def _find_shift(self, order=3):
"""
Find the best shift between image1 and image2.
Expects _load_data() to have been run first to initialize things.
order is the order of the spline used for shifting in the correlation step.
"""
# Mask pixels around the edges of the image.
# We don't have inverse-variances because sdssproc isn't run, so we can't do
# smarter masking, like bad pixel smoothing, cosmic rays, etc.
# It is important to mask out the ends of the array, because of
# spline-induced oddities there.
subimg1 = self.bigimg1[self.region].copy()
subimg2 = self.bigimg2[self.region].copy()
mask = np.ones(subimg1.shape, dtype='f8')
mask[:10, :] = 0
mask[-10:, :] = 0
mask[:, :10] = 0
mask[:, -10:] = 0
# Compute linear correlation coefficients
# Calculate the maximum product of the two images when shifting by steps of dx.
dx = 0.05
nshift = int(np.ceil(2 * self.maxshift / dx))
xshift = -self.maxshift + dx * np.arange(nshift, dtype='f8')
self.xshift = xshift # save for plotting
def calc_shift(xs, img1, img2, mask):
shifted = interpolation.shift(img2, [xs, 0],
order=order,
prefilter=False)
return (img1 * shifted * mask).sum()
self.coeff = np.zeros(nshift, dtype='f8')
filtered1 = interpolation.spline_filter(subimg1)
filtered2 = interpolation.spline_filter(subimg2)
for i in range(nshift):
# self.coeff[i] = (subimg1 * interpolation.shift(subimg2,
# [xshift[i], 0],
# order=order) * mask).sum()
# self.coeff[i] = (filtered1 * interpolation.shift(filtered2,
# [xshift[i], 0],
# order=order,
# prefilter=False) * mask).sum()
self.coeff[i] = calc_shift(xshift[i], filtered1, filtered2, mask)
ibest = self.coeff.argmax()
self.ibest = ibest # save for plotting
self.xoffset = xshift[ibest]
# If the sequence is actually R-L, instead of L-R,
# then the offset acctually goes the other way.
if self.hartpos1 == 'right':
self.xoffset = -self.xoffset
def add_filter(pic):
''' add random filter to the picture '''
val = val = random.randint(1, 2)
if val == 1:
s = random.uniform(0.8, 1.2)
pic = gaussian_filter(pic, sigma=s)
elif val == 2:
pic = spline_filter(pic)
return pic
def create_radial_spline(psf, fn, sigma, egy, dtheta, psf_scale_fn):
from scipy.ndimage.interpolation import spline_filter
z = create_kernel_function_lookup(
psf, fn, sigma, egy, dtheta, psf_scale_fn)
sp = []
for i in range(z.shape[0]):
sp += [spline_filter(z[i], order=2)]
return sp
def create_radial_spline(psf, fn, sigma, egy, dtheta, psf_scale_fn):
from scipy.ndimage.interpolation import spline_filter
z = create_kernel_function_lookup(psf, fn, sigma, egy, dtheta,
psf_scale_fn)
sp = []
for i in range(z.shape[0]):
sp += [spline_filter(z[i], order=2)]
return sp
def setBeamCube(self, beam):
"""Initializes beam cube. Beam is a 2D (or 3D) cube."""
# init cube
self._beam = beam.copy()
self._beam_ampl = abs(beam)
self._beam_real = beam.real
self._beam_imag = beam.imag
# replace with pre-filtered arrays if needed
if beam.ndim > 2 and self._spline_order > 1:
if not self._hier_interpol:
self._beam_real = interpolation.spline_filter(
beam.real, order=self._spline_order)
self._beam_imag = interpolation.spline_filter(
beam.imag, order=self._spline_order)
self._beam_ampl = interpolation.spline_filter(
self._beam_ampl, order=self._spline_order)
else:
# prefilter per frequency plane in per-frequency mode
for i in range(beam.shape[2]):
self._beam_real[..., i] = interpolation.spline_filter(
beam.real[..., i], order=self._spline_order)
self._beam_imag[..., i] = interpolation.spline_filter(
beam.imag[..., i], order=self._spline_order)
self._beam_ampl[..., i] = interpolation.spline_filter(
self._beam_ampl[..., i], order=self._spline_order)
def __init__(self,
scale_list,
values,
extrapolate=False,
num_extrapolate=2,
delta=1e-4):
shape = values.shape
ndim = len(shape)
# error checking
if ndim < 3:
raise ValueError('Data must have 3 or more dimensions.')
elif ndim != len(scale_list):
raise ValueError('input and output dimension mismatch.')
self._scale_list = scale_list
self._max = values.shape
self._ext = num_extrapolate
# linearly extrapolate given values
self._extfun = LinearInterpolator([(0, 1)] * ndim,
values,
extrapolate=True)
self._extrapolate = extrapolate
swp_values = []
ext_xi_shape = []
delta_list = []
for (offset, scale), n in zip(scale_list, shape):
swp_values.append(np.arange(-num_extrapolate, n + num_extrapolate))
ext_xi_shape.append(n + 2 * num_extrapolate)
delta_list.append(scale * delta)
ext_xi_shape.append(ndim)
xi = np.empty(ext_xi_shape)
xmat_list = np.meshgrid(*swp_values, indexing='ij', copy=False)
for idx, xmat in enumerate(xmat_list):
xi[..., idx] = xmat
values_ext = self._extfun(xi)
self._filt_values = imag_interp.spline_filter(values_ext)
DiffFunction.__init__(self, ndim, delta_list=delta_list)
def __init__(self,
scale_list,
values,
extrapolate=False,
num_extrapolate=3,
delta=1e-4):
shape = values.shape
ndim = len(shape)
# error checking
if ndim < 3:
raise ValueError('Data must have 3 or more dimensions.')
