"""Module for implementing collections of features within a Sample."""
import copy
import logging
from pathlib import Path
from typing import Optional
import CGNS.MAP as CGM
import CGNS.PAT.cgnskeywords as CGK
import CGNS.PAT.cgnslib as CGL
import CGNS.PAT.cgnsutils as CGU
import numpy as np
from CGNS.PAT.cgnsutils import __CHILDREN__, __NAME__
from plaid.constants import (
CGNS_ELEMENT_NAMES,
CGNS_FIELD_LOCATIONS,
)
from plaid.containers.utils import (
_check_names,
_read_index,
)
from plaid.types import CGNSLink, CGNSNode, CGNSPath, CGNSTree, Field
from plaid.utils import cgns_helper as CGH
logger = logging.getLogger(__name__)
logging.basicConfig(
format="[%(asctime)s:%(levelname)s:%(filename)s:%(funcName)s(%(lineno)d)]:%(message)s",
level=logging.INFO,
)
[docs]
class SampleMeshes:
"""A container for meshes within a Sample.
Args:
meshes (dict[float, CGNSTree], optional): A dictionary mapping time steps to CGNSTrees. Defaults to None.
mesh_base_name (str, optional): The base name for the mesh. Defaults to 'Base'.
mesh_zone_name (str, optional): The zone name for the mesh. Defaults to 'Zone'.
links (dict[float, list[CGNSLink]], optional): A dictionary mapping time steps to lists of links. Defaults to None.
paths (dict[float, list[CGNSPath]], optional): A dictionary mapping time steps to lists of paths. Defaults to None.
"""
def __init__(
self,
meshes: Optional[dict[float, CGNSTree]],
mesh_base_name: str = "Base",
mesh_zone_name: str = "Zone",
links: Optional[dict[float, list[CGNSLink]]] = None,
paths: Optional[dict[float, list[CGNSPath]]] = None,
):
[docs]
self.data: dict[float, CGNSTree] = meshes if meshes is not None else {}
[docs]
self._links = links if links is not None else {}
[docs]
self._paths = paths if paths is not None else {}
[docs]
self._default_active_base: Optional[str] = None
[docs]
self._default_active_zone: Optional[str] = None
[docs]
self._default_active_time: Optional[float] = None
[docs]
self._mesh_base_name: str = mesh_base_name
[docs]
self._mesh_zone_name: str = mesh_zone_name
[docs]
def get_all_mesh_times(self) -> list[float]:
"""Retrieve all time steps corresponding to the meshes, if available.
Returns:
list[float]: A list of all available time steps.
"""
return list(self.data.keys())
[docs]
def get_time_assignment(self, time: Optional[float] = None) -> float:
"""Retrieve the default time for the CGNS operations.
If there are available time steps, it will return the first one; otherwise, it will return 0.0.
Args:
time (str, optional): The time value provided for the operation. If not provided, the default time set in the system will be used.
Returns:
float: The attributed time.
Note:
- The default time step is used as a reference point for many CGNS operations.
- It is important for accessing and visualizing data at specific time points in a simulation.
"""
if self._default_active_time is None and time is None:
timestamps = self.get_all_mesh_times()
return sorted(timestamps)[0] if len(timestamps) > 0 else 0.0
return self._default_active_time if time is None else time
[docs]
def get_base_assignment(
self, base_name: Optional[str] = None, time: Optional[float] = None
) -> str:
"""Retrieve the default base name for the CGNS operations.
This function calculates the attributed base for a specific operation based on the
default base set in the system.
Args:
base_name (str, optional): The name of the base to attribute the operation to. If not provided, the default base set in the system will be used.
time (str, optional): The time value provided for the operation. If not provided, the default time set in the system will be used.
Raises:
KeyError: If no default base can be determined based on the provided or default.
KeyError: If no base node is found after following given and default parameters.
Returns:
str: The attributed base name.
Note:
- If no specific base name is provided, the function will use the default base provided by the user.
- In case the default base does not exist: If no specific time is provided, the function will use the default time provided by the user.
