From 0afb984a6bf7eaeb4a509d8addbf2c0fb120f7da Mon Sep 17 00:00:00 2001
From: Jan Caron <caron@fz-juelich.de>
Date: Tue, 30 Apr 2013 09:34:40 +0200
Subject: [PATCH] =?UTF-8?q?Found=20a=20way=20to=20use=20a=20src=20folder?=
=?UTF-8?q?=20(PYRAMID=20as=20project,=20FZ-J=FClich=20as=20workspace)=20R?=
=?UTF-8?q?emoved=20old=20scripts=20(AnalyticSolution=20and=20DataLoader)?=
=?UTF-8?q?=20Added=20several=20template=20testcases?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
scripts/AnalyticSolutionRealDisc.py | 63 --------
scripts/AnalyticSolutionRealSpaceSlab.py | 191 -----------------------
scripts/AnalyticSolutionRealSphere.py | 72 ---------
scripts/DataLoaderRealSpace.py | 105 -------------
scripts/compare_methods.py | 172 ++++++++++++++++++++
scripts/create_logo.py | 44 ++++++
scripts/create_samples.py | 172 ++++++++++++++++++++
scripts/get_jacobi.py | 172 ++++++++++++++++++++
scripts/main.py | 12 +-
{pyramid => src/pyramid}/__init__.py | 0
{pyramid => src/pyramid}/analytic.py | 0
{pyramid => src/pyramid}/dataloader.py | 0
{pyramid => src/pyramid}/holoimage.py | 0
{pyramid => src/pyramid}/magcreator.py | 2 +-
{pyramid => src/pyramid}/phasemap.py | 2 +
test/test_analytic.py | 29 ++++
test/test_dataloader.py | 29 ++++
test/test_holoimage.py | 29 ++++
test/test_magcreator.py | 29 ++++
test/test_phasemap.py | 31 ++++
20 files changed, 716 insertions(+), 438 deletions(-)
delete mode 100644 scripts/AnalyticSolutionRealDisc.py
delete mode 100644 scripts/AnalyticSolutionRealSpaceSlab.py
delete mode 100644 scripts/AnalyticSolutionRealSphere.py
delete mode 100644 scripts/DataLoaderRealSpace.py
create mode 100644 scripts/compare_methods.py
create mode 100644 scripts/create_logo.py
create mode 100644 scripts/create_samples.py
create mode 100644 scripts/get_jacobi.py
rename {pyramid => src/pyramid}/__init__.py (100%)
rename {pyramid => src/pyramid}/analytic.py (100%)
rename {pyramid => src/pyramid}/dataloader.py (100%)
rename {pyramid => src/pyramid}/holoimage.py (100%)
rename {pyramid => src/pyramid}/magcreator.py (97%)
rename {pyramid => src/pyramid}/phasemap.py (96%)
create mode 100644 test/test_analytic.py
create mode 100644 test/test_dataloader.py
create mode 100644 test/test_holoimage.py
create mode 100644 test/test_magcreator.py
create mode 100644 test/test_phasemap.py
diff --git a/scripts/AnalyticSolutionRealDisc.py b/scripts/AnalyticSolutionRealDisc.py
deleted file mode 100644
index ad49807..0000000
--- a/scripts/AnalyticSolutionRealDisc.py
+++ /dev/null
@@ -1,63 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Mar 20 10:24:40 2013
-
-@author: Jan
-"""
-
-'''IMPORT'''
-from pylab import *
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-#from matplotlib.ticker import FormatStrFormatter
-
-'''CONSTANTS'''
-PHI_0 = 2067.83 # magnetic flux in T*nm²
-
-'''INPUT VARIABLES'''
-b0 = 1.0 #in T
-v0 = 0
-Vacc = 30000
-xDim, yDim = 160, 160
-res = 10 #in nm
-beta = 300.0/360.0 * 2*pi
-x0 = res*xDim*0.5
-y0 = res*yDim*0.5
-R = res*xDim*0.2
-
-'''CREATE COORDINATE GRIDS'''
-x = np.linspace(res/2,xDim*res-res/2,num=xDim)
-y = np.linspace(res/2,yDim*res-res/2,num=yDim)
-xx, yy = np.meshgrid(x,y)
-
-'''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) DISC'''
-
-coeff = - pi * res * b0 / ( 2 * PHI_0 )
-
-def phiMag(x,y):
- r = np.sqrt((x-x0) ** 2 + (y-y0) ** 2)
- result = coeff * ((y-y0) * np.cos(beta) - (x-x0) * np.sin(beta))
- in_or_out = 1 * (r < R) + (R / r) ** 2 * (r > R)
- result *= in_or_out
- return result
-
-phaseMag = phiMag(xx, yy)
-
-def plot_phase(func, name):
- fig = plt.figure()
- ax = fig.add_subplot(111, aspect='equal')
- plt.pcolormesh(func, cmap='Greys')
- ticks = ax.get_xticks() * res
- ax.set_xticklabels(ticks.astype(int))
- ticks = ax.get_yticks() * res
- ax.set_yticklabels(ticks.astype(int))
- ax.set_title('Analytical Solution' + name)
- ax.set_xlabel('x-axis [nm]')
- ax.set_ylabel('y-axis [nm]')
- plt.colorbar()
- plt.show()
-
-plot_phase(phaseMag, ' Disc - Phase')
-plot_phase(cos(16*phaseMag), ' Disc - Cos(Phase)')
\ No newline at end of file
diff --git a/scripts/AnalyticSolutionRealSpaceSlab.py b/scripts/AnalyticSolutionRealSpaceSlab.py
deleted file mode 100644
index 775b695..0000000
--- a/scripts/AnalyticSolutionRealSpaceSlab.py
+++ /dev/null
@@ -1,191 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Mar 20 10:24:40 2013
-
-@author: Jan
-"""
-
-'''IMPORT'''
-from pylab import *
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-#from matplotlib.ticker import FormatStrFormatter
-
-'''CONSTANTS'''
-PHI_0 = 2067.83 # magnetic flux in T*nm²
-
-'''INPUT VARIABLES'''
-b0 = 1.0 #in T
-v0 = 0
-Vacc = 30000
-xDim, yDim = 160, 160
-res = 10 #in nm
-beta = 300.0/360.0 * 2*pi
-x0 = res*xDim*0.5
-y0 = res*yDim*0.5
-Lx = res*xDim*0.2
-Ly = res*yDim*0.4
-
-'''CREATE COORDINATE GRIDS'''
-x = np.linspace(res/2,xDim*res-res/2,num=xDim)
-y = np.linspace(res/2,yDim*res-res/2,num=yDim)
-#xx, yy = np.meshgrid(x,y)
-
-'''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) SLAB'''
-def F0(x,y):
- a = np.log( x**2 + y**2 )
- b = np.arctan( x / y ) # atan or atan2?
