def __setitem__(self, index, value):
"""Override built in.
This is called when instance is called to assign a value,
e.g.:
matrix[3, 'A'] = (entry1, entry2)"""
if type(index) == types.TupleType:
row, colName = index
else:
raise IndexError("index is not a tuple")
if type(value) == types.TupleType:
value1, value2 = value
elif type(value) == types.StringType:
value = value
else:
raise ValueError("value being assigned is not a tuple")
if colName in self.colList:
# find the location in order in the array
col = self.colList.index(colName)
# calculate the offsets to the actual array location
col1 = col * 2
col2 = col1 + 1
# store each element in turn
self.array[(row,col1+self.extraCount)] = asarray(value1,self._typecode)
self.array[(row,col2+self.extraCount)] = asarray(value2,self._typecode)
elif colName in self.extraList:
col = self.extraList.index(colName)
self.array[(row,col)] = asarray(value,self._typecode)
else:
raise KeyError("can't find %s column" % col)
def __setitem__(self, index, value):
"""Override built in.
This is called when instance is called to assign a value,
e.g.:
matrix[3, 'A'] = (entry1, entry2)"""
if type(index) == types.TupleType:
row, colName = index
else:
raise IndexError("index is not a tuple")
if type(value) == types.TupleType:
value1, value2 = value
elif type(value) == types.StringType:
value = value
else:
raise ValueError("value being assigned is not a tuple")
if colName in self.colList:
# find the location in order in the array
col = self.colList.index(colName)
# calculate the offsets to the actual array location
col1 = col * 2
col2 = col1 + 1
# store each element in turn
self.array[(row, col1 + self.extraCount)] = asarray(
value1, self._typecode)
self.array[(row, col2 + self.extraCount)] = asarray(
value2, self._typecode)
elif colName in self.extraList:
col = self.extraList.index(colName)
self.array[(row, col)] = asarray(value, self._typecode)
else:
raise KeyError("can't find %s column" % col)
def exercise_generalized_inverse_numpy(): #print 'Numeric' from Numeric import asarray from LinearAlgebra import generalized_inverse m = asarray([[1,1],[0,0]]) n = generalized_inverse(m) #print 'matrix \n',m #print 'inverse\n', n m = asarray([[1,1,1],[0,0,0],[0,0,0]]) n = generalized_inverse(m)
def exercise_generalized_inverse_numpy():
#print 'Numeric'
from Numeric import asarray
from LinearAlgebra import generalized_inverse
m = asarray([[1, 1], [0, 0]])
n = generalized_inverse(m)
#print 'matrix \n',m
#print 'inverse\n', n
m = asarray([[1, 1, 1], [0, 0, 0], [0, 0, 0]])
n = generalized_inverse(m)
def __rmul__(self, other):
import copy
from Numeric import asarray, matrixmultiply
a = copy.copy(self)
if asarray(other).shape == ():
a.SetBasis(other * self.GetBasis())
elif asarray(other).shape == self.GetBasis().shape:
a.SetBasis(matrixmultiply(other, self.GetBasis()))
else:
raise ValueError, 'matrices are not aligned'
return a
def __rmul__(self,other):
import copy
from Numeric import asarray,matrixmultiply
a=copy.copy(self)
if asarray(other).shape == ():
a.SetBasis(other*self.GetBasis())
elif asarray(other).shape == self.GetBasis().shape:
a.SetBasis(matrixmultiply(other,self.GetBasis()))
else:
raise ValueError, 'matrices are not aligned'
return a
def _asarray1d(arr):
"""Ensure 1d array for one array.
"""
m = asarray(arr)
if len(m.shape)==0:
m = reshape(m,(1,))
return m
def iahistogram(f):
""" o Purpose
Image histogram.
o Synopsis
h = iahistogram(f)
o Input
f:
o Output
h:
o Description
o Examples
f = iaread('woodlog.pgm')
iashow(f)
h = iahistogram(f)
g,d = iaplot(h)
g('set data style boxes')
g.plot(d)
showfig(h)
"""
from Numeric import asarray,searchsorted,sort,ravel,concatenate,product
f = asarray(f)
n = searchsorted(sort(ravel(f)), range(max(ravel(f))+1))
n = concatenate([n, [product(f.shape)]])
h = n[1:]-n[:-1]
return h
def _asarray1d(arr):
"""Ensure 1d array for one array.