"""
base_name = base_name or self._default_active_base
if base_name:
return base_name
base_names = self.get_base_names(time=time)
if len(base_names) == 0:
return None
elif len(base_names) == 1:
# logging.info(f"No default base provided. Taking the only base available: {base_names[0]}")
return base_names[0]
raise KeyError(f"No default base provided among {base_names}")
[docs]
def get_zone_assignment(
self,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> str:
"""Retrieve the default zone name for the CGNS operations.
This function calculates the attributed zone for a specific operation based on the
default zone set in the system, within the specified base.
Args:
zone_name (str, optional): The name of the zone to attribute the operation to. If not provided, the default zone set in the system within the specified base will be used.
base_name (str, optional): The name of the base within which the zone should be attributed. If not provided, the default base set in the system will be used.
time (str, optional): The time value provided for the operation. If not provided, the default time set in the system will be used.
Raises:
KeyError: If no default zone can be determined based on the provided or default values.
KeyError: If no zone node is found after following given and default parameters.
Returns:
str: The attributed zone name.
Note:
- If neither a specific zone name nor a specific base name is provided, the function will use the default zone provided by the user.
- In case the default zone does not exist: If no specific time is provided, the function will use the default time provided by the user.
"""
zone_name = zone_name or self._default_active_zone
if zone_name:
return zone_name
base_name = self.get_base_assignment(base_name, time)
zone_names = self.get_zone_names(base_name, time=time)
if len(zone_names) == 0:
return None
elif len(zone_names) == 1:
# logging.info(f"No default zone provided. Taking the only zone available: {zone_names[0]} in default base: {base_name}")
return zone_names[0]
raise KeyError(
f"No default zone provided among {zone_names} in the default base: {base_name}"
)
[docs]
def init_tree(self, time: Optional[float] = None) -> CGNSTree:
"""Initialize a CGNS tree structure at a specified time step or create a new one if it doesn't exist.
Args:
time (float, optional): The time step for which to initialize the CGNS tree structure. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
CGNSTree (list): The initialized or existing CGNS tree structure for the specified time step.
"""
time = self.get_time_assignment(time)
if not self.data:
self.data = {time: CGL.newCGNSTree()}
self._links = {time: None}
self._paths = {time: None}
elif time not in self.data:
self.data[time] = CGL.newCGNSTree()
self._links[time] = None
self._paths[time] = None
return self.data[time]
[docs]
def get_links(self, time: Optional[float] = None) -> list[CGNSLink]:
"""Retrieve the CGNS links for a specified time step, if available.
Args:
time (float, optional): The time step for which to retrieve the CGNS links. If a specific time is not provided, the method will display the links for the default time step.
Returns:
list: The CGNS links for the specified time step if available; otherwise, returns None.
"""
time = self.get_time_assignment(time)
return self._links[time] if (self._links) else None
[docs]
def get_mesh(
self, time: Optional[float] = None, apply_links: bool = False, in_memory=False
) -> Optional[CGNSTree]:
"""Retrieve the CGNS tree structure for a specified time step, if available.
Args:
time (float, optional): The time step for which to retrieve the CGNS tree structure. If a specific time is not provided, the method will display the tree structure for the default time step.
apply_links (bool, optional): Activates the following of the CGNS links to reconstruct the complete CGNS tree - in this case, a deepcopy of the tree is made to prevent from modifying the existing tree.
in_memory (bool, optional): Active if apply_links == True, ONLY WORKING if linked mesh is in the current sample. This option follows the link in memory from current sample.
Returns:
CGNSTree: The CGNS tree structure for the specified time step if available; otherwise, returns None.
"""
if not self.data:
return None
time = self.get_time_assignment(time)
tree = self.data[time]
links = self.get_links(time)
if not apply_links or links is None:
return tree
tree = copy.deepcopy(tree)
for link in links:
if not in_memory:
subtree, _, _ = CGM.load(str(Path(link[0]) / link[1]), subtree=link[2])
else:
linked_timestep = int(link[1].split(".cgns")[0].split("_")[1])
linked_timestamp = list(self.data.keys())[linked_timestep]
subtree = self.get_mesh(linked_timestamp)
node_path = "/".join(link[2].split("/")[:-1])
node_to_append = CGU.getNodeByPath(tree, node_path)
assert node_to_append is not None, (
f"nodepath {node_path} not present in tree, cannot apply link"
)
node_to_append[2].append(CGU.getNodeByPath(subtree, link[2]))
return tree
[docs]
def set_meshes(self, meshes: dict[float, CGNSTree]) -> None:
"""Set all meshes with their corresponding time step.