- return x*a - 2*x + 2*y*b
-
-coeff = b0 * res / ( 4 * PHI_0 )
-
-def phiMag(x,y):
- return coeff * ( - np.cos(beta) * ( F0(x-x0-Lx/2,y-y0-Ly/2)-F0(x-x0+Lx/2,y-y0-Ly/2)
- -F0(x-x0-Lx/2,y-y0+Ly/2)+F0(x-x0+Lx/2,y-y0+Ly/2) )
- + np.sin(beta) * ( F0(y-y0-Ly/2,x-x0-Lx/2)-F0(y-y0+Ly/2,x-x0-Lx/2)
- -F0(y-y0-Ly/2,x-x0+Lx/2)+F0(y-y0+Ly/2,x-x0+Lx/2) ) )
-
-def F0_Cos_1(x,y):
- return coeff * np.cos(beta) * F0(x-x0-Lx/2,y-y0-Ly/2)
-
-def F0_Cos_2(x,y):
- return coeff * np.cos(beta) * F0(x-x0+Lx/2,y-y0-Ly/2)
-
-def F0_Cos_3(x,y):
- return coeff * np.cos(beta) * F0(x-x0-Lx/2,y-y0+Ly/2)
-
-def F0_Cos_4(x,y):
- return coeff * np.cos(beta) * F0(x-x0+Lx/2,y-y0+Ly/2)
-
-def F0_Sin_1(x,y):
- return coeff * np.sin(beta) * F0(y-y0-Ly/2,x-x0-Lx/2)
-
-def F0_Sin_2(x,y):
- return coeff * np.sin(beta) * F0(y-y0+Ly/2,x-x0-Lx/2)
-
-def F0_Sin_3(x,y):
- return coeff * np.sin(beta) * F0(y-y0-Ly/2,x-x0+Lx/2)
-
-def F0_Sin_4(x,y):
- return coeff * np.sin(beta) * F0(y-y0+Ly/2,x-x0+Lx/2)
-
-
-def phiMag1(x,y):
- return coeff * ( - 0*np.cos(beta) + 1*( F0(x-x0-Lx/2,y-y0-Ly/2)-F0(x-x0+Lx/2,y-y0-Ly/2)) )
-
-def phiMag2(x,y):
- return coeff * ( - 0*np.cos(beta) + 1*(-F0(x-x0-Lx/2,y-y0+Ly/2)+F0(x-x0+Lx/2,y-y0+Ly/2) ) )
-
-def phiMag3(x,y):
- return coeff * ( + 0*np.sin(beta) + 1*( F0(y-y0-Ly/2,x-x0-Lx/2)-F0(y-y0+Ly/2,x-x0-Lx/2) ) )
-
-def phiMag4(x,y):
- return coeff * ( + 0*np.sin(beta) + 1*(-F0(y-y0-Ly/2,x-x0+Lx/2)+F0(y-y0+Ly/2,x-x0+Lx/2) ) )
-
-def Test(x,y):
- return ( abs(x-x0)<Lx/2 and abs(y-y0)<Ly/2 )
-
-xx, yy = np.meshgrid(x,y)
-
-phaseMag = phiMag(xx, yy)
-
-phase_F0_Cos_1 = F0_Cos_1(xx, yy)
-phase_F0_Cos_2 = F0_Cos_2(xx, yy)
-phase_F0_Cos_3 = F0_Cos_3(xx, yy)
-phase_F0_Cos_4 = F0_Cos_4(xx, yy)
-phase_F0_Sin_1 = F0_Sin_1(xx, yy)
-phase_F0_Sin_2 = F0_Sin_2(xx, yy)
-phase_F0_Sin_3 = F0_Sin_3(xx, yy)
-phase_F0_Sin_4 = F0_Sin_4(xx, yy)
-
-sinphase_F0_Cos_1 = np.sin(phase_F0_Cos_1)
-sinphase_F0_Cos_2 = np.sin(phase_F0_Cos_2)
-sinphase_F0_Cos_3 = np.sin(phase_F0_Cos_3)
-sinphase_F0_Cos_4 = np.sin(phase_F0_Cos_4)
-sinphase_F0_Sin_1 = np.sin(phase_F0_Sin_1)
-sinphase_F0_Sin_2 = np.sin(phase_F0_Sin_2)
-sinphase_F0_Sin_3 = np.sin(phase_F0_Sin_3)
-sinphase_F0_Sin_4 = np.sin(phase_F0_Sin_4)
-
-phase_F0_Cos_Complete = (phase_F0_Cos_1 + phase_F0_Cos_2
- + phase_F0_Cos_3 + phase_F0_Cos_4)
-
-phase_F0_Sin_Complete = (phase_F0_Sin_1 + phase_F0_Sin_2
- + phase_F0_Sin_3 + phase_F0_Sin_4)
-
-sinphase_F0_Cos_Complete = (sinphase_F0_Cos_1 + sinphase_F0_Cos_2
- + sinphase_F0_Cos_3 + sinphase_F0_Cos_4)
-
-sinphase_F0_Sin_Complete = (sinphase_F0_Sin_1 + sinphase_F0_Sin_2
- + sinphase_F0_Sin_3 + sinphase_F0_Sin_4)
-
-phaseMag1 = phiMag1(xx, yy)
-phaseMag2 = phiMag2(xx, yy)
-phaseMag3 = phiMag3(xx, yy)
-phaseMag4 = phiMag4(xx, yy)
-
-
-def plot_phase(func, name):
- fig = plt.figure()
- ax = fig.add_subplot(111, aspect='equal')
- plt.pcolormesh(func, cmap='jet')
- ticks = ax.get_xticks() * res
- ax.set_xticklabels(ticks.astype(int))
- ticks = ax.get_yticks() * res
- ax.set_yticklabels(ticks.astype(int))
- ax.set_title('Analytical Solution' + name)
- ax.set_xlabel('x-axis [nm]')
- ax.set_ylabel('y-axis [nm]')
- plt.colorbar()
- plt.show()
-
-
-'''PLOT'''
-
-fig = plt.figure()
-ax = fig.add_subplot(111, aspect='equal')
-plt.pcolormesh(np.cos(16*phaseMag), cmap='Greys')
-ticks = ax.get_xticks()*res
-ax.set_xticklabels(ticks.astype(int))
-ticks = ax.get_yticks()*res
-ax.set_yticklabels(ticks.astype(int))
-ax.set_title('Analytical Solution')
-ax.set_xlabel('x-axis [nm]')
-ax.set_ylabel('y-axis [nm]')
-plt.colorbar()
-plt.show()
-
-'''PLOT F0s'''
-plot_phase(phase_F0_Cos_Complete, 'F0_Cos_Complete')
-plot_phase(phase_F0_Sin_Complete, 'F0_Sin_Complete')
-plot_phase(sinphase_F0_Cos_Complete, 'Sin_F0_Cos_Complete')
-plot_phase(sinphase_F0_Sin_Complete, 'Sin_F0_Sin_Complete')
-#plot_phase(phase_F0_Cos_1, 'F0_Cos_1')
-#plot_phase(phase_F0_Cos_2, 'F0_Cos_2')
-#plot_phase(phase_F0_Cos_3, 'F0_Cos_3')
