"""Plot objects using matplotlib.
This module contains basic plotting functions using the matplotlib library.
"""
import numpy as np
[docs]
def plot_line(ax,projection,x,y,z,scales=(1.,1.,1.),line_args={}):
"""Wrapper for plot() in matplotlib. Support 3D, xy, xz and yz projections.
Args:
ax: axis to be plotted.
projection (str): support *3d, xy, xz, yz*.
x (ndarray): x coordinates.
y (ndarray): y coordinates.
z (ndarray): z coordinates.
scales (tuple): axis scales.
line_args (dic): matplotlib args for plot() func.
Returns:
matplotlib plot object.
Examples:
.. code-block:: python
import numpy as np
from genepy3d.util import plot as mypl
import matplotlib.pyplot as plt
# coordinates
x = np.array([1.,2.,3.])
y = np.array([1.,2.,3.])
z = np.array([1.,2.,3.])
# 3D plot
fig = plt.figure()
ax = fig.add_subplot(111,projection='3d')
mypl.plot_line(ax,'3d',x,y,z)
# 2D plot (XY projection)
fig = plt.figure()
ax = fig.add_subplot(111)
mypl.plot_line(ax,'xy',x,y,z)
"""
x = x / scales[0]
y = y / scales[1]
z = z / scales[2]
if projection=='3d':
pl = ax.plot(x,y,z,**line_args)
else:
if projection=='xy':
_x, _y = x, y
elif projection=='xz':
_x, _y = x, z
else:
_x, _y = y, z
pl = ax.plot(_x,_y,**line_args)
return pl
[docs]
def plot_point(ax,projection,x,y,z,scales=(1.,1.,1.),point_args={}):
"""Wrapper for scatter() in matplotlib. Support 3D, xy, xz and yz projections.
Args:
ax: axis to be plotted.
projection (str): support *3d, xy, xz, yz*.
x (ndarray): x coordinates.
y (ndarray): y coordinates.
z (ndarray): z coordinates.
scales (tuple): axis scales.
point_args (dic): matplotlib args for scatter() func.
Returns:
matplotlib scatter object.
Examples:
.. code-block:: python
import numpy as np
from genepy3d.util import plot as mypl
import matplotlib.pyplot as plt
# coordinates
x = np.array([1.,2.,3.])
y = np.array([1.,2.,3.])
z = np.array([1.,2.,3.])
# 3D plot
fig = plt.figure()
ax = fig.add_subplot(111,projection='3d')
mypl.plot_point(ax,'3d',x,y,z)
# 2D plot (XY projection)
fig = plt.figure()
ax = fig.add_subplot(111)
mypl.plot_point(ax,'xy',x,y,z)
"""
x = x / scales[0]
y = y / scales[1]
z = z / scales[2]
if projection=='3d':
pl = ax.scatter(x,y,z,**point_args)
else:
if projection=='xy':
_x, _y = x, y
elif projection=='xz':
_x, _y = x, z
else:
_x, _y = y, z
pl = ax.scatter(_x,_y,**point_args)
return pl
[docs]
def fix_equal_axis(data):
"""Fix unequal axis bug in matplotlib 3d plot.
The option ax.axis('equal') doesn't seem to work in 3D. Assuming a plot of 3D point cloud. This function attemps to fix this issue.
Args:
data (ndarray): 3D points.
Returns:
min and max values in each axis.
Notes:
The returned values are then used in ax.set_xlim(), ax.set_ylim(), ax.set_zlim() to correct the unequal axis.
Examples:
.. code-block:: python
import numpy as np
from genepy3d.util import plot as mypl
import matplotlib.pyplot as plt
# Coordinates
x = np.array([1.,50.,100.])
y = np.array([1.,50.,100.])
z = np.array([1.,50.,100.])
# 3D plot
fig = plt.figure()
ax = fig.add_subplot(111,projection='3d')
mypl.plot_point(ax,'3d',x,y,z)
# Fix unequal axis
data = np.array([x,y,z]).T # array of points whose columns are x, y and z positions
param = mypl.fix_equal_axis(data)
ax.set_xlim(param['xmin'],param['xmax']);
ax.set_ylim(param['ymin'],param['ymax']);
ax.set_zlim(param['zmin'],param['zmax']);
"""
x, y, z = data[:,0], data[:,1], data[:,2]
scalex = x.max()-x.min()
scaley = y.max()-y.min()
scalez = z.max()-z.min()
maxscale = np.round(np.max(np.array([scalex,scaley,scalez])))/2
xmed,ymed,zmed = np.median(x),np.median(y),np.median(z)
scale_params = {}
scale_params['xmin'] = xmed-maxscale
scale_params['xmax'] = xmed+maxscale
scale_params['ymin'] = ymed-maxscale
scale_params['ymax'] = ymed+maxscale
scale_params['zmin'] = zmed-maxscale
scale_params['zmax'] = zmed+maxscale
return scale_params
