From 9229ec98a8f053f61563aa8390027c3790d6a97c Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Fri, 9 Aug 2013 20:32:46 +0200
Subject: [PATCH] Added Scripts for Paper 1
---
.../ch5-0-evaluation_and_comparison.py | 85 +++++
.../paper 1/ch5-1-evaluation_real_space.py | 322 ++++++++++++++++++
.../paper 1/ch5-2-evaluation_fourier_space.py | 291 ++++++++++++++++
.../paper 1/ch5-3-comparison_of_methods.py | 283 +++++++++++++++
4 files changed, 981 insertions(+)
create mode 100644 scripts/paper 1/ch5-0-evaluation_and_comparison.py
create mode 100644 scripts/paper 1/ch5-1-evaluation_real_space.py
create mode 100644 scripts/paper 1/ch5-2-evaluation_fourier_space.py
create mode 100644 scripts/paper 1/ch5-3-comparison_of_methods.py
diff --git a/scripts/paper 1/ch5-0-evaluation_and_comparison.py b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
new file mode 100644
index 0000000..c01d0d9
--- /dev/null
+++ b/scripts/paper 1/ch5-0-evaluation_and_comparison.py
@@ -0,0 +1,85 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jul 26 14:37:20 2013
+
+@author: Jan
+"""
+import sys
+import traceback
+import pdb
+import os
+
+from numpy import pi
+
+import shelve
+
+import pyramid.magcreator as mc
+from pyramid.magdata import MagData
+
+import matplotlib.pyplot as plt
+
+
+def run():
+
+ print '\nACCESS SHELVE'
+ # Create / Open databank:
+ directory = '../../output/paper 1'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ data_shelve = shelve.open(directory + '/paper_1_shelve')
+
+ ###############################################################################################
+ print 'CH5-0 MAGNETIC DISTRIBUTIONS'
+
+ key = 'ch5-0-magnetic_distributions'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTIONS'
+ (mag_data_disc, mag_data_vort) = data_shelve[key]
+ else:
+ print '--CREATE MAGNETIC DISTRIBUTIONS'
+ # Input parameters:
+ res = 0.5 # in nm
+ phi = pi/2
+ dim = (32, 256, 256) # 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
+ mag_shape = mc.Shapes.disc(dim, center, radius, height)
+ print '--CREATE MAGN. DISTR. OF HOMOG. MAG. DISC'
+ mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ mag_data_disc.scale_down(3)
+ print '--CREATE MAGN. DISTR. OF VORTEX STATE DISC'
+ mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape, center))
+ mag_data_vort.scale_down(3)
+ # Mayavi-Plots
+ mag_data_disc.quiver_plot3d()
+ 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 'CLOSING SHELVE\n'
+ # Close shelve:
+ data_shelve.close()
+
+ ###############################################################################################
+
+if __name__ == "__main__":
+ try:
+ run()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
diff --git a/scripts/paper 1/ch5-1-evaluation_real_space.py b/scripts/paper 1/ch5-1-evaluation_real_space.py
new file mode 100644
index 0000000..0cb4305
--- /dev/null
+++ b/scripts/paper 1/ch5-1-evaluation_real_space.py
@@ -0,0 +1,322 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Fri Jul 26 14:37:30 2013
+
+@author: Jan
+"""
+import pdb
+import traceback
+import sys
+import os
+
+import numpy as np
+from numpy import pi
+
+import shelve
+
+import pyramid.magcreator as mc
+import pyramid.projector as pj
+import pyramid.phasemapper as pm
+import pyramid.holoimage as hi
+import pyramid.analytic as an
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+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():
+
+ print '\nACCESS SHELVE'
+ # Create / Open databank:
+ directory = '../../output/paper 1'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ data_shelve = shelve.open(directory + '/paper_1_shelve')
+
+ ###############################################################################################
+ print 'CH5-1 ANALYTIC SOLUTIONS'
+
+ # Input parameters:
+ res = 0.125 # in nm
+ phi = pi/2
+ dim = (128, 1024, 1024) # 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
+ print '--CALCULATE ANALYTIC SOLUTIONS'
+ # 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)
+ print '--PLOT/SAVE ANALYTIC SOLUTIONS'
+ hi.display_combined(phase_map_ana_disc, 100, 'Analytic solution: hom. magn. disc', 'bilinear')
+ axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
+ axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
+ 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')
+ axis = plt.gcf().add_subplot(1, 2, 2, aspect='equal')
+ axis.axhline(y=512, linewidth=3, linestyle='--', color='r')
