def show(self, *args, **kwargs):
""" Wrapper to imshow. Converts to gray to allow color maps.
Notes
-----
Differs from patchshow in that the collective image (bg, grid, particles)
is a series of masks, so they have to be drawn onto a single ndarray and
then plotted. Sicne patchshow is writing patchs, it can plot the background
separate from the grid and particles, which is slightly easier"""
# This will pull out "ax", leaving remaing args/kwargs
axes, kwargs = _parse_ax(*args, **kwargs)
title = kwargs.pop('title', None)
save = kwargs.pop('save', None)
bgonly = kwargs.pop('bgonly', False)
annotate = kwargs.pop('annotate', False)
grid = kwargs.pop('grid', False)
gcolor = kwargs.pop('gcolor', None)
gunder = kwargs.pop('gunder', False)
gstyle = kwargs.pop('gstyle', None) #NOT USED
nolabel = kwargs.pop('nolabel', False)
zoom = kwargs.pop('zoom', None)
if gstyle:
raise CanvasPlotError('"gstyle" only valid for patchshow()')
if 'pmap' in kwargs:
raise CanvasPlotError('"pmap" is only valid for patchshow() method')
PBINARY = False
if 'cmap' in kwargs:
if kwargs['cmap'] == 'pbinary' or kwargs['cmap'] == 'pbinary_r':
PBINARY = kwargs['cmap']
del kwargs['cmap']
# Get the background
if bgonly:
if 'cmap' not in kwargs:
raise CanvasPlotError('"bgonly" is only valid when a colormap is'
' passed.')
bg = kwargs['cmap'](self.graybackground)[... , :3]
del kwargs['cmap']
else:
bg = self.background
if PBINARY:
if PBINARY == 'pbinary_r':
bg = np.ones(bg.shape).astype(bool)
else:
bg = np.zeros(bg.shape).astype(bool)
# grid overlay
if gcolor or gunder and not grid:
grid = True
# If user enters gcolor, assume default grid
if grid and not gcolor:
gcolor = GCOLOR
# Map attributes from grid (centers, corners, grid)
gattr = np.zeros(bg.shape).astype(bool) #IE pass
if grid:
if not gcolor:
gcolor = GCOLOR
if grid == True:
grid = 'grid'
# Validate grid keyword
try:
gattr=getattr( self.grid, grid.lower() )
except Exception:
raise CanvasPlotError('Invalid grid argument, "%s". Choose from: '
'True, "grid", "centers", "corners", "hlines", "vlines"'
% grid)
gcolor = to_normrgb(gcolor)
#Draw grid over or under?
if gunder:
bg[gattr] = gcolor
image = self._draw_particles(bg, force_binary=PBINARY)
else:
image = self._draw_particles(bg, force_binary=PBINARY)
image[gattr] = gcolor
# GRAY CONVERT
if 'cmap' in kwargs:
image = rgb2uint(image)
# Matplotlib
if axes:
axes.imshow(image, **kwargs)
else:
axes = plt.imshow(image, **kwargs).axes
axes = self._annotate_plot(axes, annotate, title)
# SHOW DOESNT ACTUALLY CROP ANYTHING WHEN ZOOMING
if zoom:
xi, yi, xf, yf = zoom
axes.set_xlim(xi, xf)
axes.set_ylim(yf, yi)
if nolabel:
axes.xaxis.set_visible(False)
axes.yaxis.set_visible(False)
if nolabel == 'x':
axes.yaxis.set_visible(True)
elif nolabel == 'y':
axes.xaxis.set_visible(True)
if save:
path = _parse_path(save)
skimage.io.imsave(path, image)
return axes
def patchshow(self, *args, **kwargs):
""" ...
args/kwargs include alpha, edgecolors, linestyles
Notes:
Matplotlib API is setup that args or kwargs can be entered. Order is
important for args, but the correspond to same kwargs.
"""
axes, kwargs = _parse_ax(*args, **kwargs)
title = kwargs.pop('title', None)
bgonly = kwargs.pop('bgonly', False)
annotate = kwargs.pop('annotate', False)
zoom = kwargs.pop('zoom', None)
grid = kwargs.pop('grid', False)
gcolor = kwargs.pop('gcolor', None)
gstyle = kwargs.pop('gstyle', None)
gunder = kwargs.pop('gunder',False)
pmap = kwargs.pop('pmap', None)
nolabel = kwargs.pop('nolabel', None)
alpha = kwargs.get('alpha', None)
edgecolor = kwargs.get('edgecolor', None)
linewidth = kwargs.get('linewidth', None)
linestyle = kwargs.get('linestyle', None)
# Some keywords to savefig; not all supported
save = kwargs.pop('save', None)
dpi = kwargs.pop('dpi', None)
bbox_inches = kwargs.pop('bbox_inches', None)
# GET NOT POP
cmap = kwargs.get('cmap', None)
# Implement later
if cmap in ['pbinary', 'pbinary_r']:
raise CanvasPlotError('"pbinary(_r)" color map only valid for .show()')
# grid defaults
if gcolor or gunder or gstyle and not grid:
grid = True
# If user enters gcolor/gstyle, assume default grid
if grid and not gcolor:
gcolor = GCOLOR
if grid and not gstyle:
gstyle = 'solid'
# Corner case, don't touch
if pmap and cmap and bgonly:
bgonly = False
if bgonly and not cmap:
raise CanvasPlotError('"bgonly" is only valid when a colormap is'
' passed.')
if cmap:
bg = self.graybackground
else:
bg = self.background
if zoom:
xi, yi, xf, yf = zoom
bg = crop(bg, zoom)
#Overwrite axes image
if not axes:
fig, axes = plt.subplots()
else:
axes.images=[]
# DONT PASS ALL KWARGS
axes.imshow(bg, cmap=cmap)
# FOR PATICLES IN IMAGE ONLY.
in_and_edges = self.pin + self.pedge
# PARTICLE FACECOLOR, ALPHA and other PATCH ARGS
# http://matplotlib.org/api/artist_api.html#matplotlib.patches.Patch
patches = [p.particle.as_patch(facecolor=p.color, alpha=alpha,
edgecolor=edgecolor, linestyle=linestyle, linewidth=linewidth)
for p in in_and_edges]
# If no particles or grid, just pass to avoid deep mpl exceptiosn
if patches or grid:
if patches:
if pmap:
kwargs['cmap'] = pmap
if 'cmap' in kwargs and not bgonly:
ppatch = PatchCollection(patches, **kwargs) #cmap and Patch Args
ppatch.set_array(np.arange(len(patches)))
# Use settings passed to "patches"
else:
ppatch = PatchCollection(patches, match_original=True, **kwargs) #
# Grid under particles
if gunder:
axes.add_collection(self.grid.as_patch(
edgecolors=gcolor, linestyles=gstyle))
if patches:
axes.add_collection(ppatch)
# Grid over particles
else:
if patches:
axes.add_collection(ppatch)
if grid:
axes.add_collection(self.grid.as_patch(
edgecolors=gcolor, linestyles=gstyle))
axes = self._annotate_plot(axes, annotate, title)
if zoom:
axes.set_xlim(xi, xf)
axes.set_ylim(yf, yi)
if nolabel:
axes.xaxis.set_visible(False)
axes.yaxis.set_visible(False)
if nolabel == 'x':
axes.yaxis.set_visible(True)
elif nolabel == 'y':
axes.xaxis.set_visible(True)
if save:
path = _parse_path(save)
plt.savefig(path, dpi=dpi, bbox_inches=bbox_inches)
return axes