-#plot_phase(phase_F0_Cos_4, 'F0_Cos_4')
-#plot_phase(phase_F0_Sin_1, 'F0_Sin_1')
-#plot_phase(phase_F0_Sin_2, 'F0_Sin_2')
-#plot_phase(phase_F0_Sin_3, 'F0_Sin_3')
-#plot_phase(phase_F0_Sin_4, 'F0_Sin_4')
-#plot_phase(phase_F0_Cos_1-phase_F0_Cos_3, 'F0_Cos_1-3')
-#plot_phase(phase_F0_Cos_2-phase_F0_Cos_4, 'F0_Cos_2-4')
-#plot_phase(phase_F0_Sin_1-phase_F0_Sin_3, 'F0_Sin_1-3')
-#plot_phase(phase_F0_Sin_2-phase_F0_Sin_4, 'F0_Sin_2-4')
-#plot_phase(phase_F0_Cos_1-phase_F0_Cos_3 + phase_F0_Cos_2-phase_F0_Cos_4,
-# 'F0_Cos_Complete')
-#plot_phase(phase_F0_Sin_1-phase_F0_Sin_3 + phase_F0_Sin_2-phase_F0_Sin_4,
-# 'F0_Sin_Complete')
-# plot_phase(phase_F0_Sin_1-phase_F0_Sin_3 + phase_F0_Sin_2-phase_F0_Sin_4,
-# 'F0_Sin_Complete')
-
-
-x = np.linspace(-50,50,100)
-y = np.linspace(-50,50,100)
-
-xx, yy = np.meshgrid(x,y)
-
-Arc2 = np.arctan2(yy,xx)
-Arc = np.arctan(yy/xx)
\ No newline at end of file
diff --git a/scripts/AnalyticSolutionRealSphere.py b/scripts/AnalyticSolutionRealSphere.py
deleted file mode 100644
index 1b0899c..0000000
--- a/scripts/AnalyticSolutionRealSphere.py
+++ /dev/null
@@ -1,72 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Mar 20 10:24:40 2013
-
-@author: Jan
-"""
-
-
-'''PROBLEM: Sphere is 3D, current model is just 2D'''
-
-
-
-'''IMPORT'''
-from pylab import *
-import numpy as np
-from numpy import pi
-import matplotlib.pyplot as plt
-from mpl_toolkits.mplot3d import Axes3D
-#from matplotlib.ticker import FormatStrFormatter
-
-'''CONSTANTS'''
-PHI_0 = 2067.83 # magnetic flux in T*nm²
-
-'''INPUT VARIABLES'''
-b0 = 1.0 #in T
-v0 = 0
-Vacc = 30000
-xDim, yDim = 160, 160
-res = 10 #in nm
-beta = 300.0/360.0 * 2*pi
-x0 = res*xDim*0.5
-y0 = res*yDim*0.5
-R = res*xDim*0.2
-
-'''CREATE COORDINATE GRIDS'''
-x = np.linspace(res/2,xDim*res-res/2,num=xDim)
-y = np.linspace(res/2,yDim*res-res/2,num=yDim)
-xx, yy = np.meshgrid(x,y)
-
-'''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) DISC'''
-def F0(x,y):
- a = np.log( x**2 + y**2 )
- b = np.arctan2( x, y ) # atan or atan2?
- return x*a - 2*x + 2*y*b
-
-coeff = - 2/3 * pi * R**3 * b0 / PHI_0 * res/R
-
-def phiMag(x,y):
- r = np.sqrt((x-x0) ** 2 + (y-y0) ** 2)
- result = coeff / r**2 * ((y-y0) * np.cos(beta) - (x-x0) * np.sin(beta))
- in_or_out = 1 * (r > R) + (1 - (1-(r/R)**2)**(3/2)) * (r < R)
- result *= in_or_out
- return result
-
-phaseMag = phiMag(xx, yy)
-
-def plot_phase(func, name):
- fig = plt.figure()
- ax = fig.add_subplot(111, aspect='equal')
- plt.pcolormesh(func, cmap='Greys')
- ticks = ax.get_xticks() * res
- ax.set_xticklabels(ticks.astype(int))
- ticks = ax.get_yticks() * res
- ax.set_yticklabels(ticks.astype(int))
- ax.set_title('Analytical Solution' + name)
- ax.set_xlabel('x-axis [nm]')
- ax.set_ylabel('y-axis [nm]')
- plt.colorbar()
- plt.show()
-
-plot_phase(phaseMag, ' Sphere - Phase')
-plot_phase(cos(16*phaseMag), ' Sphere - Cos(Phase)')
\ No newline at end of file
diff --git a/scripts/DataLoaderRealSpace.py b/scripts/DataLoaderRealSpace.py
deleted file mode 100644
index ee68a3d..0000000
--- a/scripts/DataLoaderRealSpace.py
+++ /dev/null
@@ -1,105 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Wed Mar 20 10:24:40 2013
-
-@author: Jan
-"""
-
-'''IMPORT'''
-import numpy as np
-from numpy import pi, e
-import matplotlib.pyplot as plt
-import math as ma
-
-'''CONSTANTS'''
-PHI_0 = 2067.83
-
-'''INPUT VARIABLES'''
-b0 = 1.0
-v0 = 0
-Vacc = 30000
-scale=1E-7
-padFactor = 2
-filename = 'output.txt'
-
-'''READ DATA'''
-data = np.genfromtxt(filename, skip_header=2)
-xDim, yDim, zDim = np.genfromtxt(filename, dtype=int, skip_header=1, skip_footer=len(data[:,0]))
-res = (data[1,0] - data[0,0]) / scale
-xLen, yLen, zLen = [data[-1,i]/scale+res/2 for i in range(3)]
-xMag, yMag, zMag = [data[:,i].reshape(zDim,yDim,xDim).mean(0)*zLen for i in range(3,6)]
-#Reshape in Python and Igor is different, Python fills rows first, Igor columns!
