def invFile(filenameIn, filenameOut):
print " -- Checking if we need to invert?",
# Find the amount of translation we need to do!
data = ReadFile(filenameIn)
dataLines = [l for l in data.split("\n") if l.strip() and not l.strip().startswith("#") ]
CommentLines = [l for l in data.split("\n") if l.strip() and l.strip().startswith("#") ]
xmin,xmax = None,None
outData = CommentLines
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
xmin = min( [xmin,x,X] ) if xmin != None else min( [x,X] )
xmax = max( [xmax,x,X] ) if xmax != None else max( [x,X] )
if not( xmin<=0 and xmax <=0):
print " No, xmin,max:", xmin,xmax
WriteFile(filenameOut, data)
else:
print " Yes, xmin,max:", xmin,xmax
# Ok, we have no positive x's:
outData = CommentLines
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
x = x * -1
X = X * -1
outData.append( "\t".join( [str(g) for g in [i,t,x,y,z,X,Y,Z,p] ] ) )
WriteFile( filenameOut, "\n".join( outData) )
def nrnXYZToSWC(srcFilename, sinkFilename):
datestr = datetime.datetime.now().strftime("%d-%B-%Y")
print " -- Converting to SWC"
# Find the amount of translation we need to do!
data = ReadFile(srcFilename)
dataLines = [l for l in data.split("\n") if l.strip() and not l.strip().startswith("#") ]
CommentLines = [l for l in data.split("\n") if l.strip and l.strip().startswith("#") ]
outData = CommentLines + ["# Converted from xyz to swc using nrnXYZtoSWC.py" + " on: %s" %datestr] #["# Translated by (%d,%d,%d) using nrnTranslate.py"%translation + " On: %s"%datestr] + ["# Corrected for shrinkage (x1.28) using nrnScaled.py" + " On: %s"%datestr] + ["# Files Concatenated by nrnConcatenate.py" + " on: %s"%datestr] + ["# Converted from xyz to swc using nrnXYZtoSWC.py" + " on: %s" %datestr]
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
sX = (float(x)+float(X)) / 2.0
sY = (float(y)+float(Y)) / 2.0
sZ = (float(z)+float(Z)) / 2.0
dX = float(x) - float(X)
dY = float(y) - float(Y)
dZ = float(z) - float(Z)
d = math.sqrt( dX**2 + dY**2 + dZ**2 )
r = d / 2.0
r = r if r > 0.15 else 0.15
outData.append( "\t".join( [str(g) for g in [i,t,sX,sY,sZ,r,p] ] ) )
WriteFile( sinkFilename, "\n".join( outData) )
def nrnConcatenateXYZS( srcFilename1, srcFilename2, sinkFilename):
datestr = datetime.datetime.now().strftime("%d-%B-%Y")
print " -- Concatentating Files"
D1 = ReadFile(srcFilename1)
D2 = ReadFile(srcFilename2)
dataLines1 = [l for l in D1.split("\n") if l.strip() and not l.strip().startswith("#") ]
dataLines2 = [l for l in D2.split("\n") if l.strip() and not l.strip().startswith("#") ]
CommentLines1 = [l for l in D1.split("\n") if l.strip() and l.strip().startswith("#") ]
CommentLines2 = [l for l in D2.split("\n") if l.strip() and l.strip().startswith("#") ]
# copies comment lines and adds comment line showing the processing that's been done plus date.
#outData = [ "#Comment From File1: %s"%srcFilename1 ] + CommentLines1 + [ "#Comment From File2: %s"%srcFilename2 ] + CommentLines2 + ["# Files Concatenated by nrnConcatenate.py" + " on: %s"%datestr]
outData = CommentLines1 + CommentLines2 + ["# Files Concatenated by nrnConcatenate.py" + " on: %s"%datestr]
# Remap the id's
# Write Datafile 1
idMap = {}
for l in dataLines1:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
new_id = len(idMap) + 1
new_p = p if p ==-1 else idMap[ (0,p) ]
outData.append( "\t".join( [str(g) for g in [new_id,t,x,y,z,X,Y,Z,new_p] ] ) )
idMap[ (0,i) ] = new_id
#print srcFilename2
# Write Datafile 2
for l in dataLines2:
#print l
#print
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
new_id = len(idMap) + 1
#print p
new_p = p if p ==-1 else idMap[(1,p)]
outData.append( "\t".join( [str(g) for g in [new_id,t,x,y,z,X,Y,Z,new_p] ] ) )
idMap[(1,i)] = new_id
WriteFile( sinkFilename, "\n".join( outData) )
def nrnScale(srcFilename, sinkFilename, scaleFactor):
datestr = datetime.datetime.now().strftime("%d-%B-%Y")
# Find the amount of translation we need to do!
data = ReadFile(srcFilename)
dataLines = [l for l in data.split("\n") if l.strip() and not l.strip().startswith("#") ]
CommentLines = [l for l in data.split("\n") if l.strip() and l.strip().startswith("#") ]
outData = CommentLines + ["# Corrected for shrinkage (x1.28) using nrnScaled.py" + " On: %s"%datestr]
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
x *= scaleFactor
y *= scaleFactor
z *= scaleFactor
X *= scaleFactor
Y *= scaleFactor
Z *= scaleFactor
outData.append( "\t".join( [str(g) for g in [i,t,x,y,z,X,Y,Z,p] ] ) )
WriteFile( sinkFilename, "\n".join( outData) )
def TranslateFile(filenameIn, filenameOut, translation):
datestr = datetime.datetime.now().strftime("%d-%B-%Y")
# Find the amount of translation we need to do!
data = ReadFile(filenameIn)
dataLines = [l for l in data.split("\n") if l.strip() and not l.strip().startswith("#") ]
CommentLines = [l for l in data.split("\n") if l.strip() and l.strip().startswith("#") ]
# copies comment lines and adds comment line showing the processing that's been done plus date.
#outData = CommentLines + ["# Translated by (%d,%d,%d) using nrnTranslate.py"%translation] + ["# On: %s"%datestr]
outData = CommentLines + ["# Translated by (%d,%d,%d) using nrnTranslate.py"%translation + " On: %s"%datestr]
#outData = outData + ["# On: %s"%datestr]
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
x = x + translation[0]
y = y + translation[0]
z = z + translation[0]
X = X + translation[0]
Y = Y + translation[0]
Z = Z + translation[0]
outData.append( "\t".join( [str(g) for g in [i,t,x,y,z,X,Y,Z,p] ] ) )
WriteFile( filenameOut, "\n".join( outData) )
def nrnTranslate( nsFilenameSrc, nrnFilenameSrc,nsFilenameSink, nrnFilenameSink):
print " -- Finding Translation"
nsData = ReadFile(nsFilenameSrc)
# Find the amount of translation we need to do!
dataLines = [l for l in nsData.split("\n") if l.strip() and not l.strip().startswith("#") ]
tPoint = None
for l in dataLines:
i,t,x,y,z,X,Y,Z,p = extractXYZLine(l)
if p==-1 and t==9:
assert not tPoint
tPoint = (-1.0*x,-1.0*y,-1.0*z)
assert tPoint
print " -- Translating by", tPoint
TranslateFile(nsFilenameSrc, nsFilenameSink, tPoint)
TranslateFile(nrnFilenameSrc, nrnFilenameSink, tPoint)