def _hls2rgb(self,h):
"""
We use a rescaled h \in [0,1]
h von 0 .. 360
letztes argument ist ein flag 0 oder 1, der entscheided ob
die gruenen farben noch staerker auseinandergezogen werden,
da wir gruen so gut sehen koennen.
sonst: l = 0.5, s = 1 ist meist sinnvoll,
l = 0: schwarz, l=1 weiss, s: saettigung
"""
h=h**self.exponent
if(self.invert): h=1.0-h
h=h*360.0
h=Numeric.fmod(h,360.0)
if(self.hls_hls):
h=h/60.0
else:
if(h<120):
h=h/120.0 # /* 0..1 Rot..(Orange)..Gelb */
elif(h<180):
h=h/60.0 - 1.0 # /* 1..2 Gelb..Gruen */
elif(h<240):
h=h/30.0 - 4.0 # /* 2..4 Gruen..Blaugruen..Blau*/
else:
h=h/60.0 # /* 4..6 Blau..Purpur..Rot */
c=int(h)
frac=h-c
if (self.hls_l<=0.5):
maxi=self.hls_l*(1.0+self.hls_s)
else:
maxi=self.hls_l+self.hls_s-self.hls_l*self.hls_s
mini=2*self.hls_l-maxi;
diff=maxi-mini;
if(self.hls_s==0): # /* grau */
return(1.0,1.0,1.0)
else:
if(c==0):
return(maxi,mini+frac*diff,mini)
elif(c==1):
return(mini+(1.0-frac)*diff,maxi,mini)
elif(c==2):
return(mini,maxi,mini+frac*diff)
elif(c==3):
return(mini,mini+(1.0-frac)*diff,maxi)
elif(c==4):
return(mini+frac*diff,mini,maxi)
else:
return(maxi,mini,mini+(1.0-frac)*diff)
def addImproperTerm(self, data, improper, object, global_data):
if not self.arguments[2]:
return
a1 = improper.a1
a2 = improper.a2
a3 = improper.a3
a4 = improper.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.improperParameters(t1, t2, t3, t4)
if terms is not None:
atoms = [(t2,i2,a2), (t3,i3,a3), (t4,i4,a4)]
atoms.sort(_order)
i2, i3, i4 = tuple(map(lambda t: t[1], atoms))
a2, a3, a4 = tuple(map(lambda t: t[2], atoms))
v1 = a2.position()-a3.position()
v2 = a3.position()-a1.position()
v3 = a4.position()-a1.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i2, i3, i1, i4,
p[0], phase) + p[2:])
def addDihedralTerm(self, data, dihedral, object, global_data):
if not self.arguments[2]:
return
a1 = dihedral.a1
a2 = dihedral.a2
a3 = dihedral.a3
a4 = dihedral.a4
i1 = a1.index
i2 = a2.index
i3 = a3.index
i4 = a4.index
global_data.add('1_4_pairs', (i1, i4))
t1 = global_data.atom_type[a1]
t2 = global_data.atom_type[a2]
t3 = global_data.atom_type[a3]
t4 = global_data.atom_type[a4]
terms = self.dataset.dihedralParameters(t1, t2, t3, t4)
if terms is not None:
v1 = a1.position()-a2.position()
v2 = a2.position()-a3.position()
v3 = a4.position()-a3.position()
a = v1.cross(v2).normal()
b = v3.cross(v2).normal()
cos = a*b
sin = b.cross(a)*v2/v2.length()
dihedral = Transformation.angleFromSineAndCosine(sin, cos)
if dihedral > Numeric.pi:
dihedral = dihedral - 2.*Numeric.pi
for p in terms:
if p[2] != 0.:
mult = p[0]
phase = Numeric.fmod(Numeric.pi-mult*dihedral,
2.*Numeric.pi)
if phase < 0.:
phase = phase + 2.*Numeric.pi
data.add('dihedrals', (i1, i2, i3, i4,
p[0], phase) + p[2:])
def angles(imagefilename):
im=Image.open(imagefilename)
#im.thumbnail((20,50))
for i in range(0):
im=im.filter(ImageFilter.SMOOTH)
img=Numeric.reshape(Numeric.fromstring(im.convert("L").tostring(),
Numeric.UnsignedInt8),
(im.size[1],im.size[0]))
img=img.astype(Numeric.Complex16)
# img_freq=FFT.fft2d(img)
gsize=11
sigma=1
gauss=iagaussian([gsize,gsize],[gsize//2,gsize//2],
[[sigma,0],[0,sigma]]).astype(Numeric.Complex16)
#print Numeric.array2string(gauss,precision=3,suppress_small=1)
# kernel_freq=FFT.fft2d(gauss)
sys.stdout.write("convolve...")
sys.stdout.flush()
img=iaconv(img,gauss)
print "done"
# img=FFT.inverse_fft2d(img_freq)
# we can skip borders, which have blur errors anyhow
margin=gsize
img=img[margin:-1-margin,margin:-1-margin]
view(img)
ix=deriv(img,0)
view(ix)
iy=deriv(img,1)
view(iy)
x=ix-iy*1j
angs=Numeric.fmod(-Numeric.arctan2(x.imag,x.real)+pi,pi)
mags=abs(Numeric.sqrt(ix*ix+iy*iy))
view(angs)
histo={} # angle:freq
degreesperbucket=.1
buckets=180/degreesperbucket
totalcounted=0
for ang,mag in zip(Numeric.ravel(angs),Numeric.ravel(mags)):
ang=int(ang*buckets)/buckets
histo[ang]=histo.get(ang,0)+mag
totalcounted+=mag
keys=histo.keys()
keys.sort()
f=open("angles.data",'w')
for k in keys:
degrees=k*360/(2*pi)
print >>f,"%.3f %f" % (degrees,histo[k])
# remark on counts that are more than 1% of the total
if histo[k]>totalcounted*.005:
print "peak at",degrees
