From 975e30c27737e2aa6b83c0b99a98d60a484decdb Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Tue, 13 Aug 2013 16:16:08 +0200
Subject: [PATCH] Final version of paper scripts holoimage: changed colorwheel
(now without axes) magcreator: create_vortex now also allows a 3D-center (2D
is extracted) magdata: new methods: get_mask() and scale_down() phasemap:
changed plotting defaults (new kwargs) phasemapper: started on electrical
contribution
---
pyramid/analytic.py | 12 +-
pyramid/holoimage.py | 40 +-
pyramid/magcreator.py | 10 +-
pyramid/magdata.py | 77 ++-
pyramid/phasemap.py | 69 ++-
pyramid/phasemapper.py | 37 +-
.../compare_method_errors_fourier_padding.py | 2 +-
scripts/compare_methods.py | 16 +-
scripts/compare_pixel_fields.py | 6 +-
scripts/create_logo.py | 3 +-
scripts/interactive_setup.py | 2 +-
.../ch5-0-evaluation_and_comparison.py | 23 +-
.../paper 1/ch5-1-evaluation_real_space.py | 318 ++++++-----
.../paper 1/ch5-2-evaluation_fourier_space.py | 535 +++++++++++++++---
.../paper 1/ch5-3-comparison_of_methods.py | 136 ++---
scripts/reconstruct_random_pixels.py | 9 +-
setup.py | 2 +-
17 files changed, 910 insertions(+), 387 deletions(-)
diff --git a/pyramid/analytic.py b/pyramid/analytic.py
index 246c7a8..89337ce 100644
--- a/pyramid/analytic.py
+++ b/pyramid/analytic.py
@@ -12,7 +12,7 @@ PHI_0 = -2067.83 # magnetic flux in T*nm²
def phase_mag_slab(dim, res, phi, center, width, b_0=1):
- '''Get the analytic solution for a phase map of a slab of specified dimensions
+ '''Get the analytic solution for a phase map of a slab of specified dimensions.
Arguments:
dim - the dimensions of the grid, shape(z, y, x)
res - the resolution of the grid (grid spacing) in nm
@@ -40,8 +40,8 @@ def phase_mag_slab(dim, res, phi, center, width, b_0=1):
+ F0(y-y0+Ly/2, x-x0+Lx/2)))
# Process input parameters:
z_dim, y_dim, x_dim = dim
- y0 = res * (center[1] + 0.5) # y0, x0 have to be in the center of a pixel,
- x0 = res * (center[2] + 0.5) # hence: cellindex + 0.5
+ y0 = res * (center[1] + 0.5) # y0, x0 define the center of a pixel,
+ x0 = res * (center[2] + 0.5) # hence: (cellindex + 0.5) * resolution
Lz, Ly, Lx = res * width[0], res * width[1], res * width[2]
coeff = b_0 / (4*PHI_0)
# Create grid:
@@ -53,7 +53,7 @@ def phase_mag_slab(dim, res, phi, center, width, b_0=1):
def phase_mag_disc(dim, res, phi, center, radius, height, b_0=1):
- '''Get the analytic solution for a phase map of a disc of specified dimensions
+ '''Get the analytic solution for a phase map of a disc of specified dimensions.
Arguments:
dim - the dimensions of the grid, shape(z, y, x)
res - the resolution of the grid (grid spacing) in nm
@@ -89,7 +89,7 @@ def phase_mag_disc(dim, res, phi, center, radius, height, b_0=1):
def phase_mag_sphere(dim, res, phi, center, radius, b_0=1):
- '''Get the analytic solution for a phase map of a sphere of specified dimensions
+ '''Get the analytic solution for a phase map of a sphere of specified dimensions.
Arguments:
dim - the dimensions of the grid, shape(z, y, x)
res - the resolution of the grid (grid spacing) in nm
@@ -123,7 +123,7 @@ def phase_mag_sphere(dim, res, phi, center, radius, b_0=1):
def phase_mag_vortex(dim, res, center, radius, height, b_0=1):
- '''Get the analytic solution for a phase map of a sharp vortex disc of specified dimensions
+ '''Get the analytic solution for a phase map of a sharp vortex disc of specified dimensions.
Arguments:
dim - the dimensions of the grid, shape(z, y, x)
res - the resolution of the grid (grid spacing) in nm
diff --git a/pyramid/holoimage.py b/pyramid/holoimage.py
index b44e91d..cea6f96 100644
--- a/pyramid/holoimage.py
+++ b/pyramid/holoimage.py
@@ -8,6 +8,7 @@ import matplotlib.pyplot as plt
from pyramid.phasemap import PhaseMap
from numpy import pi
from PIL import Image
+from matplotlib.ticker import NullLocator
CDICT = {'red': [(0.00, 1.0, 0.0),
@@ -76,20 +77,20 @@ def make_color_wheel():
rgb = (255.999 * color_wheel_magnitude.T * rgba[:, :, :3].T).T.astype(np.uint8)
color_wheel = Image.fromarray(rgb)
# Plot the color wheel:
- fig = plt.figure()
- ax = fig.add_subplot(111, aspect='equal')
- ax.imshow(color_wheel)
- ax.set_title('Color Wheel')
- ax.set_xlabel('x-axis')
- ax.set_ylabel('y-axis')
+ fig = plt.figure(figsize=(4, 4))
+ axis = fig.add_subplot(1, 1, 1, aspect='equal')
+ axis.imshow(color_wheel, origin='lower')
+ axis.xaxis.set_major_locator(NullLocator())
+ axis.yaxis.set_major_locator(NullLocator())
-def display(holo_image, title='Holography Image', axis=None):
+def display(holo_image, title='Holography Image', axis=None, interpolation='none'):
'''Display the color coded holography image resulting from a given phase map.
Arguments:
- holo_image - holography image created with the holo_image function of this module
- title - the title of the plot (default: 'Holography Image')
- axis - the axis on which to display the plot (default: None, a new figure is created)
+ holo_image - holography image created with the holo_image function of this module
+ title - the title of the plot (default: 'Holography Image')
+ axis - the axis on which to display the plot (default: None, creates new figure)
+ interpolation - defines the interpolation method (default: 'none')
Returns:
None
@@ -99,13 +100,17 @@ def display(holo_image, title='Holography Image', axis=None):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1, aspect='equal')
# Plot the image and set axes:
- axis.imshow(holo_image, interpolation='none')
+ axis.imshow(holo_image, origin='lower', interpolation=interpolation)
+ # Set the title and the axes labels:
axis.set_title(title)
- axis.set_xlabel('x-axis')
- axis.set_ylabel('y-axis')
+ plt.tick_params(axis='both', which='major', labelsize=14)
+ axis.set_title(title, fontsize=18)
+ axis.set_xlabel('x-axis [px]', fontsize=15)
+ axis.set_ylabel('y-axis [px]', fontsize=15)
-def display_combined(phase_map, density, title='Combined Plot'):
+def display_combined(phase_map, density, title='Combined Plot', interpolation='none',
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]')):# TODO DOCSTRING
'''Display a given phase map and the resulting color coded holography image in one plot.
Arguments:
phase_map - the PhaseMap object from which the holography image is calculated
@@ -116,11 +121,12 @@ def display_combined(phase_map, density, title='Combined Plot'):
'''
# Create combined plot and set title:
- fig = plt.figure(figsize=(14, 7))
+ fig = plt.figure(figsize=(16, 7))
fig.suptitle(title, fontsize=20)
# Plot holography image:
holo_axis = fig.add_subplot(1, 2, 1, aspect='equal')
- display(holo_image(phase_map, density), axis=holo_axis)
+ display(holo_image(phase_map, density), axis=holo_axis, interpolation=interpolation)
# Plot phase map:
phase_axis = fig.add_subplot(1, 2, 2, aspect='equal')
- phase_map.display(axis=phase_axis)
+ fig.subplots_adjust(right=0.85)
+ phase_map.display(axis=phase_axis, labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
diff --git a/pyramid/magcreator.py b/pyramid/magcreator.py
index 0a389e5..7eef6d5 100644
--- a/pyramid/magcreator.py
+++ b/pyramid/magcreator.py
@@ -223,9 +223,9 @@ def create_mag_dist_vortex(mag_shape, center=None, magnitude=1):
'''Create a 3-dimensional magnetic distribution of a homogeneous magnetized object.
Arguments:
mag_shape - the magnetic shapes (numpy arrays, see Shapes.* for examples)
- phi - the azimuthal angle, describing the direction of the magnetized object
- theta - the polar angle, describing the direction of the magnetized object
- (optional, is set to pi/2 if not specified -> z-component is zero)
+ center - the vortex center, given in 2D (x,y) or 3D (x,y,z), where z is discarded
+ (optional, is set to the center of the field of view if not specified, always
+ between two pixels!)
magnitude - the relative magnitudes for the magnetic shape (optional, one if not specified)
Returns:
the 3D magnetic distribution as a MagData object (see pyramid.magdata for reference)
@@ -235,7 +235,9 @@ def create_mag_dist_vortex(mag_shape, center=None, magnitude=1):
assert len(dim) == 3, 'Magnetic shapes must describe 3-dimensional distributions!'
if center is None:
center = (int(dim[1]/2)-0.5, int(dim[2]/2)-0.5) # center has to be between (!) two pixels
- assert len(center) == 2, 'Vortex center has to be defined in 2D!'
+ if len(center) == 3: # if a 3D-center is given, just take the x and y components
+ center = (center[1], center[2])
+ assert len(center) == 2, 'Vortex center has to be defined in 3D or 2D!'
x = np.linspace(-center[1], dim[2]-1-center[1], dim[2])
y = np.linspace(-center[0], dim[1]-1-center[0], dim[1])
xx, yy = np.meshgrid(x, y)
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
index 61221c7..1d172b0 100644
--- a/pyramid/magdata.py
+++ b/pyramid/magdata.py
@@ -5,6 +5,7 @@
import numpy as np
import tables.netcdf3 as nc
import matplotlib.pyplot as plt
+from matplotlib.ticker import MaxNLocator
class MagData:
@@ -30,18 +31,42 @@ class MagData:
self.magnitude = magnitude
def get_vector(self, mask):
- # TODO: Implement!
+ # TODO: DOCSTRING!
return np.concatenate([self.magnitude[2][mask],
self.magnitude[1][mask],
self.magnitude[0][mask]])
def set_vector(self, mask, vector):
- # TODO: Implement!
