How to set zero margins of the figure - matplotlib - python-3.x

How to crop the figure to have no white space where nothing is plotted? Why plt.tight_layout(pad=0) does not work? The picture draw 3d coordinate system.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
fig = plt.figure(figsize=[5,3])
ax = fig.gca(projection = '3d')
ax.set_ylim(-2,3)
ax.set_zlim(-1,2)
vleng = 5
aleng = vleng/3.
p = np.array([vleng+200, 0, 0])
q = np.array([0, vleng-2, 0])
r = np.array([0, 0, vleng-3])
ax.plot(*np.vstack([[0,0,0], p]).T, color='black')
ax.plot(*np.vstack([[0,0,0], q]).T, color='black')
ax.plot(*np.vstack([[0,0,0], r]).T, color='black')
ax.azim = 20 # y rotation (default=270)
ax.elev = 20 # x rotation (default=0)
ax.dist = 10 # zoom (define perspective)
ax.set_axis_off( ) # hide all grid
plt.tight_layout(pad=0)
plt.show()
The output:
figure

So I tried multiple things. The only thing that would reduce these white spaces would require the three lines to be drawn along the meeting lines of the planes. So I did some measurements and here's the code where the white spaces have significantly reduced. You're free to reduce it further by tweaking it some more. Also comment out ax.set_axis_off( ) to see what's happening:
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
fig = plt.figure(figsize=[5,3])
ax = fig.gca(projection = '3d')
ax.set_ylim(0,3)
ax.set_zlim(0,2)
# ax.set_xlim(0,2)
vleng = 5
aleng = vleng/3.
p = np.array([vleng+200, 0, 0])
q = np.array([0, vleng-2, 0])
r = np.array([0, 0, vleng-3])
ax.plot(*np.vstack([[0,0,0], p]).T, color='black')
ax.plot(*np.vstack([[0,0,0], q]).T, color='black')
ax.plot(*np.vstack([[0,0,0], r]).T, color='black')
ax.azim = 20 # y rotation (default=270)
ax.elev = 20 # x rotation (default=0)
ax.dist = 10 # zoom (define perspective)
ax.set_axis_off( ) # hide all grid
plt.tight_layout(pad=0)
plt.show()

Related

Change colorbar limits without changing the values of the data it represents in scatter

I'm trying to change a colorbar attached to a scatter plot so that the minimum and maximum of the colorbar are the minimum and maximum of the data, but I want the data to be centred at zero as I'm using a colormap with white at zero. Here is my example
import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(0, 1, 61)
y = np.linspace(0, 1, 61)
C = np.linspace(-10, 50, 61)
M = np.abs(C).max() # used for vmin and vmax
fig, ax = plt.subplots(1, 1, figsize=(5,3), dpi=150)
sc=ax.scatter(x, y, c=C, marker='o', edgecolor='k', vmin=-M, vmax=M, cmap=plt.cm.RdBu_r)
cbar=fig.colorbar(sc, ax=ax, label='$R - R_0$ (mm)')
ax.set_xlabel('x')
ax.set_ylabel('y')
As you can see from the attached figure, the colorbar goes down to -M, where as I want the bar to just go down to -10, but if I let vmin=-10 then the colorbar won't be zerod at white. Normally, setting vmin to +/- M when using contourf the colorbar automatically sorts to how I want. This sort of behaviour is what I expect when contourf uses levels=np.linspace(-M,M,61) rather than setting it with vmin and vmax with levels=62. An example showing the default contourf colorbar behaviour I want in my scatter example is shown below
plt.figure(figsize=(6,5), dpi=150)
plt.contourf(x, x, np.reshape(np.linspace(-10, 50, 61*61), (61,61)),
levels=62, vmin=-M, vmax=M, cmap=plt.cm.RdBu_r)
plt.colorbar(label='$R - R_0$ (mm)')
Does anyone have any thoughts? I found this link which I thought might solve the problem, but when executing the cbar.outline.set_ydata line I get this error AttributeError: 'Polygon' object has no attribute 'set_ydata' .
EDIT a little annoyed that someone has closed this question without allowing me to clarify any questions they might have, as none of the proposed solutions are what I'm asking for.
As for Normalize.TwoSlopeNorm, I do not want to rescale the smaller negative side to use the entire colormap range, I just want the colorbar attached to the side of my graph to stop at -10.
This link also does not solve my issue, as it's the TwoSlopeNorm solution again.
After changing the ylim of the colorbar, the rectangle formed by the surrounding spines is too large. You can make this outline invisible. And then add a new rectangular border:
import numpy as np
import matplotlib.pyplot as plt
x = np.linspace(0, 1, 61)
y = np.linspace(0, 1, 61)
C = np.linspace(-10, 50, 61)
M = np.abs(C).max() # used for vmin and vmax
fig, ax = plt.subplots(1, 1, figsize=(5, 3), dpi=150)
sc = ax.scatter(x, y, c=C, marker='o', edgecolor='k', vmin=-M, vmax=M, cmap=plt.cm.RdBu_r)
cbar = fig.colorbar(sc, ax=ax, label='$R - R_0$ (mm)')
cb_ymin = C.min()
cb_ymax = C.max()
cb_xmin, cb_xmax = cbar.ax.get_xlim()
cbar.ax.set_ylim(cb_ymin, cb_ymax)
cbar.outline.set_visible(False) # hide the surrounding spines, which are too large after set_ylim
cbar.ax.add_patch(plt.Rectangle((cb_xmin, cb_ymin), cb_xmax - cb_xmin, cb_ymax - cb_ymin,
fc='none', ec='black', clip_on=False))
plt.show()
Another approach until v3.5 is released is to make a custom colormap that does what you want (see also https://matplotlib.org/stable/tutorials/colors/colormap-manipulation.html#sphx-glr-tutorials-colors-colormap-manipulation-py)
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.cm as cm
from matplotlib.colors import ListedColormap
fig, axs = plt.subplots(2, 1)
X = np.random.randn(32, 32) + 2
pc = axs[0].pcolormesh(X, vmin=-6, vmax=6, cmap='RdBu_r')
fig.colorbar(pc, ax=axs[0])
import matplotlib.pyplot as plt
import numpy as np
import matplotlib.cm as cm
from matplotlib.colors import ListedColormap
fig, axs = plt.subplots(2, 1)
X = np.random.randn(32, 32) + 2
pc = axs[0].pcolormesh(X, vmin=-6, vmax=6, cmap='RdBu_r')
fig.colorbar(pc, ax=axs[0])
def keep_center_colormap(vmin, vmax, center=0):
vmin = vmin - center
vmax = vmax - center
dv = max(-vmin, vmax) * 2
N = int(256 * dv / (vmax-vmin))
RdBu_r = cm.get_cmap('RdBu_r', N)
newcolors = RdBu_r(np.linspace(0, 1, N))
beg = int((dv / 2 + vmin)*N / dv)
end = N - int((dv / 2 - vmax)*N / dv)
newmap = ListedColormap(newcolors[beg:end])
return newmap
newmap = keep_center_colormap(-2, 6, center=0)
pc = axs[1].pcolormesh(X, vmin=-2, vmax=6, cmap=newmap)
fig.colorbar(pc, ax=axs[1])
plt.show()

