From de58b03c8d3ea1db40e3a3ea377205d68b7f5efa Mon Sep 17 00:00:00 2001
From: Jan Caron <j.caron@fz-juelich.de>
Date: Mon, 1 Sep 2014 14:32:15 +0200
Subject: [PATCH] Quality of life improvements, docstrings, and new gui-based
method! Many Doctring corrections, all plots now have a "show" parameter to
not show a plot at the end of the method (needed for guis and such). magdata:
quiver_plot: axis switch for x-projection, implemented logarithmic
arrows and scaling feature. projector: added to_mag_data() method to directly
produce a projected magnetization distribution. gui/create_logo:
removed (obsolete and unuseful). gui/mag_slicer: added!
---
pyramid/costfunction.py | 10 +-
pyramid/magdata.py | 84 ++++++---
pyramid/phasemap.py | 44 +++--
pyramid/projector.py | 22 +++
pyramid/reconstruction.py | 8 +-
pyramid/regularisator.py | 8 +-
.../vtk_conversion_nanowire_full.py | 60 +++++--
scripts/collaborations/zi_an.py | 72 ++++----
.../create_core_shell_disc.py | 9 +-
.../create_core_shell_sphere.py | 7 +-
scripts/create distributions/create_sample.py | 12 +-
scripts/create distributions/create_vortex.py | 6 +-
scripts/gui/create_logo.py | 70 --------
scripts/gui/create_logo.ui | 102 -----------
scripts/gui/gui_create_logo.py | 124 --------------
scripts/gui/mag_slicer.py | 160 ++++++++++++++++++
scripts/gui/mag_slicer.ui | 136 +++++++++++++++
.../reconstruct_random_pixels.py | 2 +-
18 files changed, 527 insertions(+), 409 deletions(-)
delete mode 100644 scripts/gui/create_logo.py
delete mode 100644 scripts/gui/create_logo.ui
delete mode 100644 scripts/gui/gui_create_logo.py
create mode 100644 scripts/gui/mag_slicer.py
create mode 100644 scripts/gui/mag_slicer.ui
diff --git a/pyramid/costfunction.py b/pyramid/costfunction.py
index 940df35..a18cc4e 100644
--- a/pyramid/costfunction.py
+++ b/pyramid/costfunction.py
@@ -14,7 +14,6 @@ import logging
class Costfunction(object):
- # TODO: Docstrings!
'''Class for calculating the cost of a 3D magnetic distributions in relation to 2D phase maps.
Represents a strategy for the calculation of the `cost` of a 3D magnetic distribution in
@@ -31,8 +30,13 @@ class Costfunction(object):
fwd_model : :class:`~.ForwardModel`
The Forward model instance which should be used for the simulation of the phase maps which
will be compared to `y`.
- lam : float, optional
- Regularization parameter used in the Hessian matrix multiplication. Default is 0.
+ Se_inv : :class:`~numpy.ndarray` (N=2), optional
+ Inverted covariance matrix of the measurement errors. The matrix has size `NxN` with N
+ being the length of the targetvector y (vectorized phase map information). Defaults to
+ an appropriate unity matrix if none is provided.
+ regularisator : :class:`~.Regularisator`, optional
+ Regularisator class that's responsible for the regularisation term. Defaults to zero
+ order Tikhonov if none is provided.
'''
diff --git a/pyramid/magdata.py b/pyramid/magdata.py
index df365f9..23c931e 100644
--- a/pyramid/magdata.py
+++ b/pyramid/magdata.py
@@ -406,8 +406,8 @@ class MagData(object):
mag_file.close()
return MagData(a, magnitude)
- def quiver_plot(self, title='Magnetization Distribution', filename=None, axis=None,
- proj_axis='z', ax_slice=None):
+ def quiver_plot(self, title='Magnetization Distribution', axis=None, proj_axis='z',
+ ax_slice=None, log=False, scaled=True, show=True):
'''Plot a slice of the magnetization as a quiver plot.
Parameters
@@ -416,15 +416,17 @@ class MagData(object):
The title for the plot.
axis : :class:`~matplotlib.axes.AxesSubplot`, optional
Axis on which the graph is plotted. Creates a new figure if none is specified.
- filename : string, optional
- The filename, specifying the location where the image is saved. If not specified,
- the image is shown instead.
proj_axis : {'z', 'y', 'x'}, optional
The axis, from which a slice is plotted. The default is 'z'.
ax_slice : int, optional
The slice-index of the axis specified in `proj_axis`. Is set to the center of
`proj_axis` if not specified.
-
+ log : boolean, optional
+ Takes the Default is False.
+ scaled : boolean, optional
+ Normalizes the plotted arrows in respect to the highest one. Default is True.
+ show: bool, optional
+ A switch which determines if the plot is shown at the end of plotting. Default is True.
Returns
-------
axis: :class:`~matplotlib.axes.AxesSubplot`
@@ -438,45 +440,62 @@ class MagData(object):
self.LOG.debug('proj_axis == z')
if ax_slice is None:
self.LOG.debug('ax_slice is None')
- ax_slice = int(self.dim[0]/2)
- mag_slice_u = self.magnitude[0][ax_slice, ...] # x-component
- mag_slice_v = self.magnitude[1][ax_slice, ...] # y-component
+ ax_slice = int(self.dim[0]/2.)
+ plot_u = np.copy(self.magnitude[0][ax_slice, ...]) # x-component
+ plot_v = np.copy(self.magnitude[1][ax_slice, ...]) # y-component
u_label = 'x [px]'
v_label = 'y [px]'
elif proj_axis == 'y': # Slice of the xz-plane with y = ax_slice
self.LOG.debug('proj_axis == y')
if ax_slice is None:
self.LOG.debug('ax_slice is None')
- ax_slice = int(self.dim[1]/2)
- mag_slice_u = self.magnitude[0][:, ax_slice, :] # x-component
- mag_slice_v = self.magnitude[2][:, ax_slice, :] # z-component
+ ax_slice = int(self.dim[1]/2.)
+ plot_u = np.copy(self.magnitude[0][:, ax_slice, :]) # x-component
+ plot_v = np.copy(self.magnitude[2][:, ax_slice, :]) # z-component
u_label = 'x [px]'
v_label = 'z [px]'
elif proj_axis == 'x': # Slice of the yz-plane with x = ax_slice
self.LOG.debug('proj_axis == x')
if ax_slice is None:
self.LOG.debug('ax_slice is None')
- ax_slice = int(self.dim[2]/2)
- mag_slice_u = self.magnitude[1][..., ax_slice] # y-component
- mag_slice_v = self.magnitude[2][..., ax_slice] # z-component
- u_label = 'y [px]'
- v_label = 'z [px]'
+ ax_slice = int(self.dim[2]/2.)
