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Commit 4725e6cf authored by Jan Caron's avatar Jan Caron
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Added fieldconverter module! 

fieldconverter: methods to convert M to A to B
magdata: a bit more parameters for quiver_plot3d(), added contour_plot3d()
phasemapper: pm() extended for different projections (not just simple)
kernel: u and v switched (now named after the unit magnetization direction, which makes much more sense)
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......
pyramid/__init__.py
+ 3
− 1
View file @ 4725e6cf
......@@ -59,6 +59,7 @@ from . import analytic
from . import magcreator
from . import reconstruction
from . import fft
from . import fieldconverter
from . import costfunction
from .costfunction import *
from . import dataset
......@@ -92,7 +93,7 @@ from .version import hg_revision as __hg_revision__
_log.info("Starting Pyramid V{} HG{}".format(__version__, __hg_revision__))
del logging
__all__ = ['analytic', 'magcreator', 'reconstruction', 'fft']
__all__ = ['analytic', 'magcreator', 'reconstruction', 'fft', 'fieldconverter']
__all__.extend(costfunction.__all__)
__all__.extend(dataset.__all__)
__all__.extend(diagnostics.__all__)
......@@ -106,3 +107,4 @@ __all__.extend(regularisator.__all__)
__all__.extend(ramp.__all__)
__all__.extend(quaternion.__all__)
__all__.extend(colormap.__all__)
__all__.extend(config.__all__)
pyramid/fieldconverter.py 0 → 100644
+ 139
− 0
View file @ 4725e6cf
# coding=utf-8
"""Convert vector fields.
The :mod:`~.fieldconverter` provides methods for converting a magnetization distribution `M` into
a vector potential `A` and convert this in turn into a magnetic field `B`. The direct way is also
possible.
"""
import logging
import numpy as np
from pyramid import fft
from pyramid.magdata import MagData
__all__ = ['convert_M_to_A', 'convert_A_to_B', 'convert_M_to_B']
_log = logging.getLogger(__name__)
def convert_M_to_A(mag_data, b_0=1.0):
"""Convert a magnetic vector distribution into a vector potential `A`.
Parameters
----------
mag_data: :class:`~pyramid.magdata.MagData` object
The magnetic vector field from which the A-field is calculated.
b_0: float, optional
The saturation magnetization which is used in the calculation.
Returns
-------
b_data: :class:`~pyramid.magdata.MagData` object
The calculated B-field.
"""
_log.debug('Calling convert_M_to_A')
# Preparations of variables:
assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
dim = mag_data.dim
dim_kern = tuple(2 * np.array(dim) - 1) # Dimensions of the kernel
if fft.BACKEND == 'pyfftw':
dim_pad = tuple(2 * np.array(dim)) # is at least even (not neccessary a power of 2)
elif fft.BACKEND == 'numpy':
dim_pad = tuple(2 ** np.ceil(np.log2(2 * np.array(dim))).astype(int)) # pow(2)
else:
raise ValueError('Backend of the fft module is not correctly initiated!')
slice_B = (slice(dim[0] - 1, dim_kern[0]), # Shift because kernel center
slice(dim[1] - 1, dim_kern[1]), # is not at (0, 0, 0)!
slice(dim[2] - 1, dim_kern[2]))
slice_M = (slice(0, dim[0]), # Magnetization is padded on the far end!
slice(0, dim[1]), # B-field cutout is shifted as listed above
slice(0, dim[2])) # because of the kernel center!
