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Use numpy to mask a row containing only zeros

I have a large array of point cloud data which is generated using the azure kinect. All erroneous measurements are assigned the coordinate [0,0,0]. I want to remove all coordinates with the value [0,0,0]. Since my array is rater large (1 million points) and since U need to do this process in real-time, speed is of the essence.
In my current approach I try to use numpy to mask out all rows that contain three zeroes ([0,0,0]). However, the np.ma.masked_equal function does not evaluate an entire row, but only evaluates single elements. As a result, rows that contain at least one 0 are already filtered by this approach. I only want rows to be filtered when all values in the row are 0. Find an example of my code below:
my_data = np.array([[1,2,3],[0,0,0],[3,4,5],[2,5,7],[0,0,1]])
my_data = np.ma.masked_equal(my_data, [0,0,0])
my_data = np.ma.compress_rows(my_data)
output
array([[1, 2, 3],
[3, 4, 5],
[2, 5, 7]])
desired output
array([[1, 2, 3],
[3, 4, 5],
[2, 5, 7],
[0, 0, 1]])`

Find all data points that are 0 (doesn't require np.ma module) and then select all rows that do not contain all zeros:
import numpy as np
my_data = np.array([[1, 2, 3], [0, 0, 0], [3, 4, 5], [2, 5, 7], [0, 0, 1]])
my_data[~(my_data == 0).all(axis= 1)]
Output:
array([[1, 2, 3],
[3, 4, 5],
[2, 5, 7],
[0, 0, 1]])

Instead of using the np.ma.masked_equal and np.ma.compress_rows functions, you can use the np.all function to check if all values in a row are equal to [0, 0, 0]. This should be faster than your method as it evaluates all values in a row at once.
mask = np.all(my_data == [0, 0, 0], axis=1)
my_data = my_data[~mask]

How would I achieve this "row in A * all rows in B by col in A" multiplication in NumPy without a loop?

Say I have two matrices, A and B:
A = np.array([[1, 3, 2],
[2, 2, 3],
[3, 1, 1]])
B = np.array([[0, 1, 0],
[1, 1, 0],
[1, 1, 1]])
I want to take one column in A and multiply it by each column in B element-wise, then proceed to the next column in A. So, using just one column as an example, I will use A[:,0] (values 1,2,3), and multiply it by each column in B to get this:
array([[0, 1, 0],
[2, 2, 0],
[3, 3, 3]])
I've implemented this using np.einsum like so:
np.einsum('i,ij->ij',A[:,0],B)
I then want to generate a 3D matrix with the depth dimension corresponding to the multiplication by each column in A, which I implemented using a for loop:
np.stack([np.einsum('i,ij->ij',A[:,i],B) for i in range(0,A.shape[1])])
This returns my desired array:
array([[[0, 1, 0],
[2, 2, 0],
[3, 3, 3]],
[[0, 3, 0],
[2, 2, 0],
[1, 1, 1]],
[[0, 2, 0],
[3, 3, 0],
[1, 1, 1]]])
How would I go about doing this without the loop? Can this be done purely with np.einsum? Is there another function in NumPy that will do this more simply?

Here's a simple way:
A.T[:,:,None]*B
adding the last None in indexing creates a new axis which is then used for broadcasting the elementwise multiplication.

How about this code?
A.T.reshape(3, 3, 1) * B
Reshaping ndarray can make doing many things...

Keeping with your usage of einsum:
np.einsum('ij,ik->jik', A, B)

Replace numpy subarray when element matches a condition

I have an n x m x 3 numpy array. This represents a middle-step towards an RGB representation of a complex-function plotter. When the function being plotted takes infinite values or has singularities, parts of the RGB data become NaNs.
I'm looking for an efficient way to replace a row containing a NaN with a row of my choice, perhaps [0, 0, 0] or [1, 1, 1]. In terms of the RGB values, this has the effect of replacing poorly-behaving pixels with white or black pixels. By efficient, I mean some way that takes advantage of numpy's vectorization and speed.
Please note that I am not looking to merely replace the NaN values with 0 (which I know how to do with numpy.where); if a row contains a NaN, I want to replace the whole row. I suspect this can be done nicely in numpy, but I'm not sure how.
Concrete Question
Suppose we are given a 2 x 2 x 3 array arr. If a row contains a 5, I want to replace the row with [0, 0, 0]. Trivial code that does this slowly is as follows.
import numpy as np
arr = np.array([[[1, 2, 3], [4, 5, 6]], [[1, 3, 5], [2, 4, 6]]])
# so arr is
# array([[[1, 2, 3],
# [4, 5, 6]],
#
# [[1, 3, 5],
# [2, 4, 6]]])
# Trivial and slow version to replace rows containing 5 with [0,0,0]
for i in range(len(arr)):
for j in range(len(arr[i])):
if 5 in arr[i][j]:
arr[i][j] = np.array([0, 0, 0])
# Now arr is
#
# array([[[1, 2, 3],
# [0, 0, 0]],
#
# [[0, 0, 0],
# [2, 4, 6]]])
How can we accomplish this taking advantage of numpy?

