I am wondering if there is a way to create a beautiful visualisation (in Python) of something like algorithm which involves graphs.
It would be really nice if there is a way to do that in Python which would help converting each executed logical step of the algorithm's code into a neat live illustration.
While reading about TSP on Wikipedia I found this:
I do it all the time by using individual plots created from matplotlib.
An example procedure is:
create multiple plots and save them as image files
loop over each saved image file and read them using opencv
use opencv to compile all image files into a single video file.
Here is some simplified example code
import cv2
import os
import matplotlib.pyplot as plt
# create a single plot
plt.plot([1,2,3], [3, 7, 11])
# save plot as an image
plt.savefig(plot_directory\plot_name.jpg, format='jpg', dpi=250)
plt.show()
def create_video(image_folder, video_name, fps=8, reverse=False):
"""Create video out of images saved in a folder."""
images = [img for img in os.listdir(image_folder) if img.endswith('.jpg')]
if reverse: images = images[::-1]
frame = cv2.imread(os.path.join(image_folder, images[0]))
height, width, layers = frame.shape
video = cv2.VideoWriter(video_name, -1, fps, (width,height))
for image in images:
video.write(cv2.imread(os.path.join(image_folder, image)))
cv2.destroyAllWindows()
video.release()
# use opencv to read all images in a directory and compile them into a video
create_video('plot_directory', 'my_video_name.avi')
In the create_video function, I added options to reverse the frame order and set frames per second (fps).
This video on Youtube was created using exactly this method.
To apply to your sample code, try putting all your plotting functions inside your for loop. This should produce plots each tome you iterate over an edge. Then each time a plot is generated, you can save that plot to file. Something like this:
import random
from itertools import combinations
from math import sqrt
import itertools
from _collections import OrderedDict
import networkx as nx
import numpy as np
from matplotlib import pyplot as plt
random.seed(42)
n_points = 10
def dist(p1, p2):
return sqrt((p1[0] - p2[0]) ** 2 + (p1[1] - p2[1]) ** 2)
points = [(random.random(), random.random()) for _ in range(n_points)]
named_points = {i: j for i, j in zip(itertools.count(), points)}
weighted_edges = dict()
tree_id = [None] * n_points
min_tree = []
for v1, v2 in combinations(named_points.values(), 2):
d = dist(v1, v2)
weighted_edges.update({d: ((list(named_points.keys())[list(named_points.values()).index(v1)]),
(list(named_points.keys())[list(named_points.values()).index(v2)]))
}
)
for i in range(n_points):
tree_id[i] = i
sorted_edges = OrderedDict(sorted(weighted_edges.items(), key=lambda t: t[0]))
list_edges = sorted_edges.values()
for edge in list_edges:
if tree_id[edge[0]] != tree_id[edge[1]]:
min_tree.append(edge)
old_id = tree_id[edge[0]]
new_id = tree_id[edge[1]]
for j in range(n_points):
if tree_id[j] == old_id:
tree_id[j] = new_id
print(min_tree)
G = nx.Graph()
G.add_nodes_from(range(n_points))
G.add_edges_from(list_edges)
green_edges = min_tree
G = nx.Graph()
G.add_nodes_from(range(n_points))
G.add_edges_from(list_edges)
edge_colors = ['black' if not edge in green_edges else 'red' for edge in G.edges()]
pos = nx.spiral_layout(G)
G2 = nx.Graph()
G2.add_nodes_from(range(n_points))
G2.add_edges_from(min_tree)
pos2 = nx.spiral_layout(G2)
plt.figure(1)
nx.draw(G, pos, node_size=700, edge_color=edge_colors, edge_cmap=plt.cm.Reds, with_labels = True)
plt.figure(2)
nx.draw(G2, pos2, node_size=700, edge_color='green', edge_cmap=plt.cm.Reds, with_labels = True)
plt.show()
Related
I have a community list as the following list_community.
