def random_circles(cls, n=50, rmin=5, rmax=50, background=BGCOLOR, pcolor=None):
""" Return a canvas populated with n randomly positioned circles.
Radius ranges vary randomly between 5 and 50."""
from random import randint as RIT
particles = ParticleManager()
# Randomize particle centers within the image default dimensions
for i in range(n):
cx, cy = RIT(0, BGRES[0]), RIT(0, BGRES[1])
radius = RIT(rmin,rmax)
particles.add('circle', center=(cx,cy), radius=radius,
color=to_normrgb(pcolor))
# Use default resolution and grid
return cls(background=background, particles=particles)
def copy(cls, obj, grid=None, background=None, particles=None,
rez=None, _threshfcn = None):
""" Returns a copied canvas object. __init__ params are taken from
object unless explicitly passed.
Notes
-----
copy grid, bg and particles separately as they are
deep objects. Particles is especially finiky so just
create a completely new instance of it.
Explicit passing is useful, for insance, if one wants to copy a
canvas with new particles. This makes the operation quicker than
copying the old particles and then overwriting.
"""
if not grid:
grid = copy.copy(obj.grid)
if not background:
background = copy.copy(obj.background)
if not particles:
particles = ParticleManager(plist=obj.plist, copy=True)
if not rez:
rez = obj.rez
if not _threshfcn:
_threshfcn = obj.threshfcn
return cls(background=background,
particles=particles,
rez=rez,
grid=grid,
_threshfcn=_threshfcn)
def __init__(self, particles=None, background=None, rez=None, grid=None,
_threshfcn=None): #No other traits
""" Load with optionally a background image and instance of Particle
Manager"""
if not particles:
particles = ParticleManager()
self._particles = particles
if background is None and rez is None:
self.reset_background() #sets default color/resolution
elif background is not None and rez is None:
self._resolution = BGRES
self.set_bg(background, keepres=False, inplace=True)
else:
self._resolution = rez
self.set_bg(background, keepres=rez, inplace=True)
if not grid:
self.reset_grid()
else:
self.grid = grid
# _threshfcn through __init__ only really for Cavnas.copy(); not users
if _threshfcn is None:
self.set_threshfcn(THRESHDEF)
else:
self._threshfcn = _threshfcn
def random_triangles(cls, n=50, lmin=5, lmax=50, background=BGCOLOR, pcolor=None):
""" Return a canvas populated with n randomly positioned circles.
Radius ranges vary randomly between 5 and 50."""
from random import randint as RIT
particles = ParticleManager()
# Randomize particle centers within the image default dimensions
for i in range(n):
# ADD PADDING ADHOC AT THE MOMENT!!
PAD = 2*lmax
cx, cy = RIT(0+PAD, BGRES[0]-PAD), RIT(0+PAD, BGRES[1]-PAD)
length = RIT(lmin,lmax)
particles.add('triangle', center=(cx,cy), length=length,
color=to_normrgb(pcolor))
# Use default resolution and grid
return cls(background=background, particles=particles)
class Canvas(HasTraits):
""" """
image = Property(Array) #chaching doesnt work
# ALL INTERNAL REFERENCES SHOULD GO TO _PARTICLES
particles = Property(Instance(ParticleManager, depends_on='_particles'))
_particles = Instance(ParticleManager)
# Background is only a property because for _set validation...
background = Property()
_background = Array
# Use this as a listener for grid
_resolution = Tuple(Int, Int)
grid = Instance(CartesianGrid)
def __init__(self, particles=None, background=None, rez=None, grid=None,
_threshfcn=None): #No other traits
""" Load with optionally a background image and instance of Particle
Manager"""
if not particles:
particles = ParticleManager()
self._particles = particles
if background is None and rez is None:
self.reset_background() #sets default color/resolution
elif background is not None and rez is None:
self._resolution = BGRES
self.set_bg(background, keepres=False, inplace=True)
else:
self._resolution = rez
self.set_bg(background, keepres=rez, inplace=True)
if not grid:
self.reset_grid()
else:
self.grid = grid
# _threshfcn through __init__ only really for Cavnas.copy(); not users
if _threshfcn is None:
self.set_threshfcn(THRESHDEF)
else:
self._threshfcn = _threshfcn
def set_threshfcn(self, fcn_or_string, *args, **kwargs):
""" Set a binarization function. """
if isinstance(fcn_or_string, str):
# Update later
if args:
raise CanvasError('Please use keyword args for threshold function')
self._threshfcn = choose_thresh(fcn_or_string, **kwargs)
self._threshtype = fcn_or_string
else:
self._threshfcn = functools.partial(fcn_or_string, *args, **kwargs)
self._threshtype = fcn_or_string.__name__
@property
def threshfcn(self):
try:
return self._threshtype
except CanvasAttributeError:
return None
@threshfcn.setter
def threshfcn(self):
raise CanvasAttributeError('Please use "set_threshfcn(fcn/str, *args, '
'**kwargs)" to set the binary function.')
