I have a for loop but where i has changes by 2 and i want to save a value in a numpy array in each iteration that that changes by 1.
n = 8 #steps
# random sequence
rand_seq = np.zeros(n-1)
for i in range(0, (n-1)*2, 2):
curr_state= i+3
I want to get curr_state outside the loop in the rand_seq array (seven values).
can you help me with that?
thanks a lot
A much simpler version (if I understand the question correctly) would be:
np.arange(3, 15+1, 2)
where 3 = start, 15 = stop, 2 = step size.
In general, when using numpy try to avoid adding elements in a for loop as this is inefficient. I would suggest checking out the documentation of np.arange(), np.array() and np.zeros() as in my experience, these will solve 90% of array - creation issues.
A straight forward list iteration:
In [313]: alist = []
...: for i in range(0,(8-1)*2,2):
...: alist.append(i+3)
...:
In [314]: alist
Out[314]: [3, 5, 7, 9, 11, 13, 15]
or cast as a list comprehension:
In [315]: [i+3 for i in range(0,(8-1)*2,2)]
Out[315]: [3, 5, 7, 9, 11, 13, 15]
Or if you make an array with the same range parameters:
In [316]: arr = np.arange(0,(8-1)*2,2)
In [317]: arr
Out[317]: array([ 0, 2, 4, 6, 8, 10, 12])
you can add the 3 with one simple expression:
In [318]: arr + 3
Out[318]: array([ 3, 5, 7, 9, 11, 13, 15])
With lists, iteration and comprehensions are great. With numpy you should try to make an array, such as with arange, and modify that with whole-array methods (not with iterations).
Related
I am trying to figure out a way to speed up this function. I am trying to do all pairwise comparisons between the rows and columns of a dataframe (pairwise_df) and store the result. The comparison requires two numpy arrays of continuous values taken from another dataframe (df).
pairwise_df = pd.DataFrame(index = ['insert1', 'insert2', 'insert3'], columns = ['insert1', 'insert2', 'insert3'])
df = pd.DataFrame(data = [[1, 2, 3, 4, 5, 6, 7, 8, 9, 10], [10, 9, 8, 7, 6, 5, 4, 3, 2, 1],
[2, 3, 4, 5, 7, 9, 10, 1, 2, 3]], index = ['insert1', 'insert2', 'insert3'], columns = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10])
for row in list(pairwise_df.index.values):
for col in list(pairwise_df):
pairwise_df.at[row, col] = cosine_sim(np.array(df.loc[row]), np.array(df.loc[col]))
This works, but takes about 18mins to run on a 2000 x 2000 dataframe, and i'm sure there are ways to speed this up, but my programming experience is minimal.
The cosine_sim function is here, but the function used will vary so it doesn't matter too much:
def cosine_sim(x, y):
dot = np.dot(x, y)
norma = np.linalg.norm(x)
normb = np.linalg.norm(y)
cos = dot / (norma * normb)
return cos
Thanks!
You can avoid loops to compute cosine similarity by creating the array of all combinations using np.tile and np.reshape. The trick here is to use np.einsum to replace the dot product.
m = df.values
x = np.tile(m, m.shape[0]).reshape(-1, m.shape[1])
y = np.tile(m.T, m.shape[0]).T
c = np.einsum('ij,ij->i', x, y) / (np.linalg.norm(x, axis=1) * np.linalg.norm(y, axis=1))
>>> c.reshape(-1, m.shape[0])
array([[1. , 0.57142857, 0.75283826],
[0.57142857, 1. , 0.74102903],
[0.75283826, 0.74102903, 1. ]])
I am (re)building up my knowledge of numpy, having used it a little while ago.
I have a question about fancy indexing with multidimenional (in this case 2D) arrays.
Given the following snippet:
>>> a = np.arange(12).reshape(3,4)
>>> a
array([[ 0, 1, 2, 3],
[ 4, 5, 6, 7],
[ 8, 9, 10, 11]])
>>> i = np.array( [ [0,1], # indices for the first dim of a
... [1,2] ] )
>>> j = np.array( [ [2,1], # indices for the second dim
... [3,3] ] )
>>>
>>> a[i,j] # i and j must have equal shape
array([[ 2, 5],
[ 7, 11]])
Could someone explain in simple English, the logic being applied to give the results produced. Ideally, the explanation would be applicable for 3D and higher rank arrays being used to index an array.
Conceptually (in terms of restrictions placed on "rows" and "columns"), what does it mean to index using a 2D array?
Conceptually (in terms of restrictions placed on "rows" and "columns"), what does it mean to index using a 2D array?
It means you are constructing a 2d array R, such that R=A[B, C]. This means that the value for rij=abijcij.
So it means that the item located at R[0,0] is the item in A with as row index B[0,0] and as column index C[0,0]. The item R[0,1] is the item in A with row index B[0,1] and as column index C[0,1], etc.
So in this specific case:
>>> b = a[i,j]
>>> b
array([[ 2, 5],
[ 7, 11]])
b[0,0] = 2 since i[0,0] = 0, and j[0,0] = 2, and thus a[0,2] = 2. b[0,1] = 5 since i[0,0] = 1, and j[0,0] = 1, and thus a[1,1] = 5. b[1,0] = 7 since i[0,0] = 1, and j[0,0] = 3, and thus a[1,3] = 7. b[1,1] = 11 since i[0,0] = 2, and j[0,0] = 3, and thus a[2,3] = 11.
So you can say that i will determine the "row indices", and j will determine the "column indices". Of course this concept holds in more dimensions as well: the first "indexer" thus determines the indices in the first index, the second "indexer" the indices in the second index, and so on.