# Set up kernels
coeff = mag_data.a * b_0 / (4 * np.pi)
zzz, yyy, xxx = np.indices(dim_kern)
xxx -= dim[2] - 1
yyy -= dim[1] - 1
zzz -= dim[0] - 1
k_x = fft.empty(dim_kern, dtype=fft.FLOAT)
k_y = fft.empty(dim_kern, dtype=fft.FLOAT)
k_z = fft.empty(dim_kern, dtype=fft.FLOAT)
k_x[...] = coeff * xxx / np.abs(xxx ** 2 + yyy ** 2 + zzz ** 2 + 1E-30) ** 3
k_y[...] = coeff * yyy / np.abs(xxx ** 2 + yyy ** 2 + zzz ** 2 + 1E-30) ** 3
k_z[...] = coeff * zzz / np.abs(xxx ** 2 + yyy ** 2 + zzz ** 2 + 1E-30) ** 3
# Calculate Fourier trafo of kernel components:
k_x_fft = fft.rfftn(k_x, dim_pad)
k_y_fft = fft.rfftn(k_y, dim_pad)
k_z_fft = fft.rfftn(k_z, dim_pad)
# Prepare magnetization:
x_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
y_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
z_mag = fft.zeros(dim_pad, dtype=fft.FLOAT)
x_mag[slice_M] = mag_data.magnitude[0, ...]
y_mag[slice_M] = mag_data.magnitude[1, ...]
z_mag[slice_M] = mag_data.magnitude[2, ...]
# Calculate Fourier trafo of magnetization components:
x_mag_fft = fft.rfftn(x_mag)
y_mag_fft = fft.rfftn(y_mag)
z_mag_fft = fft.rfftn(z_mag)
# Convolve:
a_x_fft = y_mag_fft * k_z_fft - z_mag_fft * k_y_fft
a_y_fft = z_mag_fft * k_x_fft - x_mag_fft * k_z_fft
a_z_fft = x_mag_fft * k_y_fft - y_mag_fft * k_x_fft
a_x = fft.irfftn(a_x_fft)[slice_B]
a_y = fft.irfftn(a_y_fft)[slice_B]
a_z = fft.irfftn(a_z_fft)[slice_B]
# Return A-field:
return MagData(mag_data.a, np.asarray((a_x, a_y, a_z)))
def convert_A_to_B(a_data):
"""Convert a vector potential `A` into a B-field distribution.
Parameters
----------
a_data: :class:`~pyramid.magdata.MagData` object
The vector potential field from which the A-field is calculated.
Returns
-------
b_data: :class:`~pyramid.magdata.MagData` object
The calculated B-field.
"""
_log.debug('Calling convert_A_to_B')
assert isinstance(a_data, MagData), 'Only MagData objects can be mapped!'
# Calculate gradients:
x_mag, y_mag, z_mag = a_data.magnitude
x_grad_z, x_grad_y, x_grad_x = np.gradient(x_mag)
y_grad_z, y_grad_y, y_grad_x = np.gradient(y_mag)
z_grad_z, z_grad_y, z_grad_x = np.gradient(z_mag)
# Calculate cross product:
b_x = (z_grad_y - y_grad_z)
b_y = (x_grad_z - z_grad_x)
b_z = (y_grad_x - x_grad_y)
# Return B-field:
return MagData(a_data.a, np.asarray((b_x, b_y, b_z)))
def convert_M_to_B(mag_data, b_0=1.0):
"""Convert a magnetic vector distribution into a B-field distribution.
Parameters
----------
mag_data: :class:`~pyramid.magdata.MagData` object
The magnetic vector field from which the B-field is calculated.
b_0: float, optional
The saturation magnetization which is used in the calculation.
Returns
-------
b_data: :class:`~pyramid.magdata.MagData` object
The calculated B-field.
"""
_log.debug('Calling convert_M_to_B')
assert isinstance(mag_data, MagData), 'Only MagData objects can be mapped!'
