How to create view/python reference on scipy sparse matrix? - python

I am working on an algorithm that uses diagonal and first off-diagonal blocks of a large (will be e06 x e06) block diagonal sparse matrix.
Right now I create a dict that stores the blocks in such a way that I can access the blocks in a matrix like fashion. For example B[0,0](5x5) gives the first block of matrix A(20x20), assuming 5x5 blocks and that matrix A is of type sparse.lil.
This works fine but takes horribly long too run. It is inefficient because it copies the data, as this reference revealed to my astonishment: GetItem Method
Is there a way to only store a view on a sparse matrix in a dict? I would like to change the content and still be able to use the same identifiers. It is fine if it takes a little longer as it should only be done once. The blocks will have many different dimensions and shapes.

As far as I know, all of the various sparse matricies in scipy.sparse return copies rather than a view of some sort. (Some of the others may be significantly faster at doing so than lil_matrix, though!)
One way of doing what you want is to just work with slice objects. For example:
import scipy.sparse
class SparseBlocks(object):
def __init__(self, data, chunksize=5):
self.data = data
self.chunksize = chunksize
def _convert_slices(self, slices):
newslices = []
for axslice in slices:
if isinstance(axslice, slice):
start, stop = axslice.start, axslice.stop
if axslice.start is not None:
start *= self.chunksize
if axslice.stop is not None:
stop *= self.chunksize
axslice = slice(start, stop, None)
elif axslice is not None:
axslice = slice(axslice, axslice+self.chunksize)
newslices.append(axslice)
return tuple(newslices)
def __getitem__(self, item):
item = self._convert_slices(item)
return self.data.__getitem__(item)
def __setitem__(self, item, value):
item = self._convert_slices(item)
return self.data.__setitem__(item, value)
data = scipy.sparse.lil_matrix((20,20))
s = SparseBlocks(data)
s[0,0] = 1
print s.data
Now, whenever we modify s[whatever] it will modify s.data of the appropriate chunk. In other words, s[0,0] will return or set s.data[:5, :5], and so on.

Related

Can we create a queue in form of list?

I have been learning the queue data structure recently. How do we actually create a queue? Can we just simply use a list and insert and remove items from the list? Or do I need to do something else? I have tried creating a queue class too. What is the correct method?
class Queue:
def __init__(self, capacity):
self.capacity = capacity
self.queue = []
def IsEmpty(self):
return len(self.queue) == self.capacity
def IsFull(self):
return len(self.queue) == 0
def Enqueue(self, x):
if len(self.queue) == self.capacity:
return 'Queue overloaded'
self.queue.insert(0, x)
return f'{x} enqueued into queue.'
def Dequeue(self):
return f'{self.queue[0]} dequeued fron queue.'
self.queue.pop(0)
def GetFront(self):
return self.queue[0]
def GetBack(self):
return self.queue[len(self.queue) - 1]
The common ways to implement a queue are basically:
Like an ArrayList, you use an array and reallocate a bigger one if it fills up. Unlike an array list, you need to allow the elements in the queue to wrap around from the end to the start. This is what java ArrayDeque does, and is probably the most common implementation. There are variants that waste more memory but don't wrap around, and these are usually used if you sometimes have to pass parts of the queue to some other function as a contiguous region.
Use a singly-linked list, but also keep a pointer to the tail node so you can enqueue items quickly. This is typically an intrusive list (i.e., you just and next pointers to objects you already have), or...
There's a particularly simple lock-free implementation of a thread-safe queue using a singly-linked list with an extra head node (and again a pointer to the tail node). This is what Java's ConcurrentLinkedQueue uses.
Your implementation of a queue is none of these. The python list is backed by an array like (1), but the first item is always at the start of the array. The pop() operation can therefore take a long time, because all the other items have to be moved toward the start.

