Map Domain

Internally, map domain objects (hit maps, signal maps, pixel noise covariances, etc) are stored in a distributed fashion. This enables each process to only store a subset of the sky pixels, which saves memory for large maps at high resolution. PixelData objects have methods to read and write HDF5 and FITS format files.

toast.pixels.PixelDistribution

Bases: AcceleratorObject

Class representing the distribution of submaps.

This object is used to describe the properties of a pixelization scheme and which "submaps" are strored on each process. The size of the submap can be tuned to balance storage (smaller submap size means fewer wasted pixels stored) and ease of indexing (larger submap size means faster global-to-local pixel lookups).

Parameters:

Name	Type	Description	Default
n_pix	int	the total number of pixels.	None
n_submap	int	the number of submaps to use.	1000
local_submaps	array	the list of local submaps (integers).	None
comm	Comm	The MPI communicator or None.	None

Source code in toast/pixels.py

class PixelDistribution(AcceleratorObject):
    """Class representing the distribution of submaps.

    This object is used to describe the properties of a pixelization scheme and which
    "submaps" are strored on each process.  The size of the submap can be tuned to
    balance storage (smaller submap size means fewer wasted pixels stored) and ease of
    indexing (larger submap size means faster global-to-local pixel lookups).

    Args:
        n_pix (int): the total number of pixels.
        n_submap (int): the number of submaps to use.
        local_submaps (array): the list of local submaps (integers).
        comm (mpi4py.MPI.Comm): The MPI communicator or None.

    """

    def __init__(self, n_pix=None, n_submap=1000, local_submaps=None, comm=None):
        super().__init__()
        self._n_pix = n_pix
        self._n_submap = n_submap
        if self._n_submap > self._n_pix:
            msg = "Cannot create a PixelDistribution with more submaps ({}) than pixels ({})".format(
                n_submap, n_pix
            )
            raise RuntimeError(msg)
        self._n_pix_submap = self._n_pix // self._n_submap
        if self._n_pix % self._n_submap != 0:
            self._n_pix_submap += 1

        self._local_submaps = local_submaps
        self._comm = comm

        self._n_local = 0
        self._glob2loc = AlignedI64.zeros(self._n_submap)
        self._glob2loc[:] = -1

        if self._local_submaps is not None and len(self._local_submaps) > 0:
            if np.max(self._local_submaps) > self._n_submap - 1:
                raise RuntimeError("local submap indices out of range")
            self._n_local = len(self._local_submaps)
            for ilocal_submap, iglobal_submap in enumerate(self._local_submaps):
                self._glob2loc[iglobal_submap] = ilocal_submap

        self._submap_owners = None
        self._owned_submaps = None
        self._alltoallv_info = None
        self._all_hit_submaps = None

    def __eq__(self, other):
        local_eq = True
        if self._n_pix != other._n_pix:
            local_eq = False
        if self._n_submap != other._n_submap:
            local_eq = False
        if self._n_pix_submap != other._n_pix_submap:
            local_eq = False
        if not np.array_equal(self._local_submaps, other._local_submaps):
            local_eq = False
        if self._comm is None and other._comm is not None:
            local_eq = False
        if self._comm is not None and other._comm is None:
            local_eq = False
        if self._comm is not None:
            comp = MPI.Comm.Compare(self._comm, other._comm)
            if comp not in (MPI.IDENT, MPI.CONGRUENT):
                local_eq = False
        return local_eq

    def __ne__(self, other):
        return not self.__eq__(other)

    def clear(self):
        """Delete the underlying memory.

        This will forcibly delete the C-allocated memory and invalidate all python
        references to this object.  DO NOT CALL THIS unless you are sure all references
        are no longer being used and you are about to delete the object.

        """
        if hasattr(self, "_glob2loc"):
            if self._glob2loc is not None:
                self._glob2loc.clear()
                del self._glob2loc

    def __del__(self):
        self.clear()

    @property
    def comm(self):
        """(mpi4py.MPI.Comm): The MPI communicator used (or None)"""
        return self._comm

    @property
    def n_pix(self):
        """(int): The global number of pixels."""
        return self._n_pix

    @property
    def n_pix_submap(self):
        """(int): The number of pixels in each submap."""
        return self._n_pix_submap

    @property
    def n_submap(self):
        """(int): The total number of submaps."""
        return self._n_submap

    @property
    def n_local_submap(self):
        """(int): The number of submaps stored on this process."""
        return self._n_local

    @property
    def local_submaps(self):
        """(array): The list of local submaps or None if process has no data."""
        return self._local_submaps

    @property
    def all_hit_submaps(self):
        """(array): The list of submaps local to atleast one process."""
        if self._all_hit_submaps is None:
            hits = np.zeros(self._n_submap)
            hits[self._local_submaps] += 1
            if self._comm is not None:
                self._comm.Allreduce(MPI.IN_PLACE, hits)
            self._all_hit_submaps = np.argwhere(hits != 0).ravel()
        return self._all_hit_submaps

    @property
    def global_submap_to_local(self):
        """(array): The mapping from global submap to local."""
        return self._glob2loc

    @function_timer
    def global_pixel_to_submap(self, gl):
        """Convert global pixel indices into the local submap and pixel.

        Args:
            gl (array): The global pixel numbers.

        Returns:
            (tuple):  A tuple of arrays containing the local submap index (int) and the
                pixel index local to that submap (int).

        """
        if len(gl) == 0:
            return (np.zeros_like(gl), np.zeros_like(gl))
        log = Logger.get()
        if np.max(gl) >= self._n_pix:
            msg = "Global pixel indices exceed the maximum for the pixelization"
            log.error(msg)
            raise RuntimeError(msg)
        return libtoast_global_to_local(gl, self._n_pix_submap, self._glob2loc)

    @function_timer
    def global_pixel_to_local(self, gl):
        """Convert global pixel indices into local pixel indices.

        Args:
            gl (array): The global pixel numbers.

        Returns:
            (array): The local raw (flat packed) buffer index for each pixel.

        """
        if len(gl) == 0:
            return np.zeros_like(gl)
        if np.max(gl) >= self._n_pix:
            log = Logger.get()
            msg = "Global pixel indices exceed the maximum for the pixelization"
            log.error(msg)
            raise RuntimeError(msg)
        local_sm, pixels = libtoast_global_to_local(
            gl, self._n_pix_submap, self._glob2loc
        )
        local_sm *= self._n_pix_submap
        pixels += local_sm
        return pixels

    def __repr__(self):
        val = "<PixelDistribution {} pixels, {} submaps, submap size = {}>".format(
            self._n_pix, self._n_submap, self._n_pix_submap
        )
        return val

    @property
    def submap_owners(self):
        """The owning process for every hit submap.

        This information is used in several other operations, including serializing
        PixelData objects to a single process and also communication needed for
        reducing data globally.
        """
        if self._submap_owners is not None:
            # Already computed
            return self._submap_owners

        self._submap_owners = np.empty(self._n_submap, dtype=np.int32)
        self._submap_owners[:] = -1

        if self._comm is None:
            # Trivial case
            if self._local_submaps is not None and len(self._local_submaps) > 0:
                self._submap_owners[self._local_submaps] = 0
        else:
            # Need to compute it.
            local_hit_submaps = np.zeros(self._n_submap, dtype=np.uint8)
            local_hit_submaps[self._local_submaps] = 1

            hit_submaps = None
            if self._comm.rank == 0:
                hit_submaps = np.zeros(self._n_submap, dtype=np.uint8)

            self._comm.Reduce(local_hit_submaps, hit_submaps, op=MPI.LOR, root=0)
            del local_hit_submaps

            if self._comm.rank == 0:
                total_hit_submaps = np.sum(hit_submaps.astype(np.int32))
                tdist = distribute_uniform(total_hit_submaps, self._comm.size)

                # The target number of submaps per process
                target = [x[1] for x in tdist]

                # Assign the submaps in rank order.  This ensures better load
                # distribution when serializing some operations and also reduces needed
                # memory copies when using Alltoallv.
                proc_offset = 0
                proc = 0
                for sm in range(self._n_submap):
                    if hit_submaps[sm] > 0:
                        self._submap_owners[sm] = proc
                        proc_offset += 1
                        if proc_offset >= target[proc]:
                            proc += 1
                            proc_offset = 0
                del hit_submaps

            self._comm.Bcast(self._submap_owners, root=0)
        return self._submap_owners

    @property
    def owned_submaps(self):
        """The submaps owned by this process."""
        if self._owned_submaps is not None:
            # Already computed
            return self._owned_submaps
        owners = self.submap_owners
        if self._comm is None:
            self._owned_submaps = np.array(
                [x for x, y in enumerate(owners) if y == 0], dtype=np.int32
            )
        else:
            self._owned_submaps = np.array(
                [x for x, y in enumerate(owners) if y == self._comm.rank],
                dtype=np.int32,
            )
        return self._owned_submaps

    @property
    def alltoallv_info(self):
        """Return the offset information for Alltoallv communication.

        This returns a tuple containing:
            - The send displacements for the Alltoallv submap gather
            - The send counts for the Alltoallv submap gather
            - The receive displacements for the Alltoallv submap gather
            - The receive counts for the Alltoallv submap gather
            - The locations in the receive buffer of each submap.

        """
        log = Logger.get()
        if self._alltoallv_info is not None:
            # Already computed
            return self._alltoallv_info

        owners = self.submap_owners
        our_submaps = self.owned_submaps

        send_counts = None
        send_displ = None
        recv_counts = None
        recv_displ = None
        recv_locations = None

        if self._comm is None:
            recv_counts = len(self._local_submaps) * np.ones(1, dtype=np.int32)
            recv_displ = np.zeros(1, dtype=np.int32)
            recv_locations = dict()
            for offset, sm in enumerate(self._local_submaps):
                recv_locations[sm] = np.array([offset], dtype=np.int32)
            send_counts = len(self._local_submaps) * np.ones(1, dtype=np.int32)
            send_displ = np.zeros(1, dtype=np.int32)
        else:
            # Compute the other "contributing" processes that have submaps which we own.
            # Also track the receive buffer offsets for each owned submap.
            send = [list() for x in range(self._comm.size)]
            for sm in self._local_submaps:
                # Tell the owner of this submap that we are a contributor
                send[owners[sm]].append(sm)
            recv = self._comm.alltoall(send)

            recv_counts = np.zeros(self._comm.size, dtype=np.int32)
            recv_displ = np.zeros(self._comm.size, dtype=np.int32)
            recv_locations = dict()

            offset = 0
            for proc, sms in enumerate(recv):
                recv_displ[proc] = offset
                for sm in sms:
                    if sm not in recv_locations:
                        recv_locations[sm] = list()
                    recv_locations[sm].append(offset)
                    recv_counts[proc] += 1
                    offset += 1

            for sm in list(recv_locations.keys()):
                recv_locations[sm] = np.array(recv_locations[sm], dtype=np.int32)

            # Compute the Alltoallv send offsets in terms of submaps
            send_counts = np.zeros(self._comm.size, dtype=np.int32)
            send_displ = np.zeros(self._comm.size, dtype=np.int32)
            offset = 0
            last_offset = 0
            last_own = -1
            for sm in self._local_submaps:
                if last_own != owners[sm]:
                    # Moving on to next owning process...
                    if last_own >= 0:
                        send_displ[last_own] = last_offset
                        last_offset = offset
                send_counts[owners[sm]] += 1
                offset += 1
                last_own = owners[sm]
            if last_own >= 0:
                # Finish up last process
                send_displ[last_own] = last_offset

        self._alltoallv_info = (
            send_counts,
            send_displ,
            recv_counts,
            recv_displ,
            recv_locations,
        )

        msg_rank = 0
        if self._comm is not None:
            msg_rank = self._comm.rank
        msg = f"alltoallv_info[{msg_rank}]:\n"
        msg += f"  send_counts={send_counts} "
        msg += f"send_displ={send_displ}\n"
        msg += f"  recv_counts={recv_counts} "
        msg += f"recv_displ={recv_displ} "
        msg += f"recv_locations={recv_locations}"
        log.verbose(msg)

        return self._alltoallv_info

    def _accel_exists(self):
        return accel_data_present(self._glob2loc, self._accel_name)

    def _accel_create(self):
        self._glob2loc = accel_data_create(self._glob2loc, self._accel_name)

    def _accel_update_device(self):
        self._glob2loc = accel_data_update_device(self._glob2loc, self._accel_name)

    def _accel_update_host(self):
        self._glob2loc = accel_data_update_host(self._glob2loc, self._accel_name)

    def _accel_reset(self):
        accel_data_reset(self._glob2loc, self._accel_name)

    def _accel_delete(self):
        self._glob2loc = accel_data_delete(self._glob2loc, self._accel_name)

_all_hit_submaps = None instance-attribute

_alltoallv_info = None instance-attribute

_comm = comm instance-attribute

_glob2loc = AlignedI64.zeros(self._n_submap) instance-attribute

_local_submaps = local_submaps instance-attribute

_n_local = 0 instance-attribute

_n_pix = n_pix instance-attribute

_n_pix_submap = self._n_pix // self._n_submap instance-attribute

_n_submap = n_submap instance-attribute

_owned_submaps = None instance-attribute

_submap_owners = None instance-attribute

all_hit_submaps property

(array): The list of submaps local to atleast one process.

alltoallv_info property

Return the offset information for Alltoallv communication.

This returns a tuple containing

• The send displacements for the Alltoallv submap gather
• The send counts for the Alltoallv submap gather
• The receive displacements for the Alltoallv submap gather
• The receive counts for the Alltoallv submap gather
• The locations in the receive buffer of each submap.

comm property

(mpi4py.MPI.Comm): The MPI communicator used (or None)

global_submap_to_local property

(array): The mapping from global submap to local.

local_submaps property

(array): The list of local submaps or None if process has no data.

n_local_submap property

(int): The number of submaps stored on this process.

n_pix property

(int): The global number of pixels.

n_pix_submap property

(int): The number of pixels in each submap.

n_submap property

(int): The total number of submaps.

owned_submaps property

The submaps owned by this process.

submap_owners property

The owning process for every hit submap.

This information is used in several other operations, including serializing PixelData objects to a single process and also communication needed for reducing data globally.

__del__()

Source code in toast/pixels.py

def __del__(self):
    self.clear()

__eq__(other)

Source code in toast/pixels.py

def __eq__(self, other):
    local_eq = True
    if self._n_pix != other._n_pix:
        local_eq = False
    if self._n_submap != other._n_submap:
        local_eq = False
    if self._n_pix_submap != other._n_pix_submap:
        local_eq = False
    if not np.array_equal(self._local_submaps, other._local_submaps):
        local_eq = False
    if self._comm is None and other._comm is not None:
        local_eq = False
    if self._comm is not None and other._comm is None:
        local_eq = False
    if self._comm is not None:
        comp = MPI.Comm.Compare(self._comm, other._comm)
        if comp not in (MPI.IDENT, MPI.CONGRUENT):
            local_eq = False
    return local_eq

__init__(n_pix=None, n_submap=1000, local_submaps=None, comm=None)

Source code in toast/pixels.py

def __init__(self, n_pix=None, n_submap=1000, local_submaps=None, comm=None):
    super().__init__()
    self._n_pix = n_pix
    self._n_submap = n_submap
    if self._n_submap > self._n_pix:
        msg = "Cannot create a PixelDistribution with more submaps ({}) than pixels ({})".format(
            n_submap, n_pix
        )
        raise RuntimeError(msg)
    self._n_pix_submap = self._n_pix // self._n_submap
    if self._n_pix % self._n_submap != 0:
        self._n_pix_submap += 1

    self._local_submaps = local_submaps
    self._comm = comm

    self._n_local = 0
    self._glob2loc = AlignedI64.zeros(self._n_submap)
    self._glob2loc[:] = -1

    if self._local_submaps is not None and len(self._local_submaps) > 0:
        if np.max(self._local_submaps) > self._n_submap - 1:
            raise RuntimeError("local submap indices out of range")
        self._n_local = len(self._local_submaps)
        for ilocal_submap, iglobal_submap in enumerate(self._local_submaps):
            self._glob2loc[iglobal_submap] = ilocal_submap

    self._submap_owners = None
    self._owned_submaps = None
    self._alltoallv_info = None
    self._all_hit_submaps = None

__ne__(other)

Source code in toast/pixels.py

def __ne__(self, other):
    return not self.__eq__(other)

__repr__()

Source code in toast/pixels.py

def __repr__(self):
    val = "<PixelDistribution {} pixels, {} submaps, submap size = {}>".format(
        self._n_pix, self._n_submap, self._n_pix_submap
    )
    return val

_accel_create()

Source code in toast/pixels.py

def _accel_create(self):
    self._glob2loc = accel_data_create(self._glob2loc, self._accel_name)

_accel_delete()

Source code in toast/pixels.py

def _accel_delete(self):
    self._glob2loc = accel_data_delete(self._glob2loc, self._accel_name)

_accel_exists()

Source code in toast/pixels.py

def _accel_exists(self):
    return accel_data_present(self._glob2loc, self._accel_name)

_accel_reset()

Source code in toast/pixels.py

def _accel_reset(self):
    accel_data_reset(self._glob2loc, self._accel_name)

_accel_update_device()

Source code in toast/pixels.py

def _accel_update_device(self):
    self._glob2loc = accel_data_update_device(self._glob2loc, self._accel_name)

_accel_update_host()

Source code in toast/pixels.py

def _accel_update_host(self):
    self._glob2loc = accel_data_update_host(self._glob2loc, self._accel_name)

clear()

Delete the underlying memory.

