I need to find unique rows in a numpy.array.
For example:
>>> a # I have
array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
>>> new_a # I want to get to
array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 1, 1, 0]])
I know that i can create a set and loop over the array, but I am looking for an efficient pure numpy solution. I believe that there is a way to set data type to void and then I could just use numpy.unique, but I couldn't figure out how to make it work.
As of NumPy 1.13, one can simply choose the axis for selection of unique values in any N-dim array. To get unique rows, one can do:
unique_rows = np.unique(original_array, axis=0)
Yet another possible solution
np.vstack({tuple(row) for row in a})
Another option to the use of structured arrays is using a view of a void type that joins the whole row into a single item:
a = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
b = np.ascontiguousarray(a).view(np.dtype((np.void, a.dtype.itemsize * a.shape[1])))
_, idx = np.unique(b, return_index=True)
unique_a = a[idx]
>>> unique_a
array([[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
EDIT
Added np.ascontiguousarray following #seberg's recommendation. This will slow the method down if the array is not already contiguous.
EDIT
The above can be slightly sped up, perhaps at the cost of clarity, by doing:
unique_a = np.unique(b).view(a.dtype).reshape(-1, a.shape[1])
Also, at least on my system, performance wise it is on par, or even better, than the lexsort method:
a = np.random.randint(2, size=(10000, 6))
%timeit np.unique(a.view(np.dtype((np.void, a.dtype.itemsize*a.shape[1])))).view(a.dtype).reshape(-1, a.shape[1])
100 loops, best of 3: 3.17 ms per loop
%timeit ind = np.lexsort(a.T); a[np.concatenate(([True],np.any(a[ind[1:]]!=a[ind[:-1]],axis=1)))]
100 loops, best of 3: 5.93 ms per loop
a = np.random.randint(2, size=(10000, 100))
%timeit np.unique(a.view(np.dtype((np.void, a.dtype.itemsize*a.shape[1])))).view(a.dtype).reshape(-1, a.shape[1])
10 loops, best of 3: 29.9 ms per loop
%timeit ind = np.lexsort(a.T); a[np.concatenate(([True],np.any(a[ind[1:]]!=a[ind[:-1]],axis=1)))]
10 loops, best of 3: 116 ms per loop
If you want to avoid the memory expense of converting to a series of tuples or another similar data structure, you can exploit numpy's structured arrays.
The trick is to view your original array as a structured array where each item corresponds to a row of the original array. This doesn't make a copy, and is quite efficient.
As a quick example:
import numpy as np
data = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
ncols = data.shape[1]
dtype = data.dtype.descr * ncols
struct = data.view(dtype)
uniq = np.unique(struct)
uniq = uniq.view(data.dtype).reshape(-1, ncols)
print uniq
To understand what's going on, have a look at the intermediary results.
Once we view things as a structured array, each element in the array is a row in your original array. (Basically, it's a similar data structure to a list of tuples.)
In [71]: struct
Out[71]:
array([[(1, 1, 1, 0, 0, 0)],
[(0, 1, 1, 1, 0, 0)],
[(0, 1, 1, 1, 0, 0)],
[(1, 1, 1, 0, 0, 0)],
[(1, 1, 1, 1, 1, 0)]],
dtype=[('f0', '<i8'), ('f1', '<i8'), ('f2', '<i8'), ('f3', '<i8'), ('f4', '<i8'), ('f5', '<i8')])
In [72]: struct[0]
Out[72]:
array([(1, 1, 1, 0, 0, 0)],
dtype=[('f0', '<i8'), ('f1', '<i8'), ('f2', '<i8'), ('f3', '<i8'), ('f4', '<i8'), ('f5', '<i8')])
Once we run numpy.unique, we'll get a structured array back:
In [73]: np.unique(struct)
Out[73]:
array([(0, 1, 1, 1, 0, 0), (1, 1, 1, 0, 0, 0), (1, 1, 1, 1, 1, 0)],
dtype=[('f0', '<i8'), ('f1', '<i8'), ('f2', '<i8'), ('f3', '<i8'), ('f4', '<i8'), ('f5', '<i8')])
That we then need to view as a "normal" array (_ stores the result of the last calculation in ipython, which is why you're seeing _.view...):
In [74]: _.view(data.dtype)
Out[74]: array([0, 1, 1, 1, 0, 0, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 0])
And then reshape back into a 2D array (-1 is a placeholder that tells numpy to calculate the correct number of rows, give the number of columns):
In [75]: _.reshape(-1, ncols)
Out[75]:
array([[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
Obviously, if you wanted to be more concise, you could write it as:
import numpy as np
def unique_rows(data):
uniq = np.unique(data.view(data.dtype.descr * data.shape[1]))
return uniq.view(data.dtype).reshape(-1, data.shape[1])
data = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
print unique_rows(data)
Which results in:
[[0 1 1 1 0 0]
[1 1 1 0 0 0]
[1 1 1 1 1 0]]
np.unique when I run it on np.random.random(100).reshape(10,10) returns all the unique individual elements, but you want the unique rows, so first you need to put them into tuples:
array = #your numpy array of lists
new_array = [tuple(row) for row in array]
uniques = np.unique(new_array)
That is the only way I see you changing the types to do what you want, and I am not sure if the list iteration to change to tuples is okay with your "not looping through"
np.unique works by sorting a flattened array, then looking at whether each item is equal to the previous. This can be done manually without flattening:
ind = np.lexsort(a.T)
a[ind[np.concatenate(([True],np.any(a[ind[1:]]!=a[ind[:-1]],axis=1)))]]
This method does not use tuples, and should be much faster and simpler than other methods given here.