How do I edit the code below to make the community visible?
from igraph import *
list_community = [['A', 'B', 'C', 'D'],['E','F','G'],['G', 'H','I','J']]
list_nodes = ['A', 'B', 'C', 'D','E','F','G','H','I','J']
tuple_edges = [('A','B'),('A','C'),('A','D'),('B','C'),('B','D'), ('C','D'),('C','E'),
('E','F'),('E','G'),('F','G'),('G','H'),
('G','I'), ('G','J'),('H','I'),('H','J'),('I','J'),]
# Make a graph
g_test = Graph()
g_test.add_vertices(list_nodes)
g_test.add_edges(tuple_edges)
# Plot
layout = g_test.layout("kk")
g.vs["name"] = list_nodes
visual_style = {}
visual_style["vertex_label"] = g.vs["name"]
visual_style["layout"] = layout
ig.plot(g_test, **visual_style)
I would like a plot that visualizes the community as shown below.
I can also do this by using a module other than igraph.
Thank you.
In igraph you can use the VertexCover to draw polygons around clusters (as also suggested by Szabolcs in his comment). You have to supply the option mark_groups when plotting the cover, possibly with some additional palette if you want. See some more detail in the documentation here.
In order to construct the VertexCover, you first have to make sure you get integer indices for each node in the graph you created. You can do that using g_test.vs.find.
clusters = [[g_test.vs.find(name=v).index for v in cl] for cl in list_community]
cover = ig.VertexCover(g_test, clusters)
After that, you can simply draw the cover like
ig.plot(cover,
mark_groups=True,
palette=ig.RainbowPalette(3))
resulting in the following picture
Here is a script that somewhat achieves what you're looking for. I had to handle the cases of single-, and two-nodes communities separately, but for greater than two nodes this draws a polygon within the nodes.
I had some trouble with matplotlib not accounting for overlapping edges and faces of polygons which meant the choice was between (1) not having the polygon surround the nodes or (2) having an extra outline just inside the edge of the polygon due to matplotlib overlapping the widened edge with the fill of the polygon. I left a comment on how to change the code from option (2) to option (1).
I also blatantly borrowed a convenience function from this post to handle correctly sorting the nodes in the polygon for appropriate filling by matplotlib's plt.fill().
Option 1:
Option 2:
Full code:
import networkx as nx
import matplotlib.pyplot as plt
import numpy as np
from matplotlib import cm
def sort_xy(x, y):
x0 = np.mean(x)
y0 = np.mean(y)
r = np.sqrt((x-x0)**2 + (y-y0)**2)
angles = np.where((y-y0) > 0, np.arccos((x-x0)/r), 2*np.pi-np.arccos((x-x0)/r))
mask = np.argsort(angles)
x_sorted = x[mask]
y_sorted = y[mask]
return x_sorted, y_sorted
G = nx.karate_club_graph()
pos = nx.spring_layout(G, seed=42)
fig, ax = plt.subplots(figsize=(8, 10))
nx.draw(G, pos=pos, with_labels=True)
communities = nx.community.louvain_communities(G)
alpha = 0.5
edge_padding = 10
colors = cm.get_cmap('viridis', len(communities))
for i, comm in enumerate(communities):
if len(comm) == 1:
cir = plt.Circle((pos[comm.pop()]), edge_padding / 100, alpha=alpha, color=colors(i))
ax.add_patch(cir)
elif len(comm) == 2:
comm_pos = {k: pos[k] for k in comm}
coords = [a for a in zip(*comm_pos.values())]
x, y = coords[0], coords[1]
plt.plot(x, y, linewidth=edge_padding, linestyle="-", alpha=alpha, color=colors(i))
else:
comm_pos = {k: pos[k] for k in comm}
coords = [a for a in zip(*comm_pos.values())]
x, y = sort_xy(np.array(coords[0]), np.array(coords[1]))
plt.fill(x, y, alpha=alpha, facecolor=colors(i),
edgecolor=colors(i), # set to None to remove edge padding
linewidth=edge_padding)
I am using open3d to render a 3D head together with a hairstyle (see code below). I am now looking for a way to take a screenshot of the rendered objects. How do you suggest proceeding? I need to consider a few hundred hairstyles, so I would prefer to avoid using mouse or keyboard control.
