def __init__(self, fig, rect=[0.0, 0.0, 1.0, 1.0], *args, **kwargs):
self.fig = fig
azim = cbook.popd(kwargs, 'azim', -60)
elev = cbook.popd(kwargs, 'elev', 30)
self.xy_viewLim = unit_bbox()
self.zz_viewLim = unit_bbox()
self.xy_dataLim = unit_bbox()
self.zz_dataLim = unit_bbox()
# inihibit autoscale_view until the axises are defined
# they can't be defined until Axes.__init__ has been called
self._ready = 0
Axes.__init__(self, self.fig, rect,
frameon=True,
xticks=[], yticks=[], *args, **kwargs)
self.M = None
self._ready = 1
self.view_init(elev, azim)
self.mouse_init()
self.create_axes()
self.set_top_view()
#self.axesPatch.set_edgecolor((1,0,0,0))
self.axesPatch.set_linewidth(0)
#self.axesPatch.set_facecolor((0,0,0,0))
self.fig.add_axes(self)
def _get_axes(*arrays):
""" find list of axes from a list of axis-aligned DimArray objects
"""
dims = get_dims(*arrays) # all dimensions present in objects
axes = Axes()
for dim in dims:
common_axis = None
for o in arrays:
# skip missing dimensions
if dim not in o.dims: continue
axis = o.axes[dim]
# update values
if common_axis is None or (common_axis.size==1 and axis.size > 1):
common_axis = axis
# Test alignment for non-singleton axes
if not (axis.size == 1 or np.all(axis.values==common_axis.values)):
raise ValueError("axes are not aligned")
# append new axis
axes.append(common_axis)
return axes
def __init__(self, *args, **kwargs):
if len(args) == 1:
self.xvalues, self.yvalues = meshgrid(arange(args[0].shape[0]),
arange(args[0].shape[1]))
self.zvalues = args[0]
else:
self.xvalues, self.yvalues, self.zvalues = args
# shading
self.shading = kwargs.get('shading', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add plot to axis
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
# adjust default behavior for 3D plots
self.axes.axis_on_top = False
self.axes.xlabel_near_ticks = False
self.axes.ylabel_near_ticks = False
self.axes.zlabel_near_ticks = False
def __init__(self, *args, **kwargs):
"""
Initializes plot properties.
"""
# data points
if len(args) < 1:
self.xvalues = asarray([])
self.yvalues = asarray([])
elif len(args) < 2:
self.yvalues = asarray(args[0]).flatten()
self.xvalues = arange(1, len(self.yvalues) + 1)
else:
self.xvalues = asarray(args[0]).flatten()
self.yvalues = asarray(args[1]).flatten()
# line style
self.line_style = kwargs.get('line_style', None)
self.line_width = kwargs.get('line_width', None)
self.opacity = kwargs.get('opacity', None)
self.color = kwargs.get('color', None)
self.fill = kwargs.get('fill', False)
# marker style
self.marker = kwargs.get('marker', None)
self.marker_size = kwargs.get('marker_size', None)
self.marker_edge_color = kwargs.get('marker_edge_color', None)
self.marker_face_color = kwargs.get('marker_face_color', None)
self.marker_opacity = kwargs.get('marker_opacity', None)
# error bars
self.xvalues_error = asarray(kwargs.get('xvalues_error', [])).flatten()
self.yvalues_error = asarray(kwargs.get('yvalues_error', [])).flatten()
self.error_marker = kwargs.get('error_marker', None)
self.error_color = kwargs.get('error_color', None)
self.error_style = kwargs.get('error_style', None)
self.error_width = kwargs.get('error_width', None)
# comb (or stem) plots
self.ycomb = kwargs.get('ycomb', False)
self.xcomb = kwargs.get('xcomb', False)
self.closed = kwargs.get('closed', False)
self.const_plot = kwargs.get('const_plot', False)
# legend entry for this plot
self.legend_entry = kwargs.get('legend_entry', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add plot to axes
self.axes = kwargs.get('axis', Axes.gca())
self.axes.children.append(self)
def set_w_ylim(self, *args, **kwargs):
gl,self.get_ylim = self.get_ylim,self.get_w_ylim
vl,self.viewLim = self.viewLim,self.xy_viewLim
vmin,vmax = Axes.set_ylim(self, *args, **kwargs)
self.get_ylim = gl
self.viewLim = vl
return vmin,vmax
def empty(axes=None, dims=None, shape=None, dtype=float):
""" Initialize an empty array
axes and dims have the same meaning as DimArray's initializer
shape, optional: can be provided in combination with `dims`
if `axes=` is omitted.
>>> a = empty([('time',[2000,2001]),('items',['a','b','c'])])
>>> a.fill(3)
>>> a
dimarray: 6 non-null elements (0 null)
dimensions: 'time', 'items'
0 / time (2): 2000 to 2001
1 / items (3): a to c
array([[ 3., 3., 3.],
[ 3., 3., 3.]])
>>> b = empty(dims=('time','items'), shape=(2, 3))
See also:
---------
empty_like, ones, zeros, nans
"""
axes = Axes._init(axes, dims=dims, shape=shape)
if shape is None:
shape = [ax.size for ax in axes]
values = np.empty(shape, dtype=dtype)
return DimArray(values, axes=axes, dims=dims)
def scatter3D(self, xs, ys, zs, *args, **kwargs):
had_data = self.has_data()
patches = Axes.scatter(self,xs,ys,*args,**kwargs)
patches = art3d.wrap_patch(patches, zs)
#
self.auto_scale_xyz(xs,ys,zs, had_data)
return patches
def empty(axes=None, dims=None, shape=None, dtype=float):
""" Initialize an empty array
axes and dims have the same meaning as DimArray's initializer
shape, optional: can be provided in combination with `dims`
if `axes=` is omitted.
>>> a = empty([('time',[2000,2001]),('items',['a','b','c'])])
>>> a.fill(3)
>>> a
dimarray: 6 non-null elements (0 null)
dimensions: 'time', 'items'
0 / time (2): 2000 to 2001
1 / items (3): a to c
array([[ 3., 3., 3.],
[ 3., 3., 3.]])
>>> b = empty(dims=('time','items'), shape=(2, 3))
See also:
---------
empty_like, ones, zeros, nans
"""
axes = Axes._init(axes, dims=dims, shape=shape)
if shape is None:
shape = [ax.size for ax in axes]
values = np.empty(shape, dtype=dtype)
return DimArray(values, axes=axes, dims=dims)
def __init__(self, *args, **kwargs):
if len(args) == 1:
self.xvalues, self.yvalues = meshgrid(
arange(args[0].shape[0]),
arange(args[0].shape[1]))
self.zvalues = args[0]
else:
self.xvalues, self.yvalues, self.zvalues = args
# shading
self.shading = kwargs.get('shading', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add plot to axis
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
# adjust default behavior for 3D plots
self.axes.axis_on_top = False
self.axes.xlabel_near_ticks = False
self.axes.ylabel_near_ticks = False
self.axes.zlabel_near_ticks = False
def from_pandas(cls, data, dims=None):
""" Initialize a DimArray from pandas
data: pandas object (Series, DataFrame, Panel, Panel4D)
dims, optional: dimension (axis) names, otherwise look at ax.name for ax in data.axes
>>> import pandas as pd
>>> s = pd.Series([3,5,6], index=['a','b','c'])
>>> s.index.name = 'dim0'
>>> DimArray.from_pandas(s)
dimarray: 3 non-null elements (0 null)
dimensions: 'dim0'
0 / dim0 (3): a to c
array([3, 5, 6])
Also work with Multi-Index
>>> panel = pd.Panel(np.arange(2*3*4).reshape(2,3,4))
>>> b = panel.to_frame() # pandas' method to convert Panel to DataFrame via MultiIndex
>>> DimArray.from_pandas(b) # doctest: +SKIP
dimarray: 24 non-null elements (0 null)
dimensions: 'major,minor', 'x1'
0 / major,minor (12): (0, 0) to (2, 3)
1 / x1 (2): 0 to 1
...
"""
try:
import pandas as pd
except ImportError:
raise ImportError("pandas module is required to use this method")
axisnames = []
axes = []
for i, ax in enumerate(data.axes):
# axis name
name = ax.name
if dims is not None: name = dims[i]
if name is None: name = 'x%i'% (i)
# Multi-Index: make a Grouped Axis object
if isinstance(ax, pd.MultiIndex):
# level names
names = ax.names
for j, nm in enumerate(names):
if nm is None:
names[j] = '%s_%i'%(name,j)
miaxes = Axes.from_arrays(ax.levels, dims=names)
axis = GroupedAxis(*miaxes)
# Index: Make a simple Axis
else:
axis = Axis(ax.values, name)
axes.append(axis)
#axisnames, axes = zip(*[(ax.name, ax.values) for ax in data.axes])
return cls(data.values, axes=axes)
def from_pandas(cls, data, dims=None):
""" Initialize a DimArray from pandas
data: pandas object (Series, DataFrame, Panel, Panel4D)
dims, optional: dimension (axis) names, otherwise look at ax.name for ax in data.axes
>>> import pandas as pd
>>> s = pd.Series([3,5,6], index=['a','b','c'])
>>> s.index.name = 'dim0'
>>> DimArray.from_pandas(s)
dimarray: 3 non-null elements (0 null)
dimensions: 'dim0'
0 / dim0 (3): a to c
array([3, 5, 6])
Also work with Multi-Index
>>> panel = pd.Panel(np.arange(2*3*4).reshape(2,3,4))
>>> b = panel.to_frame() # pandas' method to convert Panel to DataFrame via MultiIndex
>>> DimArray.from_pandas(b) # doctest: +SKIP
dimarray: 24 non-null elements (0 null)
dimensions: 'major,minor', 'x1'
0 / major,minor (12): (0, 0) to (2, 3)
1 / x1 (2): 0 to 1
...
"""
try:
import pandas as pd
except ImportError:
raise ImportError("pandas module is required to use this method")
axisnames = []
axes = []
for i, ax in enumerate(data.axes):
# axis name
name = ax.name
if dims is not None: name = dims[i]
if name is None: name = 'x%i' % (i)
# Multi-Index: make a Grouped Axis object
if isinstance(ax, pd.MultiIndex):
# level names
names = ax.names
for j, nm in enumerate(names):
if nm is None:
names[j] = '%s_%i' % (name, j)
miaxes = Axes.from_arrays(ax.levels, dims=names)
axis = GroupedAxis(*miaxes)
# Index: Make a simple Axis
else:
axis = Axis(ax.values, name)
axes.append(axis)
#axisnames, axes = zip(*[(ax.name, ax.values) for ax in data.axes])
return cls(data.values, axes=axes)
def draw(self, renderer):
# draw the background patch
self.axesPatch.draw(renderer)
self._frameon = False
# add the projection matrix to the renderer
self.M = self.get_proj()
renderer.M = self.M
renderer.vvec = self.vvec
renderer.eye = self.eye
renderer.get_axis_position = self.get_axis_position
#self.set_top_view()
self.w_xaxis.draw(renderer)
self.w_yaxis.draw(renderer)
self.w_zaxis.draw(renderer)
Axes.draw(self, renderer)
def plot3D(self, xs, ys, zs, *args, **kwargs):
had_data = self.has_data()
lines = Axes.plot(self, xs,ys, *args, **kwargs)
if len(lines)==1:
line = lines[0]
art3d.wrap_line(line, zs)
#
self.auto_scale_xyz(xs,ys,zs, had_data)
return lines
def add_axes(self, *args, **kwargs):
"""
Add an a axes with axes rect [left, bottom, width, height] where all
quantities are in fractions of figure width and height. kwargs are
legal Axes kwargs plus "polar" which sets whether to create a polar axes
rect = l,b,w,h
add_axes(rect)
add_axes(rect, frameon=False, axisbg='g')
add_axes(rect, polar=True)
add_axes(ax) # add an Axes instance
If the figure already has an axes with key *args, *kwargs then it will
simply make that axes current and return it. If you do not want this
behavior, eg you want to force the creation of a new axes, you must
use a unique set of args and kwargs. The artist "label" attribute has
been exposed for this purpose. Eg, if you want two axes that are
otherwise identical to be added to the figure, make sure you give them
unique labels:
add_axes(rect, label='axes1')
add_axes(rect, label='axes2')
The Axes instance will be returned
The following kwargs are supported:
%(Axes)s
"""
key = self._make_key(*args, **kwargs)
if self._seen.has_key(key):
ax = self._seen[key]
self.sca(ax)
return ax
if not len(args): return
if isinstance(args[0], Axes):
a = args[0]
assert (a.get_figure() is self)
else:
rect = args[0]
ispolar = kwargs.pop('polar', False)
if ispolar:
a = PolarAxes(self, rect, **kwargs)
else:
a = Axes(self, rect, **kwargs)
self.axes.append(a)
self._axstack.push(a)
self.sca(a)
self._seen[key] = a
return a
def add_axes(self, rect, axisbg=None, frameon=True):
"""
Add an a axes with axes rect [left, bottom, width, height]
where all quantities are in fractions of figure width and
height.
The Axes instance will be returned
"""
if axisbg is None: axisbg = rcParams['axes.facecolor']
a = Axes(self, rect, axisbg, frameon)
self.axes.append(a)
return a
def __init__(self, *args, **kwargs):
# legend entries
self.legend_entries = args
# legend properties
self.at = kwargs.get('at', None)
self.anchor = kwargs.get('anchor', None)
self.location = kwargs.get('location', None)
self.align = kwargs.get('align', 'left')
self.box = kwargs.get('box', True)
self.font_size = kwargs.get('font_size', None)
# assign legend to axis
self.axes = kwargs.get('axes', Axes.gca())
self.axes.legend = self
def __init__(self, image, **kwargs):
"""
@type image: string/array_like/PIL Image
@param image: a filepath or an image in grayscale or RGB
@param vmin:
@param vmax:
@param cmap:
"""
self.cmap = kwargs.get('cmap', 'gray')
if isinstance(image, str):
self.image = PILImage.open(image)
elif isinstance(image, PILImage.Image):
self.image = image.copy()
else:
if isinstance(image, ndarray):
# copy array
image = array(image)
if image.dtype.kind != 'i':
vmin = kwargs.get('vmin', min(image))
vmax = kwargs.get('vmax', max(image))
# rescale image
image = (image - vmin) / (vmax - vmin)
image = array(image * 256., dtype='int32')
image[image < 0] = 0
image[image > 255] = 255
image = array(image, dtype='uint8')
if image.ndim < 3:
image = repeat(image.reshape(image.shape[0], -1, 1), 3, 2)
self.image = PILImage.fromarray(image)
# add image to axis
self.axes = kwargs.get('axis', Axes.gca())
self.axes.children.append(self)
self.idx = Image._counter
Image._counter += 1
def subplot(i, j, **kwargs):
fig = gcf()
if not (fig.axes and isinstance(fig.axes[0], AxesGrid)):
# create new axis grid
fig.axes = [AxesGrid(**kwargs)]
# get axis grid
grid = fig.axes[0]
if not (i, j) in grid.keys():
# create new axis in axis grid
grid[i, j] = Axes(fig=fig, **kwargs)
# make axis active; TODO: find a less hacky solution
fig._ca = grid[i, j]
def add_axes(self, rect, axisbg=None, frameon=True, **kwargs):
"""
Add an a axes with axes rect [left, bottom, width, height]
where all quantities are in fractions of figure width and
height.
