Source code for trident.light_ray

LightRay class and member functions.


# Copyright (c) 2013-2017, yt Development Team.
# Copyright (c) 2017, Trident Development Team.
# Distributed under the terms of the Modified BSD License.
# The full license is in the file LICENSE, distributed with this software.

import numpy as np

from yt_astro_analysis.cosmological_observation.cosmology_splice import \
from yt.loaders import \
from yt.frontends.ytdata.utilities import \
from yt.frontends.ytdata.data_structures import \
from yt.units.yt_array import \
from yt.utilities.cosmology import \
from yt.utilities.logger import \
    ytLogger as mylog
from yt.utilities.parallel_tools.parallel_analysis_interface import \
    parallel_objects, \
from yt.utilities.physical_constants import \
from yt.data_objects.static_output import \

[docs]class LightRay(CosmologySplice): r""" A 1D object representing the path of a light ray passing through a simulation. LightRays can be either simple, where they pass through a single dataset, or compound, where they pass through consecutive datasets from the same cosmological simulation. One can sample any of the fields intersected by the LightRay object as it passed through the dataset(s). For compound rays, the LightRay stacks together multiple datasets in a time series in order to approximate a LightRay's path through a volume and redshift interval larger than a single simulation data output. The outcome is something akin to a synthetic QSO line of sight. Once the LightRay object is set up, use LightRay.make_light_ray to begin making rays. Different randomizations can be created with a single object by providing different random seeds to make_light_ray. **Parameters** :parameter_filename: string or :class:`~yt.data_objects.static_output.Dataset` For simple rays, one may pass either a loaded dataset object or the filename of a dataset. For compound rays, one must pass the filename of the simulation parameter file. :simulation_type: optional, string This refers to the simulation frontend type. Do not use for simple rays. Default: None :near_redshift: optional, float The near (lowest) redshift for a light ray containing multiple datasets. Do not use for simple rays. Default: None :far_redshift: optional, float The far (highest) redshift for a light ray containing multiple datasets. Do not use for simple rays. Default: None :use_minimum_datasets: optional, bool If True, the minimum number of datasets is used to connect the initial and final redshift. If false, the light ray solution will contain as many entries as possible within the redshift interval. Do not use for simple rays. Default: True. :max_box_fraction: optional, float In terms of the size of the domain, the maximum length a light ray segment can be in order to span the redshift interval from one dataset to another. If using a zoom-in simulation, this parameter can be set to the length of the high resolution region so as to limit ray segments to that size. If the high resolution region is not cubical, the smallest side should be used. Default: 1.0 (the size of the box) :deltaz_min: optional, float Specifies the minimum :math:`\Delta z` between consecutive datasets in the returned list. Do not use for simple rays. Default: 0.0. :minimum_coherent_box_fraction: optional, float Use to specify the minimum length of a ray, in terms of the size of the domain, before the trajectory is re-randomized. Set to 0 to have ray trajectory randomized for every dataset. Set to np.inf (infinity) to use a single trajectory for the entire ray. Default: 0. :time_data: optional, bool Whether or not to include time outputs when gathering datasets for time series. Do not use for simple rays. Default: True. :redshift_data: optional, bool Whether or not to include redshift outputs when gathering datasets for time series. Do not use for simple rays. Default: True. :find_outputs: optional, bool Whether or not to search for datasets in the current directory. Do not use for simple rays. Default: False. :load_kwargs: optional, dict If you are passing a filename of a dataset to LightRay rather than an already loaded dataset, then you can optionally provide this dictionary as keywords when the dataset is loaded by yt with the "load" function. Necessary for use with certain frontends. E.g. Tipsy using "bounding_box" Gadget using "unit_base", etc. Default : None """
