From 20b2d7e5854828d4effba13638f02ff1249df6fc Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Tue, 23 Jul 2013 14:09:33 +0200
Subject: [PATCH] analytic: added vortex solution holoimage: turned off
interpolation test_compliance: added scripts to be tested setup: work in
progress
---
pyramid/analytic.py | 33 ++++
pyramid/holoimage.py | 2 +-
pyramid/numcore/phase_mag_real.c | 4 +-
pyramid/test/test_compliance.py | 2 +-
scripts/compare_discs.py | 22 +--
scripts/compare_method_errors.py | 155 +-----------------
.../compare_method_errors_fourier_padding.py | 99 +++++++++++
scripts/compare_method_errors_res.py | 141 +++++++++++++++-
scripts/compare_vortices.py | 17 +-
scripts/get_revision.py | 14 ++
scripts/interactive_setup.py | 3 +-
setup.py | 35 +++-
12 files changed, 340 insertions(+), 187 deletions(-)
create mode 100644 scripts/compare_method_errors_fourier_padding.py
create mode 100644 scripts/get_revision.py
diff --git a/pyramid/analytic.py b/pyramid/analytic.py
index a19ee64..246c7a8 100644
--- a/pyramid/analytic.py
+++ b/pyramid/analytic.py
@@ -120,3 +120,36 @@ def phase_mag_sphere(dim, res, phi, center, radius, b_0=1):
xx, yy = np.meshgrid(x, y)
# Return phase:
return phiMag(xx, yy)
+
+
+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
+ Arguments:
+ dim - the dimensions of the grid, shape(z, y, x)
+ res - the resolution of the grid (grid spacing) in nm
+ center - the center of the disc in pixel coordinates, shape(z, y, x)
+ radius - the radius of the disc in pixel coordinates (scalar value)
+ height - the height of the disc in pixel coordinates (scalar value)
+ b_0 - magnetic induction corresponding to a magnetization Mo in T (default: 1)
+ Returns:
+ the analytic solution for the phase map
+
+ '''
+ # Function for the phase:
+ def phiMag(x, y):
+ r = np.hypot(x - x0, y - y0)
+ result = coeff * np.where(r <= R, r - R, 0)
+ return result
+ # 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
+ Lz = res * height
+ R = res * radius
+ coeff = pi * b_0 * Lz / PHI_0
+ # Create grid:
+ x = np.linspace(res/2, x_dim*res-res/2, num=x_dim)
+ y = np.linspace(res/2, y_dim*res-res/2, num=y_dim)
+ xx, yy = np.meshgrid(x, y)
+ # Return phase:
+ return phiMag(xx, yy)
diff --git a/pyramid/holoimage.py b/pyramid/holoimage.py
index 2aeb2c0..b44e91d 100644
--- a/pyramid/holoimage.py
+++ b/pyramid/holoimage.py
@@ -99,7 +99,7 @@ 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)
+ axis.imshow(holo_image, interpolation='none')
axis.set_title(title)
axis.set_xlabel('x-axis')
axis.set_ylabel('y-axis')
diff --git a/pyramid/numcore/phase_mag_real.c b/pyramid/numcore/phase_mag_real.c
index f762fe7..7d7b55e 100644
--- a/pyramid/numcore/phase_mag_real.c
+++ b/pyramid/numcore/phase_mag_real.c
@@ -1,4 +1,4 @@
-/* Generated by Cython 0.19.1 on Tue Jul 16 14:55:54 2013 */
+/* Generated by Cython 0.19.1 on Tue Jul 23 11:18:13 2013 */
#define PY_SSIZE_T_CLEAN