"""
m = asarray(arr)
if len(m.shape) == 0:
m = reshape(m, (1, ))
return m
def iaind2sub(dim,i):
""" o Purpose
Convert linear index to double subscripts.
o Synopsis
x,y = iaind2sub(dim,i)
o Input
dim: Dimension.
i: Index.
o Output
x:
y:
o Description
o Examples
f = Numeric.array([[0,6,0,2],[4,0,1,8],[0,0,3,0]])
print f
i = Numeric.nonzero(Numeric.ravel(f))
(x,y) = iaind2sub(f.shape, i)
print x
print y
print f[x[0],y[0]]
print f[x[4],y[4]]
"""
from Numeric import asarray
i = asarray(i)
x = i / dim[1]
y = i % dim[1]
return x,y
def setWidget(self, widget, newValue):
"""Called by AttributeControl to set our widgets' values to the observed values,
to implement refresh(). This is also used during initialization.
"""
drawingArea = widget.drawingArea
color = map(int, tuple(asarray(newValue[:3]) * 65535))
gdkColor = drawingArea.get_colormap().alloc_color(*color)
self.setColor(drawingArea, gdkColor, newValue[3])
def TranslateCoordinates(self,translation,type): """Returns a translated grid This method can be used to translate the coordinates of a grid. Two different types of translation exist * 'active' : Translates every grid point according to 'translation' * 'passive' : Translates the origin of the grid according to 'translation' This method only supports a translation vector that matches the grid coordinates and for this reason 'translation' should be specified in terms of these coordinates. """ import ArrayTools from Numeric import asarray from Vector import Vector import copy # finding the output grid translategrid=copy.copy(self) # preparing for translation and calculating origin #trunctranslation=self._GetTruncatedTranslation(translation) if type=='active': translationnumbers=self._GetTranslationNumbers(-asarray(translation)) # origin translategrid.SetOrigin(self.GetOrigin()) elif type=='passive': translationnumbers=self._GetTranslationNumbers(asarray(translation)) # origin transorigin=Vector(space=self.GetOrigin().GetSpace()) transorigin.SetCartesianCoordinates(translategrid.GetSpace().CartesianCoordinatesFromCoordinates(self.CoordinatesFromGridCoordinates(translation))) translategrid.SetOrigin(self.GetOrigin()+transorigin) else: raise ValueError, 'translation type not defined' # finding the output array translatearray=ArrayTools.Translate(self.GetArray(),translationnumbers) translategrid.SetArray(translatearray) return translategrid
def spline(x, y, yp1=None, ypn=None): """y2 = spline(x_vals,y_vals, yp1=None, ypn=None) returns the y2 table for the spline as needed by splint()""" n=len(x) u=zeros(n,Float) y2=zeros(n,Float) x=asarray(x, Float) y=asarray(y, Float) dx=x[1:]-x[:-1] dxi=1.0/dx dx2i=1.0/(x[2:]-x[:-2]) dy=(y[1:]-y[:-1]) siga=dx[:-1]*dx2i dydx=dy*dxi # u[i]=(y[i+1]-y[i])/float(x[i+1]-x[i]) - (y[i]-y[i-1])/float(x[i]-x[i-1]) u[1:-1]=dydx[1:]-dydx[:-1] #this is an incomplete rendering of u... the rest requires recursion in the loop if yp1 is None: y2[0]=u[0]=0.0 else: y2[0]= -0.5 u[0]=(3.0*dxi[0])*(dy[0]*dxi[0] -yp1) for i in range(1,n-1): sig=siga[i-1] p=sig*y2[i-1]+2.0 y2[i]=(sig-1.0)/p u[i]=(6.0*u[i]*dx2i[i-1] - sig*u[i-1])/p if ypn is None: qn=un=0.0 else: qn= 0.5 un=(3.0*dxi[-1])*(ypn- dy[-1]*dxi[-1] ) y2[-1]=(un-qn*u[-2])/(qn*y2[-2]+1.0) for k in range(n-2,-1,-1): y2[k]=y2[k]*y2[k+1]+u[k] return y2