return convert_A_to_B(convert_M_to_A(mag_data, b_0=b_0))
pyramid/kernel.py
+ 5
− 5
View file @ 4725e6cf
......@@ -94,8 +94,8 @@ class Kernel(object):
u = np.linspace(-(u_dim - 1), u_dim - 1, num=2 * u_dim - 1)
v = np.linspace(-(v_dim - 1), v_dim - 1, num=2 * v_dim - 1)
uu, vv = np.meshgrid(u, v)
self.u = fft.empty(self.dim_kern, fft.FLOAT)
self.v = fft.empty(self.dim_kern, fft.FLOAT)
self.u = fft.empty(self.dim_kern, dtype=fft.FLOAT)
self.v = fft.empty(self.dim_kern, dtype=fft.FLOAT)
self.u[...] = coeff * self._get_elementary_phase(geometry, uu, vv, a)
self.v[...] = coeff * self._get_elementary_phase(geometry, vv, uu, a)
# Include perturbed reference wave:
......@@ -123,15 +123,15 @@ class Kernel(object):
self._log.debug('Calling _get_elementary_phase')
if geometry == 'disc':
in_or_out = ~ np.logical_and(n == 0, m == 0)
return m / (n ** 2 + m ** 2 + 1E-30) * in_or_out
return n / (n ** 2 + m ** 2 + 1E-30) * in_or_out
elif geometry == 'slab':
def _F_a(n, m):
A = np.log(a ** 2 * (n ** 2 + m ** 2))
B = np.arctan(n / m)
return n * A - 2 * n + 2 * m * B
return 0.5 * (_F_a(n - 0.5, m - 0.5) - _F_a(n + 0.5, m - 0.5)
- _F_a(n - 0.5, m + 0.5) + _F_a(n + 0.5, m + 0.5))
return 0.5 * (_F_a(n - 0.5, m - 0.5) - _F_a(n + 0.5, m - 0.5) -
_F_a(n - 0.5, m + 0.5) + _F_a(n + 0.5, m + 0.5))
def print_info(self):
"""Print information about the kernel.
......
pyramid/magdata.py
+ 74
− 40
View file @ 4725e6cf
......@@ -548,7 +548,7 @@ class MagData(object):
self._log.debug('Calling save_to_hdf5')
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'magdata')
if not os.path.exists(directory):
os.makedirs(directory)
......@@ -577,7 +577,7 @@ class MagData(object):
return
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'magdata')
filename = os.path.join(directory, filename)
# Load data from file:
......@@ -605,7 +605,7 @@ class MagData(object):
data = np.array([xx, yy, zz, x_vec, y_vec, z_vec]).T
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'magdata')
if not os.path.exists(directory):
os.makedirs(directory)
......@@ -636,7 +636,7 @@ class MagData(object):
SCALE = 1.0E-9 / 1.0E-2 # From cm to nm
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'magdata')
filename = os.path.join(directory, filename)
# Load data from file:
......@@ -668,7 +668,8 @@ class MagData(object):
The slice-index of the axis specified in `proj_axis`. Is set to the center of
`proj_axis` if not specified.
log : boolean, optional
Takes the Default is False.
The loratihm of the arrow length is plotted instead. This is helpful if only the
direction of the arrows is important and the amplitude varies a lot. Default is False.
scaled : boolean, optional
Normalizes the plotted arrows in respect to the highest one. Default is True.
scale: float, optional
......@@ -691,8 +692,8 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[0] // 2
plot_u = np.copy(self.magnitude[0][ax_slice, ...]) # x-component
plot_v = np.copy(self.magnitude[1][ax_slice, ...]) # y-component
u_mag = np.copy(self.magnitude[0][ax_slice, ...]) # x-component
v_mag = np.copy(self.magnitude[1][ax_slice, ...]) # y-component
u_label = 'x [px]'
v_label = 'y [px]'
submask = self.get_mask()[ax_slice, ...]