#ifndef CYTHON_USE_PYLONG_INTERNALS
@@ -1569,7 +1569,7 @@ static char __pyx_k_43[] = "Cannot transpose memoryview with indirect dimensions
static char __pyx_k_44[] = "got differing extents in dimension %d (got %d and %d)";
static char __pyx_k_45[] = "Dimension %d is not direct";
static char __pyx_k_48[] = "phase_mag_real_helper";
-static char __pyx_k_49[] = "C:\\Users\\Jan\\PhD Thesis\\Pyramid\\pyramid\\numcore\\phase_mag_real.pyx";
+static char __pyx_k_49[] = "C:\\Users\\Jan\\Daten\\PhD Thesis\\Pyramid\\pyramid\\numcore\\phase_mag_real.pyx";
static char __pyx_k_50[] = "getbuffer(obj, view, flags)";
static char __pyx_k_51[] = "<strided and direct or indirect>";
static char __pyx_k_53[] = "<strided and direct>";
diff --git a/pyramid/test/test_compliance.py b/pyramid/test/test_compliance.py
index ab5e0eb..ec901a1 100644
--- a/pyramid/test/test_compliance.py
+++ b/pyramid/test/test_compliance.py
@@ -30,7 +30,7 @@ class TestCaseCompliance(unittest.TestCase):
def test_pep8(self):
# TODO: Docstring
- files = self.get_files_to_check('..') # search in pyramid package
+ files = self.get_files_to_check('../../pyramid') + self.get_files_to_check('../../scripts')
ignores = ('E226', 'E128')
pep8.MAX_LINE_LENGTH = 99
pep8style = pep8.StyleGuide(quiet=False)
diff --git a/scripts/compare_discs.py b/scripts/compare_discs.py
index 47ea92a..f544e61 100644
--- a/scripts/compare_discs.py
+++ b/scripts/compare_discs.py
@@ -20,27 +20,22 @@ PHI_0 = -2067.83 # magnetic flux in T*nm²
def compare_vortices():
- '''Calculate and display the Pyramid-Logo.
- Arguments:
- None
- Returns:
- None
-
+ ''' DOCSTRING
'''
# Input parameters:
dim_list = [(16, 256, 256), (8, 128, 128), (4, 64, 64), (2, 32, 32), (1, 16, 16)]
- res_list = [4., 8., 16., 32., 64.] # in nm
- density = 1
+ res_list = [1., 2., 4., 8., 16.] # in nm
+ density = 20
phi = pi/2
x = []
y = []
# Analytic solution:
- L = 1024. # in nm
- Lz = 0.5 * 64. # in nm
- R = 0.25 * L
- x0 = L / 2
+ L = dim_list[0][1] # in px/nm
+ Lz = 0.5 * dim_list[0][0] # in px/nm
+ R = 0.25 * L # in px/nm
+ x0 = L / 2 # in px/nm
def F(x):
coeff = - pi * Lz / (2*PHI_0)
result = coeff * (- (x - x0) * np.sin(phi))
@@ -73,9 +68,6 @@ def compare_vortices():
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, :])
- fig = plt.figure()
- fig.add_subplot(1, 1, 1)
- plt.plot(x[i], y[i])
# Plot:
fig = plt.figure()
diff --git a/scripts/compare_method_errors.py b/scripts/compare_method_errors.py
index 0c451b1..41bfc5d 100644
--- a/scripts/compare_method_errors.py
+++ b/scripts/compare_method_errors.py
@@ -11,7 +11,7 @@ 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
+import pyramid.analytic as an
from pyramid.magdata import MagData
from pyramid.phasemap import PhaseMap
import shelve
@@ -31,10 +31,10 @@ def phase_from_mag():
'''FOURIER PADDING->RMS|DURATION'''
# Parameters:
b_0 = 1 # in T
- res = 10.0 # in nm
- dim = (1, 128, 128)
+ res = 1.0 # in nm
