Module carray¶

Implementation of resizeable arrays of different types in Cython.

All arrays provide for the following operations:

access by indexing.

access through get/set function.

appending values at the end of the array.

reserving space for future appends.

access to internal data through a numpy array.

Each array also provides an interface to its data through a numpy array. This is done through the get_npy_array function. The returned numpy array can be used just like any other numpy array but for the following restrictions:

the array may not be resized.

references of this array should not be kept.

slices of this array may not be made.

The numpy array may however be copied and used in any manner.

class cyarray.carray.BaseArray¶

Bases: object

Base class for managed C-arrays.

align_array(self, LongArray new_indices, int stride=1)¶: Rearrange the array contents according to the new indices.

alloc¶

‘long’

Type:	alloc

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶: Copy subset of values from source to self.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶: Copy values of indexed particles from self to dest.

extend(self, ndarray in_array)¶: Extend the array with data from in_array.

get_c_type(self) → str¶: Return the c data type of this array.

get_npy_array(self) → ndarray¶: Returns a numpy array of the data: do not keep its reference.

length¶

‘long’

Type:	length

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶: Remove the particles with indices in index_list.

reserve(self, long size)¶: Resizes the internal data to required size.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes the array to the new size.

set_data(self, ndarray nparr)¶

Set data from the given numpy array.

If the numpy array is a reference to the numpy array maintained internally by this class, nothing is done. Otherwise, if the size of nparr matches this array, values are copied into the array maintained.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Update the min and max values of the array.

class cyarray.carray.BaseArrayIter(BaseArray arr)¶

Bases: object

Iteration object to support iteration over BaseArray.

class cyarray.carray.DoubleArray¶

Bases: cyarray.carray.BaseArray

Represents an array of doubles

Mallocs a memory buffer of size (n*sizeof(double)) and sets up the numpy array. The memory is aligned to 64 byte boundaries.

Parameters:	n (long) – Length of the array.

data¶

Pointer to an integer array.

Type:	pointer

length¶

Size of the array itself.

Type:	long

alloc¶

Size of the data buffer allocated.

Type:	long

Examples

>>> x = DoubleArray()
>>> x.resize(5)
>>> x.set_data(np.arange(5))
>>> x[0]
0

>>> x = DoubleArray(5)
>>> xnp = x.get_npy_array()
>>> xnp[:] = np.arange(5)
>>> x[0], x[4]
(0.0, 4.0)

append(self, double value)¶: Appends value to the end of the array.

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶

Copy a subset of values from src to self.

Parameters:	start_index (long) – the first index in self that corresponds to the 0th index in source end_index (long) – the first index in self from start_index that is not copied stride (int) – the stride along indices, basically copy over chunks of the given stride.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶

Copies values of indices in indices from self to dest.

No size check if performed, we assume the dest to of proper size i.e. atleast as long as indices.

extend(self, ndarray in_array)¶

Extend the array with data from in_array.

Parameters:	in_array (ndarray) – a numpy array with data to be added to the current array.

Notes

accessing the in_array using the indexing operation seems to be costly. Look at the annotated cython html file.

get(self, long idx) → double¶: Gets value stored at position idx.

get_c_type(self) → str¶: Return the c data type for this array as a string.

index(self, double value) → long¶: Returns the index at which value is in self, else -1.

maximum¶

‘double’

Type:	maximum

minimum¶

‘double’

Type:	minimum

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶

Remove the particles with indices in index_list.

Parameters:	index_list (ndarray) – a list of indices which should be removed. input_sorted (bool) – indicates if the input is sorted in ascending order. if not, the array will be sorted internally. stride (int) – indicates the stride size for the indices.

Notes

If the input indices are not sorted, sort them in ascending order. Starting with the last element in the index list, start replacing the element at the said index with the last element in the data and update the length of the array.

If stride is 3, then the indices are multiplied by 3 and chunks of 3 elements are removed.

reserve(self, long size)¶: Resizes the internal data to size*sizeof(double) bytes.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes internal data to size*sizeof(double) bytes and sets the length to the new size.

set(self, long idx, double value)¶: Sets location idx to value.

set_view(self, DoubleArray parent, long start, long end)¶

Create a view of a given a parent array from start to end.

