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As you can see from the link, the example is from the outdated 0.12.x version(s) of skimage, whereas 0.18.0 is current stable version.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.
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import psutil
import matplotlib.pyplot as plt
# get information about processes and memory usage
processes = []
for proc in psutil.process_iter(['pid', 'name', 'memory_info']):
try:
processes.append({
'pid': proc.info['pid'],
'name': proc.info['name'],
'memory': proc.info['memory_info'].rss
})
except (psutil.AccessDenied, psutil.NoSuchProcess):
pass
# sort processes by memory usage
processes.sort(key=lambda x: x['memory'], reverse=True)
# create a chart
fig, ax = plt.subplots()
ax.bar([p['name'] for p in processes], [p['memory'] / 1024 / 1024 for p in processes])
ax.set_xticklabels([p['name'] for p in processes], rotation=90)
ax.set_ylabel('Memory usage (MB)')
ax.set_title('Windows process memory usage')
# save chart to file
fig.savefig('memory_usage.png', bbox_inches='tight')
When executing the code, I get the following error:
C:\Users\V0lKent\PycharmProjects\pythonProject\venv\Scripts\python.ex e C:/Users/V0lKent/PycharmProjects/pythonProject/RAManalizer.py
C:\Users\V0lKent\PycharmProjects\pythonProject\RAManalizer.py:20: MatplotlibDeprecationWarning: Support for FigureCanvases without a required_interactive_framework attribute was deprecated in Matplotlib 3.6 and will be removed two minor releases later.
fig, ax = plt.subplots()
Traceback (most recent call last):
File "C:\Users\V0lKent\PycharmProjects\pythonProject\RAManalizer.py", line 20, in <module>
fig, ax = plt.subplots()
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 1474, in subplots
fig = figure(**fig_kw)
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\_api\deprecation.py", line 454, in wrapper
return func(*args, **kwargs)
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 813, in figure
manager = new_figure_manager(
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 382, in new_figure_manager
_warn_if_gui_out_of_main_thread()
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 360, in _warn_if_gui_out_of_main_thread
if _get_required_interactive_framework(_get_backend_mod()):
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 208, in _get_backend_mod
switch_backend(rcParams._get("backend"))
File "C:\Users\V0lKent\PycharmProjects\pythonProject\venv\lib\site-packages\matplotlib\pyplot.py", line 331, in switch_backend
manager_pyplot_show = vars(manager_class).get("pyplot_show")
TypeError: vars() argument must have __dict__ attribute
Process finished with exit code 1
In matplotlib, the update_from method of a Line2D object can be used to copy properties from another line (see e.g. this answer). This is not working if the two lines live on different axes. The following code:
fig, (ax1, ax2) = plt.subplots(2, 1)
line1, = ax1.plot(range(10), "r.")
line2, = ax2.plot(*line1.get_xydata().T)
line2.update_from(line1)
raises
AttributeError: 'NoneType' object has no attribute 'extents'
while the traceback leaves me puzzled.
My questions are:
Why is this error raised?
How can I copy (all) Line2D properties of line1 to line2 instead?
EDIT
After a bit more testing I can say that the AttributeError above is for example raised in a Jupyter notebook session with the %matplotlib inline backend. With the %matplotlib notebook backend or in a regular Python script (e.g. with the "qt5agg" backend), the code passes without an error but line2 is "invisible" afterwards.
For completeness, the above image was created using (Anaconda) Python 3.7.9 and matplotlib 3.3.1 with:
import matplotlib as mpl
import matplotlib.pyplot as plt
mpl.use("qt5agg")
fig, (ax1, ax2) = plt.subplots(2, 1)
line1, = ax1.plot(range(10), "r.")
line2, = ax2.plot(*line1.get_xydata().T)
line2.update_from(line1)
plt.savefig("test.png")
The problem remains that I cannot copy the Line2D properties from line1 to line2.
EDIT 2
Throwing a plt.tight_layout() into the mix brings back the AttributeError.
EDIT 3
As requested in the comments, here is the traceback for the error I get with plt.tight_layout() (EDIT 2):
Traceback (most recent call last):
File "test.py", line 11, in <module>
plt.tight_layout()
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 451, in wrapper
return func(*args, **kwargs)
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/pyplot.py", line 1490, in tight_layout
gcf().tight_layout(pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/cbook/deprecation.py", line 411, in wrapper
return func(*inner_args, **inner_kwargs)
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/figure.py", line 2615, in tight_layout
pad=pad, h_pad=h_pad, w_pad=w_pad, rect=rect)
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/tight_layout.py", line 308, in get_tight_layout_figure
pad=pad, h_pad=h_pad, w_pad=w_pad)
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/tight_layout.py", line 84, in auto_adjust_subplotpars
bb += [ax.get_tightbbox(renderer, for_layout_only=True)]
File "/home/janjoswig/.pyenv/versions/miniconda3-4.7.12/envs/md379/lib/python3.7/site-packages/matplotlib/axes/_base.py", line 4199, in get_tightbbox
if np.all(clip_extent.extents == axbbox.extents):
AttributeError: 'NoneType' object has no attribute 'extents'
It seems update_from updates too much, including the transformation and the clipbox. Maybe the error comes from the object being totally invisible after clipping to the wrong clipbox?