NOTE: A previous version of this did not have the ind right after a[, which mean that the wrong indices were used. Also, Joe Kington makes a good point that this does make a variety of intermediate copies. The following method makes fewer, by making a sorted copy and then using views of it:
b = a[np.lexsort(a.T)]
b[np.concatenate(([True], np.any(b[1:] != b[:-1],axis=1)))]
This is faster and uses less memory.
Also, if you want to find unique rows in an ndarray regardless of how many dimensions are in the array, the following will work:
b = a[lexsort(a.reshape((a.shape[0],-1)).T)];
b[np.concatenate(([True], np.any(b[1:]!=b[:-1],axis=tuple(range(1,a.ndim)))))]
An interesting remaining issue would be if you wanted to sort/unique along an arbitrary axis of an arbitrary-dimension array, something that would be more difficult.
Edit:
To demonstrate the speed differences, I ran a few tests in ipython of the three different methods described in the answers. With your exact a, there isn't too much of a difference, though this version is a bit faster:
In [87]: %timeit unique(a.view(dtype)).view('<i8')
10000 loops, best of 3: 48.4 us per loop
In [88]: %timeit ind = np.lexsort(a.T); a[np.concatenate(([True], np.any(a[ind[1:]]!= a[ind[:-1]], axis=1)))]
10000 loops, best of 3: 37.6 us per loop
In [89]: %timeit b = [tuple(row) for row in a]; np.unique(b)
10000 loops, best of 3: 41.6 us per loop
With a larger a, however, this version ends up being much, much faster:
In [96]: a = np.random.randint(0,2,size=(10000,6))
In [97]: %timeit unique(a.view(dtype)).view('<i8')
10 loops, best of 3: 24.4 ms per loop
In [98]: %timeit b = [tuple(row) for row in a]; np.unique(b)
10 loops, best of 3: 28.2 ms per loop
In [99]: %timeit ind = np.lexsort(a.T); a[np.concatenate(([True],np.any(a[ind[1:]]!= a[ind[:-1]],axis=1)))]
100 loops, best of 3: 3.25 ms per loop
I've compared the suggested alternative for speed and found that, surprisingly, the void view unique solution is even a bit faster than numpy's native unique with the axis argument. If you're looking for speed, you'll want
numpy.unique(
a.view(numpy.dtype((numpy.void, a.dtype.itemsize*a.shape[1])))
).view(a.dtype).reshape(-1, a.shape[1])
I've implemented that fastest variant in npx.unique_rows.
There is a bug report on GitHub for this, too.
Code to reproduce the plot:
import numpy
import perfplot
def unique_void_view(a):
return (
numpy.unique(a.view(numpy.dtype((numpy.void, a.dtype.itemsize * a.shape[1]))))
.view(a.dtype)
.reshape(-1, a.shape[1])
)
def lexsort(a):
ind = numpy.lexsort(a.T)
return a[
ind[numpy.concatenate(([True], numpy.any(a[ind[1:]] != a[ind[:-1]], axis=1)))]
]
def vstack(a):
return numpy.vstack([tuple(row) for row in a])
def unique_axis(a):
return numpy.unique(a, axis=0)
perfplot.show(
setup=lambda n: numpy.random.randint(2, size=(n, 20)),
kernels=[unique_void_view, lexsort, vstack, unique_axis],
n_range=[2 ** k for k in range(15)],
xlabel="len(a)",
equality_check=None,
)
Here is another variation for #Greg pythonic answer
np.vstack(set(map(tuple, a)))
I didn’t like any of these answers because none handle floating-point arrays in a linear algebra or vector space sense, where two rows being “equal” means “within some 𝜀”. The one answer that has a tolerance threshold, https://stackoverflow.com/a/26867764/500207, took the threshold to be both element-wise and decimal precision, which works for some cases but isn’t as mathematically general as a true vector distance.