+ dim = (16, 256, 256)
phi = -pi/4
- 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]
+ 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'
# Create magnetic shape:
if geometry == 'slab':
@@ -45,7 +45,7 @@ def phase_from_mag():
elif geometry == 'disc':
center = (0, 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 = 8 # in px
mag_shape = mc.Shapes.disc(dim, center, radius, height)
phase_ana = an.phase_mag_disc(dim, res, phi, center, radius, b_0)
# Project the magnetization data:
@@ -73,7 +73,8 @@ def phase_from_mag():
# Plot duration against padding:
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
- axis.set_yscale('log')
+# axis.set_xscale('log')
+# axis.set_yscale('log')
axis.plot(data[0], data[1])
axis.set_title('Fourier Space Approach: Variation of the Padding')
axis.set_xlabel('padding')
@@ -81,151 +82,13 @@ def phase_from_mag():
# Plot RMS against padding:
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+# axis.set_xscale('log')
+# axis.set_yscale('log')
axis.plot(data[0], data[2])
axis.set_title('Fourier Space Approach: Variation of the Padding')
axis.set_xlabel('padding')
axis.set_ylabel('duration [s]')
-
-
-
-
-
-
- '''VARY DIMENSIONS FOR ALL APPROACHES'''
-
- 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)]
- res_list = [64., 32., 16., 8., 4., 2., 1.] # in nm
-
-
-
- data_sl_p_fourier0 = np.zeros((3, len(res_list)))
- data_sl_w_fourier0 = np.zeros((3, len(res_list)))
- data_disc_fourier0 = np.zeros((3, len(res_list)))
-
- data_sl_p_fourier1 = np.zeros((3, len(res_list)))
- data_sl_w_fourier1 = np.zeros((3, len(res_list)))
- data_disc_fourier1 = np.zeros((3, len(res_list)))
-
- data_sl_p_fourier20 = np.zeros((3, len(res_list)))
- data_sl_w_fourier20 = np.zeros((3, len(res_list)))
- data_disc_fourier20 = np.zeros((3, len(res_list)))
-
- data_sl_p_real_s = np.zeros((3, len(res_list)))
- data_sl_w_real_s = np.zeros((3, len(res_list)))
- data_disc_real_s = np.zeros((3, len(res_list)))
-
- data_sl_p_real_d= np.zeros((3, len(res_list)))
- data_sl_w_real_d = np.zeros((3, len(res_list)))
- data_disc_real_d = np.zeros((3, len(res_list)))
-
- data_slab_perfect[0, :] = res_list
- data_slab_worst[0, :] = res_list
- data_disc[0, :] = res_list
-
-
-
- '''FOURIER UNPADDED'''
-
- for i, (dim, res) in enumerate(zip(dim_list, res_list)):
-
- print 'dim =', str(dim)
-
- # ANALYTIC SOLUTIONS:
- # Slab (perfectly aligned):
- center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
- width = (1, dim[1], dim[2]) # in px (z, y, x)
- mag_shape_slab_perfect = mc.Shapes.slab(dim, center, width)
- phase_ana_slab_perfect = an.phase_mag_slab(dim, res, phi, center, width, b_0)
- mag_data_slab_perfect = MagData(res, mc.create_mag_dist(mag_shape_slab_perfect, phi))
- projection_slab_perfect = pj.simple_axis_projection(mag_data_slab_perfect)
- # Slab (worst case):
- center = (0, dim[1]/2, dim[2]/2) # in px (z, y, x) index starts with 0!