Python: How to create an object with expandable numpy array members

I have the following use case:
I am receiving 100 samples per second of several numpy nd-arrays, say a of shape (4, 3), and b of shape (5, 6).
On other instances, I could be receiving c of shape (2, 3), and d of shape (3, 5) and e of some other shape, and so on.
These samples arrive for some variable time between a single sample and 360000 samples (an hour).
I would like to treat an entire streaming session as an object
I would like to have something like
class Aggregator_ab(object):
def __init__(self):
self.a = ???
self.b = ???
def add_sample(new_a, new_b):
self.a.update(new_a) # How can I achieve such an update?
self.b.update(new_b) # How can I achieve such an update?
Now, I would like to
access Aggregator_ab's fields as numpy arrays:
agg = Aggregator_ab() # maybe with parameters?
num_samples = 4
for i in range(num_samples):
agg.add_sample(new_a=np.zeros((4, 3), new_b=np.zeros((5, 6))
assert agg.a.shape[0] == num_samples
assert agg.b.shape[0] == num_samples
assert agg.a.shape[1:] == (4, 3)
assert agg.b.shape[1:] == (5, 6)
And I would also expect regular numpy behavior of the members of agg.
My current code has some problems, and looks something like:
class Aggregator_ab(object):
def __init__(self):
self.__as = []
self.__bs = []
def add_sample(new_a, new_b):
self.__as.append(new_a)
self.__bs.append(new_b)
#property
def a(self):
return np.vstack(self.__as)
#property
def b(self):
return np.vstack(self.__bs)
problems:
can only get a "full" numpy array after using vstack
must use expensive vstack every "get"
can't utilize previous vstacks
adding any field requires a lot of boilerplate which I would like to extract
This only supports very limited use cases, and If i ever want something more, I would have to implement myself.
going through native python lists is the only way to scale the array size without paying too much for resizing. Had I used vstack to keep a numpy array, at large sizes, I wouldn't be able to keep up with the frame rate.
This seems to me like a common use case, thus I believe someone has solved this before me.
Is there some library that does this? I know pandas sounds right, but what do I do if I have fields that are matrices?
If not, then how is this usually dealt with?
What about allocating an array that keeps growing in size? It works like vectors in most common languages:
import numpy as np
class growing_array:
def __init__(self, shape, growth):
self._arr=np.empty(shape=(*shape, growth))
self.incoming_shape=shape
self.num_entries=0
self.growth=growth
def append(self, incoming_arr):
if self.num_entries == self._arr.shape[2]:
self._arr.resize(*self.incoming_shape, self._arr.shape[2]+self.growth)
self._arr[:,:,self.num_entries] = incoming_arr
self.num_entries+=1
def get(self):
return self._arr[:,:,0:self.num_entries]

Efficient growing pools of objects

Is there an established module, or good practice, to work efficiently with large object pools in Python 3?
What I mean by "object pool" is some class capable of:
fetching new instances of specified type, while dynamically extending the memory allocation under the hood when necessary;
maintaining a consistent indexing for previously fetched objects.
Here is a basic example:
class Value:
__slots__ = ('a','b')
def __init__(self,a=None,b=None):
self.a = a
self.b = b
class BasicPool:
def __init__(self):
self.data = []
def __getitem__(self,k):
return self.data[k]
def fetch(self):
v = Value()
self.data.append(v)
return v
class BlockPool:
def __init__(self,bsize=100):
self.bsize = bsize
self.next = bsize
self.data = []
def __getitem__(self,k):
b,k = divmod(k,self.bsize)
return self.data[b][k]
def fetch(self):
self.next += 1
if self.next >= self.bsize:
self.data.append([ Value() for _ in range(self.bsize) ])
self.next = 0
return self.data[-1][self.next]
The BasicPool doesn't do anything smart: whenever a new instance is requested, it is instanciated and appended to an underlying list. On the other hand, the BlockPool grows a list of pre-allocated blocks of instances. Surprisingly though, it seems that preallocation is not beneficial in practice:
from timeit import default_timer as timer
def benchmark(P):
N = int(1e6)
start = timer()
for _ in range(N): P.fetch()
print( timer() - start )
print( 'Basic pool:' )
for _ in range(5): benchmark(BasicPool())
# Basic pool:
# 1.2352294209995307
# 0.5003506309985823
# 0.48115064000012353
# 0.48508202800076106
# 1.1760561199989752
print( 'Block pool:' )
for _ in range(5): benchmark(BlockPool())
# Block pool:
# 0.7272855400005938
# 1.4875716509995982
# 0.726611527003115
# 0.7369502859983186
# 1.4867010340021807
As you can see, the BasicPool is always faster than the BlockPool (I also don't know the cause of these large variations). Pools of objects must be a fairly common need in Python; is the best approach really to use the builtin list.append? Are there smarter containers that can be used to further improve runtime performance, or is this dominated by the instanciation time anyway?
The whole point of the geometric growth of the array underlying a list is to reduce the reallocation overhead to a constant factor. That constant can easily be smaller than that for manually making blocks (principally because of the slow, interpreted manipulation of self.next and self.data in the latter). (Asymptotically, the cost of BlockPool.fetch is still the append, of course.) Moreover, your benchmark doesn’t include the additional cost of destroying the blocks, nor that of the two-step indexing on read.
So list is surely as good as it gets (without writing your own C code). You can improve BasicPool a bit by inheriting from list rather than containing one, eliminating a dictionary lookup per fetch and the interpreted __getitem__ wrapper entirely.