elif ndim != len(scale_list):
raise ValueError('input and output dimension mismatch.')
self._scale_list = scale_list
self._max = [n - 1 + num_extrapolate for n in shape]
self._extrapolate = extrapolate
self._ext = num_extrapolate
# linearly extrapolate given values
ext_points = [
np.arange(num_extrapolate, n + num_extrapolate) for n in shape
]
points, delta_list = _scales_to_points(scale_list, values, delta)
input_ranges = [(pvec[0], pvec[-1]) for pvec in points]
self._extfun = LinearInterpolator(ext_points,
values, [delta] * ndim,
extrapolate=True)
xi_ext = np.stack(np.meshgrid(*(np.arange(0, n + 2 * num_extrapolate)
for n in shape),
indexing='ij',
copy=False),
axis=-1)
values_ext = self._extfun(xi_ext)
self._filt_values = imag_interp.spline_filter(values_ext)
DiffFunction.__init__(self, input_ranges, delta_list=delta_list)
def __init__(self, data, pix_ref, shape_out, rebin):
self._data = data
self._data_spline = []
for i in range(data.shape[0]):
self._data_spline += [spline_filter(self._data[i], order=2)]
self._axes = []
for i in range(data.ndim):
self._axes += [np.arange(0, data.shape[i], dtype=float)]
#self._coords = np.meshgrid(*self._axes[1:], indexing='ij')
self._rebin = rebin
# Shape of global output array
self._shape_out = shape_out
self._shape = np.array(self.data.shape)
for i in range(1, self.data.ndim):
self._shape[i] = int(self._shape[i] / self.rebin)
self._shape = tuple(self._shape)
# Reference pixel coordinates
self._pix_ref = pix_ref
def __init__(self, data, pix_ref, shape_out, rebin):
self._data = data
self._data_spline = []
for i in range(data.shape[0]):
self._data_spline += [spline_filter(self._data[i], order=2)]
self._axes = []
for i in range(data.ndim):
self._axes += [np.arange(0, data.shape[i], dtype=float)]
#self._coords = np.meshgrid(*self._axes[1:], indexing='ij')
self._rebin = rebin
# Shape of global output array
self._shape_out = shape_out
self._shape = np.array(self.data.shape)
for i in range(1, self.data.ndim):
self._shape[i] = int(self._shape[i] / self.rebin)
self._shape = tuple(self._shape)
# Reference pixel coordinates
self._pix_ref = pix_ref
def setBeamCube (self,beam):
"""Initializes beam cube. Beam is a 2D (or 3D) cube.""";
# init cube
self._beam = beam.copy();
self._beam_ampl = abs(beam);
self._beam_real = beam.real;
self._beam_imag = beam.imag;
# replace with pre-filtered arrays if needed
if beam.ndim > 2 and self._spline_order > 1:
if not self._hier_interpol:
self._beam_real = interpolation.spline_filter(beam.real,order=self._spline_order);
self._beam_imag = interpolation.spline_filter(beam.imag,order=self._spline_order);
self._beam_ampl = interpolation.spline_filter(self._beam_ampl,order=self._spline_order);
else:
# prefilter per frequency plane in per-frequency mode
for i in range(beam.shape[2]):
self._beam_real[...,i] = interpolation.spline_filter(beam.real[...,i],order=self._spline_order);
self._beam_imag[...,i] = interpolation.spline_filter(beam.imag[...,i],order=self._spline_order);
self._beam_ampl[...,i] = interpolation.spline_filter(self._beam_ampl[...,i],order=self._spline_order);
def spline_filter(grid,order=3):
filtered = grid.copy()
sciest.spline_filter(grid,order,filtered)
return filtered
def draw(self, painter, xmap, ymap, rect):
"""Implements QwtPlotItem.draw(), to render the image on the given painter."""
xp1, xp2, xdp, xs1, xs2, xds = xinfo = xmap.p1(), xmap.p2(
), xmap.pDist(), xmap.s1(), xmap.s2(), xmap.sDist()
yp1, yp2, ydp, ys1, ys2, yds = yinfo = ymap.p1(), ymap.p2(
), ymap.pDist(), ymap.s1(), ymap.s2(), ymap.sDist()
dprint(5, "draw:", rect, xinfo, yinfo)
self._current_rect = QRectF(QPointF(xs2, ys1), QSizeF(xds, yds))
self._current_rect_pix = QRect(
QPoint(*self.lmToPix(xs1, ys1)),
QPoint(*self.lmToPix(xs2, ys2))).intersected(
self._bounding_rect_pix)
dprint(5, "draw:", self._current_rect_pix)
# put together tuple describing current mapping
mapping = xinfo, yinfo
# if mapping has changed w.r.t. cache (i.e. zoom has changed), discard all cached QImages
if mapping != self._cache_mapping:
dprint(2, "does not match cached mapping, cache is:",
self._cache_mapping)
dprint(2, "and we have:", mapping)
self.clearDisplayCache()
self._cache_mapping = mapping
t0 = time.time()