- width = (1, dim[1], dim[2]) # in px (z, y, x)
- mag_shape_slab_worst = mc.Shapes.slab(dim, center, width)
- phase_ana_slab_worst = an.phase_mag_slab(dim, res, phi, center, width, b_0)
- mag_data_slab_worst = MagData(res, mc.create_mag_dist(mag_shape_slab_worst, phi))
- projection_slab_worst = pj.simple_axis_projection(mag_data_slab_worst)
- # Disc:
- center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
- radius = dim[1]/2 # in px
- height = 1 # in px
- mag_shape_disc = mc.Shapes.disc(dim, center, radius, height)
- 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)
-
- # NUMERICAL SOLUTIONS:
- # Slab (perfectly aligned):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding=0',
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=slab_perfect'])
- if data_shelve.has_key(key):
- data_slab_perfect[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_slab_perfect, b_0, 0)
- data_slab_perfect[2, i] = time.time() - start_time
- phase_diff = phase_ana_slab_perfect - phase_num
- data_slab_perfect[1, i] = np.std(phase_diff)
- data_shelve[key] = data_slab_perfect[:, i]
- # Slab (worst case):
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding=0',
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=slab_worst'])
- if data_shelve.has_key(key):
- data_slab_worst[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_slab_worst, b_0, 0)
- data_slab_worst[2, i] = time.time() - start_time
- phase_diff = phase_ana_slab_worst - phase_num
- data_slab_worst[1, i] = np.std(phase_diff)
- data_shelve[key] = data_slab_worst[:, i]
- # Disc:
- key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding=0',
- 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
- 'phi={}'.format(phi), 'geometry=disc'])
- if data_shelve.has_key(key):
- data_disc[:, i] = data_shelve[key]
- else:
- start_time = time.time()
- phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, 0)
- data_disc[2, i] = time.time() - start_time
- phase_diff = phase_ana_disc - phase_num
- data_disc[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc[:, i]
-
- # Plot duration against res:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.set_yscale('log')
- axis.plot(data_slab_perfect[0], data_slab_perfect[1],
- data_slab_worst[0], data_slab_worst[1],
- data_disc[0], data_disc[1])
- axis.set_title('Variation of the resolution (Fourier without padding)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('RMS')
- # Plot RMS against res:
- fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1)
- axis.plot(data_slab_perfect[0], data_slab_perfect[1],
- data_slab_worst[0], data_slab_worst[1],
- data_disc[0], data_disc[1])
- axis.set_title('Variation of the resolution (Fourier without padding)')
- axis.set_xlabel('res [nm]')
- axis.set_ylabel('duration [s]')
-
-
-
-
-
-
-
-
-
data_shelve.close()
diff --git a/scripts/compare_method_errors_fourier_padding.py b/scripts/compare_method_errors_fourier_padding.py
new file mode 100644
index 0000000..f6f7cc4
--- /dev/null
+++ b/scripts/compare_method_errors_fourier_padding.py
@@ -0,0 +1,99 @@
+# -*- coding: utf-8 -*-
+"""Compare the different methods to create phase maps."""
+
+
+import time
+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.analytic as an
+from pyramid.magdata import MagData
+from pyramid.phasemap import PhaseMap
+import shelve
+
+
+def phase_from_mag():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+ # Create / Open databank:
+ data_shelve = shelve.open('../output/method_errors_shelve')
+
+ '''FOURIER PADDING->RMS|DURATION'''
+ # Parameters:
+ b_0 = 1 # in T
+ res = 10.0 # in nm
+ dim = (1, 128, 128)
+ phi = -pi/4
