def get(self, url, sub={}):
prot, serv, path, par, q, f = parseurl(url)
if not prot:
prot='file'
if prot=='auto':
v="/"+path.lstrip('/')
v=str(v)
if self.store.has_key(v):
d=self.store[v]
else:
print "no file %s in storage" % v
return (zeros(0), {})
if not self.keepstore:
del(self.store[v])
return d
elif prot=='file':
if os.path.isfile(path):
if q:
return self.readHDF(path, q, sub)
else:
return self.readLocalFile(path, sub)
elif sub.get("Type")=="Auto":
print "referenced local file url %s not found" % path
print "The Data tag specifies the depricated attribute Type:Auto"
print "this could be do to a bug in the pre-version 1.0 url system. Try to load the file using 'auto://upath'"
else:
print "referenced local file url %s not found" % path
return (zeros(0), {})
else:
print "no support for url type %s yet" % t
return (zeros(0), {})
def __getitem__(self, key): l=len(self) if type(key)==slice: st=key.start if st<0: st=l+st if st<0: st=0 elif st>l-1: return zeros((0, self.width), self.dtype) sp= key.stop if sp<0: sp=l+sp if sp<1: return zeros((0, self.width), self.dtype) ne=min(sp, l) ne=ne-st self.file.seek(4+4*self.width*st) a=fromstring(self.file.read(self.width*4*ne), self.dtype) if self.invert: a.byteswap() a=reshape(a, (ne, self.width)) else: if key<0: key=l+key self.file.seek(4+4*self.width*key) s=self.file.read(self.width*4) a=fromstring(s, self.dtype) if self.invert: a.byteswap() return a
def add_point(a, p): if a.shape[1]>len(p): p2 = zeros(a.shape[1], p.dtype.char) p2[:len(p)]=p p=p2 elif a.shape[1]<len(p): a2=zeros((a.shape[0]+1, len(p)), a.dtype.char) a2[:-1,:a.shape[1]]=a a2[-1]=p return a2 return concatenate([a, p[NewAxis, :]])
def finishSection(accum, par, cell, points, regions):
pts=zeros((len(accum),4), float32)
reg={}
if len(accum)<2:
name="s%s" % (accum[0],)
else:
name="s%s_%s" % (accum[0], accum[-1])
for i, pid in enumerate(accum):
pts[i]=points[pid]
rp=regions[pid]
if not reg.has_key(rp):
reg[rp]=1
else:
reg[rp]+=1
if len(reg.keys())==1:
reg=reg.keys()[0]
else:
ar=reg.keys()
ar, rest=ar[0], ar[1:]
nr=reg[ar]
for k in rest:
if reg[k]>nr:
nr=reg[k]
ar=k
print "Neuron-style section %s contains points assigned to several regions (%s). Using %s (which contains the most points)" % (name, str(reg.keys()),ar)
reg=ar
if par:
try:
ppt=cell.getSection(par).getPoints()[-1]
except:
print [s.name() for s in cell.getElements('Section')]
print cell._sections
raise
def nthPoint(self, ind): '''Return a set of parameters coresponding to the index i in the 1D parameter space (0<=i<self.size()). The index is interpreted first-parameter-first. i=0 is the state where every parameter is set to the botom of its range. i=1 sets the first parameter to one precision step greater than the minimum. i=self._bins[0] sets the second parameter one step up, etc.''' indexes=zeros(self._np) for i in range(indexes.shape[0]-1, -1, -1): l, ind=divmod(ind, self._strides[i]) indexes[i]=l return self._params.indextoPar(indexes)
def readZip(f, **kwargs):
from mien.parsers.nmpml import elements as dialect
f=ZipFile(f, 'r')
xml=f.read('xml')
xml=StringIO(xml)
doc=xm.readTree(xml)
xml.close()
doc=xm.assignClasses(doc, dialect)
try:
dat=f.read('data')
except:
print "No data archive in zip file"
return doc
from mien.parsers.datahash import readMD
dat=StringIO(dat)
dat=readMD(dat, return_raw_hash=True)
des=doc.getElements('Data')
for de in des:
try:
d, h=dat[de.upath()]
except:
print "can't find data for element %s" % (de.upath(),)
d, h=(zeros(0), {})
de.datinit(d, h)
f.close()
return doc
def take(self, ai): '''Return an array containing all the rows specified in the index array ai. Ai may specify multiple occurances of the same index. This function is probably slower than numpy.take(self.toarray(), ai), but will use much less memory if ai is short and len(self) is large.''' ret=zeros((ai.shape[0],self.width), self.dtype) for i in ai: self.file.seek(4+4*self.width*i) s=self.file.read(self.width*4) ret[i,:]=fromstring(s, self.dtype) if self.invert: ret.byteswap() return ret
def codingtest(self): self.prep() q=ones(self._np)*-32768 print q print self._params.code16toPar(q) q=ones(self._np)*32767 print q print self._params.code16toPar(q) q=zeros(self._np) print q print self._params.code16toPar(q) print self._params.indextoPar(q) q=ones(self._np)*self._params._bins q-=1 print q print self._params.indextoPar(q)