def SetBasis(self, basis):
from Numeric import asarray
dim = len(basis)
v = dim * [0]
for i in range(dim):
try:
v[i] = basis[i].GetCartesianCoordinates()
except:
v[i] = basis[i]
self.Basis = asarray(v)
def MultiplyVector(self,vector,other): """ Multiplies a Vector with a scalar""" import copy from Numeric import asarray v=copy.copy(vector) if asarray(other).shape == (): v.SetCartesianCoordinates(other*vector.GetCartesianCoordinates()) return v else: raise ValueError, 'wrong multiplication of Vector'
def MultiplyVector(self, vector, other):
""" Multiplies a Vector with a scalar"""
import copy
from Numeric import asarray
v = copy.copy(vector)
if asarray(other).shape == ():
v.SetCartesianCoordinates(other * vector.GetCartesianCoordinates())
return v
else:
raise ValueError, 'wrong multiplication of Vector'
def SetBasis(self,basis): from Numeric import asarray dim=len(basis) v=dim*[0] for i in range(dim): try: v[i]=basis[i].GetCartesianCoordinates() except: v[i]=basis[i] self.Basis=asarray(v)
def SetArray(self,array): """Sets the array This method sets the array. The array should have the shape ( *a1* , *a2*,..., *ai* , *N1* , *N2* ,..., *NN* ) in case of a grid having *i* components in a *N* dimensional space. *Ni* corresponds to the number of values along each axis. Note that even though the array is given in terms of a tuple or a list it will be converted to a NumPy array. """ self.Array=asarray(array)
def validate ( self, object, name, value ):
""" Validates that a value is legal for the trait.
"""
try:
# Make sure the value is an array:
type_value = type( value )
if type_value is not ArrayType:
if type_value not in SequenceTypes:
self.error( object, name, self.repr( value ) )
value = asarray( value, self.typecode )
# Make sure the array is of the right type:
if ((self.typecode is not None) and
(value.typecode() != self.typecode)):
if self.coerce:
value = value.astype( self.typecode )
else:
value = asarray( value, self.typecode )
# If no shape requirements, then return the value:
trait_shape = self.shape
if trait_shape is None:
return value
# Else make sure that the value's shape is compatible:
value_shape = value.shape
if len( trait_shape ) == len( value_shape ):
for i, dim in enumerate( value_shape ):
item = trait_shape[i]
if item is not None:
if type( item ) is int:
if dim != item:
break
elif ((dim < item[0]) or
((item[1] is not None) and (dim > item[1]))):
break
else:
return value
except:
pass
self.error( object, name, self.repr( value ) )
def validate(self, object, name, value):
""" Validates that a value is legal for the trait.