# Public Methods
# -------------
def add(self, particle, *args, **kwargs):
""" Can't rely on __getattr__ because want *args to pass; only
kwargs pass correctly; and wrapper was more pain than worth. """
return self._particles.add(particle, *args, **kwargs)
def reset_background(self):
""" Restore default background image; restores default RES, redraws
particles over it."""
self.rez = BGRES #must be set first
self._background = self.color_background
self._bgstyle = 'default'
def reset_grid(self):
""" New grid of default x/y spacing; rez is optional """
self.grid = CartesianGrid(rez=self.rez, negative_y=True,
xspacing=GRIDYSPACE, yspacing=GRIDXSPACE)
def clear_canvas(self):
""" Background image to default; removes ALL particles."""
self.clear_particles()
self.reset_background()
self.reset_grid()
def clear_particles(self):
""" Clears all particles from image."""
self._particles.plist[:] = []
# @inplace
def pmap(self, fcn, *fcnargs, **fcnkwargs):
""" Maps a function to each particle in ParticleManger; optionally
can be done in place"""
#self._particles.map(fcn, *fcnargs, **fcnkwargs)
inplace = fcnkwargs.pop('inplace', False)
if inplace:
self._particles.map(fcn, *fcnargs, **fcnkwargs)
else:
cout = Canvas.copy(self)
cout._particles.map(fcn, *fcnargs, **fcnkwargs)
return cout
def of_ptypes(self, *types, **kwargs):
""" Retain only particles pertaining to specified *types;
optionally inplace."""
inplace = kwargs.pop('inplace', False)
if inplace:
self._particles.of_ptypes(*types)
else:
cout = Canvas.copy(self)
cout._particles.of_ptypes(*types)
return cout
def pixelmap(self, fcn, axis=0, *fcnargs, **fcnkwargs):
""" Image mapper (np.apply_along_axis)
fcn must be 1d!
Notes
-----
Calls numpy.apply_along_axis, which doesn't acces
keyword arguments.
"""
return np.apply_along_axis(fcn, axis, self.image, *fcnargs)
#http://scikit-image.org/docs/dev/api/skimage.morphology.html#skimage.morphology.label
# @inplace
def from_labels(self, bgout=None, exclude=None, binary=True, pbinary=True,
inplace=False, neighbors=4, **pmangerkwds):
""" Get morphological labels from gray or binary image.
Parameters
----------
exclude : 0, 1, 255, 'w', 'b'
Exclude white, black or specified integer from labels. For example,
'b' will prevent black pixels from being labeled.
bgout : Valid canvas array/color
Background image of resulting canvas. If exclude, then there will
be unlabled regions. bgout='r' will overlay the labels onto a red
background. By default, self.background is used.
binary : bool
Use binary image; else use grayimage.
pbinary : bool
Use self.pbinary to generate thresholded image; else, use
self.threshfcn (implicit thresholding function) to binarize.
Only valid if binary = True
Notes
-----
Use binary=False with caution. Many grayimages would lead to tends of
thousands of labels due to minute color changes in each pixel. Whitle
skimage.label can handle this, pyparty will slow down severaly trying
to make so many particles from labels.
"""
if binary:
if pbinary:
image = self.pbinary #PBINARY NOT self.binaryimage
if len(self.particles) == 0:
logger.warn('from_labels() recieved "pbinary=True", but '
'no particles are stored. Use "pbinary=False" to '
'use implicit thresholding function.')
