Thanks to visit codestin.com
Credit goes to github.com

Skip to content

2D Normalization & Colormapping for ScalerMappables #8738

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
wants to merge 35 commits into from
Closed
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
35 commits
Select commit Hold shift + click to select a range
201dc2a
Initailize class 2D norm
patniharshit Jun 9, 2017
7217536
Change name of class to BivariateNorm, take normalizer instances sepa…
patniharshit Jun 9, 2017
0178730
Bivariate works with imshow, pcolor, pcolormesh, pcolorfast
patniharshit Jul 3, 2017
575a244
add blank line between bivariate classes
patniharshit Jul 9, 2017
8425637
Add support for bivariate in scatter
patniharshit Jul 9, 2017
4a5831d
Fix missing norm2 in BivaraiteNorm
patniharshit Jul 11, 2017
85df736
Fixed bug in if condition bivariate mapping
patniharshit Jul 12, 2017
8e1bc63
Add autoscale, autoscale_None, scaled methods for BivariateNorm
patniharshit Jul 13, 2017
a9aace3
trying to show ticks and labels on both x and y axis
patniharshit Jul 16, 2017
55a7a68
commented outline code, changed gridspace to show sqaure colorbar
patniharshit Jul 17, 2017
c2eb617
2d colorbar printing now
patniharshit Jul 17, 2017
daef751
Add code for Colorsquare
patniharshit Jul 22, 2017
96af3d3
Modify axis aspect and fraction for colorsquare
patniharshit Jul 22, 2017
9285372
fix failing commits
patniharshit Jul 22, 2017
01b5932
Change PEP8 violations
patniharshit Jul 27, 2017
28288e2
Revert isBivari, remove classic locator
patniharshit Jul 29, 2017
ca2b111
Subclass normalizers from Abstract Base Class
patniharshit Aug 2, 2017
75b4eba
move _ticker function inside update_ticks
patniharshit Aug 2, 2017
bf65847
move _ticker function inside update_ticks
patniharshit Aug 2, 2017
f9dc4b1
remove cmap in imshow and pcolorfast
patniharshit Aug 5, 2017
8a985f0
Defer call to norm and cmap in imshow
patniharshit Aug 7, 2017
8f6928d
Fix bivariate handling with pcolormesh
patniharshit Aug 15, 2017
d54cb44
Make pcolor work with bivariate
patniharshit Aug 16, 2017
4d03552
Do 2D->1D mapping in call method of colormap
patniharshit Aug 20, 2017
2573610
Use list comprehensions to ravel
patniharshit Aug 20, 2017
9228480
Reflect on reviews
patniharshit Aug 21, 2017
5c8dc65
Update docstrings
patniharshit Aug 25, 2017
21ea65f
Add bivariate example
patniharshit Aug 25, 2017
b8d43a9
Treat one as slightly less than one
patniharshit Aug 25, 2017
7681d14
Change conditions for bivar
patniharshit Aug 25, 2017
59f56af
Add image comparison test for bivariate
patniharshit Aug 25, 2017
f98978f
Update is_bivar condition to expect either BivariateNorm or Bivariate…
patniharshit Aug 26, 2017
75a289f
Add line continuation in docstrings
patniharshit Aug 27, 2017
7803974
Debug doc build fail
patniharshit Aug 28, 2017
e40c87b
Add missing symbols in docs
patniharshit Aug 28, 2017
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
44 changes: 44 additions & 0 deletions examples/images_contours_and_fields/bivariate_demo.py
Original file line number Diff line number Diff line change
@@ -0,0 +1,44 @@
"""
==============
Bivariate Demo
==============

Plotting bivariate data.

imshow, pcolor, pcolormesh, pcolorfast allows you to plot bivariate data
using a bivaraite colormap.

In this example we use imshow to plot air temperature with surface pressure
alongwith a color square.
"""
import matplotlib.colors as colors
from matplotlib.cbook import get_sample_data
import matplotlib.pyplot as plt
import numpy as np


###############################################################################
# Bivariate plotting demo
# -----------------------

air_temp = np.load(get_sample_data('air_temperature.npy'))
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

How big are these data files? I have a slight preference for 'generated' data for examples (to keep the repository size small).

Copy link
Contributor Author

@patniharshit patniharshit Aug 27, 2017

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

84.2 kB each.
Couldn't come up with generated data so used these.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

That isn't too bad, suspect that is smaller than the test images.

