I'm implementing some codes using PyCharm Community Edition 2016.1.4 as environment.
I have the following simple code:
print(__doc__)
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from sklearn.cluster import KMeans
from sklearn import datasets
np.random.seed(5)
centers = [[1, 1], [-1, -1], [1, -1]]
iris = datasets.load_iris()
X = iris.data
y = iris.target
estimators = {'k_means_iris_3': KMeans(n_clusters=3),
'k_means_iris_8': KMeans(n_clusters=8),
'k_means_iris_bad_init': KMeans(n_clusters=3, n_init=1,
init='random')}
fignum = 1
name = 'k_means_iris_3'
est = KMeans(n_clusters=3)
fig = plt.figure(fignum, figsize=(4, 3))
plt.clf()
ax = Axes3D(fig, rect=[0, 0, .95, 1], elev=48, azim=134)
est.fit(X)
labels = est.labels_
ax.scatter(X[:, 3], X[:, 0], X[:, 2], c=labels.astype(np.float))
ax.w_xaxis.set_ticklabels([])
ax.w_yaxis.set_ticklabels([])
ax.w_zaxis.set_ticklabels([])
ax.set_xlabel('Petal width')
ax.set_ylabel('Sepal length')
ax.set_zlabel('Petal length')
fignum = fignum + 1
plt.show()
If I simply run it I correctly obtain the proper image:
At the contrary, if I go in debug mode, when I arrive at the line:
fig = plt.figure(fignum, figsize=(4, 3))
I get this error:
Traceback (most recent call last):
File "C:\Program Files\Anaconda\lib\site-packages\IPython\core\interactiveshell.py", line 2885, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "<ipython-input-1-36b230119a6b>", line 1, in <module>
fig = plt.figure(fignum, figsize=(4, 3))
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\pyplot.py", line 535, in figure
**kwargs)
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 44, in new_figure_manager
return new_figure_manager_given_figure(num, thisFig)
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 51, in new_figure_manager_given_figure
canvas = FigureCanvasQTAgg(figure)
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 223, in __init__
super(FigureCanvasQTAgg, self).__init__(figure=figure)
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\backends\backend_qt5agg.py", line 66, in __init__
super(FigureCanvasQTAggBase, self).__init__(figure=figure)
File "C:\Program Files\Anaconda\lib\site-packages\matplotlib\backends\backend_qt5.py", line 239, in __init__
super(FigureCanvasQT, self).__init__(figure=figure)
AttributeError: 'figure()' is not a Qt property or a signal
Can you imagine why?
The python error was kinda misleading. The real problem was the lack (for some reasons due to a double installation of Python) of a Python binding: PyQt4.
Just go here and, choose the proper installer and... just run it! You can also avoid to close-and-reopen the pyCharm (in a couple of seconds it fixes itself and no more errors).
Related
I am very new to Python. I am trying to run this script:
https://scikit-image.org/docs/0.12.x/auto_examples/segmentation/plot_local_otsu.html
But, I'm getting this error:
Traceback (most recent call last):
File "/Users/janine/Downloads/plot_local_otsu.py", line 37, in <module>
fig, ax = plt.subplots(2, 2, figsize=(8, 5), sharex=True, sharey=True,
File "/usr/local/lib/python3.9/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/matplotlib/pyplot.py", line 1440, in subplots
axs = fig.subplots(nrows=nrows, ncols=ncols, sharex=sharex, sharey=sharey,
File "/usr/local/lib/python3.9/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/matplotlib/figure.py", line 908, in subplots
axs = gs.subplots(sharex=sharex, sharey=sharey, squeeze=squeeze,
File "/usr/local/lib/python3.9/site-packages/matplotlib/gridspec.py", line 307, in subplots
axarr[row, col] = figure.add_subplot(
File "/usr/local/lib/python3.9/site-packages/matplotlib/figure.py", line 781, in add_subplot
ax = subplot_class_factory(projection_class)(self, *args, **pkw)
File "/usr/local/lib/python3.9/site-packages/matplotlib/axes/_subplots.py", line 36, in __init__
self._axes_class.__init__(self, fig, [0, 0, 1, 1], **kwargs)
File "/usr/local/lib/python3.9/site-packages/matplotlib/_api/deprecation.py", line 471, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 648, in __init__
self.update(kwargs)
File "/usr/local/lib/python3.9/site-packages/matplotlib/artist.py", line 1064, in update
ret.append(func(v))
File "/usr/local/lib/python3.9/site-packages/matplotlib/axes/_base.py", line 1531, in set_adjustable
_api.check_in_list(["box", "datalim"], adjustable=adjustable)
File "/usr/local/lib/python3.9/site-packages/matplotlib/_api/__init__.py", line 126, in check_in_list
raise ValueError(
ValueError: 'box-forced' is not a valid value for adjustable; supported values are 'box', 'datalim'
I have installed scikit-image exactly as recommended here:
https://scikit-image.org/docs/stable/install.html.
