def draw2DView(figure, raw, seg, index, color=(1,0,0)):
"""
Draw a 2D maximum intensity projection of the raw data and create
a segmentation overlay
"""
raw2d = np.max(raw, axis = 2)
mlab.imshow(raw2d, colormap='gray', figure=figure)
sother = np.multiply( (seg != 0).astype(np.int32),(seg != index).astype(np.int32) )
##max1 = np.max(np.where(np.max(np.max((seg == index).astype(np.int32), axis = 0), axis = 0)!=0))+1
##min1 = np.min(np.where(np.max(np.max((seg == index).astype(np.int32), axis = 0), axis = 0)!=0))
##max2 = np.max(np.where(np.max(np.max((seg == index).astype(np.int32), axis = 0), axis = 1)!=0))+1
##min2 = np.min(np.where(np.max(np.max((seg == index).astype(np.int32), axis = 0), axis = 1)!=0))
##d1 = int(min(max1-min1-15,0))
##d2 = int(min(max2-min2-15,0))
##min1 += d1
##max1 -= d1
##min2 += d2
##max2 -= d2
##sother = (seg == index).astype(np.int32)
##seg2dother = np.max(sother, axis = 0)
##seg2dother[min2:max2,min1:max1]=1
sindex = (seg == index).astype(np.int32)
seg2dother = np.max(sother, axis = 2)
seg2dindex = np.max(sindex, axis = 2)
mlab.contour_surf(seg2dother, color = (0,0,1), contours = 2, warp_scale = 0, figure=figure)
mlab.contour_surf(seg2dindex, color = color, contours = 2, warp_scale = 0, figure=figure)
def test1():
'''G8函数显示'''
# f = lambda x,y:-(np.sin(2*np.pi*x)**3*np.sin(2*np.pi*y))/(x**3*(x+y))
f = lambda x: -(np.sin(2 * np.pi * x[0])**3 * np.sin(2 * np.pi * x[1])) / (
x[0]**3 * (x[0] + x[1]))
g1 = lambda x: x[0]**2 - x[1] + 1
g2 = lambda x: 1 - x[0] + (x[1] - 4)**2
# min = [0.001,0.001]
# max = [10,10]
min = [1, 3]
max = [2, 5]
mesh_x, mesh_y = np.mgrid[min[0]:max[0]:500j, min[1]:max[1]:500j]
v = np.zeros_like(mesh_x)
for i in range(mesh_x.shape[0]):
for j in range(mesh_x.shape[1]):
p = np.array([mesh_x[i, j], mesh_y[i, j]])
v[i, j] = np.log(f(p) + 10000)
# if g1(p)<0 and g2(p)<0:
# v[i,j] = f(p)
# else:
# v[i,j] = 0
mlab.figure(size=[1024, 800])
mlab.imshow(mesh_x, mesh_y, v)
mlab.show()
def test12(self):
data = np.loadtxt(
'C:\\Users\\Administrator\\Documents\\GitHub\\DifferentialEvolution\\map.csv',
delimiter=',')
mlab.imshow(data, colormap='gist_earth', interpolate=False)
mlab.show()
def mayavi_imshow():
"""
绘制mayavi imshow图
:return:
"""
s = np.random.rand(3, 3) # 生成随机的3*3数组
mlab.imshow(s)
mlab.colorbar()
mlab.show()
def update_volume(self):
y, x, z = self.points
r = (y - self.y)**2 + (x - self.x)**2 + (z - self.z)**2
b = np.ones_like(y)
b[r > self.r**2] = 0
self.src.mlab_source.scalars = b
img = (self.H * b.reshape((-1, 1))).reshape((sensor_res, sensor_res))
mlab.clf(figure=self.scene2.mayavi_scene)
mlab.imshow(img, colormap='gray', figure=self.scene2.mayavi_scene)
mlab.colorbar()
def mlab_imshowColor(im, alpha=255, **kwargs):
"""
Plot a color image with mayavi.mlab.imshow.
im is a ndarray with dim (n, m, 3) and scale (0->255]
alpha is a single number or a ndarray with dim (n*m) and scale (0->255]
**kwargs is passed onto mayavi.mlab.imshow(..., **kwargs)
"""
try:
alpha[0]
except:
alpha = pl.ones(im.shape[0] * im.shape[1]) * alpha
if len(alpha.shape) != 1:
alpha = alpha.flatten()
# The lut is a Nx4 array, with the columns representing RGBA
# (red, green, blue, alpha) coded with integers going from 0 to 255,
# we create it by stacking all the pixles (r,g,b,alpha) as rows.
myLut = pl.c_[im.reshape(-1, 3), alpha]
myLutLookupArray = pl.arange(im.shape[0] * im.shape[1]).reshape(im.shape[0], im.shape[1])
#We can display an color image by using mlab.imshow, a lut color list and a lut lookup table.
theImshow = mlab.imshow(myLutLookupArray, colormap='binary', **kwargs) #temporary colormap
theImshow.module_manager.scalar_lut_manager.lut.table = myLut
mlab.draw()
return theImshow
def mcrtmv(frames,
dt,
mesh,
d_nodes,
map,
savemovie=False,
mvname='test',
vmin=-1,
vmax=1):
"""
Creates move from numpyfied results in 2d, using mencoder. Prolly does not work on mac!
"""
size = 500, 500
fig = ml.figure(size=size, bgcolor=(1., 1., 1.))
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
xaxis = np.linspace(0, 1, d_nodes[0] + 1)
yaxis = np.linspace(0, 1, d_nodes[1] + 1)
ml.clf(figure=fig)
u = np.load('solution_%06d.npy' % 1)
u = numpyfy(u, mesh, d_nodes, map)
fname = '_tmp%07d.png' % 1
s = ml.imshow(xaxis, yaxis, u, figure=fig, vmin=vmin, vmax=vmax)
#scale = 1./np.max(np.abs(u))
u = u
ml.axes(extent=[0, 1, 0, 1, 0, 2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2, frames):
u = np.load('solution_%06d.npy' % i)
u = numpyfy(u, mesh, d_nodes, map)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname) #,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
if savemovie:
os.system(
"mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg"
% mvname)
def test_imshow_colormap(self):
# Check if the pipeline is refreshed when we change colormap.
# See issue #262
a = np.random.randint(0, 10 + 1, (100, 100))
actor = mlab.imshow(a, colormap="cool")
with self.assertTraitChanges(actor, 'pipeline_changed'):
actor.module_manager.scalar_lut_manager.lut_mode = 'jet'
def test_imshow_colormap(self):