+ 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'
+ # Create magnetic shape:
+ if geometry == 'slab':
+ center = (0, dim[1]/2-0.5, dim[2]/2-0.5) # in px (z, y, x) index starts with 0!
+ width = (1, 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!
+ radius = dim[1]/4 # in px
+ height = 1 # in px
+ mag_shape = mc.Shapes.disc(dim, center, radius, height)
+ phase_ana = an.phase_mag_disc(dim, res, phi, center, radius, b_0)
+ # Project the magnetization data:
+ mag_data = MagData(res, mc.create_mag_dist(mag_shape, phi))
+ projection = pj.simple_axis_projection(mag_data)
+ # Create data:
+ data = np.zeros((3, len(padding_list)))
+ data[0, :] = padding_list
+ for (i, padding) in enumerate(padding_list):
+ print 'padding =', padding_list[i]
+ # Key:
+ key = ', '.join(['Padding->RMS|duration', 'Fourier', 'padding={}'.format(padding_list[i]),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry={}'.format(geometry)])
+ if data_shelve.has_key(key):
+ data[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_fourier(res, projection, b_0, padding_list[i])
+ data[2, i] = time.time() - start_time
+ phase_diff = phase_ana - phase_num
+ PhaseMap(res, phase_diff).display()
+ data[1, i] = np.std(phase_diff)
+ data_shelve[key] = data[:, i]
+ # Plot duration against padding:
+ fig = plt.figure()
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_yscale('log')
+ axis.plot(data[0], data[1])
+ axis.set_title('Fourier Space Approach: Variation of the Padding')
+ axis.set_xlabel('padding')
+ axis.set_ylabel('RMS')
+ # Plot RMS against padding:
+ fig = plt.figure()
+ axis = fig.add_subplot(1, 1, 1)
+ axis.plot(data[0], data[2])
+ axis.set_title('Fourier Space Approach: Variation of the Padding')
+ axis.set_xlabel('padding')
+ axis.set_ylabel('duration [s]')
+
+ data_shelve.close()
+
+
+
+if __name__ == "__main__":
+ try:
+ phase_from_mag()
+ except:
+ type, value, tb = sys.exc_info()
+ traceback.print_exc()
+ pdb.post_mortem(tb)
\ No newline at end of file
diff --git a/scripts/compare_method_errors_res.py b/scripts/compare_method_errors_res.py
index 0468de5..796d0a0 100644
--- a/scripts/compare_method_errors_res.py
+++ b/scripts/compare_method_errors_res.py
@@ -104,7 +104,6 @@ def compare_method_errors_res():
print 'i =', i, ' dim =', str(dim)
'''ANALYTIC SOLUTIONS'''
-
# Slab (perfectly aligned):
center = (0, dim[1]/2.-0.5, dim[2]/2.-0.5) # in px (z, y, x) index starts with 0!
width = (1, dim[1]/2, dim[2]/2) # in px (z, y, x)
@@ -120,6 +119,7 @@ def compare_method_errors_res():
mag_data_sl_w = MagData(res, mc.create_mag_dist(mag_shape_sl_w, phi))
projection_sl_w = pj.simple_axis_projection(mag_data_sl_w)
# Disc:
+ print center
center = (0, 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
@@ -129,7 +129,10 @@ def compare_method_errors_res():
projection_disc = pj.simple_axis_projection(mag_data_disc)
# Vortex:
center_vortex = (center[1], center[2])
-
+ mag_shape_vort = mc.Shapes.disc(dim, center, radius, height)
+ phase_ana_vort = an.phase_mag_vortex(dim, res, center, radius, height, b_0)
+ mag_data_vort = MagData(res, mc.create_mag_dist_vortex(mag_shape_vort, center_vortex))
+ projection_vort = pj.simple_axis_projection(mag_data_vort)
'''FOURIER UNPADDED'''
padding = 0
@@ -172,6 +175,19 @@ def compare_method_errors_res():
phase_diff = phase_ana_disc - phase_num
data_disc_fourier0[1, i] = np.std(phase_diff)
data_shelve[key] = data_disc_fourier0[:, i]
+ # Vortex:
+ key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry=vortex'])
+ if data_shelve.has_key(key):
+ data_vort_fourier0[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
+ data_vort_fourier0[2, i] = time.time() - start_time