A simpler way would be -
arr[np.isin(arr,5).any(-1)] = 0
If it's just a single value that you are looking for, then we could simplify to -
arr[(arr==5).any(-1)] = 0
If you are looking to match against NaN, we need to do the comparison differently and use np.isnan instead -
arr[np.isnan(arr).any(-1)] = 0
If you are looking to assign array values, instead of just 0, the solutions stay the same. Hence it would be -
arr[(arr==5).any(-1)] = new_array

Using np.broadcast_to
arr[np.broadcast_to((arr == 5).any(-1)[..., None], arr.shape)] = 0
array([[[1, 2, 3],
[0, 0, 0]],
[[0, 0, 0],
[2, 4, 6]]])
Just as FYI, based on your description, if you want to find np.nans instead of integers like 5, you shouldn't use ==, but rather np.isnan
arr[np.broadcast_to((np.isnan(arr)).any(-1)[..., None], arr.shape)] = 0

you can do it using in1d function like below
arr = np.array([[[1, 2, 3], [4, 5, 6]], [[1, 3, 5], [2, 4, 6]]])
arr[np.in1d(arr,5).reshape(arr.shape).any(axis=2)] = [0,0,0]
arr

vectorize upper level of a vectoized code - python - numpy [duplicate]

I have an array X:
X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
And I wish to find the index of the row of several values in this array:
searched_values = np.array([[4, 2],
[3, 3],
[5, 6]])
For this example I would like a result like:
[0,3,4]
I have a code doing this, but I think it is overly complicated:
X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
searched_values = np.array([[4, 2],
[3, 3],
[5, 6]])
result = []
for s in searched_values:
idx = np.argwhere([np.all((X-s)==0, axis=1)])[0][1]
result.append(idx)
print(result)
I found this answer for a similar question but it works only for 1d arrays.
Is there a way to do what I want in a simpler way?

Approach #1
One approach would be to use NumPy broadcasting, like so -
np.where((X==searched_values[:,None]).all(-1))[1]
Approach #2
A memory efficient approach would be to convert each row as linear index equivalents and then using np.in1d, like so -
dims = X.max(0)+1
out = np.where(np.in1d(np.ravel_multi_index(X.T,dims),\
np.ravel_multi_index(searched_values.T,dims)))[0]
Approach #3
Another memory efficient approach using np.searchsorted and with that same philosophy of converting to linear index equivalents would be like so -
dims = X.max(0)+1
X1D = np.ravel_multi_index(X.T,dims)
searched_valuesID = np.ravel_multi_index(searched_values.T,dims)
sidx = X1D.argsort()
out = sidx[np.searchsorted(X1D,searched_valuesID,sorter=sidx)]
Please note that this np.searchsorted method assumes there is a match for each row from searched_values in X.
How does np.ravel_multi_index work?
This function gives us the linear index equivalent numbers. It accepts a 2D array of n-dimensional indices, set as columns and the shape of that n-dimensional grid itself onto which those indices are to be mapped and equivalent linear indices are to be computed.
Let's use the inputs we have for the problem at hand. Take the case of input X and note the first row of it. Since, we are trying to convert each row of X into its linear index equivalent and since np.ravel_multi_index assumes each column as one indexing tuple, we need to transpose X before feeding into the function. Since, the number of elements per row in X in this case is 2, the n-dimensional grid to be mapped onto would be 2D. With 3 elements per row in X, it would had been 3D grid for mapping and so on.
To see how this function would compute linear indices, consider the first row of X -
In [77]: X
Out[77]:
array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
We have the shape of the n-dimensional grid as dims -
In [78]: dims
Out[78]: array([10, 7])
Let's create the 2-dimensional grid to see how that mapping works and linear indices get computed with np.ravel_multi_index -
In [79]: out = np.zeros(dims,dtype=int)
In [80]: out
Out[80]:
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
Let's set the first indexing tuple from X, i.e. the first row from X into the grid -
In [81]: out[4,2] = 1
In [82]: out
Out[82]:
array([[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]])
Now, to see the linear index equivalent of the element just set, let's flatten and use np.where to detect that 1.
In [83]: np.where(out.ravel())[0]
Out[83]: array([30])
This could also be computed if row-major ordering is taken into account.
Let's use np.ravel_multi_index and verify those linear indices -
In [84]: np.ravel_multi_index(X.T,dims)
Out[84]: array([30, 66, 61, 24, 41])
Thus, we would have linear indices corresponding to each indexing tuple from X, i.e. each row from X.
Choosing dimensions for np.ravel_multi_index to form unique linear indices
Now, the idea behind considering each row of X as indexing tuple of a n-dimensional grid and converting each such tuple to a scalar is to have unique scalars corresponding to unique tuples, i.e. unique rows in X.
Let's take another look at X -
In [77]: X
Out[77]:
array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
Now, as discussed in the previous section, we are considering each row as indexing tuple. Within each such indexing tuple, the first element would represent the first axis of the n-dim grid, second element would be the second axis of the grid and so on until the last element of each row in X. In essence, each column would represent one dimension or axis of the grid. If we are to map all elements from X onto the same n-dim grid, we need to consider the maximum stretch of each axis of such a proposed n-dim grid. Assuming we are dealing with positive numbers in X, such a stretch would be the maximum of each column in X + 1. That + 1 is because Python follows 0-based indexing. So, for example X[1,0] == 9 would map to the 10th row of the proposed grid. Similarly, X[4,1] == 6 would go to the 7th column of that grid.
So, for our sample case, we had -
In [7]: dims = X.max(axis=0) + 1 # Or simply X.max(0) + 1
In [8]: dims
Out[8]: array([10, 7])
Thus, we would need a grid of at least a shape of (10,7) for our sample case. More lengths along the dimensions won't hurt and would give us unique linear indices too.
Concluding remarks : One important thing to be noted here is that if we have negative numbers in X, we need to add proper offsets along each column in X to make those indexing tuples as positive numbers before using np.ravel_multi_index.