# Check if the pipeline is refreshed when we change colormap.
# See issue #262
a = np.random.randint(0, 10 + 1, (100, 100))
actor = mlab.imshow(a, colormap="cool")
with self.assertTraitChanges(actor, 'pipeline_changed'):
actor.module_manager.scalar_lut_manager.lut_mode = 'jet'
def test_quiver3d(a, b, c):
dphi, dtheta = np.pi / 30.0, np.pi / 30.0
[phi, theta] = np.mgrid[0:np.pi + dphi * 1.5:dphi,
0:2 * np.pi + dtheta * 1.5:dtheta]
x = a * np.sin(phi) * np.cos(theta)
y = b * np.sin(phi) * np.sin(theta)
z = c * np.cos(phi)
# outward pointing unit vectors
u = x
u = np.array([e / np.linalg.norm(e, ord=2) for e in u])
v = y
v = np.array([e / np.linalg.norm(e, ord=2) for e in v])
w = z
w = np.array([e / np.linalg.norm(e, ord=2) for e in w])
obj = mlab.quiver3d(x, y, z, u, v, w, line_width=1, scale_factor=1)
mlab.axes(obj)
mlab.outline(obj)
mlab.imshow(10)
return obj
def draw_layer(path, position):
# load a png with a scale 0->1 and four color channels (an extra alpha channel for transparency).
im = pl.imread(path, format='png') * 255
colors = tvtk.UnsignedCharArray()
colors.from_array(im.transpose((1, 0, 2)).reshape(-1, 4))
m_image = mlab.imshow(
np.ones(im.shape[:2]),
extent=[0, 0, 0, 0, position, position],
opacity=0.6)
m_image.actor.input.point_data.scalars = colors
def mcrtmv(frames, dt,mesh, d_nodes, map, savemovie=False, mvname='test', vmin=-1, vmax=1):
"""
Creates move from numpyfied results in 2d, using mencoder. Prolly does not work on mac!
"""
size = 500,500
fig = ml.figure(size= size, bgcolor=(1.,1.,1.));
#fig.scene.anti_aliasing_frames=07
#extent = [0,Nx-1,0,Ny-1,-30,30]
xaxis = np.linspace(0,1,d_nodes[0]+1)
yaxis = np.linspace(0,1,d_nodes[1]+1)
ml.clf(figure=fig)
u = np.load('solution_%06d.npy'%1);
u = numpyfy(u, mesh, d_nodes, map)
fname = '_tmp%07d.png' % 1
s = ml.imshow(xaxis, yaxis, u,figure=fig,vmin=vmin, vmax=vmax)
#scale = 1./np.max(np.abs(u))
u = u
ml.axes(extent=[0,1,0,1,0,2])
ml.colorbar()
ml.xlabel('x position')
ml.ylabel('y position')
ml.zlabel('wave amplitude')
if savemovie == True:
pl.ion()
arr = ml.screenshot()
img = pl.imshow(arr)
pl.axis('off')
for i in range(2,frames):
u = np.load('solution_%06d.npy'%i);
u = numpyfy(u, mesh, d_nodes, map)
s.mlab_source.scalars = u
fname = '_tmp%07d.png' % i
if savemovie == True:
arr = ml.screenshot()
img.set_array(arr)
pl.savefig(filename=fname)#,figure=fig)
print 'Saving frame', fname
pl.draw()
fig.scene.disable_render = False
if savemovie:
os.system("mencoder 'mf://_tmp*.png' -mf type=png:fps=20 -ovc lavc -lavcopts vcodec=wmv2 -oac copy -o %s.mpg" % mvname);
def mlab_color_imshow(image, **kwargs):
'''Imshow with color in mlab
Adapted from [1]
[1] http://stackoverflow.com/a/24471211/5451259
'''
alpha = np.ones(image.shape[0] * image.shape[1]) * 255
image_LUT_array = np.c_[image.reshape(-1, 3), alpha]
image_LUT_array[:, 0], image_LUT_array[:, 2] = np.copy(image_LUT_array[:, 2]), np.copy(image_LUT_array[:, 0])
LUT_lookup = np.arange(image.shape[0] * image.shape[1]).reshape(image.shape[0], image.shape[1])
mlab_imshow = mlab.imshow(LUT_lookup, colormap='binary', **kwargs)
mlab_imshow.module_manager.scalar_lut_manager.lut.table = image_LUT_array
return mlab_imshow
def draw_groundtrack_surface(scene):
"""Load the Earth Texture image as the surface
"""
# set scene to have simple interactor
scene.scene.interactor.interactor_style = tvtk.InteractorStyleTerrain()
surface_image = ndimage.imread('./data/earthmap1k.jpg')
surface_image = np.rot90(surface_image[:, :, 0], -1)
surface = mlab.imshow(surface_image,
figure=scene.mayavi_scene,
extent=[-180, 180, -90, 90, 0, 0])
mlab.axes(surface,
extent=[-180, 180, -90, 90, 0, 0],
z_axis_visibility=False)
return surface
def mlab_color_imshow(image, **kwargs):
'''Imshow with color in mlab
Adapted from [1]
[1] http://stackoverflow.com/a/24471211/5451259
'''
alpha = np.ones(image.shape[0] * image.shape[1]) * 255
image_LUT_array = np.c_[image.reshape(-1, 3), alpha]
image_LUT_array[:, 0], image_LUT_array[:, 2] = np.copy(
image_LUT_array[:, 2]), np.copy(image_LUT_array[:, 0])
LUT_lookup = np.arange(image.shape[0] * image.shape[1]).reshape(
image.shape[0], image.shape[1])
mlab_imshow = mlab.imshow(LUT_lookup, colormap='binary', **kwargs)
mlab_imshow.module_manager.scalar_lut_manager.lut.table = image_LUT_array
return mlab_imshow
def draw_map(height,width):
import pylab as pl
im = pl.imread('worldmap.png', format='png')
l = []
for i in im:
x = []
for j in i:
tmp = 0
for k in j: tmp += k
x.append(k)
l.append(x)
ims = mlab.imshow(l, colormap = 'binary')
print "Map shape", len(l),len(l[0])
ims.actor.position = [height/2,(width)/2,0]
ims.actor.scale = [float(height)/len(l),float(width)/len(l[0]),0]
def mlab_imshow_color(img_array, **kwargs):
"""
Plot a color image with mayavi.mlab.imshow.
img_array is a ndarray with dim (n, m, 4) and scale (0->255]
**kwargs is passed onto mayavi.mlab.imshow(..., **kwargs)
"""
my_lut = pl.c_[img_array.reshape(-1, 4)]
my_lut_lookup_array = pl.arange(img_array.shape[0] *
img_array.shape[1]).reshape(
img_array.shape[0], img_array.shape[1])
the_imshow = mlab.imshow(my_lut_lookup_array, colormap='binary',
**kwargs) # temporary colormap
the_imshow.module_manager.scalar_lut_manager.lut.table = my_lut
mlab.draw()
return the_imshow
def _plot_img(img, K, T, z=0.1):
obj = mlab.imshow(img.T)
quat = tf.quaternion_from_matrix(T)
angle, axis = angle_axis_from_quaternion(quat)
obj.actor.rotate_wxyz(angle * 180 / np.pi, *axis)
h, w = img.shape
xmax_pixel, ymax_pixel = w, h
point3d = projectionto3d(K, (xmax_pixel, ymax_pixel))[0]
origin3d = projectionto3d(K, (0, 0))[0]
point3d = point3d * z / point3d[2]
origin3d = origin3d * z / origin3d[2]
center3d = (point3d + origin3d) / 2.