+ plt.savefig(directory + '/ch5-1-analytic_solution_vort.png', bbox_inches='tight')
+ # Get colorwheel:
+ hi.make_color_wheel()
+ plt.savefig(directory + '/ch5-1-colorwheel.png', bbox_inches='tight')
+
+ ###############################################################################################
+ print 'CH5-1 PHASE SLICES REAL SPACE' # TODO: Verschieben
+
+ # Input parameters:
+ res = 0.25 # in nm
+ phi = pi/2
+ density = 20
+ 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'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTION'
+ mag_shape = 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 = []
+ # 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)
+ 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):
+ 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:
+ print '--CREATE PHASE SLICES VORTEX STATE DISC'
+ x = []
+ y = []
+ # 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
+ 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):
+ 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'
+ 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)
+
+ 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 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')
+ # 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')
+
+ ###############################################################################################
+ print 'CH5-1 PHASE DIFFERENCES REAL SPACE'
+
+ # Input parameters:
+ res = 1.0 # in nm
+ phi = pi/2
+ dim = (16, 128, 128) # 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!
+ radius = dim[1]/4 # in px
+ height = dim[0]/2 # in px
+
+ key = 'ch5-1-phase_diff_mag_dist'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTIONS'
+ (mag_data_disc, mag_data_vort) = data_shelve[key]
+ else:
+ print '--CREATE MAGNETIC DISTRIBUTIONS'
+ # Create magnetic shape (4 times the size):
+ res_big = res / 2
+ dim_big = (dim[0]*2, dim[1]*2, dim[2]*2)
+ center_big = (dim_big[0]/2-0.5, dim_big[1]/2.-0.5, dim_big[2]/2.-0.5)
+ radius_big = dim_big[1]/4 # in px
+ height_big = dim_big[0]/2 # in px
+ mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
+ # Create MagData (4 times the size):
+ mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
+ # Scale mag_data, resolution and dimensions:
+ mag_data_disc.scale_down()
+ mag_data_vort.scale_down()
+ print '--SAVE MAGNETIC DISTRIBUTIONS'
+ # Shelve magnetic distributions:
+ data_shelve[key] = (mag_data_disc, mag_data_vort)
+
+ print '--PLOT/SAVE 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)
+ # 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 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:
+ 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:
+ 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),
+ 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')
+
+ ###############################################################################################
+ print 'CLOSING SHELVE\n'
+ # Close shelve:
+ data_shelve.close()
+
+ ###############################################################################################
+
+
+if __name__ == "__main__":
+ try:
+ run()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
+
diff --git a/scripts/paper 1/ch5-2-evaluation_fourier_space.py b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
new file mode 100644
index 0000000..7b7e05f
--- /dev/null
+++ b/scripts/paper 1/ch5-2-evaluation_fourier_space.py
@@ -0,0 +1,291 @@
+"""Compare the different methods to create phase maps."""
+
+
+import time
+import pdb
+import traceback
+import sys
+import os
+
+import numpy as np
+from numpy import pi
+
+import shelve
+
+import pyramid.magcreator as mc
+import pyramid.projector as pj
+import pyramid.phasemapper as pm
+import pyramid.analytic as an
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+
+import matplotlib.pyplot as plt
+from matplotlib.colors import BoundaryNorm
+from matplotlib.ticker import MaxNLocator
+from matplotlib.cm import RdBu
+
+
+def run():
+
+ print '\nACCESS SHELVE'
+ # Create / Open databank:
+ directory = '../../output/paper 1'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ data_shelve = shelve.open(directory + '/paper_1_shelve')
+
+ ###############################################################################################
+ print 'CH5-2 PHASE DIFFERENCES FOURIER SPACE'
+
+ # Input parameters:
+ res = 1.0 # in nm
+ phi = pi/2
+ dim = (16, 128, 128) # 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!