Here’s my version:
from scipy.spatial.distance import squareform, pdist
def uniqueRows(arr, thresh=0.0, metric='euclidean'):
"Returns subset of rows that are unique, in terms of Euclidean distance"
distances = squareform(pdist(arr, metric=metric))
idxset = {tuple(np.nonzero(v)[0]) for v in distances <= thresh}
return arr[[x[0] for x in idxset]]
# With this, unique columns are super-easy:
def uniqueColumns(arr, *args, **kwargs):
return uniqueRows(arr.T, *args, **kwargs)
The public-domain function above uses scipy.spatial.distance.pdist to find the Euclidean (customizable) distance between each pair of rows. Then it compares each each distance to a threshold to find the rows that are within thresh of each other, and returns just one row from each thresh-cluster.
As hinted, the distance metric needn’t be Euclidean—pdist can compute sundry distances including cityblock (Manhattan-norm) and cosine (the angle between vectors).
If thresh=0 (the default), then rows have to be bit-exact to be considered “unique”. Other good values for thresh use scaled machine-precision, i.e., thresh=np.spacing(1)*1e3.
Why not use drop_duplicates from pandas:
>>> timeit pd.DataFrame(image.reshape(-1,3)).drop_duplicates().values
1 loops, best of 3: 3.08 s per loop
>>> timeit np.vstack({tuple(r) for r in image.reshape(-1,3)})
1 loops, best of 3: 51 s per loop
The numpy_indexed package (disclaimer: I am its author) wraps the solution posted by Jaime in a nice and tested interface, plus many more features:
import numpy_indexed as npi
new_a = npi.unique(a) # unique elements over axis=0 (rows) by default
Based on the answer in this page I have written a function that replicates the capability of MATLAB's unique(input,'rows') function, with the additional feature to accept tolerance for checking the uniqueness. It also returns the indices such that c = data[ia,:] and data = c[ic,:]. Please report if you see any discrepancies or errors.
def unique_rows(data, prec=5):
import numpy as np
d_r = np.fix(data * 10 ** prec) / 10 ** prec + 0.0
b = np.ascontiguousarray(d_r).view(np.dtype((np.void, d_r.dtype.itemsize * d_r.shape[1])))
_, ia = np.unique(b, return_index=True)
_, ic = np.unique(b, return_inverse=True)
return np.unique(b).view(d_r.dtype).reshape(-1, d_r.shape[1]), ia, ic
Beyond #Jaime excellent answer, another way to collapse a row is to uses a.strides[0] (assuming a is C-contiguous) which is equal to a.dtype.itemsize*a.shape[0]. Furthermore void(n) is a shortcut for dtype((void,n)). we arrive finally to this shortest version :
a[unique(a.view(void(a.strides[0])),1)[1]]
For
[[0 1 1 1 0 0]
[1 1 1 0 0 0]
[1 1 1 1 1 0]]
np.unique works given a list of tuples:
>>> np.unique([(1, 1), (2, 2), (3, 3), (4, 4), (2, 2)])
Out[9]:
array([[1, 1],
[2, 2],
[3, 3],
[4, 4]])
With a list of lists it raises a TypeError: unhashable type: 'list'
For general purpose like 3D or higher multidimensional nested arrays, try this:
import numpy as np
def unique_nested_arrays(ar):
origin_shape = ar.shape
origin_dtype = ar.dtype
ar = ar.reshape(origin_shape[0], np.prod(origin_shape[1:]))
ar = np.ascontiguousarray(ar)
unique_ar = np.unique(ar.view([('', origin_dtype)]*np.prod(origin_shape[1:])))
return unique_ar.view(origin_dtype).reshape((unique_ar.shape[0], ) + origin_shape[1:])
which satisfies your 2D dataset:
a = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
unique_nested_arrays(a)
gives:
array([[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
But also 3D arrays like:
b = np.array([[[1, 1, 1], [0, 1, 1]],
[[0, 1, 1], [1, 1, 1]],
[[1, 1, 1], [0, 1, 1]],
[[1, 1, 1], [1, 1, 1]]])
unique_nested_arrays(b)
gives:
array([[[0, 1, 1], [1, 1, 1]],
[[1, 1, 1], [0, 1, 1]],
[[1, 1, 1], [1, 1, 1]]])
None of these answers worked for me. I'm assuming as my unique rows contained strings and not numbers. However this answer from another thread did work:
Source: https://stackoverflow.com/a/38461043/5402386
You can use .count() and .index() list's methods
coor = np.array([[10, 10], [12, 9], [10, 5], [12, 9]])