"""
try:
# Make sure the value is an array:
type_value = type(value)
if type_value is not ArrayType:
if type_value not in SequenceTypes:
self.error(object, name, self.repr(value))
value = asarray(value, self.typecode)
# Make sure the array is of the right type:
if ((self.typecode is not None)
and (value.typecode() != self.typecode)):
if self.coerce:
value = value.astype(self.typecode)
else:
value = asarray(value, self.typecode)
# If no shape requirements, then return the value:
trait_shape = self.shape
if trait_shape is None:
return value
# Else make sure that the value's shape is compatible:
value_shape = value.shape
if len(trait_shape) == len(value_shape):
for i, dim in enumerate(value_shape):
item = trait_shape[i]
if item is not None:
if type(item) is int:
if dim != item:
break
elif ((dim < item[0])
or ((item[1] is not None) and (dim > item[1]))):
break
else:
return value
except:
pass
self.error(object, name, self.repr(value))
def ReadFromPositionsScalars(self, positions, scalars):
"""Reads vtkPolyData from positions and scalars"""
# Inserting positions
self.pointdata = vtkPointsFromArray(positions)
# Inserting scalars
#self.scalardata=vtkScalarsFromArray(scalars)
self.scalardata = vtkFloatArrayFromNumPyArray(
copy.copy(asarray(scalars)[..., NewAxis]))
# Inserting positions and scalars in vtkPolyData
self.GetvtkPolyData().SetPoints(self.pointdata.GetvtkPoints())
#self.GetvtkPolyData().GetPointData().SetScalars(self.scalardata.GetvtkScalars())
pointdata = self.GetvtkPolyData().GetPointData()
pointdata.SetScalars(self.scalardata.GetvtkFloatArray())
def setColor(self, drawingArea, color, alpha):
"""Accepts a gdkcolor and a floating point alpha, showing their values in the control widgets
and setting the attached object attribute to the new color value.
"""
drawingArea.gdkColor = color
drawingArea.modify_bg(gtk.STATE_NORMAL, color)
drawingArea.colorTuple = (color.red / 65535,
color.green / 65535,
color.blue / 65535,
alpha)
# Show the color in hex, since floating point takes too much space
drawingArea.label.set_text("#%02X%02X%02X%02X" %
tuple(asarray(drawingArea.colorTuple)*255))
drawingArea.setFunction(drawingArea.colorTuple)
def CoordinateArrayFromUnitVectors(shape,
gridunitvectors,
origin=[0, 0, 0],
indexfunction=lambda i, length: i):
"""
This method can be used to obtain an array representing the coordinates
of a space defined by 'gridunitvecors'. 'gridunitvectors' is in turn a
list containing the vectors defining the cells of the grid, i.e. the
vectors between neighboring grid points. These vectors are spanned
according to the specified shape.
'origin' -- specifies the origin of the returned coordinate array.
'indexfunction' -- is a lambda expression that defines the indices
with which each of the specified gridunitvectors are to be multiplied.
'indexfunction' must take two arguments, 'i' and 'length' - default
is 'lambda i,length:i'. During exection the input index 'i' will run
over the interval 0,1,..., 'length' -1.
**An Example**
To obtain a coordinate array of shape (10,10) with
'gridunitvectors' =[[2,0],[0,1]] and the origin at [10,0] use:
'CoordinateArrayFromUnitVectors((10,10),[[2,0],[0,1],[10,0])'
Note that the output array will be of shape
(< *dimension* > , < *spatialcoordinates* >).
"""
from Numeric import add, fromfunction, array, asarray
coordinatelist = []
gridunitvectors = asarray(gridunitvectors)
# Looping over the dimensionality of the vectors
for dim in range(gridunitvectors.shape[1]):
coordinates = origin[dim]
# Contribution from each unitvector
for nunitvector in range(gridunitvectors.shape[0]):
# Finding the indices from which the coordinate grid
# is spanned
indices = map(
lambda i, f=indexfunction, l=shape[nunitvector]: f(i, l),
range(shape[nunitvector]))
coordinatefunc = lambda i, v=gridunitvectors[nunitvector, dim
]: i * v
coordinates = add.outer(coordinates, map(coordinatefunc, indices))
coordinatelist.append(coordinates)
return array(coordinatelist)
def get_colours(n):
""" Return n pastel colours. """
base = asarray([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
if n <= 3:
return base[0:n]
# how many new colours to we need to insert between
# red and green and between green and blue?
needed = (((n - 3) + 1) / 2, (n - 3) / 2)
colours = []
for start in (0, 1):
for x in linspace(0, 1, needed[start] + 2):
colours.append((base[start] * (1.0 - x)) + (base[start + 1] * x))
return [pastel(c) for c in colours[0:n]]
def get_colours(n):
""" Return n pastel colours. """
base = asarray([[1,0,0], [0,1,0], [0,0,1]])
if n <= 3:
return base[0:n]