......@@ -701,8 +702,8 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[1] // 2
plot_u = np.copy(self.magnitude[0][:, ax_slice, :]) # x-component
plot_v = np.copy(self.magnitude[2][:, ax_slice, :]) # z-component
u_mag = np.copy(self.magnitude[0][:, ax_slice, :]) # x-component
v_mag = np.copy(self.magnitude[2][:, ax_slice, :]) # z-component
u_label = 'x [px]'
v_label = 'z [px]'
submask = self.get_mask()[:, ax_slice, :]
......@@ -711,26 +712,26 @@ class MagData(object):
if ax_slice is None:
self._log.debug('ax_slice is None')
ax_slice = self.dim[2] // 2
plot_u = np.swapaxes(np.copy(self.magnitude[2][..., ax_slice]), 0, 1) # z-component
plot_v = np.swapaxes(np.copy(self.magnitude[1][..., ax_slice]), 0, 1) # y-component
u_mag = np.swapaxes(np.copy(self.magnitude[2][..., ax_slice]), 0, 1) # z-component
v_mag = np.swapaxes(np.copy(self.magnitude[1][..., ax_slice]), 0, 1) # y-component
u_label = 'z [px]'
v_label = 'y [px]'
submask = self.get_mask()[..., ax_slice]
else:
raise ValueError('{} is not a valid argument (use x, y or z)'.format(proj_axis))
# Prepare quiver (select only used arrows if ar_dens is specified):
dim_uv = plot_u.shape
dim_uv = u_mag.shape
vv, uu = np.indices(dim_uv) + 0.5 # shift to center of pixel
uu = uu[::ar_dens, ::ar_dens]
vv = vv[::ar_dens, ::ar_dens]
plot_u = plot_u[::ar_dens, ::ar_dens]
plot_v = plot_v[::ar_dens, ::ar_dens]
amplitudes = np.hypot(plot_u, plot_v)
angles = np.angle(plot_u + 1j * plot_v, deg=True).tolist()
u_mag = u_mag[::ar_dens, ::ar_dens]
v_mag = v_mag[::ar_dens, ::ar_dens]
amplitudes = np.hypot(u_mag, v_mag)
angles = np.angle(u_mag + 1j * v_mag, deg=True).tolist()
# Calculate the arrow colors:
if coloring == 'angle':
self._log.debug('Encoding angles')
colorinds = (1 + np.arctan2(plot_v, plot_u) / np.pi) / 2 # in-plane color index (0-1).
colorinds = (1 + np.arctan2(v_mag, u_mag) / np.pi) / 2 # in-plane color index (0-1).
cmap = DirectionalColormap()
elif coloring == 'amplitude':
self._log.debug('Encoding amplitude')
......@@ -738,7 +739,7 @@ class MagData(object):
cmap = 'jet'
elif coloring == 'uniform':
self._log.debug('No color encoding')
colorinds = np.zeros_like(plot_u) # use black arrows!
colorinds = np.zeros_like(u_mag) # use black arrows!
cmap = 'gray'
else:
raise AttributeError("Invalid coloring mode! Use 'angles', 'amplitude' or 'uniform'!")
......@@ -749,20 +750,20 @@ class MagData(object):
axis = fig.add_subplot(1, 1, 1)
axis.set_aspect('equal')
# Take the logarithm of the arrows to clearly show directions (if specified):
if log:
if log and np.any(amplitudes): # If the slice is empty, skip!
cutoff = 10
amp = np.round(amplitudes, decimals=cutoff)
min_value = amp[np.nonzero(amp)].min()
plot_u = np.round(plot_u, decimals=cutoff) / min_value
plot_u = np.log10(np.abs(plot_u) + 1) * np.sign(plot_u)
plot_v = np.round(plot_v, decimals=cutoff) / min_value
plot_v = np.log10(np.abs(plot_v) + 1) * np.sign(plot_v)
amplitudes = np.hypot(plot_u, plot_v) # Recalculate!
u_mag = np.round(u_mag, decimals=cutoff) / min_value
u_mag = np.log10(np.abs(u_mag) + 1) * np.sign(u_mag)
v_mag = np.round(v_mag, decimals=cutoff) / min_value
v_mag = np.log10(np.abs(v_mag) + 1) * np.sign(v_mag)
amplitudes = np.hypot(u_mag, v_mag) # Recalculate (used if scaled)!
# Scale the magnitude of the arrows to the highest one (if specified):
if scaled:
plot_u /= amplitudes.max() + 1E-30
plot_v /= amplitudes.max() + 1E-30
axis.quiver(uu, vv, plot_u, plot_v, colorinds, cmap=cmap, clim=(0, 1), angles=angles,
u_mag /= amplitudes.max() + 1E-30
v_mag /= amplitudes.max() + 1E-30
axis.quiver(uu, vv, u_mag, v_mag, colorinds, cmap=cmap, clim=(0, 1), angles=angles,
pivot='middle', units='xy', scale_units='xy', scale=scale / ar_dens,
minlength=0.25, headwidth=6, headlength=7)
if show_mask and not np.all(submask): # Plot mask if desired and not trivial!
