/usr/lib/python2.7/dist-packages/tessa.py is in tessa 0.3.1-6.1build4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 | """Generate HDF5 optical structures for FDTD simulations"""
import Numeric,math,types,tables
_array=Numeric.array
_sqrt=math.sqrt
_resize=Numeric.resize
def _alwaystrue(x,y,z):
return True
def _spherefunc(x0,y0,z0,r,x,y,z):
return ((x0-x)**2+(y0-y)**2+(z0-z)**2<r**2)
def _ellipsefunc(x0,y0,rx,ry,x,y):
if(rx<ry):
# vertical ellipse
f1x=x0
f2x=x0
f1y=y0+_sqrt(ry**2-rx**2)
f2y=y0-_sqrt(ry**2-rx**2)
r=ry
else:
# horizontal ellipse
f1x=x0+_sqrt(rx**2-ry**2)
f2x=x0-_sqrt(rx**2-ry**2)
f1y=y0
f2y=y0
r=rx
return (_sqrt((x-f1x)**2+(y-f1y)**2)+_sqrt((x-f2x)**2+(y-f2y)**2) < 2*r)
class IndexFile:
"""Workspace class to build HDF5 index files
This class defines a workspace in which you can put geometric
structures, and finally you can write them to a HDF5 file."""
def __init__(self,lx,ly,lz,index=1):
"""Initialize an IndexFile structure
lx, ly, lz: dimensions of the workspace, in metric units
index: the default index in this workspace (default: 1)"""
self.lx=float(lx)
self.ly=float(ly)
self.lz=float(lz)
self.index=float(index)
self.structlist=[]
def write(self,filename,delta_x=1.,oversampling=4):
"""Actually write the data to a HDF5 file
filename: name of the HDF5 file to be created
delta_x: space step of the final grid (default=1.)
oversampling: the grid is subdivized in a higher resolution grid
to smooth the borders. This parameter sets how much
better it should be (default: 4)"""
delta_x=float(delta_x)
nx=int(math.ceil(self.lx/delta_x))
ny=int(math.ceil(self.ly/delta_x))
nz=int(math.ceil(self.lz/delta_x))
indexarr=_resize(float(self.index),(nx,ny,nz))
absorarr=None
do_absor=False
for struct in self.structlist:
if(struct.absor):
do_absor=True
absorarr=_resize(0.,(nx,ny,nz))
break
for i in range(nx):
x=i*delta_x
try:
for struct in self.structlist:
assert x+delta_x<struct.x1 or x>struct.x2
except AssertionError:
for j in range(ny):
y=j*delta_x
try:
for struct in self.structlist:
assert y+delta_x<struct.y1 or y>struct.y2
except AssertionError:
for k in range(nz):
z=k*delta_x
try:
for struct in self.structlist:
assert z+delta_x<struct.z1 or z>struct.z2
except AssertionError:
tmpdata=_resize(float(self.index),
(oversampling,oversampling,oversampling))
if(do_absor):
tmpdata2=_resize(0.,
(oversampling,oversampling,oversampling))
for struct in self.structlist:
struct.local_index_absor_fill(x,y,z,delta_x,
oversampling,
tmpdata,
tmpdata2)
absorarr[i][j][k]=sum(sum(sum(tmpdata2)))/oversampling**3
else:
for struct in self.structlist:
struct.local_index_fill(x,y,z,delta_x,
oversampling,
tmpdata)
indexarr[i][j][k]=sum(sum(sum(tmpdata)))/oversampling**3
if(filename[-3:]!='.h5'): filename+='.h5'
f=tables.openFile(filename,mode='w')
f.createArray(f.root, 'index', indexarr)
if(do_absor):
f.createArray(f.root, 'absor', absorarr)
f.close()
def addobj(self,struct):
"""Add a geometric object to the structure
struct: the object to add (must be a GeomStruct instance)"""
assert isinstance(struct,GeomStruct)
self.structlist.append(struct)
class GeomStruct:
"""Generic geometric object class"""
def __init__(self,func,x1,x2,y1,y2,z1,z2,index=1,absor=0,check_bounds=False):
"""Create a generic geometric object
func: a 3-argument function describing the object. func(x,y,z)
must be True when inside the object, and False outside
x1,x2,y1,y2,z1,z2: bounds outside which func(x,y,z) is always
False, i.e. a bounding box surrounding the
object
index: the refractive index inside the object (default=1.)