-#TODO interpolation (redefine xDim,yDim,zDim) thickness ramp
-
-'''COMPUTATION MAGNETIC PHASE SHIFT (REAL SPACE) SLAB'''
-# def F0(x,y):
-# a = np.log( x**2 + y**2 )
-# b = np.arctan( x / y )
-# return x*a - 2*x + 2*y*b
-#
-# coeff = b0 * res / ( 4 * PHI_0 )
-#
-# def phiMag(x,y):
-# return coeff * ( - np.cos(beta) * ( F0(x-x0-Lx/2,y-y0-Ly/2)
-# -F0(x-x0+Lx/2,y-y0-Ly/2)
-# -F0(x-x0-Lx/2,y-y0+Ly/2)
-# +F0(x-x0+Lx/2,y-y0+Ly/2) )
-# + np.sin(beta) * ( F0(y-y0-Ly/2,x-x0-Lx/2)
-# -F0(y-y0+Ly/2,x-x0-Lx/2)
-# -F0(y-y0-Ly/2,x-x0+Lx/2)
-# +F0(y-y0+Ly/2,x-x0+Lx/2) ) )
-#
-# return phiMag(xx, yy)
-
-
-
-
-
-
-def F(n,m):
- a = np.log( res**2/4 * ( (2*n-1)**2 + (2*m-1)**2 ) )
- b = np.arctan( (2*n-1) / (2*m-1) )
- return res * ( (n-1/2)*a - (2*n-1) + (2*m-1)*b )
-
-coeff = b0 / ( 4 * PHI_0 )
-
-beta = np.arctan2(yMag, xMag)
-
-absMag = np.sqrt(xMag**2 + yMag**2)
-
-def phi_ij(i,j,p,q):
- return absMag[j,i] * ( - np.cos(beta[j,i]) * (F(p-i,q-j)-F(p-i+1,q-j)
- -F(p-i,q-j+1)+F(p-i+1,q-j+1))
- + np.sin(beta[j,i]) * (F(q-j,p-i)-F(q-j+1,p-i)
- -F(q-j,p-i+1)+F(q-j+1,p-i+1)) )
-
-phaseMag = np.zeros((yDim,xDim))
-
-
-
-for q in range(yDim):
- for p in range(xDim):
- for j in range(yDim):
- for i in range(xDim):
- phaseMag[q,p] += phi_ij(i,j,p,q)
-
-phaseMag *= coeff
-
-#TODO Electrostatic Component
-
-'''PLOT'''
-fig = plt.figure()
-ax = fig.add_subplot(111, aspect='equal')
-plt.pcolormesh(phaseMag, cmap='gray')
-
-ticks = ax.get_xticks()*res
-ax.set_xticklabels(ticks.astype(int))
-
-ticks = ax.get_yticks()*res
-ax.set_yticklabels(ticks.astype(int))
-
-ax.set_title('Real Space Approach')
-ax.set_xlabel('x-axis [nm]')
-ax.set_ylabel('y-axis [nm]')
-plt.colorbar()
-plt.show()
\ No newline at end of file
diff --git a/scripts/compare_methods.py b/scripts/compare_methods.py
new file mode 100644
index 0000000..cd8a8cd
--- /dev/null
+++ b/scripts/compare_methods.py
@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 03 11:15:38 2013
+
+@author: Jan
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pyramid.magcreator as mc
+import pyramid.dataloader as dl
+import pyramid.phasemap as pm
+import pyramid.holoimage as hi
+import pyramid.analytic as an
+import time
+import pdb, traceback, sys
+from numpy import pi
+
+
+def phase_from_mag():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+
+ '''INPUT'''
+ # TODO: Input via GUI
+ filename = '../output/output.txt'
+ b_0 = 10.0 # in T
+ v_0 = 0 # TODO: units?
+ v_acc = 30000 # in V
+ padding = 20
+ density = 100
+
+ dim = (50, 50) # in px (y,x)
+ res = 1.0 # in nm
+ beta = pi/4
+
+ plot_mag_distr = True
+
+ # Slab:
+ shape_fun = mc.slab
+ center = (24, 24) # in px (y,x) index starts with 0!