The Axes instance will be returned
"""
if axisbg is None: axisbg = rcParams['axes.facecolor']
ispolar = kwargs.get('polar', False)
if ispolar:
a = PolarAxes(self, rect, axisbg, frameon)
else:
a = Axes(self, rect, axisbg, frameon)
self.axes.append(a)
return a
def add_axes(self, *args, **kwargs):
"""
Add an a axes with axes rect [left, bottom, width, height] where all
quantities are in fractions of figure width and height. kwargs are
legal Axes kwargs plus"polar" which sets whether to create a polar axes
add_axes((l,b,w,h))
add_axes((l,b,w,h), frameon=False, axisbg='g')
add_axes((l,b,w,h), polar=True)
add_axes(ax) # add an Axes instance
If the figure already has an axed with key *args, *kwargs then it
will simply make that axes current and return it
The Axes instance will be returned
"""
if iterable(args[0]):
key = tuple(args[0]), tuple(kwargs.items())
else:
key = args[0], tuple(kwargs.items())
if self._seen.has_key(key):
ax = self._seen[key]
self.sca(ax)
return ax
if not len(args): return
if isinstance(args[0], Axes):
a = args[0]
a.set_figure(self)
else:
rect = args[0]
ispolar = popd(kwargs, 'polar', False)
if ispolar:
a = PolarAxes(self, rect, **kwargs)
else:
a = Axes(self, rect, **kwargs)
self.axes.append(a)
self._axstack.push(a)
self.sca(a)
self._seen[key] = a
return a
def plot(self, *args, **kwargs):
had_data = self.has_data()
zval = cbook.popd(kwargs, 'z', 0)
zdir = cbook.popd(kwargs, 'dir', 'z')
lines = Axes.plot(self, *args, **kwargs)
#
linecs = [art3d.Line2DW(l, z=zval, dir=zdir) for l in lines]
#
xs = lines[0].get_xdata()
ys = lines[0].get_ydata()
zs = [zval for x in xs]
xs,ys,zs = art3d.juggle_axes(xs,ys,zs,zdir)
#
self.auto_scale_xyz(xs,ys,zs, had_data)
#
return linecs
def __init__(self, x, y, text, **kwargs):
self.x = x
self.y = y
self.text = text
# properties
self.color = kwargs.get('color', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add text to axes
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
def new_axes(self, *args, **kwargs):
'''
Add an axes to the figure.
:param position: (*list*) Optional, axes position specified by *position=* [left, bottom, width
height] in normalized (0, 1) units. Default is [0.13, 0.11, 0.775, 0.815].
:param outerposition: (*list*) Optional, axes size and location, including labels and margin.
:param aspect: (*string*) ['equal' | 'auto'] or a number. If a number the ratio of x-unit/y-unit in screen-space.
Default is 'auto'.
:param bgcolor: (*Color*) Optional, axes background color.
:param axis: (*boolean*) Optional, set all axis visible or not. Default is ``True`` .
:param bottomaxis: (*boolean*) Optional, set bottom axis visible or not. Default is ``True`` .
:param leftaxis: (*boolean*) Optional, set left axis visible or not. Default is ``True`` .
:param topaxis: (*boolean*) Optional, set top axis visible or not. Default is ``True`` .
:param rightaxis: (*boolean*) Optional, set right axis visible or not. Default is ``True`` .
:param xaxistype: (*string*) Optional, set x axis type as 'normal', 'lon', 'lat' or 'time'.
:param xreverse: (*boolean*) Optional, set x axis reverse or not. Default is ``False`` .
:param yreverse: (*boolean*) Optional, set yaxis reverse or not. Default is ``False`` .
:returns: The axes.
'''
axestype = kwargs.pop('axestype', 'cartesian')
polar = kwargs.pop('polar', False)
if polar:
axestype = 'polar'
kwargs['figure'] = self
if axestype == 'polar':
ax = PolarAxes(*args, **kwargs)
#self.__set_axes(ax, **kwargs)
elif axestype == 'map':
ax = MapAxes(*args, **kwargs)
#self.__set_axesm(ax, **kwargs)
elif axestype == '3d':
ax = Axes3D(*args, **kwargs)
#self.__set_axes3d(ax, **kwargs)
else:
ax = Axes(*args, **kwargs)
#self.__set_axes(ax, **kwargs)
#self.__set_axes_common(ax, *args, **kwargs)
return ax
def __init__(self, x, y, r, **kwargs):
self.x = x
self.y = y
self.r = r
# properties
self.color = kwargs.get('color', None)
self.line_style = kwargs.get('line_style', None)
self.line_width = kwargs.get('line_width', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add rectangle to axes
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
def __init__(self, x, y, r, **kwargs):
self.x = x
self.y = y
self.r = r
# properties
self.color = kwargs.get('color', None)
self.line_style = kwargs.get('line_style', None)
self.line_width = kwargs.get('line_width', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add rectangle to axes
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
def __init__(self, x, y, dx, dy, **kwargs):
self.x = x
self.y = y
self.dx = dx
self.dy = dy
# properties
self.color = kwargs.get('color', None)
self.arrow_style = kwargs.get('arrow_style', '-latex')
self.line_style = kwargs.get('line_style', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add arrow to axes
self.axes = kwargs.get('axis', Axes.gca())
self.axes.children.append(self)
def __create_axes(self, *args, **kwargs):
"""
Create an axes.
:param position: (*list*) Optional, axes position specified by *position=* [left, bottom, width
height] in normalized (0, 1) units. Default is [0.13, 0.11, 0.775, 0.815].
:param outerposition: (*list*) Optional, axes size and location, including labels and margin.
:returns: The axes.
"""
if len(args) > 0:
position = args[0]
else:
position = kwargs.pop('position', None)
outerposition = kwargs.pop('outerposition', None)
axestype = kwargs.pop('axestype', 'cartesian')
polar = kwargs.pop('polar', False)
if polar:
axestype = 'polar'
if axestype == 'polar':
ax = PolarAxes()
elif axestype == 'map':
ax = MapAxes()
elif axestype == '3d':
ax = Axes3D()
else:
ax = Axes()
if position is None:
position = [0.13, 0.11, 0.775, 0.815]
ax.active_outerposition(True)
else:
ax.active_outerposition(False)
ax.set_position(position)
if not outerposition is None:
ax.set_outerposition(outerposition)
ax.active_outerposition(True)
return ax
def __init__(self, *args, **kwargs):
# data points
if len(args) < 1:
self.xvalues = asarray([])
self.yvalues = asarray([])
elif len(args) < 2:
self.yvalues = asarray(args[0]).reshape(shape(args[0])[0], -1)
self.xvalues = arange(1, self.yvalues.shape[-1] + 1)
else:
self.xvalues = asarray(args[0]).flatten()
self.yvalues = asarray(args[1]).reshape(shape(args[1])[0], -1)
self.box_width = kwargs.get('box_width', 0.5)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add plot to axes
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
def __init__(self, *args, **kwargs):
# data points
if len(args) < 1:
self.xvalues = asarray([])
self.yvalues = asarray([])
elif len(args) < 2:
self.yvalues = asarray(args[0]).reshape(shape(args[0])[0], -1)
self.xvalues = arange(1, self.yvalues.shape[-1] + 1)
else:
self.xvalues = asarray(args[0]).flatten()
self.yvalues = asarray(args[1]).reshape(shape(args[1])[0], -1)
self.box_width = kwargs.get('box_width', 0.5);
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# add plot to axes
self.axes = kwargs.get('axis', Axes.gca())
self.axes.children.append(self)
def _take_broadcast(a, indices):
""" broadcast array-indices & integers, numpy's classical
Examples:
---------
>>> a = da.zeros(shape=(3,4,5,6))
>>> a[:,[0, 1],:,2].shape
(2, 3, 5)
>>> a[:,[0, 1],2,:].shape
(3, 2, 6)
"""
# new values
newval = a.values[indices]
# if the new values is a scalar, then just return it
if np.isscalar(newval):
return newval
# new axes: broacast indices (should do the same as above, since integers are just broadcast)
indices2 = broadcast_indices(indices)
# assert np.all(newval == a.values[indices2])
# make a multi-axis with tuples
is_array2 = np.array([np.iterable(ix) for ix in indices2])
nb_array2 = is_array2.sum()
# If none or one array is present, easy
if nb_array2 <= 1:
newaxes = [
a.axes[i][ix] for i, ix in enumerate(indices) if not np.isscalar(ix)
] # indices or indices2, does not matter
# else, finer check needed
else:
# same stats but on original indices
is_array = np.array([np.iterable(ix) for ix in indices])
array_ix_pos = np.where(is_array)[0]
# Determine where the axis will be inserted
# - need to consider the integers as well (broadcast as arrays)
# - if two indexed dimensions are not contiguous, new axis placed at first position...
# a = zeros((3,4,5,6))
# a[:,[1,2],:,0].shape ==> (2, 3, 5)
# a[:,[1,2],0,:].shape ==> (3, 2, 6)
array_ix_pos2 = np.where(is_array2)[0]
if np.any(np.diff(array_ix_pos2) > 1): # that mean, if two indexed dimensions are not contiguous
insert = 0
else:
insert = array_ix_pos2[0]
# Now determine axis value
# ...if originally only one array was provided, use these values correspondingly
if len(array_ix_pos) == 1:
i = array_ix_pos[0]
values = a.axes[i].values[indices[i]]
name = a.axes[i].name
# ...else use a list of tuples
else:
values = zip(*[a.axes[i].values[indices2[i]] for i in array_ix_pos])
name = ",".join([a.axes[i].name for i in array_ix_pos])
broadcastaxis = Axis(values, name)
newaxes = Axes()
for i, ax in enumerate(a.axes):
# axis is already part of the broadcast axis: skip
if is_array2[i]:
continue
else:
newaxis = ax[indices2[i]]
## do not append axis if scalar
# if np.isscalar(newaxis):
# continue
newaxes.append(newaxis)
# insert the right new axis at the appropriate position
newaxes.insert(insert, broadcastaxis)
return a._constructor(newval, newaxes, **a._metadata)
def text3D(self, x,y,z,s, *args, **kwargs):
text = Axes.text(self,x,y,s,*args,**kwargs)
art3d.wrap_text(text,z)
return text
def clabel(self, *args, **kwargs):
r = Axes.clabel(self, *args, **kwargs)
return r
def __init__(self, *args, **kwargs):
"""
Initializes plot properties.
"""
# data points
if len(args) < 1:
self.xvalues = asarray([])
self.yvalues = asarray([])
elif len(args) < 2:
self.yvalues = asarray(args[0]).flatten()
self.xvalues = arange(1, len(self.yvalues) + 1)
else:
self.xvalues = asarray(args[0]).flatten()
self.yvalues = asarray(args[1]).flatten()
# labels for each data point
self.labels = kwargs.get('labels', None)
if isinstance(self.labels, str):
self.labels = [self.labels]
if self.labels and len(self.labels) != len(self.xvalues):
raise ValueError('The number of labels should correspond to the number of data points.')
# line style
self.line_style = kwargs.get('line_style', None)
self.line_width = kwargs.get('line_width', None)
self.opacity = kwargs.get('opacity', None)
self.color = kwargs.get('color', None)
self.fill = kwargs.get('fill', False)
# marker style
self.marker = kwargs.get('marker', None)
self.marker_size = kwargs.get('marker_size', None)
self.marker_edge_color = kwargs.get('marker_edge_color', None)
self.marker_face_color = kwargs.get('marker_face_color', None)
self.marker_opacity = kwargs.get('marker_opacity', None)
# error bars
self.xvalues_error = asarray(kwargs.get('xvalues_error', [])).flatten()
self.yvalues_error = asarray(kwargs.get('yvalues_error', [])).flatten()
self.error_marker = kwargs.get('error_marker', None)
self.error_color = kwargs.get('error_color', None)
self.error_style = kwargs.get('error_style', None)
self.error_width = kwargs.get('error_width', None)
# PGF pattern to fill area and bar plots
self.pattern = kwargs.get('pattern', None)
# comb (or stem) plots
self.ycomb = kwargs.get('ycomb', False)
self.xcomb = kwargs.get('xcomb', False)
self.closed = kwargs.get('closed', False)
self.const_plot = kwargs.get('const_plot', False)
# legend entry for this plot
self.legend_entry = kwargs.get('legend_entry', None)
# custom plot options
self.pgf_options = kwargs.get('pgf_options', [])
# catch common mistakes
if not isinstance(self.pgf_options, list):
raise TypeError('pgf_options should be a list.')
