Referencing a numpy arrray without creating an expensive copy - python

Let's say that I have a function that requires that NumPy ndarray with 2 axes, e.g., a data matrix of rows and columns. If a "column" is sliced from such an array, this function should also work, thus it should do some internal X[:, np.newaxis] for convenience. However, I don't want to create a new array object for this since this can be expensive in certain cases.
I am wondering if there is a good way to do it. For example, would the following code be safe (by that I mean, would the global arrays always be unchanged like Python lists)?
X1 = np.array([[1,2,3], [4,5,6], [7,8,9]])
X2 = np.array([1,4,7])
def some_func(X):
if len(X.shape) == 1:
X = X[:, np.newaxis]
return X[:,0].sum()
some_func(X2)
some_func(X1[:, 0])
some_func(X1)
I am asking because I heard that NumPy arrays are sometimes copied in certain cases, however, I can't find a good resource about this. Any ideas?

It shouldn't create a copy. For illustration:
>>> A = np.ones((50000000,))
>>> B = A[:,np.newaxis]
>>> B.flags
C_CONTIGUOUS : False
F_CONTIGUOUS : False
OWNDATA : False
WRITEABLE : True
ALIGNED : True
UPDATEIFCOPY : False
Note the OWNDATA : False - it's sharing data with A.
For a few more details have a look at http://docs.scipy.org/doc/numpy/reference/arrays.indexing.html. The basic rule is that it doesn't create a copy unless you're doing indexing with either an array of indices (e.g. A[[1,2,4]]) or with a boolean array (e.g. A[[True, False, True]]). Pretty much everything else returns a view with no copy.

It shouldn't create a copy - these types of operations are all just views - a copy with changed metadata of the ndarray, but not the data.

You can reshape the input array to force it to be a M x N dimensional array, where M is the number of elements for the first dimension. Then, slice it to get the first column and sum all its elements. The reshaping and slicing must not
make copies.
So, you could have this alternative approach without the IF statement -
def some_func2(X):
return X.reshape(X.shape[0],-1)[:,0].sum()
To check and confirm that it doesn't create a copy with reshaping and slicing, you can use np.may_share_memory like so -
In [515]: X1
Out[515]:
array([[1, 2, 3],
[4, 5, 6],
[7, 8, 9]])
In [516]: np.may_share_memory(X1,X1.reshape(X1.shape[0],-1)[:,0])
Out[516]: True
In [517]: X2
Out[517]: array([1, 4, 7])
In [518]: np.may_share_memory(X2,X2.reshape(X2.shape[0],-1)[:,0])
Out[518]: True
A True value with np.may_share_memory is a good indicator that they are views and not copies.

Related

Return True/False for entire array if any value meets mask requirement(s)

