pynbody.array.IndexedSimArray

pynbody.array.IndexedSimArray#

class pynbody.array.IndexedSimArray(array: SimArray, ptr: slice | ndarray)[source]#

Bases: object

A view into a SimArray that allows for indexing and slicing.

Unlike a numpy array constructed from indexing a parent, IndexedSimArrays do not hold a copy of the underlying data.

For example:

>>> a = pynbody.array.SimArray([1, 2, 3, 4])
>>> b = a[[1, 3]]

In this case, b copies the relevant part of a into a new array. Updating the elements of b leave a untouched.

>>> b[:] = 0
>>> a
SimArray([1, 2, 3, 4])

By contrast,

>>> a = pynbody.array.SimArray([1, 2, 3, 4])
>>> b = pynbody.array.IndexedSimArray(a, [1, 3])

In this case, b provides a view into a. Changes to b are reflected in a. However, b is not a genuine numpy array.

>>> b[:] = 0
>>> a
SimArray([1, 0, 3, 0])

For most purposes, an IndexedSimArray should behave exactly like a SimArray/numpy array. However, advanced users may want to understand more about performance implications and ways to optimize code. This can be found in the Performance optimisation in pynbody section of the documentation.

Note

The methods of this class are the same as those of SimArray, and mainly therefore correspond to the equivalents within numpy.ndarray. See also the note on function documentation for SimArray.

Attributes:

ancestor: Provides the basemost SimArray that an IndexedSimArray is based on.
derived: True if this array has been derived by pynbody; False otherwise.
dtype: Data-type of the array’s elements.
name: The name of the array in the simulation snapshot, if known.
ndim: Number of array dimensions.
shape: Tuple of array dimensions.
sim: The simulation snapshot that the array belongs to, if known.
units: The units of the array, if known; otherwise units.NoUnit.

Methods

`abs`(args, *kwargs)	Return the absolute value of the array.
`all`([axis, out, keepdims, where])	Returns True if all elements evaluate to True.
`any`([axis, out, keepdims, where])	Returns True if any of the elements of a evaluate to True.
`argmax`([axis, out, keepdims])	Return indices of the maximum values along the given axis.
`argmin`([axis, out, keepdims])	Return indices of the minimum values along the given axis.
`argpartition`(kth[, axis, kind, order])	Returns the indices that would partition this array.
`argsort`([axis, kind, order])	Returns the indices that would sort this array.
`astype`(dtype[, order, casting, subok, copy])	Copy of the array, cast to a specified type.
`byteswap`([inplace])	Swap the bytes of the array elements
`choose`(choices[, out, mode])	Use an index array to construct a new array from a set of choices.
`clip`([min, max, out])	Return an array whose values are limited to `[min, max]`.
`compress`(condition[, axis, out])	Return selected slices of this array along given axis.
`conj`()	Complex-conjugate all elements.
`conjugate`()	Return the complex conjugate, element-wise.
`conversion_context`()	Return a dictionary of contextual information that may be required for unit conversion.
`convert_units`(new_unit)	Convert units of this array in-place.
`copy`([order])	Return a copy of the array.
`cumprod`([axis, dtype, out])	Return the cumulative product of the elements along the given axis.
`cumsum`([axis, dtype, out])	Return the cumulative sum of the elements along the given axis.
`diagonal`([offset, axis1, axis2])	Return specified diagonals.
`dump`(file)	Dump a pickle of the array to the specified file.
`dumps`()	Returns the pickle of the array as a string.
`fill`(value)	Fill the array with a scalar value.
`flatten`([order])	Return a copy of the array collapsed into one dimension.
`getfield`(dtype[, offset])	Returns a field of the given array as a certain type.
`in_original_units`()	Return a copy of this array expressed in the file's internal unit scheme.
`in_units`(new_unit, **context_overrides)	Return a copy of this array, expressed relative to an alternative unit `new_unit`.
`item`(*args)	Copy an element of an array to a standard Python scalar and return it.
`max`([axis, out, keepdims, initial, where])	Return the maximum along a given axis.
`mean`([axis, dtype, out, keepdims, where])	Returns the average of the array elements along given axis.
`mean_by_mass`(args, *kwargs)	Removed in pynbody 2.0.
`min`([axis, out, keepdims, initial, where])	Return the minimum along a given axis.
`nonzero`()	Return the indices of the elements that are non-zero.
`partition`(kth[, axis, kind, order])	Partially sorts the elements in the array in such a way that the value of the element in k-th position is in the position it would be in a sorted array.
`prod`([axis, dtype, out, keepdims, initial, ...])	Return the product of the array elements over the given axis
`put`(indices, values[, mode])	Set `a.flat[n] = values[n]` for all n in indices.
`ravel`([order])	Return a flattened array.
`repeat`(repeats[, axis])	Repeat elements of an array.
`reshape`(shape, /, *[, order, copy])	Returns an array containing the same data with a new shape.
`resize`(new_shape[, refcheck])	Change shape and size of array in-place.
`round`([decimals, out])	Return a with each element rounded to the given number of decimals.
`searchsorted`(v[, side, sorter])	Find indices where elements of v should be inserted in a to maintain order.
`set_default_units`([quiet])	Set the units for this array by guessing the `sim`'s unit scheme and known dimensionality information.
`set_units_like`(new_unit)	Set the units of this array using a guess the `sim`'s units for a given dimensionality.
`setfield`(val, dtype[, offset])	Put a value into a specified place in a field defined by a data-type.
`setflags`([write, align, uic])	Set array flags WRITEABLE, ALIGNED, WRITEBACKIFCOPY, respectively.
`sort`([axis, kind, order])	Sort an array in-place.
`squeeze`([axis])	Remove axes of length one from a.
`std`([axis, dtype, out, ddof, keepdims, where])	Returns the standard deviation of the array elements along given axis.
`sum`([axis, dtype, out, keepdims, initial, where])	Return the sum of the array elements over the given axis.
`swapaxes`(axis1, axis2)	Return a view of the array with axis1 and axis2 interchanged.
`take`(indices[, axis, out, mode])	Return an array formed from the elements of a at the given indices.
`tobytes`([order])	Construct Python bytes containing the raw data bytes in the array.
`tofile`(fid[, sep, format])	Write array to a file as text or binary (default).
`tolist`()	Return the array as an `a.ndim`-levels deep nested list of Python scalars.
`trace`([offset, axis1, axis2, dtype, out])	Return the sum along diagonals of the array.
`transpose`(*axes)	Returns a view of the array with axes transposed.
`ufunc_rule`()	Function decorator to mark a function as providing the output units for a given ufunc (or ufuncs).
`var`([axis, dtype, out, ddof, keepdims, where])	Returns the variance of the array elements, along given axis.
`view`([dtype][, type])	New view of array with the same data.
`write`(**kwargs)	Write this array to disk according to the standard method associated with its base file.