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

One argument in favour of this can be that the user seeing the example might relate to use case of bivariate plotting better with a real world example than with some mathematical function.

surf_pres = np.load(get_sample_data('surface_pressure.npy'))

fig, ax = plt.subplots()

bivariate = [air_temp, surf_pres]

###############################################################################
# To distinguish bivariate data either BivariateNorm or BivariateColormap must
# be passed in as argument

cax = ax.imshow(bivariate, norm=colors.BivariateNorm(),
cmap=colors.BivariateColormap())

###############################################################################
# If input data is bivariate then colorbar automatically draws colorsquare
# instead of colorbar

cbar = fig.colorbar(cax, xlabel='air_temp', ylabel='surf_pres')

plt.show()
166 changes: 128 additions & 38 deletions lib/matplotlib/axes/_axes.py
Original file line number Diff line number Diff line change
Expand Up @@ -4044,7 +4044,8 @@ def scatter(self, x, y, s=None, c=None, marker=None, cmap=None, norm=None,

if colors is None:
if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)
collection.set_array(np.asarray(c))
collection.set_cmap(cmap)
Expand Down Expand Up @@ -4403,7 +4404,8 @@ def hexbin(self, x, y, C=None, gridsize=100, bins=None,
accum = bins.searchsorted(accum)

if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)
collection.set_array(accum)
collection.set_cmap(cmap)
Expand Down Expand Up @@ -5037,23 +5039,25 @@ def imshow(self, X, cmap=None, norm=None, aspect=None,

Parameters
----------
X : array_like, shape (n, m) or (n, m, 3) or (n, m, 4)
X : array_like, shape (n, m) or (n, m, 3) or (n, m, 4) or (2, n, m)
Display the image in `X` to current axes. `X` may be an
array or a PIL image. If `X` is an array, it
can have the following shapes and types:

- MxN -- values to be mapped (float or int)
- MxN -- univariate values to be mapped (float or int)
- MxNx3 -- RGB (float or uint8)
- MxNx4 -- RGBA (float or uint8)
- 2xMxN -- bivariate values to be mapped (float or int)
Copy link

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

What happens when the input is shape (2, 3, 4)?

This sort of ambiguity should be avoided (and indicates that this API is probably not the right design choice).


The value for each component of MxNx3 and MxNx4 float arrays
should be in the range 0.0 to 1.0. MxN arrays are mapped
should be in the range 0.0 to 1.0. MxN and 2xMxN arrays are mapped
to colors based on the `norm` (mapping scalar to scalar)
and the `cmap` (mapping the normed scalar to a color).

cmap : `~matplotlib.colors.Colormap`, optional, default: None
cmap : `~matplotlib.colors.Colormap`, \
`~matplotlib.colors.BivariateColormap`, optional, default: None
If None, default to rc `image.cmap` value. `cmap` is ignored
if `X` is 3-D, directly specifying RGB(A) values.
if `X` is 3-D but not bivariate, directly specifying RGB(A) values.

aspect : ['auto' | 'equal' | scalar], optional, default: None
If 'auto', changes the image aspect ratio to match that of the
Expand All @@ -5077,7 +5081,8 @@ def imshow(self, X, cmap=None, norm=None, aspect=None,
on the Agg, ps and pdf backends. Other backends will fall back to
'nearest'.

norm : `~matplotlib.colors.Normalize`, optional, default: None
norm : `~matplotlib.colors.Normalize`, \
`matplotlib.colors.BivariateNorm`, optional, default: None
A `~matplotlib.colors.Normalize` instance is used to scale
a 2-D float `X` input to the (0, 1) range for input to the
`cmap`. If `norm` is None, use the default func:`normalize`.
Expand Down Expand Up @@ -5137,16 +5142,29 @@ def imshow(self, X, cmap=None, norm=None, aspect=None,
of pixel (0, 0).

"""

if not self._hold:
self.cla()

if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"
if norm is not None and not isinstance(norm, mcolors.Norms):
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)

temp = np.asarray(X)
is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
if temp.ndim != 3 and temp.shape[0] != 2:
raise TypeError("Expected shape like (2, n, m)")
if cmap is None:
cmap = mcolors.BivariateColormap()
if norm is None:
norm = mcolors.BivariateNorm()

if aspect is None:
aspect = rcParams['image.aspect']
self.set_aspect(aspect)

im = mimage.AxesImage(self, cmap, norm, interpolation, origin, extent,
filternorm=filternorm, filterrad=filterrad,
resample=resample, **kwargs)
Expand All @@ -5173,7 +5191,6 @@ def imshow(self, X, cmap=None, norm=None, aspect=None,

@staticmethod
def _pcolorargs(funcname, *args, **kw):
# This takes one kwarg, allmatch.
# If allmatch is True, then the incoming X, Y, C must
# have matching dimensions, taking into account that
# X and Y can be 1-D rather than 2-D. This perfect
Expand All @@ -5186,10 +5203,17 @@ def _pcolorargs(funcname, *args, **kw):
# is False.