Note that this excludes the end index.

Parameters:	parent (DoubleArray) – The parent array of which this is a view. start (long) – The starting index to start the view from. end (long) – The ending index to end the view at, excludes the end itself.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Updates the min and max values of the array.

class cyarray.carray.FloatArray¶

Bases: cyarray.carray.BaseArray

Represents an array of floats

Mallocs a memory buffer of size (n*sizeof(float)) and sets up the numpy array. The memory is aligned to 64 byte boundaries.

Parameters:	n (long) – Length of the array.

data¶

Pointer to an integer array.

Type:	pointer

length¶

Size of the array itself.

Type:	long

alloc¶

Size of the data buffer allocated.

Type:	long

Examples

>>> x = FloatArray()
>>> x.resize(5)
>>> x.set_data(np.arange(5))
>>> x[0]
0

>>> x = FloatArray(5)
>>> xnp = x.get_npy_array()
>>> xnp[:] = np.arange(5)
>>> x[0], x[4]
(0.0, 4.0)

append(self, float value)¶: Appends value to the end of the array.

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶

Copy a subset of values from src to self.

Parameters:	start_index (long) – the first index in self that corresponds to the 0th index in source end_index (long) – the first index in self from start_index that is not copied stride (int) – the stride along indices, basically copy over chunks of the given stride.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶

Copies values of indices in indices from self to dest.

No size check if performed, we assume the dest to of proper size i.e. atleast as long as indices.

extend(self, ndarray in_array)¶

Extend the array with data from in_array.

Parameters:	in_array (ndarray) – a numpy array with data to be added to the current array.

Notes

accessing the in_array using the indexing operation seems to be costly. Look at the annotated cython html file.

get(self, long idx) → float¶: Gets value stored at position idx.

get_c_type(self) → str¶: Return the c data type for this array as a string.

index(self, float value) → long¶: Returns the index at which value is in self, else -1.

maximum¶

‘float’

Type:	maximum

minimum¶

‘float’

Type:	minimum

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶

Remove the particles with indices in index_list.

Parameters:	index_list (ndarray) – a list of indices which should be removed. input_sorted (bool) – indicates if the input is sorted in ascending order. if not, the array will be sorted internally. stride (int) – indicates the stride size for the indices.

Notes

If the input indices are not sorted, sort them in ascending order. Starting with the last element in the index list, start replacing the element at the said index with the last element in the data and update the length of the array.

If stride is 3, then the indices are multiplied by 3 and chunks of 3 elements are removed.

reserve(self, long size)¶: Resizes the internal data to size*sizeof(float) bytes.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes internal data to size*sizeof(float) bytes and sets the length to the new size.

set(self, long idx, float value)¶: Sets location idx to value.

set_view(self, FloatArray parent, long start, long end)¶

Create a view of a given a parent array from start to end.

Note that this excludes the end index.

Parameters:	parent (FloatArray) – The parent array of which this is a view. start (long) – The starting index to start the view from. end (long) – The ending index to end the view at, excludes the end itself.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Updates the min and max values of the array.

class cyarray.carray.IntArray¶

Bases: cyarray.carray.BaseArray

Represents an array of ints

Mallocs a memory buffer of size (n*sizeof(int)) and sets up the numpy array. The memory is aligned to 64 byte boundaries.

Parameters:	n (long) – Length of the array.

data¶

Pointer to an integer array.

Type:	pointer

length¶

Size of the array itself.

Type:	long

alloc¶

Size of the data buffer allocated.

Type:	long

Examples

>>> x = IntArray()
>>> x.resize(5)
>>> x.set_data(np.arange(5))
>>> x[0]
0

>>> x = IntArray(5)
>>> xnp = x.get_npy_array()
>>> xnp[:] = np.arange(5)
>>> x[0], x[4]
(0.0, 4.0)

append(self, int value)¶: Appends value to the end of the array.

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶

Copy a subset of values from src to self.

