I am interpolating data from satellite imagery. My initial data is not on a regular grid. The data e.g. ch1 refers to positions given by longitude and latitude. When I try nearest neighbour interpolation the result I get is good.
from scipy import interpolate
lats = np.arange(latitude.max(), latitude.min(),-.1)
lons = np.arange(longitude.min(),longitude.max(),.1)
all_lon,all_lat = np.meshgrid(lons,lats)
ch1_all = interpolate.griddata((longitude.reshape(-1),latitude.reshape(-1)),ch1.reshape(-1),(all_lon,all_lat),'nearest')
However when I request bilinear interpolation I raise a Qhull error.
ch1_all = interpolate.griddata((longitude.reshape(-1),latitude.reshape(-1)),ch1.reshape(-1),(all_lon,all_lat),'linear')
The error I get is:
Traceback (most recent call last):
File "<interactive input>", line 1, in <module>
File "C:\Python27\lib\site-packages\scipy\interpolate\ndgriddata.py", line 206, in griddata
rescale=rescale)
File "interpnd.pyx", line 239, in scipy.interpolate.interpnd.LinearNDInterpolator.__init__ (scipy\interpolate\interpnd.c:4549)
File "qhull.pyx", line 1736, in scipy.spatial.qhull.Delaunay.__init__ (scipy\spatial\qhull.c:13719)
File "qhull.pyx", line 328, in scipy.spatial.qhull._Qhull.__init__ (scipy\spatial\qhull.c:3602)
QhullError: Qhull error
I have read the post at griddata runtime error -- Python / SciPy (Interpolation) but in my case, it interpolates data with one method but not with the other.
What am I doing wrong?
In the image below I have plotted the final point positions (red) and overlaid the initial positions (blue)
Related
I am trying to plot streamlines in matplotlib over a contour plot by combining these two plots shown below but showing my code first:
ax = plt.axes(projection=ccrs.PlateCarree())
ax.coastlines(lw=1)
clevs = np.linspace(-3., 3., 13)
cnplot = plt.contourf(lon,lat,anomspeed,clevs,add_labels=True,cmap='jet')
cbar = plt.colorbar(cnplot)
cbar.set_label('Standard Deviations')
plt.title('~50m Wind Speed Anomaly {} 2020'.format(calendar.month_name[currm-1]))
diffu = (uwndc - uwnd); diffv = (vwndc - vwnd)
lonn, latt = np.meshgrid(lon, lat)
plt.streamplot(lonn[0,:], latt[:,0], diffu, diffv, density=(3.5,3.5),
color='k',linewidth=0.4,arrowsize=0.6)#x,y 1D and u,v are 2D
I am getting this error (full traceback shown) when i try and run the code shown below but I do not understand 'ravel' error. I suppose it has something to do with matching coordinates or related between the two plots..? thank you for any help!
Traceback (most recent call last):
File "C:\Users\U321103\.spyder-
py3\MonthlyReport_mapsNCEP_contour_monthly_wspdv2.py", line 85, in <module>
plt.streamplot(lonn[0,:], latt[:,0], diffu, diffv, density=(3.5,3.5),
color='k',linewidth=0.4,arrowsize=0.6)
File "C:\Users\U321103\AppData\Local\Continuum\anaconda3\envs\Maps\lib\site-
packages\matplotlib\pyplot.py", line 2906, in streamplot
if data is not None else {}))
File "C:\Users\U321103\AppData\Local\Continuum\anaconda3\envs\Maps\lib\site-
packages\cartopy\mpl\geoaxes.py", line 1897, in streamplot
target_extent=target_extent)
File "C:\Users\U321103\AppData\Local\Continuum\anaconda3\envs\Maps\lib\site-
packages\cartopy\vector_transform.py", line 146, in vector_scalar_to_grid
return _interpolate_to_grid(nx, ny, x, y, u, v, *scalars, **kwargs)
File "C:\Users\U321103\AppData\Local\Continuum\anaconda3\envs\Maps\lib\site-
packages\cartopy\vector_transform.py", line 67, in _interpolate_to_grid
s_grid_tuple += (griddata(points, s.ravel(), (x_grid, y_grid),
AttributeError: 'Variable' object has no attribute 'ravel'
I'm looking to solving this same problem and I found an answer to a similar question that help me plotting streamlines and contour togheter. Take a look at here.