# check cached QImage for current image key.
qimg = self._cache_qimage.get(self._image_key)
if qimg:
dprint(5, "QImage found in cache, reusing")
# else regenerate image
else:
# check for cached intensity-mapped data
if self._cache_imap is not None:
dprint(5, "intensity-mapped data found in cache, reusing")
else:
if self._cache_interp is not None:
dprint(5, "interpolated data found in cache, reusing")
else:
image = self._image.transpose(
) if self._data_fortran_order else self._image
spline_order = 2
xsamp = abs(xmap.sDist() / xmap.pDist()) / abs(self._dl)
ysamp = abs(ymap.sDist() / ymap.pDist()) / abs(self._dm)
if max(xsamp, ysamp) < .33 or min(xsamp, ysamp) > 2:
spline_order = 1
dprint(2,
"regenerating drawing cache, sampling factors are",
xsamp, ysamp, "spline order is", spline_order)
self._cache_imap = None
if self._prefilter is None and spline_order > 1:
self._prefilter = interpolation.spline_filter(
image, order=spline_order)
dprint(2, "spline prefiltering took",
time.time() - t0, "secs")
t0 = time.time()
# make arrays of plot coordinates
# xp[0],yp[0] corresponds to pixel 0,0, where 0,0 is the upper-left corner of the plot
# the maps are in a funny order (w.r.t. meaning of p1/p2/s1/s2), so the indices here are determined empirically
# We also adjust by half-pixel, to get the world coordinate of the pixel _center_
xp = xmap.s1() - (xmap.sDist() / xmap.pDist()) * (
0.5 + numpy.arange(int(xmap.pDist())))
yp = ymap.s2() - (ymap.sDist() / ymap.pDist()) * (
0.5 + numpy.arange(int(ymap.pDist())))
# now convert plot coordinates into fractional image pixel coordinates
xi = self._x0 + (xp - self._l0) / self._dl
yi = self._y0 + (yp - self._m0) / self._dm
# interpolate image data
### # old code for nearest-neighbour interpolation
### # superceded by interpolation below (we simply round pixel coordinates to go to NN when oversampling)
### xi = xi.round().astype(int);
### oob_x = (xi<0)|(xi>=self._nx);
### xi[oob_x] = 0;
### yi = yi.round().astype(int);
### oob_y = (yi<0)|(yi>=self._ny);
### yi[oob_y] = 0;
### idx = (xi[:,numpy.newaxis]*self._ny + yi[numpy.newaxis,:]).ravel();
### interp_image = self._image.ravel()[idx].reshape((len(xi),len(yi)));
### interp_image[oob_x,:] = 0;
### interp_image[:,oob_y] = 0;
### self._qimage_cache = self.colormap.colorize(interp_image,self._img_range);
### self._qimage_cache_attrs = (rect,xinfo,yinfo);
# if either axis is oversampled by a factor of 3 or more, switch to nearest-neighbour interpolation by rounding pixel values
if xsamp < .33:
xi = xi.round()
if ysamp < .33:
yi = yi.round()
# make [2,nx,ny] array of interpolation coordinates
xy = numpy.zeros((2, len(xi), len(yi)))
xy[0, :, :] = xi[:, numpy.newaxis]
xy[1, :, :] = yi[numpy.newaxis, :]
# interpolate. Use NAN for out of range pixels...
# for fortran order, tranpose axes for extra speed (flip XY around then)
if self._data_fortran_order:
xy = xy[-1::-1, ...]
if spline_order > 1:
interp_image = interpolation.map_coordinates(
self._prefilter,
xy,
order=spline_order,
cval=numpy.nan,
prefilter=False)
else:
interp_image = interpolation.map_coordinates(
image, xy, order=spline_order, cval=numpy.nan)
# ...and put a mask on them (Colormap.colorize() will make these transparent).
mask = ~numpy.isfinite(interp_image)
self._cache_interp = numpy.ma.masked_array(
interp_image, mask)
dprint(2, "interpolation took",
time.time() - t0, "secs")
t0 = time.time()
# ok, we have interpolated data in _cache_interp
self._cache_imap = self.imap.remap(self._cache_interp)
dprint(2, "intensity mapping took",
time.time() - t0, "secs")
t0 = time.time()
# ok, we have intensity-mapped data in _cache_imap
qimg = self.colormap.colorize(self._cache_imap)
dprint(2, "colorizing took",
time.time() - t0, "secs")
t0 = time.time()
# cache the qimage
self._cache_qimage[self._image_key] = qimg.copy()
# now draw the image
t0 = time.time()
painter.drawImage(xp1, yp2, qimg)
dprint(2, "drawing took",
time.time() - t0, "secs")
def __init__(self,
cubefile,
convert_cube_content=False,
convert_to_rs=False,
PBC=True,
shift='edge',
order=3,
verbose=False,
precalc_weights=True):
self.cubefile = cubefile
# read the cube file
# convert means density in e / A**3
full_output = read_cube(cubefile,
full_output=True,
convert=convert_cube_content)
# conveniently map dict content to instance variables:
# self.atoms
# self.cube_data
# self.voxdim
# self.origin
self.__dict__.update(full_output)
if verbose:
print(get_cube_info(self.cubefile))
self.convert_cube_content = convert_cube_content
self.convert_to_rs = convert_to_rs
# hard coded conversion factor
self.A2au = 1. / Bohr
# PBC treatment of the interpolation function
self.PBC = PBC
if self.PBC:
self.mode = 'wrap'
else:
self.mode = 'constant'
self.Q, self.Qinv = self._create_trafo_matrices(self.voxdim)
# get the number of voxels
self.Nx, self.Ny, self.Nz = self.cube_data.shape
# get the cell
self.cell = self.atoms.get_cell()
# shifting the values
shift = shift.lower()
if shift == 'edge':
self.shift = 0.0
else:
self.shift = 0.5
# save spline order
self.order = order
# pre-calculate the spline weights (one-time process)
# instead of doing this with every call to map_coordinates.
# Acc. to Joe Kington's mail here:
# http://scipy-user.10969.n7.nabble.com/SciPy-User-3D-spline-interpolation-very-very-slow-UPDATE-td19702.html
if precalc_weights:
self._cube_data = spline_filter(self.cube_data, order=self.order)
# flag for map_coordinates
self._prefilter = False
else:
self._cube_data = self.cube_data
self._prefilter = True
def read(self, filenames):
freqs = []
for ifreq, (filename_real, filename_imag) in enumerate(filenames):
"""Reads beam patterns from FITS files. If only one file is supplied, assumes a real-only beam.