Parameters:	start_index (long) – the first index in self that corresponds to the 0th index in source end_index (long) – the first index in self from start_index that is not copied stride (int) – the stride along indices, basically copy over chunks of the given stride.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶

Copies values of indices in indices from self to dest.

No size check if performed, we assume the dest to of proper size i.e. atleast as long as indices.

extend(self, ndarray in_array)¶

Extend the array with data from in_array.

Parameters:	in_array (ndarray) – a numpy array with data to be added to the current array.

Notes

accessing the in_array using the indexing operation seems to be costly. Look at the annotated cython html file.

get(self, long idx) → int¶: Gets value stored at position idx.

get_c_type(self) → str¶: Return the c data type for this array as a string.

index(self, int value) → long¶: Returns the index at which value is in self, else -1.

maximum¶

‘int’

Type:	maximum

minimum¶

‘int’

Type:	minimum

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶

Remove the particles with indices in index_list.

Parameters:	index_list (ndarray) – a list of indices which should be removed. input_sorted (bool) – indicates if the input is sorted in ascending order. if not, the array will be sorted internally. stride (int) – indicates the stride size for the indices.

Notes

If the input indices are not sorted, sort them in ascending order. Starting with the last element in the index list, start replacing the element at the said index with the last element in the data and update the length of the array.

If stride is 3, then the indices are multiplied by 3 and chunks of 3 elements are removed.

reserve(self, long size)¶: Resizes the internal data to size*sizeof(int) bytes.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes internal data to size*sizeof(int) bytes and sets the length to the new size.

set(self, long idx, int value)¶: Sets location idx to value.

set_view(self, IntArray parent, long start, long end)¶

Create a view of a given a parent array from start to end.

Note that this excludes the end index.

Parameters:	parent (IntArray) – The parent array of which this is a view. start (long) – The starting index to start the view from. end (long) – The ending index to end the view at, excludes the end itself.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Updates the min and max values of the array.

class cyarray.carray.LongArray¶

Bases: cyarray.carray.BaseArray

Represents an array of longs

Mallocs a memory buffer of size (n*sizeof(long)) and sets up the numpy array. The memory is aligned to 64 byte boundaries.

Parameters:	n (long) – Length of the array.

data¶

Pointer to an integer array.

Type:	pointer

length¶

Size of the array itself.

Type:	long

alloc¶

Size of the data buffer allocated.

Type:	long

Examples

>>> x = LongArray()
>>> x.resize(5)
>>> x.set_data(np.arange(5))
>>> x[0]
0

>>> x = LongArray(5)
>>> xnp = x.get_npy_array()
>>> xnp[:] = np.arange(5)
>>> x[0], x[4]
(0.0, 4.0)

append(self, long value)¶: Appends value to the end of the array.

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶

Copy a subset of values from src to self.

Parameters:	start_index (long) – the first index in self that corresponds to the 0th index in source end_index (long) – the first index in self from start_index that is not copied stride (int) – the stride along indices, basically copy over chunks of the given stride.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶

Copies values of indices in indices from self to dest.

No size check if performed, we assume the dest to of proper size i.e. atleast as long as indices.

extend(self, ndarray in_array)¶

Extend the array with data from in_array.

Parameters:	in_array (ndarray) – a numpy array with data to be added to the current array.

Notes

accessing the in_array using the indexing operation seems to be costly. Look at the annotated cython html file.

get(self, long idx) → long¶: Gets value stored at position idx.

get_c_type(self) → str¶: Return the c data type for this array as a string.

index(self, long value) → long¶: Returns the index at which value is in self, else -1.

maximum¶

‘long’

Type:	maximum

minimum¶

‘long’

Type:	minimum

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶

Remove the particles with indices in index_list.

Parameters:	index_list (ndarray) – a list of indices which should be removed. input_sorted (bool) – indicates if the input is sorted in ascending order. if not, the array will be sorted internally. stride (int) – indicates the stride size for the indices.

Notes

If the input indices are not sorted, sort them in ascending order. Starting with the last element in the index list, start replacing the element at the said index with the last element in the data and update the length of the array.