This will forcibly delete the C-allocated memory and invalidate all python references to this object. DO NOT CALL THIS unless you are sure all references are no longer being used and you are about to delete the object.

Source code in toast/pixels.py

def clear(self):
    """Delete the underlying memory.

    This will forcibly delete the C-allocated memory and invalidate all python
    references to this object.  DO NOT CALL THIS unless you are sure all references
    are no longer being used and you are about to delete the object.

    """
    if hasattr(self, "_glob2loc"):
        if self._glob2loc is not None:
            self._glob2loc.clear()
            del self._glob2loc

global_pixel_to_local(gl)

Convert global pixel indices into local pixel indices.

Parameters:

Name	Type	Description	Default
gl	array	The global pixel numbers.	required

Returns:

Type	Description
array	The local raw (flat packed) buffer index for each pixel.

Source code in toast/pixels.py

@function_timer
def global_pixel_to_local(self, gl):
    """Convert global pixel indices into local pixel indices.

    Args:
        gl (array): The global pixel numbers.

    Returns:
        (array): The local raw (flat packed) buffer index for each pixel.

    """
    if len(gl) == 0:
        return np.zeros_like(gl)
    if np.max(gl) >= self._n_pix:
        log = Logger.get()
        msg = "Global pixel indices exceed the maximum for the pixelization"
        log.error(msg)
        raise RuntimeError(msg)
    local_sm, pixels = libtoast_global_to_local(
        gl, self._n_pix_submap, self._glob2loc
    )
    local_sm *= self._n_pix_submap
    pixels += local_sm
    return pixels

global_pixel_to_submap(gl)

Convert global pixel indices into the local submap and pixel.

Parameters:

Name	Type	Description	Default
gl	array	The global pixel numbers.	required

Returns:

Type	Description
tuple	A tuple of arrays containing the local submap index (int) and the pixel index local to that submap (int).

Source code in toast/pixels.py

@function_timer
def global_pixel_to_submap(self, gl):
    """Convert global pixel indices into the local submap and pixel.

    Args:
        gl (array): The global pixel numbers.

    Returns:
        (tuple):  A tuple of arrays containing the local submap index (int) and the
            pixel index local to that submap (int).

    """
    if len(gl) == 0:
        return (np.zeros_like(gl), np.zeros_like(gl))
    log = Logger.get()
    if np.max(gl) >= self._n_pix:
        msg = "Global pixel indices exceed the maximum for the pixelization"
        log.error(msg)
        raise RuntimeError(msg)
    return libtoast_global_to_local(gl, self._n_pix_submap, self._glob2loc)

toast.pixels.PixelData

Bases: AcceleratorObject

Distributed map-domain data.

The distribution information is stored in a PixelDistribution instance passed to the constructor. Each process has local data stored in one or more "submaps".

Although multiple processes may have the same submap of data stored locally, only one process is considered the "owner". This ownership is used when serializing the data and when doing reductions in certain cases. Ownership can be set to either the lowest rank process which has the submap or to a balanced distribution.

Parameters:

Name	Type	Description	Default
dist	PixelDistribution	The distribution of submaps.	required
dtype	dtype	A numpy-compatible dtype for each element of the data. The only supported types are 1, 2, 4, and 8 byte signed and unsigned integers, 4 and 8 byte floating point numbers, and 4 and 8 byte complex numbers.	required
n_value	int	The number of values per pixel.	1
units	Unit	The units of the map data.	dimensionless_unscaled

Source code in toast/pixels.py

class PixelData(AcceleratorObject):
    """Distributed map-domain data.

    The distribution information is stored in a PixelDistribution instance passed to
    the constructor.  Each process has local data stored in one or more "submaps".

    Although multiple processes may have the same submap of data stored locally, only
    one process is considered the "owner".  This ownership is used when serializing the
    data and when doing reductions in certain cases.  Ownership can be set to either
    the lowest rank process which has the submap or to a balanced distribution.

    Args:
        dist (PixelDistribution):  The distribution of submaps.
        dtype (numpy.dtype):  A numpy-compatible dtype for each element of the data.
            The only supported types are 1, 2, 4, and 8 byte signed and unsigned
            integers, 4 and 8 byte floating point numbers, and 4 and 8 byte complex
            numbers.
        n_value (int):  The number of values per pixel.
        units (Unit):  The units of the map data.

    """

    def __init__(self, dist, dtype, n_value=1, units=u.dimensionless_unscaled):
        super().__init__()
        log = Logger.get()

        self._dist = dist
        self._n_value = n_value
        self._units = units

        # construct a new dtype in case the parameter given is shortcut string
        ttype = np.dtype(dtype)

        self.storage_class = None
        if ttype.char == "b":
            self.storage_class = AlignedI8
        elif ttype.char == "B":
            self.storage_class = AlignedU8
        elif ttype.char == "h":
            self.storage_class = AlignedI16
        elif ttype.char == "H":
            self.storage_class = AlignedU16
        elif ttype.char == "i":
            self.storage_class = AlignedI32
        elif ttype.char == "I":
            self.storage_class = AlignedU32
        elif (ttype.char == "q") or (ttype.char == "l"):
            self.storage_class = AlignedI64
        elif (ttype.char == "Q") or (ttype.char == "L"):
            self.storage_class = AlignedU64
        elif ttype.char == "f":
            self.storage_class = AlignedF32
        elif ttype.char == "d":
            self.storage_class = AlignedF64
        elif ttype.char == "F":
            raise NotImplementedError("No support yet for complex numbers")
        elif ttype.char == "D":
            raise NotImplementedError("No support yet for complex numbers")
        else:
            msg = "Unsupported data typecode '{}'".format(ttype.char)
            log.error(msg)
            raise ValueError(msg)
        self._dtype = ttype

        self.mpitype = None
        self.mpibytesize = None
        if self._dist.comm is not None:
            self.mpibytesize, self.mpitype = mpi_data_type(self._dist.comm, self._dtype)

        self._shape = (
            self._dist.n_local_submap,
            self._dist.n_pix_submap,
            self._n_value,
        )
        self._flatshape = (
            self._dist.n_local_submap * self._dist.n_pix_submap * self._n_value
        )
        self._n_submap_value = self._dist.n_pix_submap * self._n_value

        self.raw = self.storage_class.zeros(self._flatshape)
        self.data = self.raw.array().reshape(self._shape)

        # Allreduce quantities
        self._all_comm_submap = None
        self._all_send = None
        self._all_send_raw = None
        self._all_recv = None
        self._all_recv_raw = None

        # Alltoallv quantities
        self._send_counts = None
        self._send_displ = None
        self._recv_counts = None
        self._recv_displ = None
        self._recv_locations = None
        self.receive = None
        self._receive_raw = None
        self.reduce_buf = None
        self._reduce_buf_raw = None

    def clear(self):
        """Delete the underlying memory.

        This will forcibly delete the C-allocated memory and invalidate all python
        references to this object.  DO NOT CALL THIS unless you are sure all references
        are no longer being used and you are about to delete the object.

        """
        if hasattr(self, "data"):
            # we keep the attribute to avoid errors in _accel_exists
            self.data = None
        if hasattr(self, "raw"):
            if self.accel_exists():
                self.accel_delete()
            if self.raw is not None:
                self.raw.clear()
            del self.raw
        if hasattr(self, "receive"):
            del self.receive
            if self._receive_raw is not None:
                self._receive_raw.clear()
            del self._receive_raw
        if hasattr(self, "reduce_buf"):
            del self.reduce_buf
            if self._reduce_buf_raw is not None:
                self._reduce_buf_raw.clear()
            del self._reduce_buf_raw
        if hasattr(self, "_all_send"):
            del self._all_send
            if self._all_send_raw is not None:
                self._all_send_raw.clear()
            del self._all_send_raw
        if hasattr(self, "_all_recv"):
            del self._all_recv
            if self._all_recv_raw is not None:
                self._all_recv_raw.clear()
            del self._all_recv_raw

    def __del__(self):
        self.clear()

    def reset(self):
        """Set memory to zero"""
        self.raw[:] = 0
        if self.accel_exists():
            self.accel_reset()

    @property
    def distribution(self):
        """(PixelDistribution): The distribution information."""
        return self._dist

    @property
    def dtype(self):
        """(numpy.dtype): The data type of the values."""
        return self._dtype

    @property
    def n_value(self):
        """(int): The number of non-zero values per pixel."""
        return self._n_value

    @property
    def units(self):
        """(Unit):  The map data units."""
        return self._units

    def update_units(self, new_units):
        """Update the units associated with the data."""
        self._units = new_units

    def __getitem__(self, key):
        return np.array(self.data[key], dtype=self._dtype, copy=False)

    def __delitem__(self, key):
        raise NotImplementedError("Cannot delete individual memory elements")
        return

    def __setitem__(self, key, value):
        self.data[key] = value

    def __iter__(self):
        return iter(self.data)

    def __len__(self):
        return len(self.data)

    def __repr__(self):
        val = (
            "<PixelData {} values per pixel, dtype = {}, units= {}, dist = {}>".format(
                self._n_value, self._dtype, self._units, self._dist
            )
        )
        return val

    def __eq__(self, other):
        if self.distribution != other.distribution:
            return False
        if self.dtype.char != other.dtype.char:
            return False
        if self.n_value != other.n_value:
            return False
        if not np.allclose(self.data, other.data):
            return False
        return True

    def __ne__(self, other):
        return not self.__eq__(other)

    def duplicate(self):
        """Create a copy of the data with the same distribution.

        Returns:
            (PixelData):  A duplicate of the instance with copied data but the same
                distribution.

        """
        dup = PixelData(
            self.distribution, self.dtype, n_value=self.n_value, units=self._units
        )
        dup.data[:] = self.data
        return dup

    def comm_nsubmap(self, bytes):
        """Given a buffer size, compute the number of submaps to communicate.

        Args:
            bytes (int):  The number of bytes.

        Returns:
            (int):  The number of submaps in each buffer.

        """
        dbytes = self._dtype.itemsize
        nsub = int(bytes / (dbytes * self._n_submap_value))
        if nsub == 0:
            nsub = 1
        allsub = int(self._dist.n_pix / self._dist.n_pix_submap)
        if nsub > allsub:
            nsub = allsub
        return nsub

    @function_timer
    def setup_allreduce(self, n_submap):
        """Check that allreduce buffers exist and create them if needed."""
        # Allocate persistent send / recv buffers that only change if number of submaps
        # change.
        if self._all_comm_submap is not None:
            # We have already done a reduce...
            if n_submap == self._all_comm_submap:
                # Already allocated with correct size
                return
            else:
                # Delete the old buffers.
                del self._all_send
                self._all_send_raw.clear()
                del self._all_send_raw
                del self._all_recv
                self._all_recv_raw.clear()
                del self._all_recv_raw
        # Allocate with the new size
        self._all_comm_submap = n_submap
        self._all_recv_raw = self.storage_class.zeros(n_submap * self._n_submap_value)
        self._all_recv = self._all_recv_raw.array()
        self._all_send_raw = self.storage_class.zeros(n_submap * self._n_submap_value)
        self._all_send = self._all_send_raw.array()

    @function_timer
    def sync_allreduce(self, comm_bytes=10000000):
        """Perform a buffered allreduce of the data.

        Args:
            comm_bytes (int): The approximate message size to use.

        Returns:
            None.

        """
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)

        if self._dist.comm is None:
            return

        comm_submap = self.comm_nsubmap(comm_bytes)
        self.setup_allreduce(comm_submap)

        dist = self._dist
        nsub = dist.n_submap

        sendview = self._all_send.reshape(
            (comm_submap, dist.n_pix_submap, self._n_value)
        )

        recvview = self._all_recv.reshape(
            (comm_submap, dist.n_pix_submap, self._n_value)
        )

        owners = dist.submap_owners

        submap_off = 0
        ncomm = comm_submap

        gt = GlobalTimers.get()

        while submap_off < nsub:
            if submap_off + ncomm > nsub:
                ncomm = nsub - submap_off
            if np.sum(owners[submap_off : submap_off + ncomm]) != -ncomm:
                # At least one submap has some hits.  Do the allreduce.
                # Otherwise we would skip this buffer to avoid reducing a
                # bunch of zeros.
                for c in range(ncomm):
                    glob = submap_off + c
                    if glob in dist.local_submaps:
                        # copy our data in.
                        loc = dist.global_submap_to_local[glob]
                        sendview[c, :, :] = self.data[loc, :, :]

                gt.start("PixelData.sync_allreduce MPI Allreduce")
                dist.comm.Allreduce(self._all_send, self._all_recv, op=MPI.SUM)
                gt.stop("PixelData.sync_allreduce MPI Allreduce")

                for c in range(ncomm):
                    glob = submap_off + c
                    if glob in dist.local_submaps:
                        # copy the reduced data
                        loc = dist.global_submap_to_local[glob]
                        self.data[loc, :, :] = recvview[c, :, :]

                self._all_send.fill(0)
                self._all_recv.fill(0)

            submap_off += ncomm

        return

    @staticmethod
    def local_reduction(n_submap_value, receive_locations, receive, reduce_buf):
        # Locally reduce owned submaps
        for sm, locs in receive_locations.items():
            reduce_buf[:] = 0
            for lc in locs:
                reduce_buf += receive[lc : lc + n_submap_value]
            for lc in locs:
                receive[lc : lc + n_submap_value] = reduce_buf

    @function_timer
    def setup_alltoallv(self):
        """Check that alltoallv buffers exist and create them if needed."""
        if self._send_counts is None:
            if self.accel_in_use():
                msg = f"PixelData {self._accel_name} currently on accelerator"
                msg += " cannot do MPI communication"
                raise RuntimeError(msg)
            log = Logger.get()
            # Get the parameters in terms of submaps.
            (
                send_counts,
                send_displ,
                recv_counts,
                recv_displ,
                recv_locations,
            ) = self._dist.alltoallv_info

            # Pixel values per submap
            scale = self._n_submap_value

            # Scale these quantites by the submap size and the number of values per
            # pixel.

            self._send_counts = scale * np.array(send_counts, dtype=np.int32)
            self._send_displ = scale * np.array(send_displ, dtype=np.int32)
            self._recv_counts = scale * np.array(recv_counts, dtype=np.int32)
            self._recv_displ = scale * np.array(recv_displ, dtype=np.int32)
            self._recv_locations = dict()
            for sm, locs in recv_locations.items():
                self._recv_locations[sm] = scale * np.array(locs, dtype=np.int32)

            msg_rank = 0
            if self._dist.comm is not None:
                msg_rank = self._dist.comm.rank
            msg = f"setup_alltoallv[{msg_rank}]:\n"
            msg += f"  send_counts={self._send_counts} "
            msg += f"send_displ={self._send_displ}\n"
            msg += f"  recv_counts={self._recv_counts} "
            msg += f"recv_displ={self._recv_displ} "
            msg += f"recv_locations={self._recv_locations}"
            log.verbose(msg)

            # Allocate a persistent single-submap buffer
            self._reduce_buf_raw = self.storage_class.zeros(self._n_submap_value)
            self.reduce_buf = self._reduce_buf_raw.array()

            buf_check_fail = False
            try:
                if self._dist.comm is None:
                    # For this case, point the receive member to the original data.
                    # This will allow codes processing locally owned submaps to work
                    # transparently in the serial case.
                    self.receive = self.data.reshape((-1,))
                else:
                    # Check that our send and receive buffers do not exceed 32bit
                    # indices required by MPI
                    max_int = 2147483647
                    recv_buf_size = self._recv_displ[-1] + self._recv_counts[-1]
                    if recv_buf_size > max_int:
                        msg = "Proc {} Alltoallv receive buffer size exceeds max 32bit integer".format(
                            self._dist.comm.rank
                        )
                        log.error(msg)
                        buf_check_fail = True
                    if len(self.raw) > max_int:
                        msg = "Proc {} Alltoallv send buffer size exceeds max 32bit integer".format(
                            self._dist.comm.rank
                        )
                        log.error(msg)
                        buf_check_fail = True

                    # Allocate a persistent receive buffer
                    msg = f"{msg_rank}:  allocate receive buffer of "
                    msg += f"{recv_buf_size} elements"
                    log.verbose(msg)
                    self._receive_raw = self.storage_class.zeros(recv_buf_size)
                    self.receive = self._receive_raw.array()
            except Exception:
                buf_check_fail = True
            if self._dist.comm is not None:
                buf_check_fail = self._dist.comm.allreduce(buf_check_fail, op=MPI.LOR)
            if buf_check_fail:
                msg = "alltoallv buffer setup failed on one or more processes"
                raise RuntimeError(msg)

    @function_timer
    def forward_alltoallv(self):
        """Communicate submaps into buffers on the owning process.