......@@ -784,7 +785,7 @@ class MagData(object):
return axis
def quiver_plot3d(self, title='Magnetization Distribution', limit=None, cmap='jet',
ar_dens=1, mode='arrow', coloring='angle', show_pipeline=False):
mode='2darrow', coloring='angle', ar_dens=1, opacity=1.0):
"""Plot the magnetization as 3D-vectors in a quiverplot.
Parameters
......@@ -799,13 +800,12 @@ class MagData(object):
Number defining the arrow density which is plotted. A higher ar_dens number skips more
arrows (a number of 2 plots every second arrow). Default is 1.
mode: string, optional
Mode, determining the glyphs used in the 3D plot. Default is 'arrow', which corresponds
to 3D arrows. For large amounts of arrows, '2darrow' should be used.
Mode, determining the glyphs used in the 3D plot. Default is '2darrow', which
corresponds to 2D arrows. For smaller amounts of arrows, 'arrow' (3D) is prettier.
coloring : string
Color coding mode of the arrows. Use 'angle' (default) or 'amplitude'.
show_pipeline : boolean, optional
If True, the mayavi pipeline, a GUI used for image manipulation is shown. The default
is False.
opacity: float, optional
Defines the opacity of the arrows. Default is 1.0 (completely opaque).
Returns
-------
......@@ -821,16 +821,17 @@ class MagData(object):
limit = np.max(self.mag_amp)
ad = ar_dens
# Create points and vector components as lists:
zz, yy, xx = (np.indices(dim) - a / 2).reshape((3,) + dim)
zz = zz[::ad, ::ad, ::ad].flatten()
yy = yy[::ad, ::ad, ::ad].flatten()
xx = xx[::ad, ::ad, ::ad].flatten()
zzz, yyy, xxx = (np.indices(dim) - a / 2).reshape((3,) + dim)
zzz = zzz[::ad, ::ad, ::ad].flatten()
yyy = yyy[::ad, ::ad, ::ad].flatten()
xxx = xxx[::ad, ::ad, ::ad].flatten()
x_mag = self.magnitude[0][::ad, ::ad, ::ad].flatten()
y_mag = self.magnitude[1][::ad, ::ad, ::ad].flatten()
z_mag = self.magnitude[2][::ad, ::ad, ::ad].flatten()
# Plot them as vectors:
mlab.figure(size=(750, 700))
plot = mlab.quiver3d(xx, yy, zz, x_mag, y_mag, z_mag, mode=mode, colormap=cmap)
plot = mlab.quiver3d(xxx, yyy, zzz, x_mag, y_mag, z_mag,
mode=mode, colormap=cmap, opacity=opacity)
if coloring == 'angle': # Encodes the full angle via colorwheel and saturation
self._log.debug('Encoding full 3D angles')
from tvtk.api import tvtk
......@@ -853,6 +854,39 @@ class MagData(object):
mlab.axes(plot)
mlab.title(title, height=0.95, size=0.35)
mlab.orientation_axes()
if show_pipeline:
mlab.show_pipeline()
# mlab.show()
return plot
def contour_plot3d(self, title='Magnetization Distribution', contours=10, opacity=0.25):
"""Plot the magnetization as 3D-vectors in a quiverplot.
Parameters
----------
title: string, optional
The title for the plot.
contours: int, optional
Number of contours which should be plotted.
opacity: float, optional
Defines the opacity of the contours. Default is 0.25.
Returns
-------
plot : :class:`mayavi.modules.vectors.Vectors`
The plot object.