else:
image = self.binaryimage
else:
image = self.grayimage
logger.warn('Labels from grayimage can be very slow (fix coming)')
if exclude is None: # scikit api doesn't accept None
labels = morphology.label(image, neighbors)
else:
# Parse various cases
if exclude == 'w' or exclude == 'white':
if binary:
exclude = 1
else:
exclude = 255
elif exclude == 'b' or exclude == 'black':
exclude = 0
labels = morphology.label(image, neighbors, background=exclude)
pout = ParticleManager.from_labels(labels, **pmangerkwds)
if inplace:
self._particles = pout
else:
cout = Canvas.copy(self)
cout.particles = pout
if bgout is not None:
cout.background = bgout
return cout
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
def _annotate_plot(self, axes, annotate, title):
""" Hacky boiler plat reduction. show() and patchshow() both do exact
same thing at end; didn't want to put it twice."""
if annotate:
axes.set_xlabel('px')
axes.set_ylabel('px')
if not title:
if len(self._particles) == 1:
pcnt_str = '1 particle'
else:
pcnt_str = '%s particles' % len(self._particles)
if len(self._particles.ptypes) == 1:
ptype_str = '%s' % self._particles.ptypes[0]
else:
ptype_str = '%s types' % len(self._particles.ptypes)
title = '%s (%s) %.2f%% coverage' % \
(pcnt_str, ptype_str, 100.0*self.pixarea)
if title:
axes.set_title(title)
return axes
#http://matplotlib.org/api/pyplot_api.html#matplotlib.pyplot.imshow
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 scatter(self, *args, **kwargs):
""" Scatter plot of two particles attributes (eg area vs ccircularity).
Parameters
----------
attr1: str
X-attribute
attr2: str
Y-attribute
annotate: False
Adds title, x and y labels
"""
# Would it make more sense to default these to something
attr1 = kwargs.pop('attr1', None)
attr2 = kwargs.pop('attr2', None)
if not attr1 or not attr2:
raise CanvasPlotError('Scatter attributes must be specified as'
' keywords (IE c.scatter(attr1=area, attr2=eccentricity ...)')
annotate = kwargs.pop('annotate', False)
title = kwargs.pop('title', None)
fancy = kwargs.pop('fancy', False)
axes, kwargs = _parse_ax(*args, **kwargs)
if fancy:
raise NotImplementedError("Fancy kwarg not yet supported.")
if not axes:
fig, axes = plt.subplots()
x, y = getattr(self, attr1), getattr(self, attr2)
axes.scatter(x, y, **kwargs)
if annotate:
if not title:
title = '%s - %s' % (attr1.title(), attr2.title())
axes.set_xlabel(attr1)
axes.set_ylabel(attr2)
if title:
axes.set_title(title)
return axes
def _draw_particles(self, image, force_binary=False):
""" Draws particles over any image (ie background, background+grid.
force_binary is a hack to allow for drawing binary particles, useful
for canvas.show(cmap=pbinary)"""
for p in self._particles:
rr_cc = p.particle.rr_cc
# Lot of crap! Need it this way or grid color will be inverted too
if force_binary:
if force_binary == 'pbinary_r':
color = False
else:
color = True
else:
color = p.color
rr_cc = coords_in_image(rr_cc, image.shape)
image[rr_cc] = color
return image
def _get_image(self):
""" Creates image array of particles. Tried fitting to a property or
Traits events interface to control the caching, but manually choosing
cache points proved to be easier."""
# self.background is always a new array; otherwise would use np.copy
return self._draw_particles(self.background)
# Image Attributes Promoted
# ------------------
@property
def shape(self):
""" Avoid recomputing image"""
return (self.rx, self.ry, 3)
@property
def ndim(self):
""" Avoid recomputing image for this purpose """
return len(self._background)
@property
def dtype(self):
# Same dtype as image
return self._background.dtype
@property
def grayimage(self):
""" Collapse multi-channel, scale to 255 (via ubyte) """
return rgb2uint(self.image)
@property
def binaryimage(self):
return self._threshfcn(self.grayimage)
@property
def graybackground(self):
return rgb2uint(self.background)
@property
def binarybackground(self):
return self._threshfcn(self.graybackground)
@property
def color_background(self):
""" Generate a colored background at current resolution """
return bgu.from_color_res(BGCOLOR, self.rx, self.ry)
# Promote most common grid attributes
@property
def gcenters(self):
return self.grid.centers
@property
def gcorners(self):
return self.grid.corners
@property
def ghlines(self):
return self.grid.hlines
@property
def gvlines(self):
return self.grid.vlines
def gpairs(self, attr):
return self.grid.pairs(attr)
#GRID LISTENER
def __resolution_changed(self):
# BACKWARDS BECAUSE GRID IS RELATIVE INVERSE
if self.grid:
self.grid.xend = self.ry
self.grid.yend = self.rx
# Image Resolution
@property
def rez(self):
""" Resoloution; since x,y is wonky on image, rx really is y dim"""
return self._resolution
@rez.setter
def rez(self, rez):
rx, ry = rint(rez[0]), rint(rez[1])
self._resolution = rx, ry
@property
def rx(self):
return self.rez[0]
@rx.setter
def rx(self, rx):
self._resolution = ( int(rx), self._resolution[1] )
@property
def ry(self):
return self.rez[1]
@ry.setter
def ry(self, ry):
self._resolution = ( self._resolution[0], int(ry) )
@property
def pbinary(self):
""" Returns boolean mask of all particles IN the image, with
background removed."""