All 3D objects (head and hairstyle) are from this dataset.
This is the script I'm using to visualize the 3D head model and the hairstyle:
import open3d as o3d
import math
from mathutils import Vector
import struct
import array
import numpy as np
# Load the head model
mesh = o3d.io.read_triangle_mesh("../head_model.obj")
# Load a 3D hairstyle
fin = open("../strands00144.data", "rb")
num_of_strands = struct.unpack('i', fin.read(4))[0]
hair = []
num_strand = 0
#print("num_of_strands: ", num_of_strands)
for i in range(num_of_strands):
num_of_vertices = struct.unpack('i', fin.read(4))[0]
if num_of_vertices == 100:
num_strand += 1
#print("num_of_vertices: ", num_of_vertices)
strand = []
for j in range(num_of_vertices):
vertex_x = struct.unpack('f', fin.read(4))[0]
vertex_y = struct.unpack('f', fin.read(4))[0]
vertex_z = struct.unpack('f', fin.read(4))[0]
vertex = [vertex_x, vertex_y, vertex_z]
#print("vertex: ", vertex)
strand.append(vertex)
hair.append(strand)
randomPoints = np.zeros([100*num_strand, 3])
for ii in range(num_strand):
randomPoints[0 + 100 * ii: 100 + 100 * ii][:] = hair[ii][:][:]
o3d.visualization.Visualizer()
pointSet = o3d.geometry.PointCloud()
pointSet.points = o3d.utility.Vector3dVector(randomPoints)
pointSet.paint_uniform_color([0, 0, 0])
mesh.compute_vertex_normals()
o3d.visualization.draw_geometries([pointSet, mesh])
I converted some audio files to spectrograms and saved them to files using the following code:
import os
from matplotlib import pyplot as plt
import librosa
import librosa.display
import IPython.display as ipd
audio_fpath = "./audios/"
spectrograms_path = "./spectrograms/"
audio_clips = os.listdir(audio_fpath)
def generate_spectrogram(x, sr, save_name):
X = librosa.stft(x)
Xdb = librosa.amplitude_to_db(abs(X))
fig = plt.figure(figsize=(20, 20), dpi=1000, frameon=False)
ax = fig.add_axes([0, 0, 1, 1], frameon=False)
ax.axis('off')
librosa.display.specshow(Xdb, sr=sr, cmap='gray', x_axis='time', y_axis='hz')
plt.savefig(save_name, quality=100, bbox_inches=0, pad_inches=0)
librosa.cache.clear()
for i in audio_clips:
audio_fpath = "./audios/"
spectrograms_path = "./spectrograms/"
audio_length = librosa.get_duration(filename=audio_fpath + i)
j=60
while j < audio_length:
x, sr = librosa.load(audio_fpath + i, offset=j-60, duration=60)
save_name = spectrograms_path + i + str(j) + ".jpg"
generate_spectrogram(x, sr, save_name)
j += 60
if j >= audio_length:
j = audio_length
x, sr = librosa.load(audio_fpath + i, offset=j-60, duration=60)
save_name = spectrograms_path + i + str(j) + ".jpg"
generate_spectrogram(x, sr, save_name)
I wanted to keep the most detail and quality from the audios, so that i could turn them back to audio without too much loss (They are 80MB each).
Is it possible to turn them back to audio files? How can I do it?
I tried using librosa.feature.inverse.mel_to_audio, but it didn't work, and I don't think it applies.
I now have 1300 spectrogram files and want to train a Generative Adversarial Network with them, so that I can generate new audios, but I don't want to do it if i wont be able to listen to the results later.