"""
self._log.debug('Calling quiver_plot3D')
from mayavi import mlab
# Create points and vector components as lists:
x_mag, y_mag, z_mag = self.magnitude
amplitudes = np.sqrt(x_mag ** 2 + y_mag ** 2 + z_mag ** 2)
# Plot them as vectors:
mlab.figure(size=(750, 700))
plot = mlab.contour3d(amplitudes, contours=contours, opacity=opacity)
mlab.outline(plot)
mlab.axes(plot)
mlab.title(title, height=0.95, size=0.35)
mlab.orientation_axes()
# mlab.show()
return plot
pyramid/phasemap.py
+ 4
− 4
View file @ 4725e6cf
......@@ -485,7 +485,7 @@ class PhaseMap(object):
self._log.debug('Calling save_to_hdf5')
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'phasemap')
if not os.path.exists(directory):
os.makedirs(directory)
......@@ -514,7 +514,7 @@ class PhaseMap(object):
return
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'phasemap')
filename = os.path.join(directory, filename)
# Load data from file:
......@@ -540,7 +540,7 @@ class PhaseMap(object):
self._log.debug('Calling save_to_txt')
# Construct path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'phasemap')
if not os.path.exists(directory):
os.makedirs(directory)
......@@ -575,7 +575,7 @@ class PhaseMap(object):
cls._log.debug('Calling load_from_txt')
# Use relative path if filename isn't already absolute:
if not os.path.isabs(filename):
from pyramid import DIR_FILES
from pyramid.config import DIR_FILES
directory = os.path.join(DIR_FILES, 'phasemap')
filename = os.path.join(directory, filename)
# Load data from file:
......
pyramid/phasemapper.py
+ 39
− 23
View file @ 4725e6cf
......@@ -18,7 +18,7 @@ from pyramid import fft
from pyramid.kernel import Kernel
from pyramid.magdata import MagData
from pyramid.phasemap import PhaseMap
from pyramid.projector import SimpleProjector
from pyramid.projector import RotTiltProjector, XTiltProjector, YTiltProjector, SimpleProjector
__all__ = ['PhaseMapperRDFC', 'PhaseMapperRDRC', 'PhaseMapperFDFC', 'pm']
_log = logging.getLogger(__name__)
......@@ -142,7 +142,7 @@ class PhaseMapperRDFC(PhaseMapper):
self.u_mag_fft = fft.rfftn(self.u_mag)
self.v_mag_fft = fft.rfftn(self.v_mag)
# Convolve the magnetization with the kernel in Fourier space:
self.phase_fft = self.u_mag_fft * self.kernel.u_fft - self.v_mag_fft * self.kernel.v_fft
self.phase_fft = self.u_mag_fft * self.kernel.v_fft - self.v_mag_fft * self.kernel.u_fft
# Return the result:
return fft.irfftn(self.phase_fft)[self.kernel.slice_phase]
......@@ -188,8 +188,8 @@ class PhaseMapperRDFC(PhaseMapper):
'vector size not compatible! vector: {}, size: {}'.format(len(vector), self.m)
self.mag_adj[self.kernel.slice_mag] = vector.reshape(self.kernel.dim_uv)
mag_adj_fft = fft.irfftn_adj(self.mag_adj)
u_phase_adj_fft = mag_adj_fft * self.kernel.u_fft
v_phase_adj_fft = mag_adj_fft * -self.kernel.v_fft
u_phase_adj_fft = mag_adj_fft * self.kernel.v_fft
v_phase_adj_fft = mag_adj_fft * -self.kernel.u_fft
u_phase_adj = fft.rfftn_adj(u_phase_adj_fft)[self.kernel.slice_phase]
v_phase_adj = fft.rfftn_adj(v_phase_adj_fft)[self.kernel.slice_phase]
result = np.concatenate((-u_phase_adj.flatten(), -v_phase_adj.flatten()))
......@@ -258,19 +258,19 @@ class PhaseMapperRDRC(PhaseMapper):
# Calculation of the phase:
phase = np.zeros(dim_uv, dtype=np.float32)
if self.numcore:
nc.phasemapper_real_convolve(dim_uv[0], dim_uv[1], v_phi, u_phi,
nc.phasemapper_real_convolve(dim_uv[0], dim_uv[1], u_phi, v_phi,
v_mag, u_mag, phase, self.threshold)
else:
for j in range(dim_uv[0]):
for i in range(dim_uv[1]):
u_phase = u_phi[dim_uv[0] - 1 - j:(2 * dim_uv[0] - 1) - j,
dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
