Related
Let's say I have a list a = [2, 1, 4, 3, 5]. I want to do the following:
I define a percentage value r%. I would like to select r% of samples having low values and get their indices.
For examples, if r=80 - The output would be the indices of 1, 2, 3, 4 i.e. 1, 0, 3, 2
Use np.percentile and np.where
a = np.array([2, 1, 4, 3, 5])
r = 80
np.where(a < np.percentile(a, r))
> (array([0, 1, 2, 3]),)
Note: in your example you return the order of the indices as if the elements were sorted. It's not clear if this is important for you but if it is it's easy in NumPy! Just replace the last line with
np.argsort(a)[a < np.percentile(a, r)]
> array([1, 0, 3, 2])
def perc(r, number_list):
# Find number of samples based on the percentage (rounding to closest integer)
number_of_samples = len(number_list) * (r/ 100)
number_list.sort()
return [number_list[index] for index in range(number_of_samples)]
Can I index NumPy N-D array with fallback to default values for out-of-bounds indexes? Example code below for some imaginary np.get_with_default(a, indexes, default):
import numpy as np
print(np.get_with_default(
np.array([[1,2,3],[4,5,6]]), # N-D array
[(np.array([0, 0, 1, 1, 2, 2]), np.array([1, 2, 2, 3, 3, 5]))], # N-tuple of indexes along each axis
13, # Default for out-of-bounds fallback
))
should print
[2 3 6 13 13 13]
I'm looking for some built-in function for this. If such not exists then at least some short and efficient implementation to do that.
I arrived at this question because I was looking for exactly the same. I came up with the following function, which does what you ask for 2 dimension. It could likely be generalised to N dimensions.
def get_with_defaults(a, xx, yy, nodata):
# get values from a, clipping the index values to valid ranges
res = a[np.clip(yy, 0, a.shape[0] - 1), np.clip(xx, 0, a.shape[1] - 1)]
# compute a mask for both x and y, where all invalid index values are set to true
myy = np.ma.masked_outside(yy, 0, a.shape[0] - 1).mask
mxx = np.ma.masked_outside(xx, 0, a.shape[1] - 1).mask
# replace all values in res with NODATA, where either the x or y index are invalid
np.choose(myy + mxx, [res, nodata], out=res)
return res
xx and yy are the index array, a is indexed by (y,x).
This gives:
>>> a=np.zeros((3,2),dtype=int)
>>> get_with_defaults(a, (-1, 1000, 0, 1, 2), (0, -1, 0, 1, 2), -1)
array([-1, -1, 0, 0, -1])
As an alternative, the following implementation achieves the same and is more concise:
def get_with_default(a, xx, yy, nodata):
# get values from a, clipping the index values to valid ranges
res = a[np.clip(yy, 0, a.shape[0] - 1), np.clip(xx, 0, a.shape[1] - 1)]
# replace all values in res with NODATA (gets broadcasted to the result array), where
# either the x or y index are invalid
res[(yy < 0) | (yy >= a.shape[0]) | (xx < 0) | (xx >= a.shape[1])] = nodata
return res
I don't know if there is anything in NumPy to do that directly, but you can always implement it yourself. This is not particularly smart or efficient, as it requires multiple advanced indexing operations, but does what you need:
import numpy as np
def get_with_default(a, indices, default=0):
# Ensure inputs are arrays
a = np.asarray(a)
indices = tuple(np.broadcast_arrays(*indices))
if len(indices) <= 0 or len(indices) > a.ndim:
raise ValueError('invalid number of indices.')
# Make mask of indices out of bounds
mask = np.zeros(indices[0].shape, np.bool)
for ind, s in zip(indices, a.shape):
mask |= (ind < 0) | (ind >= s)
# Only do masking if necessary
n_mask = np.count_nonzero(mask)
# Shortcut for the case where all is masked
if n_mask == mask.size:
return np.full_like(a, default)
if n_mask > 0:
# Ensure index arrays are contiguous so masking works right
indices = tuple(map(np.ascontiguousarray, indices))
for ind in indices:
# Replace masked indices with zeros
ind[mask] = 0
# Get values
res = a[indices]
if n_mask > 0:
# Replace values of masked indices with default value
res[mask] = default
return res
# Test
print(get_with_default(
np.array([[1,2,3],[4,5,6]]),
(np.array([0, 0, 1, 1, 2, 2]), np.array([1, 2, 2, 3, 3, 5])),
13
))
# [ 2 3 6 13 13 13]
I also needed a solution to this, but I wanted a solution that worked in N dimensions. I made Markus' solution work for N-dimensions, including selecting from an array with more dimensions than the coordinates point to.