Yes, it is possible to recover most of the signal and estimate the phase with e.g. Griffin-Lim Algorithm (GLA). Its "fast" implementation for Python can be found in librosa. Here's how you can use it:
import numpy as np
import librosa
y, sr = librosa.load(librosa.util.example_audio_file(), duration=10)
S = np.abs(librosa.stft(y))
y_inv = librosa.griffinlim(S)
And that's how the original and reconstruction look like:
The algorithm by default randomly initialises the phases and then iterates forward and inverse STFT operations to estimate the phases.
Looking at your code, to reconstruct the signal, you'd just need to do:
import numpy as np
X_inv = librosa.griffinlim(np.abs(X))
It's just an example of course. As pointed out by #PaulR, in your case you'd need to load the data from jpeg (which is lossy!) and then apply inverse transform to amplitude_to_db first.
The algorithm, especially the phase estimation, can be further improved thanks to advances in artificial neural networks. Here is one paper that discusses some enhancements.
I am trying to create a spectrogram from a .wav file in python3.
I want the final saved image to look similar to this image:
I have tried the following:
This stack overflow post:
Spectrogram of a wave file
This post worked, somewhat. After running it, I got
However, This graph does not contain the colors that I need. I need a spectrogram that has colors. I tried to tinker with this code to try and add the colors however after spending significant time and effort on this, I couldn't figure it out!
I then tried this tutorial.
This code crashed(on line 17) when I tried to run it with the error TypeError: 'numpy.float64' object cannot be interpreted as an integer.
line 17:
samples = np.append(np.zeros(np.floor(frameSize/2.0)), sig)
I tried to fix it by casting
samples = int(np.append(np.zeros(np.floor(frameSize/2.0)), sig))
and I also tried
samples = np.append(np.zeros(int(np.floor(frameSize/2.0)), sig))
However neither of these worked in the end.
I would really like to know how to convert my .wav files to spectrograms with color so that I can analyze them! Any help would be appreciated!!!!!
Please tell me if you want me to provide any more information about my version of python, what I tried, or what I want to achieve.
Use scipy.signal.spectrogram.
import matplotlib.pyplot as plt
from scipy import signal
from scipy.io import wavfile
sample_rate, samples = wavfile.read('path-to-mono-audio-file.wav')
frequencies, times, spectrogram = signal.spectrogram(samples, sample_rate)
plt.pcolormesh(times, frequencies, spectrogram)
plt.imshow(spectrogram)
plt.ylabel('Frequency [Hz]')
plt.xlabel('Time [sec]')
plt.show()
Be sure that your wav file is mono (single channel) and not stereo (dual channel) before trying to do this. I highly recommend reading the scipy documentation at https://docs.scipy.org/doc/scipy-
0.19.0/reference/generated/scipy.signal.spectrogram.html.
Putting plt.pcolormesh before plt.imshow seems to fix some issues, as pointed out by #Davidjb, and if unpacking error occurs, follow the steps by #cgnorthcutt below.