if abs(u_mag[j, i]) > self.threshold:
phase += u_mag[j, i] * u_phase
v_phase = v_phi[dim_uv[0] - 1 - j:(2 * dim_uv[0] - 1) - j,
dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
if abs(v_mag[j, i]) > self.threshold:
phase -= v_mag[j, i] * v_phase
phase += u_mag[j, i] * v_phase
u_phase = u_phi[dim_uv[0] - 1 - j:(2 * dim_uv[0] - 1) - j,
dim_uv[1] - 1 - i:(2 * dim_uv[1] - 1) - i]
if abs(u_mag[j, i]) > self.threshold:
phase -= v_mag[j, i] * u_phase
# Return the phase:
return PhaseMap(mag_data.a, phase)
......@@ -297,7 +297,7 @@ class PhaseMapperRDRC(PhaseMapper):
if self.numcore:
if vector.dtype != np.float32:
vector = vector.astype(np.float32)
nc.jac_dot_real_convolve(v_dim, u_dim, self.kernel.u, self.kernel.v, vector, result)
nc.jac_dot_real_convolve(v_dim, u_dim, self.kernel.v, self.kernel.u, vector, result)
else:
# Iterate over all contributing pixels (numbered consecutively)
for s in range(self.m): # column-wise (two columns at a time, u- and v-component)
......@@ -307,8 +307,8 @@ class PhaseMapperRDRC(PhaseMapper):
u_max = (2 * u_dim - 1) - i # = u_min + u_dim
v_min = (v_dim - 1) - j # v_dim-1: center of the kernel
v_max = (2 * v_dim - 1) - j # = v_min + v_dim
result += vector[s] * self.kernel.u[v_min:v_max, u_min:u_max].reshape(-1)
result -= vector[s + self.m] * self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1)
result += vector[s] * self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1)
result -= vector[s + self.m] * self.kernel.u[v_min:v_max, u_min:u_max].reshape(-1)
return result
def jac_T_dot(self, vector):
......@@ -334,7 +334,7 @@ class PhaseMapperRDRC(PhaseMapper):
if self.numcore:
if vector.dtype != np.float32:
vector = vector.astype(np.float32)
nc.jac_T_dot_real_convolve(v_dim, u_dim, self.kernel.u, self.kernel.v, vector, result)
nc.jac_T_dot_real_convolve(v_dim, u_dim, self.kernel.v, self.kernel.u, vector, result)
else:
# Iterate over all contributing pixels (numbered consecutively):
for s in range(self.m): # row-wise (two rows at a time, u- and v-component)
......@@ -344,9 +344,9 @@ class PhaseMapperRDRC(PhaseMapper):
u_max = (2 * u_dim - 1) - i # = u_min + u_dim
v_min = (v_dim - 1) - j # v_dim-1: center of the kernel
v_max = (2 * v_dim - 1) - j # = v_min + v_dim
result[s] = np.sum(vector * self.kernel.u[v_min:v_max, u_min:u_max].reshape(-1))
result[s] = np.sum(vector * self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1))
result[s + self.m] = np.sum(vector *
-self.kernel.v[v_min:v_max, u_min:u_max].reshape(-1))
-self.kernel.u[v_min:v_max, u_min:u_max].reshape(-1))
return result
......@@ -579,20 +579,22 @@ class PhaseMapperMIP(PhaseMapper):
raise NotImplementedError()
def pm(mag_data, axis='z', dim_uv=None, b_0=1):
def pm(mag_data, mode='z', b_0=1, **kwargs):
"""Convenience function for fast phase mapping.
Parameters
----------
mag_data : :class:`~.MagData`
A :class:`~.MagData` object, from which the projected phase map should be calculated.
axis: {'z', 'y', 'x'}, optional
Axis along which the :class:`.~SimpleProjector` projects the magnetic distribution.
dim_uv : tuple of int (N=2), optional
Dimensions of the 2-dimensional projected magnetization grid from which the phase should
be calculated.
mode: {'z', 'y', 'x', 'x-tilt', 'y-tilt', 'rot-tilt'}, optional
Projection mode which determines the :class:`~.pyramid.projector.Projector` subclass, which
is used for the projection. Default is a simple projection along the `z`-direction.
b_0 : float, optional
Saturation magnetization in Tesla, which is used for the phase calculation. Default is 1.