I have an 1 dimensional sorted array and would like to find all pairs of elements whose difference is no larger than 5.
A naive approach would to be to make N^2 comparisons doing something like
diffs = np.tile(x, (x.size,1) ) - x[:, np.newaxis]
D = np.logical_and(diffs>0, diffs<5)
indicies = np.argwhere(D)
Note here that the output of my example are indices of x. If I wanted the values of x which satisfy the criteria, I could do x[indicies].
This works for smaller arrays, but not arrays of the size with which I work.
An idea I had was to find where there are gaps larger than 5 between consecutive elements. I would split the array into two pieces, and compare all the elements in each piece.
Is this a more efficient way of finding elements which satisfy my criteria? How could I go about writing this?
Here is a small example:
x = np.array([ 9, 12,
21,
36, 39, 44, 46, 47,
58,
64, 65,])
the result should look like
array([[ 0, 1],
[ 3, 4],
[ 5, 6],
[ 5, 7],
[ 6, 7],
[ 9, 10]], dtype=int64)
Here is a solution that iterates over offsets while shrinking the set of candidates until there are none left:
import numpy as np
def f_pp(A, maxgap):
d0 = np.diff(A)
d = d0.copy()
IDX = []
k = 1
idx, = np.where(d <= maxgap)
vidx = idx[d[idx] > 0]
while vidx.size:
IDX.append(vidx[:, None] + (0, k))
if idx[-1] + k + 1 == A.size:
idx = idx[:-1]
d[idx] = d[idx] + d0[idx+k]
k += 1
idx = idx[d[idx] <= maxgap]
vidx = idx[d[idx] > 0]
return np.concatenate(IDX, axis=0)
data = np.cumsum(np.random.exponential(size=10000)).repeat(np.random.randint(1, 20, (10000,)))
pairs = f_pp(data, 1)
#pairs = set(map(tuple, pairs))
from timeit import timeit
kwds = dict(globals=globals(), number=100)
print(data.size, 'points', pairs.shape[0], 'close pairs')
print('pp', timeit("f_pp(data, 1)", **kwds)*10, 'ms')
Sample run:
99963 points 1020651 close pairs
pp 43.00256529124454 ms
Your idea of slicing the array is a very efficient approach. Since your data are sorted you can just calculate the difference and split it:
d=np.diff(x)
ind=np.where(d>5)[0]
pieces=np.split(x,ind)
Here pieces is a list, where you can then use in a loop with your own code on every element.
The best algorithm is highly dependent on the nature of your data which I'm unaware. For example another possibility is to write a nested loop:
pairs=[]
for i in range(x.size):
j=i+1
while x[j]-x[i]<=5 and j<x.size:
pairs.append([i,j])
j+=1
If you want it to be more clever, you can edit the outer loop in a way to jump when j hits a gap.
I have a 2D - array A, which contains the x and y coordinates of points
array([[ 0, 0],
[ 0, 0],
[ 0, 0],
[ 3, 4],
[ 4, 1],
[ 5, 10],
[ 9, 7]])
as you can see the point ( 0 , 0 ) appears more often.
I want to delete this point so that the array looks like this:
array([[ 3, 4],
[ 4, 1],
[ 5, 10],
[ 9, 7]])
Since the array in real is very huge, it is very important to do this without for loops, otherwise it takes very long.
I'm new to python but i'm used to matlab, where I can solve it very easily with:
A (A(:,1) == 0 & A(:,2) == 0, :) = []
I thought it is almost the same or very similar in python, but I can't figure it out - am totally stuck. Errors like "use a.any()/all()" or "ufunc "bitwise_and" not supported for the input types" appear and I don't know what I should change.
Technically what you are doing in MATLAB is not deleting elements from A. What you are actually doing is creating a new array that lacks the elements of A. It is equivalent to:
>> A = A (A(:,1) ~= 0 | A(:,2) ~= 0, :);
You can do exactly the same thing in numpy:
>>> a = a[(a[:,0] != 0) | (a[:,1] != 0), :]
However, thanks to numpy's automatic broadcasting, you can make this simpler:
>>> a = a[(a != [0, 0]).any(1)]
This will work for any target array so long as it has the same number of columns as a.
relatively new to pandas, I have a json and python files:
{"dataset":{
"id": 123,
"data": [["2015-10-16",1,2,3,4,5,6],
["2015-10-15",7,8,9,10,11,12],
["2015-10-14",13,14,15,16,17]]
}}
&
import pandas
x = pandas.read_json('sample.json')
y = x.dataset.data
print x.dataset
Printing x.dataset and y works fine, but when I go to access a sub-element y, it returns a 'buffer' type. What's going on? How can I access the data inside the array? Attempting y[0][1] it returns out of bounds error, and iterating through returns a strange series of 'nul' characters and yet, it appears to be able to return the first portion of the data after printing x.dataset...
The data attribute of a pandas Series points to the memory buffer of all the data contained in that series:
>>> df = pandas.read_json('sample.json')
>>> type(df.dataset)
pandas.core.series.Series
>>> type(df.dataset.data)
memoryview
If you have a column/row named "data", you have to access it by it's string name, e.g.:
>>> type(df.dataset['data'])
list
Because of surprises like this, it's usually considered best practice to access columns through indexing rather than through attribute access. If you do this, you will get your desired result:
>>> df['dataset']['data']
[['2015-10-16', 1, 2, 3, 4, 5, 6],
['2015-10-15', 7, 8, 9, 10, 11, 12],
['2015-10-14', 13, 14, 15, 16, 17]]
>>> arr = df['dataset']['data']
>>> arr[0][0]
'2015-10-16'