainSim is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PyBrainSim.  If not, see <http://www.gnu.org/licenses/>.
+
+__metaclass__ = type # New style classes. Is this necessary?
+
+"""
+The Head class is the main class in PyBrainSim. It holds a list of generators and connections between these generators, as well as a head model that governs the propagation of the activity of the generation throughout the modeled head, to the specified registration sites.
+
+This class is only the simplest implementation of these ideas, intended to serve as an example and a starting point for creating complex derived classes, ready for real simulation tasks.
+"""
+
+class Head:
+    def __init__(self):
+        self.samplingFrequency = 128;
+        self.generatorList = []
+    
+    def setSamplingFrequency(self, samplingFrequency):
+        self.samplingFrequency = samplingFrequency
+
+    def addGenerator(self, generator):
+        self.generatorList.append(generator)
+
+    def runSimulation(self, duration=1):
+        """Queries all generators and connections, sends the generators' output to the head model and then to the specified registration sites"""
+        recording = [];
+
+        for timePoint in range(duration * self.samplingFrequency):
+            recording.append(0)
+            for generator in self.generatorList:
+                recording[timePoint] += generator.runGenerator()
+
+        return recording

Added: trunk/src/PyBrainSim.py
===================================================================
--- trunk/src/PyBrainSim.py	                        (rev 0)
+++ trunk/src/PyBrainSim.py	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,37 @@
+# PyBrainSim
+# Copyright 2009 Roman Goj
+#
+# This file is part of PyBrainSim.
+#
+# PyBrainSim is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# PyBrainSim is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with PyBrainSim.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+PyBrainSim is an interactive tool for the simulation and visualization of the electromagnetic activity of the brain, currently under development.
+
+This script can be executed to run an example simulation, using the Head and Generator classes. Currently it only generates a list of integer numbers... but work is under way to make it simulate the brain... Have fun!
+
+pybrainsim.sourceforge.net
+"""
+
+from Head import Head
+from Generator import Generator
+
+exampleHead = Head()
+exampleHead.setSamplingFrequency(32)
+
+exampleGenerator = Generator()
+exampleHead.addGenerator(exampleGenerator)
+
+recording = exampleHead.runSimulation(1)
+print recording

Added: trunk/src/svn-commit.2.tmp
===================================================================
--- trunk/src/svn-commit.2.tmp	                        (rev 0)
+++ trunk/src/svn-commit.2.tmp	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,4 @@
+Oh well...
+--This line, and those below, will be ignored--
+
+A    src

Added: trunk/src/svn-commit.tmp
===================================================================
--- trunk/src/svn-commit.tmp	                        (rev 0)
+++ trunk/src/svn-commit.tmp	2009-07-16 19:38:35 UTC (rev 2)
@@ -0,0 +1,14 @@
+Initial import of the classes:
+* Head, with the following functionality:
+    ** setting the sampling frequency
+    ** a list of generators
+    ** running a simulation by looping through the list of generators, running them and reading their output
+* Generator, with the following functionality:
+    ** producing output when required by the running simulation, currently only incrementing a stored integer number by one
+
+Initial import of the PyBrainSim.py script, with a demo of the classes' functionalities.
+
+Initial import of the text of the license - the GNU GPL v3 in the file COPYING.
+--This line, and those below, will be ignored--
+
+A    src


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