# how many new colours to we need to insert between
# red and green and between green and blue?
needed = (((n - 3) + 1) / 2, (n - 3) / 2)
colours = []
for start in (0, 1):
for x in linspace(0, 1, needed[start]+2):
colours.append((base[start] * (1.0 - x)) +
(base[start+1] * x))
return [pastel(c) for c in colours[0:n]]
def SetRGBColors(self,colorlist): """Sets the vtkLookupTable This method can be used to change the colortable. 'colorlist' is expected to be a list of colors whose elements is either specified in terms of the RGB colorscale or in terms of the name of a color. A complete list of the recognized colors can be obtained via the method 'GetColorNames' . **An example** To generate a colortable going from red to (0.5000,0.1647,0.1647) to black use: 'SetRGBColors(["red",(0.5000,0.1647,0.1647),"black"])' . """ from Numeric import asarray,Float,array interval=256/(len(colorlist)-1) Ncolors=interval*(len(colorlist)-1) self.SetNumberOfColors(Ncolors) # Translating colors (if any) to r,g,b numbers for i in range(len(colorlist)): if type(colorlist[i]) in [type([]),type(())]: colorlist[i]=asarray(colorlist[i],Float) else: colorlist[i]=array(self.ColorNameToRGB(colorlist[i])) # Finding the difference between adjacent colors # dcolorlist is the steplenght for each color entry dcolorlist=[] for i in range(len(colorlist)-1): dcolorlist.append((colorlist[i+1]-colorlist[i])/interval) # Inserting the colors in the table color=colorlist[0] for loopnumber in range(len(colorlist)-1): for entry in range(loopnumber*interval,(loopnumber+1)*interval): r,g,b=color self.SetTableValue(entry,r,g,b,1.0) color=color+dcolorlist[loopnumber]
def Repeat(self,periods): """Returns a repeated grid This method can be used used to repeat the grid an integer number of times according to the unit cell. Note that the unit cell in the returned grid will also be expanded according to 'periods' . """ from ArrayTools import RepeatArray from Numeric import transpose,asarray a=copy.copy(self) # Finding the new grid valueorder=len(self.GetShape())-len(self.GetSpatialShape()) # Only the spatial coordinates are repeated a.SetArray(RepeatArray(a.GetArray(),valueorder*[1]+periods)) # Finding the new space newspace=copy.copy(self.GetSpace()) newspace.SetBasis(transpose(transpose(self.GetSpace().GetBasis())*asarray(periods))) a.SetSpace(newspace) return a
def pastel(colour, weight=2.4):
""" Convert colour into a nice pastel shade"""
rgb = asarray(colorConverter.to_rgb(colour))
# scale colour
maxc = max(rgb)
if maxc < 1.0 and maxc > 0:
# scale colour
scale = 1.0 / maxc
rgb = rgb * scale
# now decrease saturation
total = sum(rgb)
slack = 0
for x in rgb:
slack += 1.0 - x
# want to increase weight from total to weight
# pick x s.t. slack * x == weight - total
# x = (weight - total) / slack
x = (weight - total) / slack
rgb = [c + (x * (1.0 - c)) for c in rgb]
return rgb
def pastel(colour, weight=2.4):
""" Convert colour into a nice pastel shade"""
rgb = asarray(colorConverter.to_rgb(colour))
# scale colour
maxc = max(rgb)
if maxc < 1.0 and maxc > 0:
# scale colour
scale = 1.0 / maxc
rgb = rgb * scale
# now decrease saturation
total = sum(rgb)
slack = 0
for x in rgb:
slack += 1.0 - x
# want to increase weight from total to weight
# pick x s.t. slack * x == weight - total
# x = (weight - total) / slack
x = (weight - total) / slack
rgb = [c + (x * (1.0-c)) for c in rgb]
return rgb
def Map(function, array, coordinates):
"""Return a mapped array
This method can be used to map an array along with the coordinates
corresponding to each grid point. The arrangement of the arguments
in the input function is expected to be of the form
'function(' *arrayvalue* , *coordinate* ')' where *coordinate* is a
NumPy array having a length correspoding to the dimension.