xmax, ymax, _ = point3d - origin3d
obj.actor.scale = np.array([xmax / xmax_pixel, ymax / ymax_pixel, 1.0])
obj.actor.position = utils.apply_transform(T, center3d)
mlab.view(distance=20 * z)
return obj
def _plot_imshow(self, im, alpha,
position=(0, 0, 0),
orientation=(0, 0, 0),
scale=1.0, **kwargs):
"""
Plot a color image with mayavi.mlab.imshow.
im is a ndarray with dim (n, m, 3) and scale (0->255]
alpha is a single number or a ndarray with dim (n*m) and scale (0->255]
**kwargs is passed onto mayavi.mlab.imshow(..., **kwargs)
"""
if len(alpha.shape) != 1:
alpha = alpha.flatten()
# The lut is a Nx4 array, with the columns representing RGBA
# (red, green, blue, alpha) coded with integers going from 0 to 255,
# we create it by stacking all the pixles (r,g,b,alpha) as rows.
# lut = np.c_[im.reshape(-1, 3), alpha] / 255.0
# lut_lookup_array = np.arange(
# im.shape[0] * im.shape[1]).reshape(im.shape[0], im.shape[1])
# We can display an color image by using mlab.imshow, a lut color list and
# a lut lookup table.
# temporary colormap
# imshow = mlab.imshow(lut_lookup_array,
# colormap='binary',
# **kwargs)
colors = tvtk.UnsignedCharArray()
im_shape = im.shape
im_rgba = np.concatenate((im,
alpha.reshape(im_shape[0], im_shape[1], 1)),
axis=-1)
im_rgba_T = im_rgba.transpose((1, 0, 2))
colors.from_array(im_rgba_T.reshape(-1, 4))
image = mlab.imshow(np.ones(im_rgba_T.shape[:2]))
image.actor.input.point_data.scalars = colors
image.actor.scale = (scale, scale, 1.0)
image.actor.position = position
image.actor.orientation = orientation
#imshow.module_manager.scalar_lut_manager.lut.table = lut
# print 'xxx'
# imshow.module_manager.scalar_lut_manager.load_lut_from_list(lut)
# print 'yyy'
return image
def plot(x, y, z, nx, ny):
from mayavi import mlab
mlab.figure(size=(600, 600))
xmin, xmax = np.min(x.data), np.max(x.data)
ymin, ymax = np.min(y.data), np.max(y.data)
s = mlab.imshow(z.data.reshape((nx, ny)),
extent=[xmin, xmax, ymin, ymax, 0, 0],
colormap='jet')
s.scene.z_plus_view()
n = 2000
dt = 4 * np.pi / n
for i in range(n):
julia(z, x, y, -dt * i)
z.pull()
s.mlab_source.scalars = z.data.reshape((nx, ny))
if i % 3 == 0:
mlab.process_ui_events()
mlab.show()
def mlab_imshowColor(im, alpha = 255, **kwargs):
"""
Plot a color image with mayavi.mlab.imshow.
im is a ndarray with dim (n, m, 3) and scale (0->255]
alpha is a single number or a ndarray with dim (n*m) and scale (0->255]
**kwargs is passed onto mayavi.mlab.imshow(..., **kwargs)
"""
from tvtk.api import tvtk
# Homogenous coordinate conversion
im = np.concatenate((im, alpha * np.ones((im.shape[0], im.shape[1], 1), dtype = np.uint8)), axis = -1)
colors = tvtk.UnsignedCharArray()
colors.from_array(im.reshape(-1, 4))
m_image = mlab.imshow(np.ones(im.shape[:2][::-1]))
m_image.actor.input.point_data.scalars = colors
mlab.draw()
mlab.show()
return
def plot_frustum(Rt_list, img_list, f):
fig = mlab.figure(figure=None,
bgcolor=(0, 0, 0),
fgcolor=(1, 1, 1),
engine=None,
size=(1600, 1000))
for i in range(len(Rt_list)):
R = Rt_list[i][:3, :3]
t = Rt_list[i][:3, 3]
C = -np.dot(R.T, t)
pp = np.array([0, 0, f])
img = img_list[i][:, :, 1]
euler = rotation_to_euler(R[:3, :3])
obj = mlab.imshow(img.T, figure=fig)
obj.actor.orientation = np.rad2deg(euler)
obj.actor.position = (np.dot(R, pp) + t) + C
# obj.actor.scale = [0.01, 0.01, 0.01]
# center
mlab.orientation_axes()
mlab.show()
def setup_visu():
# Create a Mayavi figure
fig = mlab.figure('Ball tracking visualization')
# Measurements have to be whole numbers
TABLE_WIDTH = 152 # cm
TABLE_LENGTH = 274 # cm
table_structure = np.ones((TABLE_WIDTH, TABLE_LENGTH))
# Draw out the lines on the table
# Creases
table_structure[1:-2, 1] = 0
table_structure[1:-2, -2] = 0
table_structure[1, 1:-2] = 0
table_structure[-2, 1:-2] = 0
# Center line
table_structure[TABLE_WIDTH // 2, 1:-2] = 0
# Representing net
table_structure[1:-2, TABLE_LENGTH // 2 - 1] = 0.4
table_structure[1:-2, TABLE_LENGTH // 2] = 0.4
table_structure[1:-2, TABLE_LENGTH // 2 + 1] = 0.4
# Create the table layout in the figure
table = mlab.imshow(table_structure, colormap='Blues', opacity=0.6)
# Setup a 3D point plotter with
# proper shapes, ie., no. of points
# for the ball and its trail
x = y = z = s = np.zeros(5)
point_plt = mlab.points3d(x, y, z, s, scale_factor=1, color=(1, 0.4, 0))
# Put text to indicate table orientation
mlab.text3d(0, TABLE_LENGTH // 2 + 10, -40, 'Player 1',
scale=10, orient_to_camera=True)
mlab.text3d(0, -(TABLE_LENGTH // 2 + 10), -40,
'Player 2', scale=10, orient_to_camera=True)
return point_plt.mlab_source
def drawMap(mlab, scalars, mapFile):
''' 3d Visualization of the data
Parameters
----------
mlab : mlab
scalars : 3d np array
mapFile : str
Returns
-------
imshow object
'''
# Get the shape of axes
shape = scalars.shape
height = shape[0]
width = shape[1]
im = pl.imread(mapFile, format = 'png')
l = []
for i in im:
x = []
for j in i:
tmp = 0
for k in j: tmp += k
x.append(tmp)
l.append(x)
#ims = mlab.imshow(l, colormap = 'binary')
ims = mlab.imshow(l)
print "Map shape", len(l),len(l[0])
ims.actor.position = [height/2,(width)/2,0]
ims.actor.scale = [float(height)/len(l),float(width)/len(l[0]),0]
return ims
z = 100 * np.sin((x - x[0]) / 50) c = mlab.plot3d(x, y, z, tube_radius=5, color=(1, 1, 0)) ##c.visible = False # ---------------------------------------------------------------------- # Part 4 - add surface # Create a surface x, y = np.ogrid[:n:4, :n:4] z = 80 + (0.15 * (-x - 0.015 * x ** 2 + 0.3 * y + 0.01 * y ** 2)).astype(int) s = mlab.surf(x, y, z, representation='surface', colormap='summer') # Initially hide the surface. ##s.visible = False # ---------------------------------------------------------------------- # Part 5 - Evaluate the data cube on the surface, and plot it. # Do a simple linear interpolation to evaluate the data cube on the # surface. low_index = np.floor(z).astype(int) hi_index = np.ceil(z).astype(int) low_vals = data[x, y, low_index] hi_vals = data[x, y, hi_index] vals = low_vals + (z - low_index) * (hi_vals - low_vals) # Make what is effectively a 2D image plot in another figure. mlab.figure() mlab.imshow(x, y, vals, colormap='RdBu')
def test_imshow(self):
s = np.random.random((10, 10))