+ radius = dim[1]/4 # in px
+ height = dim[0]/2 # in px
+
+ key = 'ch5-1-phase_diff_mag_dist'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTIONS'
+ (mag_data_disc, mag_data_vort) = data_shelve[key]
+ else:
+ print '--CREATE MAGNETIC DISTRIBUTIONS'
+ # Create magnetic shape (4 times the size):
+ res_big = res / 2
+ dim_big = (dim[0]*2, dim[1]*2, dim[2]*2)
+ center_big = (dim_big[0]/2-0.5, dim_big[1]/2.-0.5, dim_big[2]/2.-0.5)
+ radius_big = dim_big[1]/4 # in px
+ height_big = dim_big[0]/2 # in px
+ mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
+ # Create MagData (4 times the size):
+ mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
+ # Scale mag_data, resolution and dimensions:
+ mag_data_disc.scale_down()
+ mag_data_vort.scale_down()
+ print '--SAVE MAGNETIC DISTRIBUTIONS'
+ # Shelve magnetic distributions:
+ data_shelve[key] = (mag_data_disc, mag_data_vort)
+
+ print '--PLOT/SAVE 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)
+ # 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 norm for the plots:
+ bounds = np.array([-100, -50, -25, -5, 0, 5, 25, 50, 100])
+ norm = BoundaryNorm(bounds, RdBu.N)
+ # Disc:
+ 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)'),
+ limit=np.max(bounds), norm=norm)
+ plt.savefig(directory + '/ch5-2-disc_phase_diff_no_padding.png', bbox_inches='tight')
+ # 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)'),
+ limit=np.max(bounds), norm=norm)
+ plt.savefig(directory + '/ch5-2-vortex_phase_diff_no_padding.png', bbox_inches='tight')
+
+ # 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:
+ 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)'),
+ limit=np.max(bounds), norm=norm)
+ plt.savefig(directory + '/ch5-2-disc_phase_diff_padding_10.png', bbox_inches='tight')
+ # 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)'),
+ limit=np.max(bounds), norm=norm)
+ plt.savefig(directory + '/ch5-2-vortex_phase_diff_padding_10.png', bbox_inches='tight')
+
+ ###############################################################################################
+ print 'CH5-2 FOURIER PADDING VARIATION'
+
+ # Input parameters:
+ res = 1.0 # in nm
+ phi = pi/2
+ dim = (16, 128, 128) # 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!
+ radius = dim[1]/4 # in px
+ height = dim[0]/2 # in px
+
+ key = 'ch5-2-fourier_padding_mag_dist'
+ if key in data_shelve:
+ print '--LOAD MAGNETIC DISTRIBUTIONS'
+ (mag_data_disc, mag_data_vort) = data_shelve[key]
+ else:
+ print '--CREATE MAGNETIC DISTRIBUTIONS'
+ # Create magnetic shape (4 times the size):
+ res_big = res / 2
+ dim_big = (dim[0]*2, dim[1]*2, dim[2]*2)
+ center_big = (dim_big[0]/2-0.5, dim_big[1]/2.-0.5, dim_big[2]/2.-0.5)
+ radius_big = dim_big[1]/4 # in px
+ height_big = dim_big[0]/2 # in px
+ mag_shape = mc.Shapes.disc(dim_big, center_big, radius_big, height_big)
+ # Create MagData (4 times the size):
+ mag_data_disc = MagData(res_big, mc.create_mag_dist(mag_shape, phi))
+ mag_data_vort = MagData(res_big, mc.create_mag_dist_vortex(mag_shape, center_big))
+ # Scale mag_data, resolution and dimensions:
+ mag_data_disc.scale_down()
+ mag_data_vort.scale_down()
+ print '--SAVE MAGNETIC DISTRIBUTIONS'
+ # Shelve magnetic distributions:
+ data_shelve[key] = (mag_data_disc, mag_data_vort)
+
+ # Create projections along z-axis:
+ projection_disc = pj.simple_axis_projection(mag_data_disc)
+ projection_vort = pj.simple_axis_projection(mag_data_vort)
+ # 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)
+
+ # List of applied paddings:
+ padding_list = [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16]
+
+ print '--LOAD/CREATE PADDING SERIES OF HOMOG. MAGN. DISC'
+ data_disc = np.zeros((3, len(padding_list)))
+ data_disc[0, :] = padding_list
+ for (i, padding) in enumerate(padding_list):
+ key = ', '.join(['Padding->RMS|duration', 'Fourier', 'padding={}'.format(padding_list[i]),
+ 'res={}'.format(res), 'dim={}'.format(dim), 'phi={}'.format(phi), 'disc'])
+ if key in data_shelve:
+ data_disc[:, i] = data_shelve[key]
+ else:
+ print '----calculate and save padding =', padding_list[i]
+ start_time = time.time()
+ phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=padding_list[i])
+ data_disc[2, i] = time.time() - start_time
+ phase_diff = (phase_num_disc-phase_ana_disc) * 1E3 # in mrad -> *1000)
+ phase_map_diff = PhaseMap(res, phase_diff)
+ phase_map_diff.display(labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ data_disc[1, i] = np.sqrt(np.mean(phase_diff**2))
+ data_shelve[key] = data_disc[:, i]
+
+ print '--PLOT/SAVE PADDING SERIES OF HOMOG. MAGN. DISC'
+ # 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)
+ # 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')
+ # 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')
+
+
+ print '--LOAD/CREATE PADDING SERIES OF VORTEX STATE DISC'
+ data_vort = np.zeros((3, len(padding_list)))
+ data_vort[0, :] = padding_list
+ for (i, padding) in enumerate(padding_list):
+ key = ', '.join(['Padding->RMS|duration', 'Fourier', 'padding={}'.format(padding_list[i]),
+ 'res={}'.format(res), 'dim={}'.format(dim), 'phi={}'.format(phi), 'vort'])
+ if key in data_shelve:
+ data_vort[:, i] = data_shelve[key]
+ else:
+ print '----calculate and save padding =', padding_list[i]
+ start_time = time.time()
+ phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=padding_list[i])
+ data_vort[2, i] = time.time() - start_time
+ phase_diff = (phase_num_vort-phase_ana_vort) * 1E3 # in mrad -> *1000)
+ phase_map_diff = PhaseMap(res, phase_diff)
+ phase_map_diff.display(labels=('x-axis [nm]', 'y-axis [nm]', 'phase [mrad]'))
+ data_vort[1, i] = np.sqrt(np.mean(phase_diff**2))
+ data_shelve[key] = data_vort[:, i]
+
+ print '--PLOT/SAVE PADDING SERIES OF VORTEX STATE DISC'
+ # 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()
+ # 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')
+ # 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')
+
+ ###############################################################################################
+ print 'CLOSING SHELVE\n'
+ # Close shelve:
+ data_shelve.close()
+
+ ###############################################################################################
+
+
+if __name__ == "__main__":
+ try:
+ run()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
diff --git a/scripts/paper 1/ch5-3-comparison_of_methods.py b/scripts/paper 1/ch5-3-comparison_of_methods.py
new file mode 100644
index 0000000..0b592a3
--- /dev/null
+++ b/scripts/paper 1/ch5-3-comparison_of_methods.py
@@ -0,0 +1,283 @@
+#! python
+# -*- coding: utf-8 -*-
+"""Compare the different methods to create phase maps."""