[docs] def __init__(self, parameter_filename, simulation_type=None, near_redshift=None, far_redshift=None, use_minimum_datasets=True, max_box_fraction=1.0, deltaz_min=0.0, minimum_coherent_box_fraction=0.0, time_data=True, redshift_data=True, find_outputs=False, load_kwargs=None): if near_redshift is not None and far_redshift is not None and \ near_redshift >= far_redshift: raise RuntimeError( "near_redshift must be less than far_redshift.") self.near_redshift = near_redshift self.far_redshift = far_redshift self.use_minimum_datasets = use_minimum_datasets self.deltaz_min = deltaz_min self.minimum_coherent_box_fraction = minimum_coherent_box_fraction self.parameter_filename = parameter_filename if load_kwargs is None: self.load_kwargs = {} else: self.load_kwargs = load_kwargs self.light_ray_solution = [] self._data = {} # The options here are: # 1) User passed us a dataset: use it to make a simple ray # 2) User passed us a dataset filename: use it to make a simple ray # 3) User passed us a simulation filename: use it to make a compound ray # Make a light ray from a single, given dataset: #1, #2 if simulation_type is None: self.simulation_type = simulation_type if isinstance(self.parameter_filename, Dataset): self.ds = self.parameter_filename self.parameter_filename = self.ds.basename elif isinstance(self.parameter_filename, str): self.ds = load(self.parameter_filename, **self.load_kwargs) if self.ds.cosmological_simulation: redshift = self.ds.current_redshift self.cosmology = Cosmology( hubble_constant=self.ds.hubble_constant, omega_matter=self.ds.omega_matter, omega_lambda=self.ds.omega_lambda) else: redshift = 0. self.light_ray_solution.append({"filename": self.parameter_filename, "redshift": redshift}) # Make a light ray from a simulation time-series. #3 else: self.ds = None assert isinstance(self.parameter_filename, str) # Get list of datasets for light ray solution. CosmologySplice.__init__(self, self.parameter_filename, simulation_type, find_outputs=find_outputs) self.light_ray_solution = \ self.create_cosmology_splice( self.near_redshift, self.far_redshift, minimal=self.use_minimum_datasets, max_box_fraction=max_box_fraction, deltaz_min=self.deltaz_min, time_data=time_data, redshift_data=redshift_data)
def _calculate_light_ray_solution(self, seed=None, left_edge=None, right_edge=None, min_level=None, periodic=True, start_position=None, end_position=None, trajectory=None, filename=None): "Create list of datasets to be added together to make the light ray." # Calculate dataset sizes, and get random dataset axes and centers. my_random = np.random.RandomState(seed) # If using only one dataset, set start and stop manually. if start_position is not None: if self.near_redshift is not None or self.far_redshift is not None: raise RuntimeError("LightRay Error: cannot specify both " + \ "start_position and a redshift range.") if not ((end_position is None) ^ (trajectory is None)): raise RuntimeError("LightRay Error: must specify either end_position " + \ "or trajectory, but not both.") self.light_ray_solution[0]['start'] = start_position if end_position is not None: self.light_ray_solution[0]['end'] = end_position else: # assume trajectory given as r, theta, phi if len(trajectory) != 3: raise RuntimeError("LightRay Error: trajectory must have length 3.") r, theta, phi = trajectory self.light_ray_solution[0]['end'] = self.light_ray_solution[0]['start'] + \ r * np.array([np.cos(phi) * np.sin(theta), np.sin(phi) * np.sin(theta), np.cos(theta)]) self.light_ray_solution[0]['traversal_box_fraction'] = \ vector_length(self.light_ray_solution[0]['start'], self.light_ray_solution[0]['end']) # the normal way (random start positions and trajectories for each dataset) else: # For box coherence, keep track of effective depth travelled. box_fraction_used = 0.0 for q in range(len(self.light_ray_solution)): if (q == len(self.light_ray_solution) - 1): z_next = self.near_redshift else: z_next = self.light_ray_solution[q+1]['redshift'] # Calculate fraction of box required for a depth of delta z self.light_ray_solution[q]['traversal_box_fraction'] = \ self.cosmology.comoving_radial_distance(z_next, \ self.light_ray_solution[q]['redshift']).in_units("Mpccm / h") / \ self.simulation.box_size # Get dataset axis and