If two files are supplied, uses them for the real and imaginary parts.
If 2N files are supplied, treats them as a frequency cube"""
ff_re = pyfits.open(filename_real)[0]
# form up complex beam
beam = numpy.zeros(ff_re.data.shape, complex)
beam.real = ff_re.data
# add imaginary part
if filename_imag:
im_data = pyfits.open(filename_imag)[0].data
if im_data.shape != ff_re.data.shape:
raise TypeError, "shape mismatch between FITS files %s and %s" % (
filename_real, filename_imag)
beam.imag = im_data
# change order of axis, since FITS has first axis last
beam = beam.transpose()
# figure out axes
axes = FITSAxes(ff_re.header)
used_axes = [axes.iaxis(x) for x in "L", "M", "FREQ"]
if any([x < 0 for x in used_axes]):
raise TypeError, "FITS file %s missing L, M or FREQ axis"
laxis, maxis, freqaxis = used_axes
# check the other axes
other_axes = sorted(set(range(axes.ndim())) - set(used_axes))
if any([axes.naxis(i) > 1 for i in other_axes]):
raise TypeError, "FITS file %s has other non-trivial axes besides L/M" % filename_real
# setup frequency grid
freqgrid = axes.grid(freqaxis)
if len(freqgrid) > 1:
raise TypeError, "FITS file %s has >1 frequency points"
if freqs and freqgrid[0] < freqs[-1]:
raise TypeError, "FITS file %s has lower frequency than previous file -- monotonically increasing frequencies are expected"
freqs.append(freqgrid[0])
# check if it matches previous image
if not ifreq:
baseshape = beam.shape
self._axes = axes
# setup 3D beam cube
beamcube = numpy.zeros(
(axes.naxis(laxis), axes.naxis(maxis), len(filenames)),
complex)
# setup conversion functions
self._lToPixel = Kittens.utils.curry(axes.toPixel, laxis)
self._mToPixel = Kittens.utils.curry(axes.toPixel, maxis)
for ax in laxis, maxis:
dprint(
1, "%s axis unit is %s" %
(self._axes.type(ax), self._axes.unit(ax)))
if not self._axes.unit(ax) or self._axes.unit(
ax).upper() == "DEG":
self._axes.setUnitScale(ax, DEG)
else:
if baseshape != beam.shape:
raise TypeError, "FITS file %s has differing dimensions" % filename_real
beam = beam.transpose(used_axes + other_axes)
beam = beam.reshape(beam.shape[:len(used_axes)])
beamcube[:, :, ifreq] = beam[:, :, 0]
# done reading the beam cube
dprint(1, "beam array has shape", beamcube.shape)
dprint(2, "l grid is", self._axes.grid(laxis))
dprint(2, "m grid is", self._axes.grid(maxis))
dprint(2, "freq grid is", freqs)
self._freqaxis = freqs
self._freq_interpolator = interpolate.interp1d(freqs,
range(len(freqs)),
'linear')
# prefilter beam for interpolator
self._beam = beamcube
self._beam_ampl = numpy.abs(
beamcube) if self.ampl_interpolation else None
if self._spline_order > 1:
self._beam_real = interpolation.spline_filter(
beamcube.real, order=self._spline_order)
self._beam_imag = interpolation.spline_filter(
beamcube.imag, order=self._spline_order)
if self._beam_ampl:
self._beam_ampl = interpolation.spline_filter(
self._beam_ampl, order=self._spline_order)
else:
self._beam_real = beamcube.real
self._beam_imag = beamcube.imag
def read(self, filename_real, filename_imag=None):
"""Reads beam patterns from FITS files. If only one file is supplied, assumes a real-only beam.
If two files are supplied, uses them for the real and imaginary parts.