absor: the absorption coefficient inside the object (default=0.)
check_bounds: set it to True when func(x,y,z) is not guaranteed
to be False outside the bounding box. E.g. if
func(x,y,z) is always True you can use it to
build a block (default=False)"""
self.index=float(index)
self.absor=float(absor)
assert type(func) is types.FunctionType
self.func=func
self.x1=float(x1)
self.x2=float(x2)
self.y1=float(y1)
self.y2=float(y2)
self.z1=float(z1)
self.z2=float(z2)
self.check_bounds=check_bounds
def isinside(self,x,y,z):
"""Check whether a given coordinate is inside the geometric object
x,y,z: coordinates of where to check"""
if(self.check_bounds):
if(x<self.x1 or x>=self.x2
or y<self.y1 or y>=self.y2
or z<self.z1 or z>=self.z2):
return False
return self.func(x,y,z)
def local_index_fill(self,x0,y0,z0,delta_x,nb,ar):
"""Fill an cubic array with the index of the object at the
coordinates where we are inside.
x0,y0,z0: coordinates of the starting corner of the array
delta_x: the space step between two consecutive positions in the
array
nb: number of cells in each direction
ar: the array to be filled, of size nb^3"""
if(x0+1<self.x1 or x0>self.x2 or
y0+1<self.y1 or y0>self.y2 or
z0+1<self.z1 or z0>self.z2):
return
for i in range(nb):
x=x0+i*delta_x/nb
for j in range(nb):
y=y0+j*delta_x/nb
for k in range(nb):
z=z0+k*delta_x/nb
if self.isinside(x,y,z):
ar[i,j,k]=self.index
def local_index_absor_fill(self,x0,y0,z0,delta_x,nb,ar,ar2):
"""Fill an cubic array with the index of the object at the
coordinates where we are inside, and another array with the absorption
coefficient.
x0,y0,z0: coordinates of the starting corner of the array
delta_x: the space step between two consecutive positions in the
array
nb: number of cells in each direction
ar: the array to be filled with the index, of size nb^3
ar2: the array to be filled with the absorption coefficient, same size"""
if(x0+1<self.x1 or x0>self.x2 or
y0+1<self.y1 or y0>self.y2 or
z0+1<self.z1 or z0>self.z2):
return
for i in range(nb):
x=x0+i*delta_x/nb
for j in range(nb):
y=y0+j*delta_x/nb
for k in range(nb):
z=z0+k*delta_x/nb
if self.isinside(x,y,z):
ar[i,j,k]=self.index
ar2[i,j,k]=self.absor
class Block(GeomStruct):
"""Block object class"""
def __init__(self,x1,x2,y1,y2,z1,z2,index=1,absor=0):
"""Create and initialize a block object
x1,x2,y1,y2,z1,z2: bounding coordinates for the block
index: refractive index inside the block (default=1.)
absor: the absorption coefficient inside the object (default=0.)"""
GeomStruct.__init__(self,_alwaystrue,
x1,x2,y1,y2,z1,z2,index=index,absor=absor,check_bounds=True)
class Sphere(GeomStruct):
"""Sphere object class"""
def __init__(self,x0,y0,z0,r,index=1,absor=0):
"""Create and initialize a sphere object
x0,y0,z0: center of the sphere
r: radius of the sphere
index: refractive index inside the sphere (default=1.)
absor: the absorption coefficient inside the object (default=0.)"""
self.center=(x0,y0,z0)
self.radius=r
GeomStruct.__init__(self,(lambda x,y,z:_spherefunc(x0,y0,z0,r,x,y,z)),
x0-r,x0+r,y0-r,y0+r,z0-r,z0+r,index=index,absor=absor)
# We define a prism by:
# * a projection plane: x, y or z (c=0)
# * an axis - by default it is orthogonal to the plane
# * a 2D function of the remaining variables in this plane
# * the limits of this function *in the plane* a1<a<a2, b1<b<b2
# with (a,b) = (y,z) or (x,z) or (x,y) depending on the projection
# * the height of the prism, h = c2-c1
class Prism(GeomStruct):
"""Generic prism object class"""
def __init__(self,func,a1,a2,b1,b2,c1,c2,
projplane='z',index=1,absor=0,axis=None):
"""Create and initialize a generic prism object
func: a 2-variable function returning True when inside the
object, with the two arguments being the coordinates
inside the projection plane
a1,a2,b1,b2: the bounding box outside which func(a,b)
is always False.