# This should work.
obj = mlab.imshow(s)
# -*- coding: utf-8 -*- """ Created on Mon Oct 19 21:54:55 2020 @author: lenovouser """ import numpy from mayavi import mlab s = numpy.random.random((10, 10)) img = mlab.imshow(s, colormap='gist_earth') mlab.show()
testPC[:, 1],
testPC[:, 2],
mode="point",
figure=fig)
node.glyph.scale_mode = 'scale_by_vector'
node.mlab_source.dataset.point_data.scalars = Colors0
node = mlab.points3d(keyPts[:, 0],
keyPts[:, 1],
keyPts[:, 2],
scale_factor=PtSize,
figure=fig)
node.glyph.scale_mode = 'scale_by_vector'
node.mlab_source.dataset.point_data.scalars = keyColors0
fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 500))
mlab.imshow(RespondImage)
mlab.view(270, 0, 1800, [0, 0, 0])
fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 500))
mlab.imshow(KeyPixelsImage)
mlab.view(270, 0, 1200, [0, 0, 0])
fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 1500))
node = mayavi.mlab.points3d(decodedPC[:, 0],
decodedPC[:, 1],
decodedPC[:, 2],
mode="point",
figure=fig)
mlab.show()
# basic handling of tiff 2D and 3D images
# import tif and convert to numpy array
# then visualize using mayavi2
#import os
#import sys
from mayavi import mlab
#sys.path.append('C:\\dropbox\\My Dropbox\\codes\\python')
import tifffile as tff
#blobs.tif is a 2D sample image
#tiffimg = tff.TIFFfile('D:/examples/blobs.tif')
tiffimg = tff.TIFFfile('D:/examples/g1f.tif')
#tiffimg = tff.TIFFfile('D:\\examples\\flybrain3DG.tif')
#tiffimg = tff.TIFFfile('D:/examples/flybrain3DG.tif')
imgarray = tiffimg.asarray()
# showing 2D array (blobs) as a 2D plot in mayavi.
imgwin = mlab.imshow(imgarray, colormap="gist_earth")
# showing 3D stack image
#mlab.pipeline.volume(mlab.pipeline.scalar_field(imgarray))
def test_imshow(self):
s = np.random.random((10, 10))
# This should work.
obj = mlab.imshow(s)
# Plot the data
from mayavi import mlab
# A first plot in 3D
fig = mlab.figure(1)
mlab.clf()
mesh = mlab.mesh(x, y, z, scalars=s)
cursor3d = mlab.points3d(0., 0., 0., mode='axes',
color=(0, 0, 0),
scale_factor=0.5)
mlab.title('Sousa')
# A second plot, flat
fig2d = mlab.figure(2)
mlab.clf()
im = mlab.imshow(s)
cursor = mlab.points3d(0, 0, 0, mode='2dthick_cross',
color=(0, 0, 0),
scale_factor=10)
mlab.view(90, 0)
################################################################################
# Some logic to select 'mesh' and the data index when picking.
def picker_callback(picker_obj):
picked = picker_obj.actors
if mesh.actor.actor._vtk_obj in [o._vtk_obj for o in picked]:
# m.mlab_source.points is the points array underlying the vtk
# dataset. GetPointId return the index in this array.
x_, y_ = np.lib.index_tricks.unravel_index(picker_obj.point_id,
s.shape)
# 10 contour lines (equally spaced contour levels) together with surf.
# Black color for contour lines.
plt.figure(7, fgcolor=(.0, .0, .0), bgcolor=(1.0, 1.0, 1.0))
plt.surf(xv, yv, hv, warp_scale=0.01)
plt.contour_surf(xv, yv, hv, contours=10, color=(0., 0., 0.), \
warp_scale=0.01)
# Specify the contour levels explicitly as a list.
plt.figure(8, fgcolor=(.0, .0, .0), bgcolor=(1.0, 1.0, 1.0))
levels = [500., 1000., 1500., 2000.]
plt.contour_surf(xv, yv, hv, contours=levels, warp_scale=0.01)
# View the contours by displaying as an image.
plt.figure(9, fgcolor=(.0, .0, .0), bgcolor=(1.0, 1.0, 1.0))
plt.imshow(hv)
#end contourplots
# Define a coarser grid for the vector field
x2 = y2 = np.linspace(-10.,10.,11)
x2v, y2v = np.meshgrid(x2, y2, indexing='ij', sparse=False)
h2v = h0/(1 + (x2v**2 + y2v**2)/(R**2)) # Surface on coarse grid
# endcoarsergrid
dhdx, dhdy = np.gradient(h2v)
# endgradient
# Draw contours and gradient field of h
"""
Script to generate the preview images for the mayavi2 LUTs.
Requires ImageMagick.