def get_with_defaults(arr, coords, nodata):
coords, shp = np.array(coords), np.array(arr.shape)
# Get values from arr, clipping to valid ranges
res = arr[tuple(np.clip(c, 0, s-1) for c, s in zip(coords, shp))]
# Set any output where one of the coords was out of range to nodata
res[np.any(~((0 <= coords) & (coords < shp[:len(coords), None])), axis=0)] = nodata
return res
import numpy as np
if __name__ == '__main__':
A = np.array([[1,2,3],[4,5,6]])
B = np.array([[[1, -9],[2, -8],[3, -7]],[[4, -6],[5, -5],[6, -4]]])
coords1 = [[0, 0, 1, 1, 2, 2], [1, 2, 2, 3, 3, 5]]
coords2 = [[0, 0, 1, 1, 2, 2], [1, 2, 2, 3, 3, 5], [1, 1, 1, 1, 1, 1]]
out1 = get_with_defaults(A, coords1, 13)
out2 = get_with_defaults(B, coords1, 13)
out3 = get_with_defaults(B, coords2, 13)
print(out1)
# [2, 3, 6, 13, 13, 13]
print(out2)
# [[ 2 -8]
# [ 3 -7]
# [ 6 -4]
# [13 13]
# [13 13]
# [13 13]]
print(out3)
# [-8, -7, -4, 13, 13, 13]
Let's say I have a NumPy array:
x = np.array([0, 1, 2, 0, 4, 5, 6, 7, 0, 0])
At each index, I want to find the distance to nearest zero value. If the position is a zero itself then return zero as a distance. Afterward, we are only interested in distances to the nearest zero that is to the right of the current position. The super naive approach would be something like:
out = np.full(x.shape[0], x.shape[0]-1)
for i in range(x.shape[0]):
j = 0
while i + j < x.shape[0]:
if x[i+j] == 0:
break
j += 1
out[i] = j
And the output would be:
array([0, 2, 1, 0, 4, 3, 2, 1, 0, 0])
I'm noticing a countdown/decrement pattern in the output in between the zeros. So, I might be able to do use the locations of the zeros (i.e., zero_indices = np.argwhere(x == 0).flatten())
What is the fastest way to get the desired output in linear time?
Approach #1 : Searchsorted to the rescue for linear-time in a vectorized manner (before numba guys come in)!
mask_z = x==0
idx_z = np.flatnonzero(mask_z)
idx_nz = np.flatnonzero(~mask_z)
# Cover for the case when there's no 0 left to the right
# (for same results as with posted loop-based solution)
if x[-1]!=0:
idx_z = np.r_[idx_z,len(x)]
out = np.zeros(len(x), dtype=int)
idx = np.searchsorted(idx_z, idx_nz)
out[~mask_z] = idx_z[idx] - idx_nz
Approach #2 : Another with some cumsum -
mask_z = x==0
idx_z = np.flatnonzero(mask_z)
# Cover for the case when there's no 0 left to the right
if x[-1]!=0:
idx_z = np.r_[idx_z,len(x)]
out = idx_z[np.r_[False,mask_z[:-1]].cumsum()] - np.arange(len(x))
Alternatively, last step of cumsum could be replaced by repeat functionality -
r = np.r_[idx_z[0]+1,np.diff(idx_z)]
out = np.repeat(idx_z,r)[:len(x)] - np.arange(len(x))
Approach #3 : Another with mostly just cumsum -
mask_z = x==0
idx_z = np.flatnonzero(mask_z)
pp = np.full(len(x), -1)
pp[idx_z[:-1]] = np.diff(idx_z) - 1
if idx_z[0]==0:
pp[0] = idx_z[1]
else:
pp[0] = idx_z[0]
out = pp.cumsum()
# Handle boundary case and assigns 0s at original 0s places
out[idx_z[-1]:] = np.arange(len(x)-idx_z[-1],0,-1)
out[mask_z] = 0
You could work from the other side. Keep a counter on how many non zero digits have passed and assign it to the element in the array. If you see 0, reset the counter to 0
Edit: if there is no zero on the right, then you need another check
x = np.array([0, 1, 2, 0, 4, 5, 6, 7, 0, 0])