coor_tuple = [tuple(x) for x in coor]
unique_coor = sorted(set(coor_tuple), key=lambda x: coor_tuple.index(x))
unique_count = [coor_tuple.count(x) for x in unique_coor]
unique_index = [coor_tuple.index(x) for x in unique_coor]
We can actually turn m x n numeric numpy array into m x 1 numpy string array, please try using the following function, it provides count, inverse_idx and etc, just like numpy.unique:
import numpy as np
def uniqueRow(a):
#This function turn m x n numpy array into m x 1 numpy array storing
#string, and so the np.unique can be used
#Input: an m x n numpy array (a)
#Output unique m' x n numpy array (unique), inverse_indx, and counts
s = np.chararray((a.shape[0],1))
s[:] = '-'
b = (a).astype(np.str)
s2 = np.expand_dims(b[:,0],axis=1) + s + np.expand_dims(b[:,1],axis=1)
n = a.shape[1] - 2
for i in range(0,n):
s2 = s2 + s + np.expand_dims(b[:,i+2],axis=1)
s3, idx, inv_, c = np.unique(s2,return_index = True, return_inverse = True, return_counts = True)
return a[idx], inv_, c
Example:
A = np.array([[ 3.17 9.502 3.291],
[ 9.984 2.773 6.852],
[ 1.172 8.885 4.258],
[ 9.73 7.518 3.227],
[ 8.113 9.563 9.117],
[ 9.984 2.773 6.852],
[ 9.73 7.518 3.227]])
B, inv_, c = uniqueRow(A)
Results:
B:
[[ 1.172 8.885 4.258]
[ 3.17 9.502 3.291]
[ 8.113 9.563 9.117]
[ 9.73 7.518 3.227]
[ 9.984 2.773 6.852]]
inv_:
[3 4 1 0 2 4 0]
c:
[2 1 1 1 2]
Lets get the entire numpy matrix as a list, then drop duplicates from this list, and finally return our unique list back into a numpy matrix:
matrix_as_list=data.tolist()
matrix_as_list:
[[1, 1, 1, 0, 0, 0], [0, 1, 1, 1, 0, 0], [0, 1, 1, 1, 0, 0], [1, 1, 1, 0, 0, 0], [1, 1, 1, 1, 1, 0]]
uniq_list=list()
uniq_list.append(matrix_as_list[0])
[uniq_list.append(item) for item in matrix_as_list if item not in uniq_list]
unique_matrix=np.array(uniq_list)
unique_matrix:
array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 1, 1, 0]])
The most straightforward solution is to make the rows a single item by making them strings. Each row then can be compared as a whole for its uniqueness using numpy. This solution is generalize-able you just need to reshape and transpose your array for other combinations. Here is the solution for the problem provided.
import numpy as np
original = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
uniques, index = np.unique([str(i) for i in original], return_index=True)
cleaned = original[index]
print(cleaned)
Will Give:
array([[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
Send my nobel prize in the mail
import numpy as np
original = np.array([[1, 1, 1, 0, 0, 0],
[0, 1, 1, 1, 0, 0],
[0, 1, 1, 1, 0, 0],
[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0]])
# create a view that the subarray as tuple and return unique indeies.
_, unique_index = np.unique(original.view(original.dtype.descr * original.shape[1]),
return_index=True)
# get unique set
print(original[unique_index])
Related
I have an example array that looks like array = np.array([[1,1,0,1], [0,1,0,0], [1,1,1,0], [0,0,1,2], [0,1,3,2], [1,1,0,1], [0,1,0,0]]) ...
array([[1, 1, 0, 1],
[0, 1, 0, 0],
[1, 1, 1, 0],
[0, 0, 1, 2],
[0, 1, 3, 2],
[1, 1, 0, 1],
[0, 1, 0, 0]])
With this in mind I want reformat this array into subarrays based off of the first two columns. Using How to split a numpy array based on a column? as a reference, I made this array into a list of arrays with ...
df = pd.DataFrame(array)
df['4'] = df[0].astype(str) + df[1].astype(str)
df['4'] = df['4'].astype(int)
arr = df.to_numpy()
y = [arr[arr[:,4]==k] for k in np.unique(arr[:,4])]
where y is ...
[array([[0, 0, 1, 2, 0]]),
array([[0, 1, 0, 0, 1],
[0, 1, 3, 2, 1],
[0, 1, 0, 0, 1]]),
array([[ 1, 1, 0, 1, 11],
[ 1, 1, 1, 0, 11],
[ 1, 1, 0, 1, 11]])]
This works fine but it takes far too long for y to run. The amount of time it takes increases exponentially with every row. I am playing around with hundreds of millions of rows and y = [arr[arr[:,4]==k] for k in np.unique(arr[:,4])] is not practical from a time standpoint.
Any ideas on how to speed this up?