I am on macOS Mojave.
As you can see from the link, the example is from the outdated 0.12.x version(s) of skimage, whereas 0.18.0 is current stable version. And, as the error message indicates, the error comes from this line:
fig, ax = plt.subplots(2, 2, figsize=(8, 5), sharex=True, sharey=True,
subplot_kw={'adjustable': 'box-forced'})
Obviously, the handling of the adjustable member has changed in matplotlib.pyplot over the years. By simply removing the subplot_kw parameter at all, for example, the code runs perfectly fine:
fig, ax = plt.subplots(2, 2, figsize=(8, 5), sharex=True, sharey=True)
In fact, that's also, what the updated example from the skimage documentation looks like (second example there). Notice: You'll have to add two import statements on your own, since the given code there in incomplete.
Getting an error message when I try to render a heat map using this code below. This is just a way of testing this, I have much more involved application of to a large dataset about used cars...but I cannot even get past this issue with two pieces of data.
import pandas as pd
import matplotlib as plt
from matplotlib import pyplot
import numpy as np
# initialize list of lists
#Putting in numbers for the "Name" data ends up working
#data = [[3, 10], [3, 15], [6,50]]
#initializing like this with actual strings for names gives the error
data = [["James", 10], ["Mary", 15], ["Emily", 14]]
# Create the pandas DataFrame
df = pd.DataFrame(data, columns = ['Name', 'Age'])
# print dataframe.
print(df)
plt.pyplot.pcolor(df, cmap='RdBu')
plt.pyplot.colorbar()
plt.pyplot.ylabel("Age")
plt.pyplot.xlabel("Name")
plt.pyplot.show()
The errors are as follows:
Traceback (most recent call last):
File "/home/j/dataexploratory.py", line 22, in <module>
plt.pyplot.colorbar()
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/pyplot.py", line 2320, in colorbar
ret = gcf().colorbar(mappable, cax = cax, ax=ax, **kw)
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/figure.py", line 2098, in colorbar
cb = cbar.colorbar_factory(cax, mappable, **cb_kw)
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/colorbar.py", line 1399, in colorbar_factory
cb = Colorbar(cax, mappable, **kwargs)
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/colorbar.py", line 945, in __init__
ColorbarBase.__init__(self, ax, **kw)
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/colorbar.py", line 327, in __init__
self.draw_all()
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/colorbar.py", line 349, in draw_all
self._process_values()
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/colorbar.py", line 703, in _process_values
expander=0.1)
File "/home/j/anaconda2/lib/python2.7/site-packages/matplotlib/transforms.py", line 2930, in nonsingular
if (not np.isfinite(vmin)) or (not np.isfinite(vmax)):
TypeError: ufunc 'isfinite' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''
Convert 'Name' to categorical dtype.
Except for the default ['r', 'g', 'c'... ] values for colors, every single color in matplotlib returns some sort of error.
For example, the following code:
import matplotlib.pyplot as plt
import matplotlib as mpl
fig, ax = plt.subplots()
ax.plot([2, 7], [1, 4], 'C1')
plt.show();
produces the error
Traceback (most recent call last):
File "/Users/homerlogistics/Downloads/colors-1.py", line 5, in <module>
ax.plot([2, 7], [1, 4], 'C1')
File "/Library/Python/2.7/site-packages/matplotlib-override/matplotlib/axes/_axes.py", line 1373, in plot
for line in self._get_lines(*args, **kwargs):
File "/Library/Python/2.7/site-packages/matplotlib-override/matplotlib/axes/_base.py", line 304, in _grab_next_args
for seg in self._plot_args(remaining, kwargs):
File "/Library/Python/2.7/site-packages/matplotlib-override/matplotlib/axes/_base.py", line 263, in _plot_args
linestyle, marker, color = _process_plot_format(tup[-1])
File "/Library/Python/2.7/site-packages/matplotlib-override/matplotlib/axes/_base.py", line 115, in _process_plot_format
'Unrecognized character %c in format string' % c)
ValueError: Unrecognized character C in format string
I'm trying to do a simple logarithmic bar plot:
import matplotlib.pyplot as plt
plt.bar(range(10), [4**i for i in range(10)], log=True)
plt.show()
It crashes with:
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\pyplot.py", line 2383, in bar
ret = ax.bar(left, height, width=width, bottom=bottom, **kwargs)
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\axes.py", line 4903, in bar
self.add_patch(r)
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\axes.py", line 1572, in add_patch
self._update_patch_limits(p)
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\axes.py", line 1590, in _update_patch_limits
xys = patch.get_patch_transform().transform(vertices)
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\patches.py", line 582, in get_patch_transform
self._update_patch_transform()
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\patches.py", line 578, in _update_patch_transform
bbox = transforms.Bbox.from_bounds(x, y, width, height)
File "C:\Program Files (x86)\Python33\lib\site-packages\matplotlib\transforms.py", line 786, in from_bounds
return Bbox.from_extents(x0, y0, x0 + width, y0 + height)
TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
When I use log=False, it works. I treid plt.yscale('log'), but then the bars disappeared. I'dont see, how I could use the log Parameter wrong in such a simple case.