+ plot_u = np.swapaxes(np.copy(self.magnitude[2][..., ax_slice]), 0, 1) # z-component
+ plot_v = np.swapaxes(np.copy(self.magnitude[1][..., ax_slice]), 0, 1) # y-component
+ u_label = 'z [px]'
+ v_label = 'y [px]'
# If no axis is specified, a new figure is created:
if axis is None:
self.LOG.debug('axis is None')
fig = plt.figure(figsize=(8.5, 7))
- axis = fig.add_subplot(1, 1, 1, aspect='equal')
- axis.quiver(mag_slice_u, mag_slice_v, pivot='middle', angles='xy', scale_units='xy',
- scale=1, headwidth=6, headlength=7)
- axis.set_xlim(-1, np.shape(mag_slice_u)[1])
- axis.set_ylim(-1, np.shape(mag_slice_u)[0])
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_aspect('equal')
+ angles = np.angle(plot_u+1j*plot_v, deg=True)
+ # Take the logarithm of the arrows to clearly show directions (if specified):
+ if log:
+ cutoff = 10
+ amp = np.round(np.hypot(plot_u, plot_v), decimals=cutoff)
+ min_value = amp[np.nonzero(amp)].min()
+ plot_u = np.round(plot_u, decimals=cutoff) / min_value
+ plot_u = np.log10(np.abs(plot_u)+1) * np.sign(plot_u)
+ plot_v = np.round(plot_v, decimals=cutoff) / min_value
+ plot_v = np.log10(np.abs(plot_v)+1) * np.sign(plot_v)
+ # Scale the magnitude of the arrows to the highest one (if specified):
+ if scaled:
+ plot_u /= np.hypot(plot_u, plot_v).max()
+ plot_v /= np.hypot(plot_u, plot_v).max()
+ axis.quiver(plot_u, plot_v, pivot='middle', units='xy', angles=angles,
+ scale_units='xy', scale=1, headwidth=6, headlength=7)
+ axis.set_xlim(-1, np.shape(plot_u)[1])
+ axis.set_ylim(-1, np.shape(plot_u)[0])
axis.set_title(title, fontsize=18)
axis.set_xlabel(u_label, fontsize=15)
axis.set_ylabel(v_label, fontsize=15)
axis.tick_params(axis='both', which='major', labelsize=14)
axis.xaxis.set_major_locator(MaxNLocator(nbins=9, integer=True))
axis.yaxis.set_major_locator(MaxNLocator(nbins=9, integer=True))
- plt.show()
+ # Show Plot:
+ if show:
+ plt.show()
return axis
def quiver_plot3d(self, title='Magnetization Distribution'):
@@ -514,9 +533,18 @@ class MagData(object):
mlab.colorbar(None, orientation='vertical')
def save_to_x3d(self, filename='..\..\output\magdata_output.x3d', maximum=1):
- # TODO: Docstring!
- self.LOG.debug('Calling save_to_x3d')
+ '''Output the magnetization in the .x3d format for the Fraunhofer InstantReality Player.
+
+ Parameters
+ ----------
+ None
+ Returns
+ -------
+ None
+
+ '''
+ self.LOG.debug('Calling save_to_x3d')
dim = self.dim
# Create points and vector components as lists:
zz, yy, xx = np.mgrid[0.5:(dim[0]-0.5):dim[0]*1j,
@@ -528,14 +556,14 @@ class MagData(object):
x_mag = np.reshape(self.magnitude[0], (-1))
y_mag = np.reshape(self.magnitude[1], (-1))
z_mag = np.reshape(self.magnitude[2], (-1))
-
+ # Load template, load tree and write viewpoint information:
template = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'template.x3d')
parser = etree.XMLParser(remove_blank_text=True)
tree = etree.parse(template, parser)
scene = tree.find('Scene')
etree.SubElement(scene, 'Viewpoint', position='0 0 {}'.format(1.5*dim[0]),
fieldOfView='1')
-
+ # Write each "spin"-tag separately:
for i in range(np.prod(dim)):
mag = np.sqrt(x_mag[i]**2+y_mag[i]**2+z_mag[i]**2)
if mag != 0:
@@ -562,5 +590,5 @@ class MagData(object):
value='{} {} {}'.format(*spin_color))
etree.SubElement(spin, 'fieldValue', name='spin_scale',
value='{} {} {}'.format(*spin_scale))
-
+ # Write the tree into the file in pretty print format:
tree.write(filename, pretty_print=True)
diff --git a/pyramid/phasemap.py b/pyramid/phasemap.py
index 061ade2..9dd4add 100644
--- a/pyramid/phasemap.py
+++ b/pyramid/phasemap.py
@@ -332,7 +332,8 @@ class PhaseMap(object):
# If no axis is specified, a new figure is created:
if axis is None:
fig = plt.figure(figsize=(8.5, 7))
- axis = fig.add_subplot(1, 1, 1, aspect='equal')
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_aspect('equal')
# Plot the phasemap:
im = axis.pcolormesh(phase, cmap=cmap, vmin=-limit, vmax=limit, norm=norm)
# Set the axes ticks and labels:
@@ -344,8 +345,8 @@ class PhaseMap(object):
axis.yaxis.set_major_formatter(FuncFormatter(lambda x, pos: '{:g}'.format(x*self.a)))
axis.tick_params(axis='both', which='major', labelsize=14)
axis.set_title(title, fontsize=18)
- axis.set_xlabel('x [nm]', fontsize=15)
- axis.set_ylabel('y [nm]', fontsize=15)
+ axis.set_xlabel('u-axis [nm]', fontsize=15)
+ axis.set_ylabel('v-axis [nm]', fontsize=15)
# Add colorbar:
fig = plt.gcf()
fig.subplots_adjust(right=0.8)
@@ -359,7 +360,7 @@ class PhaseMap(object):
# Return plotting axis:
return axis
- def display_phase3d(self, title='Phase Map', cmap='RdBu'):
+ def display_phase3d(self, title='Phase Map', cmap='RdBu', show=True):
'''Display the phasemap as a 3-D surface with contourplots.
Parameters
@@ -369,6 +370,8 @@ class PhaseMap(object):
cmap : string, optional
The :class:`~matplotlib.colors.Colormap` which is used for the plot as a string.
The default is 'RdBu'.
+ show: bool, optional
+ A switch which determines if the plot is shown at the end of plotting. Default is True.
Returns
-------
@@ -390,11 +393,12 @@ class PhaseMap(object):
linewidth=0, antialiased=False)
axis.contourf(uu, vv, phase, 15, zdir='z', offset=np.min(phase), cmap=cmap)
axis.view_init(45, -135)
- axis.set_xlabel('x-axis [px]')
- axis.set_ylabel('y-axis [px]')
+ axis.set_xlabel('u-axis [px]')
+ axis.set_ylabel('v-axis [px]')
axis.set_zlabel('phase shift [{}]'.format(self.unit))
# Show Plot:
- plt.show()
+ if show:
+ plt.show()
# Return plotting axis:
return axis
@@ -418,7 +422,7 @@ class PhaseMap(object):
interpolation : {'none, 'bilinear', 'cubic', 'nearest'}, optional
Defines the interpolation method. No interpolation is used in the default case.
show: bool, optional
- A switch which determines if the plot is shown at the end of plotting.
+ A switch which determines if the plot is shown at the end of plotting. Default is True.
Returns
-------
@@ -459,15 +463,16 @@ class PhaseMap(object):
# If no axis is specified, a new figure is created:
if axis is None:
fig = plt.figure()
- axis = fig.add_subplot(1, 1, 1, aspect='equal')
+ axis = fig.add_subplot(1, 1, 1)
+ axis.set_aspect('equal')
# Plot the image and set axes:
axis.imshow(holo_image, origin='lower', interpolation=interpolation)
# Set the title and the axes labels:
axis.set_title(title)
plt.tick_params(axis='both', which='major', labelsize=14)
axis.set_title(title, fontsize=18)
- axis.set_xlabel('x-axis [px]', fontsize=15)
- axis.set_ylabel('y-axis [px]', fontsize=15)
+ axis.set_xlabel('u-axis [px]', fontsize=15)
+ axis.set_ylabel('v-axis [px]', fontsize=15)
axis.set_xlim(0, self.dim_uv[1])
axis.set_ylim(0, self.dim_uv[0])
axis.xaxis.set_major_locator(MaxNLocator(nbins=9, integer=True))
@@ -479,7 +484,7 @@ class PhaseMap(object):
return axis
def display_combined(self, title='Combined Plot', cmap='RdBu', limit=None, norm=None,
- density=1, interpolation='none', grad_encode='bright'):
+ density=1, interpolation='none', grad_encode='bright', show=True):
'''Display the phase map and the resulting color coded holography image in one plot.
Parameters
@@ -506,6 +511,8 @@ class PhaseMap(object):
encodes the direction (without gradient strength), 'dark' modulates the gradient
strength with a factor between 0 and 1 and 'bright' (which is the default) encodes
the gradient strength with color saturation.
+ show: bool, optional
+ A switch which determines if the plot is shown at the end of plotting. Default is True.