# Faster to get all coords in image at once since going to paint white
out = np.zeros( self.rez, dtype=bool )
if self.particles:
rr_cc = coords_in_image( self._particles.rr_cc_all, self.rez)
out[rr_cc] = True
return out
def _whereis(self, choice='in'):
""" Wraps utils.where_is_particles for all three possibilities """
return [p.name for p in self._particles
if where_is_particle(p.rr_cc, self.rez) == choice]
@property
def pin(self):
""" Returns all particles appearing FULLY in the image"""
return self._particles[self._whereis('in')]
@property
def pedge(self):
""" Returns all particles appearing PARTIALLY in the image"""
return self._particles[self._whereis('edge')]
@property
def pout(self):
""" All particles appearing FULLY outside the image"""
return self._particles[self._whereis('out')]
@property
def pixcount(self):
""" Image pixel count """
l, w = self.rez
return int(l * w)
@property
def pixarea(self):
""" Area white pixels in pbinary """
return float(np.sum(self.pbinary)) / self.pixcount
@property
def pixperim(self):
""" Wraps measure.perimeter to estimate total perimeter of
particles in binary image."""
return skimage.measure.perimeter(self.pbinary, neighbourhood=4)
# Trait Defaults / Trait Properties
# ---------------------------------
def _get_particles(self):
""" Return a NEW INSTANCE of particles manager (ie new particles instead
of in-memory references)"""
return ParticleManager(plist=self._particles.plist,
fastnames=self._particles.fastnames)
def _set_particles(self, particles):
""" Make a copy of the particles to avoid passing by reference.
Note this is implictly controlled by _COPYPARTICLES in config.
"""
self._particles = ParticleManager(particles.plist, particles.fastnames)
def _set_image(self):
raise CanvasError('Image cannot be set; please make changes to particles'
' and/or background attributes.')
# BACKGROUND RELATED
# ------------------
# @inplace
def set_bg(self, bg, keepres=False, inplace=False):
""" Public background setting interface. """
#print 'IN SET BG', bg, keepres
#oldres = self.rez
#self._update_bg(bg)
#if keepres:
#if keepres == True:
#self.rez = oldres
#else:
#self.rez = keepres
#else:
#self.rez = self._background.shape[0:2]
if inplace:
cout = self
else:
cout = Canvas.copy(self)
oldres = cout.rez
cout._update_bg(bg)
if keepres:
if keepres == True:
cout.rez = oldres
else:
cout.rez = keepres
else:
cout.rez = cout._background.shape[0:2]
if not inplace:
return cout
def zoom_bg(self, *coords, **kwds):
""" Zoom in on current image and set the zoomed background as the
background of a new canvas. Note that because indicies will always
resume at 0, particle positions will not maintain their relative
positions.
"""
# avoid set_bg() because uses size of coords, not coords itself
inplace = kwds.pop('inplace', False)
autogrid = kwds.pop('autogrid', True)
if inplace:
cout = self
else:
cout = Canvas.copy(self)
cout._background = crop(cout._background, coords)
cout.rez = cout._background.shape[0:2]
if autogrid:
xmag = self.rx / float(cout.rx)
ymag = self.ry / float(cout.ry)
cout.grid.xdiv = rint(self.grid.xdiv / xmag)
cout.grid.ydiv = rint(self.grid.ydiv / ymag)
if not inplace:
return cout
def _get_background(self):
""" Crop or extend self._background based on self.rx, ry. Always
returns a new object to avoid accidental refernce passing."""