center. # If using box coherence, only get start point and vector if # enough of the box has been used. if (q == 0) or (box_fraction_used >= self.minimum_coherent_box_fraction): if periodic: self.light_ray_solution[q]['start'] = left_edge + \ (right_edge - left_edge) * my_random.random_sample(3) theta = np.pi * my_random.random_sample() phi = 2 * np.pi * my_random.random_sample() box_fraction_used = 0.0 else: ds = load(self.light_ray_solution[q]["filename"]) ray_length = \ ds.quan(self.light_ray_solution[q]['traversal_box_fraction'], "unitary") self.light_ray_solution[q]['start'], \ self.light_ray_solution[q]['end'] = \ non_periodic_ray(ds, left_edge, right_edge, ray_length, my_random=my_random, min_level=min_level) del ds else: # Use end point of previous segment, adjusted for periodicity, # and the same trajectory. self.light_ray_solution[q]['start'] = \ periodic_adjust(self.light_ray_solution[q-1]['end'][:], left=left_edge, right=right_edge) if "end" not in self.light_ray_solution[q]: self.light_ray_solution[q]['end'] = \ self.light_ray_solution[q]['start'] + \ self.light_ray_solution[q]['traversal_box_fraction'] * \ self.simulation.box_size * \ np.array([np.cos(phi) * np.sin(theta), np.sin(phi) * np.sin(theta), np.cos(theta)]) box_fraction_used += \ self.light_ray_solution[q]['traversal_box_fraction'] if filename is not None: self._write_light_ray_solution(filename, extra_info={'parameter_filename':self.parameter_filename, 'random_seed':seed, 'far_redshift':self.far_redshift, 'near_redshift':self.near_redshift})
[docs] def make_light_ray(self, seed=None, periodic=True, left_edge=None, right_edge=None, min_level=None, start_position=None, end_position=None, trajectory=None, fields=None, setup_function=None, solution_filename=None, data_filename=None, get_los_velocity=None, use_peculiar_velocity=True, redshift=None, field_parameters=None, njobs=-1): """ Actually generate the LightRay by traversing the desired dataset. A light ray consists of a list of field values for cells intersected by the ray and the path length of the ray through those cells. Light ray data must be written out to an hdf5 file. **Parameters** :seed: optional, int Seed for the random number generator. Default: None. :periodic: optional, bool If True, ray trajectories will make use of periodic boundaries. If False, ray trajectories will not be periodic. Default : True. :left_edge: optional, iterable of floats or YTArray The left corner of the region in which rays are to be generated. If None, the left edge will be that of the domain. If specified without units, it is assumed to be in code units. Default: None. :right_edge: optional, iterable of floats or YTArray The right corner of the region in which rays are to be generated. If None, the right edge will be that of the domain. If specified without units, it is assumed to be in code units. Default: None. :min_level: optional, int The minimum refinement level of the spatial region in which the ray passes. This can be used with zoom-in simulations where the high resolution region does not keep a constant geometry. Default: None. :start_position: optional, iterable of floats or YTArray. Used only if creating a light ray from a single dataset. The coordinates of the starting position of the ray. If specified without units, it is assumed to be in code units. Default: None. :end_position: optional, iterable of floats or YTArray. Used only if creating a light ray from a single dataset. The coordinates of the ending position of the ray. If specified without units, it is assumed to be in code units. Default: None. :trajectory: optional, list of floats Used only if creating a light ray from a single dataset. The (r, theta, phi) direction of the light ray. Use either end_position or trajectory, not both. Default: None. :fields: optional, list A list of fields for which to get data. Default: None. :setup_function: optional, callable, accepts a ds This function will be called on each dataset that is loaded to create the light ray. For, example, this can be used to add new derived fields. Default: None. :solution_filename: optional, string Path to a text file where the trajectories of each subray is written out. Default: None. :data_filename: optional, string Path to output file for ray data. Default: None. :use_peculiar_velocity: optional, bool