Returns
-------
@@ -525,17 +532,20 @@ class PhaseMap(object):
phase_axis = fig.add_subplot(1, 2, 2, aspect='equal')
fig.subplots_adjust(right=0.85)
self.display_phase(cmap='RdBu', limit=limit, norm=norm, axis=phase_axis, show=False)
- plt.show()
+ # Show Plot:
+ if show:
+ plt.show()
# Return the plotting axes:
return phase_axis, holo_axis
@classmethod
- def make_color_wheel(cls):
+ def make_color_wheel(cls, show=True):
'''Display a color wheel to illustrate the color coding of the gradient direction.
Parameters
----------
- None
+ show: bool, optional
+ A switch which determines if the plot is shown at the end of plotting. Default is True.
Returns
-------
@@ -561,4 +571,6 @@ class PhaseMap(object):
axis.imshow(color_wheel, origin='lower')
axis.xaxis.set_major_locator(NullLocator())
axis.yaxis.set_major_locator(NullLocator())
- plt.show()
+ # Show Plot:
+ if show:
+ plt.show()
diff --git a/pyramid/projector.py b/pyramid/projector.py
index 56d0a75..c18088d 100644
--- a/pyramid/projector.py
+++ b/pyramid/projector.py
@@ -12,6 +12,8 @@ import itertools
from scipy.sparse import coo_matrix, csr_matrix
+from pyramid.magdata import MagData
+
import logging
@@ -188,6 +190,26 @@ class Projector(object):
raise AssertionError('Vector size has to be suited either for '
'vector- or scalar-field-projection!')
+ def to_mag_data(self, mag_data):
+ self.LOG.debug('Calling to_mag_data')
+ '''Project a :class:`~.MagData` object and output another :class:`~.MagData` object.
+
+ Parameters
+ ----------
+ mag_data : :class:`~.MagData`
+ :class:`~.MagData` object that should be projected.
+
+ Returns
+ -------
+ mag_data_result : :class:`~.MagData`
+ :class:`~.MagData` object containing the projected magnetization distribution from
+ the input.
+
+ '''
+ mag_proj = self(mag_data.mag_vec).reshape((2,)+self.dim_uv)
+ magnitude = np.expand_dims(np.concatenate((mag_proj, np.zeros((1,)+self.dim_uv))), axis=1)
+ return MagData(mag_data.a, magnitude)
+
class XTiltProjector(Projector):
diff --git a/pyramid/reconstruction.py b/pyramid/reconstruction.py
index 22fd35b..f9b6bee 100644
--- a/pyramid/reconstruction.py
+++ b/pyramid/reconstruction.py
@@ -84,7 +84,6 @@ class PrintIterator(object):
def optimize_sparse_cg(data, Se_inv=None, regularisator=None, verbosity=0):
- # TODO: Docstring!
'''Reconstruct a three-dimensional magnetic distribution from given phase maps via the
conjugate gradient optimizaion method :func:`~.scipy.sparse.linalg.cg`.
@@ -94,6 +93,13 @@ def optimize_sparse_cg(data, Se_inv=None, regularisator=None, verbosity=0):
:class:`~.DataSet` object containing all phase maps in :class:`~.PhaseMap` objects and all
projection directions in :class:`~.Projector` objects. These provide the essential
information for the reconstruction.
+ Se_inv : :class:`~numpy.ndarray` (N=2), optional
+ Inverted covariance matrix of the measurement errors. The matrix has size `NxN` with N
+ being the length of the targetvector y (vectorized phase map information). Defaults to
+ an appropriate unity matrix if none is provided.
+ regularisator : :class:`~.Regularisator`, optional
+ Regularisator class that's responsible for the regularisation term. Defaults to zero
+ order Tikhonov if none is provided.
verbosity : {0, 1, 2}, optional
Parameter defining the verposity of the output. `2` will show the current number of the
iteration and the cost of the current distribution. `1` will just show the iteration
diff --git a/pyramid/regularisator.py b/pyramid/regularisator.py
index 5ade7c6..c3b680f 100644
--- a/pyramid/regularisator.py
+++ b/pyramid/regularisator.py
@@ -28,17 +28,17 @@ class Regularisator(object):
LOG = logging.getLogger(__name__+'.Regularisator')
@abc.abstractmethod
- def __init__(self, Sa_inv, x_a=None):
+ def __init__(self, Sa_sqrt_inv, x_a=None):
self.LOG.debug('Calling __init__')
- self.Sa_inv = Sa_inv
+ self.Sa_sqrt_inv = Sa_sqrt_inv
if x_a is None:
- x_a = np.zeros(np.shape(Sa_inv)[1])
+ x_a = np.zeros(np.shape(Sa_sqrt_inv)[1])
self.x_a = x_a
self.LOG.debug('Created '+str(self))
def __call__(self, x, x_a=None):
self.LOG.debug('Calling __call__')
- return (x-self.x_a).dot(self.Sa_inv.dot(x-self.x_a))
+ return (x-self.x_a).dot(self.Sa_sqrt_inv.dot(x-self.x_a))
def __repr__(self):
self.LOG.debug('Calling __repr__')
diff --git a/scripts/collaborations/vtk_conversion_nanowire_full.py b/scripts/collaborations/vtk_conversion_nanowire_full.py
index a0f52f9..697e6bc 100644
--- a/scripts/collaborations/vtk_conversion_nanowire_full.py
+++ b/scripts/collaborations/vtk_conversion_nanowire_full.py
@@ -16,7 +16,7 @@ from tqdm import tqdm
import pyramid
from pyramid.magdata import MagData
-from pyramid.projector import SimpleProjector, YTiltProjector, XTiltProjector
+from pyramid.projector import YTiltProjector, XTiltProjector
from pyramid.phasemapper import PMConvolve
from pyramid.phasemap import PhaseMap
from pyramid.dataset import DataSet
@@ -151,16 +151,48 @@ for i, figure in enumerate(figures):
plt.close('all')
###################################################################################################
# Close ups:
-dim_uv = (600, 200)
-mag_data_tip = MagData(mag_data.a, mag_data.magnitude[:, 600:, ...])
-pm = PMConvolve(mag_data.a, SimpleProjector(mag_data_tip.dim, 'y', dim_uv))
-phase_map_tip = PhaseMap(mag_data.a, pm(mag_data_tip).phase[350:, :])
-phase_map_tip.display_combined('Phase Map Nanowire Tip', density=density,
- interpolation='bilinear')
-plt.savefig(PATH+'_nanowire_tip.png')
-mag_data_bot = MagData(mag_data.a, mag_data.magnitude[:, :300, ...])
-pm = PMConvolve(mag_data.a, SimpleProjector(mag_data_bot.dim, 'y', dim_uv))
-phase_map_tip = PhaseMap(mag_data.a, pm(mag_data_bot).phase[:250, :])
-phase_map_tip.display_combined('Phase Map Nanowire Bottom', density=density,
- interpolation='bilinear')
-plt.savefig(PATH+'_nanowire_bot.png')
+dim = (300, 72, 72)
+dim_uv = (600, 150)
+angles = [0, 20, 40, 60, -20, -40, -60]
+for angle in angles:
+ angle_rad = angle * np.pi/180
+ shift = int(np.abs(80*np.sin(angle_rad)))
+ projector = XTiltProjector(dim, np.pi/2+angle_rad, dim_uv)
+ projector_scaled = XTiltProjector((dim[0]/2, dim[1]/2, dim[2]/2), np.pi/2+angle_rad,
+ (dim_uv[0]/2, dim_uv[1]/2))
+ # Tip:
+ mag_data_tip = MagData(mag_data.a, mag_data.magnitude[:, 608:, ...])