Args:
meshes (dict[float,CGNSTree]): Collection of time step with its corresponding CGNSTree.
Raises:
KeyError: If there is already a CGNS tree set.
"""
if not self.data:
self.data = meshes
self._links = {}
self._paths = {}
for time in self.data.keys():
self._links[time] = None
self._paths[time] = None
else:
raise KeyError(
"meshes is already set, you cannot overwrite it, delete it first or extend it with `Sample.add_tree`"
)
[docs]
def add_tree(self, tree: CGNSTree, time: Optional[float] = None) -> CGNSTree:
"""Merge a CGNS tree to the already existing tree.
Args:
tree (CGNSTree): The CGNS tree to be merged. If a Base node already exists, it is ignored.
time (float, optional): The time step for which to add the CGNS tree structure. If a specific time is not provided, the method will display the tree structure for the default time step.
Raises:
ValueError: If the provided CGNS tree is an empty list.
Returns:
CGNSTree: The merged CGNS tree.
"""
if tree == []:
raise ValueError("CGNS Tree should not be an empty list")
time = self.get_time_assignment(time)
if not self.data:
self.data = {time: tree}
self._links = {time: None}
self._paths = {time: None}
elif time not in self.data:
self.data[time] = tree
self._links[time] = None
self._paths[time] = None
else:
# TODO: gérer le cas où il y a des bases de mêmes noms... + merge
# récursif des nœuds
local_bases = self.get_base_names(time=time)
base_nodes = CGU.getNodesFromTypeSet(tree, "CGNSBase_t")
for _, node in base_nodes:
if node[__NAME__] not in local_bases: # pragma: no cover
self.data[time][__CHILDREN__].append(node)
else:
logger.warning(
f"base <{node[__NAME__]}> already exists in self._tree --> ignored"
)
base_names = self.get_base_names(time=time)
for base_name in base_names:
base_node = self.get_base(base_name, time=time)
if CGU.getValueByPath(base_node, "Time/TimeValues") is None:
baseIterativeData_node = CGL.newBaseIterativeData(base_node, "Time", 1)
TimeValues_node = CGU.newNode(
"TimeValues", None, [], CGK.DataArray_ts, baseIterativeData_node
)
CGU.setValue(TimeValues_node, np.array([time]))
return self.data[time]
[docs]
def del_tree(self, time: float) -> CGNSTree:
"""Delete the CGNS tree for a specific time.
Args:
time (float): The time step for which to delete the CGNS tree structure.
Raises:
KeyError: There is no CGNS tree in this Sample / There is no CGNS tree for the provided time.
Returns:
CGNSTree: The deleted CGNS tree.
"""
if not self.data:
raise KeyError("There is no CGNS tree in this sample.")
if time not in self.data:
raise KeyError(f"There is no CGNS tree for time {time}.")
self._links.pop(time, None)
self._paths.pop(time, None)
return self.data.pop(time)
# -------------------------------------------------------------------------#
[docs]
def get_topological_dim(
self, base_name: Optional[str] = None, time: Optional[float] = None
) -> int:
"""Get the topological dimension of a base node at a specific time.
Args:
base_name (str, optional): The name of the base node for which to retrieve the topological dimension. Defaults to None.
time (float, optional): The time at which to retrieve the topological dimension. Defaults to None.
Raises:
ValueError: If there is no base node with the specified `base_name` at the given `time` in this sample.
Returns:
int: The topological dimension of the specified base node at the given time.