# comment LaTeX code
self.comment = kwargs.get('comment', '')
# add plot to axes
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
if (unit_1 != unit_2):
return NotImplemented
return units[0]
def multiplication_rule(self, units):
non_null = [u for u in units if u]
if (len(non_null) > 1):
return NotImplemented
return non_null[0]
op_dict = {
'__mul__': multiplication_rule,
'__rmul__': multiplication_rule,
'__add__': addition_rule,
'__radd__': addition_rule,
'__sub__': addition_rule,
'__rsub__': addition_rule,
}
def __call__(self, operation, units):
if (operation not in self.op_dict):
return NotImplemented
return self.op_dict[operation](self, units)
unit_resolver = UnitResolver()
Axes.set_default_unit_to_locator_map(lambda u: u.get_tick_locators())
Axes.set_default_unit_to_formatter_map(lambda u: u.get_tick_formatters())
class LatticeDesigner(wx.Frame):
title = "Lattice Designer"
configs = {}
def __init__(self, parent):
wx.Frame.__init__(self, None, -1, self.title)
# Allow OS X users to close the window with Cmd+Q
menubar = wx.MenuBar()
self.SetMenuBar(menubar)
self.atoms_file = self.data_files = False
self.Show()
self.Maximize(True)
self.drawSidebar()
def drawSidebar(self):
layout = wx.BoxSizer(wx.HORIZONTAL)
tabs = wx.Notebook(self)
self.designSidebarPanel = scrolled.ScrolledPanel(tabs)
self.designSidebar = wx.BoxSizer(wx.VERTICAL)
self.content = content = wx.BoxSizer(wx.VERTICAL)
self.grid = BitMapGrid(self)
self.canvas = AtomsCanvas(self)
#Grid size
self.sizeBox = wx.StaticBox(self.designSidebarPanel, label='Grid size')
self.sizeBoxSizer = wx.StaticBoxSizer(self.sizeBox, wx.VERTICAL)
self.sizeBoxGrid = wx.GridSizer(1, 4, 10, 10)
self.sizeBoxWidthLabel = wx.StaticText(self.designSidebarPanel, label="Width")
self.sizeBoxWidthCtrl = wx.SpinCtrl(self.designSidebarPanel, value=str(self.grid.cols), initial=self.grid.cols, min=0, size=(50, 20))
self.sizeBoxHeightLabel = wx.StaticText(self.designSidebarPanel, label="Height")
self.sizeBoxHeightCtrl = wx.SpinCtrl(self.designSidebarPanel, value=str(self.grid.rows), initial=self.grid.rows, min=0, size=(50, 20))
self.sizeBoxGrid.AddMany([
(self.sizeBoxWidthLabel, 0, wx.EXPAND),
(self.sizeBoxWidthCtrl, 0, wx.EXPAND),
(self.sizeBoxHeightLabel, 0, wx.EXPAND),
(self.sizeBoxHeightCtrl, 0, wx.EXPAND)
])
self.sizeBoxWidthCtrl.Bind(wx.EVT_SPINCTRL, self.updateGridSize)
self.sizeBoxHeightCtrl.Bind(wx.EVT_SPINCTRL, self.updateGridSize)
self.sizeBoxSizer.Add(self.sizeBoxGrid)
#Object parameters
self.configBox = wx.StaticBox(self.designSidebarPanel, label='Object parameters')
self.configBoxSizer = wx.StaticBoxSizer(self.configBox, wx.VERTICAL)
self.configBoxGrid = wx.GridSizer(10, 2, 5, 5)
# Number of layers
self.configBoxLayersLabel = wx.StaticText(self.designSidebarPanel, label="Layers", size=(70,20))
self.configBoxLayersCtrl = wx.SpinCtrl(self.designSidebarPanel, value="3", initial=10, min=1, size=(50, 20))
# Avoid bug on OS X that auto-focus on first field and hides the default value
wx.CallAfter(self.configBoxLayersCtrl.SetFocus)
self.configBoxLayersCtrl.Bind(wx.EVT_SPINCTRL, self.updateParametersProxy)
# Type of structure
self.configBoxCellTypeLabel = wx.StaticText(self.designSidebarPanel, label="Structure")
self.configBoxCellTypeSCRadio = wx.RadioButton(self.designSidebarPanel, label='SC', style=wx.RB_GROUP)
self.configBoxCellTypeBCCRadio = wx.RadioButton(self.designSidebarPanel, label='BCC')
self.configBoxCellTypeFCCRadio = wx.RadioButton(self.designSidebarPanel, label='FCC')
self.configBoxCellTypeSCRadio.SetValue(True)
self.type = "SC"
self.configs['type'] = self.type
self.configBoxCellTypeSCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
self.configBoxCellTypeBCCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
self.configBoxCellTypeFCCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
# Net constant
self.configBoxNetConstantLabel = wx.StaticText(self.designSidebarPanel, label="Lattice constant")
self.configBoxNetConstantCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0, increment=0.1, value=0.28, agwStyle=FS.FS_LEFT)
self.configBoxNetConstantCtrl.SetFormat("%f")
self.configBoxNetConstantCtrl.SetDigits(5)
self.configBoxNetConstantCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
# Size
self.configBoxHeightLabel = wx.StaticText(self.designSidebarPanel, label="Height (nm)", size=(70, 20))
self.configBoxHeightCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0.1, increment=0.1, value=10, agwStyle=FS.FS_LEFT)
self.configBoxHeightCtrl.SetFormat("%f")
self.configBoxHeightCtrl.SetDigits(2)
self.configBoxHeightCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
# Sizes
self.configBoxWidthLabel = wx.StaticText(self.designSidebarPanel, label="Width (nm)", size=(70, 20))
self.configBoxWidthValue = wx.StaticText(self.designSidebarPanel, label="--", size=(70, 20))
self.configBoxLengthLabel = wx.StaticText(self.designSidebarPanel, label="Length (nm)", size=(70, 20))
self.configBoxLengthValue = wx.StaticText(self.designSidebarPanel, label="--", size=(70, 20))
# Scaling
self.configBoxEtaLabel = wx.StaticText(self.designSidebarPanel, label="Eta", size=(70, 20))
self.configBoxEtaCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0, increment=0.1, value=0.55, agwStyle=FS.FS_LEFT)
self.configBoxEtaCtrl.SetFormat("%f")
self.configBoxEtaCtrl.SetDigits(5)
self.configBoxEtaCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
self.configBoxXLabel = wx.StaticText(self.designSidebarPanel, label="X", size=(70, 20))
self.configBoxXValue = wx.StaticText(self.designSidebarPanel, label="--", size=(50, 20))
self.configBoxGrid.AddMany([
(self.configBoxLayersLabel, 0, wx.EXPAND),
(self.configBoxLayersCtrl, 0, wx.EXPAND),
(self.configBoxCellTypeLabel, 0, wx.EXPAND),
(self.configBoxCellTypeSCRadio, 0, wx.EXPAND),
(wx.StaticText(self, -1, ''), 0, wx.EXPAND), #Blank space
(self.configBoxCellTypeBCCRadio, 0, wx.EXPAND),
(wx.StaticText(self, -1, ''), 0, wx.EXPAND), #Blank space
(self.configBoxCellTypeFCCRadio, 0, wx.EXPAND),
(self.configBoxNetConstantLabel, 0, wx.EXPAND),
(self.configBoxNetConstantCtrl, 0, wx.EXPAND),
(self.configBoxHeightLabel, 0, wx.EXPAND),
(self.configBoxHeightCtrl, 0, wx.EXPAND),
(self.configBoxWidthLabel, 0, wx.EXPAND),
(self.configBoxWidthValue, 0, wx.EXPAND),
(self.configBoxLengthLabel, 0, wx.EXPAND),
(self.configBoxLengthValue, 0, wx.EXPAND),
(self.configBoxEtaLabel, 0, wx.EXPAND),
(self.configBoxEtaCtrl, 0, wx.EXPAND),
(self.configBoxXLabel, 0, wx.EXPAND),
(self.configBoxXValue, 0, wx.EXPAND)
])
self.configBoxSizer.Add(self.configBoxGrid)
# Figures
self.figuresBox = wx.StaticBox(self.designSidebarPanel, label='Figures')
self.figuresBoxSizer = wx.StaticBoxSizer(self.figuresBox, wx.VERTICAL)
self.figuresBoxGrid = wx.FlexGridSizer(2, 1, 10, 10)
# Quadrilateral
self.figuresQuadPane = wx.CollapsiblePane(self.designSidebarPanel, label="Quadrilateral", style=wx.CP_DEFAULT_STYLE|wx.CP_NO_TLW_RESIZE)
self.figuresQuadPane.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.quadToggled)
self.figuresQuadSizer = wx.GridSizer(1, 4, 10, 10)
self.figuresQuadPaneWin = self.figuresQuadPane.GetPane()
self.figuresQuadWidthLabel = wx.StaticText(self.figuresQuadPaneWin, label="Width")
self.figuresQuadWidthCtrl = wx.SpinCtrl(self.figuresQuadPaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresQuadHeightLabel = wx.StaticText(self.figuresQuadPaneWin, label="Height")
self.figuresQuadHeightCtrl = wx.SpinCtrl(self.figuresQuadPaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresQuadSizer.AddMany([
(self.figuresQuadWidthLabel, 0, wx.EXPAND),
(self.figuresQuadWidthCtrl, 0, wx.EXPAND),
(self.figuresQuadHeightLabel, 0, wx.EXPAND),
(self.figuresQuadHeightCtrl, 0, wx.EXPAND)
])
self.figuresQuadPaneWin.SetSizer(self.figuresQuadSizer)
# Circle
self.figuresCirclePane = wx.CollapsiblePane(self.designSidebarPanel, label="Circle", style=wx.CP_DEFAULT_STYLE|wx.CP_NO_TLW_RESIZE)
self.figuresCirclePane.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.circleToggled)
self.figuresCircleSizer = wx.GridSizer(2, 2, 10, 10)
self.figuresCirclePaneWin = self.figuresCirclePane.GetPane()
self.figuresCircleRadiusLabel = wx.StaticText(self.figuresCirclePaneWin, label="Radius")
self.figuresCircleRadiusCtrl = wx.SpinCtrl(self.figuresCirclePaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresCircleRadiusCtrl.Bind(wx.EVT_SPINCTRL, self.updateCircleWidth)
self.figuresCircleWidthLabel = wx.StaticText(self.figuresCirclePaneWin, label="Width (nm)")
self.figuresCircleWidthValue = wx.StaticText(self.figuresCirclePaneWin, label="--")
self.figuresCircleSizer.AddMany([
(self.figuresCircleRadiusLabel, 0, wx.EXPAND),
(self.figuresCircleRadiusCtrl, 0, wx.EXPAND),
(self.figuresCircleWidthLabel, 0, wx.EXPAND),
(self.figuresCircleWidthValue, 0, wx.EXPAND)
])
self.figuresCirclePaneWin.SetSizer(self.figuresCircleSizer)
self.figuresBoxGrid.AddMany([
(self.figuresQuadPane, 0, wx.EXPAND),
(self.figuresCirclePane, 0, wx.EXPAND)
])
self.figuresBoxSizer.Add(self.figuresBoxGrid)
self.clearButton = wx.Button(self.designSidebarPanel, label="Clear grid")
self.clearButton.Bind(wx.EVT_BUTTON, self.clearGrid)
self.exportFileButton = wx.Button(self.designSidebarPanel, label="Export Data")
self.exportFileButton.Bind(wx.EVT_BUTTON, self.checkParametersTrigger)
self.exportImagesButtonD = wx.Button(self.designSidebarPanel, label="Export Images")
self.exportImagesButtonD.Bind(wx.EVT_BUTTON, self.exportImagesD)
self.exportImagesButtonD.Show(False)
self.previewButton = wx.Button(self.designSidebarPanel, label="Show/hide preview")
self.previewButton.Bind(wx.EVT_BUTTON, self.togglePreview)
self.axesBoxD = wx.StaticBox(self.designSidebarPanel, label='Axes')
self.axesBoxSizerD = wx.StaticBoxSizer(self.axesBoxD, wx.VERTICAL)
self.axesD = Axes(self.designSidebarPanel)
self.axesBoxSizerD.Add(self.axesD)
self.designSidebar.Add(self.sizeBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.configBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.figuresBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.clearButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.exportFileButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.exportImagesButtonD, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.previewButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.axesBoxSizerD, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebarPanel.SetSizer(self.designSidebar)
wx.CallAfter(self.axesBoxD.Show, False)
wx.CallAfter(self.axesD.Show, False)
self.visualizationSidebarPanel = scrolled.ScrolledPanel(tabs)
visualizationSidebar = wx.BoxSizer(wx.VERTICAL)
inputDirBtn = wx.Button(self.visualizationSidebarPanel, -1, "Select Atoms file")
self.Bind(wx.EVT_BUTTON, self.openFileDialog, inputDirBtn)
self.statsBox = wx.StaticBox(self.visualizationSidebarPanel, label='Input Stats')
self.statsSizer = wx.StaticBoxSizer(self.statsBox, wx.VERTICAL)
self.statsGrid = wx.GridSizer(2, 2, 5, 5)
self.statsValidPathLabel = wx.StaticText(self.visualizationSidebarPanel, label="Valid Atom file")
self.statsValidPathValue = wx.StaticText(self.visualizationSidebarPanel, label="--")
self.statsNumberDataFilesLabel = wx.StaticText(self.visualizationSidebarPanel, label="# of Data files")
self.statsNumberDataFilesValue = wx.StaticText(self.visualizationSidebarPanel, label="--")
self.statsGrid.AddMany([
(self.statsValidPathLabel, 0, wx.EXPAND),
(self.statsValidPathValue, 0, wx.EXPAND),
(self.statsNumberDataFilesLabel, 0, wx.EXPAND),
(self.statsNumberDataFilesValue, 0, wx.EXPAND)
])
self.statsSizer.Add(self.statsGrid)
self.readInputBtn = wx.Button(self.visualizationSidebarPanel, label="Read Input files")
# Enable only if we have a valid directory
self.readInputBtn.Enable(False)
self.readInputBtn.Bind(wx.EVT_BUTTON, self.readInputFiles)
viewModeBox = wx.StaticBox(self.visualizationSidebarPanel, label='View layer')
self.viewModeSizer = wx.StaticBoxSizer(viewModeBox, wx.VERTICAL)
viewModeGrid = wx.FlexGridSizer(2, 4, 5, 5)