If stride is 3, then the indices are multiplied by 3 and chunks of 3 elements are removed.

reserve(self, long size)¶: Resizes the internal data to size*sizeof(long) bytes.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes internal data to size*sizeof(long) bytes and sets the length to the new size.

set(self, long idx, long value)¶: Sets location idx to value.

set_view(self, LongArray parent, long start, long end)¶

Create a view of a given a parent array from start to end.

Note that this excludes the end index.

Parameters:	parent (LongArray) – The parent array of which this is a view. start (long) – The starting index to start the view from. end (long) – The ending index to end the view at, excludes the end itself.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Updates the min and max values of the array.

class cyarray.carray.UIntArray¶

Bases: cyarray.carray.BaseArray

Represents an array of unsigned ints

Mallocs a memory buffer of size (n*sizeof(unsigned int)) and sets up the numpy array. The memory is aligned to 64 byte boundaries.

Parameters:	n (long) – Length of the array.

data¶

Pointer to an integer array.

Type:	pointer

length¶

Size of the array itself.

Type:	long

alloc¶

Size of the data buffer allocated.

Type:	long

Examples

>>> x = UIntArray()
>>> x.resize(5)
>>> x.set_data(np.arange(5))
>>> x[0]
0

>>> x = UIntArray(5)
>>> xnp = x.get_npy_array()
>>> xnp[:] = np.arange(5)
>>> x[0], x[4]
(0.0, 4.0)

append(self, unsigned int value)¶: Appends value to the end of the array.

copy_subset(self, BaseArray source, long start_index=-1, long end_index=-1, int stride=1)¶

Copy a subset of values from src to self.

Parameters:	start_index (long) – the first index in self that corresponds to the 0th index in source end_index (long) – the first index in self from start_index that is not copied stride (int) – the stride along indices, basically copy over chunks of the given stride.

copy_values(self, LongArray indices, BaseArray dest, int stride=1, int start=0)¶

Copies values of indices in indices from self to dest.

No size check if performed, we assume the dest to of proper size i.e. atleast as long as indices.

extend(self, ndarray in_array)¶

Extend the array with data from in_array.

Parameters:	in_array (ndarray) – a numpy array with data to be added to the current array.

Notes

accessing the in_array using the indexing operation seems to be costly. Look at the annotated cython html file.

get(self, long idx) → unsigned int¶: Gets value stored at position idx.

get_c_type(self) → str¶: Return the c data type for this array as a string.

index(self, unsigned int value) → long¶: Returns the index at which value is in self, else -1.

maximum¶

‘unsigned int’

Type:	maximum

minimum¶

‘unsigned int’

Type:	minimum

remove(self, ndarray index_list, bool input_sorted=0, int stride=1)¶

Remove the particles with indices in index_list.

Parameters:	index_list (ndarray) – a list of indices which should be removed. input_sorted (bool) – indicates if the input is sorted in ascending order. if not, the array will be sorted internally. stride (int) – indicates the stride size for the indices.

Notes

If the input indices are not sorted, sort them in ascending order. Starting with the last element in the index list, start replacing the element at the said index with the last element in the data and update the length of the array.

If stride is 3, then the indices are multiplied by 3 and chunks of 3 elements are removed.

reserve(self, long size)¶: Resizes the internal data to size*sizeof(unsigned int) bytes.

reset(self)¶: Reset the length of the array to 0.

resize(self, long size)¶: Resizes internal data to size*sizeof(unsigned int) bytes and sets the length to the new size.

set(self, long idx, unsigned int value)¶: Sets location idx to value.

set_view(self, UIntArray parent, long start, long end)¶

Create a view of a given a parent array from start to end.

Note that this excludes the end index.

Parameters:	parent (UIntArray) – The parent array of which this is a view. start (long) – The starting index to start the view from. end (long) – The ending index to end the view at, excludes the end itself.

squeeze(self)¶: Release any unused memory.

update_min_max(self)¶: Updates the min and max values of the array.

cyarray.carray.py_aligned(long n, int item_size) → long¶: Align n items each having size (in bytes) item_size to 64 bits and return the appropriate number of items that would be aligned to 64 bytes.