+ pm = PMConvolve(mag_data.a, projector)
+ phase_map_tip = PhaseMap(mag_data.a, pm(mag_data_tip).phase[350-shift:530-shift, :])
+ phase_map_tip.display_combined('Phase Map Nanowire Tip', density=density,
+ interpolation='bilinear')
+ plt.savefig(PATH+'_nanowire_tip_xtilt_{}.png'.format(angle))
+ mag_data_tip.scale_down()
+ mag_proj_tip = projector_scaled.to_mag_data(mag_data_tip)
+ axis = mag_proj_tip.quiver_plot()
+ axis.set_xlim(17, 55)
+ axis.set_ylim(180-shift/2, 240-shift/2)
+ plt.savefig(PATH+'_nanowire_tip_mag_xtilt_{}.png'.format(angle))
+ axis = mag_proj_tip.quiver_plot(log=True)
+ axis.set_xlim(17, 55)
+ axis.set_ylim(180-shift/2, 240-shift/2)
+ plt.savefig(PATH+'_nanowire_tip_mag_log_xtilt_{}.png'.format(angle))
+ # Bottom:
+ mag_data_bot = MagData(mag_data.a, mag_data.magnitude[:, :300, ...])
+ pm = PMConvolve(mag_data.a, projector)
+ phase_map_tip = PhaseMap(mag_data.a, pm(mag_data_bot).phase[50+shift:225+shift, :])
+ phase_map_tip.display_combined('Phase Map Nanowire Bottom', density=density,
+ interpolation='bilinear')
+ plt.savefig(PATH+'_nanowire_bot_xtilt_{}.png'.format(angle))
+ mag_data_bot.scale_down()
+ mag_proj_bot = projector_scaled.to_mag_data(mag_data_bot)
+ axis = mag_proj_bot.quiver_plot()
+ axis.set_xlim(17, 55)
+ axis.set_ylim(50+shift/2, 110+shift/2)
+ plt.savefig(PATH+'_nanowire_bot_mag_xtilt_{}.png'.format(angle))
+ axis = mag_proj_bot.quiver_plot(log=True)
+ axis.set_xlim(17, 55)
+ axis.set_ylim(50+shift/2, 110+shift/2)
+ plt.savefig(PATH+'_nanowire_bot_mag_log_xtilt_{}.png'.format(angle))
+ # Close plots:
+ plt.close('all')
diff --git a/scripts/collaborations/zi_an.py b/scripts/collaborations/zi_an.py
index 3d9b03e..d4a44a7 100644
--- a/scripts/collaborations/zi_an.py
+++ b/scripts/collaborations/zi_an.py
@@ -30,7 +30,6 @@ LOGGING_CONF = os.path.join(os.path.dirname(os.path.realpath(pyramid.__file__)),
logging.config.fileConfig(LOGGING_CONF, disable_existing_loggers=False)
###################################################################################################
-PATH = '../../output/zi-an/'
threshold = 1
a = 1.0 # in nm
density = 5
@@ -38,30 +37,33 @@ b_0 = 1
inter = 'none'
dim_small = (64, 64)
smoothed_pictures = True
-lam = 7.5E-5
+lam = 1E-4
order = 1
+log = True
+PATH = '../../output/zi-an/'
+if not os.path.exists(PATH+'%.0e/'%lam):
+ os.makedirs(PATH+'%.0e/'%lam)
###################################################################################################
-
# Read in files:
if smoothed_pictures:
- dm3_2_mag = dm3.DM3(PATH+'Output333_hw512.dm3').image
- dm3_4_mag = dm3.DM3(PATH+'Output334_hw512.dm3').image
- dm3_2_ele = dm3.DM3(PATH+'Output335.dm3').image
- dm3_4_ele = dm3.DM3(PATH+'Output336.dm3').image
+ dm3_2_mag = dm3.DM3(PATH+'Output334_hw512.dm3').image
+ dm3_4_mag = dm3.DM3(PATH+'Output333_hw512.dm3').image
+ dm3_2_ele = dm3.DM3(PATH+'Output336.dm3').image
+ dm3_4_ele = dm3.DM3(PATH+'Output335.dm3').image
else:
- dm3_2_mag = dm3.DM3(PATH+'07_0102mag60_q3_pha_01_sb280_sc512_vf3_med5.dm3').image
- dm3_4_mag = dm3.DM3(PATH+'18a_0102mag_ub140_62k_q3_pha_01_sb180_sc512_vf3_med5.dm3').image
- dm3_2_ele = dm3.DM3(PATH+'07_0102ele60_q3_pha_01_sb280_sc512_vf3_med5.dm3').image
- dm3_4_ele = dm3.DM3(PATH+'18a_0102ele_ub140_62k_q3_pha_01_sb180_sc512_vf3_med5.dm3').image
+ dm3_2_mag = dm3.DM3(PATH+'18a_0102mag_ub140_62k_q3_pha_01_sb180_sc512_vf3_med5.dm3').image
+ dm3_4_mag = dm3.DM3(PATH+'07_0102mag60_q3_pha_01_sb280_sc512_vf3_med5.dm3').image
+ dm3_2_ele = dm3.DM3(PATH+'18a_0102ele_ub140_62k_q3_pha_01_sb180_sc512_vf3_med5.dm3').image
+ dm3_4_ele = dm3.DM3(PATH+'07_0102ele60_q3_pha_01_sb280_sc512_vf3_med5.dm3').image
# Construct phase maps and masks
-phase_map_2 = PhaseMap(a, np.array(dm3_2_mag.resize(dim_small))+0.101)
+phase_map_2 = PhaseMap(a, np.array(dm3_2_mag.resize(dim_small))-2.546)
phase_map_2.display_combined(density=density, interpolation=inter)
-plt.savefig(PATH+'phase_map_2part.png')
+plt.savefig(PATH+'%.0e/phase_map_2part.png'%lam)
mask_2 = np.expand_dims(np.where(np.array(dm3_2_ele.resize(dim_small)) >= threshold,
True, False), axis=0)
-phase_map_4 = PhaseMap(a, np.array(dm3_4_mag.resize(dim_small))-2.546)
+phase_map_4 = PhaseMap(a, np.array(dm3_4_mag.resize(dim_small))+0.101)
phase_map_4.display_combined(density=density, interpolation=inter)
-plt.savefig(PATH+'phase_map_4part.png')
+plt.savefig(PATH+'%.0e/phase_map_4part.png'%lam)
mask_4 = np.expand_dims(np.where(np.array(dm3_4_ele.resize(dim_small)) >= threshold,
True, False), axis=0)
# Reconstruct the magnetic distribution:
@@ -74,39 +76,51 @@ print '4 particle reconstruction time:', clock() - tic
# Display the reconstructed phase map and holography image:
phase_map_rec_2 = PMConvolve(a, SimpleProjector(mag_data_rec_2.dim), b_0)(mag_data_rec_2)
phase_map_rec_2.display_combined('Reconstr. Distribution', density=density, interpolation=inter)
-plt.savefig(PATH+'phase_map_2part_rec.png')
+plt.savefig(PATH+'%.0e/phase_map_2part_rec.png'%lam)
phase_map_rec_4 = PMConvolve(a, SimpleProjector(mag_data_rec_4.dim), b_0)(mag_data_rec_4)
phase_map_rec_4.display_combined('Reconstr. Distribution', density=density, interpolation=inter)
-plt.savefig(PATH+'phase_map_4part_rec.png')
+plt.savefig(PATH+'%.0e/phase_map_4part_rec.png'%lam)
# Plot the magnetization:
axis = (mag_data_rec_2*(1/mag_data_rec_2.magnitude.max())).quiver_plot()
-#axis.set_xlim(20, 45)
-#axis.set_ylim(20, 45)
-plt.savefig(PATH+'mag_data_2part.png')
+axis.set_xlim(20, 45)
+axis.set_ylim(20, 45)
+plt.savefig(PATH+'%.0e/mag_data_2part.png'%lam)
axis = (mag_data_rec_4*(1/mag_data_rec_4.magnitude.max())).quiver_plot()
-#axis.set_xlim(20, 45)
-#axis.set_ylim(20, 45)
-plt.savefig(PATH+'mag_data_4part.png')
+axis.set_xlim(20, 45)
+axis.set_ylim(20, 45)
+plt.savefig(PATH+'%.0e/mag_data_4part.png'%lam)
# Display the Phase:
phase_diff_2 = phase_map_rec_2-phase_map_2