        On the first call, some initialization is done to compute send and receive
        displacements and counts.  A persistent receive buffer is allocated.  Submap
        data is sent to their owners simultaneously using alltoallv.

        Returns:
            None.

        """
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)

        gt = GlobalTimers.get()
        self.setup_alltoallv()

        if self._dist.comm is None:
            # No communication needed
            return

        # Gather owned submaps locally
        gt.start("PixelData.forward_alltoallv MPI Alltoallv")
        self._dist.comm.Alltoallv(
            [self.raw, self._send_counts, self._send_displ, self.mpitype],
            [self.receive, self._recv_counts, self._recv_displ, self.mpitype],
        )
        gt.stop("PixelData.forward_alltoallv MPI Alltoallv")
        return

    @function_timer
    def reverse_alltoallv(self):
        """Communicate submaps from the owning process back to all processes.

        Returns:
            None.

        """
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)

        gt = GlobalTimers.get()
        if self._dist.comm is None:
            # No communication needed
            return
        if self._send_counts is None:
            raise RuntimeError(
                "Cannot do reverse alltoallv before buffers have been setup"
            )

        # Scatter result back
        gt.start("PixelData.reverse_alltoallv MPI Alltoallv")
        self._dist.comm.Alltoallv(
            [self.receive, self._recv_counts, self._recv_displ, self.mpitype],
            [self.raw, self._send_counts, self._send_displ, self.mpitype],
        )
        gt.stop("PixelData.reverse_alltoallv MPI Alltoallv")
        return

    @function_timer
    def sync_alltoallv(self, local_func=None):
        """Perform operations on locally owned submaps using Alltoallv communication.

        On the first call, some initialization is done to compute send and receive
        displacements and counts.  A persistent receive buffer is allocated.  Submap
        data is sent to their owners simultaneously using alltoallv.  Each process does
        a local operation on their owned submaps before sending the result back with
        another alltoallv call.

        Args:
            local_func (function):  A function for processing the local submap data.

        Returns:
            None.

        """
        self.forward_alltoallv()

        if local_func is None:
            local_func = self.local_reduction

        # Run operation on locally owned submaps
        local_func(
            self._n_submap_value, self._recv_locations, self.receive, self.reduce_buf
        )

        self.reverse_alltoallv()
        return

    @function_timer
    def stats(self, comm_bytes=10000000):
        """Compute some simple statistics of the pixel data.

        The map should already be consistent across all processes with overlapping
        submaps.

        Args:
            comm_bytes (int): The approximate message size to use.

        Returns:
            (dict):  The computed properties on rank zero, None on other ranks.

        """
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)
        dist = self._dist
        nsub = dist.n_submap

        if dist.comm is None:
            return {
                "sum": [np.sum(self.data[:, :, x]) for x in range(self._n_value)],
                "mean": [np.mean(self.data[:, :, x]) for x in range(self._n_value)],
                "rms": [np.std(self.data[:, :, x]) for x in range(self._n_value)],
            }

        # The lowest rank with a locally-hit submap will contribute to the reduction
        local_hit_submaps = dist.comm.size * np.ones(nsub, dtype=np.int32)
        local_hit_submaps[dist.local_submaps] = dist.comm.rank
        hit_submaps = np.zeros_like(local_hit_submaps)
        dist.comm.Allreduce(local_hit_submaps, hit_submaps, op=MPI.MIN)
        del local_hit_submaps

        comm_submap = self.comm_nsubmap(comm_bytes)

        send_buf = np.zeros(
            comm_submap * dist.n_pix_submap * self._n_value,
            dtype=self._dtype,
        ).reshape((comm_submap, dist.n_pix_submap, self._n_value))

        recv_buf = None
        if dist.comm.rank == 0:
            # Alloc receive buffer
            recv_buf = np.zeros(
                comm_submap * dist.n_pix_submap * self._n_value,
                dtype=self._dtype,
            ).reshape((comm_submap, dist.n_pix_submap, self._n_value))
            # Variables for variance calc
            accum_sum = np.zeros(self._n_value, dtype=np.float64)
            accum_count = np.zeros(self._n_value, dtype=np.int64)
            accum_mean = np.zeros(self._n_value, dtype=np.float64)
            accum_var = np.zeros(self._n_value, dtype=np.float64)

        # Doing a two-pass variance calculation is faster than looping
        # over individual samples in python.

        submap_off = 0
        ncomm = comm_submap

        while submap_off < nsub:
            if submap_off + ncomm > nsub:
                ncomm = nsub - submap_off
            send_buf[:, :, :] = 0
            for sm in range(ncomm):
                abs_sm = submap_off + sm
                if hit_submaps[abs_sm] == dist.comm.rank:
                    # Contribute
                    loc = dist.global_submap_to_local[abs_sm]
                    send_buf[sm, :, :] = self.data[loc, :, :]

            dist.comm.Reduce(send_buf, recv_buf, op=MPI.SUM, root=0)

            if dist.comm.rank == 0:
                for sm in range(ncomm):
                    for v in range(self._n_value):
                        accum_sum[v] += np.sum(recv_buf[sm, :, v])
                        accum_count[v] += dist.n_pix_submap
            dist.comm.barrier()
            submap_off += ncomm

        if dist.comm.rank == 0:
            for v in range(self._n_value):
                accum_mean[v] = accum_sum[v] / accum_count[v]

        submap_off = 0
        ncomm = comm_submap

        while submap_off < nsub:
            if submap_off + ncomm > nsub:
                ncomm = nsub - submap_off
            send_buf[:, :, :] = 0
            for sm in range(ncomm):
                abs_sm = submap_off + sm
                if hit_submaps[abs_sm] == dist.comm.rank:
                    # Contribute
                    loc = dist.global_submap_to_local[abs_sm]
                    send_buf[sm, :, :] = self.data[loc, :, :]

            dist.comm.Reduce(send_buf, recv_buf, op=MPI.SUM, root=0)

            if dist.comm.rank == 0:
                for sm in range(ncomm):
                    for v in range(self._n_value):
                        accum_var[v] += np.sum(
                            (recv_buf[sm, :, v] - accum_mean[v]) ** 2
                        )
            dist.comm.barrier()
            submap_off += ncomm

        if dist.comm.rank == 0:
            return {
                "sum": [float(accum_sum[x]) for x in range(self._n_value)],
                "mean": [float(accum_mean[x]) for x in range(self._n_value)],
                "rms": [
                    np.sqrt(accum_var[x] / (accum_count[x] - 1))
                    for x in range(self._n_value)
                ],
            }
        else:
            return None

    @function_timer
    def broadcast_map(self, fdata, comm_bytes=10000000):
        """Distribute a map located on a single process.

        The root process takes a map in memory and distributes it.   Chunks of submaps
        are broadcast to all processes, and each process copies data to its local
        submaps.

        Args:
            fdata (array): The input data (only significant on process 0).
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)
        rank = 0
        if self._dist.comm is not None:
            rank = self._dist.comm.rank
        comm_submap = self.comm_nsubmap(comm_bytes)

        # we make the assumption that FITS binary tables are still stored in
        # blocks of 2880 bytes just like always...
        dbytes = self._dtype.itemsize
        rowbytes = self._n_value * dbytes
        optrows = int(2880 / rowbytes)

        # Get a tuple of all columns in the table.  We choose memmap here so
        # that we can (hopefully) read through all columns in chunks such that
        # we only ever have a couple FITS blocks in memory.
        if rank == 0:
            if self._n_value == 1:
                fdata = (fdata,)

        buf = np.zeros(
            comm_submap * self._dist.n_pix_submap * self._n_value, dtype=self._dtype
        )
        view = buf.reshape((comm_submap, self._dist.n_pix_submap, self._n_value))

        in_off = 0
        out_off = 0
        submap_off = 0

        rows = optrows
        while in_off < self._dist.n_pix:
            if in_off + rows > self._dist.n_pix:
                rows = self._dist.n_pix - in_off
            # is this the last block for this communication?
            islast = False
            copyrows = rows
            if out_off + rows > (comm_submap * self._dist.n_pix_submap):
                copyrows = (comm_submap * self._dist.n_pix_submap) - out_off
                islast = True

            if rank == 0:
                for col in range(self._n_value):
                    coloff = (out_off * self._n_value) + col
                    buf[
                        coloff : coloff + (copyrows * self._n_value) : self._n_value
                    ] = fdata[col][in_off : in_off + copyrows]

            out_off += copyrows
            in_off += copyrows

            if islast:
                if self._dist.comm is not None:
                    self._dist.comm.Bcast(buf, root=0)
                # loop over these submaps, and copy any that we are assigned
                for sm in range(submap_off, submap_off + comm_submap):
                    if sm in self._dist.local_submaps:
                        loc = self._dist.global_submap_to_local[sm]
                        self.data[loc, :, :] = view[sm - submap_off, :, :]
                out_off = 0
                submap_off += comm_submap
                buf.fill(0)
                islast = False

        # flush the remaining buffer

        if out_off > 0:
            if self._dist.comm is not None:
                self._dist.comm.Bcast(buf, root=0)
            # loop over these submaps, and copy any that we are assigned
            for sm in range(submap_off, submap_off + comm_submap):
                if sm in self._dist.local_submaps:
                    loc = self._dist.global_submap_to_local[sm]
                    self.data[loc, :, :] = view[sm - submap_off, :, :]
        return

    def _write_wcs(
        self,
        path,
        comm_bytes=10000000,
        report_memory=False,
        single_precision=False,
    ):
        """Write distributed PixelData to a WCS file.

        The output will be written to a WCS file in either FITS or HDF5 (determined
        by the path filename suffix).

        The data across all processes is assumed to be synchronized (the data for a
        given submap shared between processes is identical).  The submap data is sent
        to the root process which writes it out.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.
            report_memory (bool): Report the amount of available memory on
                the root node just before writing out the map.
            single_precision (bool): If True, write floats and integers in single
                precision.

        Returns:
            None

        """
        log = Logger.get()

        # The distribution
        dist = self.distribution
        rank = 0
        if dist.comm is not None:
            rank = dist.comm.rank

        # For both FITS and HDF5 formats, this type of pixel
        # data is always serialized to the root process for writing.
        image = collect_wcs_submaps(self, comm_bytes=comm_bytes)

        if rank == 0:
            dtype = None
            if single_precision:
                if image.dtype == np.dtype(np.float64):
                    dtype = np.float32
                elif image.dtype == np.dtype(np.int32):
                    dtype = np.int32
            if report_memory:
                mem = memreport(msg="(root node)", silent=True)
                log.info(f"About to write {path}:  {mem}")
            write_wcs(path, image, dist.wcs, self.units, dtype=dtype)
        del image

    def _write_healpix_fits(
        self,
        path,
        comm_bytes=10000000,
        report_memory=False,
        single_precision=False,
    ):
        """Write distributed PixelData to a healpix FITS file.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.
            report_memory (bool): Report the amount of available memory on
                the root node just before writing out the map.
            single_precision (bool): If True, write floats and integers in single
                precision.

        Returns:
            None

        """
        log = Logger.get()

        # The distribution
        dist = self.distribution
        rank = 0
        if dist.comm is not None:
            rank = dist.comm.rank

        # Healpix PixelDistribution should have the nest information.
        nest = dist.nest

        # Unit string to write
        if self.units == u.K:
            funits = "K"
        elif self.units == u.mK:
            funits = "mK"
        elif self.units == u.uK:
            funits = "uK"
        else:
            funits = str(self.units)

        fdata, fview = collect_healpix_submaps(self, comm_bytes=comm_bytes)

        if rank == 0:
            if os.path.isfile(path):
                os.remove(path)
            dtypes = [np.dtype(self.dtype) for x in range(self.n_value)]
            if single_precision:
                for i, dtype in enumerate(dtypes):
                    if dtype == np.dtype(np.float64):
                        dtypes[i] = np.float32
                    elif dtype == np.dtype(np.int64):
                        dtypes[i] = np.int32
            if report_memory:
                mem = memreport(msg="(root node)", silent=True)
                log.info(f"About to write {path}:  {mem}")
            extra = [(f"TUNIT{x}", f"{funits}") for x in range(self.n_value)]
            hp.write_map(
                path,
                fview,
                dtype=dtypes,
                fits_IDL=False,
                nest=nest,
                extra_header=extra,
            )
            del fview
            for col in range(self.n_value):
                fdata[col].clear()
            del fdata

    def _write_healpix_hdf5(
        self,
        path,
        comm_bytes=10000000,
        report_memory=False,
        single_precision=False,
        force_serial=True,
    ):
        """Write distributed PixelData to a healpix HDF5 file.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.
            report_memory (bool): Report the amount of available memory on
                the root node just before writing out the map.
            single_precision (bool): If True, write floats and integers in single
                precision.
            force_serial (bool): If True, use serial I/O, even if the HDF5
                implementation is built with MPI.

        Returns:
            None

        """
        log = Logger.get()

        # The distribution
        dist = self.distribution
        rank = 0
        nproc = 1
        if dist.comm is not None:
            rank = dist.comm.rank
            nproc = dist.comm.size

        # Healpix PixelDistribution should have the nest information.
        nest = dist.nest

        # When writing to healpix HDF5 format, we have the option to write
        # submaps in parallel.  This is a substantial performance boost when
        # dealing with many processes and large maps.

        not_owned = None
        allowners = None
        if dist.comm is None:
            not_owned = 1
            allowners = np.zeros(dist.n_submap, dtype=np.int32)
            allowners.fill(not_owned)
            for m in dist.local_submaps:
                allowners[m] = rank
        else:
            not_owned = dist.comm.size
            owners = np.zeros(dist.n_submap, dtype=np.int32)
            owners.fill(not_owned)
            for m in dist.local_submaps:
                owners[m] = dist.comm.rank
            allowners = np.zeros_like(owners)
            dist.comm.Allreduce(owners, allowners, op=MPI.MIN)

        header = {}
        if nest:
            header["ORDERING"] = "NESTED"
        else:
            header["ORDERING"] = "RING"
        header["NSIDE"] = hp.npix2nside(dist.n_pix)
        header["UNITS"] = str(self.units)

        dtype = self.dtype
        if single_precision:
            if dtype == np.dtype(np.float64):
                dtype = np.float32
            elif dtype == np.dtype(np.int64):
                dtype = np.int32

        if have_hdf5_parallel() and not force_serial:
            # Open the file for parallel access.
            with h5py.File(path, "w", driver="mpio", comm=dist.comm) as f:
                # Each process writes their own submaps to the file
                dset = f.create_dataset(
                    "map",
                    (self.n_value, dist.n_pix),
                    chunks=(self.n_value, dist.n_pix_submap),
                    dtype=dtype,
                )
                for key, value in header.items():
                    dset.attrs[key] = value
                for submap in range(dist.n_submap):
                    if allowners[submap] == rank:
                        local_submap = dist.global_submap_to_local[submap]
                        # Accommodate submap sizes that do not fit the map cleanly
                        first = submap * dist.n_pix_submap
                        last = min(first + dist.n_pix_submap, dist.n_pix)
                        dset[:, first:last] = self.data[
                            local_submap, 0 : last - first
                        ].T
        else:
            # No luck, write serially from root process
            if use_mpi and not force_serial:
                # MPI is enabled, but we are not using it.  Warn the user.
                log.warning_rank(
                    f"h5py not built with MPI support.  Writing {path} in serial mode.",
                    comm=dist.comm,
                )

            # n_send = len(dist.owned_submaps)
            n_send = np.sum(allowners == rank)
            if n_send == 0:
                sendbuffer = None
            else:
                sendbuffer = np.empty(
                    [n_send, self.n_value, dist.n_pix_submap],
                    dtype=dtype,
                )
                offset = 0
                # for submap in dist.owned_submaps:
                for submap in range(dist.n_submap):
                    if allowners[submap] == rank:
                        local_submap = dist.global_submap_to_local[submap]
                        sendbuffer[offset] = self.data[local_submap].T
                        offset += 1

            if rank == 0:
                # Root process receives the submaps from other processes and writes
                # them to file
                with h5py.File(path, "w") as f:
                    dset = f.create_dataset(
                        "map",
                        (self.n_value, dist.n_pix),
                        chunks=(self.n_value, dist.n_pix_submap),
                        dtype=dtype,
                    )
                    for rank_send in range(nproc):
                        # submaps = np.argwhere(dist.submap_owners == rank_send).ravel()
                        submaps = np.arange(dist.n_submap)[allowners == rank_send]
                        n_receive = len(submaps)
                        if n_receive > 0:
                            if rank_send == rank:
                                recvbuffer = sendbuffer
                            else:
                                recvbuffer = np.empty(
                                    [
                                        n_receive,
                                        self.n_value,
                                        dist.n_pix_submap,
                                    ],
                                    dtype=dtype,
                                )
                                dist.comm.Recv(
                                    recvbuffer, source=rank_send, tag=rank_send
                                )
                        for i, submap in enumerate(submaps):
                            # Accommodate submap sizes that do not fit the map cleanly
                            first = submap * dist.n_pix_submap
                            last = min(first + dist.n_pix_submap, dist.n_pix)
                            dset[:, first:last] = recvbuffer[i, :, 0 : last - first]

                    for key, value in header.items():
                        dset.attrs[key] = value
            else:
                # All others wait for their turn to send
                if sendbuffer is not None:
                    dist.comm.Send(sendbuffer, dest=0, tag=rank)

    def _write_healpix(
        self,
        path,
        comm_bytes=10000000,
        report_memory=False,
        single_precision=False,
        force_serial=True,
    ):
        """Write distributed PixelData to a healpix file.