If True, the peculiar velocity along the ray will be sampled for calculating the effective redshift combining the cosmological redshift and the doppler redshift. Default: True. :redshift: optional, float Used with light rays made from single datasets to specify a starting redshift for the ray. If not used, the starting redshift will be 0 for a non-cosmological dataset and the dataset redshift for a cosmological dataset. Default: None. :field_parameters: optional, dict Used to set field parameters in light rays. For example, if the 'bulk_velocity' field parameter is set, the relative velocities used to calculate peculiar velocity will be adjusted accordingly. Default: None. :njobs: optional, int The number of parallel jobs over which the segments will be split. Choose -1 for one processor per segment. Default: -1. **Examples** Make a light ray from multiple datasets: >>> import yt >>> from trident import LightRay >>> my_ray = LightRay("enzo_tiny_cosmology/32Mpc_32.enzo", "Enzo", ... 0., 0.1, time_data=False) ... >>> my_ray.make_light_ray(seed=12345, ... solution_filename="solution.txt", ... data_filename="my_ray.h5", ... fields=["temperature", "density"], ... use_peculiar_velocity=True) Make a light ray from a single dataset: >>> import yt >>> from trident import LightRay >>> my_ray = LightRay("IsolatedGalaxy/galaxy0030/galaxy0030") ... >>> my_ray.make_light_ray(start_position=[0., 0., 0.], ... end_position=[1., 1., 1.], ... solution_filename="solution.txt", ... data_filename="my_ray.h5", ... fields=["temperature", "density"], ... use_peculiar_velocity=True) """ if self.simulation_type is None: domain = self.ds else: domain = self.simulation assumed_units = "code_length" if left_edge is None: left_edge = domain.domain_left_edge elif not hasattr(left_edge, 'units'): left_edge = domain.arr(left_edge, assumed_units) left_edge.convert_to_units('unitary') if right_edge is None: right_edge = domain.domain_right_edge elif not hasattr(right_edge, 'units'): right_edge = domain.arr(right_edge, assumed_units) right_edge.convert_to_units('unitary') if start_position is not None: if hasattr(start_position, 'units'): start_position = start_position else: start_position = self.ds.arr(start_position, assumed_units) start_position.convert_to_units('unitary') if end_position is not None: if hasattr(end_position, 'units'): end_position = end_position else: end_position = self.ds.arr(end_position, assumed_units) end_position.convert_to_units('unitary') if get_los_velocity is not None: use_peculiar_velocity = get_los_velocity mylog.warning("'get_los_velocity' kwarg is deprecated. " + \ "Use 'use_peculiar_velocity' instead.") # Calculate solution. self._calculate_light_ray_solution(seed=seed, left_edge=left_edge, right_edge=right_edge, min_level=min_level, periodic=periodic, start_position=start_position, end_position=end_position, trajectory=trajectory, filename=solution_filename) if field_parameters is None: field_parameters = {} # Initialize data structures. self._data = {} # temperature field is automatically added to fields if fields is None: fields = [] if ('gas', 'temperature') not in fields: fields.append(('gas', 'temperature')) data_fields = fields[:] all_fields = fields[:] all_fields.extend(['l', 'dl', 'redshift']) all_fields.extend(['x', 'y', 'z']) data_fields.extend(['x', 'y', 'z']) if use_peculiar_velocity: all_fields.extend(['relative_velocity_x', 'relative_velocity_y', 'relative_velocity_z', 'velocity_los', 'redshift_eff', 'redshift_dopp']) data_fields.extend(['relative_velocity_x', 'relative_velocity_y', 'relative_velocity_z']) # Ensure all_fields and data_fields are all field tuples ('gas', field) all_fields = [('gas', a) if not isinstance(a, tuple) else a for a in all_fields] data_fields = [('gas', a) if not isinstance(a, tuple) else a for a in data_fields] all_ray_storage = {} for my_storage, my_segment in parallel_objects(self.light_ray_solution, storage=all_ray_storage, njobs=njobs): # In case of simple rays, use the already loaded dataset: self.ds, # otherwise, load dataset for segment. if self.ds is None: ds = load(my_segment['filename'], **self.load_kwargs) else: ds = self.ds if redshift is not None: if ds.cosmological_simulation and redshift != ds.current_redshift: mylog.warning("Generating light ray with different redshift than " + "the dataset