I have already tried looking at other similar posts however, their solutions do not solve this specific issue. Using the answer from this post I found that I get the error: "The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()" because I define my array differently from theirs. Their array is a size (n,) while my array is a size (n,m). Moreover, the solution from this post does not work either because it applies to lists. The only method I could think of was this:
When there is at least 1 True in array, then entire array is considered True:
filt = 4
tracktruth = list()
arraytruth = list()
arr1 = np.array([[1,2,4]])
for track in range(0,arr1.size):
if filt == arr1[0,track]:
tracktruth.append(True)
else:
tracktruth.append(False)
if any(tracktruth):
arraytruth.append(True)
else:
arraytruth.append(False)
When there is not a single True in array, then entire array is considered False:
filt = 5
tracktruth = list()
arraytruth = list()
arr1 = np.array([[1,2,4]])
for track in range(0,arr1.size):
if filt == arr1[0,track]:
tracktruth.append(True)
else:
tracktruth.append(False)
if any(tracktruth):
arraytruth.append(True)
else:
arraytruth.append(False)
The reason the second if-else statement is there is because I wish to apply this mask to multiple arrays and ultimately create a master list that describes which arrays are true and which are false in their entirety. However, with a for loop and two if-else statements, I think this would be very slow with larger arrays. What would be a faster way to do this?
This seems overly complicated, you can use boolean indexing to achieve results without loops
arr1=np.array([[1,2,4]])
filt=4
arr1==filt
array([[False, False, True]])
np.sum(arr1==filt).astype(bool)
True
With nmore than one row, you can use the row or column index in the np.sum or you can use the axis parameter to sum on rows or columns
As pointed out in the comments, you can use np.any() instead of the np.sum(...).astype(bool) and it runs in roughly 2/3 the time on the test dataset:
np.any(a==filt, axis=1)
array([ True])
You can do this with list comprehension. I've done it here for one array but it's easily extended to multiple arrays with a for loop
filt = 4
arr1 = np.array([[1,2,4]])
print(any([part == filt for part in arr1[0]]))
You can get the arraytruth more generally, with list comprehension for the array of size (n,m)
import numpy as np
filt = 4
a = np.array([[1, 2, 4]])
b = np.array([[1, 2, 3],
[5, 6, 7]])
array_lists = [a, b]
arraytruth = [True if a[a==filt].size>0 else False for a in array_lists]
print(arraytruth)
This will give you:
[True, False]
[edit] Use numpy hstack method.
filt = 4
arr = np.array([[1,2,3,4], [1,2,3]])
print(any([x for x in np.hstack(arr) if x < filt]))

flatten arrays in a list in python

I have multiple numpy masked arrays arr0, arr1, ..., arrn.
I put them in a list arrs = [arr0, ..., arrn].
I want to flatten these arrays et put a mask on them. I did something like:
for arr in arrs:
arr = np.ravel(arr)
arr[mask] = ma.masked
I do not understand when Python make copies and when it is just a pointer. This for loop does not flatten the arr0, ..., arrn, (whereas ravel outputs a view and not a copy) it just flattens the variable arr, although it does change their mask !
As I understand it, arr is a view of the elements in the list arrs, so when I change elements of arr it changes the elements of the corresponding array in the list. But when I assign a new value to arr it does not change the original array, even if the assignement is supposed to be a view of this array. Why ?
Edit with an example:
Arrays to flatten:
arr0 = masked_array(data=[[1,2],[3,4]], mask=False)
arr1 = masked_array(data=[[5,6],[7,8]], mask=False)
mask = [[False,True],[True,False]]
Expected output:
arr0 = masked_array(data=[[1,--],[--,4]], mask=[[False,True],[True,False]])
arr1 = masked_array(data=[[5,--],[--,8]], mask=[[False,True],[True,False]])
I'd like to do this in a loop because I have a lot of arrays (15 more or less), and I want to use the arrays name in the code. Is there no other way than do to:
arr0 = np.ravel(arr0)
...
arrn = np.ravel(arrn)
In [1032]: arr0 = np.ma.masked_array(data=[[1,2],[3,4]], mask=False)
In [1033]: arr1 = np.ma.masked_array(data=[[5,6],[7,8]], mask=False)
This is the basic way of iterating over a list, applying some action to each element, and collecting the results in another list:
In [1037]: ll=[arr0,arr1]
In [1038]: ll1=[]
In [1047]: for a in ll:
a1=a.flatten() # makes a copy
a1.mask=mask
ll1.append(a1)
In [1049]: ll1
Out[1049]:
[masked_array(data = [1 -- -- 4], mask = [False True True False],
fill_value = 999999),
masked_array(data = [5 -- -- 8], mask = [False True True False],
fill_value = 999999)]
Often that can be writen a list comprehension
[foo(a) for a in alist]
but the action here isn't a neat function
If I use ravel instead, a1 is a view (not a copy), and applying mask to it changes the mask of a as well - the result is changed masks for arr0, but no change in shape:
In [1051]: for a in ll:
......: a1=a.ravel()
......: a1.mask=mask
(the same happens with your a=a.ravel(). The a= assigns a new value to a, breaking the link to the iteration value. That's true for any Python iteration. It's best to use new variable names inside the iteration like a1 so you don't confuse yourself.)
Essentially the same as
In [1054]: for a in ll:
......: a.mask=mask
I can change the shape in the same in-place way
In [1055]: for a in ll:
......: a.shape=[-1] # short hand for inplace ravel
......: a.mask=mask
In [1056]: arr0
Out[1056]:
masked_array(data = [1 -- -- 4],
mask = [False True True False],
fill_value = 999999)
Here's a functional way of creating new arrays with new shape and mask, and using it in a list comprehension (and no change to arr0)
[np.ma.masked_array(a,mask=mask).ravel() for a in [arr0,arr1]]
Understanding these alternatives does require understanding how Python assigns iterative variables, and how numpy makes copies and views.