+ width = (25, 25) # in px (y,x)
+ params = (center, width)
+# # Disc:
+# shape_fun = mc.disc
+# center = (4, 4) # in px (y,x)
+# radius = 2.5
+# params = (center, radius)
+# # Filament:
+# shape_fun = mc.filament
+# pos = 5
+# x_or_y = 'y'
+# params = (pos, x_or_y)
+# # Alternating Filaments:
+# shape_fun = mc.alternating_filaments
+# spacing = 5
+# x_or_y = 'y'
+# params = (spacing, x_or_y)
+# # Single Pixel:
+# shape_fun = mc.single_pixel
+# pixel = (5, 5)
+# params = pixel
+
+# '''CREATE LOGO'''
+# mc.create_logo(128, res, beta, filename, plot_mag_distr)
+# mag_data = dl.MagDataLLG(filename)
+# phase= pm.real_space_slab(mag_data, b_0)
+# holo = hi.holo_image(phase, mag_data.res, density)
+# hi.display_holo(holo, '')
+
+ '''CREATE MAGNETIC DISTRIBUTION'''
+ mc.create_hom_mag(dim, res, beta, shape_fun, params,
+ filename, plot_mag_distr)
+
+ '''LOAD MAGNETIC DISTRIBUTION'''
+ mag_data = dl.MagDataLLG(filename)
+
+
+ # TODO: get it to work:
+ phase_el = pm.phase_elec(mag_data, v_0=1, v_acc=200000)
+
+
+ phi_cos_real_slab = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_slab(mag_data, b_0, pixel_map=phi_cos_real_slab)
+ pm.display_phase(phi_cos_real_slab, res, 'Phase of one Pixel-Slab (Cos - Part)')
+ phi_cos_real_disc = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_disc(mag_data, b_0, pixel_map=phi_cos_real_disc)
+ pm.display_phase(phi_cos_real_disc, res, 'Phase of one Pixel-Disc (Cos - Part)')
+ phi_cos_diff = phi_cos_real_slab - phi_cos_real_disc
+ pm.display_phase(phi_cos_diff, mag_data.res, 'Difference: One Pixel Slab - Disc')
+
+
+ '''NUMERICAL SOLUTION'''
+ # numerical solution Fourier Space:
+ tic = time.clock()
+ phase_fft = pm.fourier_space(mag_data, b_0, padding)
+ toc = time.clock()
+ print 'Time for Fourier Space Approach: ' + str(toc - tic)
+ holo_fft = hi.holo_image(phase_fft, mag_data.res, density)
+ display_combined(phase_fft, mag_data.res, holo_fft,
+ 'Fourier Space Approach')
+ # numerical solution Real Space (Slab):
+ jacobi = np.zeros((2*dim[0]*dim[1], dim[0]*dim[1]))
+ tic = time.clock()
+ phase_real_slab = pm.real_space_slab(mag_data, b_0, jacobi=None)
+ toc = time.clock()
+ np.savetxt('../output/jacobi.npy', jacobi)
+ print 'Time for Real Space Approach (Slab): ' + str(toc - tic)
+ holo_real_slab = hi.holo_image(phase_real_slab, mag_data.res, density)
+ display_combined(phase_real_slab, mag_data.res, holo_real_slab,
+ 'Real Space Approach (Slab)')
+ # numerical solution Real Space (Disc):
+ tic = time.clock()
+ phase_real_disc = pm.real_space_disc(mag_data, b_0)
+ toc = time.clock()
+ print 'Time for Real Space Approach (Disc): ' + str(toc - tic)
+ holo_real_disc = hi.holo_image(phase_real_disc, mag_data.res, density)
+ display_combined(phase_real_disc, mag_data.res, holo_real_disc,
+ 'Real Space Approach (Disc)')
+
+ '''ANALYTIC SOLUTION'''
+ # analytic solution slab:
+ phase = an.phasemap_slab(dim, res, beta, center, width, b_0)
+ holo = hi.holo_image(phase, res, density)
+ display_combined(phase, res, holo, 'Analytic Solution - Slab')
+# # analytic solution disc:
+# phase = an.phasemap_disc(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Disc')
+# # analytic solution sphere:
+# phase = an.phasemap_sphere(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Sphere')
+
+
+ '''DIFFERENCES'''
+ diff_fft_to_ana = phase_fft - phase
+ diff_real_slab_to_ana = phase_real_slab - phase
+ diff_real_disc_to_ana = phase_real_disc - phase
+ diff_slab_to_disc = phase_real_disc - phase_real_slab
+ pm.display_phase(diff_fft_to_ana, res, 'Difference: FFT - Analytic')
+ pm.display_phase(diff_real_slab_to_ana, res, 'Difference: Slab - Analytic')
+ pm.display_phase(diff_real_disc_to_ana, res, 'Difference: Disc - Analytic')
+ pm.display_phase(diff_slab_to_disc, res, 'Difference: Disc - Slab')
+
+ # TODO: Delete
+# import pdb; pdb.set_trace()
+
+
+def display_combined(phase, res, holo, title):
+ fig = plt.figure(figsize=(14, 7))
+ fig.suptitle(title, fontsize=20)
+
+ holo_axis = fig.add_subplot(1,2,1, aspect='equal')
+ hi.display_holo(holo, 'Holography Image', holo_axis)
+
+ phase_axis = fig.add_subplot(1,2,2, aspect='equal')
+ pm.display_phase(phase, res, 'Phasemap', phase_axis)
+
+
+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/create_logo.py b/scripts/create_logo.py
new file mode 100644
index 0000000..0b3c0e9
--- /dev/null
+++ b/scripts/create_logo.py
@@ -0,0 +1,44 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 03 11:15:38 2013
+
+@author: Jan
+"""
+
+import pyramid.magcreator as mc
+import pyramid.dataloader as dl
+import pyramid.phasemap as pm
+import pyramid.holoimage as hi
+import pdb, traceback, sys
+from numpy import pi
+
+
+def create_logo():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+
+ filename = '../output/logo_magnetization.txt'
+ b_0 = 1.0 # in T
+ res = 10.0 # in nm
+ beta = pi/2
+ density = 10
+
+ mc.create_logo(128, res, beta, filename)
+ mag_data = dl.MagDataLLG(filename)
+ phase= pm.real_space_slab(mag_data, b_0)
+ holo = hi.holo_image(phase, mag_data.res, density)
+ hi.display_holo(holo, '')
+
+
+if __name__ == "__main__":
+ try:
+ create_logo()
+ 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_samples.py b/scripts/create_samples.py
new file mode 100644
index 0000000..cd8a8cd
--- /dev/null
+++ b/scripts/create_samples.py
@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 03 11:15:38 2013
+
+@author: Jan
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pyramid.magcreator as mc
+import pyramid.dataloader as dl
+import pyramid.phasemap as pm
+import pyramid.holoimage as hi
+import pyramid.analytic as an
+import time
+import pdb, traceback, sys
+from numpy import pi
+
+
+def phase_from_mag():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+
+ '''INPUT'''
+ # TODO: Input via GUI
+ filename = '../output/output.txt'
+ b_0 = 10.0 # in T
+ v_0 = 0 # TODO: units?
+ v_acc = 30000 # in V
+ padding = 20
+ density = 100
+
+ dim = (50, 50) # in px (y,x)
+ res = 1.0 # in nm
+ beta = pi/4
+
+ plot_mag_distr = True
+
+ # Slab:
+ shape_fun = mc.slab
+ center = (24, 24) # in px (y,x) index starts with 0!