+
+
+import time
+import pdb
+import traceback
+import sys
+import os
+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.analytic as an
+from pyramid.magdata import MagData
+import shelve
+
+
+def run():
+
+ print '\nACCESS SHELVE'
+ # Create / Open databank:
+ directory = '../../output/paper 1'
+ if not os.path.exists(directory):
+ os.makedirs(directory)
+ data_shelve = shelve.open(directory + '/paper_1_shelve')
+
+ ###############################################################################################
+ print 'CH5-3 METHOD COMPARISON'
+
+ key = 'ch5-3-compare_method_data'
+ if key in data_shelve:
+ print '--LOAD METHOD DATA'
+ (data_disc_fourier0, data_vort_fourier0,
+ data_disc_fourier1, data_vort_fourier1,
+ data_disc_fourier10, data_vort_fourier10,
+ data_disc_real_s, data_vort_real_s,
+ data_disc_real_d, data_vort_real_d) = data_shelve[key]
+ else:
+ # Input parameters:
+ steps = 6
+ res = 0.25 # in nm
+ phi = pi/2
+ dim = (64, 512, 512) # 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!
+ radius = dim[1]/4 # in px
+ height = dim[0]/2 # in px
+
+ print '--CREATE MAGNETIC SHAPE'
+ mag_shape = mc.Shapes.disc(dim, center, radius, height)
+ # Create MagData (4 times the size):
+ print '--CREATE MAG. DIST. HOMOG. MAGN. DISC'
+ mag_data_disc = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ print '--CREATE MAG. DIST. VORTEX STATE DISC'
+ mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape, center))
+
+ # Create Data Arrays
+ res_list = [res*2**i for i in np.linspace(1, steps, steps)]
+ data_disc_fourier0 = np.vstack((res_list, np.zeros((2, steps))))
+ data_vort_fourier0 = np.vstack((res_list, np.zeros((2, steps))))
+ data_disc_fourier1 = np.vstack((res_list, np.zeros((2, steps))))
+ data_vort_fourier1 = np.vstack((res_list, np.zeros((2, steps))))
+ data_disc_fourier10 = np.vstack((res_list, np.zeros((2, steps))))
+ data_vort_fourier10 = np.vstack((res_list, np.zeros((2, steps))))
+ data_disc_real_s = np.vstack((res_list, np.zeros((2, steps))))
+ data_vort_real_s = np.vstack((res_list, np.zeros((2, steps))))
+ data_disc_real_d = np.vstack((res_list, np.zeros((2, steps))))
+ data_vort_real_d = np.vstack((res_list, np.zeros((2, steps))))
+
+ for i in range(steps):
+ # Scale mag_data, resolution and dimensions:
+ mag_data_disc.scale_down()
+ mag_data_vort.scale_down()
+ dim = mag_data_disc.dim
+ res = mag_data_disc.res
+ 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
+
+ print '--res =', res, 'nm', 'dim =', dim
+
+ print '----CALCULATE RMS/DURATION HOMOG. MAGN. DISC'
+ # Create projections along z-axis:
+ projection_disc = pj.simple_axis_projection(mag_data_disc)
+ # Analytic solution:
+ phase_ana_disc = an.phase_mag_disc(dim, res, phi, center, radius, height)
+ # Fourier unpadded:
+ padding = 0
+ start_time = time.clock()
+ phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=padding)
+ data_disc_fourier0[2, i] = time.clock() - start_time
+ print '------time (disc, fourier0) =', data_disc_fourier0[2, i]
+ phase_diff_disc = (phase_ana_disc-phase_num_disc) * 1E3 # in mrad -> *1000
+ data_disc_fourier0[1, i] = np.sqrt(np.mean(phase_diff_disc**2))
+ # Fourier padding 1:
+ padding = 1
+ start_time = time.clock()
+ phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=padding)
+ data_disc_fourier1[2, i] = time.clock() - start_time
+ print '------time (disc, fourier1) =', data_disc_fourier1[2, i]
+ phase_diff_disc = (phase_ana_disc-phase_num_disc) * 1E3 # in mrad -> *1000
+ data_disc_fourier1[1, i] = np.sqrt(np.mean(phase_diff_disc**2))
+ # Fourier padding 10:
+ padding = 10
+ start_time = time.clock()
+ phase_num_disc = pm.phase_mag_fourier(res, projection_disc, padding=padding)
+ data_disc_fourier10[2, i] = time.clock() - start_time
+ print '------time (disc, fourier10) =', data_disc_fourier10[2, i]
+ phase_diff_disc = (phase_ana_disc-phase_num_disc) * 1E3 # in mrad -> *1000
+ data_disc_fourier10[1, i] = np.sqrt(np.mean(phase_diff_disc**2))
+ # Real space slab:
+ start_time = time.clock()
+ phase_num_disc = pm.phase_mag_real(res, projection_disc, 'slab')