This appears to be a bug in your version of matplotlib. While the default for the parameter bottom of plt.bar is claimed to be 0, adding an extra keyword argument sets bottom=None which subsequently leads to arithmetic using bottom to fail.
As a workaround you can set bottom yourself to the default value again.
import numpy as np
import matplotlib.pyplot as plt
x = np.arange(10)
plt.bar(x, 4**x, bottom=0, log=True)
plt.show()
I have a fairly simple plotting routine that looks like this:
from __future__ import division
import datetime
import matplotlib
matplotlib.use('Agg')
from matplotlib.pyplot import figure, plot, show, legend, close, savefig, rcParams
import numpy
from globalconstants import *
def plotColumns(columnNumbers, t, out, showFig=False, filenamePrefix=None, saveFig=True, saveThumb=True):
lineProps = ['b', 'r', 'g', 'c', 'm', 'y', 'k', 'b--', 'r--', 'g--', 'c--', 'm--', 'y--', 'k--', 'g--', 'b.-', 'r.-', 'g.-', 'c.-', 'm.-', 'y.-', 'k.-']
rcParams['figure.figsize'] = (13,11)
for i in columnNumbers:
plot(t, out[:,i], lineProps[i])
legendStrings = list(numpy.zeros(NUMCOMPONENTS))
legendStrings[GLUCOSE] = 'GLUCOSE'
legendStrings[CELLULOSE] = 'CELLULOSE'
legendStrings[STARCH] = 'STARCH'
legendStrings[ACETATE] = 'ACETATE'
legendStrings[BUTYRATE] = 'BUTYRATE'
legendStrings[SUCCINATE] = 'SUCCINATE'
legendStrings[HYDROGEN] = 'HYDROGEN'
legendStrings[PROPIONATE] = 'PROPIONATE'
legendStrings[METHANE] = "METHANE"
legendStrings[RUMINOCOCCUS] = 'RUMINOCOCCUS'
legendStrings[METHANOBACTERIUM] = "METHANOBACTERIUM"
legendStrings[BACTEROIDES] = 'BACTEROIDES'
legendStrings[SELENOMONAS] = 'SELENOMONAS'
legendStrings[CLOSTRIDIUM] = 'CLOSTRIDIUM'
legendStrings = [legendStrings[i] for i in columnNumbers]
legend(legendStrings, loc='best')
dt = datetime.datetime.now()
dtAsString = dt.strftime('%d-%m-%Y_%H-%M-%S')
if filenamePrefix is None:
filenamePrefix = ''
if filenamePrefix != '' and filenamePrefix[-1] != '_':
filenamePrefix += '_'
if saveFig:
savefig(filenamePrefix+dtAsString+'.eps')
if saveThumb:
savefig(filenamePrefix+dtAsString+'.png', dpi=300)
if showFig: f.show()
close('all')
When I plot this in single iterations, it works fine. However, the moment I put it in a loop, matplotlib throws a hissy fit...