+ width = (25, 25) # in px (y,x)
+ params = (center, width)
+# # Disc:
+# shape_fun = mc.disc
+# center = (4, 4) # in px (y,x)
+# radius = 2.5
+# params = (center, radius)
+# # Filament:
+# shape_fun = mc.filament
+# pos = 5
+# x_or_y = 'y'
+# params = (pos, x_or_y)
+# # Alternating Filaments:
+# shape_fun = mc.alternating_filaments
+# spacing = 5
+# x_or_y = 'y'
+# params = (spacing, x_or_y)
+# # Single Pixel:
+# shape_fun = mc.single_pixel
+# pixel = (5, 5)
+# params = pixel
+
+# '''CREATE LOGO'''
+# mc.create_logo(128, res, beta, filename, plot_mag_distr)
+# mag_data = dl.MagDataLLG(filename)
+# phase= pm.real_space_slab(mag_data, b_0)
+# holo = hi.holo_image(phase, mag_data.res, density)
+# hi.display_holo(holo, '')
+
+ '''CREATE MAGNETIC DISTRIBUTION'''
+ mc.create_hom_mag(dim, res, beta, shape_fun, params,
+ filename, plot_mag_distr)
+
+ '''LOAD MAGNETIC DISTRIBUTION'''
+ mag_data = dl.MagDataLLG(filename)
+
+
+ # TODO: get it to work:
+ phase_el = pm.phase_elec(mag_data, v_0=1, v_acc=200000)
+
+
+ phi_cos_real_slab = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_slab(mag_data, b_0, pixel_map=phi_cos_real_slab)
+ pm.display_phase(phi_cos_real_slab, res, 'Phase of one Pixel-Slab (Cos - Part)')
+ phi_cos_real_disc = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_disc(mag_data, b_0, pixel_map=phi_cos_real_disc)
+ pm.display_phase(phi_cos_real_disc, res, 'Phase of one Pixel-Disc (Cos - Part)')
+ phi_cos_diff = phi_cos_real_slab - phi_cos_real_disc
+ pm.display_phase(phi_cos_diff, mag_data.res, 'Difference: One Pixel Slab - Disc')
+
+
+ '''NUMERICAL SOLUTION'''
+ # numerical solution Fourier Space:
+ tic = time.clock()
+ phase_fft = pm.fourier_space(mag_data, b_0, padding)
+ toc = time.clock()
+ print 'Time for Fourier Space Approach: ' + str(toc - tic)
+ holo_fft = hi.holo_image(phase_fft, mag_data.res, density)
+ display_combined(phase_fft, mag_data.res, holo_fft,
+ 'Fourier Space Approach')
+ # numerical solution Real Space (Slab):
+ jacobi = np.zeros((2*dim[0]*dim[1], dim[0]*dim[1]))
+ tic = time.clock()
+ phase_real_slab = pm.real_space_slab(mag_data, b_0, jacobi=None)
+ toc = time.clock()
+ np.savetxt('../output/jacobi.npy', jacobi)
+ print 'Time for Real Space Approach (Slab): ' + str(toc - tic)
+ holo_real_slab = hi.holo_image(phase_real_slab, mag_data.res, density)
+ display_combined(phase_real_slab, mag_data.res, holo_real_slab,
+ 'Real Space Approach (Slab)')
+ # numerical solution Real Space (Disc):
+ tic = time.clock()
+ phase_real_disc = pm.real_space_disc(mag_data, b_0)
+ toc = time.clock()
+ print 'Time for Real Space Approach (Disc): ' + str(toc - tic)
+ holo_real_disc = hi.holo_image(phase_real_disc, mag_data.res, density)
+ display_combined(phase_real_disc, mag_data.res, holo_real_disc,
+ 'Real Space Approach (Disc)')
+
+ '''ANALYTIC SOLUTION'''
+ # analytic solution slab:
+ phase = an.phasemap_slab(dim, res, beta, center, width, b_0)
+ holo = hi.holo_image(phase, res, density)
+ display_combined(phase, res, holo, 'Analytic Solution - Slab')
+# # analytic solution disc:
+# phase = an.phasemap_disc(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Disc')
+# # analytic solution sphere:
+# phase = an.phasemap_sphere(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Sphere')
+
+
+ '''DIFFERENCES'''
+ diff_fft_to_ana = phase_fft - phase
+ diff_real_slab_to_ana = phase_real_slab - phase
+ diff_real_disc_to_ana = phase_real_disc - phase
+ diff_slab_to_disc = phase_real_disc - phase_real_slab
+ pm.display_phase(diff_fft_to_ana, res, 'Difference: FFT - Analytic')
+ pm.display_phase(diff_real_slab_to_ana, res, 'Difference: Slab - Analytic')
+ pm.display_phase(diff_real_disc_to_ana, res, 'Difference: Disc - Analytic')
+ pm.display_phase(diff_slab_to_disc, res, 'Difference: Disc - Slab')
+
+ # TODO: Delete
+# import pdb; pdb.set_trace()
+
+
+def display_combined(phase, res, holo, title):
+ fig = plt.figure(figsize=(14, 7))
+ fig.suptitle(title, fontsize=20)
+
+ holo_axis = fig.add_subplot(1,2,1, aspect='equal')
+ hi.display_holo(holo, 'Holography Image', holo_axis)
+
+ phase_axis = fig.add_subplot(1,2,2, aspect='equal')
+ pm.display_phase(phase, res, 'Phasemap', phase_axis)
+
+
+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/get_jacobi.py b/scripts/get_jacobi.py
new file mode 100644
index 0000000..d6b04c7
--- /dev/null
+++ b/scripts/get_jacobi.py
@@ -0,0 +1,172 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 03 11:15:38 2013
+
+@author: Jan
+"""
+
+import numpy as np
+import matplotlib.pyplot as plt
+import pyramid.magcreator as mc
+import pyramid.dataloader as dl
+import pyramid.phasemap as pm
+import pyramid.holoimage as hi
+import pyramid.analytic as an
+import time
+import pdb, traceback, sys
+from numpy import pi
+
+
+def phase_from_mag():
+ '''Calculate and display the phase map from a given magnetization.
+ Arguments:
+ None
+ Returns:
+ None
+
+ '''
+
+ '''INPUT'''
+ # TODO: Input via GUI
+ filename = '../output/output.txt'
+ b_0 = 1.0 # in T
+ v_0 = 0 # TODO: units?