+ # TODO: DOCSTRING!
assert np.size(vector) % 3 == 0, 'Vector has to contain all 3 components for every pixel!'
count = np.size(vector)/3
self.magnitude[2][mask] = vector[:count] # x-component
self.magnitude[1][mask] = vector[count:2*count] # y-component
self.magnitude[0][mask] = vector[2*count:] # z-component
+
+ def get_mask(self, threshold=0):
+ # TODO: DOCSTRING!
+ z_mask = abs(self.magnitude[0]) > threshold
+ x_mask = abs(self.magnitude[1]) > threshold
+ y_mask = abs(self.magnitude[2]) > threshold
+ return np.logical_or(np.logical_or(x_mask, y_mask), z_mask)
+
+ def scale_down(self, n=1):
+ # TODO: DOCSTRING!
+ # Starting magnetic distribution:
+ assert n >= 0 and isinstance(n, (int, long)), 'n must be a positive integer!'
+ assert self.dim[0] % 2**n == 0 and self.dim[1] % 2**n == 0 and self.dim[2] % 2**n == 0, \
+ 'For downscaling, every dimension must be a multiple of 2!'
+ for t in range(n):
+ # Create coarser grid for the magnetization:
+ z_mag = self.magnitude[0].reshape(self.dim[0]/2, 2, self.dim[1]/2, 2, self.dim[2]/2, 2)
+ y_mag = self.magnitude[1].reshape(self.dim[0]/2, 2, self.dim[1]/2, 2, self.dim[2]/2, 2)
+ x_mag = self.magnitude[2].reshape(self.dim[0]/2, 2, self.dim[1]/2, 2, self.dim[2]/2, 2)
+ self.dim = (self.dim[0]/2, self.dim[1]/2, self.dim[2]/2)
+ self.res = self.res * 2
+ self.magnitude = (z_mag.mean(axis=5).mean(axis=3).mean(axis=1),
+ y_mag.mean(axis=5).mean(axis=3).mean(axis=1),
+ x_mag.mean(axis=5).mean(axis=3).mean(axis=1))
@classmethod
def load_from_llg(cls, filename):
@@ -130,30 +155,57 @@ class MagData:
print f
f.close()
- def quiver_plot(self, axis='z', ax_slice=0):
+ def quiver_plot(self, title='Magnetic Distribution)', proj_axis='z', ax_slice=None,
+ filename=None, axis=None): # TODO!!
'''Plot a slice of the magnetization as a quiver plot.
Arguments:
axis - the axis from which a slice is plotted ('x', 'y' or 'z'), default = 'z'
- ax_slice - the slice-index of the specified axis
+ ax_slice - the slice-index of the specified axis (optional, if not specified, is
+ set to the center of the specified axis)
+ filename - filename, specifying the location where the image is saved (optional, if
+ not specified, image is shown instead)
Returns:
None
'''
- assert axis == 'z' or axis == 'y' or axis == 'x', 'Axis has to be x, y or z (as string).'
- if axis == 'z': # Slice of the xy-plane with z = ax_slice
+ assert proj_axis == 'z' or proj_axis == 'y' or proj_axis == 'x', \
+ 'Axis has to be x, y or z (as string).'
+ if proj_axis == 'z': # Slice of the xy-plane with z = ax_slice
+ if ax_slice is None:
+ ax_slice = int(self.dim[0]/2)
mag_slice_u = self.magnitude[2][ax_slice, ...]
mag_slice_v = self.magnitude[1][ax_slice, ...]
- elif axis == 'y': # Slice of the xz-plane with y = ax_slice
+ u_label = 'x [px]'
+ v_label = 'y [px]'
+ elif proj_axis == 'y': # Slice of the xz-plane with y = ax_slice
+ if ax_slice is None:
+ ax_slice = int(self.dim[1]/2)
mag_slice_u = self.magnitude[2][:, ax_slice, :]
mag_slice_v = self.magnitude[0][:, ax_slice, :]
- elif axis == 'x': # Slice of the yz-plane with x = ax_slice
+ u_label = 'x [px]'
+ v_label = 'z [px]'
+ elif proj_axis == 'x': # Slice of the yz-plane with x = ax_slice
+ if ax_slice is None:
+ ax_slice = int(self.dim[2]/2)
mag_slice_u = self.magnitude[1][..., ax_slice]
mag_slice_v = self.magnitude[0][..., ax_slice]
- # Plot the magnetization vectors:
- fig = plt.figure()
- fig.add_subplot(111, aspect='equal')
- plt.quiver(mag_slice_u, mag_slice_v, pivot='middle', angles='xy', scale_units='xy',
+ u_label = 'y [px]'
+ v_label = 'z [px]'
+ # If no axis is specified, a new figure is created:
+ if axis is None:
+ fig = plt.figure(figsize=(8.5, 7))
+ axis = fig.add_subplot(1, 1, 1, aspect='equal')
+ axis.quiver(mag_slice_u, mag_slice_v, pivot='middle', angles='xy', scale_units='xy',
scale=1, headwidth=6, headlength=7)
+ axis.set_xlim(0, np.shape(mag_slice_u)[1])
+ axis.set_ylim(0, np.shape(mag_slice_u)[0])
+ axis.set_title(title, fontsize=18)
+ axis.set_xlabel(u_label, fontsize=15)
+ axis.set_ylabel(v_label, fontsize=15)
+ axis.tick_params(axis='both', which='major', labelsize=14)
+ axis.xaxis.set_major_locator(MaxNLocator(nbins=8, integer=True))
+ axis.yaxis.set_major_locator(MaxNLocator(nbins=8, integer=True))
+ plt.show()
def quiver_plot3d(self):
'''3D-Quiver-Plot of the magnetization as vectors.
@@ -178,6 +230,7 @@ class MagData:
y_mag = np.reshape(self.magnitude[1], (-1))
z_mag = np.reshape(self.magnitude[0], (-1))
# Plot them as vectors:
+ mlab.figure()
plot = mlab.quiver3d(xx, yy, zz, x_mag, y_mag, z_mag, mode='arrow', scale_factor=10.0)
mlab.outline(plot)
mlab.axes(plot)
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index 12dea2f..f2b5a04 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -88,7 +88,8 @@ class PhaseMap:
phase[:] = self.phase
f.close()
- def display(self, title='Phase Map', axis=None, cmap='gray'):
+ def display(self, title='Phase Map', labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]'),
+ cmap='RdBu', limit=None, norm=None, axis=None):
'''Display the phasemap as a colormesh.
Arguments:
title - the title of the plot (default: 'Phase Map')
@@ -97,23 +98,65 @@ class PhaseMap:
Returns:
None
- '''
+ ''' # TODO: Docstring!
+
+ # TODO: ALWAYS CENTERED around 0
+ if limit is None:
+ limit = np.max(np.abs(self.phase))
+
# If no axis is specified, a new figure is created:
if axis is None:
- fig = plt.figure()
+ fig = plt.figure(figsize=(8.5, 7))
axis = fig.add_subplot(1, 1, 1, aspect='equal')
- im = plt.pcolormesh(self.phase, cmap=cmap)
+ # Plot the phasemap:
+ im = axis.pcolormesh(self.phase, cmap=cmap, vmin=-limit, vmax=limit, norm=norm)
# Set the axes ticks and labels:
- ticks = axis.get_xticks()*self.res
+ axis.set_xlim(0, np.shape(self.phase)[1])
+ axis.set_ylim(0, np.shape(self.phase)[0])
+ ticks = (axis.get_xticks()*self.res).astype(int)
axis.set_xticklabels(ticks)
- ticks = axis.get_yticks()*self.res
+ ticks = (axis.get_yticks()*self.res).astype(int)
+ axis.tick_params(axis='both', which='major', labelsize=14)
axis.set_yticklabels(ticks)
- axis.set_title(title)
- axis.set_xlabel('x-axis [nm]')
- axis.set_ylabel('y-axis [nm]')
- # Plot the phase map:
+ axis.set_title(title, fontsize=18)
+ axis.set_xlabel(labels[0], fontsize=15)
+ axis.set_ylabel(labels[1], fontsize=15)
+ # Add colorbar:
fig = plt.gcf()
- fig.subplots_adjust(right=0.85)
- cbar_ax = fig.add_axes([0.9, 0.15, 0.02, 0.7])
- fig.colorbar(im, cax=cbar_ax)
+ fig.subplots_adjust(right=0.8)
+ cbar_ax = fig.add_axes([0.82, 0.15, 0.02, 0.7])
+ cbar = fig.colorbar(im, cax=cbar_ax)
+ cbar.ax.tick_params(labelsize=14)
+ cbar.set_label(labels[2], fontsize=15)
+
+ plt.show()
+
+ def display3d(self, title='Phase Map', labels=('x-axis [nm]', 'y-axis [nm]', 'phase [rad]'),
+ cmap='RdBu', limit=None, norm=None, axis=None):
+ '''Display the phasemap as a colormesh.
+ Arguments:
+ title - the title of the plot (default: 'Phase Map')
+ axis - the axis on which to display the plot (default: None, a new figure is created)
+ cmap - the colormap which is used for the plot (default: 'gray')
+ Returns:
+ None
+
+ ''' # TODO: Docstring!