out = x
count = 0
hasZero = False
for i in range(x.shape[0]-1,-1,-1):
if out[i] != 0:
if not hasZero:
out[i] = x.shape[0]-1
else:
count += 1
out[i] = count
else:
hasZero = True
count = 0
print(out)
You can use the difference between the indices of each position and the cumulative max of zero positions to determine the distance to the preceding zero. This can be done forward and backward. The minimum between forward and backward distance to the preceding (or next) zero will be the nearest:
import numpy as np
indices = np.arange(x.size)
zeroes = x==0
forward = indices - np.maximum.accumulate(indices*zeroes) # forward distance
forward[np.cumsum(zeroes)==0] = x.size-1 # handle absence of zero from edge
forward = forward * (x!=0) # set zero positions to zero
zeroes = zeroes[::-1]
backward = indices - np.maximum.accumulate(indices*zeroes) # backward distance
backward[np.cumsum(zeroes)==0] = x.size-1 # handle absence of zero from edge
backward = backward[::-1] * (x!=0) # set zero positions to zero
distZero = np.minimum(forward,backward) # closest distance (minimum)
results:
distZero
# [0, 1, 1, 0, 1, 2, 2, 1, 0, 0]
forward
# [0, 1, 2, 0, 1, 2, 3, 4, 0, 0]
backward
# [0, 2, 1, 0, 4, 3, 2, 1, 0, 0]
Special case where no zeroes are present on outer edges:
x = np.array([3, 1, 2, 0, 4, 5, 6, 0,8,8])
forward: [9 9 9 0 1 2 3 0 1 2]
backward: [3 2 1 0 3 2 1 0 9 9]
distZero: [3 2 1 0 1 2 1 0 1 2]
also works with no zeroes at all
[EDIT] non-numpy solutions ...
if you're looking for an O(N) solution that doesn't require numpy, you can apply this strategy using the accumulate function from itertools:
x = [0, 1, 2, 0, 4, 5, 6, 7, 0, 0]
from itertools import accumulate
maxDist = len(x) - 1
zeroes = [maxDist*(v!=0) for v in x]
forward = [*accumulate(zeroes,lambda d,v:min(maxDist,(d+1)*(v!=0)))]
backward = accumulate(zeroes[::-1],lambda d,v:min(maxDist,(d+1)*(v!=0)))
backward = [*backward][::-1]
distZero = [min(f,b) for f,b in zip(forward,backward)]
print("x",x)
print("f",forward)
print("b",backward)
print("d",distZero)
output:
x [0, 1, 2, 0, 4, 5, 6, 7, 0, 0]
f [0, 1, 2, 0, 1, 2, 3, 4, 0, 0]
b [0, 2, 1, 0, 4, 3, 2, 1, 0, 0]
d [0, 1, 1, 0, 1, 2, 2, 1, 0, 0]
If you don't want to use any library, you can accumulate the distances manually in a loop:
x = [0, 1, 2, 0, 4, 5, 6, 7, 0, 0]
forward,backward = [],[]
fDist = bDist = maxDist = len(x)-1
for f,b in zip(x,reversed(x)):
fDist = min(maxDist,(fDist+1)*(f!=0))
forward.append(fDist)
bDist = min(maxDist,(bDist+1)*(b!=0))
backward.append(bDist)
backward = backward[::-1]
distZero = [min(f,b) for f,b in zip(forward,backward)]
print("x",x)
print("f",forward)
print("b",backward)
print("d",distZero)
output:
x [0, 1, 2, 0, 4, 5, 6, 7, 0, 0]
f [0, 1, 2, 0, 1, 2, 3, 4, 0, 0]
b [0, 2, 1, 0, 4, 3, 2, 1, 0, 0]
d [0, 1, 1, 0, 1, 2, 2, 1, 0, 0]
My first intuition would be to use slicing. If x can be a normal list instead of a numpy array, then you could use
out = [x[i:].index(0) for i,_ in enumerate(x)]
if numpy is necessary then you can use
out = [np.where(x[i:]==0)[0][0] for i,_ in enumerate(x)]
but this is less efficient because you are finding all zero locations to the right of the value and then pulling out just the first. Almost definitely a better way to do this in numpy.