dot
ptp
to_device

__init__(array: SimArray, ptr: slice | ndarray)[source]#

Initialise an IndexedSimArray based on an underlying SimArray and a pointer into that array.

The pointer can be a slice or an array of indexes.

Parameters:

array (SimArray) – The underlying SimArray.
ptr (slice or numpy.ndarray) – The slice or array of indexes into the underlying array.

abs(*args, **kwargs)#: Return the absolute value of the array.

all(axis=None, out=None, keepdims=False, *, where=True)#

Returns True if all elements evaluate to True.

Refer to numpy.all for full documentation.

See also

numpy.all: equivalent function

property ancestor#: Provides the basemost SimArray that an IndexedSimArray is based on.

any(axis=None, out=None, keepdims=False, *, where=True)#

Returns True if any of the elements of a evaluate to True.

Refer to numpy.any for full documentation.

See also

numpy.any: equivalent function

argmax(axis=None, out=None, *, keepdims=False)#

Return indices of the maximum values along the given axis.

Refer to numpy.argmax for full documentation.

See also

numpy.argmax: equivalent function

argmin(axis=None, out=None, *, keepdims=False)#

Return indices of the minimum values along the given axis.

Refer to numpy.argmin for detailed documentation.

See also

numpy.argmin: equivalent function

argpartition(kth, axis=-1, kind='introselect', order=None)#

Returns the indices that would partition this array.

Refer to numpy.argpartition for full documentation.

See also

numpy.argpartition: equivalent function

argsort(axis=-1, kind=None, order=None)#

Returns the indices that would sort this array.

Refer to numpy.argsort for full documentation.

See also

numpy.argsort: equivalent function

astype(dtype, order='K', casting='unsafe', subok=True, copy=True)#

Copy of the array, cast to a specified type.

Parameters:

dtype (str or dtype) – Typecode or data-type to which the array is cast.
order ({'C', 'F', 'A', 'K'}, optional) – Controls the memory layout order of the result. ‘C’ means C order, ‘F’ means Fortran order, ‘A’ means ‘F’ order if all the arrays are Fortran contiguous, ‘C’ order otherwise, and ‘K’ means as close to the order the array elements appear in memory as possible. Default is ‘K’.
casting ({'no', 'equiv', 'safe', 'same_kind', 'unsafe'}, optional) –
Controls what kind of data casting may occur. Defaults to ‘unsafe’ for backwards compatibility.
- ’no’ means the data types should not be cast at all.
- ’equiv’ means only byte-order changes are allowed.
- ’safe’ means only casts which can preserve values are allowed.
- ’same_kind’ means only safe casts or casts within a kind, like float64 to float32, are allowed.
- ’unsafe’ means any data conversions may be done.
subok (bool, optional) – If True, then sub-classes will be passed-through (default), otherwise the returned array will be forced to be a base-class array.
copy (bool, optional) – By default, astype always returns a newly allocated array. If this is set to false, and the dtype, order, and subok requirements are satisfied, the input array is returned instead of a copy.

Returns:

arr_t – Unless copy is False and the other conditions for returning the input array are satisfied (see description for copy input parameter), arr_t is a new array of the same shape as the input array, with dtype, order given by dtype, order.

Return type:

ndarray

Raises:

ComplexWarning – When casting from complex to float or int. To avoid this, one should use a.real.astype(t).

Examples

>>> import numpy as np
>>> x = np.array([1, 2, 2.5])
>>> x
array([1. ,  2. ,  2.5])

>>> x.astype(int)
array([1, 2, 2])

byteswap(inplace=False)#

Swap the bytes of the array elements

Toggle between low-endian and big-endian data representation by returning a byteswapped array, optionally swapped in-place. Arrays of byte-strings are not swapped. The real and imaginary parts of a complex number are swapped individually.

Parameters:: inplace (bool, optional) – If True, swap bytes in-place, default is False.
Returns:: out – The byteswapped array. If inplace is True, this is a view to self.
Return type:: ndarray

Examples

>>> import numpy as np
>>> A = np.array([1, 256, 8755], dtype=np.int16)
>>> list(map(hex, A))
['0x1', '0x100', '0x2233']
>>> A.byteswap(inplace=True)
array([  256,     1, 13090], dtype=int16)
>>> list(map(hex, A))
['0x100', '0x1', '0x3322']

Arrays of byte-strings are not swapped

>>> A = np.array([b'ceg', b'fac'])
>>> A.byteswap()
array([b'ceg', b'fac'], dtype='|S3')

A.view(A.dtype.newbyteorder()).byteswap() produces an array with the same values but different representation in memory

>>> A = np.array([1, 2, 3],dtype=np.int64)
>>> A.view(np.uint8)
array([1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0, 3, 0, 0, 0, 0, 0,
       0, 0], dtype=uint8)
>>> A.view(A.dtype.newbyteorder()).byteswap(inplace=True)
array([1, 2, 3], dtype='>i8')
>>> A.view(np.uint8)
array([0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0,
       0, 3], dtype=uint8)

choose(choices, out=None, mode='raise')#

Use an index array to construct a new array from a set of choices.