+
+ from mpl_toolkits.mplot3d import Axes3D
+
+ fig = plt.figure()
+ ax = Axes3D(fig)#.gca(projection='3d')
+
+ u = range(self.dim[1])
+ v = range(self.dim[0])
+ uu, vv = np.meshgrid(u, v)
+ ax.plot_surface(uu, vv, self.phase, rstride=4, cstride=4, alpha=0.7, cmap='RdBu',
+ linewidth=0, antialiased=False)
+ ax.contourf(uu, vv, self.phase, 15, zdir='z', offset=np.min(self.phase), cmap='RdBu')
+ ax.view_init(45, -135)
+ ax.set_xlabel('x-axis [px]')
+ ax.set_ylabel('y-axis [px]')
+ ax.set_zlabel('phase [mrad]')
+
plt.show()
diff --git a/pyramid/phasemapper.py b/pyramid/phasemapper.py
index 2d53f97..61cffa1 100644
--- a/pyramid/phasemapper.py
+++ b/pyramid/phasemapper.py
@@ -4,7 +4,8 @@
import numpy as np
import numcore
-import time
+
+from numpy import pi
# Physical constants
PHI_0 = -2067.83 # magnetic flux in T*nm²
@@ -248,20 +249,20 @@ def phase_mag_real_alt(res, projection, method, b_0=1, jacobi=None): # TODO: Mo
return phase
-#def phase_elec(mag_data, v_0=0, v_acc=30000):
-# # TODO: Docstring
-#
-# res = mag_data.res
-# z_dim, y_dim, x_dim = mag_data.dim
-# z_mag, y_mag, x_mag = mag_data.magnitude
-#
-# phase = np.logical_or(x_mag, y_mag, z_mag)
-#
-# lam = H_BAR / np.sqrt(2 * M_E * v_acc * (1 + Q_E*v_acc / (2*M_E*C**2)))
-#
-# Ce = (2*pi*Q_E/lam * (Q_E*v_acc + M_E*C**2) /
-# (Q_E*v_acc * (Q_E*v_acc + 2*M_E*C**2)))
-#
-# phase *= res * v_0 * Ce
-#
-# return phase
+def phase_elec(mag_data, v_0=1, v_acc=30000):
+ # TODO: Docstring
+
+ res = mag_data.res
+ z_dim, y_dim, x_dim = mag_data.dim
+ z_mag, y_mag, x_mag = mag_data.magnitude
+
+ phase = np.logical_or(x_mag, y_mag, z_mag)
+
+ lam = H_BAR / np.sqrt(2 * M_E * v_acc * (1 + Q_E*v_acc / (2*M_E*C**2)))
+
+ Ce = (2*pi*Q_E/lam * (Q_E*v_acc + M_E*C**2) /
+ (Q_E*v_acc * (Q_E*v_acc + 2*M_E*C**2)))
+
+ phase *= res * v_0 * Ce
+
+ return phase
diff --git a/scripts/compare_method_errors_fourier_padding.py b/scripts/compare_method_errors_fourier_padding.py
index 9c0db37..e393d4a 100644
--- a/scripts/compare_method_errors_fourier_padding.py
+++ b/scripts/compare_method_errors_fourier_padding.py
@@ -36,7 +36,7 @@ def phase_from_mag():
b_0 = 1 # in T
res = 10.0 # in nm
dim = (1, 128, 128)
- phi = -pi/4
+ phi = -pi/2
padding_list = [0, 0.25, 0.5, 0.75, 1, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 21, 22]
geometry = 'disc'
diff --git a/scripts/compare_methods.py b/scripts/compare_methods.py
index ae92cf4..e6677fd 100644
--- a/scripts/compare_methods.py
+++ b/scripts/compare_methods.py
@@ -31,20 +31,20 @@ def compare_methods():
b_0 = 1 # in T
res = 10.0 # in nm
phi = pi/4
- padding = 20
- density = 10
- dim = (1, 128, 128) # in px (z, y, x)
+ padding = 12
+ density = 1
+ dim = (16, 128, 128) # in px (z, y, x)
# Create magnetic shape:
- geometry = 'slab'
+ geometry = 'disc'
if geometry == 'slab':
- center = (0, dim[1]/2., dim[2]/2.) # in px (z, y, x) index starts with 0!
- width = (1, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x)
+ center = (dim[0]/2-0.5, dim[1]/2-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ width = (dim[0]/2, dim[1]/2., dim[2]/2.) # in px (z, y, x)
mag_shape = mc.Shapes.slab(dim, center, width)
phase_ana = an.phase_mag_slab(dim, res, phi, center, width, b_0)
elif geometry == 'disc':
- center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
- height = 1 # in px
+ height = dim[0]/2 # in px
mag_shape = mc.Shapes.disc(dim, center, radius, height)
phase_ana = an.phase_mag_disc(dim, res, phi, center, radius, height, b_0)
elif geometry == 'sphere':
diff --git a/scripts/compare_pixel_fields.py b/scripts/compare_pixel_fields.py
index fff98b2..c3bd985 100644
--- a/scripts/compare_pixel_fields.py
+++ b/scripts/compare_pixel_fields.py
@@ -26,10 +26,11 @@ def compare_pixel_fields():
# Input parameters:
res = 10.0 # in nm
phi = pi/2 # in rad
- dim = (1, 11, 11)
- pixel = (0, 5, 5)
+ dim = (1, 5, 5)
+ pixel = (0, 2, 2)
# Create magnetic data, project it, get the phase map and display the holography image:
mag_data = MagData(res, mc.create_mag_dist(mc.Shapes.pixel(dim, pixel), phi))
+ mag_data.save_to_llg('../output/mag_dist_single_pixel.txt')
projection = pj.simple_axis_projection(mag_data)
phase_map_slab = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
phase_map_slab.display('Phase of one Pixel (Slab)')
@@ -38,7 +39,6 @@ def compare_pixel_fields():
phase_map_diff = PhaseMap(res, phase_map_disc.phase - phase_map_slab.phase)
phase_map_diff.display('Phase difference of one Pixel (Disc - Slab)')
-
if __name__ == "__main__":
try:
compare_pixel_fields()
diff --git a/scripts/create_logo.py b/scripts/create_logo.py
index 8fcc493..bf763f0 100644
--- a/scripts/create_logo.py
+++ b/scripts/create_logo.py
@@ -41,9 +41,10 @@ def create_logo():
mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
# Create magnetic data, project it, get the phase map and display the holography image:
mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data.quiver_plot()
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
- hi.display(hi.holo_image(phase_map, density), 'PYRAMID - LOGO')
+ hi.display(hi.holo_image(phase_map, density), 'PYRAMID - LOGO', interpolation='bilinear')
if __name__ == "__main__":
diff --git a/scripts/interactive_setup.py b/scripts/interactive_setup.py
index a7293d0..1235112 100644
--- a/scripts/interactive_setup.py
+++ b/scripts/interactive_setup.py
@@ -11,4 +11,4 @@ from pyramid.magdata import MagData
from pyramid.phasemap import PhaseMap
import os
-os.chdir('C:\Users\Jan\Daten\PhD Thesis\Pyramid\output')
+os.chdir('C:\Users\Jan\Home\PhD Thesis\Pyramid\output')
diff --git a/scripts/paper 1/ch5-0-evaluation_and_comparison.py b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
index c01d0d9..f9f6773 100644
--- a/scripts/paper 1/ch5-0-evaluation_and_comparison.py
+++ b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
@@ -57,17 +57,20 @@ def run():
mag_data_vort.quiver_plot3d()
print '--SHELVE MAGNETIC DISTRIBUTIONS'
data_shelve[key] = (mag_data_disc, mag_data_vort)
-
- print '--PLOT/SAVE HOMOG. MAGN. DISC'
- # Plot and save MagData (Disc):
- mag_data_disc.quiver_plot('Homog. magn. disc')
- plt.savefig(directory + '/ch5-0-mag_data_disc.png', bbox_inches='tight')
-
- print '--PLOT/SAVE VORTEX STATE DISC'
- # Plot and save MagData (Vortex):
- mag_data_vort.quiver_plot('Vortex state disc')
- plt.savefig(directory + '/ch5-0-mag_data_vort.png', bbox_inches='tight')
+ print '--PLOT/SAVE MAGNETIC DISTRIBUTIONS'
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Magnetic Distributions', fontsize=20)
+ # Plot MagData (Disc):
+ mag_data_disc.quiver_plot('Homog. magn. disc', axis = axes[0])
+ axes[0].set_aspect('equal')
+ # Plot MagData (Disc):
+ mag_data_vort.quiver_plot('Vortex state disc', axis = axes[1])
+ axes[1].set_aspect('equal')
+ # Save Plots:
+ plt.figtext(0.15, 0.15, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.15, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-0-magnetic_distributions.png', bbox_inches='tight')
###############################################################################################
print 'CLOSING SHELVE\n'
diff --git a/scripts/paper 1/ch5-1-evaluation_real_space.py b/scripts/paper 1/ch5-1-evaluation_real_space.py
index 0cb4305..430b9b3 100644
--- a/scripts/paper 1/ch5-1-evaluation_real_space.py
+++ b/scripts/paper 1/ch5-1-evaluation_real_space.py
@@ -56,53 +56,54 @@ def run():
# Get analytic solution:
phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height)
phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height)
- phase_map_ana_disc = PhaseMap(res, phase_ana_disc)
- phase_map_ana_vort = PhaseMap(res, phase_ana_vort)
+ phase_map_ana_disc = PhaseMap(res, phase_ana_disc*1E3) # in mrad -> *1000
+ phase_map_ana_vort = PhaseMap(res, phase_ana_vort*1E3) # in mrad -> *1000
print '--PLOT/SAVE ANALYTIC SOLUTIONS'
- hi.display_combined(phase_map_ana_disc, 100, 'Analytic solution: hom. magn. disc', 'bilinear')
+ hi.display_combined(phase_map_ana_disc, 0.1, 'Analytic solution: hom. magn. disc', 'bilinear',
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
+ plt.figtext(0.15, 0.2, 'a)', fontsize=30, color='w')
+ plt.figtext(0.52, 0.2, 'b)', fontsize=30)
plt.savefig(directory + '/ch5-1-analytic_solution_disc.png', bbox_inches='tight')
- hi.display_combined(phase_map_ana_vort, 100, 'Analytic solution: Vortex state', 'bilinear')
+ hi.display_combined(phase_map_ana_vort, 0.1, 'Analytic solution: vortex state', 'bilinear',
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
+ plt.figtext(0.15, 0.2, 'c)', fontsize=30, color='w')
+ plt.figtext(0.52, 0.2, 'd)', fontsize=30)
plt.savefig(directory + '/ch5-1-analytic_solution_vort.png', bbox_inches='tight')
# Get colorwheel:
hi.make_color_wheel()
+ plt.figtext(0.15, 0.14, 'e)', fontsize=30, color='w')
plt.savefig(directory + '/ch5-1-colorwheel.png', bbox_inches='tight')
###############################################################################################
- print 'CH5-1 PHASE SLICES REAL SPACE' # TODO: Verschieben
+ print 'CH5-1 PHASE SLICES REAL SPACE'
# Input parameters:
res = 0.25 # in nm
phi = pi/2
- density = 20
+ density = 0.1 # Because phase is in mrad -> amplification by 100 (0.001 * 100 = 0.1)
dim = (64, 512, 512) # in px (z, y, x)
# Create magnetic shape:
center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
radius = dim[1]/4 # in px
height = dim[0]/2 # in px
- key = 'ch5-1-phase_slice_mag_dist'
+ key = 'ch5-1-phase_slices_real'
if key in data_shelve:
print '--LOAD MAGNETIC DISTRIBUTION'
- mag_shape = data_shelve[key]
+ (x_d, y_d, dy_d, x_v, y_v, dy_v) = data_shelve[key]