Efficiently mapping unhashable objects to their index in a list

A Python list
f = [x0, x1, x2]
may be seen as an efficient representation of a mapping from [0, 1, ..., len(f) - 1] to the set of its elements. By "efficient" I mean that f[i] returns the element associated with i in O(1) time.
The inverse mapping may be defined as follows:
class Inverse:
def __init__(self, f):
self.f = f
def __getitem__(self, x):
return self.f.index(x)
This works, but Inverse(f)[x] takes O(n) time on average.
Alternatively, one may use a dict:
f_inv = {x: i for i, x in enumerate(f)}
This has O(1) average time complexity, but it requires the objects in the list to be hashable.
Is there a way to define an inverse mapping that provides equality-based lookups, in O(1) average time, with unhashable objects?
Edit: sample input and expected output:
>>> f = [x0, x1, x2]
>>> f_inv = Inverse(f) # this is to be defined
>>> f_inv[x0] # in O(1) time
0
>>> f_inv[x2] # in O(1) time
2
You can create an associated dictionary mapping the object ID's back to the list index.
The obvious disadvantage is that you will have to search the index for the identity object, not for on eobject that is merely equal.
On the upside, by creating a custom MutableSequence class using collections.abc, you can, with minimal code, write a class that keeps your data both as a sequence and as the reverse dictionary.
from collections.abc import MutableSequence
from threading import RLock
class MD(dict):
# No need for a full MutableMapping subclass, as the use is limited
def __getitem__(self, key):
return super().__getitem__(id(key))
class Reversible(MutableSequence):
def __init__(self, args):
self.seq = list()
self.reverse = MD()
self.lock = RLock()
for element in args:
self.append(element)
def __getitem__(self, index):
return self.seq[index]
def __setitem__(self, index, value):
with self.lock:
del self.reverse[id(self.seq[index])]
self.seq[index] = value
self.reverse[id(value)] = index
def __delitem__(self, index):
if index < 0:
index += len(self)
with self.lock:
# Increase all mapped indexes
for obj in self.seq[index:]:
self.reverse[obj] -= 1
del self.reverse[id(self.seq[index])]
del self.seq[index]
def __len__(self):
return len(self.seq)
def insert(self, index, value):
if index < 0:
index += len(self)
with self.lock:
# Increase all mapped indexes
for obj in self.seq[index:]:
self.reverse[obj] += 1
self.seq.insert(index, value)
self.reverse[id(value)] = index
And voilá: just use this object in place of your list, and the public attribute "reverse" to get the index of identity objects.
Perceive you can augment the "intelligence" of the "MD" class by trying to use different strategies, like to use the objects themselves, if they are hashable, and only resort to id, or other custom key based on other object attributes, when needed. That way you could mitigate the need for the search to be for the same object.
So, for ordinary operations on the list, this class maintain the reverted dictionary synchronized. There is no support for slice indexing, though.
For more information, check the docs at https://docs.python.org/3/library/collections.abc.html
Unfortunately you're stuck with an algorithm limitation here. Fast lookup structures, like hash tables or binary trees, are efficient because they put objects in particular buckets or order them based on their values. This requires them to be hashable or comparable consistently for the entire time you are storing them in this structure, otherwise a lookup is very likely to fail.
If the objects you need are mutable (usually the reason they are not hashable) then any time an object you are tracking changes you need to update the data structure. The safest way to do this is to create immutable objects. If you need to change an object, then create a new one, remove the old one from the dictionary, and insert the new object as a key with the same value.
The operations here are still O(1) with respect to the size of the dictionary, you just need to consider whether the cost of copying objects on every change is worth it.

Setters and getters that act like lists/tuples

I have a project that uses Numpy. One of the classes needs a set of matrices called weights. For several reasons, it's best if I store all these matrix values as one long vector, and let each separate matrix be a view of a slice of that.
self.weightvector = asmatrix(rand(nweights, 1)) # All the weights as a vector
self.weights = list() # A list of views that have the 'correct' shape
for i in range(...):
self.weights.append(...)
If the user of the class does something like foo.weights[i] = bar, then these weights will no longer be views into the original weight vector.
Does Python offer a mechanism through which can define getters and setters for when an indexing such as foo.weights[i] = bar is done?
Sure. You want to override the __setitem__ method on your class.
class Weights(list):
def __setitem__(self, key, value):
....
Here is a link to the docs:
http://docs.python.org/2/reference/datamodel.html#object.__setitem__
More options:
Instead of implementing a new container type, you could reuse the existing one that does what you want, a tuple:
self.weights = tuple()
for i in (...) :
self.weights += (<new_item>,)
Or if you really want to use a list, make weights a #property and return a copy of the original list.
#property
def weights(self) :
return [j for j in self._weights]

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