What about using the numpy_indexed library:
import numpy as np
import numpy_indexed as npi
a = np.array([[1, 1, 0, 1],
[0, 1, 0, 0],
[1, 1, 1, 0],
[0, 0, 1, 2],
[0, 1, 3, 2],
[1, 1, 0, 1],
[0, 1, 0, 0]])
key = np.dot(a[:,:2], [1, 10])
y = npi.group_by(key).split_array_as_list(arr)
Output
y
[array([[0, 0, 1, 2]]),
array([[0, 1, 0, 0],
[0, 1, 3, 2],
[0, 1, 0, 0]]),
array([[ 1, 1, 0, 1],
[ 1, 1, 1, 0],
[ 1, 1, 0, 1]])]
You can easily install the library with:
> pip install numpy-indexed
Let me know if this performs better,
from collections import defaultdict
import numpy as np
outgen = defaultdict(lambda: [])
# arr: The input numpy array, :type: np.ndarray.
c = map(lambda x: ((x[0], x[1]), x), arr)
for key, val in c:
outgen[key].append(val)
# outgen: The required output, :type: list[np.ndarray].
outgen = [np.array(x) for x in outgen.values()]
You can use np.unique directly here.
unique, indexer = np.unique(arr[:, :2], axis=0, return_inverse=True)
{i: arr[indexer == k, :] for i, k in enumerate(unique)}
This is probably about as good as it gets for your desired output. However, instead of splitting it into a list of subarrays you could sort it by the unique key and then work with slices. This might be helpful if there are many unique values leading to a long list.
arr[:] = arr[np.argsort(indexer), :] # not sure if this is guaranteed to preserve the order within each group
EDIT:
Here is a powerful solution which I have been using for a sort of 2-D factorization. It takes 8ms for 1 million rows of single digit integers (vs > 100ms for np.unique).
columns = x[:, 0], x[:, 1]
factored = map(pd.factorize, columns)
codes, unique_values = map(list, zip(*factored))
group_index = get_group_index(codes, map(len, unique_values), sort=False, xnull=False)
It uses the internal algorithm of Dataframe.drop_duplicates.
Note that the ordering of the keys is not the sort order of the unique tuples.
There is also a new open source library, riptable which emulates numpy and pandas in some ways but is can be a lot more powerful. The creation of th takes around 4ms
import riptable as rt
columns = [x[:, 0], x[:, 1]]
unique_values, key = rt.unique(columns, return_inverse=True)
Here, unique_values is a tuple containing two arrays which can be zipped to get the unique tuples
In the code that I am writing, I have three 2D numpy arrays with the same dimensions (m x n), with each 2D array containing info about a specific trait, but each corresponding cell (with a specific row/col value) across all three 2D arrays corresponding to a specific person. The three 2D arrays are trait1, trait2, and trait3. As an example, person (0, 0) will have traits 1, 2, but not three, if only trait1 and trait2 have a value of 1 at location (0,0), but trait3 does not.
What would be an efficient method of updating a 2D array at a specific location based on the values of other corresponding 2D arrays of the same dimension at the same location? That is, how can I efficiently update a 2D array at a specific location such that the other 2D arrays at this same location fulfill specific conditions?
I am currently trying to update the values of the 2D array trait1 and trait2 according to the current values of trait1 and trait2 (such that the corresponding trait1 value == 1, and the corresponding trait2 value == 0); I am also trying to update the values of trait3 according to the current values of trait1, and trait2 (under the same conditions as the previous). However, I am having trouble doing this without using nested for loops, which greatly slows down my program.
Below is my current approach, which works, but is much too slow for my purposes:
for i in range (0, m):
for j in range (0, n):
if trait1[i][j] == 1:
if trait2[i][j] == 0:
trait1[i][j] = 0
trait2[i][j] = 1
new_color(i, j, 1) #updates the color of the specific person on a grid
trait3[i][j] = 0
elif trait1[i][j] == 0:
if trait2[i][j] <= 0:
trait1[i][j] = 1
trait2[i][j] = 0
new_color(i, j, 0)
Numpy array are really slow if you use loop indeed. If you can use matrices operations / numpy function for everything, it will go much faster.