Refer to numpy.choose for full documentation.

See also

numpy.choose: equivalent function

clip(min=None, max=None, out=None, **kwargs)#

Return an array whose values are limited to [min, max]. One of max or min must be given.

Refer to numpy.clip for full documentation.

See also

numpy.clip: equivalent function

compress(condition, axis=None, out=None)#

Return selected slices of this array along given axis.

Refer to numpy.compress for full documentation.

See also

numpy.compress: equivalent function

conj()#

Complex-conjugate all elements.

Refer to numpy.conjugate for full documentation.

See also

numpy.conjugate: equivalent function

conjugate()#

Return the complex conjugate, element-wise.

Refer to numpy.conjugate for full documentation.

See also

numpy.conjugate: equivalent function

conversion_context()[source]#

Return a dictionary of contextual information that may be required for unit conversion.

This is typically cosmological scalefactor and Hubble parameter.

convert_units(new_unit)[source]#: Convert units of this array in-place. If this is a sub-view, the entire base array will be converted.

copy(order='C')#

Return a copy of the array.

Parameters:: order ({'C', 'F', 'A', 'K'}, optional) – Controls the memory layout of the copy. ‘C’ means C-order, ‘F’ means F-order, ‘A’ means ‘F’ if a is Fortran contiguous, ‘C’ otherwise. ‘K’ means match the layout of a as closely as possible. (Note that this function and numpy.copy() are very similar but have different default values for their order= arguments, and this function always passes sub-classes through.)

See also

numpy.copy: Similar function with different default behavior

numpy.copyto

Notes

This function is the preferred method for creating an array copy. The function numpy.copy() is similar, but it defaults to using order ‘K’, and will not pass sub-classes through by default.

Examples

>>> import numpy as np
>>> x = np.array([[1,2,3],[4,5,6]], order='F')

>>> y = x.copy()

>>> x.fill(0)

>>> x
array([[0, 0, 0],
       [0, 0, 0]])

>>> y
array([[1, 2, 3],
       [4, 5, 6]])

>>> y.flags['C_CONTIGUOUS']
True

For arrays containing Python objects (e.g. dtype=object), the copy is a shallow one. The new array will contain the same object which may lead to surprises if that object can be modified (is mutable):

>>> a = np.array([1, 'm', [2, 3, 4]], dtype=object)
>>> b = a.copy()
>>> b[2][0] = 10
>>> a
array([1, 'm', list([10, 3, 4])], dtype=object)

To ensure all elements within an object array are copied, use copy.deepcopy:

>>> import copy
>>> a = np.array([1, 'm', [2, 3, 4]], dtype=object)
>>> c = copy.deepcopy(a)
>>> c[2][0] = 10
>>> c
array([1, 'm', list([10, 3, 4])], dtype=object)
>>> a
array([1, 'm', list([2, 3, 4])], dtype=object)

cumprod(axis=None, dtype=None, out=None)#

Return the cumulative product of the elements along the given axis.

Refer to numpy.cumprod for full documentation.

See also

numpy.cumprod: equivalent function

cumsum(axis=None, dtype=None, out=None)#

Return the cumulative sum of the elements along the given axis.

Refer to numpy.cumsum for full documentation.

See also

numpy.cumsum: equivalent function

property derived#

True if this array has been derived by pynbody; False otherwise.

For more information on derived arrays, see derived_arrays.

diagonal(offset=0, axis1=0, axis2=1)#

Return specified diagonals. In NumPy 1.9 the returned array is a read-only view instead of a copy as in previous NumPy versions. In a future version the read-only restriction will be removed.

Refer to numpy.diagonal() for full documentation.

See also

numpy.diagonal: equivalent function

property dtype#

Data-type of the array’s elements.

Warning

Setting arr.dtype is discouraged and may be deprecated in the future. Setting will replace the dtype without modifying the memory (see also ndarray.view and ndarray.astype).

Parameters:: None
Returns:: d
Return type:: numpy dtype object

See also

ndarray.astype: Cast the values contained in the array to a new data-type.
ndarray.view: Create a view of the same data but a different data-type.

numpy.dtype

Examples

>>> import numpy as np
>>> x = np.arange(4).reshape((2, 2))
>>> x
array([[0, 1],
       [2, 3]])
>>> x.dtype
dtype('int64')   # may vary (OS, bitness)
>>> isinstance(x.dtype, np.dtype)
True

dump(file)#

Dump a pickle of the array to the specified file. The array can be read back with pickle.load or numpy.load.

Parameters:: file (str or Path) – A string naming the dump file.

dumps()#

Returns the pickle of the array as a string. pickle.loads will convert the string back to an array.

Parameters:: None

fill(value)#

Fill the array with a scalar value.

Parameters:: value (scalar) – All elements of a will be assigned this value.

Examples

>>> import numpy as np
>>> a = np.array([1, 2])
>>> a.fill(0)
>>> a
array([0, 0])
>>> a = np.empty(2)
>>> a.fill(1)
>>> a
array([1.,  1.])

