From 4d230fd8b4eb4c3de4af2379d2b944aa708b1061 Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Wed, 10 Jul 2013 16:20:13 +0200
Subject: [PATCH] Added scripts to create and compare vortices and one to setup
interactive mode
---
pyramid/magcreator.py | 27 +++++++++
scripts/compare_method_errors_res.py | 12 +++-
scripts/compare_vortices.py | 87 ++++++++++++++++++++++++++++
scripts/create_vortex.py | 54 +++++++++++++++++
scripts/interactive_setup.py | 14 +++++
5 files changed, 192 insertions(+), 2 deletions(-)
create mode 100644 scripts/compare_vortices.py
create mode 100644 scripts/create_vortex.py
create mode 100644 scripts/interactive_setup.py
diff --git a/pyramid/magcreator.py b/pyramid/magcreator.py
index 658e2ce..e2db43d 100644
--- a/pyramid/magcreator.py
+++ b/pyramid/magcreator.py
@@ -217,3 +217,30 @@ def create_mag_dist_comb(mag_shape_list, phi_list, theta_list=None, magnitude_li
y_mag += mag_object[1]
x_mag += mag_object[2]
return z_mag, y_mag, x_mag
+
+
+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)
+ 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)
+
+ '''
+ dim = np.shape(mag_shape)
+ 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!'
+ 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)
+ phi = np.arctan2(yy, xx) - pi/2
+ z_mag = np.zeros(dim)
+ y_mag = -np.ones(dim) * np.sin(phi) * mag_shape * magnitude
+ x_mag = -np.ones(dim) * np.cos(phi) * mag_shape * magnitude
+ return z_mag, y_mag, x_mag
\ No newline at end of file
diff --git a/scripts/compare_method_errors_res.py b/scripts/compare_method_errors_res.py
index 6fcc589..92bc9a3 100644
--- a/scripts/compare_method_errors_res.py
+++ b/scripts/compare_method_errors_res.py
@@ -37,7 +37,8 @@ def compare_method_errors_res():
b_0 = 1 # in T
phi = -pi/4
- dim_list = [(1, 4, 4), (1, 8, 8), (1, 16, 16), (1, 32, 32), (1, 64, 64), (1, 128, 128), (1, 256, 256), (1, 512, 512)]
+ dim_list = [(1, 4, 4), (1, 8, 8), (1, 16, 16), (1, 32, 32), (1, 64, 64),
+ (1, 128, 128), (1, 256, 256), (1, 512, 512)]
res_list = [64., 32., 16., 8., 4., 2., 1., 0.5, 0.25] # in nm
@@ -69,23 +70,27 @@ def compare_method_errors_res():
data_sl_p_fourier0[0, :] = res_list
data_sl_w_fourier0[0, :] = res_list
data_disc_fourier0[0, :] = res_list
+ data_vort_fourier0[0, :] = res_list
data_sl_p_fourier1[0, :] = res_list
data_sl_w_fourier1[0, :] = res_list
data_disc_fourier1[0, :] = res_list
+ data_vort_fourier1[0, :] = res_list
data_sl_p_fourier20[0, :] = res_list
data_sl_w_fourier20[0, :] = res_list
data_disc_fourier20[0, :] = res_list
+ data_vort_fourier20[0, :] = res_list
data_sl_p_real_s[0, :] = res_list
data_sl_w_real_s[0, :] = res_list
data_disc_real_s[0, :] = res_list
+ data_vort_real_s[0, :] = res_list
data_sl_p_real_d[0, :]= res_list
data_sl_w_real_d[0, :] = res_list
data_disc_real_d[0, :] = res_list
-
+ data_vort_real_d[0, :] = res_list
@@ -117,6 +122,9 @@ def compare_method_errors_res():
phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height, b_0)
mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape_disc, phi))
projection_disc = pj.simple_axis_projection(mag_data_disc)
+ # Vortex:
+ center_vortex = (center[1], center[2])
+
'''FOURIER UNPADDED'''
padding = 0
diff --git a/scripts/compare_vortices.py b/scripts/compare_vortices.py
new file mode 100644
index 0000000..76dca66
--- /dev/null
+++ b/scripts/compare_vortices.py
@@ -0,0 +1,87 @@
+# -*- coding: utf-8 -*-
+"""Create the Pyramid-Logo."""