Another alternative is to use asvoid (below) to view each row as a single
value of void dtype. This reduces a 2D array to a 1D array, thus allowing you to use np.in1d as usual:
import numpy as np
def asvoid(arr):
"""
Based on http://stackoverflow.com/a/16973510/190597 (Jaime, 2013-06)
View the array as dtype np.void (bytes). The items along the last axis are
viewed as one value. This allows comparisons to be performed which treat
entire rows as one value.
"""
arr = np.ascontiguousarray(arr)
if np.issubdtype(arr.dtype, np.floating):
""" Care needs to be taken here since
np.array([-0.]).view(np.void) != np.array([0.]).view(np.void)
Adding 0. converts -0. to 0.
"""
arr += 0.
return arr.view(np.dtype((np.void, arr.dtype.itemsize * arr.shape[-1])))
X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
searched_values = np.array([[4, 2],
[3, 3],
[5, 6]])
idx = np.flatnonzero(np.in1d(asvoid(X), asvoid(searched_values)))
print(idx)
# [0 3 4]

The numpy_indexed package (disclaimer: I am its author) contains functionality for performing such operations efficiently (also uses searchsorted under the hood). In terms of functionality, it acts as a vectorized equivalent of list.index:
import numpy_indexed as npi
result = npi.indices(X, searched_values)
Note that using the 'missing' kwarg, you have full control over behavior of missing items, and it works for nd-arrays (fi; stacks of images) as well.
Update: using the same shapes as #Rik X=[520000,28,28] and searched_values=[20000,28,28], it runs in 0.8064 secs, using missing=-1 to detect and denote entries not present in X.

Here is a pretty fast solution that scales up well using numpy and hashlib. It can handle large dimensional matrices or images in seconds. I used it on 520000 X (28 X 28) array and 20000 X (28 X 28) in 2 seconds on my CPU
Code:
import numpy as np
import hashlib
X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
searched_values = np.array([[4, 2],
[3, 3],
[5, 6]])
#hash using sha1 appears to be efficient
xhash=[hashlib.sha1(row).digest() for row in X]
yhash=[hashlib.sha1(row).digest() for row in searched_values]
z=np.in1d(xhash,yhash)
##Use unique to get unique indices to ind1 results
_,unique=np.unique(np.array(xhash)[z],return_index=True)
##Compute unique indices by indexing an array of indices
idx=np.array(range(len(xhash)))
unique_idx=idx[z][unique]
print('unique_idx=',unique_idx)
print('X[unique_idx]=',X[unique_idx])
Output:
unique_idx= [4 3 0]
X[unique_idx]= [[5 6]
[3 3]
[4 2]]

X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
S = np.array([[4, 2],
[3, 3],
[5, 6]])
result = [[i for i,row in enumerate(X) if (s==row).all()] for s in S]
or
result = [i for s in S for i,row in enumerate(X) if (s==row).all()]
if you want a flat list (assuming there is exactly one match per searched value).

