Source code for yt.geometry.grid_geometry_handler

AMR index container class

from __future__ import print_function

# Copyright (c) 2013, yt Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file COPYING.txt, distributed with this software.

from yt.utilities.on_demand_imports import _h5py as h5py
import numpy as np
import weakref

from collections import defaultdict

from yt.arraytypes import blankRecordArray
from yt.config import ytcfg
from yt.funcs import \
    ensure_list, ensure_numpy_array
from yt.geometry.geometry_handler import \
    Index, YTDataChunk, ChunkDataCache
from yt.utilities.definitions import MAXLEVEL
from yt.utilities.logger import ytLogger as mylog
from .grid_container import \
    GridTree, MatchPointsToGrids

class GridIndex(Index):
    """The index class for patch and block AMR datasets. """
    float_type = 'float64'
    _preload_implemented = False
    _index_properties = ("grid_left_edge", "grid_right_edge",
                         "grid_levels", "grid_particle_count",

    def _setup_geometry(self):
        mylog.debug("Counting grids.")

        mylog.debug("Initializing grid arrays.")

        mylog.debug("Parsing index.")

        mylog.debug("Constructing grid objects.")

        mylog.debug("Re-examining index")

    def __del__(self):
        del self.grid_dimensions
        del self.grid_left_edge
        del self.grid_right_edge
        del self.grid_levels
        del self.grid_particle_count
        del self.grids

    def parameters(self):
        return self.dataset.parameters

    def _detect_output_fields_backup(self):
        # grab fields from backup file as well, if present
            backup_filename = self.dataset.backup_filename
            f = h5py.File(backup_filename, 'r')
            g = f["data"]
            grid = self.grids[0] # simply check one of the grids
            grid_group = g["grid_%010i" % ( - grid._id_offset)]
            for field_name in grid_group:
                if field_name != 'particles':
        except KeyError:
        except IOError:

    def select_grids(self, level):
        Returns an array of grids at *level*.
        return self.grids[self.grid_levels.flat == level]

    def get_levels(self):
        for level in range(self.max_level+1):
            yield self.select_grids(level)

    def _initialize_grid_arrays(self):
        mylog.debug("Allocating arrays for %s grids", self.num_grids)
        self.grid_dimensions = np.ones((self.num_grids,3), 'int32')
        self.grid_left_edge = self.ds.arr(np.zeros((self.num_grids,3),
                                    self.float_type), 'code_length')
        self.grid_right_edge = self.ds.arr(np.ones((self.num_grids,3),
                                    self.float_type), 'code_length')
        self.grid_levels = np.zeros((self.num_grids,1), 'int32')
        self.grid_particle_count = np.zeros((self.num_grids,1), 'int32')

    def clear_all_data(self):
        This routine clears all the data currently being held onto by the grids
        and the data io handler.
        for g in self.grids: g.clear_data()

    def get_smallest_dx(self):
        Returns (in code units) the smallest cell size in the simulation.
        return self.select_grids(self.grid_levels.max())[0].dds[:].min()

    def _get_particle_type_counts(self):
        return {self.ds.particle_types_raw[0]: self.grid_particle_count.sum()}

    def _initialize_level_stats(self):
        # Now some statistics:
        #   0 = number of grids
        #   1 = number of cells
        #   2 = blank
        desc = {'names': ['numgrids','numcells','level'],
        self.level_stats = blankRecordArray(desc, MAXLEVEL)
        self.level_stats['level'] = [i for i in range(MAXLEVEL)]
        self.level_stats['numgrids'] = [0 for i in range(MAXLEVEL)]
        self.level_stats['numcells'] = [0 for i in range(MAXLEVEL)]
        for level in range(self.max_level+1):
            self.level_stats[level]['numgrids'] = np.sum(self.grid_levels == level)
            li = (self.grid_levels[:,0] == level)
            self.level_stats[level]['numcells'] = self.grid_dimensions[li,:].prod(axis=1).sum()

    def grid_corners(self):
        return np.array([
          [self.grid_left_edge[:,0], self.grid_left_edge[:,1], self.grid_left_edge[:,2]],
          [self.grid_right_edge[:,0], self.grid_left_edge[:,1], self.grid_left_edge[:,2]],
          [self.grid_right_edge[:,0], self.grid_right_edge[:,1], self.grid_left_edge[:,2]],
          [self.grid_left_edge[:,0], self.grid_right_edge[:,1], self.grid_left_edge[:,2]],
          [self.grid_left_edge[:,0], self.grid_left_edge[:,1], self.grid_right_edge[:,2]],
          [self.grid_right_edge[:,0], self.grid_left_edge[:,1], self.grid_right_edge[:,2]],
          [self.grid_right_edge[:,0], self.grid_right_edge[:,1], self.grid_right_edge[:,2]],
          [self.grid_left_edge[:,0], self.grid_right_edge[:,1], self.grid_right_edge[:,2]],
        ], dtype='float64')

    def lock_grids_to_parents(self):
        r"""This function locks grid edges to their parents.