In a nutshell, instead of:
plt.streamplot(lonn[0,:], latt[:,0], diffu, diffv, density=(3.5,3.5), color='k',linewidth=0.4,arrowsize=0.6)
You'd use
plt.streamplot(lonn[0,:], latt[:,0], np.array(diffu), np.array(diffv), density=(3.5,3.5), color='k',linewidth=0.4,arrowsize=0.6)
The use of np.array() solves the problem for me.
Best regards,
Mateus
I have a graph having
957267 Number of nodes ;
1860761 Number of edges and
Average degree is 3.8877
G=nx.from_edgelist(edge)
print(nx.info(G))
nx.draw_spring(G)
plt.draw()
plt.show()
till print function, every thing work, but after that when I draw graph, I got the error
All the values in edge list are integers.
I am getting memory error. Though I have 8 GB ram, and SSD hard disk Is there a way to deal with it or alternative of NetworkX
Traceback (most recent call last):
File "", line 1, in
nx.draw_spring(G)
File "C:\ProgramData\Anaconda3\lib\site-packages\networkx\drawing\nx_pylab.py", line 965, in draw_spring
draw(G, spring_layout(G), **kwargs)
File "C:\ProgramData\Anaconda3\lib\site-packages\networkx\drawing\layout.py", line 333, in fruchterman_reingold_layout
pos = _fruchterman_reingold(A, k, pos_arr, fixed, iterations, dim)
File "C:\ProgramData\Anaconda3\lib\site-packages\networkx\drawing\layout.py", line 388, in _fruchterman_reingold
distance = np.linalg.norm(delta, axis=-1)
File "C:\ProgramData\Anaconda3\lib\site-packages\numpy\linalg\linalg.py", line 2198, in norm
return sqrt(add.reduce(s, axis=axis, keepdims=keepdims))
MemoryError
Get following error when try I to use io.imsave("image.jpg",array)
Traceback (most recent call last):
File "Fourer.py", line 37, in <module>
io.imsave( "test.jpg", fImage2)
File "C:\ProgramData\Miniconda3\lib\site-packages\skimage\io\_io.py", line 131, in imsave
if is_low_contrast(arr):
File "C:\ProgramData\Miniconda3\lib\site-packages\skimage\exposure\exposure.py", line 503, in is_low_contrast
dlimits = dtype_limits(image, clip_negative=False)
File "C:\ProgramData\Miniconda3\lib\site-packages\skimage\util\dtype.py", line 49, in dtype_limits
imin, imax = dtype_range[image.dtype.type]
KeyError: <class 'numpy.complex128'>
it's a 2n complex array I use
array = [[ 3.25000000e+02+0.00000000e+00j -1.25000000e+01+1.72047740e+01j
-1.25000000e+01+4.06149620e+00j -1.25000000e+01-4.06149620e+00j
-1.25000000e+01-1.72047740e+01j]
[-6.25000000e+01+8.60238700e+01j -8.88178420e-16+8.88178420e-16j
0.00000000e+00+1.29059879e-15j 0.00000000e+00+1.29059879e-15j
-8.88178420e-16-8.88178420e-16j]
[-6.25000000e+01+2.03074810e+01j -8.88178420e-16+4.44089210e-16j
-3.55271368e-15+5.46706420e-15j -3.55271368e-15+5.46706420e-15j
-8.88178420e-16-4.44089210e-16j]
[-6.25000000e+01-2.03074810e+01j -8.88178420e-16+4.44089210e-16j
-3.55271368e-15-5.46706420e-15j -3.55271368e-15-5.46706420e-15j
-8.88178420e-16-4.44089210e-16j]
[-6.25000000e+01-8.60238700e+01j -8.88178420e-16+8.88178420e-16j
0.00000000e+00-1.29059879e-15j 0.00000000e+00-1.29059879e-15j
-8.88178420e-16-8.88178420e-16j]]
How can i save i complex array as image?
If that matrix was obtained from the FFT of an image, then you first need to do Inverse FFT. Only then, you can save it using io.imsave.
