def doAlignment(self, conv):
d=self.getElements("Data")
a=self.getElements("AbstractModel")
if a:
#FIXME: analytical fields aren't supported yet
raise StandardError('No support of analytical fields yet')
trans = [conv.get("Trans_x", 0.0), conv.get("Trans_y", 0.0), conv.get("Trans_z", 0.0)]
scale = array([conv.get("Scale_x", 1.0), conv.get("Scale_y", 1.0), conv.get("Scale_z", 1.0)])
rot = array([conv.get("Rot_x", 0.0), conv.get("Rot_y", 0.0), conv.get("Rot_z", 0.0)])
if d:
if any(rot):
vects = row_stack([self.attributes.get("Vertical", (0,1,0.0)),
self.attributes.get("Depth", (0,0,-1.0)),
self.attrib("Origin")
])
vects=rotate3D(vects, rot)
self.setAttrib("Vertical", vects[0,:].tolist())
self.setAttrib("Depth", vects[1,:].tolist())
self.setAttrib("Origin", vects[2,:].tolist())
if any(scale!=1.0):
e=array(self.attrib("Edge"))*scale
o=array(self.attrib("Origin"))*scale
self.setAttrib('Origin', o.tolist())
self.setAttrib('Edge', e.tolist())
if any(trans):
o=array(self.attrib("Origin"))+trans
self.setAttrib('Origin', o.tolist())
def arrayfromstring(s, prec=None):
if '(' in s:
shape, values=s.split(':')
return reshape(arrayfromstring(values), eval(shape))
elif ";" in s:
return vstack([arrayfromstring(l) for l in s.split(';')])
elif prec or ("." in s):
return array(map(float, s.split(',')))
else:
return array(map(int, s.split(',')))
def setPoints(self, a, append=None): '''a (array), append (bool=False) => None sets self.points to the specified array. If append is true, it adds this array to the existing self.points''' if type(a)!=ArrayType: a=array(a, Float32) if not append or self.points==None or self.points.shape[0]==0: if len(a.shape)==1: a=array([a]) self.points = a.copy() else: if len(a.shape)==2: self.points = concatenate([self.points, a]) else: self.points = add_point(self.points, a)
def getData(self):
de = self.getElements("Data")
if de:
return de[0]
else:
print "Can't find a data element. Making an empty one"
from mien.nmpml.data import newData
attrs = {"Type":"sfield", "Edge":self.attrib("Edge"), "Origin":self.attrib("Origin")}
a=array([[[]]])
d = newData(a, attrs)
self.newElement(d)
return d
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 treeToPoints(nodes):
points = []
labels={}
for i, n in enumerate(nodes):
point=[]
for v in ['x' , 'y', 'z' ]:
point.append(float(n['attributes'][v]))
if n['attributes'].has_key('d'):
point.append(float(n['attributes']['d']))
l=n['attributes'].get('Description')
if l:
labels[i]=l
points.append(point)
points=array(points)
return (points, labels)
def pypos2fed(f):
points, head = readPyPos(f)
correctedpoints = []
labels = {}
for n in points.keys():
labels[len(correctedpoints)] = n.strip()
p = points[n]
p = (p[1], p[0], -p[2])
correctedpoints.append(p)
points = array(correctedpoints)
fed = mien.nmpml.elements["Fiducial"](
attribs={"Name": "LeicaStageCoordinates", "Style": "points", "MarkerType": "OpenQuadStar"},
container=None,
points=points,
labels=labels,
)
n = mien.nmpml.elements["NmpmlDocument"](attribs={"Name": "Doc"}, tag="NmpmlDocument")
n.newElement(fed)
return n
## 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
##
from mien.math.array import array,zeros,Float32
######### Spike Wave Forms =========
SPIKE10_3={'tmin': 0.0009, 'rp':-61.0,'decay': -192151.25, 'attack': 145800.75, 'height': 76.813189999999992, 'width': 0.00050000000000000001, 'depth': 4.604920000000007, 'zc1': 0.0005, 'ahprec': -63.936369999999997, 'wave': array([ 0.54263 , 0.56312 , 0.58361 , 0.619675, 0.65574 ,
0.68033 , 0.70492 , 0.749185, 0.79345 , 0.8664 ,
0.93935 , 1.15738 , 1.37541 , 3.47299 , 6.10088 ,
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 ],
##
## 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
##
from mien.math.array import nonzero1d, zeros, Float32, array, reshape
import mien.parsers.nmpml
EDGE=4.2
EXTENT=(100,100,100)
ORIGIN=array((-161.89,-298.07,-131.32))
def writeDensityFile(of, a, **kwargs):
thresh=kwargs.get('thresh', .000001)
norm=kwargs.get('norm', None)
of.write("%.6g #Max Density\n" % a.max())
of.write("0 #Directional tuning (meaningless)\n")
if norm:
a=a*norm*(1.0/a.max())
if thresh:
nz=nonzero1d(a>thresh*a.max())
#print nz[0].min(), nz[0].max()
#print nz[1].min(), nz[1].max()
#print nz[2].min(), nz[2].max()
xr=range(nz[0].min(), nz[0].max())