"""
from Numeric import reshape, swapaxes, asarray
# Finding the dimension of the array
dim = coordinates.shape[0]
spatialshape = array.shape[-dim:]
# Reshaping array shape=(indices,)
flatarray = reshape(array, (array.shape[:-dim] + (-1, )))
# Reshaping coordinates (indices,dim)
flatcoordinates = swapaxes(reshape(coordinates, (dim, -1)), 0, 1)
maparray = asarray(map(function, flatarray, flatcoordinates))
# Reshaping back again
return reshape(maparray, spatialshape)
def CoordinatesFromCartesianCoordinates(self,coordinates): from LinearAlgebra import solve_linear_equations return solve_linear_equations(transpose(self.GetBasis()),asarray(coordinates))
def iaconv(f,h):
""" o Purpose
2D convolution.
modified by drewp to build a result array of the same typecode
as 'f', which makes this work on complex arrays.
o Synopsis
g = iaconv(f,h)
o Input
f: input image.
h: PSF (point spread function), or kernel. The origin is at the array center.
o Output
g:
o Description
Perform a 2D discrete convolution. The kernel origin is at the center of image h.
o Examples
import Numeric
f = Numeric.zeros((5,5))
f[2,2] = 1
print f
h = Numeric.array([[1,2,3],[4,5,6]])
print h
a = iaconv(f,h)
print a
f = Numeric.array([[1,0,0,0],[0,0,0,0]])
print f
h = Numeric.array([1,2,3])
print h
a = iaconv(f,h)
print a
f = Numeric.array([[1,0,0,0,0,0],[0,0,0,0,0,0]])
print f
h = Numeric.array([1,2,3,4])
print h
a = iaconv(f,h)
print a
f = iaread('cameraman.pgm')
h = [[1,2,1],[0,0,0],[-1,-2,-1]]
g = iaconv(f,h)
gn = ianormalize(g, [0,255])
iashow(gn)
"""
from Numeric import asarray,NewAxis,zeros,array,product
f, h = asarray(f), asarray(h)
if len(f.shape) == 1: f = f[NewAxis,:]
if len(h.shape) == 1: h = h[NewAxis,:]
if product(f.shape) < product(h.shape):
f, h = h, f
g = zeros(array(f.shape) + array(h.shape) - 1,f.typecode())
for i in range(h.shape[0]):
for j in range(h.shape[1]):
g[i:i+f.shape[0], j:j+f.shape[1]] += h[i,j] * f
return g
def CoordinatesFromCartesianCoordinates(self,coor): """ Returns the Cartesian coordinates (i.e 'coordinates')""" return asarray(coor)
def ReadFromArray(self, array):
"""Reads vtkScalars from array"""
# The array is copied to make it contiguous
self.scalardata = vtkFloatArrayFromNumPyArray(
copy.copy(asarray(array)[..., NewAxis]))
self.GetvtkScalars().SetScalars(self.scalardata.GetvtkFloatArray())
def closeto(x,y):
try: assert(abs(asarray(x)-asarray(y))<1e-10)
except AssertionError:
raise AssertionError('Failed: %s and %s not close' %(x,y))
def CoordinatesFromCartesianCoordinates(self, coor):
""" Returns the Cartesian coordinates (i.e 'coordinates')"""
return asarray(coor)
def CartesianCoordinatesFromCoordinates(self,coordinates): return dot(asarray(coordinates),self.GetBasis())
def CartesianCoordinatesFromCoordinates(self, coordinates):
return dot(asarray(coordinates), self.GetBasis())
def SeqToProfile(seq, alphabet=None, char_order=None,\
split_degenerates=False):
"""Generates a Profile object from a Sequence object.
seq: Sequence object
alphabet (optional): Alphabet object (if you want to split
degenerate symbols, the alphabet object should have a
Degenerates property. Default is the Alphabet associated with
the Sequence object.
char_order (optional): The order the characters occur in the Profile.