+
+
+import pdb, traceback, sys
+import numpy as np
+from numpy import pi
+import matplotlib.pyplot as plt
+
+import pyramid.magcreator as mc
+import pyramid.projector as pj
+import pyramid.phasemapper as pm
+import pyramid.holoimage as hi
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+
+def compare_vortices():
+ '''Calculate and display the Pyramid-Logo.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+ # Input parameters:
+ dim_list = [(1, 512, 512), (1, 256, 256), (1, 128, 128), (1, 64, 64), (1, 32, 32), (1, 16, 16)]
+ res_list = [2., 4., 8., 16., 32., 64.] # in nm
+ density = 10
+ height = 1
+
+ x = []
+ y = []
+
+ # Starting magnetic distribution:
+ dim_start = (1, 2*dim_list[0][1], 2*dim_list[0][2])
+ res_start = res_list[0] / 2
+ print 'dim_start = ', dim_start
+ print 'res_start = ', res_start
+ center = (0, dim_start[1]/2 - 0.5, dim_start[2]/2 - 0.5)
+ radius = 0.25 * dim_start[1]
+ mag_shape = mc.Shapes.disc(dim_start, center, radius, height)
+ mag_data = MagData(res_start, mc.create_mag_dist_vortex(mag_shape))
+ #mag_data.quiver_plot()
+
+ for i, (dim, res) in enumerate(zip(dim_list, res_list)):
+ # Create coarser grid for the magnetization:
+ z_mag = mag_data.magnitude[0].reshape(1, dim[1], 2, dim[1], 2)
+ y_mag = mag_data.magnitude[1].reshape(1, dim[1], 2, dim[1], 2)
+ x_mag = mag_data.magnitude[2].reshape(1, dim[1], 2, dim[1], 2)
+ print 'dim = ', dim
+ print 'res = ', res
+ magnitude = (z_mag.mean(axis=4).mean(axis=2) / 2,
+ y_mag.mean(axis=4).mean(axis=2) / 2,
+ x_mag.mean(axis=4).mean(axis=2) / 2)
+ mag_data = MagData(res, magnitude)
+ print np.shape(mag_data.magnitude[0])
+ #mag_data.quiver_plot()
+ projection = pj.simple_axis_projection(mag_data)
+ phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
+ hi.display_combined(phase_map, density, 'Vortex State, res = {}'.format(res))
+ x.append(np.linspace(0, dim[1]*res, dim[1]))
+ y.append(phase_map.phase[dim[1]/2, :]/pi)
+ fig = plt.figure()
+ fig.add_subplot(1, 1, 1)
+ plt.plot(x[i], y[i])
+#
+ # Plot:
+ fig = plt.figure()
+ axis = fig.add_subplot(1, 1, 1)
+ axis.plot(x[0], y[0], 'k',
+ x[1], y[1], 'r',
+ x[2], y[2], 'm',
+ x[3], y[3], 'y',
+ x[4], y[4], 'c',
+ x[5], y[5], 'g',
+ x[6], y[6], 'b')
+ axis.set_xlabel('x [nm]')
+ axis.set_ylabel('phase')
+
+if __name__ == "__main__":
+ try:
+ compare_vortices()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
\ No newline at end of file
diff --git a/scripts/create_vortex.py b/scripts/create_vortex.py
new file mode 100644
index 0000000..93c25c8
--- /dev/null
+++ b/scripts/create_vortex.py
@@ -0,0 +1,54 @@
+# -*- coding: utf-8 -*-
+"""Create the Pyramid-Logo."""
+
+
+import pdb, traceback, sys
+import numpy as np
+from numpy import pi
+import matplotlib.pyplot as plt
+
+import pyramid.magcreator as mc
+import pyramid.projector as pj
+import pyramid.phasemapper as pm
+import pyramid.holoimage as hi
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+
+def create_vortex():
+ '''Calculate and display the Pyramid-Logo.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+ # Input parameters:
+ filename = '../output/mag_dist_vortex.txt'
+ res = 10.0 # in nm
+ density = 1
+ dim = (1, 128, 128)
+ center = (0, int(dim[1]/2)-0.5, int(dim[2]/2)-0.5)
+ radius = 0.25 * dim[1]
+ height = 1
+ # Create magnetic shape:
+ mag_shape = mc.Shapes.disc(dim, center, radius, height)
+ mag_data = MagData(res, mc.create_mag_dist_vortex(mag_shape))
+ mag_data.quiver_plot()
+ mag_data.quiver_plot3d()
+ mag_data.save_to_llg(filename)
+ projection = pj.simple_axis_projection(mag_data)
+ phase_map = PhaseMap(res, pm.phase_mag_real(res, projection, 'slab'))
+ hi.display_combined(phase_map, density, 'Vortex State')
+ phase_slice = phase_map.phase[dim[1]/2, :]
+ fig = plt.figure()
+ fig.add_subplot(111)
+ plt.plot(range(dim[1]), phase_slice)
+
+if __name__ == "__main__":
+ try:
+ create_vortex()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
\ No newline at end of file
diff --git a/scripts/interactive_setup.py b/scripts/interactive_setup.py
new file mode 100644
index 0000000..660e4f5
--- /dev/null
+++ b/scripts/interactive_setup.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+"""Imports pyramid package and sets working directory to output directory"""
+
+import pyramid.analytic as an
+import pyramid.holoimage as hi
+import pyramid.magcreator as mc
+import pyramid.phasemapper as pm
+import pyramid.projector as pj
+import pyramid.reconstructor as rc
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+import os
+os.chdir('C:\Users\Jan\PhD Thesis\Pyramid\output')
\ No newline at end of file
--
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