c1,c2: the limits of our prism for the coordinate orthogonal
to the projection plane
projplane: the projection plane, defined by its normal
direction. Must be either of 'x', 'y', or 'z'
(default='z')
index: the refractive index inside the structure (default=1.)
absor: the absorption coefficient inside the object (default=0.)
axis: a tuple of length 3, defining a vector outside the
projection plane, which is the projection direction
(default= normal to the projection plane)"""
assert type(func) is types.FunctionType
self.func2d=func
xcoef,ycoef,zcoef=0.,0.,0.
# check the axis is valid
assert projplane in ('x','y','z')
foo={'x':(1,0,0),'y':(0,1,0),'z':(0,0,1)}
if(axis==None): axis=foo[projplane]
assert type(axis) is types.TupleType and len(axis)==3
assert map((lambda a,b:a*b),axis,foo[projplane]) != [0,0,0]
axis=map(float,axis)
if(projplane=='x'):
ycoef=axis[1]/axis[0]
zcoef=axis[2]/axis[0]
x1,x2=c1,c2
y1=a1+min(x1*ycoef,x2*ycoef)
y2=a2+max(x1*ycoef,x2*ycoef)
z1=b1+min(x1*zcoef,x2*zcoef)
z2=b2+max(x1*zcoef,x2*zcoef)
f=lambda x,y,z: self.func2d(y-x*ycoef,z-x*zcoef)
elif(projplane=='y'):
xcoef=axis[0]/axis[1]
zcoef=axis[2]/axis[1]
y1,y2=c1,c2
x1=a1+min(y1*xcoef,y2*xcoef)
x2=a2+max(y1*xcoef,y2*xcoef)
z1=b1+min(y1*zcoef,y2*zcoef)
z2=b2+max(y1*zcoef,y2*zcoef)
f=lambda x,y,z: self.func2d(x-y*xcoef,z-y*zcoef)
else: # projplane == 'z'
xcoef=axis[0]/axis[2]
ycoef=axis[1]/axis[2]
z1,z2=c1,c2
x1=a1+min(z1*xcoef,z2*xcoef)
x2=a2+max(z1*xcoef,z2*xcoef)
y1=b1+min(z1*ycoef,z2*ycoef)
y2=b2+max(z1*ycoef,z2*ycoef)
f=lambda x,y,z: self.func2d(x-z*xcoef,y-z*ycoef)
GeomStruct.__init__(self,f,x1,x2,y1,y2,z1,z2,index=index,absor=absor,
check_bounds=True)
class Cylinder(Prism):
"""Cylinder object class"""
def __init__(self,a0,b0,ra,rb,c1,c2,
projplane='z',index=1,absor=0,axis=None):
"""Create and initialize a cylinder object
a0,b0: the coordinates of the center of the cylinder in the
projection plane
ra,rb: the two radii of the ellipse centered at (a0,b0). If
rb=None, it is taken equal to ra and we have a circle
c1,c2: the limits of our cylinder for the coordinate orthogonal
to the projection plane
projplane: the projection plane, defined by its normal
direction. Must be either of 'x', 'y', or 'z'
(default='z')
index: the refractive index inside the structure (default=1.)
absor: the absorption coefficient inside the object (default=0.)
axis: a tuple of length 3, defining a vector outside the
projection plane, which is the projection direction
(default= normal to the projection plane)"""
if rb==None: rb=ra
Prism.__init__(self,(lambda a,b: _ellipsefunc(a0,b0,ra,rb,a,b)),
a0-ra,a0+ra,b0-rb,b0+rb,c1,c2,projplane=projplane,
index=index,absor=absor,axis=axis)
def _coneprojfunc(a,b,c,a0,b0,c0,c1,func2d):
if c==c0:
return True
return func2d(a0+(a-a0)*(c1-c0)/(c-c0),b0+(b-b0)*(c1-c0)/(c-c0))
class GenericCone(GeomStruct):
"""Generic cone object class"""
def __init__(self,func,a1,a2,b1,b2,c1,c2,x0,y0,z0,
projplane='z',index=1,absor=0):
"""Create and initialize a generic cone object
func: a 2-variable function returning True when inside the
object, with the two arguments being the coordinates
inside the projection plane (the c=c1 plane)
a1,a2,b1,b2: the bounding box outside which func(a,b)
is always False
c1,c2: the limits of our prism for the coordinate orthogonal
to the projection plane; c1 is taken as the plane
where we calculate the 2D function
x0,y0,z0: the position of the vertex
projplane: the projection plane, defined by its normal
direction. Must be either of 'x', 'y', or 'z'
(default='z')
index: the refractive index inside the structure (default=1.)