Fill expects a scalar value and always behaves the same as assigning to a single array element. The following is a rare example where this distinction is important:

>>> a = np.array([None, None], dtype=object)
>>> a[0] = np.array(3)
>>> a
array([array(3), None], dtype=object)
>>> a.fill(np.array(3))
>>> a
array([array(3), array(3)], dtype=object)

Where other forms of assignments will unpack the array being assigned:

>>> a[...] = np.array(3)
>>> a
array([3, 3], dtype=object)

flatten(order='C')#

Return a copy of the array collapsed into one dimension.

Parameters:: order ({'C', 'F', 'A', 'K'}, optional) – ‘C’ means to flatten in row-major (C-style) order. ‘F’ means to flatten in column-major (Fortran- style) order. ‘A’ means to flatten in column-major order if a is Fortran contiguous in memory, row-major order otherwise. ‘K’ means to flatten a in the order the elements occur in memory. The default is ‘C’.
Returns:: y – A copy of the input array, flattened to one dimension.
Return type:: ndarray

See also

ravel: Return a flattened array.
flat: A 1-D flat iterator over the array.

Examples

>>> import numpy as np
>>> a = np.array([[1,2], [3,4]])
>>> a.flatten()
array([1, 2, 3, 4])
>>> a.flatten('F')
array([1, 3, 2, 4])

getfield(dtype, offset=0)#

Returns a field of the given array as a certain type.

A field is a view of the array data with a given data-type. The values in the view are determined by the given type and the offset into the current array in bytes. The offset needs to be such that the view dtype fits in the array dtype; for example an array of dtype complex128 has 16-byte elements. If taking a view with a 32-bit integer (4 bytes), the offset needs to be between 0 and 12 bytes.

Parameters:

dtype (str or dtype) – The data type of the view. The dtype size of the view can not be larger than that of the array itself.
offset (int) – Number of bytes to skip before beginning the element view.

Examples

>>> import numpy as np
>>> x = np.diag([1.+1.j]*2)
>>> x[1, 1] = 2 + 4.j
>>> x
array([[1.+1.j,  0.+0.j],
       [0.+0.j,  2.+4.j]])
>>> x.getfield(np.float64)
array([[1.,  0.],
       [0.,  2.]])

By choosing an offset of 8 bytes we can select the complex part of the array for our view:

>>> x.getfield(np.float64, offset=8)
array([[1.,  0.],
       [0.,  4.]])

in_original_units()#

Return a copy of this array expressed in the file’s internal unit scheme.

For example, if sim has units of Msol and kpc and this array is the rho array, a copy of the array in units of Msol kpc^-3 will be returned, even if the current units are something else like kg m^-3.

The underlying code uses dimensional analysis; of course, simulation codes are free to use inconsistent units if they like, so in general this routine cannot be guaranteed to infer the correct units. Human cross-checks are strongly advised.

in_units(new_unit, **context_overrides)[source]#

Return a copy of this array, expressed relative to an alternative unit new_unit.

Additional keyword arguments are interpreted as context overrides for the unit conversion. For example, if the array is a comoving distance and you want to convert it to a physical distance, you might call

>>> x.in_units('kpc', a=0.1)

to get the result assuming a scalefactor 0.1. If no context overrides are given, the context of the underlying sim is adopted.

item(*args)#

Copy an element of an array to a standard Python scalar and return it.

Parameters:

*args (Arguments (variable number and type)) –

none: in this case, the method only works for arrays with one element (a.size == 1), which element is copied into a standard Python scalar object and returned.
int_type: this argument is interpreted as a flat index into the array, specifying which element to copy and return.
tuple of int_types: functions as does a single int_type argument, except that the argument is interpreted as an nd-index into the array.

Returns:

z – A copy of the specified element of the array as a suitable Python scalar

Return type:

Standard Python scalar object

Notes

When the data type of a is longdouble or clongdouble, item() returns a scalar array object because there is no available Python scalar that would not lose information. Void arrays return a buffer object for item(), unless fields are defined, in which case a tuple is returned.

item is very similar to a[args], except, instead of an array scalar, a standard Python scalar is returned. This can be useful for speeding up access to elements of the array and doing arithmetic on elements of the array using Python’s optimized math.

Examples

>>> import numpy as np
>>> np.random.seed(123)
>>> x = np.random.randint(9, size=(3, 3))
>>> x
array([[2, 2, 6],
       [1, 3, 6],
       [1, 0, 1]])
>>> x.item(3)
1
>>> x.item(7)
0
>>> x.item((0, 1))
2
>>> x.item((2, 2))
1

For an array with object dtype, elements are returned as-is.

>>> a = np.array([np.int64(1)], dtype=object)
>>> a.item() #return np.int64
np.int64(1)

max(axis=None, out=None, keepdims=False, initial=<no value>, where=True)#

Return the maximum along a given axis.

Refer to numpy.amax for full documentation.

See also

numpy.amax: equivalent function

mean(axis=None, dtype=None, out=None, keepdims=False, *, where=True)#

Returns the average of the array elements along given axis.

Refer to numpy.mean for full documentation.

See also

numpy.mean: equivalent function

mean_by_mass(*args, **kwargs)#: Removed in pynbody 2.0. Use pynbody.snapshot.simsnap.SimSnap.mean_by_mass() instead.

min(axis=None, out=None, keepdims=False, initial=<no value>, where=True)#

Return the minimum along a given axis.

Refer to numpy.amin for full documentation.

See also

numpy.amin: equivalent function

property name#: The name of the array in the simulation snapshot, if known.

property ndim#

Number of array dimensions.

Examples

>>> import numpy as np
>>> x = np.array([1, 2, 3])
>>> x.ndim
1
>>> y = np.zeros((2, 3, 4))
>>> y.ndim
3

nonzero()#

Return the indices of the elements that are non-zero.

Refer to numpy.nonzero for full documentation.

