How to properly mask a numpy 2D array?

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Say I have a two dimensional array of coordinates that looks something like

x = array([[1,2],[2,3],[3,4]])

Previously in my work so far, I generated a mask that ends up looking something like

mask = [False,False,True]

When I try to use this mask on the 2D coordinate vector, I get an error

newX =,mask))

>>> Mask and data not compatible: data size 
   is 6, mask size is 3.`

which makes sense, I suppose. So I tried to simply use the following mask instead:

mask2 = np.column_stack((mask,mask))
newX =,mask2))

And what I get is close:


to what I would expect (and want):


There must be an easier way to do this?

Is this what you are looking for?

import numpy as np
# array([[1, 2],
#        [2, 3]])

Or from numpy masked array:

newX =, mask = np.column_stack((mask, mask)))

# masked_array(data =
#  [[1 2]
#  [2 3]
#  [-- --]],
#              mask =
#  [[False False]
#  [False False]
#  [ True  True]],
#        fill_value = 999999)

How to properly mask a numpy 2D array?, Is this what you are looking for? import numpy as np x[~np.array(mask)] # array([[ 1, 2], # [2, 3]]). Or from numpy masked array: ma.count (self [, axis, keepdims]) Count the non-masked elements of the array along the given axis. ma.count_masked (arr [, axis]) Count the number of masked elements along the given axis. ma.getmask (a) Return the mask of a masked array, or nomask.

Your x is 3x2:

In [379]: x
array([[1, 2],
       [2, 3],
       [3, 4]])

Make a 3 element boolean mask:

In [380]: rowmask=np.array([False,False,True])

That can be used to select the rows where it is True, or where it is False. In both cases the result is 2d:

In [381]: x[rowmask,:]
Out[381]: array([[3, 4]])

In [382]: x[~rowmask,:]
array([[1, 2],
       [2, 3]])

This is without using the MaskedArray subclass. To make such array, we need a mask that matches x in shape. There isn't provision for masking just one dimension.

In [393]: xmask=np.stack((rowmask,rowmask),-1)  # column stack

In [394]: xmask
array([[False, False],
       [False, False],
       [ True,  True]], dtype=bool)

In [395]:,xmask)
masked_array(data =
 [[1 2]
 [2 3]
 [-- --]],
             mask =
 [[False False]
 [False False]
 [ True  True]],
       fill_value = 999999)

Applying compressed to that produces a raveled array: array([1, 2, 2, 3])

Since masking is element by element, it could mask one element in row 1, 2 in row 2 etc. So in general compressing, removing the masked elements, will not yield a 2d array. The flattened form is the only general choice. makes most sense when there's a scattering of masked values. It isn't of much value if you want want to select, or deselect, whole rows or columns.


Here are more typical masked arrays:

In [403]:,2,3)
masked_array(data =
 [[1 --]
 [-- --]
 [-- 4]],
             mask =
 [[False  True]
 [ True  True]
 [ True False]],
       fill_value = 999999)

In [404]:,2)
masked_array(data =
 [[1 --]
 [-- 3]
 [3 4]],
             mask =
 [[False  True]
 [ True False]
 [False False]],
       fill_value = 2)

In [406]:,2,3)
masked_array(data =
 [[-- 2]
 [2 3]
 [3 --]],
             mask =
 [[ True False]
 [False False]
 [False  True]],
       fill_value = 999999)

Masking a 2D array and operating on second array based off , How to properly mask a numpy 2D array?, Make a 3 element boolean mask: In [ 380]: rowmask=np.array([False,False,True]). That can be used to select the rows � I have a 3-dimensional array that I want to mask using a 2-dimensional array that has the same dimensions as the two rightmost of the 3-dimensional array. Is there a way to do this without writing

Since none of these solutions worked for me, I thought to write down what solution did, maybe it will useful for somebody else. I use python 3.x and I worked on two 3D arrays. One, which I call data_3D contains float values of recordings in a brain scan, and the other, template_3D contains integers which represent regions of the brain. I wanted to choose those values from data_3D corresponding to an integer region_code as per template_3D:

my_mask = np.in1d(template_3D, region_code).reshape(template_3D.shape)
data_3D_masked = data_3D[my_mask]

which gives me a 1D array of only relevant recordings.