Traceback (most recent call last):
File "c4hm_param_variation_h2_conc.py", line 148, in <module>
plotColumns(columnNumbers, timeVector, out, showFig=False, filenamePrefix='c
4hm_param_variation_h2_conc_'+str(hydrogen_conc), saveFig=False, saveThumb=True)
File "D:\phdproject\alexander paper\python\v3\plotcolumns.py", line 48, in plo
tColumns
savefig(filenamePrefix+dtAsString+'.png', dpi=300)
File "C:\Python25\lib\site-packages\matplotlib\pyplot.py", line 356, in savefi
g
return fig.savefig(*args, **kwargs)
File "C:\Python25\lib\site-packages\matplotlib\figure.py", line 1032, in savef
ig
self.canvas.print_figure(*args, **kwargs)
File "C:\Python25\lib\site-packages\matplotlib\backend_bases.py", line 1476, i
n print_figure
**kwargs)
File "C:\Python25\lib\site-packages\matplotlib\backends\backend_agg.py", line
358, in print_png
FigureCanvasAgg.draw(self)
File "C:\Python25\lib\site-packages\matplotlib\backends\backend_agg.py", line
314, in draw
self.figure.draw(self.renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\figure.py", line 773, in draw
for a in self.axes: a.draw(renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\axes.py", line 1735, in draw
a.draw(renderer)
File "C:\Python25\lib\site-packages\matplotlib\artist.py", line 46, in draw_wr
apper
draw(artist, renderer, *kl)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 374, in draw
bbox = self._legend_box.get_window_extent(renderer)
File "C:\Python25\lib\site-packages\matplotlib\offsetbox.py", line 209, in get
_window_extent
px, py = self.get_offset(w, h, xd, yd)
File "C:\Python25\lib\site-packages\matplotlib\offsetbox.py", line 162, in get
_offset
return self._offset(width, height, xdescent, ydescent)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 360, in findof
fset
return _findoffset(width, height, xdescent, ydescent, renderer)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 325, in _findo
ffset_best
ox, oy = self._find_best_position(width, height, renderer)
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 817, in _find_
best_position
verts, bboxes, lines = self._auto_legend_data()
File "C:\Python25\lib\site-packages\matplotlib\legend.py", line 669, in _auto_
legend_data
tpath = trans.transform_path(path)
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1911, in t
ransform_path
self._a.transform_path(path))
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1122, in t
ransform_path
return Path(self.transform(path.vertices), path.codes,
File "C:\Python25\lib\site-packages\matplotlib\transforms.py", line 1402, in t
ransform
return affine_transform(points, mtx)
MemoryError: Could not allocate memory for path
This happens on iteration 2 (counting from 1), if that makes a difference. The code is running on Windows XP 32-bit with python 2.5 and matplotlib 0.99.1, numpy 1.3.0 and scipy 0.7.1.
EDIT: The code has now been updated to reflect the fact that the crash actually occurs at the call to legend(). Commenting that call out solves the problem, though obviously, I would still like to be able to put a legend on my graphs...
Is each loop supposed to generate a new figure? I don't see you closing it or creating a new figure instance from loop to loop.
This call will clear the current figure after you save it at the end of the loop:
pyplot.clf()
I'd refactor, though, and make your code more OO and create a new figure instance on each loop:
from matplotlib import pyplot
while True:
fig = pyplot.figure()
ax = fig.add_subplot(111)
ax.plot(x,y)
ax.legend(legendStrings, loc = 'best')
fig.savefig('himom.png')
# etc....
I've also run into this error. what seems to have fixed it is
while True:
fig = pyplot.figure()
ax = fig.add_subplot(111)
ax.plot(x,y)
ax.legend(legendStrings, loc = 'best')
fig.savefig('himom.png')
#new bit here
pylab.close(fig) #where f is the figure
running my loop stably now with fluctuating memory but no consistant increase
Answer from ninjasmith worked for me too - pyplot.close() enabled my loops to work.
From the pyplot tutorial, Working with multiple figures and axes:
You can clear the current figure with clf() and the current
axes with cla(). If you find this statefulness, annoying, don’t
despair, this is just a thin stateful wrapper around an object
oriented API, which you can use instead (see Artist tutorial)
If you are making a long sequence of figures, you need to be aware of
one more thing: the memory required for a figure is not completely
released until the figure is explicitly closed with close(). Deleting
all references to the figure, and/or using the window manager to kill
the window in which the figure appears on the screen, is not enough,
because pyplot maintains internal references until close() is called.
In my case, matplotlib version 3.5.0, As Hui Liu san says,
Following method can keep memory usage low
import matplotlib
print(matplotlib.__version__) #'3.5.0'
import matplotlib.pyplot as plt
plt.savefig('your.png')
# Add both in this order for keeping memory usage low
plt.clf()
plt.close()
I had a similar issue when I was using it from jupyter, putting plt.clf() and plt.close() in the loop did not work.
But this helped:
import matplotlib
matplotlib.use('Agg')
This disables interactive backend for matplotlib.