matplotlib.patches Circle - transparent?

How to make the circle clear transparent? The desired result is a black edge and None colour to see the plots behind the circle.
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D # 3d graph
from mpl_toolkits.mplot3d import proj3d # 3d graph
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import proj3d, art3d
from matplotlib.patches import Circle
# Plot figure
figsize=[5,5]
fig = plt.figure(figsize=figsize)
ax = fig.add_subplot(111, projection='3d')
ax.azim = -57 # y rotation (default=270)
ax.elev = 29 # x rotation (default=0)
# Set limits
ax.set_xlim(-50, 50)
ax.set_ylim(0, 1)
ax.set_zlim(-50, 50)
R = 50
floor_front = Circle((0, 0), R, linewidth=2, edgecolor = 'black', alpha = 0.3) # (x, z), radius
ax.add_patch(floor_front)
art3d.pathpatch_2d_to_3d(floor_front, z=0, zdir="y") # z = corresponds to y
plt.show()
In Circle(), add facecolor="none".

How to color space between two lines with a colour transition?

How to colour space between two lines with a colour transition? For instance, with grey colour - the dark grey from the upper line should become lighter as proceeding to the lower line. Thank you
import matplotlib.pyplot as plt
import numpy as np
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [8, 8]
x = np.linspace(0, 1, 100)
y = 0.3*x
ax.set_ylim(-0.2, 0.6)
ax.plot(x, y)
width_l = ax.get_ylim()[1] - ax.get_ylim()[0]
ax.plot(x, y - 0.1*width_l)
plt.show()
Edit
And this, please? How to make the width of the coloured part the same?
import matplotlib.pyplot as plt
import numpy as np
import pywt
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [8, 8]
wavelet = pywt.ContinuousWavelet('morl')
psi, x = wavelet.wavefun(level=2)
cmap = plt.get_cmap('Greys_r')
ax.plot(x, psi)
ax.set_xlim(ax.get_xlim()[0], ax.get_xlim()[1])
y_a = ax.get_ylim()
ax.set_ylim(y_a[0],y_a[1]*1.3)
width_l = ax.get_ylim()[1] - ax.get_ylim()[0]
x_range = ax.get_xlim()[1] - ax.get_xlim()[0]
x_shift = x_range * 0.1
ax.plot([x[0]+x_shift, x[1]+x_shift], [psi[0], psi[1]])
ax.plot([x[2]-x_shift, x[3]-x_shift], [psi[2], psi[3]])
ax.plot([x[1], x[2]], [psi[1]-width_l*0.1, psi[2]-width_l*0.1])
for t in np.linspace(0, 1, 40):
ax.plot(x, psi - t * 0.1 * width_l, color=cmap(t/2 + 0.25))
plt.show()
You could draw a lot of parallel lines (or curves) using a color from a gray-scale colormap. The example code below uses a transformation u = t/2 + 0.25, so when t goes from 0 to 1, u would just go between 0.25 and 0.75 to select of specific range from the colormap, avoiding the very dark and very light parts.
import matplotlib.pyplot as plt
import numpy as np
fig, ax = plt.subplots()
plt.rcParams["figure.figsize"] = [8, 8]
x = np.linspace(0, 1, 100)
y = 0.3 * x
width_l = ax.get_ylim()[1] - ax.get_ylim()[0]
ax.set_ylim(-0.2, 0.6)
cmap = plt.get_cmap('Greys_r')
for t in np.linspace(0, 1, 40):
u = t/2 + 0.25
ax.plot(x, y - t * 0.1 * width_l, color=cmap(u))
ax.plot(x, y)
ax.plot(x, y - 0.1 * width_l)
plt.show()