def record(self, c, f):
'''Writes a chromosome and the fitness value to the arraystore. Not thread safe! (self.lockcall(self.record, (c,f)) is thread safe). f should be a tuple (fit, evalconditions) as returned by general_eval. Return value is the new size of the data store'''
if self.attrib('EvalConditions'):
evc = int(self.attrib('EvalConditions'))
evc=zeros((evc, 1))
if f[1] and type(f[1])==type(evc):
c=concatenate([[f[0]], f[1], c])
else:
c=concatenate([[f[0]], evc, c])
else:
c=concatenate([[f[0]], c])
if self._storesize!=c.shape[0]:
raise IOError("Attempt to record a parameter set of the wrong length")
n=self._store.append(c)
#print self._store[n-1]
if self.better(f[0], self._best[0]):
print "New best %.3f (%s)" % (f[0], str(c))
self._best=(f[0], n-1)
return n
def readDens(inf, **kwargs):
l=inf.readlines()
if len(l)==1000002:
l=array([float(line.split()[3]) for line in l[2:]])
l=reshape(l, (100,100,100))
else:
v=array([float(line.split()[3]) for line in l[2:]])
ind=array([map(int, line.split()[:3]) for line in l[2:]])
l=zeros((ind[:,0].max()+1, ind[:,1].max()+1, ind[:,2].max()+1), Float32)
for i in range(v.shape[0]):
l[ind[i,0],ind[i,1], ind[i,2]]=v[i]
mv = l.max()
l/=mv
o = mien.parsers.nmpml.createElement("SpatialField", {"Origin":ORIGIN.tolist(), "Edge":(EDGE,EDGE,EDGE),
"Vertical":(0.0,1.0,0.0), "Depth":(0.0,0.0,-1.0), "MaxValue":mv,
"mindensity":.0001, "maxdensity":.1})
n = mien.parsers.nmpml.blankDocument()
n.newElement(o)
d=o.getData()
d.datinit(l)
return n
def deserialize(f, **kwargs):
#st=time.time()
if not type(f) in [str, unicode]:
f=f.read()
l=struct.unpack('<I', f[:4])[0]
doc=zlib.decompress(f[4:l+4])
doc=StringIO(doc)
doc=xm.readTree(doc)
from mien.parsers.nmpml import elements as dialect
doc=xm.assignClasses(doc, dialect)
f=f[l+4:]
try:
if f:
from mien.parsers.datahash import readMD
try:
f2=StringIO(f)
f=readMD(f2, return_raw_hash=True)
except:
f=zlib.decompress(f)
f2=StringIO(f)
f=readMD(f2, return_raw_hash=True)
del(f2)
des=doc.getElements('Data')
for de in des:
try:
d, h=f[de.upath()]
except:
print "can't find data for element %s" % (de.upath(),)
d, h=(zeros(0), {})
de.datinit(d, h)
except:
print "cant load data"
#print time.time()-st;st=time.time()
return doc
11.62651 , 19.49572 , 35.26103 , 56.1815 , 72.74056 ,
76.81319 , 76.12871 , 72.58464 , 64.29499 , 48.45283 ,
27.14701 , 17.2904 , 10.02258 , 5.39836 , 2.794265,
0.19017 , -1.19344 , -2.57705 , -3.25246 , -3.92787 ,
-4.19672 , -4.46557 , -4.535245, -4.60492 , -4.56803 ,
-4.53114 , -4.430325, -4.32951 , -4.208195, -4.08688 ,
-3.929505, -3.77213 , -3.633605, -3.49508 , -3.34508 ,
-3.19508 , -3.04836 , -2.90164 , -2.77705 , -2.65246 ,
-2.535245, -2.41803 , -2.300815, -2.1836 , -2.079505,
-1.97541 , -1.854095, -1.73278 , -1.64262 , -1.55246 ,
-1.47623 , -1.4 , -1.31967 , -1.23934 , -1.174585,
-1.10983 , -1.047535, -0.98524 , -0.9336 , -0.88196 ,
-0.83606 , -0.79016 , -0.74098 , -0.6918 , -0.654915]), 't': 0.0043}
#used rp= -61.75276999, t1=-41.75, t2=-21.75
BLANKSPIKE ={'tmin': 0.004, 'decay':0, 'attack': 0, 'height': 0, 'width': 0.004, 'depth': 0, 'zc1': 0.004, 'ahprec': 0, 'wave': zeros(80, Float32), 't': 0.0043, 'rp':0}
######### Bode Plots (input and transfer)
#first sample at 1Hz, sampzed every 4 Hz, last sample at 357Hz, first col is amp, second is phase
BODE10_3SOMARin=array([[ 10. , -0.120411 ],
[ 8.76628915, -0.37065249],
[ 8.61881764, -0.35894145],
[ 8.60367746, -0.60747759],
[ 6.75429426, -0.71382487],
[ 6.7692362 , -0.69142732],
[ 5.71806099, -0.87697651],
[ 4.50451846, -0.77741426],
[ 4.50725666, -0.73454663],
[ 4.6735331 , -0.76698583],
[ 5.00659179, -0.71069939],
## 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 2 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, write to the Free Software Foundation, Inc., 59 Temple ## Place, Suite 330, Boston, MA 02111-1307 USA ## import wx from mien.math.array import zeros, vstack, ravel, reshape, array, round ArrayType=type(zeros(1)) def FileBrowse(master, dict, control): dlg=wx.FileDialog(master, message="Select file name", style=wx.OPEN) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: control.SetValue(dlg.GetPath()) dlg.Destroy() def DirBrowse(master, dict, control): dlg=wx.DirDialog(master, message="Select Directory Name", style=wx.DD_NEW_DIR_BUTTON) dlg.CenterOnParent() if dlg.ShowModal() == wx.ID_OK: control.SetValue(dlg.GetPath())