else:
print '--CREATE MAGNETIC DISTRIBUTION'
mag_shape = mc.Shapes.disc(dim, center, radius, height)
- print '--SAVE MAGNETIC DISTRIBUTION'
- data_shelve[key] = mag_shape
-
- key = 'ch5-1-phase_slice_disc'
- if key in data_shelve:
- print '--LOAD PHASE SLICES HOMOG. MAGN. DISC'
- (x, y) = data_shelve[key]
- else:
+
print '--CREATE PHASE SLICES HOMOG. MAGN. DISC'
# Arrays for plotting:
- x = []
- y = []
+ x_d = []
+ y_d = []
+ dy_d = []
# Analytic solution:
L = dim[1] * res # in px/nm
Lz = 0.5 * dim[0] * res # in px/nm
@@ -110,74 +111,35 @@ def run():
x0 = L / 2 # in px/nm
def F_disc(x):
- coeff = - pi * Lz / (2*PHI_0)
+ coeff = - pi * Lz / (2*PHI_0) * 1E3 # in mrad -> *1000
result = coeff * (- (x - x0) * np.sin(phi))
result *= np.where(np.abs(x - x0) <= R, 1, (R / (x - x0)) ** 2)
return result
- x.append(np.linspace(0, L, 5000))
- y.append(F_disc(x[0]))
- # Create and plot MagData (Disc):
+ x_d.append(np.linspace(0, L, 5000))
+ y_d.append(F_disc(x_d[0]))
+ dy_d.append(np.zeros_like(x_d[0]))
+ # Create MagData (Disc):
mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
for i in range(5):
mag_data_disc.scale_down()
print '----res =', mag_data_disc.res, 'nm', 'dim =', mag_data_disc.dim
projection = pj.simple_axis_projection(mag_data_disc)
phase_map = PhaseMap(mag_data_disc.res,
- pm.phase_mag_real(mag_data_disc.res, projection, 'slab'))
- hi.display_combined(phase_map, density, 'Disc, res = {}'.format(res))
- x.append(np.linspace(0, mag_data_disc.dim[1]*mag_data_disc.res, mag_data_disc.dim[1]))
- y.append(phase_map.phase[int(mag_data_disc.dim[1]/2), :])
- # Shelve x and y:
- print '--SAVE PHASE SLICES HOMOG. MAGN. DISC'
- data_shelve[key] = (x, y)
-
- print '--PLOT/SAVE PHASE SLICES HOMOG. MAGN. DISC'
- # Plot phase slices:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(x[0], y[0], 'k', label='analytic')
- axis.plot(x[1], y[1], 'r', label='0.5 nm')
- axis.plot(x[2], y[2], 'm', label='1 nm')
- axis.plot(x[3], y[3], 'y', label='2 nm')
- axis.plot(x[4], y[4], 'g', label='4 nm')
- axis.plot(x[5], y[5], 'c', label='8 nm')
- plt.tick_params(axis='both', which='major', labelsize=14)
- axis.set_title('DISC', fontsize=18)
- axis.set_xlabel('x [nm]', fontsize=15)
- axis.set_ylabel('phase [rad]', fontsize=15)
- axis.set_xlim(0, 128)
- axis.set_ylim(-0.22, 0.22)
- axis.legend()
- # Plot Zoombox and Arrow:
- rect1 = Rectangle((23.5, 0.16), 15, 0.04, fc='w', ec='k')
- axis.add_patch(rect1)
- plt.arrow(32.5, 0.16, 0.0, -0.16, length_includes_head=True,
- head_width=2, head_length=0.02, fc='k', ec='k')
- # Plot zoom inset:
- ins_axis = plt.axes([0.2, 0.2, 0.3, 0.3])
- ins_axis.plot(x[0], y[0], 'k', label='analytic')
- ins_axis.plot(x[1], y[1], 'r', label='0.5 nm')
- ins_axis.plot(x[2], y[2], 'm', label='1 nm')
- ins_axis.plot(x[3], y[3], 'y', label='2 nm')
- ins_axis.plot(x[4], y[4], 'g', label='4 nm')
- ins_axis.plot(x[5], y[5], 'c', label='8 nm')
- plt.tick_params(axis='both', which='major', labelsize=14)
- ins_axis.set_xlim(23.5, 38.5)
- ins_axis.set_ylim(0.16, 0.2)
- ins_axis.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis.yaxis.set_major_locator(MaxNLocator(nbins=3))
- plt.show()
- plt.savefig(directory + '/ch5-1-disc_slice_comparison.png', bbox_inches='tight')
-
- key = 'ch5-1-phase_slice_vort'
- if key in data_shelve:
- print '--LOAD PHASE SLICES VORTEX STATE DISC'
- (x, y) = data_shelve[key]
- else:
+ pm.phase_mag_real(mag_data_disc.res, projection, 'slab') * 1E3)
+ hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ x_d.append(np.linspace(mag_data_disc.res * 0.5,
+ mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
+ mag_data_disc.dim[1]))
+ slice_pos = int(mag_data_disc.dim[1]/2)
+ y_d.append(phase_map.phase[slice_pos, :])
+ dy_d.append(phase_map.phase[slice_pos, :] - F_disc(x_d[-1]))
+
print '--CREATE PHASE SLICES VORTEX STATE DISC'
- x = []
- y = []
+ x_v = []
+ y_v = []
+ dy_v = []
# Analytic solution:
L = dim[1] * res # in px/nm
Lz = 0.5 * dim[0] * res # in px/nm
@@ -185,63 +147,149 @@ def run():
x0 = L / 2 # in px/nm
def F_vort(x):
- coeff = pi*Lz/PHI_0
+ coeff = pi*Lz/PHI_0 * 1E3 # in mrad -> *1000
result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
return result
- x.append(np.linspace(0, L, 5001))
- y.append(F_vort(x[0]))
- # Create and plot MagData (Vortex):
+ x_v.append(np.linspace(0, L, 5001))
+ y_v.append(F_vort(x_v[0]))
+ dy_v.append(np.zeros_like(x_v[0]))
+ # Create MagData (Vortex):
mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape))
for i in range(5):
mag_data_vort.scale_down()
- print '----i =', i, 'dim =', mag_data_vort.dim, 'res =', mag_data_vort.res, 'nm'
+ print '----res =', mag_data_vort.res, 'nm', 'dim =', mag_data_vort.dim
projection = pj.simple_axis_projection(mag_data_vort)
phase_map = PhaseMap(mag_data_vort.res,
- pm.phase_mag_real(mag_data_vort.res, projection, 'slab'))
- hi.display_combined(phase_map, density, 'Disc, res = {}'.format(res))
- x.append(np.linspace(0, mag_data_vort.dim[1]*mag_data_vort.res, mag_data_vort.dim[1]))
- y.append(phase_map.phase[int(mag_data_vort.dim[1]/2), :])
- # Shelve x and y:
- print '--SAVE PHASE SLICES VORTEX STATE DISC'
- data_shelve[key] = (x, y)
+ pm.phase_mag_real(mag_data_vort.res, projection, 'slab') * 1E3)
+ hi.display_combined(phase_map, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ x_v.append(np.linspace(mag_data_vort.res * 0.5,
+ mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
+ mag_data_vort.dim[1]))
+ slice_pos = int(mag_data_vort.dim[1]/2)
+ y_v.append(phase_map.phase[int(mag_data_vort.dim[1]/2), :])
+ dy_v.append(phase_map.phase[slice_pos, :] - F_vort(x_v[-1]))
+
+ # Shelve x, y and dy:
+ print '--SAVE PHASE SLICES'
+ data_shelve[key] = (x_d, y_d, dy_d, x_v, y_v, dy_v)
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slices', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICES HOMOG. MAGN. DISC'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], y_d[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], y_d[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], y_d[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], y_d[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], y_d[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], y_d[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+ axes[0].set_ylim(-220, 220)
+ # Plot Zoombox and Arrow:
+ zoom = (23.5, 160, 15, 40)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[0].add_patch(rect)
+ axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+ head_width=10, head_length=4, fc='k', ec='k')
+ # Plot zoom inset:
+ ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
+ ins_axis_d.plot(x_d[0], y_d[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_d.plot(x_d[1], y_d[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_d.plot(x_d[2], y_d[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_d.plot(x_d[3], y_d[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_d.plot(x_d[4], y_d[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_d.plot(x_d[5], y_d[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC'
- # Plot:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(x[0], y[0], 'k', label='analytic')
- axis.plot(x[1], y[1], 'r', label='0.5 nm')
- axis.plot(x[2], y[2], 'm', label='1 nm')
- axis.plot(x[3], y[3], 'y', label='2 nm')
- axis.plot(x[4], y[4], 'g', label='4 nm')
- axis.plot(x[5], y[5], 'c', label='8 nm')
- plt.tick_params(axis='both', which='major', labelsize=14)
- axis.set_title('VORTEX', fontsize=18)
- axis.set_xlabel('x [nm]', fontsize=15)
- axis.set_ylabel('phase [rad]', fontsize=15)
- axis.set_xlim(0, 128)
- axis.legend()
+ # Plot phase slices:
+ axes[1].plot(x_v[0], y_v[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], y_v[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], y_v[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], y_v[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], y_v[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], y_v[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].yaxis.set_major_locator(MaxNLocator(nbins=6))
+ axes[1].legend()
# Plot Zoombox and Arrow:
- zoom = (59, 0.34, 10, 0.055)
- rect1 = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
- axis.add_patch(rect1)
- plt.arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -0.19, length_includes_head=True,
- head_width=2, head_length=0.02, fc='k', ec='k')
+ zoom = (59, 340, 10, 55)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[1].add_patch(rect)
+ axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+ head_width=2, head_length=20, fc='k', ec='k')
# Plot zoom inset:
- ins_axis = plt.axes([0.47, 0.15, 0.15, 0.3])
- ins_axis.plot(x[0], y[0], 'k', label='analytic')
- ins_axis.plot(x[1], y[1], 'r', label='0.5 nm')
- ins_axis.plot(x[2], y[2], 'm', label='1 nm')
- ins_axis.plot(x[3], y[3], 'y', label='2 nm')
- ins_axis.plot(x[4], y[4], 'g', label='4 nm')
- ins_axis.plot(x[5], y[5], 'c', label='8 nm')
- plt.tick_params(axis='both', which='major', labelsize=14)
- ins_axis.set_xlim(zoom[0], zoom[0]+zoom[2])
- ins_axis.set_ylim(zoom[1], zoom[1]+zoom[3])
- ins_axis.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
- ins_axis.yaxis.set_major_locator(MaxNLocator(nbins=4))
- plt.savefig(directory + '/ch5-1-vortex_slice_comparison.png', bbox_inches='tight')
+ ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