        This is useful in cases where the grid structure may be somewhat
        irregular, or where setting the left and right edges is a lossy
        process.  It is designed to correct situations where left/right edges
        may be set slightly incorrectly, resulting in discontinuities in images
        and the like.
        """"Locking grids to parents.")
        for i, g in enumerate(self.grids):
            si = g.get_global_startindex()
            g.LeftEdge = self.ds.domain_left_edge + * si
            g.RightEdge = g.LeftEdge + g.ActiveDimensions *
            self.grid_left_edge[i,:] = g.LeftEdge
            self.grid_right_edge[i,:] = g.RightEdge

    def print_stats(self):
        Prints out (stdout) relevant information about the simulation
        header = "%3s\t%6s\t%14s\t%14s" % ("level","# grids", "# cells",
                                           "# cells^3")
        print("%s" % (len(header.expandtabs())*"-"))
        for level in range(MAXLEVEL):
            if (self.level_stats['numgrids'][level]) == 0:
            print("% 3i\t% 6i\t% 14i\t% 14i" % \
                  (level, self.level_stats['numgrids'][level],
            dx = self.select_grids(level)[0].dds[0]
        print("-" * 46)
        print("   \t% 6i\t% 14i" % (self.level_stats['numgrids'].sum(), self.level_stats['numcells'].sum()))
            print("z = %0.8f" % (self["CosmologyCurrentRedshift"]))
        print("t = %0.8e = %0.8e s = %0.8e years" % \
        print("\nSmallest Cell:")
        for item in ("Mpc", "pc", "AU", "cm"):
            print("\tWidth: %0.3e %s" % (dx.in_units(item), item))

    def _find_field_values_at_points(self, fields, coords):
        r"""Find the value of fields at a set of coordinates.

        Returns the values [field1, field2,...] of the fields at the given
        (x, y, z) points. Returns a numpy array of field values cross coords
        coords = self.ds.arr(ensure_numpy_array(coords), 'code_length')
        grids = self._find_points(coords[:, 0], coords[:, 1], coords[:, 2])[0]
        fields = ensure_list(fields)
        mark = np.zeros(3,
        out = []

        # create point -> grid mapping
        grid_index = {}
        for coord_index, grid in enumerate(grids):
            if grid not in grid_index:
                grid_index[grid] = []

        out = []
        for field in fields:
            funit = self.ds._get_field_info(field).units
            out.append(self.ds.arr(np.empty((len(coords))), funit))

        for grid in grid_index:
            cellwidth = (grid.RightEdge - grid.LeftEdge) / grid.ActiveDimensions
            for field_index, field in enumerate(fields):
                for coord_index in grid_index[grid]:
                    mark = ((coords[coord_index, :] - grid.LeftEdge) / cellwidth)
                    mark = np.array(mark, dtype='int64')
                    out[field_index][coord_index] = \
                        grid[field][mark[0], mark[1], mark[2]]
        if len(fields) == 1:
            return out[0]
        return out

    def _find_points(self, x, y, z) :
        Returns the (objects, indices) of leaf grids containing a number of (x,y,z) points
        x = ensure_numpy_array(x)
        y = ensure_numpy_array(y)
        z = ensure_numpy_array(z)
        if not len(x) == len(y) == len(z):
            raise AssertionError("Arrays of indices must be of the same size")

        grid_tree = self._get_grid_tree()
        pts = MatchPointsToGrids(grid_tree, len(x), x, y, z)
        ind = pts.find_points_in_tree()
        return self.grids[ind], ind

    def _get_grid_tree(self):

        left_edge = self.ds.arr(np.zeros((self.num_grids, 3)),
        right_edge = self.ds.arr(np.zeros((self.num_grids, 3)),
        level = np.zeros((self.num_grids), dtype='int64')
        parent_ind = np.zeros((self.num_grids), dtype='int64')
        num_children = np.zeros((self.num_grids), dtype='int64')
        dimensions = np.zeros((self.num_grids, 3), dtype="int32")

        for i, grid in enumerate(self.grids) :

            left_edge[i,:] = grid.LeftEdge
            right_edge[i,:] = grid.RightEdge
            level[i] = grid.Level
            if grid.Parent is None :
                parent_ind[i] = -1
            else :
                parent_ind[i] = - grid.Parent._id_offset
            num_children[i] = np.int64(len(grid.Children))
            dimensions[i,:] = grid.ActiveDimensions

        return GridTree(self.num_grids, left_edge, right_edge, dimensions,
                        parent_ind, level, num_children)