        The output format (FITS or HDF5) is determined by the filename suffix.

        The data across all processes is assumed to be synchronized (the data for a
        given submap shared between processes is identical).  The submap data is sent
        to the root process which writes it out.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.
            report_memory (bool): Report the amount of available memory on
                the root node just before writing out the map.
            single_precision (bool): If True, write floats and integers in single
                precision.
            force_serial (bool): If True, use serial I/O, even if the HDF5
                implementation is built with MPI.

        Returns:
            None

        """
        if filename_is_fits(path):
            self._write_healpix_fits(
                path,
                comm_bytes=comm_bytes,
                report_memory=report_memory,
                single_precision=single_precision,
            )
        elif filename_is_hdf5(path):
            self._write_healpix_hdf5(
                path,
                comm_bytes=comm_bytes,
                report_memory=report_memory,
                single_precision=single_precision,
                force_serial=force_serial,
            )
        else:
            msg = f"Could not determine file type for '{path}'"
            raise RuntimeError(msg)

    @function_timer
    def write(
        self,
        path,
        comm_bytes=10000000,
        report_memory=False,
        single_precision=False,
        force_serial=True,
    ):
        """Write distributed PixelData to a file.

        If the internal PixelDistribution has a WCS object, then the output will be
        written to a WCS file in either FITS or HDF5 (determined by the `path`).

        If the PixelDistribution has a 'nest' member, a Healpix file is written
        in either FITS or HDF5 format.

        The data across all processes is assumed to be synchronized (the data for a
        given submap shared between processes is identical).  The submap data is sent
        to the root process which writes it out.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.
            report_memory (bool): Report the amount of available memory on
                the root node just before writing out the map.
            single_precision (bool): If True, write floats and integers in single
                precision.
            force_serial (bool): If True, use serial I/O, even if the HDF5
                implementation is built with MPI.

        Returns:
            None

        """
        dist = self.distribution

        # Check if we have WCS information
        if hasattr(dist, "wcs"):
            self._write_wcs(
                path,
                comm_bytes=comm_bytes,
                report_memory=report_memory,
                single_precision=single_precision,
            )
        elif hasattr(dist, "nest"):
            self._write_healpix(
                path,
                comm_bytes=comm_bytes,
                report_memory=report_memory,
                single_precision=single_precision,
                force_serial=force_serial,
            )
        else:
            msg = "Could not determine pixelization type.  PixelDistribution"
            msg += " does not have 'wcs' or 'nest' members."
            raise RuntimeError(msg)

    def _read_wcs(self, path, comm_bytes=10000000):
        """Read distributed PixelData from a WCS file.

        The input path should be a WCS file in either FITS or HDF5 (determined by
        the suffix).

        Args:
            path (str): The path to the input WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        dist = self.distribution
        rank = 0
        if dist.comm is not None:
            rank = dist.comm.rank

        image = None
        fscale = 1.0
        if rank == 0:
            image, funits = read_wcs(path, units=True)
            if funits is None:
                msg = f"Pixel data in {path} does not have BUNIT key.  "
                msg += f"Assuming {self.units}."
                funits = self.units
            elif funits != self.units:
                scale = 1.0 * funits
                scale.to(self.units)
                fscale = scale.value

            # Check dimensions
            impix = np.prod(image.shape)
            tot_pix = dist.n_pix * self.n_value
            if tot_pix != impix:
                raise RuntimeError(
                    f"Input file has {impix} pixel values instead of {tot_pix}"
                )
        broadcast_image(image, fscale, self, comm_bytes)

    def _read_healpix_fits(self, path, comm_bytes=10000000):
        """Read distributed PixelData from a healpix FITS file.

        Args:
            path (str): The path to the input healpix FITS file.
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        log = Logger.get()
        dist = self.distribution
        rank = 0
        if dist.comm is not None:
            rank = dist.comm.rank

        # Healpix PixelDistribution should have the nest information.
        nest = dist.nest

        # We have Healpix data
        comm_submap = self.comm_nsubmap(comm_bytes)

        # We make the assumption that FITS binary tables are still stored in
        # blocks of 2880 bytes just like always...
        dbytes = self.dtype.itemsize
        rowbytes = self.n_value * dbytes
        optrows = 2880 // rowbytes

        # get a tuple of all columns in the table.  We choose memmap here so
        # that we can (hopefully) read through all columns in chunks such that
        # we only ever have a couple FITS blocks in memory.
        fdata = None
        fscale = 1.0
        if rank == 0:
            # Check that the file is in expected format
            errors = ""
            h = hp.fitsfunc.pf.open(path, "readonly")
            nside = hp.npix2nside(dist.n_pix)
            nside_map = h[1].header["nside"]
            if "TUNIT1" in h[1].header:
                if h[1].header["TUNIT1"] == "":
                    funits = u.dimensionless_unscaled
                elif h[1].header["TUNIT1"] in ["K", "K_CMB"]:
                    funits = u.K
                elif h[1].header["TUNIT1"] in ["mK", "mK_CMB"]:
                    funits = u.mK
                elif h[1].header["TUNIT1"] in ["uK", "uK_CMB"]:
                    funits = u.uK
                else:
                    funits = u.Unit(h[1].header["TUNIT1"])
            else:
                msg = f"Pixel data in {path} does not have TUNIT1 key.  "
                msg += f"Assuming '{self.units}'."
                log.info(msg)
                funits = self.units
            if funits != self.units:
                fscale = unit_conversion(funits, self.units)
            if nside_map != nside:
                errors += f"Wrong NSide: {path} has {nside_map}, expected {nside}\n"
            map_nnz = h[1].header["tfields"]
            h.close()
            if self.n_value == 2:
                if map_nnz < 3:
                    errors += f"Wrong number of columns: {path} has {map_nnz}, "
                    errors += f"expected at least 3\n"
                # Skip I and read QU
                field = (1, 2)
            else:
                if map_nnz < self.n_value:
                    errors += f"Wrong number of columns: {path} has {map_nnz}, "
                    errors += f"expected at least {self.n_value}\n"
                field = tuple(np.arange(self.n_value))
            if len(errors) != 0:
                raise RuntimeError(errors)
            # Now read the map
            fdata = hp.read_map(
                path,
                field=field,
                dtype=[self.dtype for x in range(self.n_value)],
                memmap=True,
                nest=nest,
            )
            if self.n_value == 1:
                fdata = (fdata,)

        if dist.comm is not None:
            fscale = dist.comm.bcast(fscale, root=0)
        buf = np.zeros(comm_submap * dist.n_pix_submap * self.n_value, dtype=self.dtype)
        view = buf.reshape(comm_submap, dist.n_pix_submap, self.n_value)

        in_off = 0
        out_off = 0
        submap_off = 0

        rows = optrows
        while in_off < dist.n_pix:
            if in_off + rows > dist.n_pix:
                rows = dist.n_pix - in_off
            # is this the last block for this communication?
            islast = False
            copyrows = rows
            if out_off + rows > (comm_submap * dist.n_pix_submap):
                copyrows = (comm_submap * dist.n_pix_submap) - out_off
                islast = True

            if rank == 0:
                for col in range(self.n_value):
                    coloff = (out_off * self.n_value) + col
                    buf[coloff : coloff + (copyrows * self.n_value) : self.n_value] = (
                        fdata[col][in_off : in_off + copyrows]
                    )

            out_off += copyrows
            in_off += copyrows

            if islast:
                if dist.comm is not None:
                    dist.comm.Bcast(buf, root=0)
                # loop over these submaps, and copy any that we are assigned
                for sm in range(submap_off, submap_off + comm_submap):
                    if sm in dist.local_submaps:
                        loc = dist.global_submap_to_local[sm]
                        self.data[loc, :, :] = fscale * view[sm - submap_off, :, :]
                out_off = 0
                submap_off += comm_submap
                buf.fill(0)
                islast = False

        # flush the remaining buffer
        if out_off > 0:
            if dist.comm is not None:
                dist.comm.Bcast(buf, root=0)
            # loop over these submaps, and copy any that we are assigned
            for sm in range(submap_off, submap_off + comm_submap):
                if sm in dist.local_submaps:
                    loc = dist.global_submap_to_local[sm]
                    self.data[loc, :, :] = fscale * view[sm - submap_off, :, :]

    def _read_healpix_hdf5(self, path, comm_bytes=10000000):
        """Read distributed PixelData from a healpix HDF5 file.

        Args:
            path (str): The path to the input healpix HDF5 file.
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        log = Logger.get()
        dist = self.distribution
        rank = 0
        if dist.comm is not None:
            rank = dist.comm.rank

        # Healpix PixelDistribution should have the nest information.
        nest = dist.nest

        # We have Healpix data
        comm_submap = self.comm_nsubmap(comm_bytes)

        fscale = 1.0
        if rank == 0:
            try:
                f = h5py.File(path, "r")
            except OSError as e:
                msg = f"Failed to open {path} for reading: {e}"
                raise RuntimeError(msg)

            dset = f["map"]
            header = dict(dset.attrs)
            nside_file = header["NSIDE"]
            nside = hp.npix2nside(dist.n_pix)
            if nside_file != nside:
                msg = f"Wrong resolution in {path}: expected {nside} but found {nside_file}"
                raise RuntimeError(msg)
            if header["ORDERING"] == "NESTED":
                file_nested = True
            elif header["ORDERING"] == "RING":
                file_nested = False
            else:
                msg = f"Could not determine {path} pixel ordering."
                raise RuntimeError(msg)
            if "UNITS" in header:
                if header["UNITS"] == "":
                    funits = u.dimensionless_unscaled
                else:
                    funits = u.Unit(header["UNITS"])
            else:
                msg = f"Pixel data in {path} does not have UNITS.  "
                msg += f"Assuming {self.units}."
                log.info(msg)
                funits = self.units
            if funits != self.units:
                scale = 1.0 * funits
                scale.to(self.units)
                fscale = scale.value

            nnz, npix = dset.shape
            if nnz < self.n_value:
                msg = f"Map in {path} has {nnz} columns but we "
                msg += f"require {self.n_value}."
                raise RuntimeError(msg)
            if file_nested != nest:
                log.warning(
                    f"{path} has ORDERING={header['ORDERING']}, "
                    f"reordering serially upon load."
                )
                if file_nested and not nest:
                    mapdata = hp.reorder(dset[:], n2r=True)
                elif not file_nested and nest:
                    mapdata = hp.reorder(dset[:], r2n=True)
            else:
                # No reorder, we'll only load what we need
                mapdata = dset

        if dist.comm is not None:
            fscale = dist.comm.bcast(fscale, root=0)

        buf = np.zeros(comm_submap * self.n_value * dist.n_pix_submap, dtype=self.dtype)
        view = buf.reshape(comm_submap, self.n_value, dist.n_pix_submap)

        # Load and broadcast submaps that are used
        hit_submaps = dist.all_hit_submaps
        n_hit_submaps = len(hit_submaps)

        submap_offset = 0
        while submap_offset < n_hit_submaps:
            submap_last = min(submap_offset + comm_submap, n_hit_submaps)
            if rank == 0:
                for i, submap in enumerate(hit_submaps[submap_offset:submap_last]):
                    pix_offset = submap * dist.n_pix_submap
                    # Healpix submaps are always complete but capping the upper
                    # limit helps when users are embedding other pixelizations
                    # into Healpix
                    pix_last = min(pix_offset + dist.n_pix_submap, dist.n_pix)
                    view[i, :, 0 : pix_last - pix_offset] = mapdata[
                        0 : self.n_value, pix_offset:pix_last
                    ]

            if dist.comm is not None:
                dist.comm.Bcast(buf, root=0)

            # loop over these submaps, and copy any that we are assigned
            for i, submap in enumerate(hit_submaps[submap_offset:submap_last]):
                if submap in dist.local_submaps:
                    loc = dist.global_submap_to_local[submap]
                    self.data[loc] = fscale * view[i].T

            submap_offset = submap_last
        if rank == 0:
            f.close()

    def _read_healpix(self, path, comm_bytes=10000000):
        """Read distributed PixelData from a healpix file.

        Args:
            path (str): The path to the input healpix file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        if filename_is_fits(path):
            # FITS format
            self._read_healpix_fits(path, comm_bytes=comm_bytes)
        elif filename_is_hdf5(path):
            # HDF5 Format
            self._read_healpix_hdf5(path, comm_bytes=comm_bytes)
        else:
            msg = f"Could not determine file type for '{path}'"
            raise RuntimeError(msg)

    @function_timer
    def read(
        self,
        path,
        comm_bytes=10000000,
    ):
        """Read distributed PixelData from a file.

        If the internal PixelDistribution has a WCS object, then the input should be
        a WCS file in either FITS or HDF5 (determined by the `path`).

        If no WCS object exists in the PixelDistribution, a Healpix file is loaded
        in either FITS or HDF5 format.  The NEST or RING ordering is determined by
        the PixelDistribution.nest member.

        Args:
            path (str): The path to the output WCS file (FITS or HDF5).
            comm_bytes (int): The approximate message size to use.