+ ins_axis_v.plot(x_v[0], y_v[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_v.plot(x_v[1], y_v[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_v.plot(x_v[2], y_v[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_v.plot(x_v[3], y_v[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_v.plot(x_v[4], y_v[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_v.plot(x_v[5], y_v[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_comparison.png', bbox_inches='tight')
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slice errors', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS HOMOG. MAGN. DISC'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], dy_d[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], dy_d[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], dy_d[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], dy_d[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], dy_d[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], dy_d[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS VORTEX STATE DISC'
+ # Plot phase slices:
+ axes[1].plot(x_v[0], dy_v[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], dy_v[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], dy_v[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], dy_v[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], dy_v[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], dy_v[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].legend(loc=4)
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_errors.png', bbox_inches='tight')
###############################################################################################
print 'CH5-1 PHASE DIFFERENCES REAL SPACE'
@@ -277,7 +325,7 @@ def run():
# Shelve magnetic distributions:
data_shelve[key] = (mag_data_disc, mag_data_vort)
- print '--PLOT/SAVE PHASE DIFFERENCES'
+ print '--CALCULATE PHASE DIFFERENCES'
# Create projections along z-axis:
projection_disc = pj.simple_axis_projection(mag_data_disc)
projection_vort = pj.simple_axis_projection(mag_data_vort)
@@ -287,22 +335,32 @@ def run():
# Create norm for the plots:
bounds = np.array([-3, -0.5, -0.25, -0.1, 0, 0.1, 0.25, 0.5, 3])
norm = BoundaryNorm(bounds, RdBu.N)
- # Disc:
+ # Calculations (Disc):
phase_num_disc = pm.phase_mag_real(res, projection_disc, 'slab')
phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
- phase_diff_disc.display('Deviation (homog. magn. disc), RMS = {:3.2f} mrad'.format(RMS_disc),
- labels=('x-axis [nm]', 'y-axis [nm]', '$\Delta$phase [mrad]'),
- limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-1-disc_phase_diff.png', bbox_inches='tight')
- # Vortex:
+ # Calculations (Vortex):
phase_num_vort = pm.phase_mag_real(res, projection_vort, 'slab')
phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
- phase_diff_vort.display('Deviation (vortex state disc), RMS = {:3.2f} mrad'.format(RMS_vort),
+
+ print '--PLOT/SAVE PHASE DIFFERENCES'
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
+ # Plot MagData (Disc):
+ phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
+ labels=('x-axis [nm]', 'y-axis [nm]', '$\Delta$phase [mrad]'),
+ limit=np.max(bounds), norm=norm, axis=axes[0])
+ axes[0].set_aspect('equal')
+ # Plot MagData (Disc):
+ phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
labels=('x-axis [nm]', 'y-axis [nm]', '$\Delta$phase [mrad]'),
- limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-1-vortex_phase_diff.png', bbox_inches='tight')
+ limit=np.max(bounds), norm=norm, axis=axes[1])
+ axes[1].set_aspect('equal')
+ # Save Plots:
+ plt.figtext(0.15, 0.2, 'a)', fontsize=30)
+ plt.figtext(0.52, 0.2, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_differences.png', bbox_inches='tight')
###############################################################################################
print 'CLOSING SHELVE\n'
diff --git a/scripts/paper 1/ch5-2-evaluation_fourier_space.py b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
index 7b7e05f..b103fd9 100644
--- a/scripts/paper 1/ch5-2-evaluation_fourier_space.py
+++ b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
"""Compare the different methods to create phase maps."""
@@ -16,6 +17,7 @@ import pyramid.magcreator as mc
import pyramid.projector as pj
import pyramid.phasemapper as pm
import pyramid.analytic as an
+import pyramid.holoimage as hi
from pyramid.magdata import MagData
from pyramid.phasemap import PhaseMap
@@ -23,6 +25,10 @@ import matplotlib.pyplot as plt
from matplotlib.colors import BoundaryNorm
from matplotlib.ticker import MaxNLocator
from matplotlib.cm import RdBu
+from matplotlib.patches import Rectangle
+
+
+PHI_0 = -2067.83 # magnetic flux in T*nm²
def run():
@@ -34,6 +40,359 @@ def run():
os.makedirs(directory)
data_shelve = shelve.open(directory + '/paper_1_shelve')
+ ###############################################################################################
+ print 'CH5-1 PHASE SLICES FOURIER SPACE'
+
+ # Input parameters:
+ res = 0.25 # in nm
+ phi = pi/2
+ density = 0.1 # Because phase is in mrad -> amplification by 100 (0.001 * 100 = 0.1)
+ dim = (64, 512, 512) # in px (z, y, x)
+ # Create magnetic shape:
+ center = (dim[0]/2-0.5, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
+ radius = dim[1]/4 # in px
+ height = dim[0]/2 # in px
+
+ key = 'ch5-2-phase_slices_fourier'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTION'
+ (x_d, y_d0, y_d10, dy_d0, dy_d10, x_v, y_v0, y_v10, dy_v0, dy_v10) = data_shelve[key]
+ else:
+ print '--CREATE MAGNETIC DISTRIBUTION'
+ mag_shape = mc.Shapes.disc(dim, center, radius, height)
+
+ print '--CREATE PHASE SLICES HOMOG. MAGN. DISC'
+ # Arrays for plotting:
+ x_d = []
+ y_d0 = []
+ y_d10 = []
+ dy_d0 = []
+ dy_d10 = []
+ # Analytic solution:
+ L = dim[1] * res # in px/nm
+ Lz = 0.5 * dim[0] * res # in px/nm
+ R = 0.25 * L # in px/nm
+ x0 = L / 2 # in px/nm
+
+ def F_disc(x):
+ coeff = - pi * Lz / (2*PHI_0) * 1E3 # in mrad -> *1000
+ result = coeff * (- (x - x0) * np.sin(phi))
+ result *= np.where(np.abs(x - x0) <= R, 1, (R / (x - x0)) ** 2)
+ return result
+
+ x_d.append(np.linspace(0, L, 5000))
+ y_d0.append(F_disc(x_d[0]))
+ y_d10.append(F_disc(x_d[0]))
+ dy_d0.append(np.zeros_like(x_d[0]))
+ dy_d10.append(np.zeros_like(x_d[0]))
+ # Create MagData (Disc):
+ mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ for i in range(5):
+ mag_data_disc.scale_down()
+ print '----res =', mag_data_disc.res, 'nm', 'dim =', mag_data_disc.dim
+ projection = pj.simple_axis_projection(mag_data_disc)
+ phase_map0 = PhaseMap(mag_data_disc.res,
+ pm.phase_mag_fourier(mag_data_disc.res, projection,
+ padding=0) * 1E3)
+ phase_map10 = PhaseMap(mag_data_disc.res,
+ pm.phase_mag_fourier(mag_data_disc.res, projection,
+ padding=10) * 1E3)
+ hi.display_combined(phase_map0, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ hi.display_combined(phase_map10, density, 'Disc, res = {} nm'.format(mag_data_disc.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ x_d.append(np.linspace(mag_data_disc.res * 0.5,
+ mag_data_disc.res * (mag_data_disc.dim[1]-0.5),
+ mag_data_disc.dim[1]))
+ slice_pos = int(mag_data_disc.dim[1]/2)
+ y_d0.append(phase_map0.phase[slice_pos, :])
+ y_d10.append(phase_map10.phase[slice_pos, :])
+ dy_d0.append(phase_map0.phase[slice_pos, :] - F_disc(x_d[-1]))
+ dy_d10.append(phase_map10.phase[slice_pos, :] - F_disc(x_d[-1]))
+
+ print '--CREATE PHASE SLICES VORTEX STATE DISC'
+ x_v = []
+ y_v0 = []
+ y_v10 = []
+ dy_v0 = []
+ dy_v10 = []
+ # Analytic solution:
+ L = dim[1] * res # in px/nm
+ Lz = 0.5 * dim[0] * res # in px/nm
+ R = 0.25 * L # in px/nm
+ x0 = L / 2 # in px/nm
+
+ def F_vort(x):
+ coeff = pi*Lz/PHI_0 * 1E3 # in mrad -> *1000
+ result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
+ return result
+
+ x_v.append(np.linspace(0, L, 5000))
+ y_v0.append(F_vort(x_v[0]))
+ y_v10.append(F_vort(x_v[0]))
+ dy_v0.append(np.zeros_like(x_v[0]))
+ dy_v10.append(np.zeros_like(x_v[0]))
+ # Create MagData (Vortex):
+ mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape))
+ for i in range(5):
+ mag_data_vort.scale_down()
+ print '----res =', mag_data_vort.res, 'nm', 'dim =', mag_data_vort.dim
+ projection = pj.simple_axis_projection(mag_data_vort)
+ phase_map0 = PhaseMap(mag_data_vort.res,
+ pm.phase_mag_fourier(mag_data_vort.res, projection,
+ padding=0) * 1E3)
+ phase_map10 = PhaseMap(mag_data_vort.res,
+ pm.phase_mag_fourier(mag_data_vort.res, projection,
+ padding=10) * 1E3)
+ hi.display_combined(phase_map0, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ hi.display_combined(phase_map10, density, 'Disc, res = {} nm'.format(mag_data_vort.res),
+ labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ x_v.append(np.linspace(mag_data_vort.res * 0.5,
+ mag_data_vort.res * (mag_data_vort.dim[1]-0.5),
+ mag_data_vort.dim[1]))
+ slice_pos = int(mag_data_vort.dim[1]/2)
+ y_v0.append(phase_map0.phase[slice_pos, :])
+ y_v10.append(phase_map10.phase[slice_pos, :])
+ dy_v0.append(phase_map0.phase[slice_pos, :] - F_vort(x_v[-1]))
+ dy_v10.append(phase_map10.phase[slice_pos, :] - F_vort(x_v[-1]))
+
+ # Shelve x, y and dy:
+ print '--SAVE PHASE SLICES'
+ data_shelve[key] = (x_d, y_d0, y_d10, dy_d0, dy_d10, x_v, y_v0, y_v10, dy_v0, dy_v10)
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slices (padding = 0)', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICES HOMOG. MAGN. DISC PADDING = 0'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], y_d0[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], y_d0[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], y_d0[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], y_d0[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], y_d0[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], y_d0[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+ axes[0].set_ylim(-220, 220)