If 2N files are supplied, treats them as a frequency cube"""
ff_re = pyfits.open(filename_real)[0]
# form up complex beam
beam = numpy.zeros(ff_re.data.shape, complex)
beam.real = ff_re.data
beam_ampl = None
# add imaginary part
if filename_imag:
im_data = pyfits.open(filename_imag)[0].data
if im_data.shape != ff_re.data.shape:
raise TypeError, "shape mismatch between FITS files %s and %s" % (
filename_real, filename_imag)
beam.imag = im_data
if self.ampl_interpolation:
beam_ampl = numpy.abs(beam)
# change order of axis, since FITS has first axis last
beam = beam.transpose()
if not beam_ampl is None:
beam_ampl = beam_ampl.transpose()
# figure out axes
self._axes = axes = FITSAxes(ff_re.header)
# find L/M axes
laxis = axes.iaxis(self._l_axis)
maxis = axes.iaxis(self._m_axis)
if laxis < 0 or maxis < 0:
raise TypeError, "FITS file %s missing %s or %s axis" % (
filename_real, self._l_axis, self._m_axis)
# setup conversion functions
self._lToPixel = Kittens.utils.curry(axes.toPixel,
laxis,
sign=self._l_axis_sign)
self._mToPixel = Kittens.utils.curry(axes.toPixel,
maxis,
sign=self._m_axis_sign)
# find frequency grid. self._freqToPixel will be None if no frequency axis
freqaxis = axes.iaxis('FREQ')
if freqaxis >= 0 and axes.naxis(freqaxis) > 1:
dprint(1, "FREQ axis has %d points" % axes.naxis(freqaxis))
self._freqgrid = axes.grid(freqaxis)
self._freqToPixel = Kittens.utils.curry(axes.toPixel, freqaxis)
used_axes = [laxis, maxis, freqaxis]
else:
self._freqToPixel = None
used_axes = [laxis, maxis]
# used_axes is either (l,m,freq) or (l,m)
# other_axes is all that remains, and they had better be all trivial
other_axes = sorted(set(range(axes.ndim())) - set(used_axes))
if any([axes.naxis(i) > 1 for i in other_axes]):
raise TypeError, "FITS file %s has other non-trivial axes besides L/M" % filename_real
# setup units
for ax in laxis, maxis:
dprint(1, "%s axis unit is %s" % (axes.type(ax), axes.unit(ax)))
if not axes.unit(ax) or axes.unit(ax).upper() == "DEG":
axes.setUnitScale(ax, DEG)
# transpose array into L,M order and reshape
dprint(1, "beam array has shape", beam.shape)
beam = beam.transpose(used_axes + other_axes)
beam = beam.reshape(beam.shape[:len(used_axes)])
if not beam_ampl is None:
beam_ampl = beam_ampl.transpose(used_axes + other_axes)
beam_ampl = beam_ampl.reshape(beam_ampl.shape[:len(used_axes)])
dprint(1, "beam array has shape", beam.shape)
dprint(2, "l grid is", axes.grid(laxis))
dprint(2, "m grid is", axes.grid(maxis))
if self._freqToPixel:
dprint(2, "freq grid is", axes.grid(freqaxis))
# prefilter beam for interpolator
self._beam = beam
if self._spline_order > 1:
self._beam_real = interpolation.spline_filter(
beam.real, order=self._spline_order)
self._beam_imag = interpolation.spline_filter(
beam.imag, order=self._spline_order)
if not beam_ampl is None:
self._beam_ampl = interpolation.spline_filter(
beam_ampl, order=self._spline_order)
else:
self._beam_ampl = beam_ampl
else:
self._beam_real = beam.real
self._beam_imag = beam.imag
self._beam_ampl = beam_ampl
def calc_splinecoeffs(self):
self.u_coeffs = spline_filter(self.u)
self.v_coeffs = spline_filter(self.v)
self.p0 = self.grid[:, 0, 0, 0]
self.inv_dp = 1. / (self.grid[:, 1, 1, 1] - self.p0)
def calc_splinecoeffs(self):
self.u_coeffs = spline_filter(self.u)
self.v_coeffs = spline_filter(self.v)
self.p0 = self.grid[:,0,0,0]
self.inv_dp = 1. / (self.grid[:,1,1,1] - self.p0)
def smoothPlot(self):
if not self.plotted_ticket is None:
try:
if self.filter==0 or 2<=self.filter<=5:
congruence.checkStrictlyPositiveNumber(self.filter_sigma_h, "Sigma/Size H")
congruence.checkStrictlyPositiveNumber(self.filter_sigma_v, "Sigma/Size V")
if self.filter == 1: congruence.checkStrictlyPositiveNumber(self.filter_spline_order, "Spline Order")
ticket = self.plotted_ticket.copy()
mask = numpy.where(self.plotted_ticket["histogram"] <= self.plotted_ticket["histogram"].max()*self.masking_level)
histogram = ticket["histogram"]
h_coord = ticket["bin_h_center"]
v_coord = ticket["bin_v_center"]
norm = histogram.sum()
pixel_area = (h_coord[1]-h_coord[0])*(v_coord[1]-v_coord[0])
filter_mode = self.cb_filter_mode.currentText()
if self.filter == 0:
histogram = filters.gaussian_filter(histogram, sigma=(self.filter_sigma_h, self.filter_sigma_v), mode=filter_mode, cval=self.filter_cval)
elif self.filter == 1:
histogram = interpolation.spline_filter(histogram, order=int(self.filter_spline_order))
elif self.filter == 2:
histogram = filters.uniform_filter(histogram, size=(int(self.filter_sigma_h), int(self.filter_sigma_v)), mode=filter_mode, cval=self.filter_cval)
elif self.filter == 3:
histogram = numpy.real(numpy.fft.ifft2(fourier.fourier_gaussian(numpy.fft.fft2(histogram), sigma=(self.filter_sigma_h, self.filter_sigma_v))))
elif self.filter == 4:
histogram = numpy.real(numpy.fft.ifft2(fourier.fourier_ellipsoid(numpy.fft.fft2(histogram), size=(self.filter_sigma_h, self.filter_sigma_v))))
elif self.filter == 5:
histogram = numpy.real(numpy.fft.ifft2(fourier.fourier_uniform(numpy.fft.fft2(histogram), size=(self.filter_sigma_h, self.filter_sigma_v))))
elif self.filter == 6:
histogram = self.apply_fill_holes(histogram)
histogram[mask] = 0.0
norm /= histogram.sum()
ticket["histogram"] = histogram*norm
if self.plot_canvas is None:
self.plot_canvas = PowerPlotXYWidget()
self.image_box.layout().addWidget(self.plot_canvas)
cumulated_power_plot = numpy.sum(histogram)*pixel_area
energy_min=0.0
energy_max=0.0
energy_step=0.0
self.plot_canvas.cumulated_power_plot = cumulated_power_plot
self.plot_canvas.plot_power_density_ticket(ticket,
ticket["h_label"],
ticket["v_label"],
cumulated_total_power=0.0,
energy_min=energy_min,
energy_max=energy_max,
energy_step=energy_step)
self.plotted_ticket = ticket
except Exception as e:
QMessageBox.critical(self, "Error", str(e), QMessageBox.Ok)
if self.IS_DEVELOP: raise e
def zoom(input, zoom, output=None, order=3, mode='constant', cval=0.0,
prefilter=True):
"""
Zoom an array.