itself.") my_segment["redshift"] = redshift if setup_function is not None: setup_function(ds) if not ds.cosmological_simulation: next_redshift = my_segment["redshift"] elif self.near_redshift == self.far_redshift: if isinstance(my_segment["traversal_box_fraction"], YTArray) and \ not my_segment["traversal_box_fraction"].units.is_dimensionless: segment_length = \ my_segment["traversal_box_fraction"].in_units("Mpccm / h") else: segment_length = my_segment["traversal_box_fraction"] * \ ds.domain_width[0].in_units("Mpccm / h") next_redshift = my_segment["redshift"] - \ self._deltaz_forward(my_segment["redshift"], segment_length) elif my_segment.get("next", None) is None: next_redshift = self.near_redshift else: next_redshift = my_segment['next']['redshift'] # Make sure start, end, left, right # are using the dataset's unit system. my_start = ds.arr(my_segment['start']) my_end = ds.arr(my_segment['end']) my_left = ds.arr(left_edge) my_right = ds.arr(right_edge)"Getting segment at z = %s: %s to %s." % (my_segment['redshift'], my_start, my_end)) # Break periodic ray into non-periodic segments. sub_segments = periodic_ray(my_start, my_end, left=my_left, right=my_right) # Prepare data structure for subsegment. sub_data = {} # Put supplementary data that we want communicated across # processors in here. sub_data[('gas', 'extra_data')] = {} sub_data[('gas', 'extra_data')]['segment_redshift'] = \ my_segment['redshift'] sub_data[('gas', 'extra_data')]['unique_identifier'] = \ ds.unique_identifier for field in all_fields: sub_data[field] = [] # Keep track of length along full ray. ray_length = ds.quan(0, 'code_length') # Get data for all subsegments in segment. for sub_segment in sub_segments:"Getting subsegment: %s to %s." % (sub_segment[0], sub_segment[1])) sub_ray = ds.ray(sub_segment[0], sub_segment[1]) for key, val in field_parameters.items(): sub_ray.set_field_parameter(key, val) asort = np.argsort(sub_ray["t"]) sub_length = vector_length( sub_ray.start_point, sub_ray.end_point) # redshifts derived from l values sub_data[('gas', 'l')].extend( sub_ray['t'][asort] * sub_length + ray_length) ray_length += sub_length # column densities derived from dl values sub_data[('gas', 'dl')].extend(sub_ray['dts'][asort] * sub_length) for field in data_fields: sub_data[field].extend(sub_ray[field][asort]) if use_peculiar_velocity: line_of_sight = sub_segment[0] - sub_segment[1] line_of_sight /= ((line_of_sight**2).sum())**0.5 sub_vel = ds.arr([sub_ray[('gas', 'relative_velocity_x')], sub_ray[('gas', 'relative_velocity_y')], sub_ray[('gas', 'relative_velocity_z')]]) # Line of sight velocity = vel_los sub_vel_los = (np.rollaxis(sub_vel, 1) * \ line_of_sight).sum(axis=1) sub_data[('gas', 'velocity_los')].extend(sub_vel_los[asort]) # doppler redshift: # See and # Peebles eqns: 5.48, 5.49 # 1 + redshift_dopp = (1 + v*cos(theta)/c) / # sqrt(1 - v**2/c**2) # where v is the peculiar velocity (ie physical velocity # without the hubble flow, but no hubble flow in sim, so # just the physical velocity). # the bulk of the doppler redshift is from line of sight # motion, but there is a small amount from time dilation # of transverse motion, hence the inclusion of theta (the # angle between line of sight and the velocity). # theta is the angle between the ray vector (i.e. line of # sight) and the velocity vectors: a dot b = ab cos(theta) sub_vel_mag = sub_ray[('gas', 'velocity_magnitude')] cos_theta = / sub_vel_mag # Protect against stituations where velocity mag is exactly # zero, in which case zero / zero = NaN. cos_theta = np.nan_to_num(cos_theta) redshift_dopp = \ (1 + sub_vel_mag * cos_theta / speed_of_light_cgs) / \ np.sqrt(1 - sub_vel_mag**2 / speed_of_light_cgs**2) - 1 sub_data[('gas', 'redshift_dopp')].extend(redshift_dopp[asort]) del sub_vel, sub_vel_los, sub_vel_mag, cos_theta, \ redshift_dopp sub_ray.clear_data() del sub_ray, asort for key in sub_data: if key == ('gas', "extra_data"): continue sub_data[key] = ds.arr(sub_data[key]).in_cgs() # Get redshift for each lixel. Assume linear relation between l # and z. so z = z_start - z_range * (l / l_range) sub_data[('gas', 'redshift')] = my_segment['redshift'] - \ (sub_data[('gas', 'l')] / ray_length) * \ (my_segment['redshift'] - next_redshift) # When using the peculiar velocity, create effective redshift # (redshift_eff) field