+ # Plot Zoombox and Arrow:
+ zoom = (23.5, 160, 15, 40)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[0].add_patch(rect)
+ axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+ head_width=10, head_length=4, fc='k', ec='k')
+ # Plot zoom inset:
+ ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
+ ins_axis_d.plot(x_d[0], y_d0[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_d.plot(x_d[1], y_d0[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_d.plot(x_d[2], y_d0[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_d.plot(x_d[3], y_d0[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_d.plot(x_d[4], y_d0[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_d.plot(x_d[5], y_d0[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
+
+ print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC PADDING = 0'
+ # Plot phase slices:
+ axes[1].plot(x_v[0], y_v0[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], y_v0[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], y_v0[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], y_v0[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], y_v0[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], y_v0[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].yaxis.set_major_locator(MaxNLocator(nbins=6))
+ axes[1].legend()
+ # Plot Zoombox and Arrow:
+ zoom = (59, 340, 10, 55)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[1].add_patch(rect)
+ axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+ head_width=2, head_length=20, fc='k', ec='k')
+ # Plot zoom inset:
+ ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
+ ins_axis_v.plot(x_v[0], y_v0[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_v.plot(x_v[1], y_v0[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_v.plot(x_v[2], y_v0[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_v.plot(x_v[3], y_v0[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_v.plot(x_v[4], y_v0[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_v.plot(x_v[5], y_v0[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_padding_0.png', bbox_inches='tight')
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slices (padding = 10)', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICES HOMOG. MAGN. DISC PADDING = 10'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], y_d10[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], y_d10[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], y_d10[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], y_d10[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], y_d10[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], y_d10[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+ axes[0].set_ylim(-220, 220)
+ # Plot Zoombox and Arrow:
+ zoom = (23.5, 160, 15, 40)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[0].add_patch(rect)
+ axes[0].arrow(zoom[0]+zoom[2], zoom[1]+zoom[3]/2, 36, 0, length_includes_head=True,
+ head_width=10, head_length=4, fc='k', ec='k')
+ # Plot zoom inset:
+ ins_axis_d = plt.axes([0.33, 0.57, 0.14, 0.3])
+ ins_axis_d.plot(x_d[0], y_d10[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_d.plot(x_d[1], y_d10[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_d.plot(x_d[2], y_d10[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_d.plot(x_d[3], y_d10[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_d.plot(x_d[4], y_d10[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_d.plot(x_d[5], y_d10[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_d.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_d.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_d.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_d.yaxis.set_major_locator(MaxNLocator(nbins=3))
+
+ print '--PLOT/SAVE PHASE SLICES VORTEX STATE DISC PADDING = 10'
+ # Plot phase slices:
+ axes[1].plot(x_v[0], y_v10[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], y_v10[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], y_v10[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], y_v10[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], y_v10[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], y_v10[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].yaxis.set_major_locator(MaxNLocator(nbins=6))
+ axes[1].legend()
+ # Plot Zoombox and Arrow:
+ zoom = (59, 340, 10, 55)
+ rect = Rectangle((zoom[0], zoom[1]), zoom[2], zoom[3], fc='w', ec='k')
+ axes[1].add_patch(rect)
+ axes[1].arrow(zoom[0]+zoom[2]/2, zoom[1], 0, -193, length_includes_head=True,
+ head_width=2, head_length=20, fc='k', ec='k')
+ # Plot zoom inset:
+ ins_axis_v = plt.axes([0.695, 0.15, 0.075, 0.3])
+ ins_axis_v.plot(x_v[0], y_v10[0], '-k', linewidth=1.5, label='analytic')
+ ins_axis_v.plot(x_v[1], y_v10[1], '-r', linewidth=1.5, label='0.5 nm')
+ ins_axis_v.plot(x_v[2], y_v10[2], '-m', linewidth=1.5, label='1 nm')
+ ins_axis_v.plot(x_v[3], y_v10[3], '-y', linewidth=1.5, label='2 nm')
+ ins_axis_v.plot(x_v[4], y_v10[4], '-g', linewidth=1.5, label='4 nm')
+ ins_axis_v.plot(x_v[5], y_v10[5], '-c', linewidth=1.5, label='8 nm')
+ ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
+ ins_axis_v.set_xlim(zoom[0], zoom[0]+zoom[2])
+ ins_axis_v.set_ylim(zoom[1], zoom[1]+zoom[3])
+ ins_axis_v.xaxis.set_major_locator(MaxNLocator(nbins=4, integer= True))
+ ins_axis_v.yaxis.set_major_locator(MaxNLocator(nbins=4))
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_padding_10.png', bbox_inches='tight')
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slice errors (padding = 0)', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS HOMOG. MAGN. DISC PADDING = 0'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], dy_d0[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], dy_d0[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], dy_d0[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], dy_d0[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], dy_d0[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], dy_d0[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS VORTEX STATE DISC PADDING = 0'
+ # Plot phase slices:
+ axes[1].plot(x_v[0], dy_v0[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], dy_v0[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], dy_v0[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], dy_v0[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], dy_v0[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], dy_v0[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].legend(loc=4)
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'c)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'd)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_errors_padding_0.png', bbox_inches='tight')
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Central phase slice errors (padding = 10)', fontsize=20)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS HOMOG. MAGN. DISC PADDING = 10'
+ # Plot phase slices:
+ axes[0].plot(x_d[0], dy_d10[0], '-k', linewidth=1.5, label='analytic')
+ axes[0].plot(x_d[1], dy_d10[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[0].plot(x_d[2], dy_d10[2], '-m', linewidth=1.5, label='1 nm')
+ axes[0].plot(x_d[3], dy_d10[3], '-y', linewidth=1.5, label='2 nm')
+ axes[0].plot(x_d[4], dy_d10[4], '-g', linewidth=1.5, label='4 nm')
+ axes[0].plot(x_d[5], dy_d10[5], '-c', linewidth=1.5, label='8 nm')
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].set_title('Homog. magn. disc', fontsize=18)
+ axes[0].set_xlabel('x [nm]', fontsize=15)
+ axes[0].set_ylabel('phase [mrad]', fontsize=15)
+ axes[0].set_xlim(0, 128)
+
+ print '--PLOT/SAVE PHASE SLICE ERRORS VORTEX STATE DISC PADDING = 10'
+ # Plot phase slices:
+ axes[1].plot(x_v[0], dy_v10[0], '-k', linewidth=1.5, label='analytic')
+ axes[1].plot(x_v[1], dy_v10[1], '-r', linewidth=1.5, label='0.5 nm')
+ axes[1].plot(x_v[2], dy_v10[2], '-m', linewidth=1.5, label='1 nm')
+ axes[1].plot(x_v[3], dy_v10[3], '-y', linewidth=1.5, label='2 nm')
+ axes[1].plot(x_v[4], dy_v10[4], '-g', linewidth=1.5, label='4 nm')
+ axes[1].plot(x_v[5], dy_v10[5], '-c', linewidth=1.5, label='8 nm')
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1].set_title('Vortex state disc', fontsize=18)
+ axes[1].set_xlabel('x [nm]', fontsize=15)
+ axes[1].set_ylabel('phase [mrad]', fontsize=15)
+ axes[1].set_xlim(0, 128)
+ axes[1].legend(loc=4)
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'c)', fontsize=30)
+ plt.figtext(0.57, 0.13, 'd)', fontsize=30)
+ plt.savefig(directory + '/ch5-1-phase_slice_errors_padding_10.png', bbox_inches='tight')
+
###############################################################################################
print 'CH5-2 PHASE DIFFERENCES FOURIER SPACE'
@@ -75,6 +434,10 @@ def run():
# Get analytic solutions:
phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height)
phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height)
+
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
# Create norm for the plots:
bounds = np.array([-100, -50, -25, -5, 0, 5, 25, 50, 100])
norm = BoundaryNorm(bounds, RdBu.N)
@@ -82,21 +445,29 @@ def run():
phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=0)
phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
- phase_diff_disc.display('Deviation (homog. magn. disc), RMS = {:3.2f} mrad'.format(RMS_disc),
- labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 0)'),
+ phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
+ axis=axes[0], labels=('x-axis [nm]', 'y-axis [nm]',