self.viewModeAllLayers = wx.RadioButton(self.visualizationSidebarPanel, label='All', style=wx.RB_GROUP)
self.viewModeLayerX = wx.RadioButton(self.visualizationSidebarPanel, label='X')
self.viewLayerX = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeLayerY = wx.RadioButton(self.visualizationSidebarPanel, label='Y')
self.viewLayerY = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeLayerZ = wx.RadioButton(self.visualizationSidebarPanel, label='Z')
self.viewLayerZ = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeAllLayers.SetValue(True)
self.viewModeAllLayers.Enable(False)
self.viewModeLayerX.Enable(False)
self.viewModeLayerY.Enable(False)
self.viewModeLayerZ.Enable(False)
self.viewLayerX.Enable(False)
self.viewLayerY.Enable(False)
self.viewLayerZ.Enable(False)
self.viewModeAllLayers.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerX.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerY.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerZ.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewLayerX.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
self.viewLayerY.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
self.viewLayerZ.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
viewModeGrid.AddMany([
(self.viewModeAllLayers, 0, wx.EXPAND),
(self.viewModeLayerX, 0, wx.EXPAND),
(self.viewModeLayerY, 0, wx.EXPAND),
(self.viewModeLayerZ, 0, wx.EXPAND),
((1,1)), #Blank space
(self.viewLayerX, 0, wx.EXPAND),
(self.viewLayerY, 0, wx.EXPAND),
(self.viewLayerZ, 0, wx.EXPAND)
])
self.viewModeSizer.Add(viewModeGrid, flag=wx.ALL, border=1)
self.exportImagesButtonV = wx.Button(self.visualizationSidebarPanel, label="Export Images")
self.exportImagesButtonV.Bind(wx.EVT_BUTTON, self.exportImagesV)
self.exportImagesButtonV.Show(False)
self.exportVideoButton = wx.Button(self.visualizationSidebarPanel, label="Export Video")
self.exportVideoButton.Bind(wx.EVT_BUTTON, self.exportVideo)
self.exportVideoButton.Show(False)
controlsBox = wx.StaticBox(self.visualizationSidebarPanel, label='Controls')
self.controlsSizer = wx.StaticBoxSizer(controlsBox, wx.VERTICAL)
controlsGrid = wx.FlexGridSizer(1, 6, 5, 5)
self.playBitmap = wx.Bitmap("images/play.png", wx.BITMAP_TYPE_ANY)
self.stopBitmap = wx.Bitmap("images/pause.png", wx.BITMAP_TYPE_ANY)
self.backBitmap = wx.Bitmap("images/back.png", wx.BITMAP_TYPE_ANY)
self.forwardBitmap = wx.Bitmap("images/forward.png", wx.BITMAP_TYPE_ANY)
self.previousBitmap = wx.Bitmap("images/previous.png", wx.BITMAP_TYPE_ANY)
self.nextBitmap = wx.Bitmap("images/next.png", wx.BITMAP_TYPE_ANY)
self.backBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.backBitmap, (0,0), ((30,30)))
self.previousBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.previousBitmap, (0,0), ((30,30)))
self.playStopBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.playBitmap, (0,0), ((30,30)))
self.nextBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.nextBitmap, (0,0), ((30,30)))
self.forwardBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.forwardBitmap, (0,0), ((30,30)))
self.previousBtn.Bind(wx.EVT_BUTTON, self.previousT)
self.backBtn.Bind(wx.EVT_BUTTON, self.backT)
self.playStopBtn.Bind(wx.EVT_BUTTON, self.playStop)
self.forwardBtn.Bind(wx.EVT_BUTTON, self.forwardT)
self.nextBtn.Bind(wx.EVT_BUTTON, self.nextT)
self.backBtn.Enable(False)
self.previousBtn.Enable(False)
self.playStopBtn.Enable(False)
self.forwardBtn.Enable(False)
self.nextBtn.Enable(False)
self.currentTCtrl = wx.TextCtrl(self.visualizationSidebarPanel, value="0", style=wx.TE_CENTRE, size=(70, 10))
font = wx.Font(18, wx.SWISS, wx.NORMAL, wx.NORMAL)
self.currentTCtrl.SetFont(font)
self.currentTCtrl.Enable(False)
self.currentTCtrl.Bind(wx.EVT_TEXT, self.startCurrentTTimer)
self.currentTTimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.setCurrentT, self.currentTTimer)
controlsGrid.AddMany([
(self.backBtn, 0, wx.EXPAND),
(self.previousBtn, 0, wx.EXPAND),
(self.playStopBtn, 0, wx.EXPAND),
(self.nextBtn, 0, wx.EXPAND),
(self.forwardBtn, 0, wx.EXPAND),
(self.currentTCtrl, 0, wx.EXPAND)
])
self.controlsSizer.Add(controlsGrid)
axesBoxV = wx.StaticBox(self.visualizationSidebarPanel, label='Axes')
axesBoxSizerV = wx.StaticBoxSizer(axesBoxV, wx.VERTICAL)
self.axesV = Axes(self.visualizationSidebarPanel)
axesBoxSizerV.Add(self.axesV)
self.plotBox = wx.StaticBox(self.visualizationSidebarPanel, label='Plot')
plotSizer = wx.StaticBoxSizer(self.plotBox, wx.VERTICAL)
self.plotter = plot.PlotCanvas(self.visualizationSidebarPanel)
self.plotter.SetInitialSize(size=(220, 220))
plotSizer.Add(self.plotter)
self.plotBox.Show(False)
self.plotter.Show(False)
visualizationSidebar.AddMany([
(inputDirBtn, 0, wx.EXPAND | wx.ALL, 5),
(self.statsSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.readInputBtn, 0, wx.EXPAND | wx.ALL, 5),
(self.controlsSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.viewModeSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.exportImagesButtonV, 0, wx.EXPAND | wx.ALL, 5),
(self.exportVideoButton, 0, wx.EXPAND | wx.ALL, 5),
(axesBoxSizerV, 0, wx.EXPAND | wx.ALL, 5),
(plotSizer, 0, wx.EXPAND | wx.ALL, 5)
])
self.visualizationSidebarPanel.SetSizer(visualizationSidebar)
self.viewModeSizer.ShowItems(False)
self.controlsSizer.ShowItems(False)
tabs.AddPage(self.designSidebarPanel, "Design")
tabs.AddPage(self.visualizationSidebarPanel, "Visualization")
tabs.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
content.Add(self.grid, 1, wx.EXPAND)
content.Add(self.canvas, 1, wx.EXPAND)
self.grid.Show()
self.canvas.Hide()
self.togglePreviewStatus = 0
layout.Add(tabs, 0, wx.EXPAND)
layout.Add(content, 1, wx.EXPAND)
self.designSidebarPanel.SetupScrolling(scroll_x=False)
self.visualizationSidebarPanel.SetupScrolling(scroll_x=False)
self.SetSizer(layout)
self.Layout()
self.Refresh()
self.grid.updateSize()
self.updateParameters()
def validateAtomsFile(self):
line_number = 0
valid_first_line = re.compile("[0-9]+\t[0-9]+\t[0-9]+\t[0-9]+(\.[0-9+])*")
valid_n_line = re.compile("[0-9]+(\t\-?[0-9]+(\.[0-9]+)*){3}(\t[0-9]+){2,}")
valid = False
f = open(self.atoms_file, "r")
for line in f:
# Verify we have at least 1 line
if line_number == 0:
valid = True
if line_number == 0 and valid_first_line.match(line) == None:
valid = False
break
if line_number > 0 and valid_n_line.match(line) == None:
valid = False
break
line_number += 1
f.close()
if valid:
error = False
self.statsValidPathValue.SetLabel("Yes")
os.chdir(os.path.dirname(self.atoms_file))
data_files = glob.glob("*_*_*.dat")
if(len(data_files)):
self.data_files = data_files
self.statsNumberDataFilesValue.SetLabel(str(len(data_files)))
self.readInputBtn.Enable(True)
else:
error = 'No data files'
else:
error = 'Path does not exist'
self.statsValidPathValue.SetLabel("No")
if error:
self.atoms_file = self.data_files = False
# print "Invalid directory: %s" % error
def readInputFiles(self, evt):
atoms = {}
dataset = {}
x_param = 0
f = open(self.atoms_file, "r")
first_line = True
for line in f:
line = line.replace("\n", "").split("\t")
if first_line:
x_param = float(line[3])
else:
# We get the first 4 elements from the line
atom_id = int(line.pop(0))
atom_x = float(line.pop(0))
atom_y = float(line.pop(0))
atom_z = float(line.pop(0))
atoms[atom_id] = (atom_x, atom_y, atom_z)
first_line = False
f.close()
regex = re.compile(".*_([0-9]*)_.*.dat")
self.max_Mx = 0
self.max_My = 0
self.max_Mz = 0
for data_file in self.data_files:
data_at_t = { 'intensity': 0, 'Mx': 0, 'My': 0, 'Mz': 0, 'atoms': {} }
direction = 'x'
find_t = regex.search(data_file)
if find_t:
t = find_t.group(1)
f = open(data_file)
first_line = True
for line in f:
line = line.replace("\n", "").split("\t")
try:
atom_id = int(line.pop(0))
vector_x = float(line.pop(0))
vector_y = float(line.pop(0))
vector_z = float(line.pop(0))
data_at_t['Mx'] += vector_x
data_at_t['My'] += vector_y
data_at_t['Mz'] += vector_z
data_at_t['atoms'][atom_id] = (vector_x, vector_y, vector_z)
if first_line:
data_at_t['intensity'] = float(line.pop(0))
except:
pass
first_line = False
if data_at_t['Mx'] > self.max_Mx:
self.max_Mx = data_at_t['Mx']
if data_at_t['My'] > self.max_My:
self.max_My = data_at_t['My']
if data_at_t['Mz'] > self.max_Mz:
self.max_Mz = data_at_t['Mz']
dataset[int(t)] = data_at_t
f.close()
first_t = None
for t, data in dataset.iteritems():
if first_t == None or t < first_t:
first_t = t
if self.max_Mx:
dataset[t]['Mx'] = (dataset[t]['Mx'] + 0.0) / self.max_Mx
if self.max_My:
dataset[t]['My'] = (dataset[t]['My'] + 0.0) / self.max_My
if self.max_Mz:
dataset[t]['Mz'] = (dataset[t]['Mz'] + 0.0) / self.max_Mz
self.canvas.setDataset(atoms, dataset)
self.setT(first_t)
self.backBtn.Enable(True)
self.previousBtn.Enable(True)
self.playStopBtn.Enable(True)
self.nextBtn.Enable(True)
self.forwardBtn.Enable(True)
self.viewModeAllLayers.Enable(True)
self.viewModeLayerX.Enable(True)
self.viewModeLayerY.Enable(True)
self.viewModeLayerZ.Enable(True)
self.currentTCtrl.Enable(True)
self.readInputBtn.Show(False)
self.exportImagesButtonV.Show(True)
if _platform == "darwin":
self.exportVideoButton.Show(True)
self.statsBox.Show(False)
self.statsValidPathLabel.Show(False)
self.statsValidPathValue.Show(False)
self.statsNumberDataFilesLabel.Show(False)
self.statsNumberDataFilesValue.Show(False)
self.viewModeSizer.ShowItems(True)
self.controlsSizer.ShowItems(True)
self.plotBox.Show(True)
self.plotter.Show(True)
self.designSidebarPanel.SetupScrolling(scroll_x=False)
self.visualizationSidebarPanel.SetupScrolling(scroll_x=False)
self.Layout()
layersX = self.canvas.layersX.keys()
layersX.sort()
layersX = [str(x) for x in layersX]
layersY = self.canvas.layersY.keys()
layersY.sort()
layersY = [str(x) for x in layersY]
layersZ = self.canvas.layersZ.keys()
layersZ.sort()
layersZ = [str(x) for x in layersZ]
self.viewLayerX.Clear()
self.viewLayerX.AppendItems(layersX)
self.viewLayerX.SetSelection(0)
self.viewLayerY.Clear()
self.viewLayerY.AppendItems(layersY)
self.viewLayerY.SetSelection(0)
self.viewLayerZ.Clear()
self.viewLayerZ.AppendItems(layersZ)
self.viewLayerZ.SetSelection(0)
def exportImagesD(self, evt):
if self.atoms_file:
currentPath = os.path.dirname(self.atoms_file)
dlg = wx.DirDialog(self, message="Choose a directory",
style=wx.OPEN | wx.CHANGE_DIR
)
exportDir = None
if dlg.ShowModal() == wx.ID_OK:
exportDir = dlg.GetPath()
dlg.Destroy()
if exportDir:
os.chdir(exportDir)
existingFiles = []
files = ['atoms.png', 'axes.png']
for f in files:
if os.path.isfile(f):
existingFiles.append(f)
write = True
if len(existingFiles):
write = False
dlg = wx.MessageDialog(self,
'The following files already exists on the directory:\n\n%s' % ('\n'.join(existingFiles)),
'Overwrite files',
wx.OK | wx.CANCEL | wx.ICON_WARNING
)
if dlg.ShowModal() == wx.ID_OK:
write = True
dlg.Destroy()
if write:
self.canvas.export('atoms.png')
self.axesD.export('axes.png')
dlg = wx.MessageDialog(self,
'The files were exported succesfully.',
'Files exported',
wx.OK | wx.ICON_INFORMATION
)
dlg.ShowModal()
dlg.Destroy()
if self.atoms_file:
os.chdir(currentPath)
def exportImagesV(self, evt):
currentPath = os.path.dirname(self.atoms_file)
dlg = wx.DirDialog(self, message="Choose a directory",
style=wx.OPEN | wx.CHANGE_DIR
)
exportDir = None
if dlg.ShowModal() == wx.ID_OK:
exportDir = dlg.GetPath()
dlg.Destroy()
if exportDir:
os.chdir(exportDir)
existingFiles = []
files = ['vectors.png', 'axes.png', 'plot.png']
for f in files:
if os.path.isfile(f):
existingFiles.append(f)
write = True
if len(existingFiles):
write = False
dlg = wx.MessageDialog(self,
'The following files already exists on the directory:\n\n%s' % ('\n'.join(existingFiles)),
'Overwrite files',
wx.OK | wx.CANCEL | wx.ICON_WARNING
)
if dlg.ShowModal() == wx.ID_OK:
write = True
dlg.Destroy()
if write:
self.canvas.export('vectors.png')
self.axesV.export('axes.png')
self.plotter.SaveFile('plot.png')
dlg = wx.MessageDialog(self,
'The files were exported succesfully.',
'Files exported',
