topo

Source Code for Package topo

1 """ 2 Topographica cortical map simulator package. 3 4 Topographica is designed as a collection of packages from which 5 elements can be selected to model specific systems. For more 6 information, see the individual subpackages:: 7 8 base - Core Topographica functions and classes 9 plotting - Visualization functions and classes 10 analysis - Analysis functions and classes (besides plotting) 11 tkgui - Tk-based graphical user interface (GUI) 12 command - High-level user commands 13 misc - Various useful independent modules 14 15 The Topographica primitives library consists of a family of classes 16 that can be used with the above functions and classes:: 17 18 sheet - Sheet classes: 2D arrays of processing units 19 projection - Projection classes: connections between Sheets 20 pattern - PatternGenerator classes: 2D input or weight patterns 21 ep - EventProcessor classes: other simulation objects 22 transferfn - Transfer functions, for e.g. normalization or squashing 23 responsefn - Calculate the response of a Projection 24 learningfn - Adjust weights for a Projection 25 coordmapper - CoordinateMapperFn classes: map coords between Sheets 26 27 Each of the library directories can be extended with new classes of 28 the appropriate type, just by adding a new .py file to that directory. 29 E.g. new PatternGenerator classes can be added to pattern/, and will 30 then show up in the GUI menus as potential input patterns. 31 32 $Id: __init__.py 11201 2010-07-14 13:07:21Z ceball $ 33 """ 34 __version__ = "$Revision: 11201 $" 35 36 # The tests and the GUI are omitted from this list, and have to be 37 # imported explicitly if desired. 38 __all__ = ['analysis', 39 'base', 40 'command', 41 'coordmapper', 42 'ep', 43 'learningfn', 44 'misc', 45 'numbergen', 46 'transferfn', 47 'pattern', 48 'plotting', 49 'projection', 50 'responsefn', 51 'sheet'] 52 53 # get set by the topographica script 54 release = '' 55 version = '' 56 57 58 import param 59 import os 60 61 62 # Default location in which to create files 63 _default_output_path = os.path.join(os.path.expanduser("~"),'topographica') 64 if not os.path.exists(_default_output_path): 65 print "Creating %s"%_default_output_path 66 os.mkdir(_default_output_path) 67 68 # Location of topo/ package. This kind of thing won't work with py2exe 69 # etc. Need to see if we can get rid of it. 70 _package_path = os.path.split(__file__)[0] 71 72 param.normalize_path.prefix = _default_output_path 73 param.resolve_path.search_paths+=([_default_output_path] + [_package_path]) 74 75 76 77 # CEBALERT: (about PIL) 78 # PIL (i.e. the Imaging package) can be installed so that it's 79 # e.g. "from PIL import Image" or just "import Image". 80 try: 81 import Image 82 except ImportError: 83 from PIL import Image, ImageOps, ImageDraw, ImageFont 84 import sys 85 sys.modules['Image']=Image 86 sys.modules['ImageOps']=ImageOps 87 sys.modules['ImageDraw']=ImageDraw 88 sys.modules['ImageFont']=ImageFont 89 90 # ImageTk is completely optional 91 try: 92 import ImageTk 93 except ImportError: 94 try: 95 from PIL import ImageTk 96 import sys 97 sys.modules['ImageTk']=ImageTk 98 except ImportError: 99 pass 100 101 102 # CEBALERT: can we move these pickle support functions elsewhere? 103 # In fact, can we just gather all the non-legacy pickle garbage into one 104 # place? I'd even like to get stuff out of classes, but I guess that 105 # wouldn't always be desirable. 106 # (What prompted this note is that, apart from the clutter the pickle 107 # methods add to classes, I cannot remember all the ways one can 108 # support pickling; the answer to any new pickle problem is often 109 # spread throughout all the pickle methods I've ever added...) 110 111 112 # (note that these _pickle_support functions also work for deep copying)

113 -def _numpy_ufunc_pickle_support():