python numpy strange boolean arithmetic behaviour

Why is it, in python/numpy:
from numpy import asarray
bools=asarray([False,True])
print(bools)
[False True]
print(1*bools, 0+bools, 0-bools) # False, True are valued as 0, 1
[0 1] [0 1] [ 0 -1]
print(-2*bools, -bools*2) # !? expected same result! :-/
[0 -2] [2 0]
print(-bools) # this is the reason!
[True False]
I consider it weird that -bools returns logical_not(bools), because in all other cases the behaviour is "arithmetic", not "logical".
One who wants to use an array of booleans as a 0/1 mask (or "characteristic function") is forced to use somehow involute expressions such as (0-bools) or (-1)*bools, and can easily incur into bugs if he forgets about this.
Why is it so, and what would be the best acceptable way to obtain the desired behaviour? (beside commenting of course)
Its all about operator order and data types.
>>> import numpy as np
>>> B = np.array([0, 1], dtype=np.bool)
>>> B
array([False, True], dtype=bool)
With numpy, boolean arrays are treated as that, boolean arrays. Every operation applied to them, will first try to maintain the data type. That is way:
>>> -B
array([ True, False], dtype=bool)
and
>>> ~B
array([ True, False], dtype=bool)
which are equivalent, return the element-wise negation of its elements. Note however that using -B throws a warning, as the function is deprecated.
When you use things like:
>>> B + 1
array([1, 2])
B and 1 are first casted under the hood to the same data type. In data-type promotions, the boolean array is always casted to a numeric array. In the above case, B is casted to int, which is similar as:
>>> B.astype(int) + 1
array([1, 2])
In your example:
>>> -B * 2
array([2, 0])
First the array B is negated by the operator - and then multiplied by 2. The desired behaviour can be adopted either by explicit data conversion, or adding brackets to ensure proper operation order:
>>> -(B * 2)
array([ 0, -2])
or
>>> -B.astype(int) * 2
array([ 0, -2])
Note that B.astype(int) can be replaced without data-copy by B.view(np.int8), as boolean are represented by characters and have thus 8 bits, the data can be viewed as integer with the .view method without needing to convert it.
>>> B.view(np.int8)
array([0, 1], dtype=int8)
So, in short, B.view(np.int8) or B.astype(yourtype) will always ensurs that B is a [0,1] numeric array.
Numpy arrays are homogenous—all elements have the same type for a given array, and the array object stores what type that is. When you create an array with True and False, it is an array of type bool and operators behave on the array as such. It's not surprising, then, that you get logical negation happening in situations that would be logical negation for a normal bool. When you use the arrays for integer math, then they are converted to 1's and 0's. Of all your examples, those are the more anomalous cases, that is, it's behavior that shouldn't be relied upon in good code.
As suggested in the comments, if you want to do math with an array of 0's and 1's, it's better to just make an array of 0's and 1's. However, depending on what you want to do with them, you might be better served looking into functions like numpy.where().

Difference between nonzero(a), where(a) and argwhere(a). When to use which?

