Documentation and cleanup of the pyramid package!

Renames:
datacollection --> dataset
optimizer      --> reconstruction

scripts:
interactive_setup is now implemented in an extended Spyder startup file.
some other scripts are now
the rest is NOT adapted, yet, which is the next task at hand
furthermore scripts will be sorted and unused ones deleted in the next commit

scripts/abstract_pictures.py

+# -*- coding: utf-8 -*-
+"""
+Created on Mon Mar 17 14:28:10 2014
+
+@author: Jan
+"""
+
+
+from numpy import pi
+import numpy as np
+import matplotlib.pyplot as plt
+from matplotlib.ticker import FuncFormatter
+
+import pyramid.magcreator as mc
+from pyramid.magdata import MagData
+from pyramid.projector import SimpleProjector, YTiltProjector
+from pyramid.phasemapper import PMConvolve
+
+
+###################################################################################################
+print('Jan')
+
+dim = (128, 128, 128)
+center = (int(dim[0]/2), int(dim[1]/2), int(dim[2]/2))
+radius = dim[0]/4.
+a = 1.
+
+magnitude = mc.create_mag_dist_homog(mc.Shapes.sphere(dim, center, radius), pi/4)
+
+mag_data = MagData(a, magnitude)
+
+projector = SimpleProjector(dim)
+
+phase_map = PMConvolve(a, projector)(mag_data)
+
+axis = phase_map.display_phase()
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Phase map', fontsize=24)
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+axis = phase_map.display_holo(density=20, interpolation='bilinear')
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Magnetic induction map', fontsize=24)
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+mag_data.scale_down(2)
+
+mag_data.quiver_plot()
+axis = plt.gca()
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Magnetization distribution', fontsize=24)
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+phase_map.make_color_wheel()
+
+shape_vort = mc.Shapes.disc((64, 64, 64), (31.5, 31.5, 31.5), 24, 10)
+
+magnitude_vort = mc.create_mag_dist_vortex(shape_vort)
+
+mag_vort = MagData(a, magnitude_vort)
+
+mag_vort.scale_down(2)
+
+mag_vort.quiver_plot()
+
+
+###################################################################################################
+print('Patrick')
+
+a = 10.0  # nm
+b_0 = 3  # T
+
+dim = (128, 128, 128)
+center = (int(dim[0]/2), int(dim[1]/2), int(dim[2]/2))  # in px (z, y, x), index starts with 0!
+
+mag_data = MagData(a, mc.create_mag_dist_homog(mc.Shapes.ellipse(dim, center, (20., 60.), 5.), 0))
+
+tilts = np.array([0., 60.])/180.*pi
+
+projectors = [YTiltProjector(mag_data.dim, tilt) for tilt in tilts]
+phasemappers = [PMConvolve(mag_data.a, proj, b_0) for proj in projectors]
+
+phase_maps = [pm(mag_data) for pm in phasemappers]
+
+axis = phase_maps[0].display_holo(density=1, interpolation='bilinear')
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Magnetic induction map', fontsize=24)
+axis.xaxis.set_major_formatter(FuncFormatter(lambda x, pos: '{:g}'.format(x*a)))
+axis.yaxis.set_major_formatter(FuncFormatter(lambda x, pos: '{:g}'.format(x*a)))
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+axis = phase_maps[0].display_phase(limit=17)
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Phase map', fontsize=24)
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+axis = phase_maps[1].display_holo(density=1, interpolation='bilinear')
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Magnetic induction map', fontsize=24)
+axis.xaxis.set_major_formatter(FuncFormatter(lambda x, pos: '{:g}'.format(x*a)))
+axis.yaxis.set_major_formatter(FuncFormatter(lambda x, pos: '{:g}'.format(x*a)))
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+
+axis = phase_maps[1].display_phase(limit=17)
+axis.tick_params(axis='both', which='major', labelsize=18)
+axis.set_title('Phase map', fontsize=24)
+axis.set_xlabel('x [nm]', fontsize=18)
+axis.set_ylabel('y [nm]', fontsize=18)
+