absor: the absorption coefficient inside the object (default=0.)"""
assert type(func) is types.FunctionType
self.func2d=func
assert projplane in ('x','y','z')
c1=float(c1)
c2=float(c2)
if(projplane=='x'):
x1=min(c1,c2)
x2=max(c1,c2)
lis=(a1,a2,y0+(a1-y0)*(c2-x0)/(c1-x0),y0+(a2-y0)*(c2-x0)/(c1-x0))
y1=min(lis)
y2=max(lis)
lis=(b1,b2,z0+(b1-z0)*(c2-x0)/(c1-x0),z0+(b2-z0)*(c2-x0)/(c1-x0))
z1=min(lis)
z2=max(lis)
f=lambda x,y,z: _coneprojfunc(y,z,x,y0,z0,x0,c1,self.func2d)
elif(projplane=='y'):
y1=min(c1,c2)
y2=max(c1,c2)
lis=(a1,a2,x0+(a1-x0)*(c2-y0)/(c1-y0),x0+(a2-x0)*(c2-y0)/(c1-y0))
x1=min(lis)
x2=max(lis)
lis=(b1,b2,z0+(b1-z0)*(c2-y0)/(c1-y0),z0+(b2-z0)*(c2-y0)/(c1-y0))
z1=min(lis)
z2=max(lis)
f=lambda x,y,z: _coneprojfunc(x,z,y,x0,z0,y0,c1,self.func2d)
else: # projplane == 'z'
z1=min(c1,c2)
z2=max(c1,c2)
lis=(a1,a2,x0+(a1-x0)*(c2-z0)/(c1-z0),x0+(a2-x0)*(c2-z0)/(c1-z0))
x1=min(lis)
x2=max(lis)
lis=(b1,b2,y0+(b1-y0)*(c2-z0)/(c1-z0),y0+(b2-y0)*(c2-z0)/(c1-z0))
y1=min(lis)
y2=max(lis)
f=lambda x,y,z: _coneprojfunc(x,y,z,x0,y0,z0,c1,self.func2d)
GeomStruct.__init__(self,f,x1,x2,y1,y2,z1,z2,index=index,absor=absor,
check_bounds=True)
class Cone(GenericCone):
"""Ellipsoidal cone object class"""
def __init__(self,a0,b0,ra,rb,c1,c2,cvertex,
avertex=None,bvertex=None,
projplane='z',index=1,absor=0):
"""Create and initialize an ellipsoidal cone object
a0,b0: the coordinates of the center of the ellipse in the
projection plane
ra,rb: the two radii of the ellipse centered at (a0,b0). If
rb=None, it is taken equal to ra and we have a circle
c1,c2: the limits where to truncate the cone for the coordinate
orthogonal to the projection plane; c1 is the coordinate
where we calculate the ellipse
cvertex: the coordinate of the vertex in the direction orthogonal
to the projection plane
avertex,bvertex: same in the other directions (default to a0,b0)
projplane: the projection plane, defined by its normal
direction. Must be either of 'x', 'y', or 'z'
(default='z')
index: the refractive index inside the structure (default=1.)
absor: the absorption coefficient inside the object (default=0.)"""
if rb==None: rb=ra
if avertex==None: avertex=a0
if bvertex==None: bvertex=b0
assert projplane in ('x','y','z')
if(projplane=='x'):
x0,y0,z0=cvertex,avertex,bvertex
elif(projplane=='y'):
x0,y0,z0=avertex,cvertex,bvertex
else:
x0,y0,z0=avertex,bvertex,cvertex
GenericCone.__init__(self,(lambda a,b: _ellipsefunc(a0,b0,ra,rb,a,b)),
a0-ra,a0+ra,b0-rb,b0+rb,c1,c2,x0,y0,z0,
projplane=projplane,index=index,absor=absor)
|