See also

numpy.nonzero: equivalent function

partition(kth, axis=-1, kind='introselect', order=None)#

Partially sorts the elements in the array in such a way that the value of the element in k-th position is in the position it would be in a sorted array. In the output array, all elements smaller than the k-th element are located to the left of this element and all equal or greater are located to its right. The ordering of the elements in the two partitions on the either side of the k-th element in the output array is undefined.

Parameters:

kth (int or sequence of ints) –
Element index to partition by. The kth element value will be in its final sorted position and all smaller elements will be moved before it and all equal or greater elements behind it. The order of all elements in the partitions is undefined. If provided with a sequence of kth it will partition all elements indexed by kth of them into their sorted position at once.

Deprecated since version 1.22.0: Passing booleans as index is deprecated.
axis (int, optional) – Axis along which to sort. Default is -1, which means sort along the last axis.
kind ({'introselect'}, optional) – Selection algorithm. Default is ‘introselect’.
order (str or list of str, optional) – When a is an array with fields defined, this argument specifies which fields to compare first, second, etc. A single field can be specified as a string, and not all fields need to be specified, but unspecified fields will still be used, in the order in which they come up in the dtype, to break ties.

See also

numpy.partition: Return a partitioned copy of an array.
argpartition: Indirect partition.
sort: Full sort.

Notes

See np.partition for notes on the different algorithms.

Examples

>>> import numpy as np
>>> a = np.array([3, 4, 2, 1])
>>> a.partition(3)
>>> a
array([2, 1, 3, 4]) # may vary

>>> a.partition((1, 3))
>>> a
array([1, 2, 3, 4])

prod(axis=None, dtype=None, out=None, keepdims=False, initial=1, where=True)#

Return the product of the array elements over the given axis

Refer to numpy.prod for full documentation.

See also

numpy.prod: equivalent function

put(indices, values, mode='raise')#

Set a.flat[n] = values[n] for all n in indices.

Refer to numpy.put for full documentation.

See also

numpy.put: equivalent function

ravel([order])#

Return a flattened array.

Refer to numpy.ravel for full documentation.

See also

numpy.ravel: equivalent function
ndarray.flat: a flat iterator on the array.

repeat(repeats, axis=None)#

Repeat elements of an array.

Refer to numpy.repeat for full documentation.

See also

numpy.repeat: equivalent function

reshape(shape, /, *, order='C', copy=None)#

Returns an array containing the same data with a new shape.

Refer to numpy.reshape for full documentation.

See also

numpy.reshape: equivalent function

Notes

Unlike the free function numpy.reshape, this method on ndarray allows the elements of the shape parameter to be passed in as separate arguments. For example, a.reshape(10, 11) is equivalent to a.reshape((10, 11)).

resize(new_shape, refcheck=True)#

Change shape and size of array in-place.

Parameters:

new_shape (tuple of ints, or n ints) – Shape of resized array.
refcheck (bool, optional) – If False, reference count will not be checked. Default is True.

Return type:

None

Raises:

ValueError – If a does not own its own data or references or views to it exist, and the data memory must be changed. PyPy only: will always raise if the data memory must be changed, since there is no reliable way to determine if references or views to it exist.
SystemError – If the order keyword argument is specified. This behaviour is a bug in NumPy.

See also

resize: Return a new array with the specified shape.

Notes

This reallocates space for the data area if necessary.

Only contiguous arrays (data elements consecutive in memory) can be resized.

The purpose of the reference count check is to make sure you do not use this array as a buffer for another Python object and then reallocate the memory. However, reference counts can increase in other ways so if you are sure that you have not shared the memory for this array with another Python object, then you may safely set refcheck to False.

Examples

Shrinking an array: array is flattened (in the order that the data are stored in memory), resized, and reshaped:

>>> import numpy as np

>>> a = np.array([[0, 1], [2, 3]], order='C')
>>> a.resize((2, 1))
>>> a
array([[0],
       [1]])

>>> a = np.array([[0, 1], [2, 3]], order='F')
>>> a.resize((2, 1))
>>> a
array([[0],
       [2]])

Enlarging an array: as above, but missing entries are filled with zeros:

>>> b = np.array([[0, 1], [2, 3]])
>>> b.resize(2, 3) # new_shape parameter doesn't have to be a tuple
>>> b
array([[0, 1, 2],
       [3, 0, 0]])

Referencing an array prevents resizing…

>>> c = a
>>> a.resize((1, 1))
Traceback (most recent call last):
...
ValueError: cannot resize an array that references or is referenced ...

Unless refcheck is False:

>>> a.resize((1, 1), refcheck=False)
>>> a
array([[0]])
>>> c
array([[0]])

round(decimals=0, out=None)#

Return a with each element rounded to the given number of decimals.

Refer to numpy.around for full documentation.

See also

numpy.around: equivalent function

searchsorted(v, side='left', sorter=None)#

Find indices where elements of v should be inserted in a to maintain order.

For full documentation, see numpy.searchsorted

See also

numpy.searchsorted: equivalent function

set_default_units(quiet=False)#

Set the units for this array by guessing the sim’s unit scheme and known dimensionality information.

For example, if sim has units of Msol and kpc and this array is the rho array, the units of this array will be set to Msol kpc^-3.

Note that this does not convert the array to the new units, it only sets the units attribute. To convert, use in_units(), convert_units() or in_original_units().

set_units_like(new_unit)[source]#

Set the units of this array using a guess the sim’s units for a given dimensionality.

For example, if sim has units of Msol and kpc, and new_unit is kg m^-3, the units of this array will be set to Msol kpc^-3.

Note that this does not convert the array to the new units, it only sets the units attribute. To convert, use in_units(), convert_units() or in_original_units().

setfield(val, dtype, offset=0)#

Put a value into a specified place in a field defined by a data-type.