+ v_acc = 30000 # in V
+ padding = 20
+ density = 100
+
+ dim = (50, 50) # in px (y,x)
+ res = 1.0 # in nm
+ beta = pi/4
+
+ plot_mag_distr = True
+
+ # Slab:
+ shape_fun = mc.slab
+ center = (24, 24) # in px (y,x) index starts with 0!
+ width = (25, 25) # in px (y,x)
+ params = (center, width)
+# # Disc:
+# shape_fun = mc.disc
+# center = (4, 4) # in px (y,x)
+# radius = 2.5
+# params = (center, radius)
+# # Filament:
+# shape_fun = mc.filament
+# pos = 5
+# x_or_y = 'y'
+# params = (pos, x_or_y)
+# # Alternating Filaments:
+# shape_fun = mc.alternating_filaments
+# spacing = 5
+# x_or_y = 'y'
+# params = (spacing, x_or_y)
+# # Single Pixel:
+# shape_fun = mc.single_pixel
+# pixel = (5, 5)
+# params = pixel
+
+# '''CREATE LOGO'''
+# mc.create_logo(128, res, beta, filename, plot_mag_distr)
+# mag_data = dl.MagDataLLG(filename)
+# phase= pm.real_space_slab(mag_data, b_0)
+# holo = hi.holo_image(phase, mag_data.res, density)
+# hi.display_holo(holo, '')
+
+ '''CREATE MAGNETIC DISTRIBUTION'''
+ mc.create_hom_mag(dim, res, beta, shape_fun, params,
+ filename, plot_mag_distr)
+
+ '''LOAD MAGNETIC DISTRIBUTION'''
+ mag_data = dl.MagDataLLG(filename)
+
+
+ # TODO: get it to work:
+ phase_el = pm.phase_elec(mag_data, v_0=1, v_acc=200000)
+
+
+ phi_cos_real_slab = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_slab(mag_data, b_0, pixel_map=phi_cos_real_slab)
+ pm.display_phase(phi_cos_real_slab, res, 'Phase of one Pixel-Slab (Cos - Part)')
+ phi_cos_real_disc = np.zeros((2*dim[0]-1, 2*dim[1]-1))
+ pm.real_space_disc(mag_data, b_0, pixel_map=phi_cos_real_disc)
+ pm.display_phase(phi_cos_real_disc, res, 'Phase of one Pixel-Disc (Cos - Part)')
+ phi_cos_diff = phi_cos_real_slab - phi_cos_real_disc
+ pm.display_phase(phi_cos_diff, mag_data.res, 'Difference: One Pixel Slab - Disc')
+
+
+ '''NUMERICAL SOLUTION'''
+ # numerical solution Fourier Space:
+ tic = time.clock()
+ phase_fft = pm.fourier_space(mag_data, b_0, padding)
+ toc = time.clock()
+ print 'Time for Fourier Space Approach: ' + str(toc - tic)
+ holo_fft = hi.holo_image(phase_fft, mag_data.res, density)
+ display_combined(phase_fft, mag_data.res, holo_fft,
+ 'Fourier Space Approach')
+ # numerical solution Real Space (Slab):
+ jacobi = np.zeros((2*dim[0]*dim[1], dim[0]*dim[1]))
+ tic = time.clock()
+ phase_real_slab = pm.real_space_slab(mag_data, b_0, jacobi=None)
+ toc = time.clock()
+ np.savetxt('../output/jacobi.npy', jacobi)
+ print 'Time for Real Space Approach (Slab): ' + str(toc - tic)
+ holo_real_slab = hi.holo_image(phase_real_slab, mag_data.res, density)
+ display_combined(phase_real_slab, mag_data.res, holo_real_slab,
+ 'Real Space Approach (Slab)')
+ # numerical solution Real Space (Disc):
+ tic = time.clock()
+ phase_real_disc = pm.real_space_disc(mag_data, b_0)
+ toc = time.clock()
+ print 'Time for Real Space Approach (Disc): ' + str(toc - tic)
+ holo_real_disc = hi.holo_image(phase_real_disc, mag_data.res, density)
+ display_combined(phase_real_disc, mag_data.res, holo_real_disc,
+ 'Real Space Approach (Disc)')
+
+ '''ANALYTIC SOLUTION'''
+ # analytic solution slab:
+ phase = an.phasemap_slab(dim, res, beta, center, width, b_0)
+ holo = hi.holo_image(phase, res, density)
+ display_combined(phase, res, holo, 'Analytic Solution - Slab')
+# # analytic solution disc:
+# phase = an.phasemap_disc(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Disc')
+# # analytic solution sphere:
+# phase = an.phasemap_sphere(dim, res, beta, center, radius, b_0)
+# holo = hi.holo_image(phase, res, density)
+# display_combined(phase, res, holo, 'Analytic Solution - Sphere')
+
+
+ '''DIFFERENCES'''
+ diff_fft_to_ana = phase_fft - phase
+ diff_real_slab_to_ana = phase_real_slab - phase
+ diff_real_disc_to_ana = phase_real_disc - phase
+ diff_slab_to_disc = phase_real_disc - phase_real_slab
+ pm.display_phase(diff_fft_to_ana, res, 'Difference: FFT - Analytic')
+ pm.display_phase(diff_real_slab_to_ana, res, 'Difference: Slab - Analytic')
+ pm.display_phase(diff_real_disc_to_ana, res, 'Difference: Disc - Analytic')
+ pm.display_phase(diff_slab_to_disc, res, 'Difference: Disc - Slab')
+
+ # TODO: Delete
+# import pdb; pdb.set_trace()
+
+
+def display_combined(phase, res, holo, title):
+ fig = plt.figure(figsize=(14, 7))
+ fig.suptitle(title, fontsize=20)
+
+ holo_axis = fig.add_subplot(1,2,1, aspect='equal')
+ hi.display_holo(holo, 'Holography Image', holo_axis)
+
+ phase_axis = fig.add_subplot(1,2,2, aspect='equal')
+ pm.display_phase(phase, res, 'Phasemap', phase_axis)
+
+
+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/main.py b/scripts/main.py
index 104e85d..6ccadb5 100644
--- a/scripts/main.py
+++ b/scripts/main.py
@@ -28,15 +28,15 @@ def phase_from_mag():
'''INPUT'''
# TODO: Input via GUI
- filename = 'output.txt'
- b_0 = 10.0 # in T
+ filename = '../output/output.txt'
+ b_0 = 1.0 # in T
v_0 = 0 # TODO: units?