phase_diff_2.display_phase('Difference')
-plt.savefig(PATH+'phase_map_2part_diff.png')
+plt.savefig(PATH+'%.0e/phase_map_2part_diff.png'%lam)
phase_diff_4 = phase_map_rec_4-phase_map_4
phase_diff_4.display_phase('Difference')
-plt.savefig(PATH+'phase_map_4part_diff.png')
+plt.savefig(PATH+'%.0e/phase_map_4part_diff.png'%lam)
# Get the average difference from the experimental results:
print 'Average difference (2 cubes):', np.average(phase_diff_2.phase)
print 'Average difference (4 cubes):', np.average(phase_diff_4.phase)
# Plot holographic contour maps with overlayed magnetic distributions:
axis = phase_map_rec_2.display_holo('Magnetization Overlay', density=0.1, interpolation=inter)
-(mag_data_rec_2*(1/mag_data_rec_2.magnitude.max())).quiver_plot(axis=axis)
+mag_data_rec_2.quiver_plot(axis=axis)
+axis = plt.gca()
+axis.set_xlim(20, 45)
+axis.set_ylim(20, 45)
+plt.savefig(PATH+'%.0e/phase_map_2part_holo.png'%lam)
+axis = phase_map_rec_4.display_holo('Magnetization Overlay', density=0.1, interpolation=inter)
+mag_data_rec_4.quiver_plot(axis=axis)
+axis = plt.gca()
+axis.set_xlim(20, 45)
+axis.set_ylim(20, 45)
+plt.savefig(PATH+'%.0e/phase_map_4part_holo.png'%lam)
+axis = phase_map_rec_2.display_holo('Magnetization Overlay', density=0.1, interpolation=inter)
+mag_data_rec_2.quiver_plot(axis=axis, log=log)
axis = plt.gca()
axis.set_xlim(20, 45)
axis.set_ylim(20, 45)
-plt.savefig(PATH+'phase_map_2part_holo.png')
+plt.savefig(PATH+'%.0e/phase_map_2part_holo_log.png'%lam)
axis = phase_map_rec_4.display_holo('Magnetization Overlay', density=0.1, interpolation=inter)
-(mag_data_rec_4*(1/mag_data_rec_4.magnitude.max())).quiver_plot(axis=axis)
+mag_data_rec_4.quiver_plot(axis=axis, log=log)
axis = plt.gca()
axis.set_xlim(20, 45)
axis.set_ylim(20, 45)
-plt.savefig(PATH+'phase_map_4part_holo.png')
+plt.savefig(PATH+'%.0e/phase_map_4part_holo_log.png'%lam)
diff --git a/scripts/create distributions/create_core_shell_disc.py b/scripts/create distributions/create_core_shell_disc.py
index 920b4e5..930a40e 100644
--- a/scripts/create distributions/create_core_shell_disc.py
+++ b/scripts/create distributions/create_core_shell_disc.py
@@ -29,7 +29,6 @@ if not os.path.exists(directory):
# Input parameters:
filename = directory + '/mag_dist_core_shell_disc.txt'
a = 1.0 # in nm
-density = 1
dim = (32, 32, 32)
center = (dim[0]/2-0.5, int(dim[1]/2)-0.5, int(dim[2]/2)-0.5)
radius_core = dim[1]/8
@@ -42,13 +41,13 @@ mag_shape_shell = np.logical_xor(mag_shape_outer, mag_shape_core)
mag_data = MagData(a, mc.create_mag_dist_vortex(mag_shape_shell, magnitude=0.75))
mag_data += MagData(a, mc.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
mag_data.quiver_plot('z-projection', proj_axis='z')
-mag_data.quiver_plot('x-projection', proj_axis='x')
-mag_data.quiver_plot3d()
+mag_data.quiver_plot('y-projection', proj_axis='y')
mag_data.save_to_llg(filename)
+mag_data.quiver_plot3d()
phase_map_z = PMConvolve(a, SimpleProjector(dim, axis='z'))(mag_data)
phase_map_x = PMConvolve(a, SimpleProjector(dim, axis='x'))(mag_data)
-phase_map_z.display_holo(density, 'Core-Shell structure (z-proj.)')
-phase_axis, holo_axis = phase_map_x.display_combined(density, 'Core-Shell structure (x-proj.)')
+phase_map_z.display_holo('Core-Shell structure (z-proj.)', density=1E2)
+phase_axis, holo_axis = phase_map_x.display_combined('Core-Shell structure (x-proj.)', density=1E3)
phase_axis.set_xlabel('y [nm]')
phase_axis.set_ylabel('z [nm]')
holo_axis.set_xlabel('y-axis [px]')
diff --git a/scripts/create distributions/create_core_shell_sphere.py b/scripts/create distributions/create_core_shell_sphere.py
index d2dbe8a..d6033cc 100644
--- a/scripts/create distributions/create_core_shell_sphere.py
+++ b/scripts/create distributions/create_core_shell_sphere.py
@@ -29,7 +29,6 @@ if not os.path.exists(directory):
# Input parameters:
filename = directory + '/mag_dist_core_shell_sphere.txt'
a = 1.0 # in nm
-density = 500
dim = (32, 32, 32)
center = (dim[0]/2-0.5, int(dim[1]/2)-0.5, int(dim[2]/2)-0.5)
radius_core = dim[1]/8
@@ -43,12 +42,12 @@ mag_data = MagData(a, mc.create_mag_dist_vortex(mag_shape_shell, magnitude=0.75)
mag_data += MagData(a, mc.create_mag_dist_homog(mag_shape_core, phi=0, theta=0))
mag_data.quiver_plot('z-projection', proj_axis='z')
mag_data.quiver_plot('x-projection', proj_axis='x')
-mag_data.quiver_plot3d()
mag_data.save_to_llg(filename)
+mag_data.quiver_plot3d()
phase_map_z = PMConvolve(a, SimpleProjector(dim, axis='z'))(mag_data)
phase_map_x = PMConvolve(a, SimpleProjector(dim, axis='x'))(mag_data)
-phase_map_z.display_holo(density, 'Core-Shell structure (z-proj.)')
-phase_axis, holo_axis = phase_map_x.display_combined(density, 'Core-Shell structure (x-proj.)')
+phase_map_z.display_holo('Core-Shell structure (z-proj.)', density=1E2)
+phase_axis, holo_axis = phase_map_x.display_combined('Core-Shell structure (x-proj.)', density=1E3)
phase_axis.set_xlabel('y [nm]')
phase_axis.set_ylabel('z [nm]')
holo_axis.set_xlabel('y-axis [px]')
diff --git a/scripts/create distributions/create_sample.py b/scripts/create distributions/create_sample.py
index b69ad17..949d852 100644
--- a/scripts/create distributions/create_sample.py
+++ b/scripts/create distributions/create_sample.py
@@ -24,12 +24,12 @@ if not os.path.exists(directory):
os.makedirs(directory)
###################################################################################################
# Input parameters:
-key = 'sphere'
+key = 'slab'
###################################################################################################
filename = directory + '/mag_dist_' + key + '.txt'
-dim = (64, 64, 64) # in px (z, y, x)
+dim = (32, 32, 32) # in px (z, y, x)
a = 1.0 # in nm
-phi = pi/2
+phi = pi/4
# Geometry parameters:
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!