A workaround can be to save both before updating and setting them back:
from matplotlib import pyplot as plt
fig, (ax1, ax2) = plt.subplots(2, 1)
line1, = ax1.plot(range(10), "r.")
line2, = ax2.plot(*line1.get_xydata().T)
old_transform = line2.get_transform()
old_clipbox = line2.clipbox
line2.update_from(line1)
line2.set_transform(old_transform)
line2.clipbox = old_clipbox
plt.tight_layout()
plt.draw()
I have a list size of 1247746130. I want to get a histogram for this list:
bins = np.linspace(-100, 1, 100)
plt.hist(refList, bins, alpha=0.5, label='reference')
plt.legend(loc='upper right')
plt.savefig('reference.png')
but I get an error:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/local/lib/python2.7/dist-packages/matplotlib/pyplot.py", line 3081, in hist
stacked=stacked, data=data, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/__init__.py", line 1898, in inner
return func(ax, *args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/matplotlib/axes/_axes.py", line 6146, in hist
x = _normalize_input(x, 'x')
File "/usr/local/lib/python2.7/dist-packages/matplotlib/axes/_axes.py", line 6083, in _normalize_input
inp = np.asarray(inp)
File "/usr/local/lib/python2.7/dist-packages/numpy/core/numeric.py", line 531, in asarray
return array(a, dtype, copy=False, order=order)
MemoryError
I have 8GB RAM. Is it somehow possible to get a histogram for my data?
Thanks in advance!
I've had problems with plt.hist in the past so now use numpy.histogram. (although I think plt.hist does actually use numpy.histogram behind the scenes). An example is shown below:
import numpy as np
import matplotlib.pyplot as plt
bins = np.linspace(-100, 1, 100)
heights, edges = np.histogram(data, bins)
edges = edges[:-1]+(edges[1]-edges[0])
fig, ax = plt.subplots()
ax.plot(edges, heights)
plt.show()
Here is my code:
import matplotlib.pyplot as plt
plt.figure(1) # the first figure
plt.subplot(211) # the first subplot in the first figure
plt.plot([1, 2, 3])
plt.subplot(212) # the second subplot in the first figure
plt.plot([4, 5, 6])
plt.figure(2) # a second figure
plt.plot([4, 5, 6]) # creates a subplot(111) by default
plt.text(.5,1.5,'211',figure = 211) #tring to add text in previous subplot
plt.figure(1) # figure 1 current; subplot(212) still current
plt.subplot(211) # make subplot(211) in figure1 current
plt.title('Easy as 1, 2, 3') # subplot 211 title
The error:
Traceback (most recent call last):
File "C:/Users/ezhou/Desktop/python/test3.py", line 11, in <module>
plt.text(.5,1.5,'211',figure = 211)
File "C:\Python27\lib\site-packages\matplotlib\pyplot.py", line 3567, in text
ret = gca().text(x, y, s, fontdict=fontdict, withdash=withdash, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\axes\_axes.py", line 619, in text
self._add_text(t)
File "C:\Python27\lib\site-packages\matplotlib\axes\_base.py", line 1720, in _add_text
self._set_artist_props(txt)
File "C:\Python27\lib\site-packages\matplotlib\axes\_base.py", line 861, in _set_artist_props
a.set_figure(self.figure)
File "C:\Python27\lib\site-packages\matplotlib\artist.py", line 640, in set_figure
raise RuntimeError("Can not put single artist in "
RuntimeError: Can not put single artist in more than one figure
I was trying to understand the kwargs 'figure' in class matplotlib.text.Text(), but it will always reply 'Can not put single artist in more than one figure'. So I was confused about how to use this 'figure' kwarg. Can anyone give me some advise? Thanks!
You shouldn't pass figure as a kwarg, instead use text method of a Figure (or Axes) instance. Example:
import matplotlib.pyplot as plt
fig1, fig2 = plt.figure(1), plt.figure(2)
sp1, sp2 = fig1.add_subplot(211), fig2.add_subplot(211)
sp1.plot([1, 2, 3])
sp2.plot([0, 1, 3])
fig1.text(.5, .3, 'whole figure')
sp2.text(.5, .5, 'subplot')
Please note that coordinates are relative (0, 1).
P.S if you find matplotlib needlessly complicated (as I do), you may wish to have a look at Plotly
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.