wx.OK | wx.ICON_INFORMATION
)
dlg.ShowModal()
dlg.Destroy()
os.chdir(currentPath)
def exportVideo(self, evt):
currentPath = os.path.dirname(self.atoms_file)
dlg = wx.DirDialog(self, message="Choose a directory",
style=wx.OPEN | wx.CHANGE_DIR
)
exportDir = None
if dlg.ShowModal() == wx.ID_OK:
exportDir = dlg.GetPath()
dlg.Destroy()
if exportDir:
os.chdir(exportDir)
existingFiles = []
files = ['output.avi']
for f in files:
if os.path.isfile(f):
existingFiles.append(f)
write = True
if len(existingFiles):
write = False
dlg = wx.MessageDialog(self,
'The following files already exists on the directory:\n\n%s' % ('\n'.join(existingFiles)),
'Overwrite files',
wx.OK | wx.CANCEL | wx.ICON_WARNING
)
if dlg.ShowModal() == wx.ID_OK:
write = True
dlg.Destroy()
if write:
Ts = self.canvas.dataset.keys()
Ts.sort()
dlg = wx.ProgressDialog("Creating video",
"",
maximum = len(Ts),
parent=self,
style = 0
| wx.PD_APP_MODAL
| wx.PD_CAN_ABORT
#| wx.PD_CAN_SKIP
#| wx.PD_ELAPSED_TIME
| wx.PD_ESTIMATED_TIME
| wx.PD_REMAINING_TIME
#| wx.PD_AUTO_HIDE
)
t = Ts.pop(0)
self.currentTCtrl.ChangeValue(str(t))
self.canvas.currentT = t
self.canvas.OnDraw()
canvas_image = self.canvas.getCurrentImage()
image = numpy.asarray(canvas_image)
height, width, layers = image.shape
fps = 15
capSize = (width,height)
fourcc = cv2.cv.CV_FOURCC('m', 'p', '4', 'v')
video = cv2.VideoWriter()
success = video.open('output.avi',fourcc,fps,capSize,True)
video.write(image)
keepGoing = True
count = 1
while len(Ts) and keepGoing:
t = Ts.pop(0)
count += 1
self.canvas.currentT = t
self.canvas.OnDraw()
canvas_image = self.canvas.getCurrentImage()
image = numpy.asarray(canvas_image)
video.write(image)
if count%10 == 0:
self.currentTCtrl.ChangeValue(str(t))
(keepGoing, skip) = dlg.Update(count)
gc.collect()
cv2.destroyAllWindows()
video.release()
dlg.Destroy()
video = None
os.chdir(os.path.dirname(self.atoms_file))
def plot(self, data, markerPoint, axis, max_y):
line = plot.PolyLine(data, colour='red', width=1)
marker = plot.PolyMarker([markerPoint])
# set up text, axis and draw
gc = plot.PlotGraphics([line, marker], '', '', '')
max_y = math.fabs(max_y)
max_y += 0.5
self.plotter.Draw(gc, yAxis=(-1.5,1.5), xAxis=(-max_y,max_y))
def startCurrentTTimer(self, evt):
self.currentTTimer.Start(500, wx.TIMER_ONE_SHOT)
def validateNewT(self, t):
t = int(t)
if t not in self.canvas.dataset.keys():
t = self.canvas.currentT
Ts = self.canvas.dataset.keys()
Ts.sort()
min_t = Ts[0]
Ts.sort(reverse=True)
max_t = Ts[0]
if t > max_t:
t = max_t
if t < min_t:
t = min_t
self.setT(t)
self.canvas.currentT = t
self.canvas.OnDraw()
def setCurrentT(self, evt):
t = int(self.currentTCtrl.GetValue())
self.validateNewT(t)
def previousT(self, evt):
t = self.canvas.currentT - 1
Ts = self.canvas.dataset.keys()
Ts.sort()
min_t = Ts[0]
if t < min_t:
t = min_t
if t > min_t:
self.backBtn.Enable(True)
self.previousBtn.Enable(True)
self.validateNewT(t)
def backT(self, evt):
t = self.canvas.currentT - 50
Ts = self.canvas.dataset.keys()
Ts.sort()
min_t = Ts[0]
if t < min_t:
t = min_t
if t > min_t:
self.backBtn.Enable(True)
self.previousBtn.Enable(True)
self.validateNewT(t)
def forwardT(self, evt):
t = self.canvas.currentT + 50
Ts = self.canvas.dataset.keys()
Ts.sort(reverse=True)
max_t = Ts[0]
if t > max_t:
t = max_t
if t < max_t:
self.forwardBtn.Enable(True)
self.nextBtn.Enable(True)
self.validateNewT(t)
def nextT(self, evt):
t = self.canvas.currentT + 1
Ts = self.canvas.dataset.keys()
Ts.sort(reverse=True)
max_t = Ts[0]
if t > max_t:
t = max_t
if t < max_t:
self.forwardBtn.Enable(True)
self.nextBtn.Enable(True)
self.validateNewT(t)
def setT(self, t):
self.currentTCtrl.ChangeValue(str(t))
Ts = self.canvas.dataset.keys()
Ts.sort()
min_t = Ts[0]
Ts.sort(reverse=True)
max_t = Ts[0]
if t == max_t:
self.forwardBtn.Enable(False)
self.nextBtn.Enable(False)
if t == min_t:
self.backBtn.Enable(False)
self.previousBtn.Enable(False)
plotData = self.canvas.plotData
axis = self.canvas.colorDirection
max_y = self.canvas.dataset[min_t]['intensity']
markerPoint = (self.canvas.dataset[t]['intensity'], self.canvas.dataset[t]['Mx'])
if axis == 'y':
markerPoint = (self.canvas.dataset[t]['intensity'], self.canvas.dataset[t]['My'])
if axis == 'z':
markerPoint = (self.canvas.dataset[t]['intensity'], self.canvas.dataset[t]['Mz'])
self.plot(plotData, markerPoint, axis, max_y)
def playStop(self, evt):
if self.canvas.playStatus == 'stop':
self.canvas.playStatus = 'play'
self.playStopBtn.SetBitmapLabel(self.stopBitmap)
self.currentTCtrl.Enable(False)
self.backBtn.Enable(False)
self.previousBtn.Enable(False)
self.forwardBtn.Enable(False)
self.nextBtn.Enable(False)
self.canvas.play(True)
else:
self.canvas.playStatus = 'stop'
self.currentTCtrl.Enable(True)
self.backBtn.Enable(True)
self.previousBtn.Enable(True)
self.forwardBtn.Enable(True)
self.nextBtn.Enable(True)
self.playStopBtn.SetBitmapLabel(self.playBitmap)
self.Layout()
def openFileDialog(self, evt):
self.statsValidPathValue.SetLabel("--")
self.statsNumberDataFilesValue.SetLabel("--")
self.statsGrid.ShowItems(True)
self.readInputBtn.Enable(False)
self.backBtn.Enable(False)
self.previousBtn.Enable(False)
self.playStopBtn.Enable(False)
self.forwardBtn.Enable(False)
self.nextBtn.Enable(False)
self.viewModeAllLayers.Enable(False)
self.viewModeLayerX.Enable(False)
self.viewModeLayerY.Enable(False)
self.viewModeLayerZ.Enable(False)
self.readInputBtn.Show(True)
self.exportImagesButtonV.Show(False)
self.exportVideoButton.Show(False)
self.statsBox.Show(True)
self.statsValidPathLabel.Show(True)
self.statsValidPathValue.Show(True)
self.statsNumberDataFilesLabel.Show(True)
self.statsNumberDataFilesValue.Show(True)
self.viewModeSizer.ShowItems(False)
self.controlsSizer.ShowItems(False)
self.plotBox.Show(False)
self.plotter.Show(False)
self.Layout()
self.canvas.playStatus = 'stop'
self.playStopBtn.SetBitmapLabel(self.playBitmap)
self.canvas.setDataset({}, {})
dlg = wx.FileDialog(self, message="Choose a file",
style=wx.OPEN | wx.CHANGE_DIR
)
if dlg.ShowModal() == wx.ID_OK:
self.atoms_file = dlg.GetPath()
wx.CallAfter(self.validateAtomsFile)
dlg.Destroy()
def OnPageChanged(self, evt):
# 0 = Design
# 1 = Visualization
selection = evt.GetSelection()
if selection == 0:
self.canvas.Hide()
self.grid.Show()
self.togglePreviewStatus = 0
self.designSidebar.ShowItems(True)
self.axesD.Show(False)
self.axesBoxD.Show(False)
self.sizeBoxSizer.ShowItems(True)
self.exportImagesButtonD.Show(False)
self.figuresBoxSizer.ShowItems(True)
self.allowParameterInput(True)
else:
self.canvas.setAtoms({}, {})
self.canvas.restartPosition()
wx.CallAfter(self.canvas.OnDraw)
self.canvas.Show()
self.grid.Hide()
self.designSidebar.ShowItems(False)
self.readInputBtn.Show(True)
self.exportImagesButtonV.Show(False)
self.exportVideoButton.Show(False)
self.statsBox.Show(True)
self.statsValidPathLabel.Show(True)
self.statsValidPathValue.Show(True)
self.statsNumberDataFilesLabel.Show(True)
self.statsNumberDataFilesValue.Show(True)
self.viewModeSizer.ShowItems(False)
self.controlsSizer.ShowItems(False)
self.plotBox.Show(False)
self.plotter.Show(False)
self.axesD.Show(True)
self.axesBoxD.Show(True)
self.togglePreviewStatus = 1
self.allowParameterInput(False)
self.Layout()
evt.Skip()
def allowParameterInput(self, allow):
inputs = [
self.sizeBoxWidthCtrl,
self.sizeBoxHeightCtrl,
self.configBoxLayersCtrl,
self.configBoxCellTypeSCRadio,
self.configBoxCellTypeBCCRadio,
self.configBoxCellTypeFCCRadio,
self.configBoxNetConstantCtrl,
self.configBoxHeightCtrl,
self.configBoxEtaCtrl,
self.figuresQuadPane,
self.figuresCirclePane,
self.clearButton,
]
for input in inputs:
input.Enable(allow)
def quadToggled(self, evt):
self.Layout()
if not evt.GetCollapsed():
self.grid.figure = 'quad'
self.setFigure(self.figuresQuadPane)
else:
self.grid.figure = False
def circleToggled(self, evt):
self.Layout()
if not evt.GetCollapsed():
self.grid.figure = 'circle'
self.setFigure(self.figuresCirclePane)
else:
self.grid.figure = False
def clearGrid(self, evt):
self.grid.clearGrid()
def setFigure(self, openedPane):
panes = [self.figuresQuadPane, self.figuresCirclePane]
for pane in panes:
if not pane == openedPane:
pane.Collapse()
self.Layout()
def updateCircleWidth(self, evt):
radius = self.figuresCircleRadiusCtrl.GetValue()
width = radius * self.a / (self.x ** self.eta)
self.figuresCircleWidthValue.SetLabel(str(width))
def updateGridSize(self, evt):
self.grid.cols = self.sizeBoxWidthCtrl.GetValue()
self.grid.rows = self.sizeBoxHeightCtrl.GetValue()
self.grid.updateSize()
def updateType(self, evt):
if self.configBoxCellTypeSCRadio.GetValue():
self.type = "SC"
if self.configBoxCellTypeBCCRadio.GetValue():
self.type = "BCC"
if self.configBoxCellTypeFCCRadio.GetValue():
self.type = "FCC"
self.configs['type'] = self.type
self.updateParameters()
def updateViewMode(self, evt):
self.viewLayerX.Enable(False)
self.viewLayerY.Enable(False)
self.viewLayerZ.Enable(False)
if self.viewModeAllLayers.GetValue():
self.canvas.viewMode = 'all'
if self.viewModeLayerX.GetValue():
self.canvas.viewMode = 'x'
self.viewLayerX.Enable(True)
self.canvas.viewLayer = float(self.viewLayerX.GetStringSelection())
if self.viewModeLayerY.GetValue():
self.canvas.viewMode = 'y'
self.viewLayerY.Enable(True)
self.canvas.viewLayer = float(self.viewLayerY.GetStringSelection())
if self.viewModeLayerZ.GetValue():
self.canvas.viewMode = 'z'
self.viewLayerZ.Enable(True)
self.canvas.viewLayer = float(self.viewLayerZ.GetStringSelection())
self.canvas.OnDraw()
def updateParametersProxy(self, evt):
self.updateParameters()
def updateParameters(self):
layers = self.configBoxLayersCtrl.GetValue()
heightReal = self.configBoxHeightCtrl.GetValue()
widthPixels = self.grid.getWidth()
lengthPixels = self.grid.getLength()
widthReal = heightReal * widthPixels / layers
lengthReal = heightReal * lengthPixels / layers
self.configBoxWidthValue.SetLabel(str('{0:.5f}'.format(widthReal)))
self.configBoxLengthValue.SetLabel(str('{0:.5f}'.format(lengthReal)))
self.a = a = self.configBoxNetConstantCtrl.GetValue()
self.eta = eta = self.configBoxEtaCtrl.GetValue()
factor = 1.0
if self.type == "BCC" or self.type == "FCC":
factor = 0.5
self.x = (layers * a * factor / heightReal) ** (1/eta)
self.configBoxXValue.SetLabel('{0:.5f}'.format(self.x))
# self.configBoxXValue.SetLabel(str(self.x))
def checkParametersTrigger(self, evt):
self.checkParameters()
self.exportFile()
def checkParameters(self):
valid = True
if not is_number(self.configBoxLayersCtrl.GetValue()):
valid = False
if not (self.configBoxCellTypeSCRadio.GetValue() or self.configBoxCellTypeBCCRadio.GetValue() or self.configBoxCellTypeFCCRadio.GetValue()):
valid = False
if not is_number(self.configBoxNetConstantCtrl.GetValue()):
valid = False
if not is_number(self.configBoxHeightCtrl.GetValue()):
valid = False
if not valid:
wx.MessageBox('You must have valid values for each parameter.', 'Info', wx.OK | wx.ICON_WARNING)
else:
self.configs['layers'] = self.configBoxLayersCtrl.GetValue()
self.configs['cells'] = self.grid.cells
if self.type == 'SC':
self.cube = SC(self.configs)
if self.type == 'BCC':
self.cube = BCC(self.configs)
if self.type == 'FCC':
self.cube = FCC(self.configs)
self.cube.calculate()
#self.exportFile()
# wx.MessageBox('Data exported to export.dat file.', 'Info', wx.OK | wx.ICON_INFORMATION)
def exportFile(self):
currentPath = None
if self.atoms_file:
currentPath = os.path.dirname(self.atoms_file)
dlg = wx.DirDialog(self, message="Choose a directory",
style=wx.OPEN | wx.CHANGE_DIR
)
exportDir = None
if dlg.ShowModal() == wx.ID_OK:
exportDir = dlg.GetPath()
dlg.Destroy()
if exportDir:
os.chdir(exportDir)
existingFiles = []
files = ['export.dat']
for f in files:
if os.path.isfile(f):
existingFiles.append(f)
write = True
if len(existingFiles):
write = False
dlg = wx.MessageDialog(self,
'The following files already exists on the directory:\n\n%s' % ('\n'.join(existingFiles)),
'Overwrite files',
wx.OK | wx.CANCEL | wx.ICON_WARNING
)