The array is zoomed using spline interpolation of the requested order.
Parameters
----------
input : ndarray
The input array.
zoom : float or sequence, optional
The zoom factor along the axes. If a float, `zoom` is the same for each
axis. If a sequence, `zoom` should contain one value for each axis.
output : ndarray or dtype, optional
The array in which to place the output, or the dtype of the returned
array.
order : int, optional
The order of the spline interpolation, default is 3.
The order has to be in the range 0-5.
mode : str, optional
Points outside the boundaries of the input are filled according
to the given mode ('constant', 'nearest', 'reflect' or 'wrap').
Default is 'constant'.
cval : scalar, optional
Value used for points outside the boundaries of the input if
``mode='constant'``. Default is 0.0
prefilter : bool, optional
The parameter prefilter determines if the input is pre-filtered with
`spline_filter` before interpolation (necessary for spline
interpolation of order > 1). If False, it is assumed that the input is
already filtered. Default is True.
Returns
-------
return_value : ndarray or None
The zoomed input. If `output` is given as a parameter, None is
returned.
"""
if order < 0 or order > 5:
raise RuntimeError('spline order not supported')
input = numpy.asarray(input)
if numpy.iscomplexobj(input):
raise TypeError('Complex type not supported')
if input.ndim < 1:
raise RuntimeError('input and output rank must be > 0')
mode = _extend_mode_to_code(mode)
if prefilter and order > 1:
filtered = spline_filter(input, order, output = numpy.float64)
else:
filtered = input
zoom = _ni_support._normalize_sequence(zoom, input.ndim)
output_shape = tuple([int(ii * jj) for ii, jj in zip(input.shape, zoom)])
zoom_div = numpy.array(output_shape, float)
zoom = (numpy.array(input.shape)) / zoom_div
# Zooming to non-finite values in unpredictable, so just choose
# zoom factor 1 instead
zoom[~numpy.isfinite(zoom)] = 1
output, return_value = _ni_support._get_output(output, input,
shape=output_shape)
zoom = numpy.asarray(zoom, dtype = numpy.float64)
zoom = numpy.ascontiguousarray(zoom)
_nd_image.zoom_shift(filtered, zoom, None, output, order, mode, cval)
return return_value
def read (self,filenames):
freqs = [];
for ifreq,(filename_real,filename_imag) in enumerate(filenames):
"""Reads beam patterns from FITS files. If only one file is supplied, assumes a real-only beam.
If two files are supplied, uses them for the real and imaginary parts.
If 2N files are supplied, treats them as a frequency cube"""
ff_re = pyfits.open(filename_real)[0];
# form up complex beam
beam = numpy.zeros(ff_re.data.shape,complex);
beam.real = ff_re.data;
# add imaginary part
if filename_imag:
im_data = pyfits.open(filename_imag)[0].data;
if im_data.shape != ff_re.data.shape:
raise TypeError,"shape mismatch between FITS files %s and %s"%(filename_real,filename_imag);
beam.imag = im_data;
# change order of axis, since FITS has first axis last
beam = beam.transpose();
# figure out axes
axes = FITSAxes(ff_re.header);
used_axes = [ axes.iaxis(x) for x in "L","M","FREQ" ];
if any([x<0 for x in used_axes]):
raise TypeError,"FITS file %s missing L, M or FREQ axis";
laxis,maxis,freqaxis = used_axes;
# check the other axes
other_axes = sorted(set(range(axes.ndim())) - set(used_axes));
if any([axes.naxis(i)>1 for i in other_axes]):
raise TypeError,"FITS file %s has other non-trivial axes besides L/M"%filename_real;
# setup frequency grid
freqgrid = axes.grid(freqaxis);
if len(freqgrid) > 1:
raise TypeError,"FITS file %s has >1 frequency points";
if freqs and freqgrid[0] < freqs[-1]:
raise TypeError,"FITS file %s has lower frequency than previous file -- monotonically increasing frequencies are expected";
freqs.append(freqgrid[0]);
# check if it matches previous image
if not ifreq:
baseshape = beam.shape;
self._axes = axes;
# setup 3D beam cube
beamcube = numpy.zeros((axes.naxis(laxis),axes.naxis(maxis),len(filenames)),complex);
# setup conversion functions
self._lToPixel = Kittens.utils.curry(axes.toPixel,laxis);
self._mToPixel = Kittens.utils.curry(axes.toPixel,maxis);
for ax in laxis,maxis:
dprint(1,"%s axis unit is %s"%(self._axes.type(ax),self._axes.unit(ax)));
if not self._axes.unit(ax) or self._axes.unit(ax).upper() == "DEG":
self._axes.setUnitScale(ax,DEG);
else:
if baseshape != beam.shape:
raise TypeError,"FITS file %s has differing dimensions"%filename_real;
beam = beam.transpose(used_axes+other_axes);
beam = beam.reshape(beam.shape[:len(used_axes)]);
beamcube[:,:,ifreq] = beam[:,:,0];
# done reading the beam cube
dprint(1,"beam array has shape",beamcube.shape);
dprint(2,"l grid is",self._axes.grid(laxis));
dprint(2,"m grid is",self._axes.grid(maxis));
dprint(2,"freq grid is",freqs);
self._freqaxis = freqs;
self._freq_interpolator = interpolate.interp1d(freqs,range(len(freqs)),'linear');
# prefilter beam for interpolator
self._beam = beamcube;
self._beam_ampl = numpy.abs(beamcube) if self.ampl_interpolation else None;
if self._spline_order > 1:
self._beam_real = interpolation.spline_filter(beamcube.real,order=self._spline_order);
self._beam_imag = interpolation.spline_filter(beamcube.imag,order=self._spline_order);
if self._beam_ampl:
self._beam_ampl = interpolation.spline_filter(self._beam_ampl,order=self._spline_order);
else:
self._beam_real = beamcube.real;
self._beam_imag = beamcube.imag;
def read (self,filename_real,filename_imag=None):
"""Reads beam patterns from FITS files. If only one file is supplied, assumes a real-only beam.