bgx, bgy = self._background.shape[0:2]
rx, ry = self.rez
if bgx == rx and bgy == ry:
return np.copy(self._background)
def _smaller(idx1, idx2):
if idx1 < idx2:
return idx1
return idx2
xs, ys = _smaller(rx, bgx), _smaller(ry, bgy)
out = np.empty( (rx, ry, 3) )
out[:] = BGCOLOR #.fill only works with scalar
out[:xs, :ys] = self._background[:xs, :ys] #no copy needed
return out
def _set_background(self, bg):
""" Set background and use new resolution if there is one """
self.set_bg(bg, keepres=False, inplace=True)
# REDO THIS WITH COLOR NORM AND STUFF! Also, dtype warning?
def _update_bg(self, background):
""" Parses several valid inputs including: None, Path, Color (of any
valid to_normRGB() type, ndarray, (Color, Resolution)."""
if background is None:
self._background = self.color_background
self._bgstyle = 'default'
elif isinstance(background, Grid):
self._background = bgu.from_grid(background)
self._bgstyle = 'grid'
elif isinstance(background, np.ndarray):
self._background = background
self._bgstyle = 'ndarray'
# colorstring or hex
elif isinstance(background, basestring):
self._background = bgu.from_string(background, self.rx, self.ry)
self._bgstyle = 'file/colorstring/url'
# If not array, color is assume as valid to_norm_rgb(color) arg
# It will raise its own error if failure occurs
else:
self._background = bgu.from_color_res(background, self.rx, self.ry)
self._bgstyle = 'color'
# Float-color convert array
self._background = any2rgb(self._background, 'background')
# IMAGE IS CACHED AT END OF _set_bg()
# Delegate dictionary interface to ParticleManager
# -----------
def __getitem__(self, keyslice):
""" Employs particle manager interface; however, returns single entry
as a list to allow slicing directly into get_item[]"""
return self._particles.__getitem__(keyslice)
#IF WANT TO RETURN CANVAS ALWAYS SEE BELOW
#pout = self._particles.__getitem__(keyslice)
#return Canvas(background=self.background, particles=pout, rez=self.rez)
def __delitem__(self, keyslice):
return self._particles.__delitem__(keyslice)
def __setitem__(self, key, particle):
return self._particles.__setitem__(key, particles)
def __getattr__(self, attr):
""" Look for missing attributes on particle manager.
Notes
-----
*args are NOT passed to called methods; kwargs are. If absolutely
need ARGS, see how I handled add. Could not get wrapper
to work correctly because it generally wanted to return a function
but sometimes this returns objects, lists etc... not just functions
so doing for example c.plist would try to give c.plist() and so on.
"""
try:
return getattr(self._particles, attr)
except ParticleError:
raise CanvasAttributeError('"%s" could not be found on %s, '
'underlying manager, or on one-or multiple of the '
'Particles' % (attr, self.__class__.__name__) )
def __iter__(self):
""" Iteration is blocked """
raise CanvasError("Iteration on canvas is ambiguous. Iterate over "
"canvas.image or canvas.particles")
@property
def _address(self):
""" Property to make easily accesible by multicanvas """
return mem_address(super(Canvas, self).__repr__())
def __repr__(self):
_bgstyle = self._bgstyle #REPLACE
res = '(%s X %s)' % (self.rx, self.ry )
g=self.grid
xd, yd = g.xdiv, g.ydiv
gridstring = "%sxygrid[%s] --> (%sp X %sp) : (%.1f X %.1f) [pix/tile]" \
% (_PAD, xd*yd, xd, yd, g.xspacing, g.yspacing)
# MAY WANT TO USE COLUMN ALIGNMENT
outstring = "%s (%s):\n" % (self.__class__.__name__, self._address)
outstring += "%sbackground --> %s : %s\n" % (_PAD, res, _bgstyle)
outstring += "%sparticles --> %s particles : %s types\n" % (_PAD, \
len(self._particles), len(self._particles.ptype_count))
outstring += gridstring
return outstring
def __len__(self):
return self._particles.__len__()
# Arithmetic Operation
# --------------------
def __add__(self, c2):
return concat_canvas(self, c2, bg_resolve='c2')
def __sub__(self, c2):
raise CanvasError("%s does not support subtraction" %
self.__class__.__name__)
# Class methods
# ------------
@classmethod
def copy(cls, obj, grid=None, background=None, particles=None,
rez=None, _threshfcn = None):
""" Returns a copied canvas object. __init__ params are taken from
object unless explicitly passed.
Notes
-----
copy grid, bg and particles separately as they are
deep objects. Particles is especially finiky so just
create a completely new instance of it.