width = (dim[0]/2, dim[1]/2, dim[2]/2) # in px (z, y, x)
@@ -49,7 +49,7 @@ elif key == 'filament':
elif key == 'pixel':
mag_shape = mc.Shapes.pixel(dim, pixel)
# Create magnetic distribution
-magnitude = mc.create_mag_dist_homog(mag_shape, phi)
-mag_data = MagData(a, magnitude)
-mag_data.quiver_plot()
+mag_data = MagData(a, mc.create_mag_dist_homog(mag_shape, phi, magnitude=0.75))
mag_data.save_to_llg(filename)
+mag_data.quiver_plot()
+mag_data.quiver_plot3d()
diff --git a/scripts/create distributions/create_vortex.py b/scripts/create distributions/create_vortex.py
index cd70c5f..699832f 100644
--- a/scripts/create distributions/create_vortex.py
+++ b/scripts/create distributions/create_vortex.py
@@ -28,13 +28,14 @@ if not os.path.exists(directory):
filename = directory + '/mag_dist_vortex.txt'
a = 10.0 # in nm
# density = 1
-dim = (64, 64, 64)
+dim = (32, 32, 32)
center = (int(dim[0]/2)-0.5, int(dim[1]/2)-0.5, int(dim[2]/2)-0.5)
+print 'center', center
radius = 0.25 * dim[1]
height = dim[0]/4
# Create magnetic shape:
mag_shape = mc.Shapes.disc(dim, center, radius, height)
-mag_data = MagData(a, mc.create_mag_dist_vortex(mag_shape))
+mag_data = MagData(a, mc.create_mag_dist_vortex(mag_shape, magnitude=0.75))
mag_data.quiver_plot()
mag_data.save_to_llg(filename)
projector = SimpleProjector(dim)
@@ -44,3 +45,4 @@ phase_slice = phase_map.phase[dim[1]/2, :]
fig = plt.figure()
fig.add_subplot(111)
plt.plot(range(dim[1]), phase_slice)
+mag_data.quiver_plot3d()
diff --git a/scripts/gui/create_logo.py b/scripts/gui/create_logo.py
deleted file mode 100644
index b7269a2..0000000
--- a/scripts/gui/create_logo.py
+++ /dev/null
@@ -1,70 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Form implementation generated from reading ui file 'create_logo.ui'
-#
-# Created: Tue May 21 14:29:03 2013
-# by: PyQt4 UI code generator 4.9.5
-#
-# WARNING! All changes made in this file will be lost!
-
-
-from PyQt4 import QtCore, QtGui
-from matplotlibwidget import MatplotlibWidget
-
-
-try:
- _fromUtf8 = QtCore.QString.fromUtf8
-except AttributeError:
- _fromUtf8 = lambda s: s
-
-
-class Ui_CreateLogoWidget(object):
- def setupUi(self, CreateLogoWidget):
- CreateLogoWidget.setObjectName(_fromUtf8("CreateLogoWidget"))
- CreateLogoWidget.resize(520, 492)
- self.verticalLayout_2 = QtGui.QVBoxLayout(CreateLogoWidget)
- self.verticalLayout_2.setObjectName(_fromUtf8("verticalLayout_2"))
- self.verticalLayout = QtGui.QVBoxLayout()
- self.verticalLayout.setObjectName(_fromUtf8("verticalLayout"))
- self.horizontalLayout = QtGui.QHBoxLayout()
- self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
- self.xLabel = QtGui.QLabel(CreateLogoWidget)
- self.xLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
- self.xLabel.setObjectName(_fromUtf8("xLabel"))
- self.horizontalLayout.addWidget(self.xLabel)
- self.xSpinBox = QtGui.QSpinBox(CreateLogoWidget)
- self.xSpinBox.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
- self.xSpinBox.setMaximum(512)
- self.xSpinBox.setProperty("value", 128)
- self.xSpinBox.setObjectName(_fromUtf8("xSpinBox"))
- self.horizontalLayout.addWidget(self.xSpinBox)
- self.yLabel = QtGui.QLabel(CreateLogoWidget)
- self.yLabel.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
- self.yLabel.setObjectName(_fromUtf8("yLabel"))
- self.horizontalLayout.addWidget(self.yLabel)
- self.ySpinBox = QtGui.QSpinBox(CreateLogoWidget)
- self.ySpinBox.setAlignment(QtCore.Qt.AlignRight|QtCore.Qt.AlignTrailing|QtCore.Qt.AlignVCenter)
- self.ySpinBox.setMaximum(512)
- self.ySpinBox.setProperty("value", 128)
- self.ySpinBox.setObjectName(_fromUtf8("ySpinBox"))
- self.horizontalLayout.addWidget(self.ySpinBox)
- self.logoPushButton = QtGui.QPushButton(CreateLogoWidget)
- self.logoPushButton.setObjectName(_fromUtf8("logoPushButton"))
- self.horizontalLayout.addWidget(self.logoPushButton)
- self.verticalLayout.addLayout(self.horizontalLayout)
- self.verticalLayout_2.addLayout(self.verticalLayout)
- self.mplWidget = MatplotlibWidget(CreateLogoWidget)
- self.mplWidget.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
- self.mplWidget.setLayoutDirection(QtCore.Qt.LeftToRight)
- self.mplWidget.setAutoFillBackground(False)
- self.mplWidget.setObjectName(_fromUtf8("mplWidget"))
- self.verticalLayout_2.addWidget(self.mplWidget)
-
- self.retranslateUi(CreateLogoWidget)
- QtCore.QMetaObject.connectSlotsByName(CreateLogoWidget)
-
- def retranslateUi(self, CreateLogoWidget):
- CreateLogoWidget.setWindowTitle(QtGui.QApplication.translate("CreateLogoWidget", "Form", None, QtGui.QApplication.UnicodeUTF8))
- self.xLabel.setText(QtGui.QApplication.translate("CreateLogoWidget", "X [px] :", None, QtGui.QApplication.UnicodeUTF8))
- self.yLabel.setText(QtGui.QApplication.translate("CreateLogoWidget", "Y [px] :", None, QtGui.QApplication.UnicodeUTF8))
- self.logoPushButton.setText(QtGui.QApplication.translate("CreateLogoWidget", "Create Logo", None, QtGui.QApplication.UnicodeUTF8))
diff --git a/scripts/gui/create_logo.ui b/scripts/gui/create_logo.ui
deleted file mode 100644
index e785b90..0000000
--- a/scripts/gui/create_logo.ui
+++ /dev/null
@@ -1,102 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>CreateLogoWidget</class>
- <widget class="QWidget" name="CreateLogoWidget">
- <property name="geometry">
- <rect>
- <x>0</x>
- <y>0</y>
- <width>520</width>
- <height>492</height>
- </rect>
- </property>
- <property name="windowTitle">
- <string>Create Pyramid Logo</string>
- </property>
- <layout class="QVBoxLayout" name="verticalLayout_2">
- <item>
- <layout class="QVBoxLayout" name="verticalLayout">
- <item>
- <layout class="QHBoxLayout" name="horizontalLayout">
- <item>
- <widget class="QLabel" name="xLabel">
- <property name="text">
- <string>X [px] :</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="xSpinBox">
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="maximum">
- <number>512</number>
- </property>
- <property name="value">
- <number>128</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QLabel" name="yLabel">
- <property name="text">
- <string>Y [px] :</string>
- </property>
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QSpinBox" name="ySpinBox">
- <property name="alignment">
- <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
- </property>
- <property name="maximum">
- <number>512</number>
- </property>
- <property name="value">
- <number>128</number>
- </property>
- </widget>
- </item>
- <item>
- <widget class="QPushButton" name="logoPushButton">
- <property name="text">
- <string>Create Logo</string>
- </property>
- </widget>
- </item>
- </layout>
- </item>
- </layout>
- </item>
- <item>
- <widget class="MatplotlibWidget" name="mplWidget">
- <property name="cursor">
- <cursorShape>ArrowCursor</cursorShape>
- </property>
- <property name="layoutDirection">
- <enum>Qt::LeftToRight</enum>
- </property>
- <property name="autoFillBackground">
- <bool>false</bool>
- </property>
- </widget>
- </item>
- </layout>
- </widget>
- <customwidgets>
- <customwidget>
- <class>MatplotlibWidget</class>
- <extends>QWidget</extends>
- <header>matplotlibwidget</header>
- </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>
diff --git a/scripts/gui/gui_create_logo.py b/scripts/gui/gui_create_logo.py
deleted file mode 100644
index 3e00bf5..0000000
--- a/scripts/gui/gui_create_logo.py
+++ /dev/null
@@ -1,124 +0,0 @@
-# -*- coding: utf-8 -*-
-"""Create the Pyramid-Logo via GUI-Input."""
