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annotate with two different colors based on threshold #104

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Jul 9, 2014
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annotate with two different colors based on threshold #104

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53 changes: 46 additions & 7 deletions trackpy/plots.py
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Original file line number Diff line number Diff line change
Expand Up @@ -136,8 +136,8 @@ def plot_traj(traj, colorby='particle', mpp=1, label=False, superimpose=None,
ptraj = plot_traj # convenience alias

@make_axes
def annotate(centroids, image, circle_size=170, color='g',
invert=False, ax=None):
def annotate(centroids, image, circle_size=170, color=None,
invert=False, ax=None, split_category=None, split_thresh=None):
"""Mark identified features with white circles.

Parameters
Expand All @@ -146,17 +146,36 @@ def annotate(centroids, image, circle_size=170, color='g',
image : image array (or string path to image file)
circle_size : size of circle annotations in matplotlib's annoying
arbitrary units, default 170
color : string
default 'g'
color : single matplotlib color or a list of multiple colors
default None
invert : If you give a filepath as the image, specify whether to invert
black and white. Default True.
ax : matplotlib axes object, defaults to current axes

split_category : string, parameter to use to split the data into sections
default None
split_thresh : single value or list of ints or floats threshold to split
particles into sections for plotting in multiple colors
default None

Returns
------
axes
"""
import matplotlib.pyplot as plt
from itertools import tee, izip
from collections import Iterable

# https://docs.python.org/2/library/itertools.html
def pairwise(iterable):
"s -> (s0,s1), (s1,s2), (s2, s3), ..."
a, b = tee(iterable)
next(b, None)
return izip(a, b)

if color is None:
color = 'g'
if not (split_thresh, Iterable):
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I know the train's already left the station, but I don't see how this test wouldn't always evaluate to True. Did you mean to write if not isinstance(split_thresh, Iterable)?

In any case, a string also counts as iterable, so there has to be another way.

Sorry I've been doing nothing but writing comments. I'll be back on my development computer by tomorrow, I promise :).

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My fault. This is what I get for late-night merging.

On Wednesday, July 9, 2014, Nathan Keim notifications@github.com wrote:

In trackpy/plots.py:

 Returns
 ------
 axes
 """
 import matplotlib.pyplot as plt
  • from itertools import tee, izip
  • from collections import Iterable

I know the train's already left the station, but I don't see how this test
wouldn't always evaluate to True. Did you mean to write if not
isinstance(split_thresh, Iterable)?

In any case, a string also counts as iterable, so there has to be another
way.

Sorry I've been doing nothing but writing comments. I'll be back on my
development computer by tomorrow, I promise :).

—
Reply to this email directly or view it on GitHub
https://github.com/soft-matter/trackpy/pull/104/files#r14724711.

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This bit of code is to handle the case where split_thresh is a single number. I turn it into a list because split_thresh[0] needs to be valid

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I think that the code, as written, will never put anything into a list, scalar or not. A multi-element tuple always evaluates to True.

I can say that I definitely get the wrong behavior when I try this code at the IPython prompt.

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This is the case I was trying to handle:
tp.annotate(f, frames[0],color=['purple','green'],split_category='signal',split_thresh=10)
I see now that it is broken. What is the proper way to check if something is iterable?

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isinstance(foo, Iterable) will return True if foo is iterable (and properly implements the ABC stuff from collections).

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Thanks, Tom! I've been doing it a much less elegant way. I guess the only complication is if you'd like strings to count as single values; then you'd need something like isinstance(foo, Iterable) and not isinstance(foo, str). But it looks like that's not the case in this code.

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A wonderful phrase I learned last night, 'duck typing brings a can of worms: either you go fishing with them or eat them'

split_thresh = [split_thresh]

# The parameter image can be an image object or a filename.
if isinstance(image, basestring):
Expand All @@ -167,10 +186,30 @@ def annotate(centroids, image, circle_size=170, color='g',
ax.imshow(image, origin='upper', shape=image.shape, cmap=plt.cm.gray)
ax.set_xlim(0, image.shape[1])
ax.set_ylim(0, image.shape[0])
ax.scatter(centroids['x'], centroids['y'],
s=circle_size, facecolors='none', edgecolors=color)

if split_category is None:
if np.size(color) > 1:
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does this interact badly with strings?

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It's fine with strings. One of my successful test cases was: tp.annotate(f, frames[0],color='purple'). I added this exception after trying tp.annotate(f, frames[0],color=['purple','green']), and the annotation circles alternated between the two colors-- not a good result. np.size('green')=1, np.size(['green','purple']=2

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Indeed: np.size('green') is 1 even though len('green') is five. This was news to me.

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I'll have to remember that. Thanks, Becca!

raise ValueError("multiple colors specified, no split category specified")
ax.scatter(centroids['x'], centroids['y'],
s=circle_size, facecolors='none', edgecolors=color)
else:
if len(color) != len(split_thresh) + 1:
raise ValueError("number of colors must be number of thresholds plus 1")
low = centroids[split_category] < split_thresh[0]
ax.scatter(centroids['x'][low], centroids['y'][low],
s=circle_size, facecolors='none', edgecolors=color[0])

for c, (bot, top) in izip(color[1:-1], pairwise(split_thresh)):
indx = ((centroids[split_category]) >= bot) & ((centroids[split_category]) < top)
ax.scatter(centroids['x'][indx], centroids['y'][indx],
s=circle_size, facecolors='none', edgecolors=c)

high = centroids[split_category] >= split_thresh[-1]
ax.scatter(centroids['x'][high], centroids['y'][high],
s=circle_size, facecolors='none', edgecolors=color[-1])
return ax


@make_axes
def mass_ecc(f, ax=None):
"""Plot each particle's mass versus eccentricity."""
Expand Down