scripts/edinburgh_test.py

@@ -9,7 +9,7 @@ Created on Tue Jan 28 15:15:08 2014
 import numpy as np
 from pyramid.magdata import MagData
 from pyramid.projector import SimpleProjector
-from pyramid.phasemapper import PMAdapterFM
+from pyramid.phasemapper import PMAdapterFM, PMFourier
 from matplotlib.ticker import FuncFormatter
 
 data = np.loadtxt('../output/data from Edinburgh/long_grain_remapped_0p0035.txt', delimiter=',')
@@ -28,17 +28,18 @@ magnitude = np.array((x_mag, y_mag, z_mag))
 
 mag_data = MagData(a, magnitude)
 
-mag_data.pad(30, 20, 0)
-
-mag_data.scale_up()
-
-mag_data.quiver_plot()
+#mag_data.pad(30, 20, 0)
+#
+#mag_data.scale_up()
+#
+#mag_data.quiver_plot()
 
 #mag_data.quiver_plot3d()
 
 projector = SimpleProjector(mag_data.dim)
 
 phasemapper = PMAdapterFM(mag_data.a, projector)
+phasemapper = PMFourier(mag_data.a, projector, padding = 1)
 
 phase_map = phasemapper(mag_data)
 

scripts/interactive_setup.py

 # -*- coding: utf-8 -*-
 """Imports pyramid package and sets working directory to output directory"""
 
-import pyramid.analytic as an
-import pyramid.holoimage as hi
+
 import pyramid.magcreator as mc
-import pyramid.phasemapper as pm
-import pyramid.projector as pj
-import pyramid.reconstructor as rc
-from pyramid.magdata import MagData
-from pyramid.phasemap import PhaseMap
+import pyramid.analytic as an
+import pyramid.reconstruction as rc
+
+from pyramid.magdata import *
+from pyramid.projector import *
+from pyramid.kernel import *
+from pyramid.phasemapper import *
+from pyramid.phasemap import *
+from pyramid.dataset import *
+from pyramid.forwardmodel import *
+from pyramid.costfunction import *
 
 import os
-os.chdir('C:\\Users\\Jan\\Home\\PhD Thesis\\Pyramid\\tests')
+
+
+os.chdir('C:\\Users\\Jan\\Home\\PhD Thesis\\Pyramid\\output')

scripts/paper 1/logfile.log

-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling __init__
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling __init__
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Created <pyramid.projector.SimpleProjector object at 0x0DC7ECD0>
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Created <pyramid.projector.SimpleProjector object at 0x0DC7ECD0>
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling as function
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    mode == vector
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling _vector_field_projection
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __neg__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Adding two PhaseMap objects
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling display_phase
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling as function
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    mode == vector
-2014-02-18 09:30:30: INFO     @ <pyramid.projector>:    Calling _vector_field_projection
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __neg__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Adding two PhaseMap objects
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __isub__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Adding an offset
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:30: INFO     @ <pyramid.phasemap>:    Calling display_phase
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    Calling as function
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    mode == vector
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    Calling _vector_field_projection
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __neg__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Adding two PhaseMap objects
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:31: INFO     @ <pyramid.phasemap>:    Calling display_phase
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    Calling as function
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    mode == vector
-2014-02-18 09:30:31: INFO     @ <pyramid.projector>:    Calling _vector_field_projection
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __neg__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Adding two PhaseMap objects
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __isub__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __sub__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __add__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Adding an offset
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:32: INFO     @ <pyramid.phasemap>:    Calling display_phase
-2014-02-18 09:30:33: INFO     @ <pyramid.projector>:    Calling __init__
-2014-02-18 09:30:33: INFO     @ <pyramid.projector>:    Calling __init__
-2014-02-18 09:30:33: INFO     @ <pyramid.projector>:    Created <pyramid.projector.SimpleProjector object at 0x0DC7EB70>
-2014-02-18 09:30:33: INFO     @ <pyramid.projector>:    Created <pyramid.projector.SimpleProjector object at 0x0DC7EB70>
-2014-02-18 09:30:33: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:33: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))
-2014-02-18 09:30:33: INFO     @ <pyramid.phasemap>:    Calling __str__
-2014-02-18 09:30:33: INFO     @ <pyramid.phasemap>:    Created PhaseMap(a=1.0, dim_uv=(128, 128))