+ '$\Delta$phase [mrad] (padding = 0)'),
limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-2-disc_phase_diff_no_padding.png', bbox_inches='tight')
+ axes[0].set_aspect('equal')
# Vortex:
phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=0)
phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
- phase_diff_vort.display('Deviation (vortex state disc), RMS = {:3.2f} mrad'.format(RMS_vort),
- labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 0)'),
+ phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
+ axis=axes[1], labels=('x-axis [nm]', 'y-axis [nm]',
+ '$\Delta$phase [mrad] (padding = 0)'),
limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-2-vortex_phase_diff_no_padding.png', bbox_inches='tight')
+ axes[1].set_aspect('equal')
+
+ plt.show()
+ plt.figtext(0.15, 0.2, 'a)', fontsize=30)
+ plt.figtext(0.52, 0.2, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-2-fourier_phase_differe_no_padding.png', bbox_inches='tight')
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Difference of the real space approach from the analytical solution', fontsize=20)
# Create norm for the plots:
bounds = np.array([-3, -0.5, -0.25, -0.1, 0, 0.1, 0.25, 0.5, 3])
norm = BoundaryNorm(bounds, RdBu.N)
@@ -104,20 +475,25 @@ def run():
phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=10)
phase_diff_disc = PhaseMap(res, (phase_num_disc-phase_ana_disc)*1E3) # in mrad -> *1000)
RMS_disc = np.sqrt(np.mean(phase_diff_disc.phase**2))
- phase_diff_disc.display('Deviation (homog. magn. disc), RMS = {:3.2f} mrad'.format(RMS_disc),
- labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 10)'),
+ phase_diff_disc.display('Homog. magn. disc, RMS = {:3.2f} mrad'.format(RMS_disc),
+ axis=axes[0], labels=('x-axis [nm]', 'y-axis [nm]',
+ '$\Delta$phase [mrad] (padding = 10)'),
limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-2-disc_phase_diff_padding_10.png', bbox_inches='tight')
+ axes[0].set_aspect('equal')
# Vortex:
phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=10)
phase_diff_vort = PhaseMap(res, (phase_num_vort-phase_ana_vort)*1E3) # in mrad -> *1000
RMS_vort = np.sqrt(np.mean(phase_diff_vort.phase**2))
- phase_diff_vort.display('Deviation (vortex state disc), RMS = {:3.2f} mrad'.format(RMS_vort),
- labels=('x-axis [nm]', 'y-axis [nm]',
- '$\Delta$phase [mrad] (padding = 10)'),
+ phase_diff_vort.display('Vortex state disc, RMS = {:3.2f} mrad'.format(RMS_vort),
+ axis=axes[1], labels=('x-axis [nm]', 'y-axis [nm]',
+ '$\Delta$phase [mrad] (padding = 10)'),
limit=np.max(bounds), norm=norm)
- plt.savefig(directory + '/ch5-2-vortex_phase_diff_padding_10.png', bbox_inches='tight')
+ axes[1].set_aspect('equal')
+
+ plt.show()
+ plt.figtext(0.15, 0.2, 'c)', fontsize=30)
+ plt.figtext(0.52, 0.2, 'd)', fontsize=30)
+ plt.savefig(directory + '/ch5-2-fourier_phase_differe_padding_10.png', bbox_inches='tight')
###############################################################################################
print 'CH5-2 FOURIER PADDING VARIATION'
@@ -183,42 +559,41 @@ def run():
data_shelve[key] = data_disc[:, i]
print '--PLOT/SAVE PADDING SERIES OF HOMOG. MAGN. DISC'
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Variation of the padding (homog. magn. disc)', fontsize=20)
# Plot RMS against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.axhline(y=0.18, linestyle='--', color='g', label='RMS [mrad] (real space)')
- axis.plot(data_disc[0], data_disc[1], 'go-', label='RMS [mrad] (Fourier space)')
- axis.set_title('Variation of the Padding (homog. magn. disc)', fontsize=18)
- axis.set_xlabel('padding', fontsize=15)
- axis.set_ylabel('RMS [mrad]', fontsize=15)
- axis.set_xlim(-0.5, 16.5)
- axis.set_ylim(-5, 45)
- axis.xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
- axis.legend()
- plt.tick_params(axis='both', which='major', labelsize=14)
+ axes[0].axhline(y=0.18, linestyle='--', color='g', label='RMS [mrad] (real space)')
+ axes[0].plot(data_disc[0], data_disc[1], 'go-', label='RMS [mrad] (Fourier space)')
+ axes[0].set_xlabel('padding', fontsize=15)
+ axes[0].set_ylabel('RMS [mrad]', fontsize=15)
+ axes[0].set_xlim(-0.5, 16.5)
+ axes[0].set_ylim(-5, 45)
+ axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].legend()
# Plot zoom inset:
- ins_axis = plt.axes([0.3, 0.3, 0.55, 0.4])
- ins_axis.axhline(y=0.18, linestyle='--', color='g')
- ins_axis.plot(data_disc[0], data_disc[1], 'go-')
- ins_axis.set_yscale('log')
- ins_axis.set_xlim(5.5, 16.5)
- ins_axis.set_ylim(0.1, 1.1)
- plt.tick_params(axis='both', which='major', labelsize=14)
- plt.savefig(directory + '/ch5-2-disc_padding_RMS.png', bbox_inches='tight')
+ ins_axis_d = plt.axes([0.2, 0.35, 0.25, 0.4])
+ ins_axis_d.axhline(y=0.18, linestyle='--', color='g')
+ ins_axis_d.plot(data_disc[0], data_disc[1], 'go-')
+ ins_axis_d.set_yscale('log')
+ ins_axis_d.set_xlim(5.5, 16.5)
+ ins_axis_d.set_ylim(0.1, 1.1)
+ ins_axis_d.tick_params(axis='both', which='major', labelsize=14)
# Plot duration against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(data_disc[0], data_disc[2], 'bo-')
- axis.set_title('Variation of the Padding (homog. magn. disc)', fontsize=18)
- axis.set_xlabel('padding', fontsize=15)
- axis.set_ylabel('duration [s]', fontsize=15)
- axis.set_xlim(-0.5, 16.5)
- axis.set_ylim(-0.05, 1.5)
- axis.xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
- axis.yaxis.set_major_locator(MaxNLocator(nbins=10))
- plt.tick_params(axis='both', which='major', labelsize=14)
- plt.savefig(directory + '/ch5-2-disc_padding_duration.png', bbox_inches='tight')
-
+ axes[1].plot(data_disc[0], data_disc[2], 'bo-')
+ axes[1].set_xlabel('padding', fontsize=15)
+ axes[1].set_ylabel('duration [s]', fontsize=15)
+ axes[1].set_xlim(-0.5, 16.5)
+ axes[1].set_ylim(-0.05, 1.5)
+ axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[1].yaxis.set_major_locator(MaxNLocator(nbins=10))
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.17, 'b)', fontsize=30)
+ plt.savefig(directory + '/ch5-2-disc_padding_variation.png', bbox_inches='tight')
print '--LOAD/CREATE PADDING SERIES OF VORTEX STATE DISC'
data_vort = np.zeros((3, len(padding_list)))
@@ -240,39 +615,41 @@ def run():
data_shelve[key] = data_vort[:, i]
print '--PLOT/SAVE PADDING SERIES OF VORTEX STATE DISC'
+ # Create figure:
+ fig, axes = plt.subplots(1, 2, figsize=(16, 7))
+ fig.suptitle('Variation of the padding (Vortex state disc)', fontsize=20)
# Plot RMS against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.axhline(y=0.22, linestyle='--', color='g', label='RMS [mrad] (real space)')
- axis.plot(data_vort[0], data_vort[1], 'go-', label='RMS [mrad] (Fourier space)')
- axis.set_title('Variation of the Padding (vortex state disc)', fontsize=18)
- axis.set_xlabel('padding', fontsize=15)
- axis.set_ylabel('RMS [mrad]', fontsize=15)
- axis.set_xlim(-0.5, 16.5)
- axis.set_ylim(-5, 45)
- plt.tick_params(axis='both', which='major', labelsize=14)
- axis.xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
- axis.legend()
+ axes[0].axhline(y=0.22, linestyle='--', color='g', label='RMS [mrad] (real space)')
+ axes[0].plot(data_vort[0], data_vort[1], 'go-', label='RMS [mrad] (Fourier space)')
+ axes[0].set_xlabel('padding', fontsize=15)
+ axes[0].set_ylabel('RMS [mrad]', fontsize=15)
+ axes[0].set_xlim(-0.5, 16.5)
+ axes[0].set_ylim(-5, 45)
+ axes[0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[0].legend()
# Plot zoom inset:
- ins_axis = plt.axes([0.3, 0.3, 0.55, 0.4])
- ins_axis.axhline(y=0.22, linestyle='--', color='g')
- ins_axis.plot(data_vort[0], data_vort[1], 'go-')
- ins_axis.set_yscale('log')
- ins_axis.set_xlim(5.5, 16.5)
- ins_axis.set_ylim(0.1, 1.1)
- plt.tick_params(axis='both', which='major', labelsize=14)
- plt.savefig(directory + '/ch5-2-vortex_padding_RMS.png', bbox_inches='tight')
+ ins_axis_v = plt.axes([0.2, 0.35, 0.25, 0.4])
+ ins_axis_v.axhline(y=0.22, linestyle='--', color='g')
+ ins_axis_v.plot(data_vort[0], data_vort[1], 'go-')
+ ins_axis_v.set_yscale('log')
+ ins_axis_v.set_xlim(5.5, 16.5)
+ ins_axis_v.set_ylim(0.1, 1.1)
+ ins_axis_v.tick_params(axis='both', which='major', labelsize=14)
# Plot duration against padding:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(data_vort[0], data_vort[2], 'bo-')
- axis.set_title('Variation of the Padding (vortex state disc)', fontsize=18)
- axis.set_xlabel('padding', fontsize=15)
- axis.set_ylabel('duration [s]', fontsize=15)
- axis.set_xlim(-0.5, 16.5)
- axis.set_ylim(-0.05, 1.5)
- plt.tick_params(axis='both', which='major', labelsize=14)
- plt.savefig(directory + '/ch5-2-vortex_padding_duration.png', bbox_inches='tight')
+ axes[1].plot(data_vort[0], data_vort[2], 'bo-')
+ axes[1].set_xlabel('padding', fontsize=15)
+ axes[1].set_ylabel('duration [s]', fontsize=15)
+ axes[1].set_xlim(-0.5, 16.5)
+ axes[1].set_ylim(-0.05, 1.5)
+ axes[1].xaxis.set_major_locator(MaxNLocator(nbins=10, integer= True))
+ axes[1].yaxis.set_major_locator(MaxNLocator(nbins=10))
+ axes[1].tick_params(axis='both', which='major', labelsize=14)
+
+ plt.show()
+ plt.figtext(0.15, 0.13, 'c)', fontsize=30)
+ plt.figtext(0.57, 0.17, 'd)', fontsize=30)
+ plt.savefig(directory + '/ch5-2-vortex_padding_variation.png', bbox_inches='tight')
###############################################################################################
print 'CLOSING SHELVE\n'
diff --git a/scripts/paper 1/ch5-3-comparison_of_methods.py b/scripts/paper 1/ch5-3-comparison_of_methods.py
index 0b592a3..d5b886a 100644
--- a/scripts/paper 1/ch5-3-comparison_of_methods.py
+++ b/scripts/paper 1/ch5-3-comparison_of_methods.py