Default is the list(alphabet)
split_degenerates (optional): Whether you want the counts for the
degenerate symbols to be divided over the non-degenerate symbols they
code for.
A Profile is a position x character matrix describing which characters
occur at each position. In a sequence (as opposed to an alignment) only
one character occurs at each position. In general a sequence profile
will only contain ones and zeros. However, you have the possibility of
splitting degenerate characters. For example, if a position is R, it
means that you have 50/50% chance of A and G. It's also possible to
ignore characters, which in a sequence profile will lead to positions
(rows) containing only zeros.
Example:
Sequence = ACGU
Profile(seq, CharOrder=UCAG):
U C A G
0 0 1 0 first pos
0 1 0 0 second pos
0 0 0 1 third pos
1 0 0 0 fourth pos
Sequence= GURY
Profile(seq,CharOrder=UCAG, split_degenerates=True)
U C A G
0 0 0 1 first pos
1 0 0 0 second pos
0 0 .5 .5 third pos
.5 .5 0 0 fourth pos
Characters can also be ignored
Sequence = ACN-
Profile(seq, CharOrder=UCAGN, split_degenerates=True)
U C A G
0 0 1 0 first pos
0 1 0 0 second pos
.25 .25 .25 .25 third pos
0 0 0 0 fourth pos <--contains only zeros
"""
if alphabet is None:
alphabet = seq.Alphabet
if char_order is None:
char_order = list(alphabet)
#Determine the meaning of each character based on the alphabet, the
#character order, and the option to split degenerates
char_meaning = CharMeaningProfile(alphabet, char_order,\
split_degenerates)
#construct profile data
result_data = take(char_meaning.Data, asarray(seq.upper(), UInt8))
return Profile(result_data, alphabet, char_order)
def SetCoordinates(self,coordinates):
"""Sets the coordinates of the vector in the basis of the 'VectorSpace'."""
self.Coordinates=asarray(coordinates)
def SetCoordinates(self, coordinates):
"""Sets the coordinates of the vector in the basis of the 'VectorSpace'."""
self.Coordinates = asarray(coordinates)
def closeto(x, y):
try:
assert (abs(asarray(x) - asarray(y)) < 1e-10)
except AssertionError:
raise AssertionError('Failed: %s and %s not close' % (x, y))
def ReadFromArray(self, array):
"""Read vtkPoints from array"""
self.pointdata = vtkFloatArrayFromNumPyArray(asarray(array))
self.GetvtkPoints().SetData(self.pointdata.GetvtkFloatArray())
def CoordinatesFromCartesianCoordinates(self, coordinates):
from LinearAlgebra import solve_linear_equations
return solve_linear_equations(transpose(self.GetBasis()),
asarray(coordinates))
def CoordinatesFromGridCoordinates(self,gridcoor): """Returns a list containing the scaled coordinates """ from Numeric import Float return list(asarray(gridcoor,Float)/self.GetSpatialShape())
def AlnToProfile(aln, alphabet=None, char_order=None, split_degenerates=False,\
weights=None):
"""Generates a Profile object from an Alignment.
aln: Alignment object
alphabet (optional): an Alphabet object (or list of chars, but if you
want to split degenerate symbols, the alphabet must have a
Degenerates property. Default is the alphabet of the first seq in
the alignment.
char_order (optional): order of the characters in the profile. Default
is list(alphabet)
split_degenerates (optional): Whether you want the counts for the
degenerate symbols to be divided over the non-degenerate symbols they
code for.
weights (optional): dictionary of seq_id: weight. If not entered all seqs
are weighted equally
A Profile is a position x character matrix describing which characters
occur at each position of an alignment. The Profile is always normalized,
so it gives the probabilities of each character at each position.
Ignoring chars: you can ignore characters in the alignment by not putting
the char in the CharOrder. If you ignore all characters at a particular
position, an error will be raised, because the profile can't be normalized.