allmatch = kw.pop("allmatch", False)
norm = kw.pop("norm", None)
cmap = kw.pop("cmap", None)

if len(args) == 1:
C = np.asanyarray(args[0])
numRows, numCols = C.shape
is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
numRows, numCols = C.shape[1:]
else:
numRows, numCols = C.shape
if allmatch:
X, Y = np.meshgrid(np.arange(numCols), np.arange(numRows))
else:
Expand All @@ -5200,7 +5224,12 @@ def _pcolorargs(funcname, *args, **kw):

if len(args) == 3:
X, Y, C = [np.asanyarray(a) for a in args]
numRows, numCols = C.shape
is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
numRows, numCols = C.shape[1:]
else:
numRows, numCols = C.shape
else:
raise TypeError(
'Illegal arguments to %s; see help(%s)' % (funcname, funcname))
Expand Down Expand Up @@ -5235,7 +5264,7 @@ def _pcolorargs(funcname, *args, **kw):
@docstring.dedent_interpd
def pcolor(self, *args, **kwargs):
"""
Create a pseudocolor plot of a 2-D array.
Create a pseudocolor plot of a 2-D univariate or 3-D bivariate array.

Call signatures::

Expand Down Expand Up @@ -5273,10 +5302,12 @@ def pcolor(self, *args, **kwargs):
vectors, they will be expanded as needed into the appropriate 2-D
arrays, making a rectangular grid.

cmap : `~matplotlib.colors.Colormap`, optional, default: None
cmap : `~matplotlib.colors.Colormap` or \
`matplotlib.colors.BivariateColormap`, optional, default: None
If `None`, default to rc settings.

norm : `matplotlib.colors.Normalize`, optional, default: None
norm : `matplotlib.colors.Normalize` or \
`matplotlib.colors.BivariateNorm`, optional, default: None
An instance is used to scale luminance data to (0, 1).
If `None`, defaults to :func:`normalize`.

Expand Down Expand Up @@ -5382,9 +5413,20 @@ def pcolor(self, *args, **kwargs):
vmin = kwargs.pop('vmin', None)
vmax = kwargs.pop('vmax', None)

X, Y, C = self._pcolorargs('pcolor', *args, allmatch=False)
kw = {'norm': norm, 'cmap': cmap, 'allmatch': False}
X, Y, C = self._pcolorargs('pcolor', *args, **kw)
Ny, Nx = X.shape

is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
if C.ndim != 3 and C.shape[0] != 2:
raise TypeError("Expected shape like (2, n, m)")
if cmap is None:
cmap = mcolors.BivariateColormap()
if norm is None:
norm = mcolors.BivariateNorm()

# unit conversion allows e.g. datetime objects as axis values
self._process_unit_info(xdata=X, ydata=Y, kwargs=kwargs)
X = self.convert_xunits(X)
Expand All @@ -5399,7 +5441,10 @@ def pcolor(self, *args, **kwargs):
xymask = (mask[0:-1, 0:-1] + mask[1:, 1:] +
mask[0:-1, 1:] + mask[1:, 0:-1])
# don't plot if C or any of the surrounding vertices are masked.
mask = ma.getmaskarray(C) + xymask
if isinstance(norm, mcolors.BivariateNorm):
mask = ma.getmaskarray(C[0]) + ma.getmaskarray(C[1]) + xymask
else:
mask = ma.getmaskarray(C) + xymask

newaxis = np.newaxis
compress = np.compress
Expand All @@ -5423,7 +5468,15 @@ def pcolor(self, *args, **kwargs):
axis=1)
verts = xy.reshape((npoly, 5, 2))

C = compress(ravelmask, ma.filled(C[0:Ny - 1, 0:Nx - 1]).ravel())
if isinstance(norm, mcolors.BivariateNorm):
C = np.array([
compress(
ravelmask,
ma.filled(c[0:Ny - 1, 0:Nx - 1]).ravel()
) for c in C
])
else:
C = compress(ravelmask, ma.filled(C[0:Ny - 1, 0:Nx - 1]).ravel())

linewidths = (0.25,)
if 'linewidth' in kwargs:
Expand All @@ -5450,9 +5503,12 @@ def pcolor(self, *args, **kwargs):

collection.set_alpha(alpha)
collection.set_array(C)
if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"

if norm is not None and not isinstance(norm, mcolors.Norms):
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)

collection.set_cmap(cmap)
collection.set_norm(norm)
collection.set_clim(vmin, vmax)
Expand Down Expand Up @@ -5518,11 +5574,13 @@ def pcolormesh(self, *args, **kwargs):
Keyword arguments:

*cmap*: [ *None* | Colormap ]
A :class:`matplotlib.colors.Colormap` instance. If *None*, use
rc settings.
A :class:`matplotlib.colors.Colormap` or
:class:`matplotlib.colors.BivariateColormap` instance. If *None*,
use rc settings.