if dlg.ShowModal() == wx.ID_OK:
write = True
dlg.Destroy()
if write:
f = open("export.dat", "w")
number_of_neighbors = 6
if self.type == 'BCC':
number_of_neighbors = 8
if self.type == 'FCC':
number_of_neighbors = 12
line = [len(self.cube.atoms), 1, number_of_neighbors, '{0:.5f}'.format(self.x)]
f.write("\t".join(str(x) for x in line) + "\n")
atom_keys = [int(x) for x in self.cube.atoms.keys()]
atom_keys.sort()
for atom_id in atom_keys:
atom = self.cube.atoms[atom_id]
neighbors = self.cube.neighborhood[atom_id]
line = [atom_id] + ['{0:.5f}'.format(x * self.x) for x in atom] + [len(neighbors)] + neighbors + ([0] * (number_of_neighbors - len(neighbors)))
f.write("\t".join(str(x) for x in line) + "\n")
f.close()
dlg = wx.MessageDialog(self,
'The file was exported succesfully.',
'File exported',
wx.OK | wx.ICON_INFORMATION
)
dlg.ShowModal()
dlg.Destroy()
def togglePreview(self, evt):
if self.togglePreviewStatus:
self.canvas.Hide()
self.grid.Show()
self.togglePreviewStatus = 0
self.axesD.Show(False)
self.axesBoxD.Show(False)
self.exportImagesButtonD.Show(False)
self.sizeBoxSizer.ShowItems(True)
self.figuresBoxSizer.ShowItems(True)
self.allowParameterInput(True)
else:
self.checkParameters()
self.canvas.setAtoms(self.cube.atoms, self.cube.atom_type)
self.canvas.restartPosition()
self.canvas.Show()
self.grid.Hide()
self.togglePreviewStatus = 1
self.axesD.Show(True)
self.axesBoxD.Show(True)
self.exportImagesButtonD.Show(True)
self.sizeBoxSizer.ShowItems(False)
self.figuresBoxSizer.ShowItems(False)
self.allowParameterInput(False)
self.Layout()
for unit_1, unit_2 in zip(units[:-1], units[1:]):
if (unit_1 != unit_2):
return NotImplemented
return units[0]
def multiplication_rule(self, units):
non_null = [u for u in units if u]
if (len(non_null) > 1):
return NotImplemented
return non_null[0]
op_dict = {
'__mul__':multiplication_rule,
'__rmul__':multiplication_rule,
'__add__':addition_rule,
'__radd__':addition_rule,
'__sub__':addition_rule,
'__rsub__':addition_rule,
}
def __call__(self, operation, units):
if (operation not in self.op_dict):
return NotImplemented
return self.op_dict[operation](self, units)
unit_resolver = UnitResolver()
Axes.set_default_unit_to_locator_map(lambda u:u.get_tick_locators())
Axes.set_default_unit_to_formatter_map(lambda u:u.get_tick_formatters())
def __init__(self, image, **kwargs):
"""
@type image: string/array_like/PIL Image
@param image: a filepath or an image in grayscale or RGB
@param vmin:
@param vmax:
@param cmap:
@param xmin:
@param xmax:
@param ymin:
@param ymax:
@param limits:
"""
self._cmap = kwargs.get('cmap', 'gray')
if isinstance(image, str):
self.image = PILImage.open(image)
elif isinstance(image, PILImage.Image):
self.image = image.copy()
else:
if isinstance(image, ndarray):
# copy array
image = array(image)
if image.dtype.kind not in ['u', 'i']:
self.vmin = kwargs.get('vmin', min(image))
self.vmax = kwargs.get('vmax', max(image))
# rescale image
image = (image - self.vmin) / (self.vmax - self.vmin)
image = array(image * 256., dtype='int32')
image[image < 0] = 0
image[image > 255] = 255
image = array(image, dtype='uint8')
if image.ndim < 3:
image = repeat(image.reshape(image.shape[0], -1, 1), 3, 2)
for i in range(image.shape[0]):
for j in range(image.shape[1]):
image[i, j, :] = colormaps[self._cmap][image[i, j,
0]]
self.image = PILImage.fromarray(image)
# specify pixel coordinates
self.xmin = kwargs.get('xmin', 0)
self.xmax = kwargs.get('xmax', self.image.size[0])
self.ymin = kwargs.get('ymin', 0)
self.ymax = kwargs.get('ymax', self.image.size[1])
if 'limits' in kwargs:
self.xmin, self.xmax, \
self.ymin, self.ymax = kwargs['limits']
# add image to axis
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
self.idx = Image._counter
Image._counter += 1
def subplot(self, nrows, ncols, plot_number, **kwargs):
"""
Returen a subplot axes positioned by the given grid definition.
:param nrows, nrows: (*int*) Whree *nrows* and *ncols* are used to notionally spli the
figure into ``nrows * ncols`` sub-axes.
:param plot_number: (*int) Is used to identify the particular subplot that this function
is to create within the notional gird. It starts at 1, increments across rows first
and has a maximum of ``nrows * ncols`` .
:returns: Current axes specified by ``plot_number`` .
"""
chart = self.getChart()
chart.setRowNum(nrows)
chart.setColumnNum(ncols)
polar = kwargs.pop('polar', False)
isnew = True
if isnew:
polar = kwargs.pop('polar', False)
if polar:
ax = PolarAxes()
else:
ax = Axes()
ax.axes.isSubPlot = True
else:
chart.setCurrentPlot(plot_number - 1)
position = kwargs.pop('position', None)
if position is None:
if isnew:
if isinstance(plot_number, (list, tuple)):
i = 0
for pnum in plot_number:
pnum -= 1
rowidx = pnum / ncols
colidx = pnum % ncols
width = 1. / ncols
height = 1. / nrows
x = width * colidx
y = 1. - height * (rowidx + 1)
if i == 0:
minx = x
miny = y
maxx = x + width
maxy = y + height
else:
minx = min(x, minx)
miny = min(y, miny)
maxx = max(x + width, maxx)
maxy = max(y + height, maxy)
i += 1
x = minx
y = miny
width = maxx - minx
height = maxy - miny
else:
plot_number -= 1
rowidx = plot_number / ncols
colidx = plot_number % ncols
width = 1. / ncols
height = 1. / nrows
x = width * colidx
y = 1. - height * (rowidx + 1)
ax.set_position([x, y, width, height])
ax.set_outerposition([x, y, width, height])
ax.active_outerposition(True)
else:
ax.set_position(position)
ax.active_outerposition(False)
outerposition = kwargs.pop('outerposition', None)
if not outerposition is None:
ax.set_outerposition(outerposition)
ax.active_outerposition(True)
if isinstance(ax, MapAxes):
self.__set_axesm(ax, **kwargs)
else:
self.__set_axes(ax, **kwargs)
if isnew:
chart.addPlot(ax.axes)
chart.setCurrentPlot(chart.getPlots().size() - 1)
return ax
def aggregate(arrays, check_overlap=True):
""" like a multi-dimensional concatenate
input:
arrays: sequence of DimArrays
check_overlap, optional: if True, check that arrays do not overlap (to avoid data loss)
If any two elements overlap, keep the one which is not NaN, if applicable
or raise an error if two valid values overlap
Default is True to reduce the risk of errors, but this makes the operation
less performant since every time a copy of the subarray is extracted
and tested for NaNs. Consider setting check_overlap to False for large
arrays for a well-tested problems, if the valid-nan selection is not
required.
Note:
Probably a bad idea to have duplicate axis values (not tested)
TODO: add support for missing values other than np.nan
Examples:
---------
>>> a = DimArray([[1.,2,3]],axes=[('line',[0]), ('col',['a','b','c'])])
>>> b = DimArray([[4],[5]], axes=[('line',[1,2]), ('col',['d'])])
>>> c = DimArray([[22]], axes=[('line',[2]), ('col',['b'])])
>>> d = DimArray([-99], axes=[('line',[4])])
>>> aggregate((a,b,c,d))
dimarray: 10 non-null elements (6 null)
dimensions: 'line', 'col'
0 / line (4): 0 to 4
1 / col (4): a to d
array([[ 1., 2., 3., nan],
[ nan, nan, nan, 4.],
[ nan, 22., nan, 5.],
[-99., -99., -99., -99.]])
But beware of overlapping arrays. The following will raise an error:
>>> a = DimArray([[1.,2,3]],axes=[('line',[0]), ('col',['a','b','c'])])
>>> b = DimArray([[4],[5]], axes=[('line',[0,1]), ('col',['b'])])
>>> try:
... aggregate((a,b))
... except ValueError, msg:
... print msg
Overlapping arrays: set check_overlap to False to suppress this error.
Can set check_overlap to False to let it happen anyway (the latter array wins)
>>> aggregate((a,b), check_overlap=False)
dimarray: 4 non-null elements (2 null)
dimensions: 'line', 'col'
0 / line (2): 0 to 1
1 / col (3): a to c
array([[ 1., 4., 3.],
[ nan, 5., nan]])
Note that if NaNs are present on overlapping, the valid data are kept
>>> a = DimArray([[1.,2,3]],axes=[('line',[1]), ('col',['a','b','c'])])
>>> b = DimArray([[np.nan],[5]], axes=[('line',[1,2]), ('col',['b'])])
>>> aggregate((a,b)) # does not overwrite `2` at location (1, 'b')
dimarray: 4 non-null elements (2 null)
dimensions: 'line', 'col'
0 / line (2): 1 to 2
1 / col (3): a to c
array([[ 1., 2., 3.],
[ nan, 5., nan]])
"""
# list of common dimensions
dims = get_dims(*arrays)
# build a common Axes object
axes = Axes()
for d in dims:
newaxis = concatenate_axes([a.axes[d] for a in arrays if d in a.dims])
newaxis.values = np.unique(newaxis.values) # unique values
axes.append(newaxis)
# Fill in an array
newarray = arrays[0]._constructor(None, axes=axes, dtype=arrays[0].dtype)
for a in arrays:
indices = {ax.name:ax.values for ax in a.axes}
if check_overlap:
# look for nans in replaced and replacing arrays
subarray = newarray.take(indices, broadcast_arrays=False).values
subarray_is_nan = np.isnan(subarray)
newvalues_is_nan = np.isnan(a.values)
# check overlapping
overlap_values = ~subarray_is_nan & ~newvalues_is_nan
if np.any(overlap_values):
raise ValueError("Overlapping arrays: set check_overlap to False to suppress this error.")
# only take new non-nan values
newvalues = np.where(newvalues_is_nan, subarray, a.values)
else:
newvalues = a.values
# The actual operation is done by put
newarray.put(newvalues, indices=indices, inplace=True, convert=True, broadcast_arrays=False)
# That's it !
return newarray
def subplots(self, nrows=1, ncols=1, position=None, sharex=False, sharey=False, \
wspace=None, hspace=None, axestype='Axes', **kwargs):
'''
Create a figure and a set of subplots.
:param nrows: (*int*) Number of rows.
:param ncols: (*int*) Number of cols.
:param position: (*list*) All axes' position specified by *position=* [left, bottom, width
height] in normalized (0, 1) units. Default is [0,0,1,1].
:param sharex: (*boolean*) If share x axis.
:param sharey: (*boolean*) If share y axis.
:param subplot_kw: (*dict*) Subplot key words.
:param wspace: (*float*) The amount of width reserved for blank space between subplots,
expressed as a fraction of the average axis width.
:param hspace: (*float*) The amount of height reserved for blank space between subplots,
expressed as a fraction of the average axis height.
:param axestype: (*string*) Axes type [Axes | Axes3D | MapAxes | PolarAxes].
:returns: The figure and the axes tuple.
'''
if position is None:
if wspace is None and hspace is None:
position = [0, 0, 1, 1]
else:
position = [0.13, 0.11, 0.775, 0.815]
left = float(position[0])
bottom = float(position[1])
width = float(position[2])
height = float(position[3])
chart = self.getChart()
chart.setRowNum(nrows)
chart.setColumnNum(ncols)
axs = []
ax2d = nrows > 1 and ncols > 1
w = width / ncols
h = height / nrows
iswspace = False
ishspace = False
if not wspace is None and ncols > 1:
w = (width - wspace * (ncols - 1)) / ncols
iswspace = True
if not hspace is None and nrows > 1:
h = (height - hspace * (nrows - 1)) / nrows
ishspace = True
axestype = axestype.lower()
y = bottom + height - h
for i in range(nrows):
if ax2d:
axs2d = []
x = left
if ishspace:
if i > 0:
y -= hspace
for j in range(ncols):
if axestype == 'axes3d':
ax = Axes3D()
self.__set_axes3d(ax, **kwarg)
elif axestype == 'mapaxes':
ax = MapAxes()
self.__set_axesm(ax, **kwargs)
elif axestype == 'polaraxes':
ax = PolarAxes()
else:
ax = Axes()
self.__set_axes(ax, **kwargs)
ax.axes.isSubPlot = True
if not iswspace and not ishspace:
x = left + w * j
y = (bottom + height) - h * (i + 1)
ax.set_position([x, y, w, h])
ax.set_outerposition([x, y, w, h])
ax.active_outerposition(True)
else:
if iswspace:
if j > 0:
x += wspace
ax.set_position([x, y, w, h])
ax.active_outerposition(False)
x += w
if sharex:
if i < nrows - 1:
ax.axes.getAxis(
Location.BOTTOM).setDrawTickLabel(False)
if sharey:
if j > 0:
ax.axes.getAxis(Location.LEFT).setDrawTickLabel(False)
chart.addPlot(ax.axes)
if ax2d:
axs2d.append(ax)
else:
axs.append(ax)
if ax2d:
axs.append(tuple(axs2d))
y -= h
chart.setCurrentPlot(0)
return tuple(axs)
def __init__(self, values=None, axes=None, dims=None, labels=None, copy=False, dtype=None, _indexing=None, _indexing_broadcast=None, **kwargs):
""" Initialization. See help on DimArray.