In your case, you could first extract the indices you're interested about, and then update your matrices like this:
import numpy as np
np.random.seed(1)
# Generate some sample data
trait1, trait2, trait3 = ( np.random.randint(0,2, [4,4]) for _ in range(3) )
In [4]: trait1
Out[4]:
array([[1, 1, 0, 0],
[1, 1, 1, 1],
[1, 0, 0, 1],
[0, 1, 1, 0]])
In [5]: trait2
Out[5]:
array([[0, 1, 0, 0],
[0, 1, 0, 0],
[1, 0, 0, 0],
[1, 0, 0, 0]])
In [6]: trait3
Out[6]:
array([[1, 1, 1, 1],
[1, 0, 0, 0],
[1, 1, 1, 1],
[1, 1, 0, 1]])
And then:
cond1_idx = np.where((trait1 == 1) & (trait2==0))
cond2_idx = np.where((trait1 == 0) & (trait2<=0))
trait1[cond1_idx] = 0
trait2[cond1_idx] = 1
trait3[cond1_idx] = 0
[ new_color(i, j, 1) for i,j in zip(*cond1_idx) ]
trait1[cond2_idx] = 1
trait2[cond2_idx] = 0
[ new_color(i, j, 0) for i,j in zip(*cond2_idx) ]
Result:
In [2]: trait1
Out[2]:
array([[0, 1, 1, 1],
[0, 1, 0, 0],
[1, 1, 1, 0],
[0, 0, 0, 1]])
In [3]: trait2
Out[3]:
array([[1, 1, 0, 0],
[1, 1, 1, 1],
[1, 0, 0, 1],
[1, 1, 1, 0]])
In [4]: trait3
Out[4]:
array([[0, 1, 1, 1],
[0, 0, 0, 0],
[1, 1, 1, 0],
[1, 0, 0, 1]])
I cannot really test the new_color though since I don't have the function
I have a numpy array of various one hot encoded numpy arrays, eg;
x = np.array([[1, 0, 0], [0, 0, 1], [1, 0, 0]])
I would like to count the occurances of each unique one hot vector,
{[1, 0, 0]: 2, [0, 0, 1]: 1}
Approach #1
Seems like a perfect setup to use the new functionality of numpy.unique (v1.13 and newer) that lets us work along an axis of a NumPy array -
unq_rows, count = np.unique(x,axis=0, return_counts=1)
out = {tuple(i):j for i,j in zip(unq_rows,count)}
Sample outputs -
In [289]: unq_rows
Out[289]:
array([[0, 0, 1],
[1, 0, 0]])
In [290]: count
Out[290]: array([1, 2])
In [291]: {tuple(i):j for i,j in zip(unq_rows,count)}
Out[291]: {(0, 0, 1): 1, (1, 0, 0): 2}
Approach #2
For NumPy versions older than v1.13, we can make use of the fact that the input array is one-hot encoded array, like so -
_, idx, count = np.unique(x.argmax(1), return_counts=1, return_index=1)
out = {tuple(i):j for i,j in zip(x[idx],count)} # x[idx] is unq_rows
You could convert your arrays to tuples and use a Counter:
import numpy as np
from collections import Counter
x = np.array([[1, 0, 0], [0, 0, 1], [1, 0, 0]])
Counter([tuple(a) for a in x])
# Counter({(1, 0, 0): 2, (0, 0, 1): 1})
The fastest way given your data format is:
x.sum(axis=0)
which gives:
array([2, 0, 1])
Where the 1st result is the count of arrays where the 1st is hot:
[1, 0, 0] [2
[0, 1, 0] 0
[0, 0, 1] 1]
This exploits the fact that only one can be on at a time, so we can decompose the direct sum.
If you absolutely need it expanded to the same format, it can be converted via:
sums = x.sum(axis=0)
{tuple(int(k == i) for k in range(len(sums))): e for i, e in enumerate(sums)}
or, similarly to tarashypka:
{tuple(row): count for row, count in zip(np.eye(len(sums), dtype=np.int64), sums)}
yields:
{(1, 0, 0): 2, (0, 1, 0): 0, (0, 0, 1): 1}
Here is another interesting solution with sum
>> {tuple(v): n for v, n in zip(np.eye(x.shape[1], dtype=int), np.sum(x, axis=0))
if n > 0}
{(0, 0, 1): 1, (1, 0, 0): 2}
Lists (including numpy arrays) are unhashable, i.e. they can't be keys of a dictionary. So your precise desired output, a dictionary with keys that look like [1, 0, 0] is never possible in Python. To deal with this you need to map your vectors to tuples.
from collections import Counter
import numpy as np
x = np.array([[1, 0, 0], [0, 0, 1], [1, 0, 0]])
counts = Counter(map(tuple, x))
That will get you:
In [12]: counts
Out[12]: Counter({(0, 0, 1): 1, (1, 0, 0): 2})
I am working on an image analysis project. I have gotten my picture of interest (a NxM numpy array) to a binary format. The '1' in the matrix are regions of interest. There are regions of interest, and there is noise that cannot possibly represent features on an image. For example, in a horizontal snap of the image, isolated 1's, or groups of 2 up to, say, 5 consecutive 1's are not of interest to me. I would like to find a quick way to flip these (i.e make them =0).
my MWE for flipping isolated 1's:
import numpy as np
img = np.random.choice([0,1],size=(1000,1000), p=[1./2,1./2])
#now we take the second derivative of the matrix in the horizontal axis
#since we have a binary matrix, an isolated 1, that is [...010...] is captured
#by a second derivative entry equal to -2
#because ([...010...]->dx->[...1,-1,...]->dx->[...-2...]