        Returns:
            None

        """
        dist = self.distribution

        # Check if we have WCS information
        if hasattr(dist, "wcs"):
            # We have WCS data.
            self._read_wcs(path, comm_bytes=comm_bytes)
        elif hasattr(dist, "nest"):
            self._read_healpix(path, comm_bytes=comm_bytes)
        else:
            msg = "Could not determine pixelization type.  PixelDistribution"
            msg += " does not have 'wcs' or 'nest' members."
            raise RuntimeError(msg)

    def _accel_exists(self):
        if use_accel_omp:
            return accel_data_present(self.raw, self._accel_name)
        elif use_accel_jax:
            return accel_data_present(self.data)
        else:
            return False

    def _accel_create(self, zero_out=False):
        if use_accel_omp:
            self.raw = accel_data_create(self.raw, self._accel_name, zero_out=zero_out)
        elif use_accel_jax:
            self.data = accel_data_create(self.data, zero_out=zero_out)

    def _accel_update_device(self):
        if use_accel_omp:
            self.raw = accel_data_update_device(self.raw, self._accel_name)
        elif use_accel_jax:
            self.data = accel_data_update_device(self.data)

    def _accel_update_host(self):
        if use_accel_omp:
            self.raw = accel_data_update_host(self.raw, self._accel_name)
        elif use_accel_jax:
            self.data = accel_data_update_host(self.data)

    def _accel_reset(self):
        if use_accel_omp:
            accel_data_reset(self.raw, self._accel_name)
        elif use_accel_jax:
            accel_data_reset(self.data)

    def _accel_delete(self):
        if use_accel_omp:
            self.raw = accel_data_delete(self.raw, self._accel_name)
        elif use_accel_jax:
            self.data = accel_data_delete(self.data)

_all_comm_submap = None instance-attribute

_all_recv = None instance-attribute

_all_recv_raw = None instance-attribute

_all_send = None instance-attribute

_all_send_raw = None instance-attribute

_dist = dist instance-attribute

_dtype = ttype instance-attribute

_flatshape = self._dist.n_local_submap * self._dist.n_pix_submap * self._n_value instance-attribute

_n_submap_value = self._dist.n_pix_submap * self._n_value instance-attribute

_n_value = n_value instance-attribute

_receive_raw = None instance-attribute

_recv_counts = None instance-attribute

_recv_displ = None instance-attribute

_recv_locations = None instance-attribute

_reduce_buf_raw = None instance-attribute

_send_counts = None instance-attribute

_send_displ = None instance-attribute

_shape = (self._dist.n_local_submap, self._dist.n_pix_submap, self._n_value) instance-attribute

_units = units instance-attribute

data = self.raw.array().reshape(self._shape) instance-attribute

distribution property

(PixelDistribution): The distribution information.

dtype property

(numpy.dtype): The data type of the values.

mpibytesize = None instance-attribute

mpitype = None instance-attribute

n_value property

(int): The number of non-zero values per pixel.

raw = self.storage_class.zeros(self._flatshape) instance-attribute

receive = None instance-attribute

reduce_buf = None instance-attribute

storage_class = None instance-attribute

units property

(Unit): The map data units.

__del__()

Source code in toast/pixels.py

def __del__(self):
    self.clear()

__delitem__(key)

Source code in toast/pixels.py

def __delitem__(self, key):
    raise NotImplementedError("Cannot delete individual memory elements")
    return

__eq__(other)

Source code in toast/pixels.py

def __eq__(self, other):
    if self.distribution != other.distribution:
        return False
    if self.dtype.char != other.dtype.char:
        return False
    if self.n_value != other.n_value:
        return False
    if not np.allclose(self.data, other.data):
        return False
    return True

__getitem__(key)

Source code in toast/pixels.py

def __getitem__(self, key):
    return np.array(self.data[key], dtype=self._dtype, copy=False)

__init__(dist, dtype, n_value=1, units=u.dimensionless_unscaled)

Source code in toast/pixels.py

def __init__(self, dist, dtype, n_value=1, units=u.dimensionless_unscaled):
    super().__init__()
    log = Logger.get()

    self._dist = dist
    self._n_value = n_value
    self._units = units

    # construct a new dtype in case the parameter given is shortcut string
    ttype = np.dtype(dtype)

    self.storage_class = None
    if ttype.char == "b":
        self.storage_class = AlignedI8
    elif ttype.char == "B":
        self.storage_class = AlignedU8
    elif ttype.char == "h":
        self.storage_class = AlignedI16
    elif ttype.char == "H":
        self.storage_class = AlignedU16
    elif ttype.char == "i":
        self.storage_class = AlignedI32
    elif ttype.char == "I":
        self.storage_class = AlignedU32
    elif (ttype.char == "q") or (ttype.char == "l"):
        self.storage_class = AlignedI64
    elif (ttype.char == "Q") or (ttype.char == "L"):
        self.storage_class = AlignedU64
    elif ttype.char == "f":
        self.storage_class = AlignedF32
    elif ttype.char == "d":
        self.storage_class = AlignedF64
    elif ttype.char == "F":
        raise NotImplementedError("No support yet for complex numbers")
    elif ttype.char == "D":
        raise NotImplementedError("No support yet for complex numbers")
    else:
        msg = "Unsupported data typecode '{}'".format(ttype.char)
        log.error(msg)
        raise ValueError(msg)
    self._dtype = ttype

    self.mpitype = None
    self.mpibytesize = None
    if self._dist.comm is not None:
        self.mpibytesize, self.mpitype = mpi_data_type(self._dist.comm, self._dtype)

    self._shape = (
        self._dist.n_local_submap,
        self._dist.n_pix_submap,
        self._n_value,
    )
    self._flatshape = (
        self._dist.n_local_submap * self._dist.n_pix_submap * self._n_value
    )
    self._n_submap_value = self._dist.n_pix_submap * self._n_value

    self.raw = self.storage_class.zeros(self._flatshape)
    self.data = self.raw.array().reshape(self._shape)

    # Allreduce quantities
    self._all_comm_submap = None
    self._all_send = None
    self._all_send_raw = None
    self._all_recv = None
    self._all_recv_raw = None

    # Alltoallv quantities
    self._send_counts = None
    self._send_displ = None
    self._recv_counts = None
    self._recv_displ = None
    self._recv_locations = None
    self.receive = None
    self._receive_raw = None
    self.reduce_buf = None
    self._reduce_buf_raw = None

__iter__()

Source code in toast/pixels.py

def __iter__(self):
    return iter(self.data)

__len__()

Source code in toast/pixels.py

def __len__(self):
    return len(self.data)

__ne__(other)

Source code in toast/pixels.py

def __ne__(self, other):
    return not self.__eq__(other)

__repr__()

Source code in toast/pixels.py

def __repr__(self):
    val = (
        "<PixelData {} values per pixel, dtype = {}, units= {}, dist = {}>".format(
            self._n_value, self._dtype, self._units, self._dist
        )
    )
    return val

__setitem__(key, value)

Source code in toast/pixels.py

def __setitem__(self, key, value):
    self.data[key] = value

_accel_create(zero_out=False)

Source code in toast/pixels.py

def _accel_create(self, zero_out=False):
    if use_accel_omp:
        self.raw = accel_data_create(self.raw, self._accel_name, zero_out=zero_out)
    elif use_accel_jax:
        self.data = accel_data_create(self.data, zero_out=zero_out)

_accel_delete()

Source code in toast/pixels.py

def _accel_delete(self):
    if use_accel_omp:
        self.raw = accel_data_delete(self.raw, self._accel_name)
    elif use_accel_jax:
        self.data = accel_data_delete(self.data)

_accel_exists()

Source code in toast/pixels.py

def _accel_exists(self):
    if use_accel_omp:
        return accel_data_present(self.raw, self._accel_name)
    elif use_accel_jax:
        return accel_data_present(self.data)
    else:
        return False

_accel_reset()

Source code in toast/pixels.py

def _accel_reset(self):
    if use_accel_omp:
        accel_data_reset(self.raw, self._accel_name)
    elif use_accel_jax:
        accel_data_reset(self.data)

_accel_update_device()

Source code in toast/pixels.py

def _accel_update_device(self):
    if use_accel_omp:
        self.raw = accel_data_update_device(self.raw, self._accel_name)
    elif use_accel_jax:
        self.data = accel_data_update_device(self.data)

_accel_update_host()

Source code in toast/pixels.py

def _accel_update_host(self):
    if use_accel_omp:
        self.raw = accel_data_update_host(self.raw, self._accel_name)
    elif use_accel_jax:
        self.data = accel_data_update_host(self.data)

_read_healpix(path, comm_bytes=10000000)

Read distributed PixelData from a healpix file.

Parameters:

Name	Type	Description	Default
path	str	The path to the input healpix file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _read_healpix(self, path, comm_bytes=10000000):
    """Read distributed PixelData from a healpix file.

    Args:
        path (str): The path to the input healpix file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    if filename_is_fits(path):
        # FITS format
        self._read_healpix_fits(path, comm_bytes=comm_bytes)
    elif filename_is_hdf5(path):
        # HDF5 Format
        self._read_healpix_hdf5(path, comm_bytes=comm_bytes)
    else:
        msg = f"Could not determine file type for '{path}'"
        raise RuntimeError(msg)

_read_healpix_fits(path, comm_bytes=10000000)

Read distributed PixelData from a healpix FITS file.

Parameters:

Name	Type	Description	Default
path	str	The path to the input healpix FITS file.	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _read_healpix_fits(self, path, comm_bytes=10000000):
    """Read distributed PixelData from a healpix FITS file.

    Args:
        path (str): The path to the input healpix FITS file.
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    log = Logger.get()
    dist = self.distribution
    rank = 0
    if dist.comm is not None:
        rank = dist.comm.rank

    # Healpix PixelDistribution should have the nest information.
    nest = dist.nest

    # We have Healpix data
    comm_submap = self.comm_nsubmap(comm_bytes)

    # We make the assumption that FITS binary tables are still stored in
    # blocks of 2880 bytes just like always...
    dbytes = self.dtype.itemsize
    rowbytes = self.n_value * dbytes
    optrows = 2880 // rowbytes

    # get a tuple of all columns in the table.  We choose memmap here so
    # that we can (hopefully) read through all columns in chunks such that
    # we only ever have a couple FITS blocks in memory.
    fdata = None
    fscale = 1.0
    if rank == 0:
        # Check that the file is in expected format
        errors = ""
        h = hp.fitsfunc.pf.open(path, "readonly")
        nside = hp.npix2nside(dist.n_pix)
        nside_map = h[1].header["nside"]
        if "TUNIT1" in h[1].header:
            if h[1].header["TUNIT1"] == "":
                funits = u.dimensionless_unscaled
            elif h[1].header["TUNIT1"] in ["K", "K_CMB"]:
                funits = u.K
            elif h[1].header["TUNIT1"] in ["mK", "mK_CMB"]:
                funits = u.mK
            elif h[1].header["TUNIT1"] in ["uK", "uK_CMB"]:
                funits = u.uK
            else:
                funits = u.Unit(h[1].header["TUNIT1"])
        else:
            msg = f"Pixel data in {path} does not have TUNIT1 key.  "
            msg += f"Assuming '{self.units}'."
            log.info(msg)
            funits = self.units
        if funits != self.units:
            fscale = unit_conversion(funits, self.units)
        if nside_map != nside:
            errors += f"Wrong NSide: {path} has {nside_map}, expected {nside}\n"
        map_nnz = h[1].header["tfields"]
        h.close()
        if self.n_value == 2:
            if map_nnz < 3:
                errors += f"Wrong number of columns: {path} has {map_nnz}, "
                errors += f"expected at least 3\n"
            # Skip I and read QU
            field = (1, 2)
        else:
            if map_nnz < self.n_value:
                errors += f"Wrong number of columns: {path} has {map_nnz}, "
                errors += f"expected at least {self.n_value}\n"
            field = tuple(np.arange(self.n_value))
        if len(errors) != 0:
            raise RuntimeError(errors)
        # Now read the map
        fdata = hp.read_map(
            path,
            field=field,
            dtype=[self.dtype for x in range(self.n_value)],
            memmap=True,
            nest=nest,
        )
        if self.n_value == 1:
            fdata = (fdata,)

    if dist.comm is not None:
        fscale = dist.comm.bcast(fscale, root=0)
    buf = np.zeros(comm_submap * dist.n_pix_submap * self.n_value, dtype=self.dtype)
    view = buf.reshape(comm_submap, dist.n_pix_submap, self.n_value)

    in_off = 0
    out_off = 0
    submap_off = 0

    rows = optrows
    while in_off < dist.n_pix:
        if in_off + rows > dist.n_pix:
            rows = dist.n_pix - in_off
        # is this the last block for this communication?
        islast = False
        copyrows = rows
        if out_off + rows > (comm_submap * dist.n_pix_submap):
            copyrows = (comm_submap * dist.n_pix_submap) - out_off
            islast = True

        if rank == 0:
            for col in range(self.n_value):
                coloff = (out_off * self.n_value) + col
                buf[coloff : coloff + (copyrows * self.n_value) : self.n_value] = (
                    fdata[col][in_off : in_off + copyrows]
                )

        out_off += copyrows
        in_off += copyrows

        if islast:
            if dist.comm is not None:
                dist.comm.Bcast(buf, root=0)
            # loop over these submaps, and copy any that we are assigned
            for sm in range(submap_off, submap_off + comm_submap):
                if sm in dist.local_submaps:
                    loc = dist.global_submap_to_local[sm]
                    self.data[loc, :, :] = fscale * view[sm - submap_off, :, :]
            out_off = 0
            submap_off += comm_submap
            buf.fill(0)
            islast = False

    # flush the remaining buffer
    if out_off > 0:
        if dist.comm is not None:
            dist.comm.Bcast(buf, root=0)
        # loop over these submaps, and copy any that we are assigned
        for sm in range(submap_off, submap_off + comm_submap):
            if sm in dist.local_submaps:
                loc = dist.global_submap_to_local[sm]
                self.data[loc, :, :] = fscale * view[sm - submap_off, :, :]

_read_healpix_hdf5(path, comm_bytes=10000000)

Read distributed PixelData from a healpix HDF5 file.

Parameters:

Name	Type	Description	Default
path	str	The path to the input healpix HDF5 file.	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _read_healpix_hdf5(self, path, comm_bytes=10000000):
    """Read distributed PixelData from a healpix HDF5 file.

    Args:
        path (str): The path to the input healpix HDF5 file.
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    log = Logger.get()
    dist = self.distribution
    rank = 0
    if dist.comm is not None:
        rank = dist.comm.rank

    # Healpix PixelDistribution should have the nest information.
    nest = dist.nest

    # We have Healpix data
    comm_submap = self.comm_nsubmap(comm_bytes)

    fscale = 1.0
    if rank == 0:
        try:
            f = h5py.File(path, "r")
        except OSError as e:
            msg = f"Failed to open {path} for reading: {e}"
            raise RuntimeError(msg)

        dset = f["map"]
        header = dict(dset.attrs)
        nside_file = header["NSIDE"]
        nside = hp.npix2nside(dist.n_pix)
        if nside_file != nside:
            msg = f"Wrong resolution in {path}: expected {nside} but found {nside_file}"
            raise RuntimeError(msg)
        if header["ORDERING"] == "NESTED":
            file_nested = True
        elif header["ORDERING"] == "RING":
            file_nested = False
        else:
            msg = f"Could not determine {path} pixel ordering."
            raise RuntimeError(msg)
        if "UNITS" in header:
            if header["UNITS"] == "":
                funits = u.dimensionless_unscaled
            else:
                funits = u.Unit(header["UNITS"])
        else:
            msg = f"Pixel data in {path} does not have UNITS.  "
            msg += f"Assuming {self.units}."
            log.info(msg)
            funits = self.units
        if funits != self.units:
            scale = 1.0 * funits
            scale.to(self.units)
            fscale = scale.value

        nnz, npix = dset.shape
        if nnz < self.n_value:
            msg = f"Map in {path} has {nnz} columns but we "
            msg += f"require {self.n_value}."
            raise RuntimeError(msg)
        if file_nested != nest:
            log.warning(
                f"{path} has ORDERING={header['ORDERING']}, "
                f"reordering serially upon load."
            )
            if file_nested and not nest:
                mapdata = hp.reorder(dset[:], n2r=True)
            elif not file_nested and nest:
                mapdata = hp.reorder(dset[:], r2n=True)
        else:
            # No reorder, we'll only load what we need
            mapdata = dset

    if dist.comm is not None:
        fscale = dist.comm.bcast(fscale, root=0)

    buf = np.zeros(comm_submap * self.n_value * dist.n_pix_submap, dtype=self.dtype)
    view = buf.reshape(comm_submap, self.n_value, dist.n_pix_submap)

    # Load and broadcast submaps that are used
    hit_submaps = dist.all_hit_submaps
    n_hit_submaps = len(hit_submaps)

    submap_offset = 0
    while submap_offset < n_hit_submaps:
        submap_last = min(submap_offset + comm_submap, n_hit_submaps)
        if rank == 0:
            for i, submap in enumerate(hit_submaps[submap_offset:submap_last]):
                pix_offset = submap * dist.n_pix_submap
                # Healpix submaps are always complete but capping the upper
                # limit helps when users are embedding other pixelizations
                # into Healpix
                pix_last = min(pix_offset + dist.n_pix_submap, dist.n_pix)
                view[i, :, 0 : pix_last - pix_offset] = mapdata[
                    0 : self.n_value, pix_offset:pix_last
                ]

        if dist.comm is not None:
            dist.comm.Bcast(buf, root=0)

        # loop over these submaps, and copy any that we are assigned
        for i, submap in enumerate(hit_submaps[submap_offset:submap_last]):
            if submap in dist.local_submaps:
                loc = dist.global_submap_to_local[submap]
                self.data[loc] = fscale * view[i].T

        submap_offset = submap_last
    if rank == 0:
        f.close()

_read_wcs(path, comm_bytes=10000000)

Read distributed PixelData from a WCS file.