"""
import os
from mayavi import mlab
from mayavi.core.lut_manager import lut_mode_list, lut_image_dir
import numpy as np
# Create some data
X = np.arange(0, 255)
X = X * np.ones((200, 1))
mlab.clf()
image = mlab.imshow(X.T)
mlab.view(0, 0, 118)
# Make a preview for each possible lut
for lut in lut_mode_list():
filebasename = os.path.join(lut_image_dir, lut.lower())
if not lut == 'file':
image.module_manager.scalar_lut_manager.lut_mode = lut
mlab.savefig(filebasename + '.png', size=(80, 20))
#os.system('convert %s.png %s.gif &' %(filebasename, filebasename))
os.system('montage -geometry -0-0 -label "%s" %s.png %s.gif &'
% (lut, filebasename, filebasename) )
# PtSize = 0.1
# node = mlab.points3d(ExtendedKeyPts[:,0], ExtendedKeyPts[:,1], ExtendedKeyPts[:,2], scale_factor=PtSize, figure=fig)
# node.glyph.scale_mode = 'scale_by_vector'
# node.mlab_source.dataset.point_data.scalars = ExtendedKeyColors
#PtSize = 0.1
#node = mlab.points3d(PlanarPts[:,0], PlanarPts[:,1], PlanarPts[:,2], scale_factor=PtSize, figure=fig)
#node.glyph.scale_mode = 'scale_by_vector'
#node.mlab_source.dataset.point_data.scalars = PlanarColors
#
#mlab.quiver3d(PlanarPts[:,0], PlanarPts[:,1], PlanarPts[:,2], \
# PlanarPts[:,3], PlanarPts[:,4], PlanarPts[:,5], \
# figure=fig, line_width=0.5, scale_factor=1)
fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 500))
mlab.imshow(RangeImage)
mlab.view(270, 0, 1800, [0,0,0])
mlab.show()
print('cntkeyPts =', KeyPts.shape[0])
t1 = time()
print(round(t1 - t0, 2), 's, GetKeyPixels')
#t5 = time()
#print(round(t5-t4, 2), 's')
color0 = np.ones((PC.shape[0], 1), dtype=np.float32) * 0.0
color3 = np.ones((KeyPts.shape[0], 1), dtype=np.float32) * 0.9
#fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 500))
#mlab.imshow(SphericalRingImage)
#mlab.view(270, 0, 1200, [0,0,0])
fig = mlab.figure(bgcolor=(0, 0, 0), size=(1640, 500))
mlab.imshow(RespondImage)
mlab.view(270, 0, 1200, [0, 0, 0])
fig = mayavi.mlab.figure(bgcolor=(0, 0, 0), size=(1640, 1500))
node_PC = mayavi.mlab.points3d(PC[:, 0],
PC[:, 1],
PC[:, 2],
mode="point",
figure=fig)
node_PC.mlab_source.dataset.point_data.scalars = color0
node_KeyPC = mayavi.mlab.points3d(KeyPts[:, 0],
KeyPts[:, 1],
KeyPts[:, 2],
scale_factor=0.15,
figure=fig)
def test_imshow_extent(self):
mlab.imshow(np.random.rand(10, 20), extent=[-1, 11, -1, 21, 0, 0])
u=numpy.zeros((N,N), dtype=float)
v=numpy.zeros((N,N), dtype=float)
u_y=numpy.zeros((N,N), dtype=float)
v_x=numpy.zeros((N,N), dtype=float)
omega=numpy.zeros((N,N), dtype=float)
# Initial conditions
for i in range(len(x)):
for j in range(len(y)):
u[i][j]=numpy.sin(2*math.pi*x[i])*numpy.cos(2*math.pi*y[j])
v[i][j]=-numpy.cos(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
u_y[i][j]=-2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
v_x[i][j]=2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
omega[i][j]=v_x[i][j]-u_y[i][j]
src = mlab.imshow(xx,yy,omega,colormap='jet')
mlab.scalarbar(object=src)
mlab.xlabel('x',object=src)
mlab.ylabel('y',object=src)
# Wavenumber
k_x = 2*math.pi*numpy.array([complex(0,1)*n for n in range(0,N/2) \
+ [0] + range(-N/2+1,0)])
k_y=k_x
kx=numpy.zeros((N,N), dtype=complex)
ky=numpy.zeros((N,N), dtype=complex)
kxx=numpy.zeros((N,N), dtype=complex)
kyy=numpy.zeros((N,N), dtype=complex)
ridge0 = final[789] mlab.points3d(ridge0[:,0],ridge0[:,1],ridge0[:,2],4*ones(size(ridge0)/3),resolution=16,scale_factor=1,color=(0,0,0)) ridge1 = final[780] mlab.points3d(ridge1[:,0],ridge1[:,1],ridge1[:,2],4*ones(size(ridge1)/3),resolution=16,scale_factor=1,color=(1,0,0)) filename = 'shellstack215.tif' image1 = io.imread(filename) image[image<12000]=False obj = mlab.imshow(image1[0:,0:].T, opacity = .3, transparent = True) #obj.actor.orientation = [0, 0, 0] # the required orientation obj.actor.position = [shape(image1)[0]/2.+20, shape(image1)[1]/2.-20, 215] # the required position #obj.actor.scale = [0, 0, 0] filename = 'shellstack345.tif' image2 = io.imread(filename) image[image<12000]=False obj = mlab.imshow(image2[0:,0:].T, opacity = .3, transparent=True) #obj.actor.orientation = [0, 0, 0] # the required orientation obj.actor.position = [shape(image2)[0]/2.+20, shape(image2)[1]/2.-20, 345] # the required position
import numpy as np
from mayavi import mlab
#SHA3 state vizualizer
#1600 bit block size
#5 x 5 x 64 array
#this input string does not represent a message, but instead a value already stored in the state about to be fed through the permutation function
inString = "1100111010000001000010010101001110101010111011100010001101111000111111110000010111000111001101010101001010000111000010000001111001101101011011001111010101100001101111110011101011011110001100000000100100101011011101111101100001110110001001010100101001110101010110100110001100001001111000110110101100110111101111100100100111010110110111011110111011100101000011110010111100011100010111000101110001111101111101100101110011010110010111111010110101000110011101101111111010101101111100010011111101100101100111100100110011100101100011100011100101100111011010000110011000011010100101110100010101110010101000100001100101111010001110000000010101010110110010111100100000010000010101011011110011110111001111111001001000000100111110010101101001101110000011010000000011110110001101100110110001010110100000011000101011110101110011010101111101110101000110101100000100100111101000110100101010101001010011110011000100001100110101011100101001111100111010100101010100000110100111100011100000101110000010010001100011101010011101010010101110001011111110100110100110000001111011010010010100100011000000001111100111000100011110000001011011110010011101011001000110111000010010110001110010011101111000100101000100110011001001000011010011101110011111110000111011101011000011011111011101101101000011101110101010101101101000000101110110010101111001110101111011100110011110100100111110001001001010110111000100110010011001101000000100100111011101111111111110010011111001001111100011101011111001001101101011101000011010110100110111100011110100101111100011011000000001110000100101111110000001111001011100110110001001001010011100010101"
stateOneDimensionalList = list(inString)
#convert to digits from characters
for index in range(0, len(stateOneDimensionalList)):
stateOneDimensionalList[index] = int(stateOneDimensionalList[index])
state = []
stateIterator = 0
for i in range(0, 64):
twoDSlice = []
for j in range(0, 5):
oneDSlice = []
for k in range(0, 5):
oneDSlice.append(stateOneDimensionalList[stateIterator])
stateIterator += 1
twoDSlice.append(oneDSlice)
state.append(twoDSlice)
stateNumpyArray = np.array(state)
print stateNumpyArray
print stateNumpyArray.shape
frame = 0
for i in stateNumpyArray:
mlab.imshow(i, interpolate=False)
mlab.savefig("frame" + str(frame) + ".png")
frame += 1
sys.exit(-1)
data.shape = shape
nx = shape[0]
ny = shape[1]
nz = shape[2]
dx = nx / 2 + 1
dy = ny / 2 + 1
dz = nz / 2 + 1
if hslice:
amp = np.sqrt(data[:, :, dz, 0]**2 + data[:, :, dz, 1]**2 +
data[:, :, dz, 2]**2)
mlab.imshow(amp, opacity=0.6, reset_zoom=False)
mlab.quiver3d(data[:, :, :, 0],
data[:, :, :, 1],
data[:, :, :, 2],
mask_points=mask_points,
scale_factor=scale_factor,
extent=[-dx, dx, -dy, dy, -dz, dz])
if axes:
mlab.axes()
if colorbar:
mlab.vectorbar()
mlab.show()
def plot_events(xs,
ys,
ts,
ps,
save_path=None,
num_compress='auto',
num_show=1000,
event_size=2,
elev=0,
azim=45,
imgs=[],
img_ts=[],
show_events=True,
show_frames=True,
show_plot=False,
crop=None,
compress_front=False,
marker='.',
stride=1,
invert=False,
img_size=None,
show_axes=False,
ts_scale=100000):
"""
Given events, plot these in a spatiotemporal volume.