"""
# get_base will look for default time and base_name
base_node = self.get_base(base_name, time)
if base_node is None: # pragma: no cover
raise ValueError(
f"there is no base called {base_name} at the time {time} in this sample"
)
return base_node[1][0]
[docs]
def get_physical_dim(
self, base_name: Optional[str] = None, time: Optional[float] = None
) -> int:
"""Get the physical dimension of a base node at a specific time.
Args:
base_name (str, optional): The name of the base node for which to retrieve the topological dimension. Defaults to None.
time (float, optional): The time at which to retrieve the topological dimension. Defaults to None.
Raises:
ValueError: If there is no base node with the specified `base_name` at the given `time` in this sample.
Returns:
int: The topological dimension of the specified base node at the given time.
"""
base_node = self.get_base(base_name, time)
if base_node is None: # pragma: no cover
raise ValueError(
f"there is no base called {base_name} at the time {time} in this sample"
)
return base_node[1][1]
[docs]
def init_base(
self,
topological_dim: int,
physical_dim: int,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> CGNSNode:
"""Create a Base node named `base_name` if it doesn't already exists.
Args:
topological_dim (int): Cell dimension, see [CGNS standard](https://pycgns.github.io/PAT/lib.html#CGNS.PAT.cgnslib.newCGNSBase).
physical_dim (int): Ambient space dimension, see [CGNS standard](https://pycgns.github.io/PAT/lib.html#CGNS.PAT.cgnslib.newCGNSBase).
base_name (str): If not specified, uses `mesh_base_name` specified in Sample initialization. Defaults to None.
time (float, optional): The time at which to initialize the base. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
CGNSNode: The created Base node.
"""
_check_names([base_name])
time = self.get_time_assignment(time)
if base_name is None:
base_name = (
self._mesh_base_name
+ "_"
+ str(topological_dim)
+ "_"
+ str(physical_dim)
)
self.init_tree(time)
if not (self.has_base(base_name, time)):
base_node = CGL.newCGNSBase(
self.data[time], base_name, topological_dim, physical_dim
)
base_names = self.get_base_names(time=time)
for base_name in base_names:
base_node = self.get_base(base_name, time=time)
if CGU.getValueByPath(base_node, "Time/TimeValues") is None:
base_iterative_data_node = CGL.newBaseIterativeData(
base_node, "Time", 1
)
time_values_node = CGU.newNode(
"TimeValues", None, [], CGK.DataArray_ts, base_iterative_data_node
)
CGU.setValue(time_values_node, np.array([time]))
return base_node
[docs]
def del_base(self, base_name: str, time: float) -> CGNSTree:
"""Delete a CGNS base node for a specific time.
Args:
base_name (str): The name of the base node to be deleted.
time (float): The time step for which to delete the CGNS base node.
Raises:
KeyError: There is no CGNS tree in this sample / There is no CGNS tree for the provided time.
KeyError: If there is no base node with the given base name or time.
Returns:
CGNSTree: The tree at the provided time (without the deleted node)
"""
if not self.data:
raise KeyError("There is no CGNS tree in this sample.")
if time not in self.data:
raise KeyError(f"There is no CGNS tree for time {time}.")
base_node = self.get_base(base_name, time)
mesh_tree = self.data[time]
if base_node is None:
raise KeyError(
f"There is no base node with name {base_name} for time {time}."
)
return CGU.nodeDelete(mesh_tree, base_node)
[docs]
def get_base_names(
self,
full_path: bool = False,
unique: bool = False,
time: Optional[float] = None,
) -> list[str]:
"""Return Base names.
Args:
full_path (bool, optional): If True, returns full paths instead of only Base names. Defaults to False.
unique (bool, optional): If True, returns unique names instead of potentially duplicated names. Defaults to False.
time (float, optional): The time at which to check for the Base. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
list[str]:
"""
time = self.get_time_assignment(time)
if self.data and time in self.data and self.data[time] is not None:
return CGH.get_base_names(
self.data[time], full_path=full_path, unique=unique
)
else:
return []
[docs]
def has_base(self, base_name: str, time: Optional[float] = None) -> bool:
"""Check if a CGNS tree contains a Base with a given name at a specified time.