Another way is to use cdist function from scipy.spatial.distance like this:
np.nonzero(cdist(X, searched_values) == 0)[0]
Basically, we get row numbers of X which have distance zero to a row in searched_values, meaning they are equal. Makes sense if you look on rows as coordinates.

I had similar requirement and following worked for me:
np.argwhere(np.isin(X, searched_values).all(axis=1))

Here's what worked out for me:
def find_points(orig: np.ndarray, search: np.ndarray) -> np.ndarray:
equals = [np.equal(orig, p).all(1) for p in search]
exists = np.max(equals, axis=1)
indices = np.argmax(equals, axis=1)
indices[exists == False] = -1
return indices
test:
X = np.array([[4, 2],
[9, 3],
[8, 5],
[3, 3],
[5, 6]])
searched_values = np.array([[4, 2],
[3, 3],
[5, 6],
[0, 0]])
find_points(X, searched_values)
output:
[0,3,4,-1]

How to get a value from every column in a Numpy matrix

I'd like to get the index of a value for every column in a matrix M. For example:
M = matrix([[0, 1, 0],
[4, 2, 4],
[3, 4, 1],
[1, 3, 2],
[2, 0, 3]])
In pseudocode, I'd like to do something like this:
for col in M:
idx = numpy.where(M[col]==0) # Only for columns!
and have idx be 0, 4, 0 for each column.
I have tried to use where, but I don't understand the return value, which is a tuple of matrices.

The tuple of matrices is a collection of items suited for indexing. The output will have the shape of the indexing matrices (or arrays), and each item in the output will be selected from the original array using the first array as the index of the first dimension, the second as the index of the second dimension, and so on. In other words, this:
>>> numpy.where(M == 0)
(matrix([[0, 0, 4]]), matrix([[0, 2, 1]]))
>>> row, col = numpy.where(M == 0)
>>> M[row, col]
matrix([[0, 0, 0]])
>>> M[numpy.where(M == 0)] = 1000
>>> M
matrix([[1000, 1, 1000],
[ 4, 2, 4],
[ 3, 4, 1],
[ 1, 3, 2],
[ 2, 1000, 3]])
The sequence may be what's confusing you. It proceeds in flattened order -- so M[0,2] appears second, not third. If you need to reorder them, you could do this:
>>> row[0,col.argsort()]
matrix([[0, 4, 0]])
You also might be better off using arrays instead of matrices. That way you can manipulate the shape of the arrays, which is often useful! Also note ajcr's transpose-based trick, which is probably preferable to using argsort.
Finally, there is also a nonzero method that does the same thing as where in this case. Using the transpose trick now:
>>> (M == 0).T.nonzero()
(matrix([[0, 1, 2]]), matrix([[0, 4, 0]]))

As an alternative to np.where, you could perhaps use np.argwhere to return an array of indexes where the array meets the condition:
>>> np.argwhere(M == 0)
array([[[0, 0]],
[[0, 2]],
[[4, 1]]])
This tells you each the indexes in the format [row, column] where the condition was met.
If you'd prefer the format of this output array to be grouped by column rather than row, (that is, [column, row]), just use the method on the transpose of the array:
>>> np.argwhere(M.T == 0).squeeze()
array([[0, 0],
[1, 4],
[2, 0]])
I also used np.squeeze here to get rid of axis 1, so that we are left with a 2D array. The sequence you want is the second column, i.e. np.argwhere(M.T == 0).squeeze()[:, 1].

The result of where(M == 0) would look something like this
(matrix([[0, 0, 4]]), matrix([[0, 2, 1]])) First matrix tells you the rows where 0s are and second matrix tells you the columns where 0s are.
Out[4]:
matrix([[0, 1, 0],
[4, 2, 4],
[3, 4, 1],
[1, 3, 2],
[2, 0, 3]])
In [5]: np.where(M == 0)
Out[5]: (matrix([[0, 0, 4]]), matrix([[0, 2, 1]]))
In [6]: M[0,0]
Out[6]: 0
In [7]: M[0,2] #0th row 2nd column
Out[7]: 0
In [8]: M[4,1] #4th row 1st column
Out[8]: 0

This isn't anything new on what's been already suggested, but a one-line solution is:
>>> np.where(np.array(M.T)==0)[-1]
array([0, 4, 0])
(I agree that NumPy matrix objects are more trouble than they're worth).

>>> M = np.array([[0, 1, 0],
... [4, 2, 4],
... [3, 4, 1],
... [1, 3, 2],
... [2, 0, 3]])
>>> [np.where(M[:,i]==0)[0][0] for i in range(M.shape[1])]
[0, 4, 0]