Edit: I am sorry, I misunderstood. This will give you the distance to the nearest zeros - may it be at left or right. But you can use d_right as intermediate result. This does not cover the edge case of not having any zero to the right though.
import numpy as np
x = np.array([0, 1, 2, 0, 4, 5, 6, 7, 0, 0])
# Get the distance to the closest zero from the left:
zeros = x == 0
zero_locations = np.argwhere(x == 0).flatten()
zero_distances = np.diff(np.insert(zero_locations, 0, 0))
temp = x.copy()
temp[~zeros] = 1
temp[zeros] = -(zero_distances-1)
d_left = np.cumsum(temp) - 1
# Get the distance to the closest zero from the right:
zeros = x[::-1] == 0
zero_locations = np.argwhere(x[::-1] == 0).flatten()
zero_distances = np.diff(np.insert(zero_locations, 0, 0))
temp = x.copy()
temp[~zeros] = 1
temp[zeros] = -(zero_distances-1)
d_right = np.cumsum(temp) - 1
d_right = d_right[::-1]
# Get the smallest distance from both sides:
smallest_distances = np.min(np.stack([d_left, d_right]), axis=0)
# np.array([0, 1, 1, 0, 1, 2, 2, 1, 0, 0])
I have a signal where I want to find the average height of the values. This is done by finding the zero crossings and calculating the max and min between each zero crossing, then averaging these values.
My problem occurs when I want to use np.where() to find where the signal is crossing zero. When I use np.where() I get the result in a tuple, but I want it in an array where I can count the amount of times zero is crossed.
I am new to Python and coming from Matlab it is a bit confusing with all the different classes. As you can see, I get an error because nu = len(zero_u) gives 1 as a result, because the whole array is written in a tuple as one element.
Any ideas how to go around this?
The code looks like this:
import numpy as np
def averageheight(f):
rms = np.std(f)
f = f + (rms * 10**-6)
# Find zero crossing
fsign = np.sign(f)
fdiff = np.diff(fsign)
zero_u = np.asarray(np.where(fdiff > 0)) + 1
zero_d = np.asarray(np.where(fdiff < 0)) + 1
nu = len(zero_u)
nd = len(zero_d)
value_max = np.zeros((nu, 1))
value_min = np.zeros((nu, 1))
imaxvec = np.zeros((nu, 1))
iminvec = np.zeros((nu, 1))
if (nu > 2) and (nd > 2):
if zero_u[0] > zero_d[0]:
zero_d[0] = []
nu = len(zero_u)
nd = len(zero_d)
ncross = np.fmin(nu, nd)
# Find Maxima:
for ic in range(0, ncross - 1):
up = int(zero_u[ic])
down = int(zero_d[ic])
fvec = f[up:down]
value_max[ic] = np.amax(fvec)
index_max = value_max.argmax()
imaxvec[ic] = up + index_max - 1
# Find Minima:
for ic in range(0, ncross - 2):
down = int(zero_d[ic])
up = int(zero_u[ic+1])
fvec = f[down:up]
value_min[ic] = np.amin(fvec)
index_min = value_min.argmin()
iminvec[ic] = down + index_min - 1
# Remove spurious values, bumps and zero_d
thr = rms/3
maxfind = np.where(value_max < thr)
for i in range(0, len(maxfind)):
imaxfind = np.where(value_max == maxfind[i])
imaxvec[imaxfind] = 0
value_max[imaxfind] = 0
minfind = np.where(value_min > -thr)
for j in range(0, len(minfind)):
iminfind = np.where(value_min == minfind[j])
value_min[iminfind] = 0
iminvec[iminfind] = 0
# Find Average Height
avh = np.mean(value_max) - np.mean(value_min)
else:
avh = 0
return avh
np.where, and np.nonzero even more so, clearly explains that it returns a tuple, with one array for each dimension of the condition array:
In [71]: arr = np.random.randint(-5,5,10)
In [72]: arr
Out[72]: array([ 3, 4, 2, -3, -1, 0, -5, 4, 2, -3])
In [73]: arr.shape
Out[73]: (10,)
In [74]: np.where(arr>=0)
Out[74]: (array([0, 1, 2, 5, 7, 8]),)
In [75]: arr[_]
Out[75]: array([3, 4, 2, 0, 4, 2])
That Out[74] tuple can be used directly as an index.
You can also extract the array from the tuple:
In [76]: np.where(arr>=0)[0]
Out[76]: array([0, 1, 2, 5, 7, 8])
That, I think is a better choice than the np.asarray(np.where(...))