:param: xs x coords of events
:param: ys y coords of events
:param: ts t coords of events
:param: ps p coords of events
:param: save_path if set, will save plot to here
:param: num_compress will take this number of events from the end
and create an event image from these. This event image will
be displayed at the end of the spatiotemporal volume
:param: num_show sets the number of events to plot. If set to -1
will plot all of the events (can be potentially expensive)
:param: event_size sets the size of the plotted events
:param: elev sets the elevation of the plot
:param: azim sets the azimuth of the plot
:param: imgs a list of images to draw into the spatiotemporal volume
:param: img_ts a list of the position on the temporal axis where each
image from 'imgs' is to be placed (the timestamp of the images, usually)
:param: show_events if False, will not plot the events (only images)
:param: crop a list of length 4 that sets the crop of the plot (must
be in the format [top_left_y, top_left_x, height, width]
"""
print("plot all")
#Crop events
if img_size is None:
img_size = [max(ys), max(ps)] if len(imgs) == 0 else imgs[0].shape[0:2]
crop = [0, img_size[0], 0, img_size[1]] if crop is None else crop
xs, ys, ts, ps = clip_events_to_bounds(xs,
ys,
ts,
ps,
crop,
set_zero=False)
xs, ys = xs - crop[2], ys - crop[0]
#Defaults and range checks
num_show = len(xs) if num_show == -1 else num_show
skip = max(len(xs) // num_show, 1)
print("Has {} events, show only {}, skip = {}".format(
len(xs), num_show, skip))
num_compress = len(xs) if num_compress == -1 else num_compress
num_compress = min(img_size[0] * img_size[1] * 0.5,
len(xs)) if num_compress == 'auto' else num_compress
xs, ys, ts, ps = xs[::skip], ys[::skip], ts[::skip], ps[::skip]
t0 = ts[0]
ts = ts - t0
#mlab.options.offscreen = True
#Plot images
if len(imgs) > 0 and show_frames:
for imgidx, (img, img_t) in enumerate(zip(imgs, img_ts)):
img = img[crop[0]:crop[1], crop[2]:crop[3]]
mlab.imshow(img,
colormap='gray',
extent=[
0, img.shape[0],
0, img.shape[1], (img_t - t0) * ts_scale,
(img_t - t0) * ts_scale + 0.01
],
opacity=1.0,
transparent=False)
colors = [0 if p > 0 else 240 for p in ps]
ones = np.array([0 if p == 0 else 1 for p in ps])
p3d = mlab.quiver3d(ys,
xs,
ts * ts_scale,
ones,
ones,
ones,
scalars=colors,
mode='sphere',
scale_factor=event_size)
p3d.glyph.color_mode = 'color_by_scalar'
p3d.module_manager.scalar_lut_manager.lut.table = colors
#mlab.draw()
#mlab.view(84.5, 54, 5400, np.array([ 187, 175, 2276]), roll=95)
if show_plot:
mlab.show()
tries = 0
# ]:
for outOrder in outorders[2:3]:
for R in RList:
print 'R', R
for vector, color in zip([[100, 0, 0], [0, 100, 0], [0, 0, 100]],
[(1., 0., 0.), (0., 1., 0.), (0., 0., 1.)]):
c = pl.c_[[0, tries * 1000, ii * 1000]]
if ii == 0 and tries == 0:
vector = pl.r_[vector] * 5 # point out the first vector
lin = R_orig.dot(pl.c_[[0, 0, 0], vector]) + c
mlab.plot3d(*lin,
color=color,
tube_radius=5)
lin3D = mlab.imshow(im, colormap="gray")
print 'inOrder', inOrder
rxyz = pl.array(
euler_from_matrix(R, inOrder)) * 180 / pl.pi
print 'outOrder', outOrder
i, j, k = outOrder
print 'o', [rxyz[i], rxyz[j], rxyz[k]]
lin3D.actor.orientation = [rxyz[i], rxyz[j], rxyz[k]]
lin3D.actor.position = c.flatten()
lin3D.actor.scale = (6, 6, 1)
tries += 1
mlab.draw()
mlab.show()
def test_imshow_extent(self):
mlab.imshow(np.random.rand(10, 20), extent=[-1, 11, -1, 21, 0, 0])
def plot_colorbar(min_q, max_q, max_val=0.35, num_interp=100, width=25):
""" Plot a colorbar """
vals = np.linspace(0, max_val, num=num_interp)
vals = vals[:,np.newaxis]
image = np.tile(vals, [1, width])
mv.imshow(image, colormap='hsv')
def draw_poses(title,
parents,
pose_sequence,
frame_paths=None,
fps=50 / 3.0,
crossover=None):
T, _, J = pose_sequence.shape
fig = mlab.figure()
xmin, ymin = pose_sequence.min(axis=0).min(axis=1)
xmax, ymax = pose_sequence.max(axis=0).max(axis=1)
# ax.set_xlim(xmin, xmax)
# ax.set_zlim(ymin, ymax)
# ax.set_ylim(0, T/fps)
# # ax.set_aspect('equal')
# ax.invert_zaxis()
if frame_paths:
# Decide on plot indices ahead of time. Main constraints are:
# - I don't want more than five frames in a 1s time period.
# - I'd like to display the first and last frames
inner_seconds = int(np.floor((T - 2) / fps))
num_keyframes = min(T - 2, inner_seconds * 5) + 2
skip = int(np.round(float(T) / num_keyframes))
keyframe_inds = np.arange(0, T, skip)
if keyframe_inds[-1] != T - 1:
keyframe_inds = np.concatenate([keyframe_inds, [T - 1]])
keyframe_inds = set(keyframe_inds)
print('Keyframe inds: ', keyframe_inds)
for t in range(T):
# plot joints
pose_xy_j = pose_sequence[t]
depth = 10 * float(t) / fps
for joint in range(1, len(parents)):
joint_coord = pose_xy_j[:, joint]
parent = parents[joint]
parent_coord = pose_xy_j[:, parent]
if (parent_coord == joint_coord).all():
# mayavi will complain if we plot this zero-length line
continue
x_data = np.array((parent_coord[0], joint_coord[0]), dtype='int16')
z_data = np.array((parent_coord[1], joint_coord[1]), dtype='int16')
depth_data = np.full_like(x_data, depth, dtype='int16')
x_data = np.array((parent_coord[0], joint_coord[0]))
z_data = np.array((parent_coord[1], joint_coord[1]))
depth_data = np.full_like(x_data, depth)
mlab.plot3d(x_data, depth_data, z_data)
# plot frame (TODO: only plot frames occasionally; don't want to overdo
# it and make the plot unreadable)
if frame_paths and t in keyframe_inds:
im = imread(frame_paths[t])
# mayavi wants a 2D array of integers instead of a real image; it
# looks up colours in a colourmap
im2d = np.arange(np.prod(im.shape[:2])).reshape(im.shape[:2])
cmap = im.reshape((im.shape[0] * im.shape[1], im.shape[2]))
# add alpha channel
cmap = np.concatenate(
[cmap, np.full((cmap.shape[0], 1), 255, dtype='uint8')],
axis=1)
assert cmap.dtype == np.uint8
# extent = [xmin, xmax, ymin, ymax, zmin, zmaax]
extent = np.array([0, im.shape[1], depth, depth, 0, im.shape[0]])
ims = mlab.imshow(im2d,
colormap='binary',
extent=extent,
opacity=0.5)
# Documentation? What's that?
# http://stackoverflow.com/a/24471211
ims.module_manager.scalar_lut_manager.lut.table = cmap
mlab.draw()
# TODO:
# - Back-connection to previous frames
# - Thicken original pose tubes relative to back-connections
# - Add crossover colour for predictions
# - Make surex/y/z are going in the right direction, and that camera is
# in the right place
# - Maybe plot action labels
return fig
def draw(self):
sz = self.size
anc = self.anchor
mlab.imshow(self.cur,
extent=[anc[0], sz[0], anc[1], sz[1], anc[2], sz[2]],
colormap='gist_earth')
byold=numpy.zeros((N,N), dtype=float)
# Initial conditions
for i in range(len(x)):
for j in range(len(y)):
u[i][j]=numpy.sin(2*math.pi*x[i])*numpy.cos(2*math.pi*y[j])
v[i][j]=-numpy.cos(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
u_y[i][j]=-2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
v_x[i][j]=2*math.pi*numpy.sin(2*math.pi*x[i])*numpy.sin(2*math.pi*y[j])
omega[i][j]=v_x[i][j]-u_y[i][j]
theta[i][j]=numpy.exp(-2.0*((4*math.pi*(x[i]-0.3))**2+(4*math.pi*(y[j]-0.3))**2))
alpha[i][j]=numpy.sin(4*math.pi*x[i])*numpy.cos(6*math.pi*y[j])
src = mlab.imshow(xx,yy,theta,colormap='jet')
mlab.scalarbar(object=src)
mlab.xlabel('x',object=src)
mlab.ylabel('y',object=src)
# Wavenumber
k_x = 2*math.pi*numpy.array([complex(0,1)*n for n in range(0,N/2) \
+ [0] + range(-N/2+1,0)])
k_y=k_x
kx=numpy.zeros((N,N), dtype=complex)
ky=numpy.zeros((N,N), dtype=complex)
kxx=numpy.zeros((N,N), dtype=complex)
kyy=numpy.zeros((N,N), dtype=complex)
def plot3d(data,
xvar,
yvar,
zvar,
fvar,
ival='Dive',
day=None,
filament=None,
cmap='RdYlBu',
rev_cmap=True,
alpha=1,
cmin=None,
cmax=None,
title='',
temp=None,
chl=None,
intdat=None):
"""
Create 3D curtain plot
Parameters
----------
data : dataframe
Pandas dataframe containing the needed data.
xvar : character
Name of the x axis variable, in the data dataframe (normally lon - or however longitude is name in the dataframe) .
yvar : character
Name of the y axis variable, in the data dataframe (normally lat - or however latitude is name in the dataframe) .
zvar : character
Name of the z axis variable, in the data dataframe (normally a rounded Depth or Pressure value).
fvar : character
Name of the variable used for the filling (for example temperature, salinity, Sv1000 or whtaever you want it to be).
ival : character, optional
This is a grouping value, if not using 'Dive', make sure to define it. The default is 'Dive'.
day : dataframe, optional
Reference to a dataframe containing day/night information, if defined, this will put a bar on top of the plot. The default is None.
filament : dataframe, optional
This will put a bar below the plot, for example to delimit certain regions. The default is None.
cmap : colormap, optional
Character describing a valid colormap. The default is 'RdYlBu'.
rev_cmap : boolean, optional
Define if the colormap should be reversed. The default is True.
alpha : float, optional
Sets the transparenct. The default is 1.
cmin : float, optional
Define the color scale minimum. The default is None.
cmax : float, optional
Define the color scale maximum. The default is None.
title : character, optional
Add a title to the plot. The default is ''.
temp : TYPE, optional
Add temperature background map. The default is None.
chl : TYPE, optional
Add chlorophyll background map. The default is None.
intdat : TYPE, optional
DESCRIPTION. The default is None.
Returns
-------
None.