Plotting colorbar in Python 3

I am trying to color the errorbar points based on the color from an array. But getting an error. My code is shown below:
import numpy as np
import matplotlib.pyplot as plt
from matplotlib.cm import ScalarMappable, coolwarm as cmap
from matplotlib.colors import Normalize
fig = plt.figure(1)
sp = fig.add_subplot(1, 1, 1)
sp.set_xlabel(r'$x$')
sp.set_ylabel(r'$y$')
x = np.random.rand(10)
y = np.random.rand(10)
M = np.logspace(9, 10, 10)
norm = Normalize(vmin=8, vmax=11,clip=False) # controls the min and max of the colorbar
smap = ScalarMappable(cmap=cmap, norm=norm)
for xi, yi, Mi in zip(x, y, M):
c = cmap(norm(np.log10(Mi))) # make sure to color by log of mass, not mass
sp.errorbar(
xi,
yi,
yerr=[[.1], [.1]],
xerr=[[.1], [.1]],
ecolor=c,
marker='o',
mec=c,
mfc=c
)
cb = plt.colorbar(smap)
cb.set_label(r'$\log_{10}M$')
I am getting the following error:
TypeError: You must first set_array for mappable
For matplotlib < 3.1, you need to set an array - which can be empty
sm = ScalarMappable(cmap=cmap, norm=norm)
sm.set_array([])
fig.colorbar(sm)
For matplotlib >= 3.1, this is not necessary any more.
sm = ScalarMappable(cmap=cmap, norm=norm)
fig.colorbar(sm)

matplotlib plot rotation 90 degree is not happening

I am finding the edges of the images using matplotlib.I have done almost.And i want to rotate the image as 90 degree in plot.But it is not working for me.I have tried many things.Below is my code what i have tried.
from scipy import misc
from skimage import color,measure
import matplotlib.pyplot as plt
from skimage.draw import ellipse
from skimage.measure import find_contours, approximate_polygon, subdivide_polygon
from PIL import Image
import numpy as np
filename = r"images/5601.jpg"
fimg = misc.imread(filename)
gimg = color.colorconv.rgb2grey(fimg)
contours = measure.find_contours(gimg, 0.8)
for n, contour in enumerate(contours):
plt.plot(contour[:, 1], contour[:, 0], linewidth=2)
contour = contours[0]
new_s = contour.copy()
appr_s = approximate_polygon(new_s, tolerance=0.8)
fig, ax2 = plt.subplots(ncols=1, figsize=(7, 5))
ax2.plot(contour[:, 0], contour[:, 1])
#these are all what i have tried
#plt.xticks(rotation='vertical')
# for tick in ax2.get_xticklabels():
# tick.set_rotation(45)
#plt.setp(ax2.xaxis.get_majorticklabels(), rotation=70 )
#ax2.tick_params(axis='both', rotation=45)
#fig.autofmt_xdate(bottom=0.5, rotation=90, ha='right')
#plt.hist(ax2, bins=10, orientation='horizontal')
plt.axis('off')
plt.tick_params(axis='both' , left='off', top='off', right='off', bottom='off', labelleft='off', labeltop='off', labelright='off', labelbottom='off')
plt.savefig("test.svg", format="svg")
The output is:
Expected output is:
Thanks in advance.
There are a lot of options here. It is important to note that rotating the ticks will not help here. Instead, use either of the following.
Flip the axes using invert_yaxis(). This would not rotate the image, but flip the axes the image is shown in vertically.
ax2.plot(contour[:, 1], contour[:, 0])
ax2.invert_yaxis()
Flip the image using numpy.flipud. This would not rotate the image, but flip it vertically before processing it further.
fimg = plt.imread(filename)
fimg = np.flipud(fimg)
# ...
ax2.plot(contour[:, 1], contour[:, 0])
Rotate the image using numpy.rot90. In fact you would need to rotate it by 180 degrees (k=2).
fimg = plt.imread(filename)
fimg = np.rot90(fimg,k=2)
# ...
ax2.plot(contour[:, 1], contour[:, 0])
Rotate the output curve
mat = lambda angle: np.array([[ np.cos(angle), np.sin(angle)],
[-np.sin(angle), np.cos(angle)]])
rotcontour = np.dot(contour, mat(np.deg2rad(180)))
ax2.plot(rotcontour[:, 1], rotcontour[:, 0])

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