+ phase_diff = phase_ana_vort - phase_num
+ data_vort_fourier0[1, i] = np.std(phase_diff)
+ data_shelve[key] = data_vort_fourier0[:, i]
'''FOURIER PADDED ONCE'''
@@ -214,7 +230,20 @@ def compare_method_errors_res():
data_disc_fourier1[2, i] = time.time() - start_time
phase_diff = phase_ana_disc - phase_num
data_disc_fourier1[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_fourier1[:, i]
+ data_shelve[key] = data_disc_fourier1[:, i]
+ # Vortex:
+ key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry=vortex'])
+ if data_shelve.has_key(key):
+ data_vort_fourier1[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
+ data_vort_fourier1[2, i] = time.time() - start_time
+ phase_diff = phase_ana_vort - phase_num
+ data_vort_fourier1[1, i] = np.std(phase_diff)
+ data_shelve[key] = data_vort_fourier1[:, i]
'''FOURIER PADDED 20'''
@@ -259,7 +288,19 @@ def compare_method_errors_res():
phase_diff = phase_ana_disc - phase_num
data_disc_fourier20[1, i] = np.std(phase_diff)
data_shelve[key] = data_disc_fourier20[:, i]
-
+ # Vortex:
+ key = ', '.join(['Resolution->RMS|duration', 'Fourier', 'padding={}'.format(padding),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry=vortex'])
+ if data_shelve.has_key(key):
+ data_vort_fourier20[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_fourier(res, projection_disc, b_0, padding)
+ data_vort_fourier20[2, i] = time.time() - start_time
+ phase_diff = phase_ana_vort - phase_num
+ data_vort_fourier20[1, i] = np.std(phase_diff)
+ data_shelve[key] = data_vort_fourier20[:, i]
'''REAL SLAB'''
method = 'slab'
@@ -301,8 +342,20 @@ def compare_method_errors_res():
data_disc_real_s[2, i] = time.time() - start_time
phase_diff = phase_ana_disc - phase_num
data_disc_real_s[1, i] = np.std(phase_diff)
- data_shelve[key] = data_disc_real_s[:, i]
-
+ data_shelve[key] = data_disc_real_s[:, i]
+ # Vortex:
+ key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry=vortex'])
+ if data_shelve.has_key(key):
+ data_disc_real_s[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
+ data_vort_real_s[2, i] = time.time() - start_time
+ phase_diff = phase_ana_vort - phase_num
+ data_vort_real_s[1, i] = np.std(phase_diff)
+ data_shelve[key] = data_vort_real_s[:, i]
'''REAL DISC'''
method = 'disc'
@@ -345,11 +398,24 @@ def compare_method_errors_res():
phase_diff = phase_ana_disc - phase_num
data_disc_real_d[1, i] = np.std(phase_diff)
data_shelve[key] = data_disc_real_d[:, i]
-
+ # Vortex:
+ key = ', '.join(['Resolution->RMS|duration', 'Real', 'method={}'.format(method),
+ 'B0={}'.format(b_0), 'res={}'.format(res), 'dim={}'.format(dim),
+ 'phi={}'.format(phi), 'geometry=vortex'])
+ if data_shelve.has_key(key):
+ data_vort_real_d[:, i] = data_shelve[key]
+ else:
+ start_time = time.time()
+ phase_num = pm.phase_mag_real(res, projection_disc, method, b_0)
+ data_vort_real_d[2, i] = time.time() - start_time
+ phase_diff = phase_ana_vort - phase_num
+ data_vort_real_d[1, i] = np.std(phase_diff)
+ data_shelve[key] = data_vort_real_d[:, i]
# Plot duration against res (perfect slab):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_sl_p_fourier0[0], data_sl_p_fourier0[1], 'b+',
data_sl_p_fourier1[0], data_sl_p_fourier1[1], 'bx',
@@ -362,6 +428,7 @@ def compare_method_errors_res():
# Plot RMS against res (perfect slab):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_sl_p_fourier0[0], data_sl_p_fourier0[2], 'b+',
data_sl_p_fourier1[0], data_sl_p_fourier1[2], 'bx',
@@ -371,10 +438,18 @@ def compare_method_errors_res():
axis.set_title('Variation of the resolution (perfectly adjusted slab)')
axis.set_xlabel('res [nm]')