Splitting degenerates: you can split degenerate characters over the
non-degenerate characters they code for. For example: R = A or G. So,
an R at a position counts for 0.5 A and 0.5 G.
Example:
seq1 TCAG weight: 0.5
seq2 TAR- weight: 0.25
seq3 YAG- weight: 0.25
Profile(aln,alphabet=DnaAlphabet,char_order="TACG",weights=w,
split_degenerates=True)
Profile:
T A C G
[[ 0.875 0. 0.125 0. ]
[ 0. 0.5 0.5 0. ]
[ 0. 0.625 0. 0.375]
[ 0. 0. 0. 1. ]]
"""
if alphabet is None:
alphabet = aln.values()[0].Alphabet
if char_order is None:
char_order = list(alphabet)
if weights is None:
weights = dict.fromkeys(aln.keys(),1/len(aln))
char_meaning = CharMeaningProfile(alphabet, char_order,\
split_degenerates)
profiles = []
for k,v in aln.items():
profiles.append(take(char_meaning.Data, asarray(v.upper(), UInt8))\
* weights[k])
s = reduce(add,profiles)
result = Profile(s,alphabet, char_order)
try:
result.normalizePositions()
except:
raise ValueError,\
"Probably one of the rows in your profile adds up to zero,\n "+\
"because you are ignoring all of the characters in the "+\
"corresponding\n column in the alignment"
return result
def iagaussian(s,mu,sigma):
""" o Purpose
Generate a 2D Gaussian image.
o Synopsis
g = iagaussian(s,mu,sigma)
o Input
s: [rows columns]
mu: Mean vector. 2D point (x;y). Point of maximum value.
sigma: covariance matrix (square). [ Sx^2 Sxy; Syx Sy^2]
o Output
g:
o Description
A 2D Gaussian image is an image with a Gaussian distribution. It can be used to generate test patterns or Gaussian filters both for spatial and frequency domain. The integral of the gaussian function is 1.0.
o Examples
import Numeric
f = iagaussian([8,4], [3,1], [[1,0],[0,1]])
print Numeric.array2string(f, precision=4, suppress_small=1)
g = ianormalize(f, [0,255]).astype(Numeric.UnsignedInt8)
print g
f = iagaussian(100, 50, 10*10)
g = ianormalize(f, [0,1])
g,d = iaplot(g)
showfig(g)
f = iagaussian([50,50], [25,10], [[10*10,0],[0,20*20]])
g = ianormalize(f, [0,255]).astype(Numeric.UnsignedInt8)
iashow(g)
"""
from Numeric import asarray,product,arange,NewAxis,transpose,matrixmultiply,reshape,concatenate,resize,sum,zeros,Float,ravel,pi,sqrt,exp
from LinearAlgebra import inverse,determinant
if type(sigma).__name__ in ['int', 'float', 'complex']: sigma = [sigma]
s, mu, sigma = asarray(s), asarray(mu), asarray(sigma)
if (product(s) == max(s)):
x = arange(product(s))
d = x - mu
if len(d.shape) == 1:
tmp1 = d[:,NewAxis]
tmp3 = d
else:
tmp1 = transpose(d)
tmp3 = tmp1
if len(sigma) == 1:
tmp2 = 1./sigma
else:
tmp2 = inverse(sigma)
k = matrixmultiply(tmp1, tmp2) * tmp3
else:
aux = arange(product(s))
x, y = iaind2sub(s, aux)
xx = reshape(concatenate((x,y)), (2, product(x.shape)))
d = transpose(xx) - resize(reshape(mu,(len(mu),1)), (s[0]*s[1],len(mu)))
if len(sigma) == 1:
tmp = 1./sigma
else:
tmp = inverse(sigma)
k = matrixmultiply(d, tmp) * d
k = sum(transpose(k))
g = zeros(s, Float)
aux = ravel(g)
if len(sigma) == 1:
tmp = sigma
else:
tmp = determinant(sigma)
aux[:] = 1./(2*pi*sqrt(tmp)) * exp(-1./2 * k)
return g