I have fixed the errors you are facing for http://www.frank-zalkow.de/en/code-snippets/create-audio-spectrograms-with-python.html
This implementation is better because you can change the binsize (e.g. binsize=2**8)
import numpy as np
from matplotlib import pyplot as plt
import scipy.io.wavfile as wav
from numpy.lib import stride_tricks
""" short time fourier transform of audio signal """
def stft(sig, frameSize, overlapFac=0.5, window=np.hanning):
win = window(frameSize)
hopSize = int(frameSize - np.floor(overlapFac * frameSize))
# zeros at beginning (thus center of 1st window should be for sample nr. 0)
samples = np.append(np.zeros(int(np.floor(frameSize/2.0))), sig)
# cols for windowing
cols = np.ceil( (len(samples) - frameSize) / float(hopSize)) + 1
# zeros at end (thus samples can be fully covered by frames)
samples = np.append(samples, np.zeros(frameSize))
frames = stride_tricks.as_strided(samples, shape=(int(cols), frameSize), strides=(samples.strides[0]*hopSize, samples.strides[0])).copy()
frames *= win
return np.fft.rfft(frames)
""" scale frequency axis logarithmically """
def logscale_spec(spec, sr=44100, factor=20.):
timebins, freqbins = np.shape(spec)
scale = np.linspace(0, 1, freqbins) ** factor
scale *= (freqbins-1)/max(scale)
scale = np.unique(np.round(scale))
# create spectrogram with new freq bins
newspec = np.complex128(np.zeros([timebins, len(scale)]))
for i in range(0, len(scale)):
if i == len(scale)-1:
newspec[:,i] = np.sum(spec[:,int(scale[i]):], axis=1)
else:
newspec[:,i] = np.sum(spec[:,int(scale[i]):int(scale[i+1])], axis=1)
# list center freq of bins
allfreqs = np.abs(np.fft.fftfreq(freqbins*2, 1./sr)[:freqbins+1])
freqs = []
for i in range(0, len(scale)):
if i == len(scale)-1:
freqs += [np.mean(allfreqs[int(scale[i]):])]
else:
freqs += [np.mean(allfreqs[int(scale[i]):int(scale[i+1])])]
return newspec, freqs
""" plot spectrogram"""
def plotstft(audiopath, binsize=2**10, plotpath=None, colormap="jet"):
samplerate, samples = wav.read(audiopath)
s = stft(samples, binsize)
sshow, freq = logscale_spec(s, factor=1.0, sr=samplerate)
ims = 20.*np.log10(np.abs(sshow)/10e-6) # amplitude to decibel
timebins, freqbins = np.shape(ims)
print("timebins: ", timebins)
print("freqbins: ", freqbins)
plt.figure(figsize=(15, 7.5))
plt.imshow(np.transpose(ims), origin="lower", aspect="auto", cmap=colormap, interpolation="none")
plt.colorbar()
plt.xlabel("time (s)")
plt.ylabel("frequency (hz)")
plt.xlim([0, timebins-1])
plt.ylim([0, freqbins])
xlocs = np.float32(np.linspace(0, timebins-1, 5))
plt.xticks(xlocs, ["%.02f" % l for l in ((xlocs*len(samples)/timebins)+(0.5*binsize))/samplerate])
ylocs = np.int16(np.round(np.linspace(0, freqbins-1, 10)))
plt.yticks(ylocs, ["%.02f" % freq[i] for i in ylocs])
if plotpath:
plt.savefig(plotpath, bbox_inches="tight")
else:
plt.show()
plt.clf()
return ims
ims = plotstft(filepath)
import os
import wave
import pylab
def graph_spectrogram(wav_file):
sound_info, frame_rate = get_wav_info(wav_file)
pylab.figure(num=None, figsize=(19, 12))
pylab.subplot(111)
pylab.title('spectrogram of %r' % wav_file)
pylab.specgram(sound_info, Fs=frame_rate)
pylab.savefig('spectrogram.png')
def get_wav_info(wav_file):
wav = wave.open(wav_file, 'r')
frames = wav.readframes(-1)
sound_info = pylab.fromstring(frames, 'int16')
frame_rate = wav.getframerate()
wav.close()
return sound_info, frame_rate
for A Capella Science - Bohemian Gravity! this gives:
Use graph_spectrogram(path_to_your_wav_file).
I don't remember the blog from where I took this snippet. I will add the link whenever I see it again.