"""
ne = 0
#bring x,y,z data into shape, create 3 pivot tables
x = pd.pivot(data=data.reset_index(),
index=ival,
columns=zvar,
values=xvar)
y = pd.pivot(data=data.reset_index(),
index=ival,
columns=zvar,
values=yvar)
z = -pd.pivot(
data=data.reset_index(), index=ival, columns=zvar, values=zvar)
#create pivot table with fill value, where ival become the index
fill = pd.pivot(data=data.reset_index(),
index=ival,
columns=zvar,
values=fvar)
#define cmax and cmin if they are not given
if cmax is None:
cmax = np.ceil(np.nanmax(fill))
if cmin is None:
cmin = np.floor(np.nanmin(fill))
#create a mayavi figure
fig = mlab.figure(size = (2048,1526),\
bgcolor = (1,1,1), fgcolor = (0.5, 0.5, 0.5), figure=title)
#create a mesh from the x,y,z and fill info
svp = mlab.mesh(x,
y,
z,
scalars=fill,
colormap=cmap,
opacity=alpha,
extent=[0.2, 1, 0.1, 1, 0.22, .69],
figure=fig,
representation='surface')
#reverse color map if needed
if rev_cmap == True:
svp.module_manager.scalar_lut_manager.reverse_lut = True
#set color range
svp.module_manager.scalar_lut_manager.data_range = (cmin, cmax)
#svp.module_manager.scalar_lut_manager.use_below_range_color = True
#svp.module_manager.scalar_lut_manager.below_range_color = (0,0,0,0)
#svp.module_manager.scalar_lut_manager.lut.number_of_colors = 64
#add colorbar
cb = mlab.colorbar(object=svp, title=title, orientation='vertical')
cb.scalar_bar.unconstrained_font_size = True
cb.label_text_property.font_size = 20
cb.title_text_property.font_size = 46
#make plot window
mlab.gcf()
#set plot limits
xmin = x.values[np.isfinite(x.values)].min()
xmax = x.values[np.isfinite(x.values)].max()
ymin = y.values[np.isfinite(y.values)].min()
ymax = y.values[np.isfinite(y.values)].max()
zmin = z.values[np.isfinite(z.values)].min()
zmax = z.values[np.isfinite(z.values)].max()
#change the aesthetics
ax = mlab.axes(nb_labels=5,
xlabel='Longitude',
ylabel='Latitude',
zlabel='Depth [m]',
ranges=[xmin, xmax, ymin, ymax, zmin, zmax])
ax.axes.font_factor = 0.5
ax.axes.label_format = ' %6.2f'
#add day night at top
if day is not None:
lut = np.zeros((2, 4))
lut[1, :] = [0, 0, 0, 100]
lut[0, :] = [100, 100, 0, 100]
p3d = mlab.plot3d(day.lon.values,
day.lat.values,
day['depth'].values,
day['numSun'].values,
tube_radius=0.001,
figure=fig,
opacity=1,
extent=[0.2, 1, 0.1, 1, 0.695, 0.71])
p3d.module_manager.scalar_lut_manager.lut.number_of_colors = 2
p3d.module_manager.scalar_lut_manager.lut.table = lut
#add line at bottom of plot
if filament is not None:
mlab.plot3d(filament.lon.values,
filament.lat.values,
filament['fildep'].values,
filament['numfil'].values,
tube_radius=0.01,
figure=fig,
opacity=1,
extent=[0.2, 1, 0.1, 1, 0.19, 0.21],
colormap='Set1')
#add chl background map
if chl is not None:
if ne == 0:
zl = 0.2
else:
zl = 0.72
ne += 1
x1 = chl.longitude.values.min()
x2 = chl.longitude.values.max()
y1 = chl.latitude.values.min()
y2 = chl.latitude.values.max()
dx = xmax - xmin
dy = ymax - ymin
xl1 = -(xmin - x1) / dx
xl2 = -(xmax - x2) / dx
yl1 = -(ymin - y1) / dy
yl2 = -(ymax - y2) / dy
zs = pd.pivot_table(data=chl,
index='latitude',
columns='longitude',
values='chlorophyll').transpose()
#cmap2 = matplotlib.cm.get_cmap()
#cmap2.set_bad('white',1.)
sat1 = mlab.imshow(
zs,
figure=fig,
extent=[0.2 + xl1, 1 + xl2, 0.1 + yl1, 1 + yl2, zl, zl],
opacity=0.8,
colormap=cmap,
interpolate=False)
sat1.module_manager.scalar_lut_manager.reverse_lut = True
sat1.module_manager.scalar_lut_manager.data_range = (0, 10)
sat1.module_manager.scalar_lut_manager.lut.nan_color = (0, 0, 0, 0)
cb2 = mlab.colorbar(object=sat1,
title='CHla',
orientation='horizontal')
cb2.scalar_bar.unconstrained_font_size = True
cb2.label_text_property.font_size = 20
cb2.title_text_property.font_size = 46
#add temp backgorund map
if temp is not None:
if ne == 0:
zl = 0.2
else:
zl = 0.72
ne += 1
x1 = temp.longitude.values.min()
x2 = temp.longitude.values.max()
y1 = temp.latitude.values.min()
y2 = temp.latitude.values.max()
dx = xmax - xmin
dy = ymax - ymin
xl1 = -(xmin - x1) / dx
xl2 = -(xmax - x2) / dx
yl1 = -(ymin - y1) / dy
yl2 = -(ymax - y2) / dy
zs2 = pd.pivot_table(data=temp,
index='latitude',
columns='longitude',
values='sst').transpose()
sat2 = mlab.imshow(
zs2,
figure=fig,
extent=[0.2 + xl1, 1 + xl2, 0.1 + yl1, 1 + yl2, zl, zl],
colormap=cmap,
opacity=0.8,
interpolate=False)
sat2.module_manager.scalar_lut_manager.reverse_lut = True
sat2.module_manager.scalar_lut_manager.lut.nan_color = (0, 0, 0, 0)
#sat2.module_manager.scalar_lut_manager.data_range = (10, 25)
#ignore this, as this was specific for the 38 kHz map for calibration
if intdat is not None:
x1 = intdat.Lon_S.values.min()
x2 = intdat.Lon_S.values.max()
y1 = intdat.Lat_S.values.min()
y2 = intdat.Lat_S.values.max()
dx = xmax - xmin
dy = ymax - ymin
xi1 = -(xmin - x1) / dx
xi2 = -(xmin - x2) / dx
yi1 = -(ymin - y1) / dy
yi2 = -(ymin - y2) / dy
xi = pd.pivot(data=intdat,
index='Ping_S',
columns='Depth_mean',
values='Lon_S')
yi = pd.pivot(data=intdat,
index='Ping_S',
columns='Depth_mean',
values='Lat_S')
zi = pd.pivot(data=intdat,
index='Ping_S',
columns='Depth_mean',
values='Depth_mean')
filli = pd.pivot(data=intdat,
index='Ping_S',
columns='Depth_mean',
values='Sv38')
ivp = mlab.mesh(xi,
yi,
zi,
scalars=filli,
colormap=cmap,
opacity=alpha,
extent=[xi1, xi2, yi1, yi2, 0.2, .7],
figure=fig,
representation='surface')
if rev_cmap == True:
ivp.module_manager.scalar_lut_manager.reverse_lut = True
ivp.module_manager.scalar_lut_manager.data_range = (cmin, cmax)
#set initial view
mlab.view(90, 110, -2)