+ data_disc_real_s[2, i] = time.clock() - start_time
+ print '------time (disc, real slab) =', data_disc_real_s[2, i]
+ phase_diff_disc = (phase_ana_disc-phase_num_disc) * 1E3 # in mrad -> *1000
+ data_disc_real_s[1, i] = np.sqrt(np.mean(phase_diff_disc**2))
+ # Real space disc:
+ start_time = time.clock()
+ phase_num_disc = pm.phase_mag_real(res, projection_disc, 'disc')
+ data_disc_real_d[2, i] = time.clock() - start_time
+ print '------time (disc, real disc) =', data_disc_real_d[2, i]
+ phase_diff_disc = (phase_ana_disc-phase_num_disc) * 1E3 # in mrad -> *1000
+ data_disc_real_d[1, i] = np.sqrt(np.mean(phase_diff_disc**2))
+
+ print '----CALCULATE RMS/DURATION HOMOG. MAGN. DISC'
+ # Create projections along z-axis:
+ projection_vort = pj.simple_axis_projection(mag_data_vort)
+ # Analytic solution:
+ phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height)
+ # Fourier unpadded:
+ padding = 0
+ start_time = time.clock()
+ phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=padding)
+ data_vort_fourier0[2, i] = time.clock() - start_time
+ print '------time (vortex, fourier0) =', data_vort_fourier0[2, i]
+ phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
+ data_vort_fourier0[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
+ # Fourier padding 1:
+ padding = 1
+ start_time = time.clock()
+ phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=padding)
+ data_vort_fourier1[2, i] = time.clock() - start_time
+ print '------time (vortex, fourier1) =', data_vort_fourier1[2, i]
+ phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
+ data_vort_fourier1[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
+ # Fourier padding 10:
+ padding = 10
+ start_time = time.clock()
+ phase_num_vort = pm.phase_mag_fourier(res, projection_vort, padding=padding)
+ data_vort_fourier10[2, i] = time.clock() - start_time
+ print '------time (vortex, fourier10) =', data_vort_fourier10[2, i]
+ phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
+ data_vort_fourier10[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
+ # Real space slab:
+ start_time = time.clock()
+ phase_num_vort = pm.phase_mag_real(res, projection_vort, 'slab')
+ data_vort_real_s[2, i] = time.clock() - start_time
+ print '------time (vortex, real slab) =', data_vort_real_s[2, i]
+ phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
+ data_vort_real_s[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
+ # Real space disc:
+ start_time = time.clock()
+ phase_num_vort = pm.phase_mag_real(res, projection_vort, 'disc')
+ data_vort_real_d[2, i] = time.clock() - start_time
+ print '------time (vortex, real disc) =', data_vort_real_d[2, i]
+ phase_diff_vort = (phase_ana_vort-phase_num_vort) * 1E3 # in mrad -> *1000
+ data_vort_real_d[1, i] = np.sqrt(np.mean(phase_diff_vort**2))
+
+ print '--SHELVE METHOD DATA'
+ data_shelve[key] = (data_disc_fourier0, data_vort_fourier0,
+ data_disc_fourier1, data_vort_fourier1,
+ data_disc_fourier10, data_vort_fourier10,
+ data_disc_real_s, data_vort_real_s,
+ data_disc_real_d, data_vort_real_d)
+
+ 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)
+ 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[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].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')
+
+ # Plot duration against res (vortex):
+# fig = plt.figure()
+# axis = fig.add_subplot(1, 1, 1)
+ 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].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[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].set_xlim(-0.5, 16.5)
+ 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')
+
+
+
+
+
+
+
+
+
+
+ ###############################################################################################
+ print 'CLOSING SHELVE\n'
+ # Close shelve:
+ data_shelve.close()
+
+ ###############################################################################################
+
+
+if __name__ == "__main__":
+ try:
+ run()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
--
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