114 """ 115 Allow instances of numpy.ufunc to pickle. 116 """ 117 # Remove this when numpy.ufuncs themselves support pickling. 118 # Code from Robert Kern; see: 119 #http://news.gmane.org/find-root.php?group=gmane.comp.python.numeric.general&article=13400 120 from numpy import ufunc 121 import copy_reg 122 123 def ufunc_pickler(ufunc): 124 """Return the ufunc's name""" 125 return ufunc.__name__

126 127 copy_reg.pickle(ufunc,ufunc_pickler) 128 129 _numpy_ufunc_pickle_support() 130 131 132 # CBENHANCEMENT: should investigate Python 2.6's fraction module (at 133 # least to replace the FixedPoint fallback). 134 # http://docs.python.org/whatsnew/2.6.html 135

136 -def _mpq_pickle_support():

137 """Allow instances of gmpy.mpq to pickle.""" 138 from gmpy import mpq 139 mpq_type = type(mpq(1,10)) # CEBALERT: any idea how to get this properly? 140 import copy_reg 141 copy_reg.pickle(mpq_type,lambda q: (mpq,(q.digits(),)))

142 143 144

145 -def _instance_method_pickle_support():

146 """Allow instance methods to pickle.""" 147 # CB: well, it seems to work - maybe there are cases where this 148 # wouldn't work? 149 # Alternative technique (totally different approach), but would 150 # only work with pickle (not cPickle): 151 # http://code.activestate.com/recipes/572213/ 152 def _pickle_instance_method(mthd): 153 mthd_name = mthd.im_func.__name__ 154 obj = mthd.im_self 155 return getattr, (obj,mthd_name)

156 157 import copy_reg, types 158 copy_reg.pickle(types.MethodType, _pickle_instance_method) 159 160 _instance_method_pickle_support() 161 162 163 # Set the default value of Simulation.time_type to gmpy.mpq. If gmpy 164 # is unavailable, use the slower fixedpoint.FixedPoint. Also, in that 165 # case, provide a fake gmpy.mpq (to allow e.g. pickled test data to be 166 # loaded). If neither gmpy nor fixedpoint is available, the default 167 # will be float. Python 2.7 has suitable fraction.Fraction() 168 time_type = None 169 try: 170 import gmpy 171 time_type = gmpy.mpq 172 time_type_args = () 173 _mpq_pickle_support() 174 except ImportError: 175 import topo.misc.fixedpoint as fixedpoint 176 param.Parameterized().warning('gmpy.mpq not available; using slower fixedpoint.FixedPoint for simulation time.') 177 time_type = fixedpoint.FixedPoint 178 time_type_args = (4,) # gives precision=4 179 180 from topo.misc.util import gmpyImporter 181 import sys 182 sys.meta_path.append(gmpyImporter()) 183 184 from topo.base.simulation import Simulation 185 186 if time_type is not None: 187 Simulation.time_type = time_type 188 Simulation.time_type_args = time_type_args 189 190 sim = Simulation() 191 192 193 194 195

196 -def about(display=True):

197 """Print release and licensing information.""" 198 199 ABOUT_TEXT = """ 200 Pre-release version %s (%s) of Topographica; an updated 201 version may be available from topographica.org. 202 203 This program is free, open-source software available under the BSD 204 license (http://www.opensource.org/licenses/bsd-license.php). 205 """%(release,version) 206 if display: 207 print ABOUT_TEXT 208 else: 209 return ABOUT_TEXT

210 211 212 # Set most floating-point errors to be fatal for safety; see 213 # topo/misc/patternfn.py for examples of how to disable 214 # the exceptions when doing so is safe. Underflow is always 215 # considered safe; e.g. input patterns can be very small 216 # at large distances, and when they are scaled by small 217 # weights underflows are common and not a problem. 218 from numpy import seterr 219 old_seterr_settings=seterr(all="raise",under="ignore") 220