"""
# check if attached to values (e.g. DimArray object)
if hasattr(values, "axes") and axes is None:
axes = values.axes
# default options
if _indexing is None: _indexing = get_option('indexing.by')
if _indexing_broadcast is None: _indexing_broadcast = get_option('indexing.broadcast')
#
# array values
#
# if masked array, replace mask by NaN
if isinstance(values, np.ma.MaskedArray):
try:
values = values.filled(np.nan) # fill mask with nans
# first convert to float
except:
values = np.ma.asarray(values, dtype=float).filled(np.nan) # fill mask with nans
if values is not None:
values = np.array(values, copy=copy, dtype=dtype)
#
# Initialize the axes
#
if axes is None and labels is None:
assert values is not None, "values= or/and axes=, labels= required to determine dimensions"
axes = Axes._init(axes, dims=dims, labels=labels, shape=values.shape if values is not None else None)
assert type(axes) is Axes
# if values not provided, create empty data, filled with NaNs if dtype is float
if values is None:
values = np.empty([ax.size for ax in axes], dtype=dtype)
if dtype in (float, None, np.dtype(float)):
values.fill(np.nan)
else:
warnings.warn("no nan representation for {}, array left empty".format(repr(dtype)))
#
# store all fields
#
self.values = values
self.axes = axes
## options
self._indexing = _indexing
self._indexing_broadcast = _indexing_broadcast
#
# metadata (see Metadata type in metadata.py)
#
#for k in kwargs:
# setncattr(self, k, kwargs[k]) # perform type-checking and store in self._metadata
self._metadata = kwargs
# Check consistency between axes and values
inferred = tuple([ax.size for ax in self.axes])
if inferred != self.values.shape:
msg = """\
shape inferred from axes: {}
shape inferred from data: {}
mismatch between values and axes""".format(inferred, self.values.shape)
raise Exception(msg)
# If a general ordering relationship of the class is assumed,
# always sort the class
if self._order is not None and self.dims != tuple(dim for dim in self._order if dim in self.dims):
present = filter(lambda x: x in self.dims, self._order) # prescribed
missing = filter(lambda x: x not in self._order, self.dims) # not
order = missing + present # prepend dimensions not found in ordering relationship
obj = self.transpose(order)
self.values = obj.values
self.axes = obj.axes
def drawSidebar(self):
layout = wx.BoxSizer(wx.HORIZONTAL)
tabs = wx.Notebook(self)
self.designSidebarPanel = scrolled.ScrolledPanel(tabs)
self.designSidebar = wx.BoxSizer(wx.VERTICAL)
self.content = content = wx.BoxSizer(wx.VERTICAL)
self.grid = BitMapGrid(self)
self.canvas = AtomsCanvas(self)
#Grid size
self.sizeBox = wx.StaticBox(self.designSidebarPanel, label='Grid size')
self.sizeBoxSizer = wx.StaticBoxSizer(self.sizeBox, wx.VERTICAL)
self.sizeBoxGrid = wx.GridSizer(1, 4, 10, 10)
self.sizeBoxWidthLabel = wx.StaticText(self.designSidebarPanel, label="Width")
self.sizeBoxWidthCtrl = wx.SpinCtrl(self.designSidebarPanel, value=str(self.grid.cols), initial=self.grid.cols, min=0, size=(50, 20))
self.sizeBoxHeightLabel = wx.StaticText(self.designSidebarPanel, label="Height")
self.sizeBoxHeightCtrl = wx.SpinCtrl(self.designSidebarPanel, value=str(self.grid.rows), initial=self.grid.rows, min=0, size=(50, 20))
self.sizeBoxGrid.AddMany([
(self.sizeBoxWidthLabel, 0, wx.EXPAND),
(self.sizeBoxWidthCtrl, 0, wx.EXPAND),
(self.sizeBoxHeightLabel, 0, wx.EXPAND),
(self.sizeBoxHeightCtrl, 0, wx.EXPAND)
])
self.sizeBoxWidthCtrl.Bind(wx.EVT_SPINCTRL, self.updateGridSize)
self.sizeBoxHeightCtrl.Bind(wx.EVT_SPINCTRL, self.updateGridSize)
self.sizeBoxSizer.Add(self.sizeBoxGrid)
#Object parameters
self.configBox = wx.StaticBox(self.designSidebarPanel, label='Object parameters')
self.configBoxSizer = wx.StaticBoxSizer(self.configBox, wx.VERTICAL)
self.configBoxGrid = wx.GridSizer(10, 2, 5, 5)
# Number of layers
self.configBoxLayersLabel = wx.StaticText(self.designSidebarPanel, label="Layers", size=(70,20))
self.configBoxLayersCtrl = wx.SpinCtrl(self.designSidebarPanel, value="3", initial=10, min=1, size=(50, 20))
# Avoid bug on OS X that auto-focus on first field and hides the default value
wx.CallAfter(self.configBoxLayersCtrl.SetFocus)
self.configBoxLayersCtrl.Bind(wx.EVT_SPINCTRL, self.updateParametersProxy)
# Type of structure
self.configBoxCellTypeLabel = wx.StaticText(self.designSidebarPanel, label="Structure")
self.configBoxCellTypeSCRadio = wx.RadioButton(self.designSidebarPanel, label='SC', style=wx.RB_GROUP)
self.configBoxCellTypeBCCRadio = wx.RadioButton(self.designSidebarPanel, label='BCC')
self.configBoxCellTypeFCCRadio = wx.RadioButton(self.designSidebarPanel, label='FCC')
self.configBoxCellTypeSCRadio.SetValue(True)
self.type = "SC"
self.configs['type'] = self.type
self.configBoxCellTypeSCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
self.configBoxCellTypeBCCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
self.configBoxCellTypeFCCRadio.Bind(wx.EVT_RADIOBUTTON, self.updateType)
# Net constant
self.configBoxNetConstantLabel = wx.StaticText(self.designSidebarPanel, label="Lattice constant")
self.configBoxNetConstantCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0, increment=0.1, value=0.28, agwStyle=FS.FS_LEFT)
self.configBoxNetConstantCtrl.SetFormat("%f")
self.configBoxNetConstantCtrl.SetDigits(5)
self.configBoxNetConstantCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
# Size
self.configBoxHeightLabel = wx.StaticText(self.designSidebarPanel, label="Height (nm)", size=(70, 20))
self.configBoxHeightCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0.1, increment=0.1, value=10, agwStyle=FS.FS_LEFT)
self.configBoxHeightCtrl.SetFormat("%f")
self.configBoxHeightCtrl.SetDigits(2)
self.configBoxHeightCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
# Sizes
self.configBoxWidthLabel = wx.StaticText(self.designSidebarPanel, label="Width (nm)", size=(70, 20))
self.configBoxWidthValue = wx.StaticText(self.designSidebarPanel, label="--", size=(70, 20))
self.configBoxLengthLabel = wx.StaticText(self.designSidebarPanel, label="Length (nm)", size=(70, 20))
self.configBoxLengthValue = wx.StaticText(self.designSidebarPanel, label="--", size=(70, 20))
# Scaling
self.configBoxEtaLabel = wx.StaticText(self.designSidebarPanel, label="Eta", size=(70, 20))
self.configBoxEtaCtrl = FS.FloatSpin(self.designSidebarPanel, -1, min_val=0, increment=0.1, value=0.55, agwStyle=FS.FS_LEFT)
self.configBoxEtaCtrl.SetFormat("%f")
self.configBoxEtaCtrl.SetDigits(5)
self.configBoxEtaCtrl.Bind(FS.EVT_FLOATSPIN, self.updateParametersProxy)
self.configBoxXLabel = wx.StaticText(self.designSidebarPanel, label="X", size=(70, 20))
self.configBoxXValue = wx.StaticText(self.designSidebarPanel, label="--", size=(50, 20))
self.configBoxGrid.AddMany([
(self.configBoxLayersLabel, 0, wx.EXPAND),
(self.configBoxLayersCtrl, 0, wx.EXPAND),
(self.configBoxCellTypeLabel, 0, wx.EXPAND),
(self.configBoxCellTypeSCRadio, 0, wx.EXPAND),
(wx.StaticText(self, -1, ''), 0, wx.EXPAND), #Blank space
(self.configBoxCellTypeBCCRadio, 0, wx.EXPAND),
(wx.StaticText(self, -1, ''), 0, wx.EXPAND), #Blank space
(self.configBoxCellTypeFCCRadio, 0, wx.EXPAND),
(self.configBoxNetConstantLabel, 0, wx.EXPAND),
(self.configBoxNetConstantCtrl, 0, wx.EXPAND),
(self.configBoxHeightLabel, 0, wx.EXPAND),
(self.configBoxHeightCtrl, 0, wx.EXPAND),
(self.configBoxWidthLabel, 0, wx.EXPAND),
(self.configBoxWidthValue, 0, wx.EXPAND),
(self.configBoxLengthLabel, 0, wx.EXPAND),
(self.configBoxLengthValue, 0, wx.EXPAND),
(self.configBoxEtaLabel, 0, wx.EXPAND),
(self.configBoxEtaCtrl, 0, wx.EXPAND),
(self.configBoxXLabel, 0, wx.EXPAND),
(self.configBoxXValue, 0, wx.EXPAND)
])
self.configBoxSizer.Add(self.configBoxGrid)
# Figures
self.figuresBox = wx.StaticBox(self.designSidebarPanel, label='Figures')
self.figuresBoxSizer = wx.StaticBoxSizer(self.figuresBox, wx.VERTICAL)
self.figuresBoxGrid = wx.FlexGridSizer(2, 1, 10, 10)
# Quadrilateral
self.figuresQuadPane = wx.CollapsiblePane(self.designSidebarPanel, label="Quadrilateral", style=wx.CP_DEFAULT_STYLE|wx.CP_NO_TLW_RESIZE)
self.figuresQuadPane.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.quadToggled)
self.figuresQuadSizer = wx.GridSizer(1, 4, 10, 10)
self.figuresQuadPaneWin = self.figuresQuadPane.GetPane()
self.figuresQuadWidthLabel = wx.StaticText(self.figuresQuadPaneWin, label="Width")
self.figuresQuadWidthCtrl = wx.SpinCtrl(self.figuresQuadPaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresQuadHeightLabel = wx.StaticText(self.figuresQuadPaneWin, label="Height")
self.figuresQuadHeightCtrl = wx.SpinCtrl(self.figuresQuadPaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresQuadSizer.AddMany([
(self.figuresQuadWidthLabel, 0, wx.EXPAND),
(self.figuresQuadWidthCtrl, 0, wx.EXPAND),
(self.figuresQuadHeightLabel, 0, wx.EXPAND),
(self.figuresQuadHeightCtrl, 0, wx.EXPAND)
])
self.figuresQuadPaneWin.SetSizer(self.figuresQuadSizer)
# Circle
self.figuresCirclePane = wx.CollapsiblePane(self.designSidebarPanel, label="Circle", style=wx.CP_DEFAULT_STYLE|wx.CP_NO_TLW_RESIZE)
self.figuresCirclePane.Bind(wx.EVT_COLLAPSIBLEPANE_CHANGED, self.circleToggled)
self.figuresCircleSizer = wx.GridSizer(2, 2, 10, 10)
self.figuresCirclePaneWin = self.figuresCirclePane.GetPane()
self.figuresCircleRadiusLabel = wx.StaticText(self.figuresCirclePaneWin, label="Radius")
self.figuresCircleRadiusCtrl = wx.SpinCtrl(self.figuresCirclePaneWin, value="1", initial=1, min=1, size=(50,20))
self.figuresCircleRadiusCtrl.Bind(wx.EVT_SPINCTRL, self.updateCircleWidth)
self.figuresCircleWidthLabel = wx.StaticText(self.figuresCirclePaneWin, label="Width (nm)")
self.figuresCircleWidthValue = wx.StaticText(self.figuresCirclePaneWin, label="--")
self.figuresCircleSizer.AddMany([
(self.figuresCircleRadiusLabel, 0, wx.EXPAND),
(self.figuresCircleRadiusCtrl, 0, wx.EXPAND),
(self.figuresCircleWidthLabel, 0, wx.EXPAND),
(self.figuresCircleWidthValue, 0, wx.EXPAND)
])
self.figuresCirclePaneWin.SetSizer(self.figuresCircleSizer)
self.figuresBoxGrid.AddMany([
(self.figuresQuadPane, 0, wx.EXPAND),
(self.figuresCirclePane, 0, wx.EXPAND)
])
self.figuresBoxSizer.Add(self.figuresBoxGrid)
self.clearButton = wx.Button(self.designSidebarPanel, label="Clear grid")
self.clearButton.Bind(wx.EVT_BUTTON, self.clearGrid)
self.exportFileButton = wx.Button(self.designSidebarPanel, label="Export Data")
self.exportFileButton.Bind(wx.EVT_BUTTON, self.checkParametersTrigger)
self.exportImagesButtonD = wx.Button(self.designSidebarPanel, label="Export Images")
self.exportImagesButtonD.Bind(wx.EVT_BUTTON, self.exportImagesD)
self.exportImagesButtonD.Show(False)
self.previewButton = wx.Button(self.designSidebarPanel, label="Show/hide preview")
self.previewButton.Bind(wx.EVT_BUTTON, self.togglePreview)
self.axesBoxD = wx.StaticBox(self.designSidebarPanel, label='Axes')
self.axesBoxSizerD = wx.StaticBoxSizer(self.axesBoxD, wx.VERTICAL)
self.axesD = Axes(self.designSidebarPanel)
self.axesBoxSizerD.Add(self.axesD)
self.designSidebar.Add(self.sizeBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.configBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.figuresBoxSizer, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.clearButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.exportFileButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.exportImagesButtonD, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.previewButton, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebar.Add(self.axesBoxSizerD, 0, wx.EXPAND | wx.ALL, 5)