The input path should be a WCS file in either FITS or HDF5 (determined by the suffix).

Parameters:

Name	Type	Description	Default
path	str	The path to the input WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _read_wcs(self, path, comm_bytes=10000000):
    """Read distributed PixelData from a WCS file.

    The input path should be a WCS file in either FITS or HDF5 (determined by
    the suffix).

    Args:
        path (str): The path to the input WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    dist = self.distribution
    rank = 0
    if dist.comm is not None:
        rank = dist.comm.rank

    image = None
    fscale = 1.0
    if rank == 0:
        image, funits = read_wcs(path, units=True)
        if funits is None:
            msg = f"Pixel data in {path} does not have BUNIT key.  "
            msg += f"Assuming {self.units}."
            funits = self.units
        elif funits != self.units:
            scale = 1.0 * funits
            scale.to(self.units)
            fscale = scale.value

        # Check dimensions
        impix = np.prod(image.shape)
        tot_pix = dist.n_pix * self.n_value
        if tot_pix != impix:
            raise RuntimeError(
                f"Input file has {impix} pixel values instead of {tot_pix}"
            )
    broadcast_image(image, fscale, self, comm_bytes)

_write_healpix(path, comm_bytes=10000000, report_memory=False, single_precision=False, force_serial=True)

Write distributed PixelData to a healpix file.

The output format (FITS or HDF5) is determined by the filename suffix.

The data across all processes is assumed to be synchronized (the data for a given submap shared between processes is identical). The submap data is sent to the root process which writes it out.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000
report_memory	bool	Report the amount of available memory on the root node just before writing out the map.	False
single_precision	bool	If True, write floats and integers in single precision.	False
force_serial	bool	If True, use serial I/O, even if the HDF5 implementation is built with MPI.	True

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _write_healpix(
    self,
    path,
    comm_bytes=10000000,
    report_memory=False,
    single_precision=False,
    force_serial=True,
):
    """Write distributed PixelData to a healpix file.

    The output format (FITS or HDF5) is determined by the filename suffix.

    The data across all processes is assumed to be synchronized (the data for a
    given submap shared between processes is identical).  The submap data is sent
    to the root process which writes it out.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.
        report_memory (bool): Report the amount of available memory on
            the root node just before writing out the map.
        single_precision (bool): If True, write floats and integers in single
            precision.
        force_serial (bool): If True, use serial I/O, even if the HDF5
            implementation is built with MPI.

    Returns:
        None

    """
    if filename_is_fits(path):
        self._write_healpix_fits(
            path,
            comm_bytes=comm_bytes,
            report_memory=report_memory,
            single_precision=single_precision,
        )
    elif filename_is_hdf5(path):
        self._write_healpix_hdf5(
            path,
            comm_bytes=comm_bytes,
            report_memory=report_memory,
            single_precision=single_precision,
            force_serial=force_serial,
        )
    else:
        msg = f"Could not determine file type for '{path}'"
        raise RuntimeError(msg)

_write_healpix_fits(path, comm_bytes=10000000, report_memory=False, single_precision=False)

Write distributed PixelData to a healpix FITS file.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000
report_memory	bool	Report the amount of available memory on the root node just before writing out the map.	False
single_precision	bool	If True, write floats and integers in single precision.	False

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _write_healpix_fits(
    self,
    path,
    comm_bytes=10000000,
    report_memory=False,
    single_precision=False,
):
    """Write distributed PixelData to a healpix FITS file.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.
        report_memory (bool): Report the amount of available memory on
            the root node just before writing out the map.
        single_precision (bool): If True, write floats and integers in single
            precision.

    Returns:
        None

    """
    log = Logger.get()

    # The distribution
    dist = self.distribution
    rank = 0
    if dist.comm is not None:
        rank = dist.comm.rank

    # Healpix PixelDistribution should have the nest information.
    nest = dist.nest

    # Unit string to write
    if self.units == u.K:
        funits = "K"
    elif self.units == u.mK:
        funits = "mK"
    elif self.units == u.uK:
        funits = "uK"
    else:
        funits = str(self.units)

    fdata, fview = collect_healpix_submaps(self, comm_bytes=comm_bytes)

    if rank == 0:
        if os.path.isfile(path):
            os.remove(path)
        dtypes = [np.dtype(self.dtype) for x in range(self.n_value)]
        if single_precision:
            for i, dtype in enumerate(dtypes):
                if dtype == np.dtype(np.float64):
                    dtypes[i] = np.float32
                elif dtype == np.dtype(np.int64):
                    dtypes[i] = np.int32
        if report_memory:
            mem = memreport(msg="(root node)", silent=True)
            log.info(f"About to write {path}:  {mem}")
        extra = [(f"TUNIT{x}", f"{funits}") for x in range(self.n_value)]
        hp.write_map(
            path,
            fview,
            dtype=dtypes,
            fits_IDL=False,
            nest=nest,
            extra_header=extra,
        )
        del fview
        for col in range(self.n_value):
            fdata[col].clear()
        del fdata

_write_healpix_hdf5(path, comm_bytes=10000000, report_memory=False, single_precision=False, force_serial=True)

Write distributed PixelData to a healpix HDF5 file.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000
report_memory	bool	Report the amount of available memory on the root node just before writing out the map.	False
single_precision	bool	If True, write floats and integers in single precision.	False
force_serial	bool	If True, use serial I/O, even if the HDF5 implementation is built with MPI.	True

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _write_healpix_hdf5(
    self,
    path,
    comm_bytes=10000000,
    report_memory=False,
    single_precision=False,
    force_serial=True,
):
    """Write distributed PixelData to a healpix HDF5 file.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.
        report_memory (bool): Report the amount of available memory on
            the root node just before writing out the map.
        single_precision (bool): If True, write floats and integers in single
            precision.
        force_serial (bool): If True, use serial I/O, even if the HDF5
            implementation is built with MPI.

    Returns:
        None

    """
    log = Logger.get()

    # The distribution
    dist = self.distribution
    rank = 0
    nproc = 1
    if dist.comm is not None:
        rank = dist.comm.rank
        nproc = dist.comm.size

    # Healpix PixelDistribution should have the nest information.
    nest = dist.nest

    # When writing to healpix HDF5 format, we have the option to write
    # submaps in parallel.  This is a substantial performance boost when
    # dealing with many processes and large maps.

    not_owned = None
    allowners = None
    if dist.comm is None:
        not_owned = 1
        allowners = np.zeros(dist.n_submap, dtype=np.int32)
        allowners.fill(not_owned)
        for m in dist.local_submaps:
            allowners[m] = rank
    else:
        not_owned = dist.comm.size
        owners = np.zeros(dist.n_submap, dtype=np.int32)
        owners.fill(not_owned)
        for m in dist.local_submaps:
            owners[m] = dist.comm.rank
        allowners = np.zeros_like(owners)
        dist.comm.Allreduce(owners, allowners, op=MPI.MIN)

    header = {}
    if nest:
        header["ORDERING"] = "NESTED"
    else:
        header["ORDERING"] = "RING"
    header["NSIDE"] = hp.npix2nside(dist.n_pix)
    header["UNITS"] = str(self.units)

    dtype = self.dtype
    if single_precision:
        if dtype == np.dtype(np.float64):
            dtype = np.float32
        elif dtype == np.dtype(np.int64):
            dtype = np.int32

    if have_hdf5_parallel() and not force_serial:
        # Open the file for parallel access.
        with h5py.File(path, "w", driver="mpio", comm=dist.comm) as f:
            # Each process writes their own submaps to the file
            dset = f.create_dataset(
                "map",
                (self.n_value, dist.n_pix),
                chunks=(self.n_value, dist.n_pix_submap),
                dtype=dtype,
            )
            for key, value in header.items():
                dset.attrs[key] = value
            for submap in range(dist.n_submap):
                if allowners[submap] == rank:
                    local_submap = dist.global_submap_to_local[submap]
                    # Accommodate submap sizes that do not fit the map cleanly
                    first = submap * dist.n_pix_submap
                    last = min(first + dist.n_pix_submap, dist.n_pix)
                    dset[:, first:last] = self.data[
                        local_submap, 0 : last - first
                    ].T
    else:
        # No luck, write serially from root process
        if use_mpi and not force_serial:
            # MPI is enabled, but we are not using it.  Warn the user.
            log.warning_rank(
                f"h5py not built with MPI support.  Writing {path} in serial mode.",
                comm=dist.comm,
            )

        # n_send = len(dist.owned_submaps)
        n_send = np.sum(allowners == rank)
        if n_send == 0:
            sendbuffer = None
        else:
            sendbuffer = np.empty(
                [n_send, self.n_value, dist.n_pix_submap],
                dtype=dtype,
            )
            offset = 0
            # for submap in dist.owned_submaps:
            for submap in range(dist.n_submap):
                if allowners[submap] == rank:
                    local_submap = dist.global_submap_to_local[submap]
                    sendbuffer[offset] = self.data[local_submap].T
                    offset += 1

        if rank == 0:
            # Root process receives the submaps from other processes and writes
            # them to file
            with h5py.File(path, "w") as f:
                dset = f.create_dataset(
                    "map",
                    (self.n_value, dist.n_pix),
                    chunks=(self.n_value, dist.n_pix_submap),
                    dtype=dtype,
                )
                for rank_send in range(nproc):
                    # submaps = np.argwhere(dist.submap_owners == rank_send).ravel()
                    submaps = np.arange(dist.n_submap)[allowners == rank_send]
                    n_receive = len(submaps)
                    if n_receive > 0:
                        if rank_send == rank:
                            recvbuffer = sendbuffer
                        else:
                            recvbuffer = np.empty(
                                [
                                    n_receive,
                                    self.n_value,
                                    dist.n_pix_submap,
                                ],
                                dtype=dtype,
                            )
                            dist.comm.Recv(
                                recvbuffer, source=rank_send, tag=rank_send
                            )
                    for i, submap in enumerate(submaps):
                        # Accommodate submap sizes that do not fit the map cleanly
                        first = submap * dist.n_pix_submap
                        last = min(first + dist.n_pix_submap, dist.n_pix)
                        dset[:, first:last] = recvbuffer[i, :, 0 : last - first]

                for key, value in header.items():
                    dset.attrs[key] = value
        else:
            # All others wait for their turn to send
            if sendbuffer is not None:
                dist.comm.Send(sendbuffer, dest=0, tag=rank)

_write_wcs(path, comm_bytes=10000000, report_memory=False, single_precision=False)

Write distributed PixelData to a WCS file.

The output will be written to a WCS file in either FITS or HDF5 (determined by the path filename suffix).

The data across all processes is assumed to be synchronized (the data for a given submap shared between processes is identical). The submap data is sent to the root process which writes it out.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000
report_memory	bool	Report the amount of available memory on the root node just before writing out the map.	False
single_precision	bool	If True, write floats and integers in single precision.	False

Returns:

Type	Description
	None

Source code in toast/pixels.py

def _write_wcs(
    self,
    path,
    comm_bytes=10000000,
    report_memory=False,
    single_precision=False,
):
    """Write distributed PixelData to a WCS file.

    The output will be written to a WCS file in either FITS or HDF5 (determined
    by the path filename suffix).

    The data across all processes is assumed to be synchronized (the data for a
    given submap shared between processes is identical).  The submap data is sent
    to the root process which writes it out.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.
        report_memory (bool): Report the amount of available memory on
            the root node just before writing out the map.
        single_precision (bool): If True, write floats and integers in single
            precision.

    Returns:
        None

    """
    log = Logger.get()

    # The distribution
    dist = self.distribution
    rank = 0
    if dist.comm is not None:
        rank = dist.comm.rank

    # For both FITS and HDF5 formats, this type of pixel
    # data is always serialized to the root process for writing.
    image = collect_wcs_submaps(self, comm_bytes=comm_bytes)

    if rank == 0:
        dtype = None
        if single_precision:
            if image.dtype == np.dtype(np.float64):
                dtype = np.float32
            elif image.dtype == np.dtype(np.int32):
                dtype = np.int32
        if report_memory:
            mem = memreport(msg="(root node)", silent=True)
            log.info(f"About to write {path}:  {mem}")
        write_wcs(path, image, dist.wcs, self.units, dtype=dtype)
    del image

broadcast_map(fdata, comm_bytes=10000000)

Distribute a map located on a single process.

The root process takes a map in memory and distributes it. Chunks of submaps are broadcast to all processes, and each process copies data to its local submaps.

Parameters:

Name	Type	Description	Default
fdata	array	The input data (only significant on process 0).	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

@function_timer
def broadcast_map(self, fdata, comm_bytes=10000000):
    """Distribute a map located on a single process.

    The root process takes a map in memory and distributes it.   Chunks of submaps
    are broadcast to all processes, and each process copies data to its local
    submaps.

    Args:
        fdata (array): The input data (only significant on process 0).
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    if self.accel_in_use():
        msg = f"PixelData {self._accel_name} currently on accelerator"
        msg += " cannot do MPI communication"
        raise RuntimeError(msg)
    rank = 0
    if self._dist.comm is not None:
        rank = self._dist.comm.rank
    comm_submap = self.comm_nsubmap(comm_bytes)

    # we make the assumption that FITS binary tables are still stored in
    # blocks of 2880 bytes just like always...
    dbytes = self._dtype.itemsize
    rowbytes = self._n_value * dbytes
    optrows = int(2880 / rowbytes)

    # Get a tuple of all columns in the table.  We choose memmap here so
    # that we can (hopefully) read through all columns in chunks such that
    # we only ever have a couple FITS blocks in memory.
    if rank == 0:
        if self._n_value == 1:
            fdata = (fdata,)

    buf = np.zeros(
        comm_submap * self._dist.n_pix_submap * self._n_value, dtype=self._dtype
    )
    view = buf.reshape((comm_submap, self._dist.n_pix_submap, self._n_value))

    in_off = 0
    out_off = 0
    submap_off = 0

    rows = optrows
    while in_off < self._dist.n_pix:
        if in_off + rows > self._dist.n_pix:
            rows = self._dist.n_pix - in_off
        # is this the last block for this communication?
        islast = False
        copyrows = rows
        if out_off + rows > (comm_submap * self._dist.n_pix_submap):
            copyrows = (comm_submap * self._dist.n_pix_submap) - out_off
            islast = True

        if rank == 0:
            for col in range(self._n_value):
                coloff = (out_off * self._n_value) + col
                buf[
                    coloff : coloff + (copyrows * self._n_value) : self._n_value
                ] = fdata[col][in_off : in_off + copyrows]

        out_off += copyrows
        in_off += copyrows

        if islast:
            if self._dist.comm is not None:
                self._dist.comm.Bcast(buf, root=0)
            # loop over these submaps, and copy any that we are assigned
            for sm in range(submap_off, submap_off + comm_submap):
                if sm in self._dist.local_submaps:
                    loc = self._dist.global_submap_to_local[sm]
                    self.data[loc, :, :] = view[sm - submap_off, :, :]
            out_off = 0
            submap_off += comm_submap
            buf.fill(0)
            islast = False

    # flush the remaining buffer

    if out_off > 0:
        if self._dist.comm is not None:
            self._dist.comm.Bcast(buf, root=0)
        # loop over these submaps, and copy any that we are assigned
        for sm in range(submap_off, submap_off + comm_submap):
            if sm in self._dist.local_submaps:
                loc = self._dist.global_submap_to_local[sm]
                self.data[loc, :, :] = view[sm - submap_off, :, :]
    return

clear()

Delete the underlying memory.

This will forcibly delete the C-allocated memory and invalidate all python references to this object. DO NOT CALL THIS unless you are sure all references are no longer being used and you are about to delete the object.

Source code in toast/pixels.py

def clear(self):
    """Delete the underlying memory.

    This will forcibly delete the C-allocated memory and invalidate all python
    references to this object.  DO NOT CALL THIS unless you are sure all references
    are no longer being used and you are about to delete the object.