scripts/simple_reconstruction.py

@@ -10,15 +10,17 @@ import numpy as np
 from numpy import pi
 
 from pyramid.magdata import MagData
-from pyramid.projector import YTiltProjector
+from pyramid.projector import YTiltProjector, XTiltProjector
 from pyramid.phasemapper import PMConvolve
-from pyramid.datacollection import DataCollection
+from pyramid.dataset import DataSet
+import pyramid.magcreator as mc
 
 from pyramid.kernel import Kernel
 from pyramid.forwardmodel import ForwardModel
 from pyramid.costfunction import Costfunction
+import pyramid.reconstruction as rc
 
-from scipy.sparse.linalg import cg
+from scipy.sparse.linalg import cg, LinearOperator
 
 
 ###################################################################################################
@@ -41,7 +43,7 @@ phase_maps = [pm(mag_data) for pm in phasemappers]
 
 dim_uv = dim[1:3]
 
-data_collection = DataCollection(a, dim_uv, b_0)
+data_collection = DataSet(a, dim_uv, b_0)
 
 [data_collection.append((phase_maps[i], projectors[i])) for i in range(count)]
 
@@ -100,7 +102,7 @@ phase_maps = [pm(mag_data) for pm in phasemappers]
 
 dim_uv = dim[1:3]
 
-data_collection = DataCollection(a, dim_uv, b_0)
+data_collection = DataSet(a, dim_uv, b_0)
 
 [data_collection.append((phase_maps[i], projectors[i])) for i in range(count)]
 
@@ -166,35 +168,40 @@ print('--STARTING RECONSTRUCTION')
 ###################################################################################################
 print('--Generating input phase_maps')
 
-a = 1.
+a = 10.
 b_0 = 1000.
-dim = (9, 9, 9)
-count = 8
+dim = (8, 8, 8)
+count = 32
 
 magnitude = np.zeros((3,)+dim)
-magnitude[0, int(dim[0]/2), int(dim[1]/2), int(dim[2]/2)] = 1.
+magnitude[:, 3:6, 3:6, 3:6] = 1# int(dim[0]/2), int(dim[1]/2), int(dim[2]/2)] = 1.
+magnitude = mc.create_mag_dist_vortex(mc.Shapes.disc(dim, (3.5, 3.5, 3.5), 3, 4))
 
 mag_data = MagData(a, magnitude)
 mag_data.quiver_plot3d()
 
-tilts = np.linspace(0, 2*pi, num=count, endpoint=False)
-projectors = [YTiltProjector(mag_data.dim, tilt) for tilt in tilts]
+tilts = np.linspace(0, 2*pi, num=count/2, endpoint=False)
+projectors = []
+projectors.extend([XTiltProjector(mag_data.dim, tilt) for tilt in tilts])
+projectors.extend([YTiltProjector(mag_data.dim, tilt) for tilt in tilts])
 phasemappers = [PMConvolve(mag_data.a, projector, b_0) for projector in projectors]
 phase_maps = [pm(mag_data) for pm in phasemappers]
 
-[phase_map.display_phase(title=u'Tilt series $(\phi = {:2.1f} \pi)$'.format(tilts[i]/pi))
-                         for i, phase_map in enumerate(phase_maps)]
+#[phase_map.display_phase(title=u'Tilt series $(\phi = {:2.1f} \pi)$'.format(tilts[i%(count/2)]/pi))
+#                         for i, phase_map in enumerate(phase_maps)]
 
 ###################################################################################################
 print('--Setting up data collection')
 
 dim_uv = dim[1:3]
 
+lam =  10. ** -10
+
 size_2d = np.prod(dim_uv)
 size_3d = np.prod(dim)
 