-
-
-import sys
-import numpy as np
-from numpy import pi
-from PyQt4 import QtCore, QtGui, uic
-
-import pyramid.magcreator as mc
-from pyramid.projector import SimpleProjector
-from pyramid.phasemapper import PMConvolve
-from pyramid.magdata import MagData
-
-from create_logo import Ui_CreateLogoWidget
-
-
-class Overlay(QtGui.QWidget):
- def __init__(self, parent=None):
- QtGui.QWidget.__init__(self, parent)
- palette = QtGui.QPalette(self.palette())
- palette.setColor(palette.Background, QtCore.Qt.transparent)
- self.setPalette(palette)
-
- def paintEvent(self, event):
- painter = QtGui.QPainter()
- painter.begin(self)
- painter.setRenderHint(QtGui.QPainter.Antialiasing)
- painter.fillRect(event.rect(), QtGui.QBrush(QtGui.QColor(255, 255, 255, 127)))
- painter.setPen(QtGui.QPen(QtCore.Qt.NoPen))
- for i in range(6):
- if (self.counter / 5) % 6 == i:
- painter.setBrush(QtGui.QBrush(QtGui.QColor(127, 127 + (self.counter % 5)*32, 127)))
- else:
- painter.setBrush(QtGui.QBrush(QtGui.QColor(127, 127, 127)))
- painter.drawEllipse(
- self.width()/2 + 30 * np.cos(2 * pi * i / 6.0) - 10,
- self.height()/2 + 30 * np.sin(2 * pi * i / 6.0) - 10,
- 20, 20)
- painter.end()
-
- def showEvent(self, event):
- self.timer = self.startTimer(50)
- self.counter = 0
-
- def hideEvent(self, event):
- self.killTimer(self.timer)
-
- def timerEvent(self, event):
- self.counter += 1
- self.update()
-
-
-class CreateLogoWidget(QtGui.QWidget, Ui_CreateLogoWidget):
-
- def __init__(self):
- # Call parent constructor
- QtGui.QWidget.__init__(self)
- self.setupUi(self)
- self.ui = uic.loadUi('create_logo.ui')
-# self.setCentralWidget(self.ui)
- # Connect Widgets with locally defined functions:
- self.connect(self.logoPushButton, QtCore.SIGNAL('clicked()'), self.buttonPushed)
- # Create overlay to indicate busy state:
- self.overlay = Overlay(self)
-# self.ui.overlay = Overlay(self.ui)
- self.overlay.hide()
- # Show Widget:
- self.show()
-
- self.workerThread = WorkerThread()
-
- def buttonPushed(self):
- self.overlay.show()
- x = self.xSpinBox.value()
- y = self.ySpinBox.value()
- create_logo((1, y, x), self.mplWidget.axes)
- self.mplWidget.draw()
-# self.workerThread.start()
- self.overlay.hide()
-
- def resizeEvent(self, event):
- self.overlay.resize(event.size())
- event.accept()
-
-
-class WorkerThread(QtCore.QThread):
-
- def __init__(self, parent=None):
- QtCore.QThread.__init__(self)
-
- def run(self):
- x = self.xSpinBox.value()
- y = self.ySpinBox.value()
- create_logo((1, y, x), self.mplWidget.axes)
- self.mplWidget.draw()
-
-
-def create_logo(dim, axis):
- '''Calculate and display the Pyramid-Logo.'''
- # Input parameters:
- a = 10.0 # in nm
- phi = -pi/2 # in rad
- density = 10
- # Create magnetic shape:
- mag_shape = np.zeros(dim)
- x = range(dim[2])
- y = range(dim[1])
- xx, yy = np.meshgrid(x, y)
- bottom = (yy >= 0.25*dim[1])
- left = (yy <= 0.75/0.5 * dim[1]/dim[2] * xx)
- right = np.fliplr(left)
- mag_shape[0, ...] = np.logical_and(np.logical_and(left, right), bottom)
- # Create magnetic data, project it, get the phase map and display the holography image:
- mag_data = MagData(a, mc.create_mag_dist_homog(mag_shape, phi))
- phase_map = PMConvolve(a, SimpleProjector(dim))(mag_data)
- phase_map.display_holo(density, 'PYRAMID - LOGO', interpolation='bilinear',
- axis=axis, show=False)
-
-
-if __name__ == '__main__':
- app = QtGui.QApplication(sys.argv)
- gui = CreateLogoWidget()
- sys.exit(app.exec_())
diff --git a/scripts/gui/mag_slicer.py b/scripts/gui/mag_slicer.py
new file mode 100644
index 0000000..fcce907
--- /dev/null
+++ b/scripts/gui/mag_slicer.py
@@ -0,0 +1,160 @@
+# -*- coding: utf-8 -*-
+
+# Form implementation generated from reading ui file 'mag_slicer2.ui'
+#
+# Created: Sun Aug 31 20:39:52 2014
+# by: PyQt4 UI code generator 4.9.6
+#
+# WARNING! All changes made in this file will be lost!
+
+
+import sys
+
+from PyQt4 import QtCore, QtGui
+
+from matplotlibwidget import MatplotlibWidget
+
+from pyramid.magdata import MagData
+
+
+try:
+ _fromUtf8 = QtCore.QString.fromUtf8
+except AttributeError:
+ def _fromUtf8(s):
+ return s
+
+try:
+ _encoding = QtGui.QApplication.UnicodeUTF8
+
+ def _translate(context, text, disambig):
+ return QtGui.QApplication.translate(context, text, disambig, _encoding)
+
+except AttributeError:
+
+ def _translate(context, text, disambig):
+ return QtGui.QApplication.translate(context, text, disambig)
+
+
+class UI_MagSlicerMain(QtGui.QWidget):
+ def __init__(self, parent=None):
+ QtGui.QWidget.__init__(self, parent)
+ Form = self
+ self.setGeometry(100, 100, 650, 650)
+ self.setWindowTitle('Mag Slicer')
+ self.gridLayout = QtGui.QGridLayout(Form)
+ self.gridLayout.setObjectName(_fromUtf8("gridLayout"))
+ self.horizontalLayout = QtGui.QHBoxLayout()
+ self.horizontalLayout.setObjectName(_fromUtf8("horizontalLayout"))
+ self.pushButton = QtGui.QPushButton(Form)
+ self.pushButton.setObjectName(_fromUtf8("pushButton"))
+ self.horizontalLayout.addWidget(self.pushButton)
+ self.scaleCheckBox = QtGui.QCheckBox(Form)
+ self.scaleCheckBox.setChecked(True)
+ self.scaleCheckBox.setTristate(False)
+ self.scaleCheckBox.setObjectName(_fromUtf8("scaleCheckBox"))
+ self.horizontalLayout.addWidget(self.scaleCheckBox)
+ self.logCheckBox = QtGui.QCheckBox(Form)
+ self.logCheckBox.setObjectName(_fromUtf8("logCheckBox"))
+ self.horizontalLayout.addWidget(self.logCheckBox)
+ self.comboBox = QtGui.QComboBox(Form)
+ self.comboBox.setObjectName(_fromUtf8("comboBox"))
+ self.comboBox.addItem(_fromUtf8(""))
+ self.comboBox.addItem(_fromUtf8(""))
+ self.comboBox.addItem(_fromUtf8(""))
+ self.horizontalLayout.addWidget(self.comboBox)
+ self.label = QtGui.QLabel(Form)
+ self.label.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
+ QtCore.Qt.AlignVCenter)
+ self.label.setObjectName(_fromUtf8("label"))
+ self.horizontalLayout.addWidget(self.label)
+ self.spinBox = QtGui.QSpinBox(Form)
+ self.spinBox.setAlignment(QtCore.Qt.AlignRight | QtCore.Qt.AlignTrailing |
+ QtCore.Qt.AlignVCenter)
+ self.spinBox.setMaximum(0)
+ self.spinBox.setProperty("value", 0)
+ self.spinBox.setObjectName(_fromUtf8("spinBox"))
+ self.horizontalLayout.addWidget(self.spinBox)
+ self.scrollBar = QtGui.QScrollBar(Form)
+ sizePolicy = QtGui.QSizePolicy(QtGui.QSizePolicy.Expanding, QtGui.QSizePolicy.Fixed)
+ sizePolicy.setHorizontalStretch(0)
+ sizePolicy.setVerticalStretch(0)
+ sizePolicy.setHeightForWidth(self.scrollBar.sizePolicy().hasHeightForWidth())