Args:
base_name (str): The name of the Base to check for in the CGNS tree.
time (float, optional): The time at which to check for the Base. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
bool: `True` if the CGNS tree has a Base called `base_name`, else return `False`.
"""
# get_base_names will look for the default time
return base_name in self.get_base_names(time=time)
[docs]
def get_base(
self, base_name: Optional[str] = None, time: Optional[float] = None
) -> CGNSNode:
"""Return Base node named `base_name`.
If `base_name` is not specified, checks that there is **at most** one base, else raises an error.
Args:
base_name (str, optional): The name of the Base node to retrieve. Defaults to None. Defaults to None.
time (float, optional): Time at which you want to retrieve the Base node. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
CGNSNode or None: The Base node with the specified name or None if it is not found.
"""
time = self.get_time_assignment(time)
base_name = self.get_base_assignment(base_name, time)
if time not in self.data or self.data[time] is None:
logger.warning(f"No mesh exists in the sample at {time=}")
return None
return CGU.getNodeByPath(self.data[time], f"/CGNSTree/{base_name}")
# -------------------------------------------------------------------------#
[docs]
def init_zone(
self,
zone_shape: np.ndarray,
zone_type: str = CGK.Unstructured_s,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> CGNSNode:
"""Initialize a new zone within a CGNS base.
Args:
zone_shape (np.ndarray): An array specifying the shape or dimensions of the zone.
zone_type (str, optional): The type of the zone. Defaults to CGK.Unstructured_s.
zone_name (str, optional): The name of the zone to initialize. If not provided, uses `mesh_zone_name` specified in Sample initialization. Defaults to None.
base_name (str, optional): The name of the base to which the zone will be added. If not provided, the zone will be added to the currently active base. Defaults to None.
time (float, optional): The time at which to initialize the zone. If a specific time is not provided, the method will display the tree structure for the default time step.
Raises:
KeyError: If the specified base does not exist. You can create a base using `Sample.init_base(base_name)`.
Returns:
CGLNode: The newly initialized zone node within the CGNS tree.
"""
_check_names([zone_name])
# init_tree will look for default time
self.init_tree(time)
# get_base will look for default base_name and time
base_node = self.get_base(base_name, time)
if base_node is None:
raise KeyError(
f"there is no base <{base_name}>, you should first create one with `Sample.init_base({base_name=})`"
)
zone_name = self.get_zone_assignment(zone_name, base_name, time)
if zone_name is None:
zone_name = self._mesh_zone_name
zone_node = CGL.newZone(base_node, zone_name, zone_shape, zone_type)
return zone_node
[docs]
def del_zone(self, zone_name: str, base_name: str, time: float) -> CGNSTree:
"""Delete a zone within a CGNS base.
Args:
zone_name (str): The name of the zone to be deleted.
base_name (str, optional): The name of the base from which the zone will be deleted. If not provided, the zone will be deleted from the currently active base. Defaults to None.
time (float, optional): The time step for which to delete the zone. Defaults to None.
Raises:
KeyError: There is no CGNS tree in this sample / There is no CGNS tree for the provided time.
KeyError: If there is no base node with the given base name or time.
Returns:
CGNSTree: The tree at the provided time (without the deleted node)
"""
if self.data is None: # pragma: no cover
raise KeyError("There is no CGNS tree in this sample.")
if time not in self.data:
raise KeyError(f"There is no CGNS tree for time {time}.")
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
mesh_tree = self.data[time]
if zone_node is None:
raise KeyError(
f"There is no zone node with name {zone_name} or base node with name {base_name}."
)
return CGU.nodeDelete(mesh_tree, zone_node)
[docs]
def get_zone_names(
self,
base_name: Optional[str] = None,
full_path: bool = False,
unique: bool = False,
time: Optional[float] = None,
) -> list[str]:
"""Return list of Zone names in Base named `base_name` with specific time.
Args:
base_name (str, optional): Name of Base where to search Zones. If not specified, checks if there is at most one Base. Defaults to None.
full_path (bool, optional): If True, returns full paths instead of only Zone names. Defaults to False.
unique (bool, optional): If True, returns unique names instead of potentially duplicated names. Defaults to False.
time (float, optional): The time at which to check for the Zone. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
list[str]: List of Zone names in Base named `base_name`, empty if there is none or if the Base doesn't exist.