*norm*: [ *None* | Normalize ]
A :class:`matplotlib.colors.Normalize` instance is used to
A :class:`matplotlib.colors.Normalize` or
:class:`matplotlib.colors.BivariateNorm` instance is used to
scale luminance data to 0,1. If *None*, defaults to
:func:`normalize`.

Expand Down Expand Up @@ -5582,25 +5640,41 @@ def pcolormesh(self, *args, **kwargs):

allmatch = (shading == 'gouraud')

X, Y, C = self._pcolorargs('pcolormesh', *args, allmatch=allmatch)
kw = {'norm': norm, 'cmap': cmap, 'allmatch': allmatch}
X, Y, C = self._pcolorargs('pcolormesh', *args, **kw)
Ny, Nx = X.shape

is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
if C.ndim != 3 and C.shape[0] != 2:
raise TypeError("Expected shape like (2, n, m)")
if cmap is None:
cmap = mcolors.BivariateColormap()
if norm is None:
norm = mcolors.BivariateNorm()

# unit conversion allows e.g. datetime objects as axis values
self._process_unit_info(xdata=X, ydata=Y, kwargs=kwargs)
X = self.convert_xunits(X)
Y = self.convert_yunits(Y)

# convert to one dimensional arrays
C = C.ravel()
# convert to one dimensional arrays if univariate
if isinstance(norm, mcolors.BivariateNorm):
C = np.asarray([c.ravel() for c in C])
else:
C = C.ravel()

coords = np.column_stack((X.flat, Y.flat)).astype(float, copy=False)

collection = mcoll.QuadMesh(Nx - 1, Ny - 1, coords,
antialiased=antialiased, shading=shading,
**kwargs)
collection.set_alpha(alpha)
collection.set_array(C)
if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"
if norm is not None and not isinstance(norm, mcolors.Norms):
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)
collection.set_cmap(cmap)
collection.set_norm(norm)
Expand Down Expand Up @@ -5634,7 +5708,7 @@ def pcolormesh(self, *args, **kwargs):
@docstring.dedent_interpd
def pcolorfast(self, *args, **kwargs):
"""
pseudocolor plot of a 2-D array
pseudocolor plot of a 2-D univariate or 3-D bivariate array

Experimental; this is a pcolor-type method that
provides the fastest possible rendering with the Agg
Expand Down Expand Up @@ -5693,11 +5767,13 @@ def pcolorfast(self, *args, **kwargs):
Optional keyword arguments:

*cmap*: [ *None* | Colormap ]
A :class:`matplotlib.colors.Colormap` instance from cm. If *None*,
use rc settings.
A :class:`matplotlib.colors.Colormap` or
:class:`matplotlib.colors.BivariateColormap` instance from cm.
If *None*, use rc settings.

*norm*: [ *None* | Normalize ]
A :class:`matplotlib.colors.Normalize` instance is used to scale
A :class:`matplotlib.colors.Normalize` or
:class:`matplotlib.colors.BivariateNorm` instance is used to scale
luminance data to 0,1. If *None*, defaults to normalize()

*vmin*/*vmax*: [ *None* | scalar ]
Expand All @@ -5723,12 +5799,26 @@ def pcolorfast(self, *args, **kwargs):
cmap = kwargs.pop('cmap', None)
vmin = kwargs.pop('vmin', None)
vmax = kwargs.pop('vmax', None)
if norm is not None and not isinstance(norm, mcolors.Normalize):
msg = "'norm' must be an instance of 'mcolors.Normalize'"

if norm is not None and not isinstance(norm, mcolors.Norms):
msg = ("'norm' must be an instance of 'mcolors.Normalize' or "
"'mcolors.BivariateNorm'")
raise ValueError(msg)

C = args[-1]
nr, nc = C.shape
C = np.asarray(args[-1])

is_bivari = (isinstance(norm, mcolors.BivariateNorm) or
isinstance(cmap, mcolors.BivariateColormap))
if is_bivari:
if C.ndim != 3 and C.shape[0] != 2:
raise TypeError("Expected shape like (2, n, m)")
if cmap is None:
cmap = mcolors.BivariateColormap()
if norm is None:
norm = mcolors.BivariateNorm()
nr, nc = C.shape[1:]
else:
nr, nc = C.shape
if len(args) == 1:
style = "image"
x = [0, nc]
Expand Down
1 change: 0 additions & 1 deletion lib/matplotlib/axes/_subplots.py
Original file line number Diff line number Diff line change
Expand Up @@ -177,7 +177,6 @@ def subplot_class_factory(axes_class=None):
(SubplotBase, axes_class),
{'_axes_class': axes_class})
_subplot_classes[axes_class] = new_class

return new_class

# This is provided for backward compatibility
Expand Down
Loading