@@ -10,7 +10,9 @@ import sys
import os
import numpy as np
from numpy import pi
+
import matplotlib.pyplot as plt
+from matplotlib.ticker import IndexLocator
import pyramid.magcreator as mc
import pyramid.projector as pj
@@ -180,91 +182,75 @@ def run():
print '--PLOT/SAVE METHOD DATA'
- # row and column sharing
- fig, axes = plt.subplots(2, 2, sharex='col', sharey='row', figsize=(16, 7))
-# ax1.plot(x, y)
-# ax1.set_title('Sharing x per column, y per row')
-# ax2.scatter(x, y)
-# ax3.scatter(x, 2 * y ** 2 - 1, color='r')
-# ax4.plot(x, 2 * y ** 2 - 1, color='r')
-
-
-
- # Plot duration against res (disc):
-# fig = plt.figure()
-# axis = fig.add_subplot(1, 1, 1)
- plt.tick_params(axis='both', which='major', labelsize=14)
+ # Plot using shared rows and colums:
+ fig, axes = plt.subplots(2, 2, sharex='col', sharey='row', figsize=(12, 8))
+ fig.tight_layout(rect=(0.05, 0.05, 0.95, 0.95))
+ fig.suptitle('Method Comparison', fontsize=20)
+
+ # Plot duration against res (disc) [top/left]:
axes[1, 0].set_yscale('log')
- axes[1, 0].plot(data_disc_fourier0[0], data_disc_fourier0[1], '--b+', label='Fourier padding=0')
- axes[1, 0].plot(data_disc_fourier1[0], data_disc_fourier1[1], '--bx', label='Fourier padding=1')
- axes[1, 0].plot(data_disc_fourier10[0], data_disc_fourier10[1], '--b*', label='Fourier padding=10')
- axes[1, 0].plot(data_disc_real_s[0], data_disc_real_s[1], '--rs', label='Real space (slab)')
- axes[1, 0].plot(data_disc_real_d[0], data_disc_real_d[1], '--ro', label='Real space (disc)')
- axes[1, 0].set_title('Variation of the resolution (disc)', fontsize=18)
-# axes[1, 0].set_xlabel('res [nm]', fontsize=15)
-# axes[1, 0].set_ylabel('RMS [mrad]', fontsize=15)
-# axes[1, 0].set_xlim(-0.5, 16.5)
-# axes[1, 0].legend(loc=4)
-# plt.tick_params(axis='both', which='major', labelsize=14)
-# plt.savefig(directory + '/ch5-3-disc_RMS_against_res.png', bbox_inches='tight')
- # Plot RMS against res (disc):
-# fig = plt.figure()
-# axis = fig.add_subplot(1, 1, 1)
+ axes[1, 0].plot(data_disc_fourier0[0], data_disc_fourier0[1], ':bs')
+ axes[1, 0].plot(data_disc_fourier1[0], data_disc_fourier1[1], ':bo')
+ axes[1, 0].plot(data_disc_fourier10[0], data_disc_fourier10[1], ':b^')
+ axes[1, 0].plot(data_disc_real_s[0], data_disc_real_s[1], '--rs')
+ axes[1, 0].plot(data_disc_real_d[0], data_disc_real_d[1], '--ro')
+ axes[1, 0].set_xlabel('res [nm]', fontsize=15)
+ axes[1, 0].set_ylabel('RMS [mrad]', fontsize=15)
+ axes[1, 0].set_xlim(-0.5, 16.5)
+ axes[1, 0].tick_params(axis='both', which='major', labelsize=14)
+ axes[1, 0].xaxis.set_major_locator(IndexLocator(base=4, offset=-0.5))
+
+ # Plot RMS against res (disc) [bottom/left]:
+ plt.tick_params(axis='both', which='major', labelsize=14)
axes[0, 0].set_yscale('log')
- axes[0, 0].plot(data_disc_fourier0[0], data_disc_fourier0[2], '--b+', label='Fourier padding=0')
- axes[0, 0].plot(data_disc_fourier1[0], data_disc_fourier1[2], '--bx', label='Fourier padding=1')
- axes[0, 0].plot(data_disc_fourier10[0], data_disc_fourier10[2], '--b*', label='Fourier padding=10')
- axes[0, 0].plot(data_disc_real_s[0], data_disc_real_s[2], '--rs', label='Real space (slab)')
- axes[0, 0].plot(data_disc_real_d[0], data_disc_real_d[2], '--ro', label='Real space (disc)')
- axes[0, 0].set_title('Variation of the resolution (disc)', fontsize=18)
-# axes[0, 0].set_xlabel('res [nm]', fontsize=15)
+ axes[0, 0].plot(data_disc_fourier0[0], data_disc_fourier0[2], ':bs')
+ axes[0, 0].plot(data_disc_fourier1[0], data_disc_fourier1[2], ':bo')
+ axes[0, 0].plot(data_disc_fourier10[0], data_disc_fourier10[2], ':b^')
+ axes[0, 0].plot(data_disc_real_s[0], data_disc_real_s[2], '--rs')
+ axes[0, 0].plot(data_disc_real_d[0], data_disc_real_d[2], '--ro')
+ axes[0, 0].set_title('Homog. magn. disc', fontsize=18)
axes[0, 0].set_ylabel('duration [s]', fontsize=15)
-# axes[0, 0].set_xlim(-0.5, 16.5)
-# axes[0, 0].legend(loc=1)
-# plt.tick_params(axis='both', which='major', labelsize=14)
-# plt.savefig(directory + '/ch5-3-disc_duration_against_res.png', bbox_inches='tight')
+ axes[0, 0].set_xlim(-0.5, 16.5)
+ axes[0, 0].tick_params(axis='both', which='major', labelsize=14)
+ axes[0, 0].xaxis.set_major_locator(IndexLocator(base=4, offset=-0.5))
- # Plot duration against res (vortex):
-# fig = plt.figure()
-# axis = fig.add_subplot(1, 1, 1)
+ # Plot duration against res (vortex) [top/right]:
axes[1, 1].set_yscale('log')
- axes[1, 1].plot(data_vort_fourier0[0], data_vort_fourier0[1], '--b+', label='Fourier padding=0')
- axes[1, 1].plot(data_vort_fourier1[0], data_vort_fourier1[1], '--bx', label='Fourier padding=1')
- axes[1, 1].plot(data_vort_fourier10[0], data_vort_fourier10[1], '--b*', label='Fourier padding=10')
- axes[1, 1].plot(data_vort_real_s[0], data_vort_real_s[1], '--rs', label='Real space (slab)')
- axes[1, 1].plot(data_vort_real_d[0], data_vort_real_d[1], '--ro', label='Real space (disc)')
-# axes[1, 1].set_title('Variation of the resolution (vortex)', fontsize=18)
+ axes[1, 1].plot(data_vort_fourier0[0], data_vort_fourier0[1], ':bs')
+ axes[1, 1].plot(data_vort_fourier1[0], data_vort_fourier1[1], ':bo')
+ axes[1, 1].plot(data_vort_fourier10[0], data_vort_fourier10[1], ':b^')
+ axes[1, 1].plot(data_vort_real_s[0], data_vort_real_s[1], '--rs')
+ axes[1, 1].plot(data_vort_real_d[0], data_vort_real_d[1], '--ro')
axes[1, 1].set_xlabel('res [nm]', fontsize=15)
-# axes[1, 1].set_ylabel('RMS [mrad]', fontsize=15)
axes[1, 1].set_xlim(-0.5, 16.5)
-# axes[1, 1].legend(loc=4)
-# plt.tick_params(axis='both', which='major', labelsize=14)
-# plt.savefig(directory + '/ch5-3-vortex_RMS_against_res.png', bbox_inches='tight')
- # Plot RMS against res (vort):
-# fig = plt.figure()
-# axis = fig.add_subplot(1, 1, 1)
+ axes[1, 1].tick_params(axis='both', which='major', labelsize=14)
+ axes[1, 1].xaxis.set_major_locator(IndexLocator(base=4, offset=-0.5))
+
+ # Plot RMS against res (vortex) [bottom/right]:
axes[0, 1].set_yscale('log')
- axes[0, 1].plot(data_vort_fourier0[0], data_vort_fourier0[2], '--b+', label='Fourier padding=0')
- axes[0, 1].plot(data_vort_fourier1[0], data_vort_fourier1[2], '--bx', label='Fourier padding=1')
- axes[0, 1].plot(data_vort_fourier10[0], data_vort_fourier10[2], '--b*', label='Fourier padding=10')
- axes[0, 1].plot(data_vort_real_s[0], data_vort_real_s[2], '--rs', label='Real space (slab)')
- axes[0, 1].plot(data_vort_real_d[0], data_vort_real_d[2], '--ro', label='Real space (disc)')
- axes[0, 1].set_title('Variation of the resolution (vortex)', fontsize=18)
-# axes[0, 1].set_xlabel('res [nm]', fontsize=15)
-# axes[0, 1].set_ylabel('duration [s]', fontsize=15)
+ axes[0, 1].plot(data_vort_fourier0[0], data_vort_fourier0[2], ':bs',
+ label='Fourier padding=0')
+ axes[0, 1].plot(data_vort_fourier1[0], data_vort_fourier1[2], ':bo',
+ label='Fourier padding=1')
+ axes[0, 1].plot(data_vort_fourier10[0], data_vort_fourier10[2], ':b^',
+ label='Fourier padding=10')
+ axes[0, 1].plot(data_vort_real_s[0], data_vort_real_s[2], '--rs',
+ label='Real space (slab)')
+ axes[0, 1].plot(data_vort_real_d[0], data_vort_real_d[2], '--ro',
+ label='Real space (disc)')
+ axes[0, 1].set_title('Vortex state disc', fontsize=18)
axes[0, 1].set_xlim(-0.5, 16.5)
+ axes[0, 1].tick_params(axis='both', which='major', labelsize=14)
+ axes[0, 1].xaxis.set_major_locator(IndexLocator(base=4, offset=-0.5))
axes[0, 1].legend(loc=1)
-# plt.tick_params(axis='both', which='major', labelsize=14)
- plt.savefig(directory + '/ch5-3-vortex_duration_against_res.png', bbox_inches='tight')
-
-
-
-
-
-
-
-
-
+
+ # Save figure as .png:
+ plt.show()
+ plt.figtext(0.45, 0.85, 'a)', fontsize=30)
+ plt.figtext(0.57, 0.85, 'b)', fontsize=30)
+ plt.figtext(0.45, 0.15, 'c)', fontsize=30)
+ plt.figtext(0.57, 0.15, 'd)', fontsize=30)
+ plt.savefig(directory + '/ch5-3-method comparison.png', bbox_inches='tight')
###############################################################################################
print 'CLOSING SHELVE\n'
diff --git a/scripts/reconstruct_random_pixels.py b/scripts/reconstruct_random_pixels.py
index a09bb09..c4d62a6 100644
--- a/scripts/reconstruct_random_pixels.py
+++ b/scripts/reconstruct_random_pixels.py
@@ -32,7 +32,6 @@ def reconstruct_random_distribution():
b_0 = 1 # in T
res = 10.0 # in nm
rnd.seed(18)
- threshold = 0
# Create lists for magnetic objects:
mag_shape_list = np.zeros((n_pixel,) + dim)
@@ -51,15 +50,9 @@ def reconstruct_random_distribution():
projection = pj.simple_axis_projection(mag_data)
phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab', b_0))
hi.display_combined(phase_map, 10, 'Generated Distribution')
- # Get the locations of the magnetized pixels (mask):
- z_mag, y_mag, x_mag = mag_data.magnitude
- z_mask = abs(z_mag) > threshold
- x_mask = abs(x_mag) > threshold
- y_mask = abs(y_mag) > threshold
- mask = np.logical_or(np.logical_or(x_mask, y_mask), z_mask)
# Reconstruct the magnetic distribution:
- mag_data_rec = rc.reconstruct_simple_leastsq(phase_map, mask, b_0)
+ mag_data_rec = rc.reconstruct_simple_leastsq(phase_map, mag_data.get_mask(), b_0)
# Display the reconstructed phase map and holography image:
projection_rec = pj.simple_axis_projection(mag_data_rec)
diff --git a/setup.py b/setup.py
index 9efd3c4..9d9a4ea 100644
--- a/setup.py
+++ b/setup.py
@@ -57,7 +57,7 @@ setup(
packages = find_packages(exclude=['tests']),
include_dirs = [numpy.get_include()],
- requires = ['numpy', 'matplotlib'],
+ requires = ['numpy', 'matplotlib', 'mayavi'],
scripts = get_files('scripts'),
--
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