axis.set_ylabel('duration [s]')
+ # Save to file:
+ data_sl_p = np.concatenate((data_sl_p_fourier0,
+ data_sl_p_fourier1[1:,:],
+ data_sl_p_fourier20[1:,:],
+ data_sl_p_real_s[1:,:],
+ data_sl_p_real_d[1:,:]))
+ np.savetxt('../output/data_slab_perfect.txt', data_sl_p.T)
# Plot duration against res (worst case slab):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_sl_w_fourier0[0], data_sl_w_fourier0[1], 'b+',
data_sl_w_fourier1[0], data_sl_w_fourier1[1], 'bx',
@@ -387,6 +462,7 @@ def compare_method_errors_res():
# Plot RMS against res (worst case slab):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_sl_w_fourier0[0], data_sl_w_fourier0[2], 'b+',
data_sl_w_fourier1[0], data_sl_w_fourier1[2], 'bx',
@@ -396,10 +472,18 @@ def compare_method_errors_res():
axis.set_title('Variation of the resolution (worst case slab)')
axis.set_xlabel('res [nm]')
axis.set_ylabel('duration [s]')
+ # Save to file:
+ data_sl_w = np.concatenate((data_sl_w_fourier0,
+ data_sl_w_fourier1[1:,:],
+ data_sl_w_fourier20[1:,:],
+ data_sl_w_real_s[1:,:],
+ data_sl_w_real_d[1:,:]))
+ np.savetxt('../output/data_slab_worstcase.txt', data_sl_w.T)
- # Plot duration against res (disc<):
+ # Plot duration against res (disc):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_disc_fourier0[0], data_disc_fourier0[1], 'b+',
data_disc_fourier1[0], data_disc_fourier1[1], 'bx',
@@ -412,6 +496,7 @@ def compare_method_errors_res():
# Plot RMS against res (disc):
fig = plt.figure()
axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
axis.set_yscale('log')
axis.plot(data_disc_fourier0[0], data_disc_fourier0[2], 'b+',
data_disc_fourier1[0], data_disc_fourier1[2], 'bx',
@@ -421,7 +506,47 @@ def compare_method_errors_res():
axis.set_title('Variation of the resolution (disc)')
axis.set_xlabel('res [nm]')
axis.set_ylabel('duration [s]')
+ # Save to file:
+ data_disc = np.concatenate((data_disc_fourier0,
+ data_disc_fourier1[1:,:],
+ data_disc_fourier20[1:,:],
+ data_disc_real_s[1:,:],
+ data_disc_real_d[1:,:]))
+ np.savetxt('../output/data_disc.txt', data_disc.T)
+ # Plot duration against res (vortex):
+ fig = plt.figure()
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
+ axis.set_yscale('log')
+ axis.plot(data_vort_fourier0[0], data_vort_fourier0[1], 'b+',
+ data_vort_fourier1[0], data_vort_fourier1[1], 'bx',
+ data_vort_fourier20[0], data_vort_fourier20[1], 'b*',
+ data_vort_real_s[0], data_vort_real_s[1], 'rs',
+ data_vort_real_d[0], data_vort_real_d[1], 'ro')
+ axis.set_title('Variation of the resolution (vortex)')
+ axis.set_xlabel('res [nm]')
+ axis.set_ylabel('RMS')
+ # Plot RMS against res (vort):
+ fig = plt.figure()
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_xscale('log')
+ axis.set_yscale('log')
+ axis.plot(data_vort_fourier0[0], data_vort_fourier0[2], 'b+',
+ data_vort_fourier1[0], data_vort_fourier1[2], 'bx',
+ data_vort_fourier20[0], data_vort_fourier20[2], 'b*',
+ data_vort_real_s[0], data_vort_real_s[2], 'rs',
+ data_vort_real_d[0], data_vort_real_d[2], 'ro')
+ axis.set_title('Variation of the resolution (vortex)')
+ axis.set_xlabel('res [nm]')
+ axis.set_ylabel('duration [s]')
+ # Save to file:
+ data_vort = np.concatenate((data_vort_fourier0,
+ data_vort_fourier1[1:,:],
+ data_vort_fourier20[1:,:],
+ data_vort_real_s[1:,:],
+ data_vort_real_d[1:,:]))
+ np.savetxt('../output/data_vortex.txt', data_vort.T)
data_shelve.close()
diff --git a/scripts/compare_vortices.py b/scripts/compare_vortices.py
index c24f668..2c89820 100644
--- a/scripts/compare_vortices.py
+++ b/scripts/compare_vortices.py
@@ -28,8 +28,8 @@ def compare_vortices():
'''