+ self.scrollBar.setSizePolicy(sizePolicy)
+ self.scrollBar.setMaximum(0)
+ self.scrollBar.setOrientation(QtCore.Qt.Horizontal)
+ self.scrollBar.setObjectName(_fromUtf8("scrollBar"))
+ self.horizontalLayout.addWidget(self.scrollBar)
+ self.gridLayout.addLayout(self.horizontalLayout, 0, 0, 1, 1)
+ self.mplWidget = MatplotlibWidget(Form)
+ self.mplWidget.setCursor(QtGui.QCursor(QtCore.Qt.ArrowCursor))
+ self.mplWidget.setLayoutDirection(QtCore.Qt.LeftToRight)
+ self.mplWidget.setAutoFillBackground(False)
+ self.mplWidget.setObjectName(_fromUtf8("mplWidget"))
+ self.gridLayout.addWidget(self.mplWidget, 1, 0, 1, 1)
+ self.retranslateUi(Form)
+ self.connect(self.scrollBar, QtCore.SIGNAL(_fromUtf8("valueChanged(int)")),
+ self.spinBox.setValue)
+ self.connect(self.spinBox, QtCore.SIGNAL(_fromUtf8("valueChanged(int)")),
+ self.scrollBar.setValue)
+ self.connect(self.logCheckBox, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.update_plot)
+ self.connect(self.scaleCheckBox, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.update_plot)
+ self.connect(self.spinBox, QtCore.SIGNAL(_fromUtf8('valueChanged(int)')),
+ self.update_plot)
+ self.connect(self.comboBox, QtCore.SIGNAL(_fromUtf8('currentIndexChanged(int)')),
+ self.update_ui)
+ self.connect(self.pushButton, QtCore.SIGNAL(_fromUtf8('clicked()')),
+ self.load)
+ QtCore.QMetaObject.connectSlotsByName(Form)
+
+ def retranslateUi(self, Form):
+ Form.setWindowTitle(_translate("Form", "Mag Slicer", None))
+ self.pushButton.setText(_translate("Form", "Laden", None))
+ self.scaleCheckBox.setText(_translate("Form", "Scaled", None))
+ self.logCheckBox.setText(_translate("Form", "Log", None))
+ self.comboBox.setItemText(0, _translate("Form", "xy-plane", None))
+ self.comboBox.setItemText(1, _translate("Form", "xz-plane", None))
+ self.comboBox.setItemText(2, _translate("Form", "zy-plane", None))
+ self.label.setText(_translate("Form", "Slice:", None))
+
+ def update_ui(self):
+ if self.mag_data_loaded:
+ mode_ind = self.comboBox.currentIndex()
+ if mode_ind == 0:
+ self.mode = 'z'
+ length = self.mag_data.dim[0]-1
+ elif mode_ind == 1:
+ self.mode = 'y'
+ length = self.mag_data.dim[1]-1
+ else:
+ self.mode = 'x'
+ length = self.mag_data.dim[2]-1
+ self.spinBox.setMaximum(length)
+ self.scrollBar.setMaximum(length)
+ self.spinBox.setValue(int(length/2.))
+ self.update_plot()
+
+ def update_plot(self):
+ if self.mag_data_loaded:
+ self.mag_data.quiver_plot(axis=self.mplWidget.axes, proj_axis=self.mode,
+ ax_slice=self.spinBox.value(),
+ log=self.logCheckBox.isChecked(),
+ scaled=self.scaleCheckBox.isChecked(),
+ show=False)
+ self.mplWidget.draw()
+
+ def load(self):
+ mag_file = QtGui.QFileDialog.getOpenFileName(self, 'Open Data File', '',
+ 'NetCDF files (*.nc)')
+ self.mag_data = MagData.load_from_netcdf4(mag_file)
+ self.mag_data_loaded = True
+ self.comboBox.setCurrentIndex(0)
+ self.update_ui()
+
+
+if __name__ == '__main__':
+ app = QtGui.QApplication(sys.argv)
+ widget = UI_MagSlicerMain()
+ widget.show()
+ sys.exit(app.exec_())
diff --git a/scripts/gui/mag_slicer.ui b/scripts/gui/mag_slicer.ui
new file mode 100644
index 0000000..030f735
--- /dev/null
+++ b/scripts/gui/mag_slicer.ui
@@ -0,0 +1,136 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>Form</class>
+ <widget class="QWidget" name="Form">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>652</width>
+ <height>646</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Mag Slicer</string>
+ </property>
+ <layout class="QGridLayout" name="gridLayout">
+ <item row="0" column="0">
+ <layout class="QHBoxLayout" name="horizontalLayout">
+ <item>
+ <widget class="QPushButton" name="pushButton">
+ <property name="text">
+ <string>Laden</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="scaleCheckBox">
+ <property name="text">
+ <string>Scaled</string>
+ </property>
+ <property name="checked">
+ <bool>true</bool>
+ </property>
+ <property name="tristate">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="logCheckBox">
+ <property name="text">
+ <string>Log</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QComboBox" name="comboBox">
+ <item>
+ <property name="text">
+ <string>xy-plane</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>xz-plane</string>
+ </property>
+ </item>
+ <item>
+ <property name="text">
+ <string>zy-plane</string>
+ </property>
+ </item>
+ </widget>
+ </item>
+ <item>
+ <widget class="QLabel" name="label">
+ <property name="text">
+ <string>Slice:</string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QSpinBox" name="spinBox">
+ <property name="alignment">
+ <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="value">
+ <number>0</number>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QScrollBar" name="scrollBar">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="maximum">
+ <number>0</number>
+ </property>
+ <property name="orientation">
+ <enum>Qt::Horizontal</enum>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ <item row="1" column="0">
+ <widget class="MatplotlibWidget" name="mplWidget">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Expanding" vsizetype="Expanding">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="cursor">
+ <cursorShape>ArrowCursor</cursorShape>
+ </property>
+ <property name="layoutDirection">
+ <enum>Qt::LeftToRight</enum>
+ </property>
+ <property name="autoFillBackground">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>MatplotlibWidget</class>
+ <extends>QWidget</extends>
+ <header>matplotlibwidget</header>
+ </customwidget>
+ </customwidgets>
+ <resources/>
+ <connections/>
+</ui>
diff --git a/scripts/reconstruction/reconstruct_random_pixels.py b/scripts/reconstruction/reconstruct_random_pixels.py
index ca7e212..65c5289 100644
--- a/scripts/reconstruction/reconstruct_random_pixels.py
+++ b/scripts/reconstruction/reconstruct_random_pixels.py
@@ -46,7 +46,7 @@ phase_map = PMConvolve(a, SimpleProjector(dim), b_0)(mag_data)
phase_map.display_combined('Generated Distribution', density=10)
# Reconstruct the magnetic distribution:
-mag_data_rec = rc.optimize_simple_leastsq(phase_map, mag_data.get_mask(), b_0)
+mag_data_rec = rc.optimize_simple_leastsq(phase_map, mag_data.get_mask(), b_0, lam=1E-4, order=1)
# Display the reconstructed phase map and holography image:
phase_map_rec = PMConvolve(a, SimpleProjector(dim), b_0)(mag_data_rec)
--
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