 
-data_collection = DataCollection(a, dim_uv, b_0)
+data_collection = DataSet(a, dim_uv, b_0)
 
 [data_collection.append((phase_maps[i], projectors[i])) for i in range(count)]
 
@@ -202,37 +209,62 @@ data = data_collection
 y = data.phase_vec
 kern = Kernel(data.a, data.dim_uv, data.b_0)
 F = ForwardModel(data.projectors, kern)
-C = Costfunction(y, F)
+C = Costfunction(y, F, lam)
 
 ###################################################################################################
 print('--Test simple solver')
 
-M = np.asmatrix([F.jac_dot(None, np.eye(3*size_3d)[:, i]) for i in range(3*size_3d)]).T
-lam = 1*10. ** -10
-MTM = M.T * M + lam * np.asmatrix(np.eye(3*size_3d))
-
-A = MTM#np.array([F(np.eye(81)[:, i]) for i in range(81)])
-
-b = F.jac_T_dot(None, y)
-
-b_test = np.asarray((M.T.dot(y)).T)[0]
+#M = np.asmatrix([F.jac_dot(None, np.eye(3*size_3d)[:, i]) for i in range(3*size_3d)]).T
+#MTM = M.T * M + lam * np.asmatrix(np.eye(3*size_3d))
+#A = MTM#np.array([F(np.eye(81)[:, i]) for i in range(81)])
 
-x_f = cg(A, b)[0]
-
-mag_data_rec = MagData(a, np.zeros((3,)+dim))
-
-mag_data_rec.mag_vec = x_f
-
-mag_data_rec.quiver_plot3d()
+#class A_adapt(LinearOperator):
+#
+#    def __init__(self, FwdModel, lam, shape):
+#        self.fwd = FwdModel
+#        self.lam = lam
+#        self.shape = shape
+#
+#    def matvec(self, vector):
+#        return self.fwd.jac_T_dot(None, self.fwd.jac_dot(None, vector)) + self.lam*vector
+#
+#    @property
+#    def shape(self):
+#        return self.shape
+#
+#    @property
+#    def dtype(self):
+#        return np.dtype("d") # None #np.ones(1).dtype
+#
+## TODO: .shape in F und C
+#
+#b = F.jac_T_dot(None, y)
+#
+#A_fast = A_adapt(F, lam, (3*size_3d, 3*size_3d))
+#
+#i = 0
+#def printit(_):
+#    global i
+#    i += 1
+#    print i
+#
+#x_f, info = cg(A_fast, b, callback=printit)
+#
+#mag_data_rec = MagData(a, np.zeros((3,)+dim))
+#
+#mag_data_rec.mag_vec = x_f
+#
+#mag_data_rec.quiver_plot3d()
 
-phase_maps_rec = [pm(mag_data_rec) for pm in phasemappers]
-[phase_map.display_phase(title=u'Tilt series (rec.) $(\phi = {:2.1f} \pi)$'.format(tilts[i]/pi))
-                         for i, phase_map in enumerate(phase_maps_rec)]
+#phase_maps_rec = [pm(mag_data_rec) for pm in phasemappers]
+#[phase_map.display_phase(title=u'Tilt series (rec.) $(\phi = {:2.1f} \pi)$'.format(tilts[i%(count/2)]/pi))
+#                         for i, phase_map in enumerate(phase_maps_rec)]
 
+mag_data_opt = rc.optimize_sparse_cg(data_collection)
 
+mag_data_opt.quiver_plot3d()
 
 
-#
 #first_guess = MagData(a, np.zeros((3,)+dim))
 #
 #first_guess.magnitude[1, int(dim[0]/2), int(dim[1]/2), int(dim[2]/2)] = 1
@@ -253,6 +285,77 @@ phase_maps_rec = [pm(mag_data_rec) for pm in phasemappers]
 #phase_opt.display_phase()
 