combining cosmological redshift and # doppler redshift. # then to add cosmological redshift and doppler redshifts, follow # eqn 3.75 in Peacock's Cosmological Physics: # 1 + z_eff = (1 + z_cosmo) * (1 + z_doppler) if use_peculiar_velocity: sub_data[('gas', 'redshift_eff')] = \ ((1 + sub_data[('gas', 'redshift_dopp')]) * \ (1 + sub_data[('gas', 'redshift')])) - 1 # Remove empty lixels. sub_dl_nonzero = sub_data[('gas', 'dl')].nonzero() for field in all_fields: sub_data[field] = sub_data[field][sub_dl_nonzero] del sub_dl_nonzero # Add to storage. my_storage.result = sub_data del ds # Reconstruct ray data from parallel_objects storage. all_data = [my_data for my_data in all_ray_storage.values()] # This is now a list of segments where each one is a dictionary # with all the fields. all_data.sort(key=lambda a:a[('gas', 'extra_data')]['segment_redshift'], reverse=True) # Gather segment data to add to the light ray solution. for segment_data, my_segment in \ zip(all_data, self.light_ray_solution): my_segment["unique_identifier"] = \ segment_data[('gas', "extra_data")]["unique_identifier"] # Flatten the list into a single dictionary containing fields # for the whole ray. all_data = _flatten_dict_list( all_data, exceptions=[('gas', 'extra_data')]) self._data = all_data if data_filename is not None: self._write_light_ray(data_filename, all_data) ray_ds = YTDataLightRayDataset(data_filename) # temporary fix for yt-4.0 ytdata selection issue ray_ds.domain_left_edge ='code_length') ray_ds.domain_right_edge ='code_length') return ray_ds else: return None
def __getitem__(self, field): return self._data[field] @parallel_root_only def _write_light_ray(self, filename, data): """ _write_light_ray(filename, data) Write light ray data to hdf5 file. """ extra_attrs = {"data_type": "yt_light_ray"} if self.simulation_type is None: ds = self.ds else: ds = {} ds["periodicity"] = (True, True, True) ds["current_redshift"] = self.near_redshift for attr in ["dimensionality", "cosmological_simulation", "domain_left_edge", "domain_right_edge", "length_unit", "time_unit"]: ds[attr] = getattr(self.simulation, attr) if self.simulation.cosmological_simulation: for attr in ["omega_lambda", "omega_matter", "hubble_constant"]: ds[attr] = getattr(self.cosmology, attr) ds["current_time"] = \ self.cosmology.t_from_z(ds["current_redshift"]) if isinstance(ds["hubble_constant"], YTArray): ds["hubble_constant"] = \ ds["hubble_constant"].to("100*km/(Mpc*s)").d extra_attrs["unit_registry_json"] = \ self.simulation.unit_registry.to_json() # save the light ray solution if len(self.light_ray_solution) > 0: for key in self.light_ray_solution[0]: if key in ["next", "previous", "index"]: continue lrsa = [sol[key] for sol in self.light_ray_solution] if isinstance(lrsa[-1], YTArray): to_arr = YTArray else: to_arr = np.array arr = to_arr(lrsa) # If we somehow create an object array, convert it to a string # to avoid errors later if arr.dtype == 'O': arr = arr.astype(str) if arr.dtype.kind == 'U': arr = arr.astype('|S') extra_attrs["light_ray_solution_%s" % key] = arr field_types = dict([(field, "grid") for field in data.keys()]) # Only return LightRay elements with non-zero density if 'temperature' in data: f = 'temperature' if ('gas', 'temperature') in data: f = ('gas', 'temperature') if 'temperature' in data or ('gas', 'temperature') in data: mask = data[f] > 0 if not np.any(mask): raise RuntimeError( "No zones along light ray with nonzero %s. " "Please modify your light ray trajectory." % (f,)) for key in data.keys(): data[key] = data[key][mask] save_as_dataset(ds, filename, data, field_types=field_types, extra_attrs=extra_attrs) @parallel_root_only def _write_light_ray_solution(self, filename, extra_info=None): """ _write_light_ray_solution(filename, extra_info=None) Write light ray solution to a file. """"Writing light ray solution to %s." % filename) f = open(filename, 'w') if extra_info is not None: for par, val in extra_info.items(): f.write("%s = %s\n" % (par, val)) f.write("\nSegment Redshift dl/box Start x y " + \ "z End x y z Dataset\n") for q, my_segment in enumerate(self.light_ray_solution): f.write("%04d %.6f %.6f % .10f % .10f % .10f % .10f % .10f % .10f %s\n" % \ (q, my_segment['redshift'], my_segment['traversal_box_fraction'], my_segment['start'][0], my_segment['start'][1], my_segment['start'][2], my_segment['end'][0], my_segment['end'][1], my_segment['end'][2], my_segment['filename'])) f.close()