ddx_img = np.diff(np.diff(img,1),1)
to_flip = np.where(ddx_img==-2) #returns a tuple of [x,y] matrix entries
# the second derivative eats up an index position on horizontally, so I need to add
# +1 to the horizontal axis of the tuple
temp_copy = to_flip[1].copy() #cannot modify tuple directly, for some reason its read only
temp_copy+=1
to_flip = (to_flip[0],temp_copy)
#now we can flip the entries by adding +1 to the entries to flip and taking mod 2
img[to_flip]=mod(img[to_flip]+1,2)
This takes around 9ms on my machine. I could do with routines of up to 1 second.
I would welcome any criticism on the code ( I am not a good python programmer ), and any ideas on how to efficiently extend this procedure to eliminate isolated islands of consecutive 1s up to islands of generic size S.
Thanks in advance
edit: I realize the mod is unnecessary. At the time I did this I wanted also to flip too small islands of 0's. One could replace the =mod.... by =0
Question-specific case
After the edits, it seems you could use some slicing and thus avoid making intermediate copies for some performance improvement. Here's two-lines of codes to achieve the desired output -
# Calculate second derivative
ddx_img = np.diff(np.diff(img,1),1)
# Get sliced version of img excluding the first and last columns
# and use mask with ddx elements as "-2" to zeros
img[:,1:-1][ddx_img==-2] = 0
Runtime tests and verify results -
In [42]: A = np.random.choice([0,1],size=(1000,1000), p=[1./2,1./2])
In [43]: def slicing_based(A):
...: img = A.copy()
...: ddx_img = np.diff(np.diff(img,1),1)
...: img[:,1:-1][ddx_img==-2] = 0
...: return img
...:
...:
...: def original_approach(A):
...:
...: img = A.copy()
...:
...: ddx_img = np.diff(np.diff(img,1),1)
...: to_flip = np.where(ddx_img==-2)
...:
...: temp_copy = to_flip[1].copy()
...: temp_copy+=1
...: to_flip = (to_flip[0],temp_copy)
...:
...: img[to_flip] = 0
...:
...: return img
...:
In [44]: %timeit slicing_based(A)
100 loops, best of 3: 15.3 ms per loop
In [45]: %timeit original_approach(A)
10 loops, best of 3: 20.1 ms per loop
In [46]: np.allclose(slicing_based(A),original_approach(A))
Out[46]: True
Generic case
To make the solution generic, one can use some signal processing, specifically 2D convolution as shown here -
# Define kernel
K1 = np.array([[0,1,1,0]]) # Edit this for different island lengths
K2 = 1-K1
# Generate masks of same shape as img amd based on TRUE and inverted versions of
# kernels being convolved and those convolved sums being compared against the
# kernel sums indicating those spefic positions have fulfiled both the ONES
# and ZEROS criteria
mask1 = convolve2d(img, K1, boundary='fill',fillvalue=0, mode='same')==K1.sum()
mask2 = convolve2d(img==0, K2, boundary='fill',fillvalue=0, mode='same')==K2.sum()
# Use a combined mask to create that expanses through the kernel length
# and use it to set those in img to zeros
K3 = np.ones((1,K1.size))
mask3 = convolve2d(mask1 & mask2, K3, boundary='fill',fillvalue=0, mode='same')>0
img_out = img*(~mask3)
Sample input, output -
In [250]: img
Out[250]:
array([[0, 1, 1, 1, 0, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 0, 1],
[1, 0, 1, 1, 1, 1, 0, 0],
[1, 1, 1, 1, 0, 1, 0, 1],
[1, 1, 0, 1, 1, 0, 1, 1],
[1, 0, 1, 1, 1, 1, 1, 1],
[1, 1, 0, 1, 1, 0, 1, 0],
[1, 1, 1, 0, 1, 1, 1, 1]])
In [251]: img_out
Out[251]:
array([[0, 1, 1, 1, 0, 1, 1, 1],
[1, 1, 1, 1, 1, 1, 0, 1],
[1, 0, 1, 1, 1, 1, 0, 0],
[1, 1, 1, 1, 0, 1, 0, 1],
[1, 1, 0, 0, 0, 0, 0, 1],
[1, 0, 1, 1, 1, 1, 1, 1],
[1, 1, 0, 0, 0, 0, 0, 0],
[1, 1, 1, 0, 1, 1, 1, 1]])
I am trying to count a number each row shows in a np.array, for example:
import numpy as np
my_array = np.array([[1, 2, 0, 1, 1, 1],
[1, 2, 0, 1, 1, 1], # duplicate of row 0
[9, 7, 5, 3, 2, 1],
[1, 1, 1, 0, 0, 0],
[1, 2, 0, 1, 1, 1], # duplicate of row 0
[1, 1, 1, 1, 1, 0]])
Row [1, 2, 0, 1, 1, 1] shows up 3 times.