    """
    if hasattr(self, "data"):
        # we keep the attribute to avoid errors in _accel_exists
        self.data = None
    if hasattr(self, "raw"):
        if self.accel_exists():
            self.accel_delete()
        if self.raw is not None:
            self.raw.clear()
        del self.raw
    if hasattr(self, "receive"):
        del self.receive
        if self._receive_raw is not None:
            self._receive_raw.clear()
        del self._receive_raw
    if hasattr(self, "reduce_buf"):
        del self.reduce_buf
        if self._reduce_buf_raw is not None:
            self._reduce_buf_raw.clear()
        del self._reduce_buf_raw
    if hasattr(self, "_all_send"):
        del self._all_send
        if self._all_send_raw is not None:
            self._all_send_raw.clear()
        del self._all_send_raw
    if hasattr(self, "_all_recv"):
        del self._all_recv
        if self._all_recv_raw is not None:
            self._all_recv_raw.clear()
        del self._all_recv_raw

comm_nsubmap(bytes)

Given a buffer size, compute the number of submaps to communicate.

Parameters:

Name	Type	Description	Default
bytes	int	The number of bytes.	required

Returns:

Type	Description
int	The number of submaps in each buffer.

Source code in toast/pixels.py

def comm_nsubmap(self, bytes):
    """Given a buffer size, compute the number of submaps to communicate.

    Args:
        bytes (int):  The number of bytes.

    Returns:
        (int):  The number of submaps in each buffer.

    """
    dbytes = self._dtype.itemsize
    nsub = int(bytes / (dbytes * self._n_submap_value))
    if nsub == 0:
        nsub = 1
    allsub = int(self._dist.n_pix / self._dist.n_pix_submap)
    if nsub > allsub:
        nsub = allsub
    return nsub

duplicate()

Create a copy of the data with the same distribution.

Returns:

Type	Description
PixelData	A duplicate of the instance with copied data but the same distribution.

Source code in toast/pixels.py

def duplicate(self):
    """Create a copy of the data with the same distribution.

    Returns:
        (PixelData):  A duplicate of the instance with copied data but the same
            distribution.

    """
    dup = PixelData(
        self.distribution, self.dtype, n_value=self.n_value, units=self._units
    )
    dup.data[:] = self.data
    return dup

forward_alltoallv()

Communicate submaps into buffers on the owning process.

On the first call, some initialization is done to compute send and receive displacements and counts. A persistent receive buffer is allocated. Submap data is sent to their owners simultaneously using alltoallv.

Returns:

Type	Description
	None.

Source code in toast/pixels.py

@function_timer
def forward_alltoallv(self):
    """Communicate submaps into buffers on the owning process.

    On the first call, some initialization is done to compute send and receive
    displacements and counts.  A persistent receive buffer is allocated.  Submap
    data is sent to their owners simultaneously using alltoallv.

    Returns:
        None.

    """
    if self.accel_in_use():
        msg = f"PixelData {self._accel_name} currently on accelerator"
        msg += " cannot do MPI communication"
        raise RuntimeError(msg)

    gt = GlobalTimers.get()
    self.setup_alltoallv()

    if self._dist.comm is None:
        # No communication needed
        return

    # Gather owned submaps locally
    gt.start("PixelData.forward_alltoallv MPI Alltoallv")
    self._dist.comm.Alltoallv(
        [self.raw, self._send_counts, self._send_displ, self.mpitype],
        [self.receive, self._recv_counts, self._recv_displ, self.mpitype],
    )
    gt.stop("PixelData.forward_alltoallv MPI Alltoallv")
    return

local_reduction(n_submap_value, receive_locations, receive, reduce_buf) staticmethod

Source code in toast/pixels.py

@staticmethod
def local_reduction(n_submap_value, receive_locations, receive, reduce_buf):
    # Locally reduce owned submaps
    for sm, locs in receive_locations.items():
        reduce_buf[:] = 0
        for lc in locs:
            reduce_buf += receive[lc : lc + n_submap_value]
        for lc in locs:
            receive[lc : lc + n_submap_value] = reduce_buf

read(path, comm_bytes=10000000)

Read distributed PixelData from a file.

If the internal PixelDistribution has a WCS object, then the input should be a WCS file in either FITS or HDF5 (determined by the path).

If no WCS object exists in the PixelDistribution, a Healpix file is loaded in either FITS or HDF5 format. The NEST or RING ordering is determined by the PixelDistribution.nest member.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None

Source code in toast/pixels.py

@function_timer
def read(
    self,
    path,
    comm_bytes=10000000,
):
    """Read distributed PixelData from a file.

    If the internal PixelDistribution has a WCS object, then the input should be
    a WCS file in either FITS or HDF5 (determined by the `path`).

    If no WCS object exists in the PixelDistribution, a Healpix file is loaded
    in either FITS or HDF5 format.  The NEST or RING ordering is determined by
    the PixelDistribution.nest member.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.

    Returns:
        None

    """
    dist = self.distribution

    # Check if we have WCS information
    if hasattr(dist, "wcs"):
        # We have WCS data.
        self._read_wcs(path, comm_bytes=comm_bytes)
    elif hasattr(dist, "nest"):
        self._read_healpix(path, comm_bytes=comm_bytes)
    else:
        msg = "Could not determine pixelization type.  PixelDistribution"
        msg += " does not have 'wcs' or 'nest' members."
        raise RuntimeError(msg)

reset()

Set memory to zero

Source code in toast/pixels.py

def reset(self):
    """Set memory to zero"""
    self.raw[:] = 0
    if self.accel_exists():
        self.accel_reset()

reverse_alltoallv()

Communicate submaps from the owning process back to all processes.

Returns:

Type	Description
	None.

Source code in toast/pixels.py

@function_timer
def reverse_alltoallv(self):
    """Communicate submaps from the owning process back to all processes.

    Returns:
        None.

    """
    if self.accel_in_use():
        msg = f"PixelData {self._accel_name} currently on accelerator"
        msg += " cannot do MPI communication"
        raise RuntimeError(msg)

    gt = GlobalTimers.get()
    if self._dist.comm is None:
        # No communication needed
        return
    if self._send_counts is None:
        raise RuntimeError(
            "Cannot do reverse alltoallv before buffers have been setup"
        )

    # Scatter result back
    gt.start("PixelData.reverse_alltoallv MPI Alltoallv")
    self._dist.comm.Alltoallv(
        [self.receive, self._recv_counts, self._recv_displ, self.mpitype],
        [self.raw, self._send_counts, self._send_displ, self.mpitype],
    )
    gt.stop("PixelData.reverse_alltoallv MPI Alltoallv")
    return

setup_allreduce(n_submap)

Check that allreduce buffers exist and create them if needed.

Source code in toast/pixels.py

@function_timer
def setup_allreduce(self, n_submap):
    """Check that allreduce buffers exist and create them if needed."""
    # Allocate persistent send / recv buffers that only change if number of submaps
    # change.
    if self._all_comm_submap is not None:
        # We have already done a reduce...
        if n_submap == self._all_comm_submap:
            # Already allocated with correct size
            return
        else:
            # Delete the old buffers.
            del self._all_send
            self._all_send_raw.clear()
            del self._all_send_raw
            del self._all_recv
            self._all_recv_raw.clear()
            del self._all_recv_raw
    # Allocate with the new size
    self._all_comm_submap = n_submap
    self._all_recv_raw = self.storage_class.zeros(n_submap * self._n_submap_value)
    self._all_recv = self._all_recv_raw.array()
    self._all_send_raw = self.storage_class.zeros(n_submap * self._n_submap_value)
    self._all_send = self._all_send_raw.array()

setup_alltoallv()

Check that alltoallv buffers exist and create them if needed.

Source code in toast/pixels.py

@function_timer
def setup_alltoallv(self):
    """Check that alltoallv buffers exist and create them if needed."""
    if self._send_counts is None:
        if self.accel_in_use():
            msg = f"PixelData {self._accel_name} currently on accelerator"
            msg += " cannot do MPI communication"
            raise RuntimeError(msg)
        log = Logger.get()
        # Get the parameters in terms of submaps.
        (
            send_counts,
            send_displ,
            recv_counts,
            recv_displ,
            recv_locations,
        ) = self._dist.alltoallv_info

        # Pixel values per submap
        scale = self._n_submap_value

        # Scale these quantites by the submap size and the number of values per
        # pixel.

        self._send_counts = scale * np.array(send_counts, dtype=np.int32)
        self._send_displ = scale * np.array(send_displ, dtype=np.int32)
        self._recv_counts = scale * np.array(recv_counts, dtype=np.int32)
        self._recv_displ = scale * np.array(recv_displ, dtype=np.int32)
        self._recv_locations = dict()
        for sm, locs in recv_locations.items():
            self._recv_locations[sm] = scale * np.array(locs, dtype=np.int32)

        msg_rank = 0
        if self._dist.comm is not None:
            msg_rank = self._dist.comm.rank
        msg = f"setup_alltoallv[{msg_rank}]:\n"
        msg += f"  send_counts={self._send_counts} "
        msg += f"send_displ={self._send_displ}\n"
        msg += f"  recv_counts={self._recv_counts} "
        msg += f"recv_displ={self._recv_displ} "
        msg += f"recv_locations={self._recv_locations}"
        log.verbose(msg)

        # Allocate a persistent single-submap buffer
        self._reduce_buf_raw = self.storage_class.zeros(self._n_submap_value)
        self.reduce_buf = self._reduce_buf_raw.array()

        buf_check_fail = False
        try:
            if self._dist.comm is None:
                # For this case, point the receive member to the original data.
                # This will allow codes processing locally owned submaps to work
                # transparently in the serial case.
                self.receive = self.data.reshape((-1,))
            else:
                # Check that our send and receive buffers do not exceed 32bit
                # indices required by MPI
                max_int = 2147483647
                recv_buf_size = self._recv_displ[-1] + self._recv_counts[-1]
                if recv_buf_size > max_int:
                    msg = "Proc {} Alltoallv receive buffer size exceeds max 32bit integer".format(
                        self._dist.comm.rank
                    )
                    log.error(msg)
                    buf_check_fail = True
                if len(self.raw) > max_int:
                    msg = "Proc {} Alltoallv send buffer size exceeds max 32bit integer".format(
                        self._dist.comm.rank
                    )
                    log.error(msg)
                    buf_check_fail = True

                # Allocate a persistent receive buffer
                msg = f"{msg_rank}:  allocate receive buffer of "
                msg += f"{recv_buf_size} elements"
                log.verbose(msg)
                self._receive_raw = self.storage_class.zeros(recv_buf_size)
                self.receive = self._receive_raw.array()
        except Exception:
            buf_check_fail = True
        if self._dist.comm is not None:
            buf_check_fail = self._dist.comm.allreduce(buf_check_fail, op=MPI.LOR)
        if buf_check_fail:
            msg = "alltoallv buffer setup failed on one or more processes"
            raise RuntimeError(msg)

stats(comm_bytes=10000000)

Compute some simple statistics of the pixel data.

The map should already be consistent across all processes with overlapping submaps.

Parameters:

Name	Type	Description	Default
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
dict	The computed properties on rank zero, None on other ranks.

Source code in toast/pixels.py

@function_timer
def stats(self, comm_bytes=10000000):
    """Compute some simple statistics of the pixel data.

    The map should already be consistent across all processes with overlapping
    submaps.

    Args:
        comm_bytes (int): The approximate message size to use.

    Returns:
        (dict):  The computed properties on rank zero, None on other ranks.

    """
    if self.accel_in_use():
        msg = f"PixelData {self._accel_name} currently on accelerator"
        msg += " cannot do MPI communication"
        raise RuntimeError(msg)
    dist = self._dist
    nsub = dist.n_submap

    if dist.comm is None:
        return {
            "sum": [np.sum(self.data[:, :, x]) for x in range(self._n_value)],
            "mean": [np.mean(self.data[:, :, x]) for x in range(self._n_value)],
            "rms": [np.std(self.data[:, :, x]) for x in range(self._n_value)],
        }

    # The lowest rank with a locally-hit submap will contribute to the reduction
    local_hit_submaps = dist.comm.size * np.ones(nsub, dtype=np.int32)
    local_hit_submaps[dist.local_submaps] = dist.comm.rank
    hit_submaps = np.zeros_like(local_hit_submaps)
    dist.comm.Allreduce(local_hit_submaps, hit_submaps, op=MPI.MIN)
    del local_hit_submaps

    comm_submap = self.comm_nsubmap(comm_bytes)

    send_buf = np.zeros(
        comm_submap * dist.n_pix_submap * self._n_value,
        dtype=self._dtype,
    ).reshape((comm_submap, dist.n_pix_submap, self._n_value))

    recv_buf = None
    if dist.comm.rank == 0:
        # Alloc receive buffer
        recv_buf = np.zeros(
            comm_submap * dist.n_pix_submap * self._n_value,
            dtype=self._dtype,
        ).reshape((comm_submap, dist.n_pix_submap, self._n_value))
        # Variables for variance calc
        accum_sum = np.zeros(self._n_value, dtype=np.float64)
        accum_count = np.zeros(self._n_value, dtype=np.int64)
        accum_mean = np.zeros(self._n_value, dtype=np.float64)
        accum_var = np.zeros(self._n_value, dtype=np.float64)

    # Doing a two-pass variance calculation is faster than looping
    # over individual samples in python.

    submap_off = 0
    ncomm = comm_submap

    while submap_off < nsub:
        if submap_off + ncomm > nsub:
            ncomm = nsub - submap_off
        send_buf[:, :, :] = 0
        for sm in range(ncomm):
            abs_sm = submap_off + sm
            if hit_submaps[abs_sm] == dist.comm.rank:
                # Contribute
                loc = dist.global_submap_to_local[abs_sm]
                send_buf[sm, :, :] = self.data[loc, :, :]

        dist.comm.Reduce(send_buf, recv_buf, op=MPI.SUM, root=0)

        if dist.comm.rank == 0:
            for sm in range(ncomm):
                for v in range(self._n_value):
                    accum_sum[v] += np.sum(recv_buf[sm, :, v])
                    accum_count[v] += dist.n_pix_submap
        dist.comm.barrier()
        submap_off += ncomm

    if dist.comm.rank == 0:
        for v in range(self._n_value):
            accum_mean[v] = accum_sum[v] / accum_count[v]

    submap_off = 0
    ncomm = comm_submap

    while submap_off < nsub:
        if submap_off + ncomm > nsub:
            ncomm = nsub - submap_off
        send_buf[:, :, :] = 0
        for sm in range(ncomm):
            abs_sm = submap_off + sm
            if hit_submaps[abs_sm] == dist.comm.rank:
                # Contribute
                loc = dist.global_submap_to_local[abs_sm]
                send_buf[sm, :, :] = self.data[loc, :, :]

        dist.comm.Reduce(send_buf, recv_buf, op=MPI.SUM, root=0)

        if dist.comm.rank == 0:
            for sm in range(ncomm):
                for v in range(self._n_value):
                    accum_var[v] += np.sum(
                        (recv_buf[sm, :, v] - accum_mean[v]) ** 2
                    )
        dist.comm.barrier()
        submap_off += ncomm

    if dist.comm.rank == 0:
        return {
            "sum": [float(accum_sum[x]) for x in range(self._n_value)],
            "mean": [float(accum_mean[x]) for x in range(self._n_value)],
            "rms": [
                np.sqrt(accum_var[x] / (accum_count[x] - 1))
                for x in range(self._n_value)
            ],
        }
    else:
        return None

sync_allreduce(comm_bytes=10000000)

Perform a buffered allreduce of the data.

Parameters:

Name	Type	Description	Default
comm_bytes	int	The approximate message size to use.	10000000

Returns:

Type	Description
	None.

Source code in toast/pixels.py

@function_timer
def sync_allreduce(self, comm_bytes=10000000):
    """Perform a buffered allreduce of the data.

    Args:
        comm_bytes (int): The approximate message size to use.

    Returns:
        None.