If that is the case, take a look at skimage's:
----> Inverse Fourier Transform
I'm trying to visualize graph in NetworkX. I need to colorize the graph like this: center node needs to be colored dark. Then, all nodes that are further away will need to be colored lighter, but when i run the code i get this error :
error: Cannot convert argument type < class 'numpy.ndarray' > to rgba array on the line :
nx.draw_networkx_nodes(G,pos,nodelist=p.keys(),node_size=90,
node_color=p.values(),cmap=plt.cm.Reds_r)
I think the problem is in:
node_color=p.values()
The code is:
import numpy
import pandas
import networkx as nx
import unicodecsv as csv
import community
import matplotlib.pyplot as plt
# Generate the Graph
G=nx.davis_southern_women_graph()
# Create a Spring Layout
pos=nx.spring_layout(G)
# Find the center Node
dmin=1
ncenter=0
for n in pos:
x,y=pos[n]
d=(x-0.5)**2+(y-0.5)**2
if d<dmin:
ncenter=n
dmin=d
""" returns a dictionary of nodes and their distance to the node
supplied as an argument. We will then use these distances
to determine colors"""
p=nx.single_source_shortest_path_length(G,ncenter)
plt.figure(figsize=(8,8))
nx.draw_networkx_edges(G,pos,nodelist=[ncenter],alpha=0.4)
nx.draw_networkx_nodes(G,pos,nodelist=p.keys(),node_size=90,
node_color=p.values(),cmap=plt.cm.Reds_r)
plt.show()
Full Traceback
Traceback (most recent call last):
File "<ipython-input-4-da1414ba5e14>", line 1, in <module>
runfile('C:/Users/Desktop/Marvel/finding_key_players.py', wdir='C:/Users/Desktop/Marvel')
File "C:\Users\Anaconda33\lib\site- packages\spyderlib\widgets\externalshell\sitecustomize.py", line 685, in runfile
execfile(filename, namespace)
File "C:\Users\Anaconda33\lib\site packages\spyderlib\widgets\externalshell\sitecustomize.py", line 85, in execfile
exec(compile(open(filename, 'rb').read(), filename, 'exec'), namespace)
File "C:/Users/Desktop/Marvel/finding_key_players.py", line 70, in
<module>
cmap=plt.cm.Reds_r)
File "C:\Users\Anaconda33\lib\site-packages\networkx\drawing\nx_pylab.py", line 399, in draw_networkx_nodes
label=label)
File "C:\Users\Anaconda33\lib\site-packages\matplotlib\axes\_axes.py", line 3606, in scatter
colors = mcolors.colorConverter.to_rgba_array(c, alpha)
File "C:\Users\Anaconda33\lib\site-packages\matplotlib\colors.py", line 391, in to_rgba_array
if alpha > 1 or alpha < 0:
ValueError: Cannot convert argument type <class 'numpy.ndarray'> to rgba array
The error is in the function for drawing nodes.
p.keys()values must be put in a list for nodelist, and node_color, otherwise it's not working.
So the correct line is:
nx.draw_networkx_nodes(G,pos,nodelist=list(p.keys()),node_size=80,node_color=list(p.values()), cmap=plt.cm.Reds_r)
plt.axis('off')
plt.show()
I'm trying to write a short script that takes a .csv file with some distance data, and outputs the psd file for it. the code is here:
import math
import matplotlib.pyplot as plt
name = raw_input('File:')
data = open(name + '.csv', 'r')
distances = []
for row in data:
distances.append(row.replace("\n",""))
for i in range(len(distances)):
distances[i] = float(distances[i])
Pxx, freqs = plt.psd(distances, NFFT=16,Fs=2,detrend='detrend_mean',window='window_none',noverlap=128,sides='onesided',scale_by_freq=True)
plot(Pxx,freqs)
plt.savefig(name + 'psd.png', bbox_inches = 'tight')
As you can see, it's pretty simple. the csv file just features one column of numbers, so distances is a vector.
The error I'm getting is as follows:
Traceback (most recent call last):
File "C:psdplot.py", line 15, in <module>
Pxx, freqs = plt.psd(distances, NFFT=16,Fs=2,detrend='detrend_mean',window='window_none',noverlap=128,sides='onesided',scale_by_freq=True)
File "C:\Python27\lib\site-packages\matplotlib\pyplot.py", line 3029, in psd
sides=sides, scale_by_freq=scale_by_freq, **kwargs)
File "C:\Python27\lib\site-packages\matplotlib\axes.py", line 8696, in psd
sides, scale_by_freq)
File "C:\Python27\lib\site-packages\matplotlib\mlab.py", line 389, in psd
scale_by_freq)
File "C:\Python27\lib\site-packages\matplotlib\mlab.py", line 423, in csd
noverlap, pad_to, sides, scale_by_freq)
File "C:\Python27\lib\site-packages\matplotlib\mlab.py", line 251, in _spectral_helper
assert(len(window) == NFFT)
AssertionError
Could someone direct me on how to fix this? I'm sure it's rather obvious, but I haven't been able to find anything on fixing it in this particular context.
Thanks in advance!