If two files are supplied, uses them for the real and imaginary parts.
If 2N files are supplied, treats them as a frequency cube"""
ff_re = pyfits.open(filename_real)[0];
# form up complex beam
beam = numpy.zeros(ff_re.data.shape,complex);
beam.real = ff_re.data;
beam_ampl = None
# add imaginary part
if filename_imag:
im_data = pyfits.open(filename_imag)[0].data;
if im_data.shape != ff_re.data.shape:
raise TypeError,"shape mismatch between FITS files %s and %s"%(filename_real,filename_imag);
beam.imag = im_data;
if self.ampl_interpolation:
beam_ampl = numpy.abs(beam)
# change order of axis, since FITS has first axis last
beam = beam.transpose();
if not beam_ampl is None:
beam_ampl = beam_ampl.transpose()
# figure out axes
self._axes = axes = FITSAxes(ff_re.header);
# find L/M axes
laxis = axes.iaxis('L');
maxis = axes.iaxis('M');
if laxis<0 or maxis<0:
raise TypeError,"FITS file %s missing L or M axis"%filename_real;
# setup conversion functions
self._lToPixel = Kittens.utils.curry(axes.toPixel,laxis);
self._mToPixel = Kittens.utils.curry(axes.toPixel,maxis);
# find frequency grid. self._freqToPixel will be None if no frequency axis
freqaxis = axes.iaxis('FREQ');
if freqaxis >= 0 and axes.naxis(freqaxis) > 1:
dprint(1,"FREQ axis has %d points"%axes.naxis(freqaxis));
self._freqgrid = axes.grid(freqaxis);
self._freqToPixel = Kittens.utils.curry(axes.toPixel,freqaxis);
used_axes = [laxis,maxis,freqaxis];
else:
self._freqToPixel = None;
used_axes = [laxis,maxis];
# used_axes is either (l,m,freq) or (l,m)
# other_axes is all that remains, and they had better be all trivial
other_axes = sorted(set(range(axes.ndim())) - set(used_axes));
if any([axes.naxis(i)>1 for i in other_axes]):
raise TypeError,"FITS file %s has other non-trivial axes besides L/M"%filename_real;
# setup units
for ax in laxis,maxis:
dprint(1,"%s axis unit is %s"%(axes.type(ax),axes.unit(ax)));
if not axes.unit(ax) or axes.unit(ax).upper() == "DEG":
axes.setUnitScale(ax,DEG);
# transpose array into L,M order and reshape
dprint(1,"beam array has shape",beam.shape);
beam = beam.transpose(used_axes+other_axes);
beam = beam.reshape(beam.shape[:len(used_axes)]);
if not beam_ampl is None:
beam_ampl = beam_ampl.transpose(used_axes+other_axes)
beam_ampl = beam_ampl.reshape(beam_ampl.shape[:len(used_axes)]);
dprint(1,"beam array has shape",beam.shape);
dprint(2,"l grid is",axes.grid(laxis));
dprint(2,"m grid is",axes.grid(maxis));
if self._freqToPixel:
dprint(2,"freq grid is",axes.grid(freqaxis));
# prefilter beam for interpolator
self._beam = beam;
if self._spline_order > 1:
self._beam_real = interpolation.spline_filter(beam.real,order=self._spline_order);
self._beam_imag = interpolation.spline_filter(beam.imag,order=self._spline_order);
if not beam_ampl is None:
self._beam_ampl = interpolation.spline_filter(beam_ampl,order=self._spline_order);
else:
self._beam_ampl = beam_ampl
else:
self._beam_real = beam.real;
self._beam_imag = beam.imag;
self._beam_ampl = beam_ampl
def draw (self,painter,xmap,ymap,rect):
"""Implements QwtPlotItem.draw(), to render the image on the given painter.""";
xp1,xp2,xdp,xs1,xs2,xds = xinfo = xmap.p1(),xmap.p2(),xmap.pDist(),xmap.s1(),xmap.s2(),xmap.sDist();
yp1,yp2,ydp,ys1,ys2,yds = yinfo = ymap.p1(),ymap.p2(),ymap.pDist(),ymap.s1(),ymap.s2(),ymap.sDist();
dprint(5,"draw:",rect,xinfo,yinfo);
self._current_rect = QRectF(QPointF(xs2,ys1),QSizeF(xds,yds));
self._current_rect_pix = QRect(QPoint(*self.lmToPix(xs1,ys1)),QPoint(*self.lmToPix(xs2,ys2))).intersected(self._bounding_rect_pix);
dprint(5,"draw:",self._current_rect_pix);
# put together tuple describing current mapping
mapping = xinfo,yinfo;
# if mapping has changed w.r.t. cache (i.e. zoom has changed), discard all cached QImages
if mapping != self._cache_mapping:
dprint(2,"does not match cached mapping, cache is:",self._cache_mapping);
dprint(2,"and we have:",mapping);
self.clearDisplayCache();
self._cache_mapping = mapping;
t0 = time.time();