self.designSidebarPanel.SetSizer(self.designSidebar)
wx.CallAfter(self.axesBoxD.Show, False)
wx.CallAfter(self.axesD.Show, False)
self.visualizationSidebarPanel = scrolled.ScrolledPanel(tabs)
visualizationSidebar = wx.BoxSizer(wx.VERTICAL)
inputDirBtn = wx.Button(self.visualizationSidebarPanel, -1, "Select Atoms file")
self.Bind(wx.EVT_BUTTON, self.openFileDialog, inputDirBtn)
self.statsBox = wx.StaticBox(self.visualizationSidebarPanel, label='Input Stats')
self.statsSizer = wx.StaticBoxSizer(self.statsBox, wx.VERTICAL)
self.statsGrid = wx.GridSizer(2, 2, 5, 5)
self.statsValidPathLabel = wx.StaticText(self.visualizationSidebarPanel, label="Valid Atom file")
self.statsValidPathValue = wx.StaticText(self.visualizationSidebarPanel, label="--")
self.statsNumberDataFilesLabel = wx.StaticText(self.visualizationSidebarPanel, label="# of Data files")
self.statsNumberDataFilesValue = wx.StaticText(self.visualizationSidebarPanel, label="--")
self.statsGrid.AddMany([
(self.statsValidPathLabel, 0, wx.EXPAND),
(self.statsValidPathValue, 0, wx.EXPAND),
(self.statsNumberDataFilesLabel, 0, wx.EXPAND),
(self.statsNumberDataFilesValue, 0, wx.EXPAND)
])
self.statsSizer.Add(self.statsGrid)
self.readInputBtn = wx.Button(self.visualizationSidebarPanel, label="Read Input files")
# Enable only if we have a valid directory
self.readInputBtn.Enable(False)
self.readInputBtn.Bind(wx.EVT_BUTTON, self.readInputFiles)
viewModeBox = wx.StaticBox(self.visualizationSidebarPanel, label='View layer')
self.viewModeSizer = wx.StaticBoxSizer(viewModeBox, wx.VERTICAL)
viewModeGrid = wx.FlexGridSizer(2, 4, 5, 5)
self.viewModeAllLayers = wx.RadioButton(self.visualizationSidebarPanel, label='All', style=wx.RB_GROUP)
self.viewModeLayerX = wx.RadioButton(self.visualizationSidebarPanel, label='X')
self.viewLayerX = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeLayerY = wx.RadioButton(self.visualizationSidebarPanel, label='Y')
self.viewLayerY = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeLayerZ = wx.RadioButton(self.visualizationSidebarPanel, label='Z')
self.viewLayerZ = wx.ComboBox(self.visualizationSidebarPanel, choices=["0.000"], style=wx.CB_DROPDOWN|wx.CB_READONLY, size=(60, 27))
self.viewModeAllLayers.SetValue(True)
self.viewModeAllLayers.Enable(False)
self.viewModeLayerX.Enable(False)
self.viewModeLayerY.Enable(False)
self.viewModeLayerZ.Enable(False)
self.viewLayerX.Enable(False)
self.viewLayerY.Enable(False)
self.viewLayerZ.Enable(False)
self.viewModeAllLayers.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerX.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerY.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewModeLayerZ.Bind(wx.EVT_RADIOBUTTON, self.updateViewMode)
self.viewLayerX.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
self.viewLayerY.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
self.viewLayerZ.Bind(wx.EVT_COMBOBOX, self.updateViewMode)
viewModeGrid.AddMany([
(self.viewModeAllLayers, 0, wx.EXPAND),
(self.viewModeLayerX, 0, wx.EXPAND),
(self.viewModeLayerY, 0, wx.EXPAND),
(self.viewModeLayerZ, 0, wx.EXPAND),
((1,1)), #Blank space
(self.viewLayerX, 0, wx.EXPAND),
(self.viewLayerY, 0, wx.EXPAND),
(self.viewLayerZ, 0, wx.EXPAND)
])
self.viewModeSizer.Add(viewModeGrid, flag=wx.ALL, border=1)
self.exportImagesButtonV = wx.Button(self.visualizationSidebarPanel, label="Export Images")
self.exportImagesButtonV.Bind(wx.EVT_BUTTON, self.exportImagesV)
self.exportImagesButtonV.Show(False)
self.exportVideoButton = wx.Button(self.visualizationSidebarPanel, label="Export Video")
self.exportVideoButton.Bind(wx.EVT_BUTTON, self.exportVideo)
self.exportVideoButton.Show(False)
controlsBox = wx.StaticBox(self.visualizationSidebarPanel, label='Controls')
self.controlsSizer = wx.StaticBoxSizer(controlsBox, wx.VERTICAL)
controlsGrid = wx.FlexGridSizer(1, 6, 5, 5)
self.playBitmap = wx.Bitmap("images/play.png", wx.BITMAP_TYPE_ANY)
self.stopBitmap = wx.Bitmap("images/pause.png", wx.BITMAP_TYPE_ANY)
self.backBitmap = wx.Bitmap("images/back.png", wx.BITMAP_TYPE_ANY)
self.forwardBitmap = wx.Bitmap("images/forward.png", wx.BITMAP_TYPE_ANY)
self.previousBitmap = wx.Bitmap("images/previous.png", wx.BITMAP_TYPE_ANY)
self.nextBitmap = wx.Bitmap("images/next.png", wx.BITMAP_TYPE_ANY)
self.backBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.backBitmap, (0,0), ((30,30)))
self.previousBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.previousBitmap, (0,0), ((30,30)))
self.playStopBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.playBitmap, (0,0), ((30,30)))
self.nextBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.nextBitmap, (0,0), ((30,30)))
self.forwardBtn = wx.BitmapButton(self.visualizationSidebarPanel, -1, self.forwardBitmap, (0,0), ((30,30)))
self.previousBtn.Bind(wx.EVT_BUTTON, self.previousT)
self.backBtn.Bind(wx.EVT_BUTTON, self.backT)
self.playStopBtn.Bind(wx.EVT_BUTTON, self.playStop)
self.forwardBtn.Bind(wx.EVT_BUTTON, self.forwardT)
self.nextBtn.Bind(wx.EVT_BUTTON, self.nextT)
self.backBtn.Enable(False)
self.previousBtn.Enable(False)
self.playStopBtn.Enable(False)
self.forwardBtn.Enable(False)
self.nextBtn.Enable(False)
self.currentTCtrl = wx.TextCtrl(self.visualizationSidebarPanel, value="0", style=wx.TE_CENTRE, size=(70, 10))
font = wx.Font(18, wx.SWISS, wx.NORMAL, wx.NORMAL)
self.currentTCtrl.SetFont(font)
self.currentTCtrl.Enable(False)
self.currentTCtrl.Bind(wx.EVT_TEXT, self.startCurrentTTimer)
self.currentTTimer = wx.Timer(self)
self.Bind(wx.EVT_TIMER, self.setCurrentT, self.currentTTimer)
controlsGrid.AddMany([
(self.backBtn, 0, wx.EXPAND),
(self.previousBtn, 0, wx.EXPAND),
(self.playStopBtn, 0, wx.EXPAND),
(self.nextBtn, 0, wx.EXPAND),
(self.forwardBtn, 0, wx.EXPAND),
(self.currentTCtrl, 0, wx.EXPAND)
])
self.controlsSizer.Add(controlsGrid)
axesBoxV = wx.StaticBox(self.visualizationSidebarPanel, label='Axes')
axesBoxSizerV = wx.StaticBoxSizer(axesBoxV, wx.VERTICAL)
self.axesV = Axes(self.visualizationSidebarPanel)
axesBoxSizerV.Add(self.axesV)
self.plotBox = wx.StaticBox(self.visualizationSidebarPanel, label='Plot')
plotSizer = wx.StaticBoxSizer(self.plotBox, wx.VERTICAL)
self.plotter = plot.PlotCanvas(self.visualizationSidebarPanel)
self.plotter.SetInitialSize(size=(220, 220))
plotSizer.Add(self.plotter)
self.plotBox.Show(False)
self.plotter.Show(False)
visualizationSidebar.AddMany([
(inputDirBtn, 0, wx.EXPAND | wx.ALL, 5),
(self.statsSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.readInputBtn, 0, wx.EXPAND | wx.ALL, 5),
(self.controlsSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.viewModeSizer, 0, wx.EXPAND | wx.ALL, 5),
(self.exportImagesButtonV, 0, wx.EXPAND | wx.ALL, 5),
(self.exportVideoButton, 0, wx.EXPAND | wx.ALL, 5),
(axesBoxSizerV, 0, wx.EXPAND | wx.ALL, 5),
(plotSizer, 0, wx.EXPAND | wx.ALL, 5)
])
self.visualizationSidebarPanel.SetSizer(visualizationSidebar)
self.viewModeSizer.ShowItems(False)
self.controlsSizer.ShowItems(False)
tabs.AddPage(self.designSidebarPanel, "Design")
tabs.AddPage(self.visualizationSidebarPanel, "Visualization")
tabs.Bind(wx.EVT_NOTEBOOK_PAGE_CHANGED, self.OnPageChanged)
content.Add(self.grid, 1, wx.EXPAND)
content.Add(self.canvas, 1, wx.EXPAND)
self.grid.Show()
self.canvas.Hide()
self.togglePreviewStatus = 0
layout.Add(tabs, 0, wx.EXPAND)
layout.Add(content, 1, wx.EXPAND)
self.designSidebarPanel.SetupScrolling(scroll_x=False)
self.visualizationSidebarPanel.SetupScrolling(scroll_x=False)
self.SetSizer(layout)
self.Layout()
self.Refresh()
self.grid.updateSize()
self.updateParameters()
def __init__(self, image, **kwargs):
"""
@type image: string/array_like/PIL Image
@param image: a filepath or an image in grayscale or RGB
@param vmin:
@param vmax:
@param cmap:
@param xmin:
@param xmax:
@param ymin:
@param ymax:
@param limits:
"""
self._cmap = kwargs.get('cmap', 'gray')
if isinstance(image, str):
self.image = PILImage.open(image)
elif isinstance(image, PILImage.Image):
self.image = image.copy()
else:
if isinstance(image, ndarray):
# copy array
image = array(image)
if image.dtype.kind not in ['u', 'i']:
self.vmin = kwargs.get('vmin', min(image))
self.vmax = kwargs.get('vmax', max(image))
# rescale image
image = (image - self.vmin) / (self.vmax - self.vmin)
image = array(image * 256., dtype='int32')
image[image < 0] = 0
image[image > 255] = 255
image = array(image, dtype='uint8')
if image.ndim < 3:
image = repeat(image.reshape(image.shape[0], -1, 1), 3, 2)
for i in range(image.shape[0]):
for j in range(image.shape[1]):
image[i, j, :] = colormaps[self._cmap][image[i, j, 0]]
self.image = PILImage.fromarray(image)
# specify pixel coordinates
self.xmin = kwargs.get('xmin', 0)
self.xmax = kwargs.get('xmax', self.image.size[0])
self.ymin = kwargs.get('ymin', 0)
self.ymax = kwargs.get('ymax', self.image.size[1])
if 'limits' in kwargs:
self.xmin, self.xmax, \
self.ymin, self.ymax = kwargs['limits']
# add image to axis
self.axes = kwargs.get('axes', Axes.gca())
self.axes.children.append(self)
self.idx = Image._counter
Image._counter += 1
def gca(): """ Returns currently active axis. """ return Axes.gca()
def _take_broadcast(a, indices):
""" broadcast array-indices & integers, numpy's classical
Examples:
---------
>>> a = da.zeros(shape=(3,4,5,6))
>>> a[:,[0, 1],:,2].shape
(2, 3, 5)
>>> a[:,[0, 1],2,:].shape
(3, 2, 6)
"""
# new values
newval = a.values[indices]
# if the new values is a scalar, then just return it
if np.isscalar(newval):
return newval
# new axes: broacast indices (should do the same as above, since integers are just broadcast)
indices2 = broadcast_indices(indices)
# assert np.all(newval == a.values[indices2])
# make a multi-axis with tuples
is_array2 = np.array([np.iterable(ix) for ix in indices2])
nb_array2 = is_array2.sum()
# If none or one array is present, easy
if nb_array2 <= 1:
newaxes = [
a.axes[i][ix] for i, ix in enumerate(indices)
if not np.isscalar(ix)
] # indices or indices2, does not matter
# else, finer check needed
else:
# same stats but on original indices
is_array = np.array([np.iterable(ix) for ix in indices])
array_ix_pos = np.where(is_array)[0]
# Determine where the axis will be inserted
# - need to consider the integers as well (broadcast as arrays)
# - if two indexed dimensions are not contiguous, new axis placed at first position...
# a = zeros((3,4,5,6))
# a[:,[1,2],:,0].shape ==> (2, 3, 5)
# a[:,[1,2],0,:].shape ==> (3, 2, 6)
array_ix_pos2 = np.where(is_array2)[0]
if np.any(np.diff(array_ix_pos2) > 1
): # that mean, if two indexed dimensions are not contiguous
insert = 0
else:
insert = array_ix_pos2[0]
# Now determine axis value
# ...if originally only one array was provided, use these values correspondingly
if len(array_ix_pos) == 1:
i = array_ix_pos[0]
values = a.axes[i].values[indices[i]]
name = a.axes[i].name
# ...else use a list of tuples
else:
values = zip(
*[a.axes[i].values[indices2[i]] for i in array_ix_pos])
name = ",".join([a.axes[i].name for i in array_ix_pos])
broadcastaxis = Axis(values, name)
newaxes = Axes()
for i, ax in enumerate(a.axes):
# axis is already part of the broadcast axis: skip
if is_array2[i]:
continue
else:
newaxis = ax[indices2[i]]
## do not append axis if scalar
#if np.isscalar(newaxis):
# continue
newaxes.append(newaxis)
# insert the right new axis at the appropriate position
newaxes.insert(insert, broadcastaxis)
return a._constructor(newval, newaxes, **a._metadata)