v_acc = 30000 # in V
padding = 20
- density = 100
+ density = 10
dim = (50, 50) # in px (y,x)
- res = 1.0 # in nm
+ res = 10.0 # in nm
beta = pi/4
plot_mag_distr = True
@@ -105,11 +105,11 @@ def phase_from_mag():
display_combined(phase_fft, mag_data.res, holo_fft,
'Fourier Space Approach')
# numerical solution Real Space (Slab):
-# jacobi = np.zeros((2*dim[0]*dim[1], dim[0]*dim[1]))
+ jacobi = np.zeros((2*dim[0]*dim[1], dim[0]*dim[1]))
tic = time.clock()
phase_real_slab = pm.real_space_slab(mag_data, b_0, jacobi=None)
toc = time.clock()
-# np.savetxt('jacobi.npy', jacobi)
+ np.savetxt('../output/jacobi.npy', jacobi)
print 'Time for Real Space Approach (Slab): ' + str(toc - tic)
holo_real_slab = hi.holo_image(phase_real_slab, mag_data.res, density)
display_combined(phase_real_slab, mag_data.res, holo_real_slab,
diff --git a/pyramid/__init__.py b/src/pyramid/__init__.py
similarity index 100%
rename from pyramid/__init__.py
rename to src/pyramid/__init__.py
diff --git a/pyramid/analytic.py b/src/pyramid/analytic.py
similarity index 100%
rename from pyramid/analytic.py
rename to src/pyramid/analytic.py
diff --git a/pyramid/dataloader.py b/src/pyramid/dataloader.py
similarity index 100%
rename from pyramid/dataloader.py
rename to src/pyramid/dataloader.py
diff --git a/pyramid/holoimage.py b/src/pyramid/holoimage.py
similarity index 100%
rename from pyramid/holoimage.py
rename to src/pyramid/holoimage.py
diff --git a/pyramid/magcreator.py b/src/pyramid/magcreator.py
similarity index 97%
rename from pyramid/magcreator.py
rename to src/pyramid/magcreator.py
index b4f84c9..ac00677 100644
--- a/pyramid/magcreator.py
+++ b/src/pyramid/magcreator.py
@@ -168,7 +168,7 @@ def create_logo(edge, res, beta = pi/2, filename='logo.txt', plot_mag_distr=Fals
y_mag = np.array(np.ones(dim)) * np.sin(beta) * shape_mag
z_mag = np.array(np.zeros(dim))
- if (True):
+ if (plot_mag_distr):
fig = plt.figure()
fig.add_subplot(111, aspect='equal')
plt.quiver(x_mag, y_mag, pivot='middle', angles='xy', scale_units='xy',
diff --git a/pyramid/phasemap.py b/src/pyramid/phasemap.py
similarity index 96%
rename from pyramid/phasemap.py
rename to src/pyramid/phasemap.py
index 9464545..96cdccb 100644
--- a/pyramid/phasemap.py
+++ b/src/pyramid/phasemap.py
@@ -71,6 +71,8 @@ def real_space_slab(mag_data, b_0=1, v_0=0, v_acc=30000,
the phasemap as a 2 dimensional array
'''
+ # TODO: combine with disc and sphere approach, pixel field as function
+
# TODO: Expand docstring!
# TODO: Delete
diff --git a/test/test_analytic.py b/test/test_analytic.py
new file mode 100644
index 0000000..b26bfd4
--- /dev/null
+++ b/test/test_analytic.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 24 07:10:28 2013
+
+@author: Jan
+"""
+# py.test
+
+import unittest
+
+
+class TestSuite(unittest.TestCase):
+
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test(self):
+ self.assertTrue(True)
+
+ def test_almost(self):
+ self.assertAlmostEqual(0, 0.01, places=1)
+
+
+if __name__ == '__main__':
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+ unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file
diff --git a/test/test_dataloader.py b/test/test_dataloader.py
new file mode 100644
index 0000000..b26bfd4
--- /dev/null
+++ b/test/test_dataloader.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 24 07:10:28 2013
+
+@author: Jan
+"""
+# py.test
+
+import unittest
+
+
+class TestSuite(unittest.TestCase):
+
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test(self):
+ self.assertTrue(True)
+
+ def test_almost(self):
+ self.assertAlmostEqual(0, 0.01, places=1)
+
+
+if __name__ == '__main__':
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+ unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file
diff --git a/test/test_holoimage.py b/test/test_holoimage.py
new file mode 100644
index 0000000..b26bfd4
--- /dev/null
+++ b/test/test_holoimage.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 24 07:10:28 2013
+
+@author: Jan
+"""
+# py.test
+
+import unittest
+
+
+class TestSuite(unittest.TestCase):
+
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test(self):
+ self.assertTrue(True)
+
+ def test_almost(self):
+ self.assertAlmostEqual(0, 0.01, places=1)
+
+
+if __name__ == '__main__':
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+ unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file
diff --git a/test/test_magcreator.py b/test/test_magcreator.py
new file mode 100644
index 0000000..b26bfd4
--- /dev/null
+++ b/test/test_magcreator.py
@@ -0,0 +1,29 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 24 07:10:28 2013
+
+@author: Jan
+"""
+# py.test
+
+import unittest
+
+
+class TestSuite(unittest.TestCase):
+
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test(self):
+ self.assertTrue(True)
+
+ def test_almost(self):
+ self.assertAlmostEqual(0, 0.01, places=1)
+
+
+if __name__ == '__main__':
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+ unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file
diff --git a/test/test_phasemap.py b/test/test_phasemap.py
new file mode 100644
index 0000000..1c2af41
--- /dev/null
+++ b/test/test_phasemap.py
@@ -0,0 +1,31 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Wed Apr 24 07:10:28 2013
+
+@author: Jan
+"""
+# py.test
+
+import unittest
+import numpy as np
+
+
+class TestSuite(unittest.TestCase):
+
+ def setUp(self):
+ pass
+
+ def tearDown(self):
+ pass
+
+ def test(self):
+ self.assertTrue(True)
+
+ def test_almost(self):
+ self.assertAlmostEqual(0, 0.01, places=1)
+ np.testing.assert_array_almost_equal()
+
+
+if __name__ == '__main__':
+ suite = unittest.TestLoader().loadTestsFromTestCase(TestSuite)
+ unittest.TextTestRunner(verbosity=2).run(suite)
\ No newline at end of file
--
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