# check cached QImage for current image key.
qimg = self._cache_qimage.get(self._image_key);
if qimg:
dprint(5,"QImage found in cache, reusing");
# else regenerate image
else:
# check for cached intensity-mapped data
if self._cache_imap is not None:
dprint(5,"intensity-mapped data found in cache, reusing");
else:
if self._cache_interp is not None:
dprint(5,"interpolated data found in cache, reusing");
else:
image = self._image.transpose() if self._data_fortran_order else self._image;
spline_order = 2;
xsamp = abs(xmap.sDist()/xmap.pDist())/abs(self._dl);
ysamp = abs(ymap.sDist()/ymap.pDist())/abs(self._dm);
if max(xsamp,ysamp) < .33 or min(xsamp,ysamp) > 2:
spline_order = 1;
dprint(2,"regenerating drawing cache, sampling factors are",xsamp,ysamp,"spline order is",spline_order);
self._cache_imap = None;
if self._prefilter is None and spline_order>1:
self._prefilter = interpolation.spline_filter(image,order=spline_order);
dprint(2,"spline prefiltering took",time.time()-t0,"secs"); t0 = time.time();
# make arrays of plot coordinates
# xp[0],yp[0] corresponds to pixel 0,0, where 0,0 is the upper-left corner of the plot
# the maps are in a funny order (w.r.t. meaning of p1/p2/s1/s2), so the indices here are determined empirically
# We also adjust by half-pixel, to get the world coordinate of the pixel _center_
xp = xmap.s1() - (xmap.sDist()/xmap.pDist())*(0.5+numpy.arange(int(xmap.pDist())));
yp = ymap.s2() - (ymap.sDist()/ymap.pDist())*(0.5+numpy.arange(int(ymap.pDist())));
# now convert plot coordinates into fractional image pixel coordinates
xi = self._x0 + (xp - self._l0)/self._dl;
yi = self._y0 + (yp - self._m0)/self._dm;
# interpolate image data
### # old code for nearest-neighbour interpolation
### # superceded by interpolation below (we simply round pixel coordinates to go to NN when oversampling)
### xi = xi.round().astype(int);
### oob_x = (xi<0)|(xi>=self._nx);
### xi[oob_x] = 0;
### yi = yi.round().astype(int);
### oob_y = (yi<0)|(yi>=self._ny);
### yi[oob_y] = 0;
### idx = (xi[:,numpy.newaxis]*self._ny + yi[numpy.newaxis,:]).ravel();
### interp_image = self._image.ravel()[idx].reshape((len(xi),len(yi)));
### interp_image[oob_x,:] = 0;
### interp_image[:,oob_y] = 0;
### self._qimage_cache = self.colormap.colorize(interp_image,self._img_range);
### self._qimage_cache_attrs = (rect,xinfo,yinfo);
# if either axis is oversampled by a factor of 3 or more, switch to nearest-neighbour interpolation by rounding pixel values
if xsamp < .33:
xi = xi.round();
if ysamp < .33:
yi = yi.round();
# make [2,nx,ny] array of interpolation coordinates
xy = numpy.zeros((2,len(xi),len(yi)));
xy[0,:,:] = xi[:,numpy.newaxis];
xy[1,:,:] = yi[numpy.newaxis,:];
# interpolate. Use NAN for out of range pixels...
# for fortran order, tranpose axes for extra speed (flip XY around then)
if self._data_fortran_order:
xy = xy[-1::-1,...];
if spline_order > 1:
interp_image = interpolation.map_coordinates(self._prefilter,xy,order=spline_order,cval=numpy.nan,prefilter=False);
else:
interp_image = interpolation.map_coordinates(image,xy,order=spline_order,cval=numpy.nan);
# ...and put a mask on them (Colormap.colorize() will make these transparent).
mask = ~numpy.isfinite(interp_image);
self._cache_interp = numpy.ma.masked_array(interp_image,mask);
dprint(2,"interpolation took",time.time()-t0,"secs"); t0 = time.time();
# ok, we have interpolated data in _cache_interp
self._cache_imap = self.imap.remap(self._cache_interp);
dprint(2,"intensity mapping took",time.time()-t0,"secs"); t0 = time.time();
# ok, we have intensity-mapped data in _cache_imap
qimg = self.colormap.colorize(self._cache_imap);
dprint(2,"colorizing took",time.time()-t0,"secs"); t0 = time.time();
# cache the qimage
self._cache_qimage[self._image_key] = qimg.copy();
# now draw the image
t0 = time.time();
painter.drawImage(xp1,yp2,qimg);
dprint(2,"drawing took",time.time()-t0,"secs");