Explicit passing is useful, for insance, if one wants to copy a
canvas with new particles. This makes the operation quicker than
copying the old particles and then overwriting.
"""
if not grid:
grid = copy.copy(obj.grid)
if not background:
background = copy.copy(obj.background)
if not particles:
particles = ParticleManager(plist=obj.plist, copy=True)
if not rez:
rez = obj.rez
if not _threshfcn:
_threshfcn = obj.threshfcn
return cls(background=background,
particles=particles,
rez=rez,
grid=grid,
_threshfcn=_threshfcn)
# Extend to polygons/other partciles in future
# May want to refactor into particle manager method actually
@classmethod
def random_circles(cls, n=50, rmin=5, rmax=50, background=BGCOLOR, pcolor=None):
""" Return a canvas populated with n randomly positioned circles.
Radius ranges vary randomly between 5 and 50."""
from random import randint as RIT
particles = ParticleManager()
# Randomize particle centers within the image default dimensions
for i in range(n):
cx, cy = RIT(0, BGRES[0]), RIT(0, BGRES[1])
radius = RIT(rmin,rmax)
particles.add('circle', center=(cx,cy), radius=radius,
color=to_normrgb(pcolor))
# Use default resolution and grid
return cls(background=background, particles=particles)
@classmethod
def random_triangles(cls, n=50, lmin=5, lmax=50, background=BGCOLOR, pcolor=None):
""" Return a canvas populated with n randomly positioned circles.
Radius ranges vary randomly between 5 and 50."""
from random import randint as RIT
particles = ParticleManager()
# Randomize particle centers within the image default dimensions
for i in range(n):
# ADD PADDING ADHOC AT THE MOMENT!!
PAD = 2*lmax
cx, cy = RIT(0+PAD, BGRES[0]-PAD), RIT(0+PAD, BGRES[1]-PAD)
length = RIT(lmin,lmax)
particles.add('triangle', center=(cx,cy), length=length,
color=to_normrgb(pcolor))
# Use default resolution and grid
return cls(background=background, particles=particles)
def _set_particles(self, particles):
""" Make a copy of the particles to avoid passing by reference.
Note this is implictly controlled by _COPYPARTICLES in config.
"""
self._particles = ParticleManager(particles.plist, particles.fastnames)
def _get_particles(self):
""" Return a NEW INSTANCE of particles manager (ie new particles instead
of in-memory references)"""
return ParticleManager(plist=self._particles.plist,
fastnames=self._particles.fastnames)
def from_labels(self, bgout=None, exclude=None, binary=True, pbinary=True,
inplace=False, neighbors=4, **pmangerkwds):
""" Get morphological labels from gray or binary image.
Parameters
----------
exclude : 0, 1, 255, 'w', 'b'
Exclude white, black or specified integer from labels. For example,
'b' will prevent black pixels from being labeled.
bgout : Valid canvas array/color
Background image of resulting canvas. If exclude, then there will
be unlabled regions. bgout='r' will overlay the labels onto a red
background. By default, self.background is used.
binary : bool
Use binary image; else use grayimage.
pbinary : bool
Use self.pbinary to generate thresholded image; else, use
self.threshfcn (implicit thresholding function) to binarize.
Only valid if binary = True
Notes
-----
Use binary=False with caution. Many grayimages would lead to tends of
thousands of labels due to minute color changes in each pixel. Whitle
skimage.label can handle this, pyparty will slow down severaly trying
to make so many particles from labels.
"""
if binary:
if pbinary:
image = self.pbinary #PBINARY NOT self.binaryimage
if len(self.particles) == 0:
logger.warn('from_labels() recieved "pbinary=True", but '
'no particles are stored. Use "pbinary=False" to '
'use implicit thresholding function.')
else:
image = self.binaryimage
else:
image = self.grayimage
logger.warn('Labels from grayimage can be very slow (fix coming)')
if exclude is None: # scikit api doesn't accept None
labels = morphology.label(image, neighbors)
else:
# Parse various cases
if exclude == 'w' or exclude == 'white':
if binary:
exclude = 1
else:
exclude = 255
elif exclude == 'b' or exclude == 'black':
exclude = 0
labels = morphology.label(image, neighbors, background=exclude)
pout = ParticleManager.from_labels(labels, **pmangerkwds)
if inplace:
self._particles = pout
else:
cout = Canvas.copy(self)
cout.particles = pout
if bgout is not None:
cout.background = bgout
return cout