Place val into a’s field defined by dtype and beginning offset bytes into the field.

Parameters:

val (object) – Value to be placed in field.
dtype (dtype object) – Data-type of the field in which to place val.
offset (int, optional) – The number of bytes into the field at which to place val.

Return type:

None

See also

getfield

Examples

>>> import numpy as np
>>> x = np.eye(3)
>>> x.getfield(np.float64)
array([[1.,  0.,  0.],
       [0.,  1.,  0.],
       [0.,  0.,  1.]])
>>> x.setfield(3, np.int32)
>>> x.getfield(np.int32)
array([[3, 3, 3],
       [3, 3, 3],
       [3, 3, 3]], dtype=int32)
>>> x
array([[1.0e+000, 1.5e-323, 1.5e-323],
       [1.5e-323, 1.0e+000, 1.5e-323],
       [1.5e-323, 1.5e-323, 1.0e+000]])
>>> x.setfield(np.eye(3), np.int32)
>>> x
array([[1.,  0.,  0.],
       [0.,  1.,  0.],
       [0.,  0.,  1.]])

setflags(write=None, align=None, uic=None)#

Set array flags WRITEABLE, ALIGNED, WRITEBACKIFCOPY, respectively.

These Boolean-valued flags affect how numpy interprets the memory area used by a (see Notes below). The ALIGNED flag can only be set to True if the data is actually aligned according to the type. The WRITEBACKIFCOPY flag can never be set to True. The flag WRITEABLE can only be set to True if the array owns its own memory, or the ultimate owner of the memory exposes a writeable buffer interface, or is a string. (The exception for string is made so that unpickling can be done without copying memory.)

Parameters:

write (bool, optional) – Describes whether or not a can be written to.
align (bool, optional) – Describes whether or not a is aligned properly for its type.
uic (bool, optional) – Describes whether or not a is a copy of another “base” array.

Notes

Array flags provide information about how the memory area used for the array is to be interpreted. There are 7 Boolean flags in use, only three of which can be changed by the user: WRITEBACKIFCOPY, WRITEABLE, and ALIGNED.

WRITEABLE (W) the data area can be written to;

ALIGNED (A) the data and strides are aligned appropriately for the hardware (as determined by the compiler);

WRITEBACKIFCOPY (X) this array is a copy of some other array (referenced by .base). When the C-API function PyArray_ResolveWritebackIfCopy is called, the base array will be updated with the contents of this array.

All flags can be accessed using the single (upper case) letter as well as the full name.

Examples

>>> import numpy as np
>>> y = np.array([[3, 1, 7],
...               [2, 0, 0],
...               [8, 5, 9]])
>>> y
array([[3, 1, 7],
       [2, 0, 0],
       [8, 5, 9]])
>>> y.flags
  C_CONTIGUOUS : True
  F_CONTIGUOUS : False
  OWNDATA : True
  WRITEABLE : True
  ALIGNED : True
  WRITEBACKIFCOPY : False
>>> y.setflags(write=0, align=0)
>>> y.flags
  C_CONTIGUOUS : True
  F_CONTIGUOUS : False
  OWNDATA : True
  WRITEABLE : False
  ALIGNED : False
  WRITEBACKIFCOPY : False
>>> y.setflags(uic=1)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ValueError: cannot set WRITEBACKIFCOPY flag to True

property shape#

Tuple of array dimensions.

The shape property is usually used to get the current shape of an array, but may also be used to reshape the array in-place by assigning a tuple of array dimensions to it. As with numpy.reshape, one of the new shape dimensions can be -1, in which case its value is inferred from the size of the array and the remaining dimensions. Reshaping an array in-place will fail if a copy is required.

Warning

Setting arr.shape is discouraged and may be deprecated in the future. Using ndarray.reshape is the preferred approach.

Examples

>>> import numpy as np
>>> x = np.array([1, 2, 3, 4])
>>> x.shape
(4,)
>>> y = np.zeros((2, 3, 4))
>>> y.shape
(2, 3, 4)
>>> y.shape = (3, 8)
>>> y
array([[ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.],
       [ 0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.]])
>>> y.shape = (3, 6)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ValueError: cannot reshape array of size 24 into shape (3,6)
>>> np.zeros((4,2))[::2].shape = (-1,)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: Incompatible shape for in-place modification. Use
`.reshape()` to make a copy with the desired shape.

See also

numpy.shape: Equivalent getter function.
numpy.reshape: Function similar to setting shape.
ndarray.reshape: Method similar to setting shape.

property sim#: The simulation snapshot that the array belongs to, if known.

sort(axis=-1, kind=None, order=None)#

Sort an array in-place. Refer to numpy.sort for full documentation.

Parameters:

axis (int, optional) – Axis along which to sort. Default is -1, which means sort along the last axis.
kind ({'quicksort', 'mergesort', 'heapsort', 'stable'}, optional) – Sorting algorithm. The default is ‘quicksort’. Note that both ‘stable’ and ‘mergesort’ use timsort under the covers and, in general, the actual implementation will vary with datatype. The ‘mergesort’ option is retained for backwards compatibility.
order (str or list of str, optional) – When a is an array with fields defined, this argument specifies which fields to compare first, second, etc. A single field can be specified as a string, and not all fields need be specified, but unspecified fields will still be used, in the order in which they come up in the dtype, to break ties.

See also

numpy.sort: Return a sorted copy of an array.
numpy.argsort: Indirect sort.
numpy.lexsort: Indirect stable sort on multiple keys.
numpy.searchsorted: Find elements in sorted array.
numpy.partition: Partial sort.

Notes

See numpy.sort for notes on the different sorting algorithms.