In Numpy, nonzero(a), where(a) and argwhere(a), with a being a numpy array, all seem to return the non-zero indices of the array. What are the differences between these three calls?
On argwhere the documentation says:
np.argwhere(a) is the same as np.transpose(np.nonzero(a)).
Why have a whole function that just transposes the output of nonzero ? When would that be so useful that it deserves a separate function?
What about the difference between where(a) and nonzero(a)? Wouldn't they return the exact same result?
nonzero and argwhere both give you information about where in the array the elements are True. where works the same as nonzero in the form you have posted, but it has a second form:
np.where(mask,a,b)
which can be roughly thought of as a numpy "ufunc" version of the conditional expression:
a[i] if mask[i] else b[i]
(with appropriate broadcasting of a and b).
As far as having both nonzero and argwhere, they're conceptually different. nonzero is structured to return an object which can be used for indexing. This can be lighter-weight than creating an entire boolean mask if the 0's are sparse:
mask = a == 0 # entire array of bools
mask = np.nonzero(a)
Now you can use that mask to index other arrays, etc. However, as it is, it's not very nice conceptually to figure out which indices correspond to 0 elements. That's where argwhere comes in.
I can't comment on the usefulness of having a separate convenience function that transposes the result of another, but I can comment on where vs nonzero. In it's simplest use case, where is indeed the same as nonzero.
>>> np.where(np.array([[0,4],[4,0]]))
(array([0, 1]), array([1, 0]))
>>> np.nonzero(np.array([[0,4],[4,0]]))
(array([0, 1]), array([1, 0]))
or
>>> a = np.array([[1, 2],[3, 4]])
>>> np.where(a == 3)
(array([1, 0]),)
>>> np.nonzero(a == 3)
(array([1, 0]),)
where is different from nonzero in the case when you wish to pick elements of from array a if some condition is True and from array b when that condition is False.
>>> a = np.array([[6, 4],[0, -3]])
>>> b = np.array([[100, 200], [300, 400]])
>>> np.where(a > 0, a, b)
array([[6, 4], [300, 400]])
Again, I can't explain why they added the nonzero functionality to where, but this at least explains how the two are different.
EDIT: Fixed the first example... my logic was incorrect previously

Efficiently sum a small numpy array, broadcast across a ginormous numpy array?