def _flatten_dict_list(data, exceptions=None): """ _flatten_dict_list(data, exceptions=None) Flatten the list of dicts into one dict. """ if exceptions is None: exceptions = [] new_data = {} for datum in data: for field in [field for field in datum.keys() if field not in exceptions]: if field not in new_data: new_data[field] = [] new_data[field].extend(datum[field]) for field in new_data: new_data[field] = YTArray(new_data[field]) return new_data def vector_length(start, end): """ vector_length(start, end) Calculate vector length. """ return np.sqrt(np.power((end - start), 2).sum()) def periodic_adjust(p, left=None, right=None): """ Return the point p adjusted for periodic boundaries. """ if isinstance(p, YTArray): p.convert_to_units("unitary") if left is None: left = np.zeros_like(p) if right is None: right = np.ones_like(p) w = right - left p -= left return np.mod(p, w) def periodic_distance(coord1, coord2): """ periodic_distance(coord1, coord2) Calculate length of shortest vector between to points in periodic domain. """ dif = coord1 - coord2 dim = np.ones(coord1.shape,dtype=int) def periodic_bind(num): pos = np.abs(num % dim) neg = np.abs(num % -dim) return np.min([pos,neg],axis=0) dif = periodic_bind(dif) return np.sqrt((dif * dif).sum(axis=-1)) def periodic_ray(start, end, left=None, right=None): """ periodic_ray(start, end, left=None, right=None) Break up periodic ray into non-periodic segments. Accepts start and end points of periodic ray as YTArrays. Accepts optional left and right edges of periodic volume as YTArrays. Returns a list of lists of coordinates, where each element of the top-most list is a 2-list of start coords and end coords of the non-periodic ray: [[[x0start,y0start,z0start], [x0end, y0end, z0end]], [[x1start,y1start,z1start], [x1end, y1end, z1end]], ...,] """ if left is None: left = np.zeros(start.shape) if right is None: right = np.ones(start.shape) dim = right - left vector = end - start wall = np.zeros_like(start) close = np.zeros(start.shape, dtype=object) left_bound = vector < 0 right_bound = vector > 0 no_bound = vector == 0.0 bound = vector != 0.0 wall[left_bound] = left[left_bound] close[left_bound] = np.max wall[right_bound] = right[right_bound] close[right_bound] = np.min wall[no_bound] = np.inf close[no_bound] = np.min segments = [] this_start = start.copy() this_end = end.copy() t = 0.0 tolerance = 1e-6 while t < 1.0 - tolerance: hit_left = (this_start <= left) & (vector < 0) if (hit_left).any(): this_start[hit_left] += dim[hit_left] this_end[hit_left] += dim[hit_left] hit_right = (this_start >= right) & (vector > 0) if (hit_right).any(): this_start[hit_right] -= dim[hit_right] this_end[hit_right] -= dim[hit_right] nearest = vector.unit_array * \ np.array([close[q]([this_end[q], wall[q]]) \ for q in range(start.size)]) dt = ((nearest - this_start) / vector)[bound].min() now = this_start + vector * dt close_enough = np.abs(now - nearest) / np.abs(vector.max()) < 1e-10 now[close_enough] = nearest[close_enough] segments.append([this_start.copy(), now.copy()]) this_start = now.copy() t += dt return segments def non_periodic_ray(ds, left_edge, right_edge, ray_length, max_iter=5000, min_level=None, my_random=None): max_length = vector_length(left_edge, right_edge) if ray_length > max_length: raise RuntimeError( ("The maximum segment length in the region %s to %s is %s, " + "but the ray length requested is %s. Decrease ray length.") % (left_edge, right_edge, max_length, ray_length)) if my_random is None: my_random = np.random.RandomState() i = 0 while True: start = my_random.random_sample(3) * \ (right_edge - left_edge) + left_edge theta = np.pi * my_random.random_sample() phi = 2 * np.pi * my_random.random_sample() end = start + ray_length * \ np.array([np.cos(phi) * np.sin(theta), np.sin(phi) * np.sin(theta), np.cos(theta)]) i += 1 test_ray = ds.ray(start, end) if (end >= left_edge).all() and (end <= right_edge).all() and \ (min_level is None or min_level <= 0 or (test_ray["grid_level"] >= min_level).all()):"Found ray after %d attempts." % i) del test_ray return start, end del test_ray if i > max_iter: raise RuntimeError( ("Failed to create segment in %d attempts. " + "Decreasing ray length is recommended") % i)