Beginner's answer above is excellent. I dont have 50 rep so I can't comment on it, but if you want the correct amplitude in the frequency domain the stft function should look like this:
import numpy as np
from matplotlib import pyplot as plt
import scipy.io.wavfile as wav
from numpy.lib import stride_tricks
""" short time fourier transform of audio signal """
def stft(sig, frameSize, overlapFac=0, window=np.hanning):
win = window(frameSize)
hopSize = int(frameSize - np.floor(overlapFac * frameSize))
# zeros at beginning (thus center of 1st window should be for sample nr. 0)
samples = np.append(np.zeros(int(np.floor(frameSize/2.0))), sig)
# cols for windowing
cols = np.ceil( (len(samples) - frameSize) / float(hopSize)) + 1
# zeros at end (thus samples can be fully covered by frames)
samples = np.append(samples, np.zeros(frameSize))
frames = stride_tricks.as_strided(samples, shape=(int(cols), frameSize), strides=(samples.strides[0]*hopSize, samples.strides[0])).copy()
frames *= win
fftResults = np.fft.rfft(frames)
windowCorrection = 1/(np.sum(np.hanning(frameSize))/frameSize) #This is amplitude correct (1/mean(window)). Energy correction is 1/rms(window)
FFTcorrection = 2/frameSize
scaledFftResults = fftResults*windowCorrection*FFTcorrection
return scaledFftResults
You can use librosa for your mp3 spectogram needs. Here is some code I found, thanks to Parul Pandey from medium. The code I used is this,
# Method described here https://stackoverflow.com/questions/15311853/plot-spectogram-from-mp3
import librosa
import librosa.display
from pydub import AudioSegment
import matplotlib.pyplot as plt
from scipy.io import wavfile
from tempfile import mktemp
def plot_mp3_matplot(filename):
"""
plot_mp3_matplot -- using matplotlib to simply plot time vs amplitude waveplot
Arguments:
filename -- filepath to the file that you want to see the waveplot for
Returns -- None
"""
# sr is for 'sampling rate'
# Feel free to adjust it
x, sr = librosa.load(filename, sr=44100)
plt.figure(figsize=(14, 5))
librosa.display.waveplot(x, sr=sr)
def convert_audio_to_spectogram(filename):
"""
convert_audio_to_spectogram -- using librosa to simply plot a spectogram
Arguments:
filename -- filepath to the file that you want to see the waveplot for
Returns -- None
"""
# sr == sampling rate
x, sr = librosa.load(filename, sr=44100)
# stft is short time fourier transform
X = librosa.stft(x)
# convert the slices to amplitude
Xdb = librosa.amplitude_to_db(abs(X))
# ... and plot, magic!
plt.figure(figsize=(14, 5))
librosa.display.specshow(Xdb, sr = sr, x_axis = 'time', y_axis = 'hz')
plt.colorbar()
# same as above, just changed the y_axis from hz to log in the display func
def convert_audio_to_spectogram_log(filename):
x, sr = librosa.load(filename, sr=44100)
X = librosa.stft(x)
Xdb = librosa.amplitude_to_db(abs(X))
plt.figure(figsize=(14, 5))
librosa.display.specshow(Xdb, sr = sr, x_axis = 'time', y_axis = 'log')
plt.colorbar()
Cheers!
I am trying to plot a very big file (~5 GB) using python and matplotlib. I am able to load the whole file in memory (the total available in the machine is 16 GB) but when I plot it using simple imshow I get a segmentation fault. This is most probable to the ulimit which I have set to 15000 but I cannot set higher. I have come to the conclusion that I need to plot my array in batches and therefore made a simple code to do that. My main isue is that when I plot a batch of the big array the x coordinates start always from 0 and there is no way I can overlay the images to create a final big one. If you have any suggestion please let me know. Also I am not able to install new packages like "Image" on this machine due to administrative rights. Here is a sample of the code that reads the first 12 lines of my array and make 3 plots.