**kwargs : additional arguments
Additional arguments like `dim_uv`, 'tilt' or 'rotation', which are passed to the
projector-constructor, defined by the `mode`.
Returns
-------
phase_map : :class:`~pyramid.phasemap.PhaseMap`
......@@ -600,9 +602,23 @@ def pm(mag_data, axis='z', dim_uv=None, b_0=1):
"""
_log.debug('Calling pm')
projector = SimpleProjector(mag_data.dim, axis=axis, dim_uv=dim_uv)
# Determine projection mode:
if mode == 'rot-tilt':
projector = RotTiltProjector(mag_data.dim, **kwargs)
elif mode == 'x-tilt':
projector = XTiltProjector(mag_data.dim, **kwargs)
elif mode == 'y-tilt':
projector = YTiltProjector(mag_data.dim, **kwargs)
elif mode in ['x', 'y', 'z']:
projector = SimpleProjector(mag_data.dim, axis=mode, **kwargs)
else:
raise ValueError("Invalid mode (use 'x', 'y', 'z', 'x-tilt', 'y-tilt' or 'rot-tilt')")
# Project:
mag_proj = projector(mag_data)
# Set up phasemapper and map phase:
phasemapper = PhaseMapperRDFC(Kernel(mag_data.a, projector.dim_uv, b_0=b_0))
phase_map = phasemapper(mag_proj)
# Get mask from magdata:
phase_map.mask = mag_proj.get_mask()[0, ...]
# Return phase:
return phase_map
pyramid/tests/test_kernel/ref_u_fft.npy
+ 0
− 0
View file @ 4725e6cf
No preview for this file type
pyramid/tests/test_kernel/ref_v_fft.npy
+ 0
− 0
View file @ 4725e6cf
No preview for this file type
scripts/gui/mag_slicer.py
+ 5
− 5
View file @ 4725e6cf
......@@ -11,15 +11,15 @@
import os
import sys
from PyQt4 import QtCore, QtGui
from matplotlibwidget import MatplotlibWidget
import pyramid
from pyramid.kernel import Kernel
from pyramid.magdata import MagData
from pyramid.phasemapper import PhaseMapperRDFC
from pyramid.projector import SimpleProjector
from PyQt4 import QtCore, QtGui
from matplotlibwidget import MatplotlibWidget
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
......@@ -230,8 +230,8 @@ class UI_MagSlicerMain(QtGui.QWidget):
def load(self):
directory = os.path.join(pyramid.DIR_FILES, 'magdata')
mag_file = QtGui.QFileDialog.getOpenFileName(self, 'Open Data File', directory,
'NetCDF files (*.nc)')
self.mag_data = MagData.load_from_netcdf4(mag_file)
'HDF5 files (*.hdf5)')
self.mag_data = MagData.load_from_hdf5(mag_file)
self.mag_data_loaded = True
self.mplWidgetMag.axes.set_visible(True)
self.mplWidgetHolo.axes.set_visible(True)
......
scripts/phasemap/phasemap_tilt_series.py
+ 2
− 2
View file @ 4725e6cf
......@@ -19,7 +19,7 @@ angles = np.linspace()
###################################################################################################
mag_data = py.MagData.load_from_netcdf4(filename)
phase_map = py.pm(mag_data, axis=axis, dim_uv=dim_uv, b_0=b_0)
phase_map = py.pm(mag_data, mode=axis, dim_uv=dim_uv, b_0=b_0)
phase_map.save_to_netcdf4('phasemap_{}_axis={}'.format(filename.replace('magdata_', ''), axis))
phase_map.display_combined()
......@@ -56,4 +56,4 @@ for angle in angles:
plt.close('all')
gc.collect()
print 'RSS = {:.2f} MB'.format(proc.memory_info().rss/1024.**2)
print angle, 'deg. done!'
\ No newline at end of file
print angle, 'deg. done!'
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