# Input parameters:
dim_list = [(16, 256, 256), (8, 128, 128), (4, 64, 64), (2, 32, 32), (1, 16, 16)]
- res_list = [4., 8., 16., 32., 64.] # in nm
- density = 1
+ res_list = [1., 2., 4., 8., 16.] # in nm
+ density = 20
x = []
y = []
@@ -44,15 +44,15 @@ def compare_vortices():
mag_data = MagData(res_start, mc.create_mag_dist_vortex(mag_shape))
# Analytic solution:
- L = 1024. # in nm
- Lz = 0.5 * 64. # in nm
- R = 0.25 * L
- x0 = L / 2
+ L = dim_list[0][1] # in px/nm
+ Lz = 0.5 * dim_list[0][0] # in px/nm
+ R = 0.25 * L # in px/nm
+ x0 = L / 2 # in px/nm
def F(x):
coeff = pi*Lz/PHI_0
result = coeff * np.where(np.abs(x - x0) <= R, (np.abs(x-x0)-R), 0)
return result
- x_an = np.linspace(0, L, 1000)
+ x_an = np.linspace(0, L, 1001)
y_an = F(x_an)
for i, (dim, res) in enumerate(zip(dim_list, res_list)):
@@ -71,9 +71,6 @@ def compare_vortices():
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, :])
- fig = plt.figure()
- fig.add_subplot(1, 1, 1)
- plt.plot(x[i], y[i])
# Plot:
fig = plt.figure()
diff --git a/scripts/get_revision.py b/scripts/get_revision.py
new file mode 100644
index 0000000..62af71c
--- /dev/null
+++ b/scripts/get_revision.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Jul 22 15:01:55 2013
+
+@author: Jan
+"""
+
+def make_hgrevision(target, source, env):
+ import subprocess as sp
+ output = sp.Popen(["hg", "id", "-i"], stdout=sp.PIPE).communicate()[0]
+
+ hgrevision_cc = file(str(target[0]), "w")
+ hgrevision_cc.write('HG_Revision = "{0}"\n'.format(output.strip()))
+ hgrevision_cc.close()
\ No newline at end of file
diff --git a/scripts/interactive_setup.py b/scripts/interactive_setup.py
index 660e4f5..5c4ebd4 100644
--- a/scripts/interactive_setup.py
+++ b/scripts/interactive_setup.py
@@ -11,4 +11,5 @@ 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
+os.chdir('C:\Users\Jan\Daten\PhD Thesis\Pyramid\output')
+# TODO: Path not hard-coded!!!
\ No newline at end of file
diff --git a/setup.py b/setup.py
index ded1e12..1b9a5b4 100644
--- a/setup.py
+++ b/setup.py
@@ -11,10 +11,30 @@ Created on Fri May 03 10:27:04 2013
import numpy
+
+import os
+import sys
+import sysconfig
+
from distutils.core import setup
+from distutils.command.build import build
from distutils.extension import Extension
from Cython.Distutils import build_ext
+class custom_build(build):
+ def run(self):
+ build.run(self)
+ print 'Test'
+
+def distutils_dir_name(dname):
+ '''Returns the name of a distutils build directory'''
+ path = "{dirname}.{platform}-{version[0]}.{version[1]}"
+ return path.format(dirname=dname, platform=sysconfig.get_platform(), version=sys.version_info)
+
+
+print '\n------------------------------------------------------------------------------'
+
+build_path = os.path.join('build', distutils_dir_name('lib'))
setup(
@@ -24,16 +44,25 @@ setup(
author = 'Jan Caron',
author_email = 'j.caron@fz-juelich.de',
- packages = ['pyramid', 'pyramid.numcore'],
+ packages = ['pyramid', 'pyramid.numcore', 'pyramid.test'],
include_dirs = [numpy.get_include()],
+ requires = ['numpy', 'matplotlib'],
- cmdclass = {'build_ext': build_ext},
+ cmdclass = {'build_ext': build_ext, 'build': custom_build},
ext_package = 'pyramid/numcore',
ext_modules = [
Extension('phase_mag_real', ['pyramid/numcore/phase_mag_real.pyx'],
include_dirs = [numpy.get_include(), numpy.get_numarray_include()],
- extra_compile_args=["-march=pentium", "-mtune=pentium"]
+ extra_compile_args=["-march=native", "-mtune=native"]
)
]
)
+
+import os
+print os.getcwd()
+
+print '------------------------------------------------------------------------------\n'
+
+#import pyramid.test as test
+#test.run_tests()
--
GitLab