This convention for where becomes clearer when we use it on a 2d array
In [77]: arr2 = arr.reshape(2,5)
In [78]: np.where(arr2>=0)
Out[78]: (array([0, 0, 0, 1, 1, 1]), array([0, 1, 2, 0, 2, 3]))
In [79]: arr2[_]
Out[79]: array([3, 4, 2, 0, 4, 2])
Again we are indexing with a tuple. arr2[1,3] is really arr2[(1,3)]. The values in [] indexing brackets are actually passed to the indexing function as a tuple of values.
np.argwhere applies transpose to the result of where, producing an array:
In [80]: np.transpose(np.where(arr2>=0))
Out[80]:
array([[0, 0],
[0, 1],
[0, 2],
[1, 0],
[1, 2],
[1, 3]])
That's the same indexing arrays, but arranged in a 2d column matrix.
If you need the count of where without the actual values, a slightly faster function is
In [81]: np.count_nonzero(arr>=0)
Out[81]: 6
In fact np.nonzero uses the count to first determine the size of the arrays that it will return.
Say I have two lists of data as follows:
x = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
y = [1, 2, 3, 4, 5, 6, 8, 10, 12, 14]
That is, it's pretty clear that merely fitting a line to this data doesn't work, but instead the slope changed at a point in the data. (Obviously, one can pinpoint from this data set pretty easily where that change is, but it's not as clear in the set I'm working with so let's ignore that.) Something with the derivative, I'm guessing, but the point here is I want to treat this as a free parameter where I say "it's this point, +/- this uncertainty, and here is the linear slope before and after this point."
Note, I can do this with an array if it's easier. Thanks!
Here is a plot of your data:
You need to find two slopes (== taking two derivatives). First, find the slope between every two points (using numpy):
import numpy as np
x = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10],dtype=np.float)
y = np.array([1, 2, 3, 4, 5, 6, 8, 10, 12, 14],dtype=np.float)
m = np.diff(y)/np.diff(x)
print (m)
# [ 1. 1. 1. 1. 1. 2. 2. 2. 2.]
Clearly, slope changes from 1 to 2 in the sixth interval (between sixth and seventh points). Then take the derivative of this array, which tells you when the slope changes:
print (np.diff(m))
[ 0. 0. 0. 0. 1. 0. 0. 0.]
To find the index of the non-zero value:
idx = np.nonzero(np.diff(m))[0]
print (idx)
# 4
Since we took one derivative with respect to x, and indices start from zero in Python, idx+2 tells you that the slope is different before and after the sixth point.
I'm not sure to understand very well what you want but you can see the evolution this way (derivative):
>>> y = [1, 2, 3, 4, 5, 6, 8, 10, 12, 14]
>>> dy=[y[i+1]-y[i] for i in range(len(y)-1)]
>>> dy
[1, 1, 1, 1, 1, 2, 2, 2, 2]
and then find the point where it change (second derivative):
>>> dpy=[dy[i+1]-dy[i] for i in range(len(dy)-1)]
>>> dpy
[0, 0, 0, 0, 1, 0, 0, 0]
if you want the index of this point :
>>> dpy.index(1)
4
that can give you the value of the last point before change of slope :
>>> change=dpy.index(1)
>>> y[change]
5
In your y = [1, 2, 3, 4, 5, 6, 8, 10, 12, 14] the change happen at the index [4] (list indexing start to 0) and the value of y at this point is 5.
You can calculate the slope as the difference between each pair of points (the first derivative). Then check where the slope changes (the second derivative). If it changes, append the index location to idx, the collection of points where the slope changes.
Note that the first point does not have a unique slope. The second pair of points will give you the slope, but you need the third pair before you can measure the change in slope.
idx = []
prior_slope = float(y[1] - y[0]) / (x[1] - x[0])
for n in range(2, len(x)): # Start from 3rd pair of points.
slope = float(y[n] - y[n - 1]) / (x[n] - x[n - 1])
if slope != prior_slope:
idx.append(n)
prior_slope = slope
>>> idx
[6]
Of course this could be done more efficiently in Pandas or Numpy, but I am just giving you a simple Python 2 solution.
A simple conditional list comprehension should also be pretty efficient, although it is more difficult to understand.
idx = [n for n in range(2, len(x))
if float(y[n] - y[n - 1]) / (x[n] - x[n - 1])
!= float(y[n - 1] - y[n - 2]) / (x[n - 1] - x[n - 2])]
Knee point might be a potential solution.
from kneed import KneeLocator
import numpy as np
x = np.array([1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
y = np.array([1, 2, 3, 4, 5, 6, 8, 10, 12, 14])
kn = KneeLocator(x, y, curve='convex', direction='increasing')
# You can use array y to automatically determine 'convex' and 'increasing' if y is well-behaved
idx = (np.abs(x - kn.knee)).argmin()
>>> print(x[idx], y[idx])
6 6