Masked array operations — NumPy v1.20.dev0 Manual, Stack 1-D arrays as columns into a 2-D array. ma.concatenate (arrays[, axis]). Concatenate a sequence of arrays along the given axis. In both NumPy and Pandas we can create masks to filter data. Masks are ’Boolean’ arrays – that is arrays of true and false values and provide a powerful and flexible method to selecting data. NumPy creating a mask. Let’s begin by creating an array of 4 rows of 10 columns of uniform random number between 0 and 100.

In your last example, the problem is not the mask. It is your use of compressed. From the docstring of compressed:

Return all the non-masked data as a 1-D array.

So compressed flattens the nonmasked values into a 1-d array. (It has to, because there is no guarantee that the compressed data will have an n-dimensional structure.)

Take a look at the masked array before you compress it:

In [8]:, mask2)

masked_array(data =
 [[1 2]
 [2 3]
 [-- --]],
             mask =
 [[False False]
 [False False]
 [ True  True]],
       fill_value = 999999) — Astropy v4.2.dev526+gbe39265ca, : a package to handle missing or invalid values. If we're indexing a multidimensional field in a # structured array (such as dtype("(2,)i2,(2 A masked array does not own its data and therefore cannot safely be resized in place. NumPy library provides objects for multi-dimensional arrays, whereas Pandas is capable of offering an in-memory 2d table object called DataFrame. The corresponding non-zero values can be obtained with: a[numpy. mask_rows (a[, axis]) Mask rows of a 2D array that contain masked values. Starting from numpy 1. The fourth channel is an alpha channel.

With np.where you can do all sorts of things:

x_maskd = np.where(mask, x, 0)

Comparisons, Masks, and Boolean Logic, Working with Boolean Arrays�. Given a Boolean array, there are a host of useful operations you can do. We'll work with x , the two-� Creating arrays in NumPy 3. mask_rows (a[, axis]) Mask rows of a 2D array that contain masked values. In fact, both sliding windows and image pyramids are both used in my 6-step. concatenate ( [a1,a2]) operation does not actually link the two arrays but returns a new one, filled with the entries from both given arrays in sequence.

20. Masked Arrays, To create a masked array where all values "near" 1.e20 are invalid, we can do: Return the Python list self.filled(fill_value).tolist(); note that masked values are filled. Note that a new array is created only if necessary to create a correctly filled, contiguous, Numeric array. Averaging an entire multidimensional array. import numpy as np import matplotlib.pyplot as plt # Construct a random 50x50 RGB image image = np.random.random((50, 50, 3)) # Construct mask according to some condition; # in this case, select all pixels with a red value > 0.3 mask = image[, 0] > 0.3 # Set all masked pixels to zero masked = image.copy() masked[mask] = 0 # Display original and masked images side-by-side f, (ax0, ax1) = plt.subplots(1, 2) ax0.imshow(image) ax1.imshow(masked)

Nodata Masks — rasterio documentation, The other kind of mask is Numpy's masked array which has the inverse sense: True values in a With care, you can safely navigate convert between the two mask types. This 2D array is a valid data mask in the sense of GDAL RFC 15. a.shape[0] is the number of rows and the size of the first dimension, while a.shape[1] is the size of the second dimension. You need to write: for x in range(0, rows): for y in range(0, cols): print a[x,y]

Look Ma, No For-Loops: Array Programming With NumPy – Real , In NumPy, an axis refers to a single dimension of a multidimensional array: A trick for doing this is to first mask the array of NumPy “shape-tuples” in places� Numpy convert 2d array to float. Numpy convert 2d array to float

  • Ah I see, so what I was trying does work, I just can't compress it. Hm. is there a way to remove masked elements of an array without loosing dimensionality of the array? does both.
  • I don't too much about masked array either, probably the same level as you. Just trying to make it work. Well, if you are trying to remove elements, I think logic index is not a bad way.
  • You're right, its correct before I compress it. I will read the documentation for a way to remove masked elements while preserving array dimensionality. Thanks
  • If I understand what you are trying to do, @Psidom's first suggestion looks reasonable. In particular, you probably don't need a masked array. Just index a regular array with a boolean array.