import os
import sys
import scipy
import numpy as np
import pylab as pl
import matplotlib as mpl
import matplotlib.cm as cm
from optparse import OptionParser
from scipy import fftpack
from scipy.fftpack import *
from cmath import *
from pylab import *
import pp
import fileinput
import matplotlib.pylab as plt
import pickle
def readalllines(file1,rows,freqs):
file = open(file1,'r')
sizer = int(rows*freqs)
i = 0
q = np.zeros(sizer,'float')
for i in range(rows*freqs):
s =file.readline()
s = s.split()
#print s[4],q[i]
q[i] = float(s[4])
if i%262144 == 0:
print '\r ',int(i*100.0/(337*262144)),' percent complete',
i += 1
file.close()
return q
parser = OptionParser()
parser.add_option('-f',dest="filename",help="Read dynamic spectrum from FILE",metavar="FILE")
parser.add_option('-t',dest="dtime",help="The time integration used in seconds, default 10",default=10)
parser.add_option('-n',dest="dfreq",help="The bandwidth of each frequency channel in Hz",default=11.92092896)
parser.add_option('-w',dest="reduce",help="The chuncker divider in frequency channels, integer default 16",default=16)
(opts,args) = parser.parse_args()
rows=12
freqs = 262144
file1 = opts.filename
s = readalllines(file1,rows,freqs)
s = np.reshape(s,(rows,freqs))
s = s.T
print s.shape
#raw_input()
#s_shift = scipy.fftpack.fftshift(s)
#fig = plt.figure()
#fig.patch.set_alpha(0.0)
#axes = plt.axes()
#axes.patch.set_alpha(0.0)
###plt.ylim(0,8)
plt.ion()
i = 0
for o in range(0,rows,4):
fig = plt.figure()
#plt.clf()
plt.imshow(s[:,o:o+4],interpolation='nearest',aspect='auto', cmap=cm.gray_r, origin='lower')
if o == 0:
axis([0,rows,0,freqs])
fdf, fdff = xticks()
print fdf
xticks(fdf+o)
print xticks()
#axis([o,o+4,0,freqs])
plt.draw()
#w, h = fig.canvas.get_width_height()
#buf = np.fromstring(fig.canvas.tostring_argb(), dtype=np.uint8)
#buf.shape = (w,h,4)
#buf = np.rol(buf, 3, axis=2)
#w,h,_ = buf.shape
#img = Image.fromstring("RGBA", (w,h),buf.tostring())
#if prev:
# prev.paste(img)
# del prev
#prev = img
i += 1
pl.colorbar()
pl.show()
If you plot any array with more than ~2k pixels across something in your graphics chain will down sample the image in some way to display it on your monitor. I would recommend down sampling in a controlled way, something like
data = convert_raw_data_to_fft(args) # make sure data is row major
def ds_decimate(row,step = 100):
return row[::step]
def ds_sum(row,step):
return np.sum(row[:step*(len(row)//step)].reshape(-1,step),1)
# as per suggestion from tom10 in comments
def ds_max(row,step):
return np.max(row[:step*(len(row)//step)].reshape(-1,step),1)
data_plotable = [ds_sum(d) for d in data] # plug in which ever function you want
or interpolation.
Matplotlib is pretty memory-inefficient when plotting images. It creates several full-resolution intermediate arrays, which is probably why your program is crashing.
One solution is to downsample the image before feeding it into matplotlib, as #tcaswell suggests.
I also wrote some wrapper code to do this downsampling automatically, based on your screen resolution. It's at https://github.com/ChrisBeaumont/mpl-modest-image, if it's useful. It also has the advantage that the image is resampled on the fly, so you can still pan and zoom without sacrificing resolution where you need it.
I think you're just missing the extent=(left, right, bottom, top) keyword argument in plt.imshow.
x = np.random.randn(2, 10)
y = np.ones((4, 10))
x[0] = 0 # To make it clear which side is up, etc
y[0] = -1
plt.imshow(x, extent=(0, 10, 0, 2))
plt.imshow(y, extent=(0, 10, 2, 6))
# This is necessary, else the plot gets scaled and only shows the last array
plt.ylim(0, 6)
plt.colorbar()
plt.show()