    """
    if self.accel_in_use():
        msg = f"PixelData {self._accel_name} currently on accelerator"
        msg += " cannot do MPI communication"
        raise RuntimeError(msg)

    if self._dist.comm is None:
        return

    comm_submap = self.comm_nsubmap(comm_bytes)
    self.setup_allreduce(comm_submap)

    dist = self._dist
    nsub = dist.n_submap

    sendview = self._all_send.reshape(
        (comm_submap, dist.n_pix_submap, self._n_value)
    )

    recvview = self._all_recv.reshape(
        (comm_submap, dist.n_pix_submap, self._n_value)
    )

    owners = dist.submap_owners

    submap_off = 0
    ncomm = comm_submap

    gt = GlobalTimers.get()

    while submap_off < nsub:
        if submap_off + ncomm > nsub:
            ncomm = nsub - submap_off
        if np.sum(owners[submap_off : submap_off + ncomm]) != -ncomm:
            # At least one submap has some hits.  Do the allreduce.
            # Otherwise we would skip this buffer to avoid reducing a
            # bunch of zeros.
            for c in range(ncomm):
                glob = submap_off + c
                if glob in dist.local_submaps:
                    # copy our data in.
                    loc = dist.global_submap_to_local[glob]
                    sendview[c, :, :] = self.data[loc, :, :]

            gt.start("PixelData.sync_allreduce MPI Allreduce")
            dist.comm.Allreduce(self._all_send, self._all_recv, op=MPI.SUM)
            gt.stop("PixelData.sync_allreduce MPI Allreduce")

            for c in range(ncomm):
                glob = submap_off + c
                if glob in dist.local_submaps:
                    # copy the reduced data
                    loc = dist.global_submap_to_local[glob]
                    self.data[loc, :, :] = recvview[c, :, :]

            self._all_send.fill(0)
            self._all_recv.fill(0)

        submap_off += ncomm

    return

sync_alltoallv(local_func=None)

Perform operations on locally owned submaps using Alltoallv communication.

On the first call, some initialization is done to compute send and receive displacements and counts. A persistent receive buffer is allocated. Submap data is sent to their owners simultaneously using alltoallv. Each process does a local operation on their owned submaps before sending the result back with another alltoallv call.

Parameters:

Name	Type	Description	Default
local_func	function	A function for processing the local submap data.	None

Returns:

Type	Description
	None.

Source code in toast/pixels.py

@function_timer
def sync_alltoallv(self, local_func=None):
    """Perform operations on locally owned submaps using Alltoallv communication.

    On the first call, some initialization is done to compute send and receive
    displacements and counts.  A persistent receive buffer is allocated.  Submap
    data is sent to their owners simultaneously using alltoallv.  Each process does
    a local operation on their owned submaps before sending the result back with
    another alltoallv call.

    Args:
        local_func (function):  A function for processing the local submap data.

    Returns:
        None.

    """
    self.forward_alltoallv()

    if local_func is None:
        local_func = self.local_reduction

    # Run operation on locally owned submaps
    local_func(
        self._n_submap_value, self._recv_locations, self.receive, self.reduce_buf
    )

    self.reverse_alltoallv()
    return

update_units(new_units)

Update the units associated with the data.

Source code in toast/pixels.py

def update_units(self, new_units):
    """Update the units associated with the data."""
    self._units = new_units

write(path, comm_bytes=10000000, report_memory=False, single_precision=False, force_serial=True)

Write distributed PixelData to a file.

If the internal PixelDistribution has a WCS object, then the output will be written to a WCS file in either FITS or HDF5 (determined by the path).

If the PixelDistribution has a 'nest' member, a Healpix file is written in either FITS or HDF5 format.

The data across all processes is assumed to be synchronized (the data for a given submap shared between processes is identical). The submap data is sent to the root process which writes it out.

Parameters:

Name	Type	Description	Default
path	str	The path to the output WCS file (FITS or HDF5).	required
comm_bytes	int	The approximate message size to use.	10000000
report_memory	bool	Report the amount of available memory on the root node just before writing out the map.	False
single_precision	bool	If True, write floats and integers in single precision.	False
force_serial	bool	If True, use serial I/O, even if the HDF5 implementation is built with MPI.	True

Returns:

Type	Description
	None

Source code in toast/pixels.py

@function_timer
def write(
    self,
    path,
    comm_bytes=10000000,
    report_memory=False,
    single_precision=False,
    force_serial=True,
):
    """Write distributed PixelData to a file.

    If the internal PixelDistribution has a WCS object, then the output will be
    written to a WCS file in either FITS or HDF5 (determined by the `path`).

    If the PixelDistribution has a 'nest' member, a Healpix file is written
    in either FITS or HDF5 format.

    The data across all processes is assumed to be synchronized (the data for a
    given submap shared between processes is identical).  The submap data is sent
    to the root process which writes it out.

    Args:
        path (str): The path to the output WCS file (FITS or HDF5).
        comm_bytes (int): The approximate message size to use.
        report_memory (bool): Report the amount of available memory on
            the root node just before writing out the map.
        single_precision (bool): If True, write floats and integers in single
            precision.
        force_serial (bool): If True, use serial I/O, even if the HDF5
            implementation is built with MPI.

    Returns:
        None

    """
    dist = self.distribution

    # Check if we have WCS information
    if hasattr(dist, "wcs"):
        self._write_wcs(
            path,
            comm_bytes=comm_bytes,
            report_memory=report_memory,
            single_precision=single_precision,
        )
    elif hasattr(dist, "nest"):
        self._write_healpix(
            path,
            comm_bytes=comm_bytes,
            report_memory=report_memory,
            single_precision=single_precision,
            force_serial=force_serial,
        )
    else:
        msg = "Could not determine pixelization type.  PixelDistribution"
        msg += " does not have 'wcs' or 'nest' members."
        raise RuntimeError(msg)

Map domain objects can be saved to and loaded from different formats on disk depending on the pixelization. Healpix maps support both FITS and a more performant HDF5 format. Maps in WCS flat projections only support FITS formats.

toast.pixels_io_healpix.read_healpix(filename, *args, **kwargs)

Read a FITS or HDF5 map serially.

This reads the file into simple numpy arrays on the calling process. Units in the file are ignored.

Parameters:

Name	Type	Description	Default
filename	str	The path to the file.	required

Returns:

Type	Description
tuple	The map data and optionally header.

Source code in toast/pixels_io_healpix.py

@function_timer
def read_healpix(filename, *args, **kwargs):
    """Read a FITS or HDF5 map serially.

    This reads the file into simple numpy arrays on the calling process.
    Units in the file are ignored.

    Args:
        filename (str):  The path to the file.

    Returns:
        (tuple):  The map data and optionally header.

    """

    filename = filename.strip()

    if filename_is_fits(filename):
        # Load a FITS map with healpy
        result = hp.read_map(filename, *args, **kwargs)

    elif filename_is_hdf5(filename):
        # Translate positional arguments to keyword arguments
        if len(args) == 0:
            if "field" not in kwargs:
                kwargs["field"] = (0,)
        else:
            if "field" in kwargs:
                raise ValueError("'field' defined twice")
            field = args[0]
            if field is not None and not hasattr(field, "__len__"):
                field = (field,)
            kwargs["field"] = field

        if len(args) > 1:
            if "dtype" in kwargs:
                raise ValueError("'dtype' defined twice")
            kwargs["dtype"] = args[1]

        if len(args) > 2:
            if "nest" in kwargs:
                raise ValueError("'nest' defined twice")
            kwargs["nest"] = args[2]
        if "nest" in kwargs:
            nest = kwargs["nest"]
        else:
            nest = False

        if len(args) > 3:
            if "partial" in kwargs:
                raise ValueError("'partial' defined twice")
            kwargs["partial"] = args[3]
        if "partial" in kwargs and kwargs["partial"]:
            raise ValueError("HDF5 maps are never explicitly indexed")

        if len(args) > 4:
            if "hdu" in kwargs:
                raise ValueError("'hdu' defined twice")
            kwargs["hdu"] = args[4]
        if "hdu" in kwargs and kwargs["hdu"] != 1:
            raise ValueError("HDF5 maps do not have HDUs")

        if len(args) > 5:
            if "h" in kwargs:
                raise ValueError("'h' defined twice")
            kwargs["h"] = args[5]

        if len(args) > 6:
            if "verbose" in kwargs:
                raise ValueError("'verbose' defined twice")
            kwargs["verbose"] = args[6]
        if "verbose" in kwargs:
            verbose = kwargs["verbose"]
        else:
            # healpy default
            verbose = True

        if len(args) > 7:
            if "memmap" in kwargs:
                raise ValueError("'memmap' defined twice")
            kwargs["memmap"] = args[7]
        if "memmap" in kwargs and kwargs["memmap"]:
            raise ValueError("HDF5 maps do not have explicit memmap")

        # Load an HDF5 map
        try:
            f = h5py.File(filename, "r")
        except OSError as e:
            msg = f"Failed to open {filename} for reading: {e}"
            raise RuntimeError(msg)

        dset = f["map"]
        if "field" in kwargs and kwargs["field"] is not None:
            mapdata = []
            for field in kwargs["field"]:
                mapdata.append(dset[field])
            mapdata = np.vstack(mapdata)
        else:
            mapdata = dset[:]

        header = dict(dset.attrs)
        if "ORDERING" not in header or header["ORDERING"] not in ["NESTED", "RING"]:
            raise RuntimeError("Cannot determine pixel ordering")
        if header["ORDERING"] == "NESTED" and nest == False:
            if verbose:
                print(f"\nReordering {filename} to RING")
            mapdata = hp.reorder(mapdata, n2r=True)
        elif header["ORDERING"] == "RING" and nest == True:
            if verbose:
                print(f"\nReordering {filename} to NESTED")
            mapdata = hp.reorder(mapdata, r2n=True)
        else:
            if verbose:
                print(f"\n{filename} is already {header['ORDERING']}")
        f.close()

        if "dtype" in kwargs and kwargs["dtype"] is not None:
            mapdata = mapdata.astype(kwargs["dtype"])

        if mapdata.shape[0] == 1:
            mapdata = mapdata[0]

        if "h" in kwargs and kwargs["h"] == True:
            result = mapdata, header
        else:
            result = mapdata
    else:
        msg = f"Could not ascertain file type for '{filename}'"
        raise RuntimeError(msg)

    return result

toast.pixels_io_healpix.write_healpix(filename, mapdata, nside_submap=16, *args, **kwargs)

Write a FITS or HDF5 map serially.

This writes the map data from a simple numpy array on the calling process.

Parameters:

Name	Type	Description	Default
filename	str	The path to the file.	required
mapdata	array	The data array.	required
nside_submap	int	The submap NSIDE, used for dataset chunking.	16

Returns:

Type	Description
	None

Source code in toast/pixels_io_healpix.py

@function_timer
def write_healpix(filename, mapdata, nside_submap=16, *args, **kwargs):
    """Write a FITS or HDF5 map serially.

    This writes the map data from a simple numpy array on the calling process.

    Args:
        filename (str):  The path to the file.
        mapdata (array):  The data array.
        nside_submap (int):  The submap NSIDE, used for dataset chunking.

    Returns:
        None

    """

    if filename_is_fits(filename):
        # Write a FITS map with healpy
        return hp.write_map(filename, mapdata, *args, **kwargs)

    elif filename_is_hdf5(filename):
        if len(args) != 0:
            raise ValueError("No positional arguments supported")

        # Write an HDF5 map
        mapdata = np.atleast_2d(mapdata)
        n_value, n_pix = mapdata.shape
        nside = hp.npix2nside(n_pix)

        nside_submap = min(nside_submap, nside)
        n_pix_submap = 12 * nside_submap**2

        mode = "w-"
        if "overwrite" in kwargs and kwargs["overwrite"] == True:
            mode = "w"
        elif os.path.isfile(filename):
            raise FileExistsError(f"'{filename}' exists and `overwrite` is False")

        dtype = mapdata.dtype
        if "dtype" in kwargs and kwargs["dtype"] is not None:
            dtype = kwargs["dtype"]

        if "fits_IDL" in kwargs and kwargs["fits_IDL"]:
            raise ValueError("HDF5 does not support fits_IDL")

        if "partial" in kwargs and kwargs["partial"]:
            raise ValueError("HDF5 does not support partial; map is always chunked.")

        if "column_names" in kwargs and kwargs["column_names"] is not None:
            raise ValueError("HDF5 does not support column_names")

        ordering = "RING"
        if "nest" in kwargs and kwargs["nest"] == True:
            ordering = "NESTED"

        coord = None
        if "coord" in kwargs:
            coord = kwargs["coord"]

        units = None
        if "column_units" in kwargs:
            units = kwargs["column_units"]
            # Only one units attribute is supported
            if not isinstance(units, str):
                msg = f"ERROR: HDF5 map units must be a single string, "
                msg += f"not {units}"
                raise RuntimeError(msg)

        with h5py.File(filename, mode) as f:
            dset = f.create_dataset(
                "map",
                (n_value, n_pix),
                chunks=(n_value, n_pix_submap),
                dtype=dtype,
            )
            dset[:] = mapdata

            if "extra_header" in kwargs:
                header = kwargs["extra_header"]
                for key, value in header:
                    dset.attrs[key] = value

            dset.attrs["ORDERING"] = ordering
            dset.attrs["NSIDE"] = nside
            if units is not None:
                dset.attrs["UNITS"] = units
            if coord is not None:
                dset.attrs["COORDSYS"] = coord

    return

toast.pixels_io_wcs.write_wcs(filename, image, wcs, units=None, dtype=None)

Write a FITS or HDF5 WCS map on the calling process

Parameters:

Name	Type	Description	Default
filename	str	The path to the file	required
image	ndarray	2 or 3-dimensional image	required
wcs	WCS	The World Coordinate System	required
units	str	Image units	None

Returns:

Type	Description
	None

Source code in toast/pixels_io_wcs.py

@function_timer
def write_wcs(filename, image, wcs, units=None, dtype=None):
    """Write a FITS or HDF5 WCS map on the calling process

    Args:
        filename (str):  The path to the file
        image (ndarray): 2 or 3-dimensional image
        wcs (astropy.WCS):  The World Coordinate System
        units (str):  Image units

    Returns:
        None
    """

    filename = filename.strip()
    if os.path.isfile(filename):
        os.remove(filename)

    # Basic wcs header
    header = wcs.to_header(relax=True)

    # Output units
    if dtype is None:
        dtype = image.dtype

    # Row-major to column major (FITS standanrd)
    # image = np.atleast_3d(image).transpose([0, 2, 1]).astype(dtype)
    image = np.atleast_3d(image).astype(dtype)

    if filename_is_fits(filename):
        # Add map dimensions
        header["NAXIS"] = image.ndim
        for i, n in enumerate(image.shape[::-1]):
            header[f"NAXIS{i + 1}"] = n
        if units is not None:
            # Add units
            header["BUNIT"] = str(units)
        hdus = af.HDUList([af.PrimaryHDU(image, header)])
        hdus.writeto(filename)
        del hdus
    elif filename_is_hdf5(filename):
        with h5py.File(filename, "w") as hfile:
            hfile["data"] = image
            for key, value in header.items():
                hfile[f"wcs/{key}"] = value
            if units is not None:
                # Add units
                hfile["bunit"] = str(units)
    else:
        msg = f"Could not ascertain file type for '{filename}'"
        raise RuntimeError(msg)
    return

toast.pixels_io_wcs.read_wcs(filename, units=False, extension=0, dtype=None)

Read a FITS or HDF5 WCS map serially.

This reads the file into simple numpy arrays on the calling process. Units in the file are ignored.

Parameters:

Name	Type	Description	Default
filename	str	The path to the file.	required
units	bool	If True, return the units of the map	False

Returns:

Type	Description
tuple	The map data and the appropriate astropy units.

Source code in toast/pixels_io_wcs.py

@function_timer
def read_wcs(filename, units=False, extension=0, dtype=None):
    """Read a FITS or HDF5 WCS map serially.

    This reads the file into simple numpy arrays on the calling process.
    Units in the file are ignored.

    Args:
        filename (str):  The path to the file.
        units (bool):  If True, return the units of the map

    Returns:
        (tuple):  The map data and the appropriate astropy units.

    """

    log = Logger.get()

    filename = filename.strip()
    funits = None

    if filename_is_fits(filename):
        # Load a FITS format image
        with af.open(filename, mode="readonly") as hdul:
            hdu = hdul[extension]
            image = np.array(hdu.data)
            if units and "BUNIT" in hdu.header:
                bunit = hdu.header["BUNIT"]
    elif filename_is_hdf5(filename):
        # Load an HDF5 format image
        with h5py.File(filename, "r") as hfile:
            image = np.array(hfile["data"][()])
            if units and "bunit" in hfile:
                # Separately read the units
                bunit = hfile["bunit"][()].decode()
    else:
        msg = f"Could not ascertain file type for '{filename}'"
        raise RuntimeError(msg)

    # Column-major to row major
    # image = np.transpose(image, [0, 2, 1]).astype(dtype)
    image = np.atleast_3d(image).astype(dtype)

    # Optionally parse units
    if units:
        if bunit == "":
            funits = u.dimensionless_unscaled
        else:
            try:
                funits = u.Unit(bunit)
            except ValueError as e:
                log.warning(f"WARNING: failed to parse units in {filename}:\n{e}")
        result = (image, funits)
    else:
        result = image

    return result