Examples

>>> import numpy as np
>>> a = np.array([[1,4], [3,1]])
>>> a.sort(axis=1)
>>> a
array([[1, 4],
       [1, 3]])
>>> a.sort(axis=0)
>>> a
array([[1, 3],
       [1, 4]])

Use the order keyword to specify a field to use when sorting a structured array:

>>> a = np.array([('a', 2), ('c', 1)], dtype=[('x', 'S1'), ('y', int)])
>>> a.sort(order='y')
>>> a
array([(b'c', 1), (b'a', 2)],
      dtype=[('x', 'S1'), ('y', '<i8')])

squeeze(axis=None)#

Remove axes of length one from a.

Refer to numpy.squeeze for full documentation.

See also

numpy.squeeze: equivalent function

std(axis=None, dtype=None, out=None, ddof=0, keepdims=False, *, where=True)#

Returns the standard deviation of the array elements along given axis.

Refer to numpy.std for full documentation.

See also

numpy.std: equivalent function

sum(axis=None, dtype=None, out=None, keepdims=False, initial=0, where=True)#

Return the sum of the array elements over the given axis.

Refer to numpy.sum for full documentation.

See also

numpy.sum: equivalent function

swapaxes(axis1, axis2)#

Return a view of the array with axis1 and axis2 interchanged.

Refer to numpy.swapaxes for full documentation.

See also

numpy.swapaxes: equivalent function

take(indices, axis=None, out=None, mode='raise')#

Return an array formed from the elements of a at the given indices.

Refer to numpy.take for full documentation.

See also

numpy.take: equivalent function

tobytes(order='C')#

Construct Python bytes containing the raw data bytes in the array.

Constructs Python bytes showing a copy of the raw contents of data memory. The bytes object is produced in C-order by default. This behavior is controlled by the order parameter.

Parameters:: order ({'C', 'F', 'A'}, optional) – Controls the memory layout of the bytes object. ‘C’ means C-order, ‘F’ means F-order, ‘A’ (short for Any) means ‘F’ if a is Fortran contiguous, ‘C’ otherwise. Default is ‘C’.
Returns:: s – Python bytes exhibiting a copy of a’s raw data.
Return type:: bytes

See also

frombuffer: Inverse of this operation, construct a 1-dimensional array from Python bytes.

Examples

>>> import numpy as np
>>> x = np.array([[0, 1], [2, 3]], dtype='<u2')
>>> x.tobytes()
b'\x00\x00\x01\x00\x02\x00\x03\x00'
>>> x.tobytes('C') == x.tobytes()
True
>>> x.tobytes('F')
b'\x00\x00\x02\x00\x01\x00\x03\x00'

tofile(fid, sep='', format='%s')#

Write array to a file as text or binary (default).

Data is always written in ‘C’ order, independent of the order of a. The data produced by this method can be recovered using the function fromfile().

Parameters:

fid (file or str or Path) – An open file object, or a string containing a filename.
sep (str) – Separator between array items for text output. If “” (empty), a binary file is written, equivalent to file.write(a.tobytes()).
format (str) – Format string for text file output. Each entry in the array is formatted to text by first converting it to the closest Python type, and then using “format” % item.

Notes

This is a convenience function for quick storage of array data. Information on endianness and precision is lost, so this method is not a good choice for files intended to archive data or transport data between machines with different endianness. Some of these problems can be overcome by outputting the data as text files, at the expense of speed and file size.

When fid is a file object, array contents are directly written to the file, bypassing the file object’s write method. As a result, tofile cannot be used with files objects supporting compression (e.g., GzipFile) or file-like objects that do not support fileno() (e.g., BytesIO).

tolist()#

Return the array as an a.ndim-levels deep nested list of Python scalars.

Return a copy of the array data as a (nested) Python list. Data items are converted to the nearest compatible builtin Python type, via the ~numpy.ndarray.item function.

If a.ndim is 0, then since the depth of the nested list is 0, it will not be a list at all, but a simple Python scalar.

Parameters:: none
Returns:: y – The possibly nested list of array elements.
Return type:: object, or list of object, or list of list of object, or …

Notes

The array may be recreated via a = np.array(a.tolist()), although this may sometimes lose precision.

Examples

For a 1D array, a.tolist() is almost the same as list(a), except that tolist changes numpy scalars to Python scalars:

>>> import numpy as np
>>> a = np.uint32([1, 2])
>>> a_list = list(a)
>>> a_list
[np.uint32(1), np.uint32(2)]
>>> type(a_list[0])
<class 'numpy.uint32'>
>>> a_tolist = a.tolist()
>>> a_tolist
[1, 2]
>>> type(a_tolist[0])
<class 'int'>

Additionally, for a 2D array, tolist applies recursively:

>>> a = np.array([[1, 2], [3, 4]])
>>> list(a)
[array([1, 2]), array([3, 4])]
>>> a.tolist()
[[1, 2], [3, 4]]

The base case for this recursion is a 0D array:

>>> a = np.array(1)
>>> list(a)
Traceback (most recent call last):
  ...
TypeError: iteration over a 0-d array
>>> a.tolist()
1

trace(offset=0, axis1=0, axis2=1, dtype=None, out=None)#

Return the sum along diagonals of the array.

Refer to numpy.trace for full documentation.

See also

numpy.trace: equivalent function

transpose(*axes)#

Returns a view of the array with axes transposed.

Refer to numpy.transpose for full documentation.

Parameters:

axes (None, tuple of ints, or n ints) –

None or no argument: reverses the order of the axes.
tuple of ints: i in the j-th place in the tuple means that the array’s i-th axis becomes the transposed array’s j-th axis.
n ints: same as an n-tuple of the same ints (this form is intended simply as a “convenience” alternative to the tuple form).