I want to calculate an indexed weight sum across a large (1,000,000 x
3,000) boolean numpy array. The large boolean array changes
infrequently, but the weights come at query time, and I need answers
very fast, without copying the whole large array, or expanding the
small weight array to the size of the large array.
The result should be an array with 1,000,000 entries, each having the
sum of the weights array entries corresponding to that row's True
values.
I looked into using masked arrays, but they seem to require building a
weights array the size of my large boolean array.
The code below gives the correct results, but I can't afford that copy
during the multiply step. The multiply isn't even necessary, since
the values array is boolean, but at least it handles the broadcasting
properly.
I'm new to numpy, and loving it, but I'm about to give up on it for
this particular problem. I've learned enough numpy to know to stay
away from anything that loops in python.
My next step will be to write this routine in C (which has the added
benefit of letting me save memory by using bits instead of bytes, by
the way.)
Unless one of you numpy gurus can save me from cython?
from numpy import array, multiply, sum
# Construct an example values array, alternating True and False.
# This represents four records of three attributes each:
# array([[False, True, False],
# [ True, False, True],
# [False, True, False],
# [ True, False, True]], dtype=bool)
values = array([(x % 2) for x in range(12)], dtype=bool).reshape((4,3))
# Construct example weights, one for each attribute:
# array([1, 2, 3])
weights = array(range(1, 4))
# Create expensive NEW array with the weights for the True attributes.
# Broadcast the weights array into the values array.
# array([[0, 2, 0],
# [1, 0, 3],
# [0, 2, 0],
# [1, 0, 3]])
weighted = multiply(values, weights)
# Add up the weights:
# array([2, 4, 2, 4])
answers = sum(weighted, axis=1)
print answers
# Rejected masked_array solution is too expensive (and oddly inverts
# the results):
masked = numpy.ma.array([[1,2,3]] * 4, mask=values)
The dot product (or inner product) is what you want. It allows you to take a matrix of size mĂ—n and a vector of length n and multiply them together yielding a vector of length m, where each entry is the weighted sum of a row of the matrix with the entries of the vector of as weights.
Numpy implements this as array1.dot(array2) (or numpy.dot(array1, array2) in older versions). e.g.:
from numpy import array
values = array([(x % 2) for x in range(12)], dtype=bool).reshape((4,3))
weights = array(range(1, 4))
answers = values.dot(weights)
print answers
# output: [ 2 4 2 4 ]
(You should benchmark this though, using the timeit module.)
It seems likely that dbaupp's answer is the correct one. But just for the sake of diversity, here's another solution that saves memory. This will work even for operations that don't have a built-in numpy equivalent.
>>> values = numpy.array([(x % 2) for x in range(12)], dtype=bool).reshape((4,3))
>>> weights = numpy.array(range(1, 4))
>>> weights_stretched = numpy.lib.stride_tricks.as_strided(weights, (4, 3), (0, 8))
numpy.lib.stride_tricks.as_strided is a wonderful little function! It allows you to specify shape and strides values that allow a small array to mimic a much larger array. Observe -- there aren't really four rows here; it just looks that way:
>>> weights_stretched[0][0] = 4
>>> weights_stretched
array([[4, 2, 3],
[4, 2, 3],
[4, 2, 3],
[4, 2, 3]])
So instead of passing a huge array to MaskedArray, you can pass a smaller one. (But as you've already noticed, numpy masking works in the opposite way you might expect; truth masks, rather than revealing, so you'll have to store your values inverted.) As you can see, MaskedArray doesn't copy any data; it just reflects whatever is in weights_stretched:
>>> masked = numpy.ma.MaskedArray(weights_stretched, numpy.logical_not(values))
>>> weights_stretched[0][0] = 1
>>> masked
masked_array(data =
[[-- 2 --]
[1 -- 3]
[-- 2 --]
[1 -- 3]],
mask =
[[ True False True]
[False True False]
[ True False True]
[False True False]],
fill_value=999999)
Now we can just pass it to sum:
>>> sum(masked, axis=1)
masked_array(data = [2 4 2 4],
mask = [False False False False],
fill_value=999999)
I benchmarked numpy.dot and the above against a 1,000,000 x 30 array. This is the result on a relatively modern MacBook Pro (numpy.dot is dot1; mine is dot2):
>>> %timeit dot1(values, weights)
1 loops, best of 3: 194 ms per loop
>>> %timeit dot2(values, weights)
1 loops, best of 3: 459 ms per loop
As you can see, the built-in numpy solution is faster. But stride_tricks is worth knowing about regardless, so I'm leaving this.
Would this work for you?
a = np.array([sum(row * weights) for row in values])
This uses sum() to immediately sum the row * weights values, so you don't need the memory to store all the intermediate values. Then the list comprehension collects all the values.
You said you want to avoid anything that "loops in Python". This at least does the looping with the C guts of Python, rather than an explicit Python loop, but it can't be as fast as a NumPy solution because that uses compiled C or Fortran.
I don't think you need numpy for something like that. And 1000000 by 3000 is a huge array; this will not fit in your RAM, most likely.
I would do it this way:
Let's say that you data is originally in a text file:
False,True,False
True,False,True
False,True,False
True,False,True
My code:
weight = range(1,4)
dicto = {'True':1, 'False':0}
with open ('my_data.txt') as fin:
a = sum(sum(dicto[ele]*w for ele,w in zip(line.strip().split(','),weight)) for line in fin)
Result:
>>> a
12
EDIT:
I think I slightly misread the question first time around, and summed up the everything together. Here is the solution that gives the exact solution that OP is after:
weight = range(1,4)
dicto = {'True':1, 'False':0}
with open ('my_data.txt') as fin:
a = [sum(dicto[ele]*w for ele,w in zip(line.strip().split(','),weight)) for line in fin]
Result:
>>> a
[2, 4, 2, 4]

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