    def convert(self, unit):
        return self.dataset.conversion_factors[unit]

    def _identify_base_chunk(self, dobj):
        fast_index = None
        def _gsort(g):
            if g.filename is None:
            return g.filename
        if dobj._type_name == "grid":
            dobj._chunk_info = np.empty(1, dtype='object')
            dobj._chunk_info[0] = weakref.proxy(dobj)
        elif getattr(dobj, "_grids", None) is None:
            gi = dobj.selector.select_grids(self.grid_left_edge,
            grids = list(sorted(self.grids[gi], key = _gsort))
            dobj._chunk_info = np.empty(len(grids), dtype='object')
            for i, g in enumerate(grids):
                dobj._chunk_info[i] = g
        # These next two lines, when uncommented, turn "on" the fast index.
        #if dobj._type_name != "grid":
        #    fast_index = self._get_grid_tree()
        if getattr(dobj, "size", None) is None:
            dobj.size = self._count_selection(dobj, fast_index = fast_index)
        if getattr(dobj, "shape", None) is None:
            dobj.shape = (dobj.size,)
        dobj._current_chunk = list(self._chunk_all(dobj, cache = False,
                                   fast_index = fast_index))[0]

    def _count_selection(self, dobj, grids = None, fast_index = None):
        if fast_index is not None:
            return fast_index.count(dobj.selector)
        if grids is None: grids = dobj._chunk_info
        count = sum((g.count(dobj.selector) for g in grids))
        return count

    def _chunk_all(self, dobj, cache = True, fast_index = None):
        gobjs = getattr(dobj._current_chunk, "objs", dobj._chunk_info)
        fast_index = fast_index or getattr(dobj._current_chunk, "_fast_index",
        yield YTDataChunk(dobj, "all", gobjs, dobj.size, 
                        cache, fast_index = fast_index)
    def _chunk_spatial(self, dobj, ngz, sort = None, preload_fields = None):
        gobjs = getattr(dobj._current_chunk, "objs", dobj._chunk_info)
        if sort in ("+level", "level"):
            giter = sorted(gobjs, key=lambda g: g.Level)
        elif sort == "-level":
            giter = sorted(gobjs, key=lambda g: -g.Level)
        elif sort is None:
            giter = gobjs
        if preload_fields is None: preload_fields = []
        preload_fields, _ = self._split_fields(preload_fields)
        if self._preload_implemented and len(preload_fields) > 0 and ngz == 0:
            giter = ChunkDataCache(list(giter), preload_fields, self)
        for i, og in enumerate(giter):
            if ngz > 0:
                g = og.retrieve_ghost_zones(ngz, [], smoothed=True)
                g = og
            size = self._count_selection(dobj, [og])
            if size == 0: continue
            # We don't want to cache any of the masks or icoords or fcoords for
            # individual grids.
            yield YTDataChunk(dobj, "spatial", [g], size, cache = False)

    _grid_chunksize = 1000
    def _chunk_io(self, dobj, cache=True, local_only=False,
                  preload_fields=None, chunk_sizing="auto"):
        # local_only is only useful for inline datasets and requires
        # implementation by subclasses.
        if preload_fields is None:
            preload_fields = []
        preload_fields, _ = self._split_fields(preload_fields)
        gfiles = defaultdict(list)
        gobjs = getattr(dobj._current_chunk, "objs", dobj._chunk_info)
        fast_index = dobj._current_chunk._fast_index
        for g in gobjs:
        # We can apply a heuristic here to make sure we aren't loading too
        # many grids all at once.
        if chunk_sizing == "auto":
            chunk_ngrids = len(gobjs)
            if chunk_ngrids > 0:
                nproc = np.float(ytcfg.getint("yt", "__global_parallel_size"))
                chunking_factor = np.ceil(self._grid_chunksize*nproc/chunk_ngrids).astype("int")
                size = max(self._grid_chunksize//chunking_factor, 1)
                size = self._grid_chunksize
        elif chunk_sizing == "config_file":
            size = ytcfg.getint("yt", "chunk_size")
        elif chunk_sizing == "just_one":
            size = 1
        elif chunk_sizing == "old":
            size = self._grid_chunksize
            raise RuntimeError("%s is an invalid value for the 'chunk_sizing' argument." % chunk_sizing)
        for fn in sorted(gfiles):
            gs = gfiles[fn]
            for grids in (gs[pos:pos + size] for pos
                          in range(0, len(gs), size)):
                dc = YTDataChunk(dobj, "io", grids,
                        self._count_selection(dobj, grids),
                        cache = cache, fast_index = fast_index)
                # We allow four full chunks to be included.
                with, preload_fields, 
                            4.0 * size):
                    yield dc