 
+
+###################################################################################################
+print('--Singular value decomposition')
+
+#a = 1.
+#b_0 = 1000.
+#dim = (3, 3, 3)
+#count = 8
+#
+#magnitude = np.zeros((3,)+dim)
+#magnitude[:, int(dim[0]/2), int(dim[1]/2), int(dim[2]/2)] = 1.
+#
+#mag_data = MagData(a, magnitude)
+#mag_data.quiver_plot3d()
+#
+#tilts = np.linspace(0, 2*pi, num=count/2, endpoint=False)
+#projectors = []
+#projectors.extend([XTiltProjector(mag_data.dim, tilt) for tilt in tilts])
+#projectors.extend([YTiltProjector(mag_data.dim, tilt) for tilt in tilts])
+#phasemappers = [PMConvolve(mag_data.a, projector, b_0) for projector in projectors]
+#phase_maps = [pm(mag_data) for pm in phasemappers]
+#
+##[phase_map.display_phase(title=u'Tilt series $(\phi = {:2.1f} \pi)$'.format(tilts[i%(count/2)]/pi))
+##                         for i, phase_map in enumerate(phase_maps)]
+#
+#dim_uv = dim[1:3]
+#
+#lam =  10. ** -10
+#
+#size_2d = np.prod(dim_uv)
+#size_3d = np.prod(dim)
+#
+#
+#data_collection = DataCollection(a, dim_uv, b_0)
+#
+#[data_collection.append((phase_maps[i], projectors[i])) for i in range(count)]
+#
+#data = data_collection
+#y = data.phase_vec
+#kern = Kernel(data.a, data.dim_uv, data.b_0)
+#F = ForwardModel(data.projectors, kern)
+#C = Costfunction(y, F, lam)
+#
+#mag_data_opt = opt.optimize_sparse_cg(data_collection)
+#mag_data_opt.quiver_plot3d()
+
+
+
+#M = np.asmatrix([F.jac_dot(None, np.eye(3*size_3d)[:, i]) for i in range(3*size_3d)]).T
+#MTM = M.T * M + lam * np.asmatrix(np.eye(3*size_3d))
+#A = MTM#np.array([F(np.eye(81)[:, i]) for i in range(81)])
+#
+#
+#
+#U, s, V = np.linalg.svd(M)
+##np.testing.assert_almost_equal(U.T, V, decimal=5)
+#
+#for value in range(20):
+#    print 'Singular value:', s[value]
+#    MagData(data.a, np.array(V[value,:]).reshape((3,)+dim)).quiver_plot3d()
+#
+#
+#for value in range(-10,0):
+#    print 'Singular value:', s[value]
+#    MagData(data.a, np.array(V[value,:]).reshape((3,)+dim)).quiver_plot3d()
+
+
+# TODO: print all singular vectors for a 2x2x2 distribution for each single and both tilt series!
+
+# TODO: Separate the script for SVD and compliance tests
+
 ####################################################################################################
 #print('--Further testing')
 #
@@ -281,7 +384,7 @@ phase_maps_rec = [pm(mag_data_rec) for pm in phasemappers]
 #K = np.asmatrix(K)
 #lam = 10. ** -10
 #KTK = K.T * K + lam * np.asmatrix(np.eye(81))
-#print lam, 
+#print lam,
 ##print pylab.cond(KTK),
 #x_f = KTK.I * K.T * y
 #print (np.asarray(K * x_f - y) ** 2).sum(),

tests/test_optimize.py → tests/test_reconstruction.py

@@ -5,10 +5,10 @@
 import os
 import unittest
 
-import pyramid.reconstructor as rc
+import pyramid.reconstruction as rc
 
 
-class TestCaseReconstructor(unittest.TestCase):
+class TestCaseReconstruction(unittest.TestCase):
 
     def setUp(self):
         self.path = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'test_phasemapper')
@@ -21,5 +21,5 @@ class TestCaseReconstructor(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseReconstructor)
+    suite = unittest.TestLoader().loadTestsFromTestCase(TestCaseReconstruction)
     unittest.TextTestRunner(verbosity=2).run(suite)