A simple naive solution would involve converting all my rows to tuples, and applying collections.Counter, like this:
from collections import Counter
def row_counter(my_array):
list_of_tups = [tuple(ele) for ele in my_array]
return Counter(list_of_tups)
Which yields:
In [2]: row_counter(my_array)
Out[2]: Counter({(1, 2, 0, 1, 1, 1): 3, (1, 1, 1, 1, 1, 0): 1, (9, 7, 5, 3, 2, 1): 1, (1, 1, 1, 0, 0, 0): 1})
However, I am concerned about the efficiency of my approach. And maybe there is a library that provides a built-in way of doing this. I tagged the question as pandas because I think that pandas might have the tool I am looking for.
You can use the answer to this other question of yours to get the counts of the unique items.
In numpy 1.9 there is a return_counts optional keyword argument, so you can simply do:
>>> my_array
array([[1, 2, 0, 1, 1, 1],
[1, 2, 0, 1, 1, 1],
[9, 7, 5, 3, 2, 1],
[1, 1, 1, 0, 0, 0],
[1, 2, 0, 1, 1, 1],
[1, 1, 1, 1, 1, 0]])
>>> dt = np.dtype((np.void, my_array.dtype.itemsize * my_array.shape[1]))
>>> b = np.ascontiguousarray(my_array).view(dt)
>>> unq, cnt = np.unique(b, return_counts=True)
>>> unq = unq.view(my_array.dtype).reshape(-1, my_array.shape[1])
>>> unq
array([[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0],
[1, 2, 0, 1, 1, 1],
[9, 7, 5, 3, 2, 1]])
>>> cnt
array([1, 1, 3, 1])
In earlier versions, you can do it as:
>>> unq, _ = np.unique(b, return_inverse=True)
>>> cnt = np.bincount(_)
>>> unq = unq.view(my_array.dtype).reshape(-1, my_array.shape[1])
>>> unq
array([[1, 1, 1, 0, 0, 0],
[1, 1, 1, 1, 1, 0],
[1, 2, 0, 1, 1, 1],
[9, 7, 5, 3, 2, 1]])
>>> cnt
array([1, 1, 3, 1])
I think just specifying axis in np.unique gives what you need.
import numpy as np
unq, cnt = np.unique(my_array, axis=0, return_counts=True)
Note: this feature is available only in numpy>=1.13.0.
(This assumes that the array is fairly small, e.g. fewer than 1000 rows.)
Here's a short NumPy way to count how many times each row appears in an array:
>>> (my_array[:, np.newaxis] == my_array).all(axis=2).sum(axis=1)
array([3, 3, 1, 1, 3, 1])
This counts how many times each row appears in my_array, returning an array where the first value shows how many times the first row appears, the second value shows how many times the second row appears, and so on.
A pandas approach might look like this
import pandas as pd
df = pd.DataFrame(my_array,columns=['c1','c2','c3','c4','c5','c6'])
df.groupby(['c1','c2','c3','c4','c5','c6']).size()
Note: supplying column names is not necessary
You solution is not bad, but if your matrix is large you will probably want to use a more efficient hash (compared to the default one Counter uses) for the rows before counting. You can do that with joblib:
A = np.random.rand(5, 10000)
%timeit (A[:,np.newaxis,:] == A).all(axis=2).sum(axis=1)
10000 loops, best of 3: 132 µs per loop
%timeit Counter(joblib.hash(row) for row in A).values()
1000 loops, best of 3: 1.37 ms per loop
%timeit Counter(tuple(ele) for ele in A).values()
100 loops, best of 3: 3.75 ms per loop
%timeit pd.DataFrame(A).groupby(range(A.shape[1])).size()
1 loops, best of 3: 2.24 s per loop
The pandas solution is extremely slow (about 2s per loop) with this many columns. For a small matrix like the one you showed your method is faster than joblib hashing but slower than numpy:
numpy: 100000 loops, best of 3: 15.1 µs per loop
joblib:1000 loops, best of 3: 885 µs per loop
tuple: 10000 loops, best of 3: 27 µs per loop
pandas: 100 loops, best of 3: 2.2 ms per loop
If you have a large number of rows then you can probably find a better substitute for Counter to find hash frequencies.
Edit: Added numpy benchmarks from #acjr's solution in my system so that it is easier to compare. The numpy solution is the fastest one in both cases.
A solution identical to Jaime's can be found in the numpy_indexed package (disclaimer: I am its author)
import numpy_indexed as npi
npi.count(my_array)