Returns:

p – View of the array with its axes suitably permuted.

Return type:

ndarray

See also

transpose: Equivalent function.
ndarray.T: Array property returning the array transposed.
ndarray.reshape: Give a new shape to an array without changing its data.

Examples

>>> import numpy as np
>>> a = np.array([[1, 2], [3, 4]])
>>> a
array([[1, 2],
       [3, 4]])
>>> a.transpose()
array([[1, 3],
       [2, 4]])
>>> a.transpose((1, 0))
array([[1, 3],
       [2, 4]])
>>> a.transpose(1, 0)
array([[1, 3],
       [2, 4]])

>>> a = np.array([1, 2, 3, 4])
>>> a
array([1, 2, 3, 4])
>>> a.transpose()
array([1, 2, 3, 4])

ufunc_rule()#

Function decorator to mark a function as providing the output units for a given ufunc (or ufuncs).

The function should take the same number of arguments as the ufunc, and return the output units. The function may optionally also return a tuple of the output units and the modified input arguments, in which case the input arguments will be passed to the ufunc in place of the original arguments.

Note that while this is predominantly used for ufuncs, in fact it can also be used for things which are not strictly ufuncs, like numpy.linalg.norm

property units#: The units of the array, if known; otherwise units.NoUnit.

var(axis=None, dtype=None, out=None, ddof=0, keepdims=False, *, where=True)#

Returns the variance of the array elements, along given axis.

Refer to numpy.var for full documentation.

See also

numpy.var: equivalent function

view([dtype][, type])#

New view of array with the same data.

Note

Passing None for dtype is different from omitting the parameter, since the former invokes dtype(None) which is an alias for dtype('float64').

Parameters:

dtype (data-type or ndarray sub-class, optional) – Data-type descriptor of the returned view, e.g., float32 or int16. Omitting it results in the view having the same data-type as a. This argument can also be specified as an ndarray sub-class, which then specifies the type of the returned object (this is equivalent to setting the type parameter).
type (Python type, optional) – Type of the returned view, e.g., ndarray or matrix. Again, omission of the parameter results in type preservation.

Notes

a.view() is used two different ways:

a.view(some_dtype) or a.view(dtype=some_dtype) constructs a view of the array’s memory with a different data-type. This can cause a reinterpretation of the bytes of memory.

a.view(ndarray_subclass) or a.view(type=ndarray_subclass) just returns an instance of ndarray_subclass that looks at the same array (same shape, dtype, etc.) This does not cause a reinterpretation of the memory.

For a.view(some_dtype), if some_dtype has a different number of bytes per entry than the previous dtype (for example, converting a regular array to a structured array), then the last axis of a must be contiguous. This axis will be resized in the result.

Changed in version 1.23.0: Only the last axis needs to be contiguous. Previously, the entire array had to be C-contiguous.

Examples

>>> import numpy as np
>>> x = np.array([(-1, 2)], dtype=[('a', np.int8), ('b', np.int8)])

Viewing array data using a different type and dtype:

>>> nonneg = np.dtype([("a", np.uint8), ("b", np.uint8)])
>>> y = x.view(dtype=nonneg, type=np.recarray)
>>> x["a"]
array([-1], dtype=int8)
>>> y.a
array([255], dtype=uint8)

Creating a view on a structured array so it can be used in calculations

>>> x = np.array([(1, 2),(3,4)], dtype=[('a', np.int8), ('b', np.int8)])
>>> xv = x.view(dtype=np.int8).reshape(-1,2)
>>> xv
array([[1, 2],
       [3, 4]], dtype=int8)
>>> xv.mean(0)
array([2.,  3.])

Making changes to the view changes the underlying array

>>> xv[0,1] = 20
>>> x
array([(1, 20), (3,  4)], dtype=[('a', 'i1'), ('b', 'i1')])

Using a view to convert an array to a recarray:

>>> z = x.view(np.recarray)
>>> z.a
array([1, 3], dtype=int8)

Views share data:

>>> x[0] = (9, 10)
>>> z[0]
np.record((9, 10), dtype=[('a', 'i1'), ('b', 'i1')])

Views that change the dtype size (bytes per entry) should normally be avoided on arrays defined by slices, transposes, fortran-ordering, etc.:

>>> x = np.array([[1, 2, 3], [4, 5, 6]], dtype=np.int16)
>>> y = x[:, ::2]
>>> y
array([[1, 3],
       [4, 6]], dtype=int16)
>>> y.view(dtype=[('width', np.int16), ('length', np.int16)])
Traceback (most recent call last):
    ...
ValueError: To change to a dtype of a different size, the last axis must be contiguous
>>> z = y.copy()
>>> z.view(dtype=[('width', np.int16), ('length', np.int16)])
array([[(1, 3)],
       [(4, 6)]], dtype=[('width', '<i2'), ('length', '<i2')])

However, views that change dtype are totally fine for arrays with a contiguous last axis, even if the rest of the axes are not C-contiguous:

>>> x = np.arange(2 * 3 * 4, dtype=np.int8).reshape(2, 3, 4)
>>> x.transpose(1, 0, 2).view(np.int16)
array([[[ 256,  770],
        [3340, 3854]],

       [[1284, 1798],
        [4368, 4882]],

       [[2312, 2826],
        [5396, 5910]]], dtype=int16)

write(**kwargs)[source]#

Write this array to disk according to the standard method associated with its base file. This is equivalent to calling

>>> sim.gas.write_array('array')

in the case of writing out the array ‘array’ for the gas particle family. See the description of pynbody.snapshot.SimSnap.write_array() for options.

pynbody.array.IndexedSimArray

Contents

pynbody.array.IndexedSimArray#