"""
zone_paths = []
# get_base will look for default base_name and time
base_node = self.get_base(base_name, time)
if base_node is not None:
z_paths = CGU.getPathsByTypeSet(base_node, "CGNSZone_t")
for pth in z_paths:
s_pth = pth.split("/")
assert len(s_pth) == 2
assert s_pth[0] == base_name or base_name is None
if full_path:
zone_paths.append(pth)
else:
zone_paths.append(s_pth[1])
if unique:
return list(set(zone_paths))
else:
return zone_paths
[docs]
def has_zone(
self,
zone_name: str,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> bool:
"""Check if the CGNS tree contains a Zone with the specified name within a specific Base and time.
Args:
zone_name (str): The name of the Zone to check for.
base_name (str, optional): The name of the Base where the Zone should be located. If not provided, the function checks all bases. Defaults to None.
time (float, optional): The time at which to check for the Zone. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
bool: `True` if the CGNS tree has a Zone called `zone_name` in a Base called `base_name`, else return `False`.
"""
# get_zone_names will look for default base_name and time
return zone_name in self.get_zone_names(base_name, time=time)
[docs]
def get_zone(
self,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> CGNSNode:
"""Retrieve a CGNS Zone node by its name within a specific Base and time.
Args:
zone_name (str, optional): The name of the Zone node to retrieve. If not specified, checks that there is **at most** one zone in the base, else raises an error. Defaults to None.
base_name (str, optional): The Base in which to seek to zone retrieve. If not specified, checks that there is **at most** one base, else raises an error. Defaults to None.
time (float, optional): Time at which you want to retrieve the Zone node.
Returns:
CGNSNode: Returns a CGNS Zone node if found; otherwise, returns None.
"""
# get_base will look for default base_name and time
base_node = self.get_base(base_name, time)
if base_node is None:
logger.warning(f"No base with name {base_name} in this tree")
return None
# _zone_attribution will look for default base_name
zone_name = self.get_zone_assignment(zone_name, base_name, time)
if zone_name is None:
logger.warning(f"No zone with name {zone_name} in this base ({base_name})")
return None
return CGU.getNodeByPath(base_node, zone_name)
[docs]
def get_zone_type(
self,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> str:
"""Get the type of a specific zone at a specified time.
Args:
zone_name (str, optional): The name of the zone whose type you want to retrieve. Default is None.
base_name (str, optional): The name of the base in which the zone is located. Default is None.
time (float, optional): The timestamp for which you want to retrieve the zone type. Default is 0.0.
Raises:
KeyError: Raised when the specified zone or base does not exist. You should first create the base/zone using `Sample.init_zone(zone_name, base_name)`.
Returns:
str: The type of the specified zone as a string.
"""
# get_zone will look for default base_name, zone_name and time
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if zone_node is None:
raise KeyError(
f"there is no base/zone <{base_name}/{zone_name}>, you should first create one with `Sample.init_zone({zone_name=},{base_name=})`"
)
return CGU.getValueByPath(zone_node, "ZoneType").tobytes().decode()
# -------------------------------------------------------------------------#
# -------------------------------------------------------------------------#
[docs]
def get_nodes(
self,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> Optional[np.ndarray]:
"""Get grid node coordinates from a specified base, zone, and time.
Args:
zone_name (str, optional): The name of the zone to search for. Defaults to None.
base_name (str, optional): The name of the base to search for. Defaults to None.
time (float, optional): The time value to consider when searching for the zone. If a specific time is not provided, the method will display the tree structure for the default time step.
Raises:
TypeError: Raised if multiple <GridCoordinates> nodes are found. Only one is expected.
Returns:
Optional[np.ndarray]: A NumPy array containing the grid node coordinates.
If no matching zone or grid coordinates are found, None is returned.
Seealso:
This function can also be called using `get_points()` or `get_vertices()`.
"""
# get_zone will look for default base_name, zone_name and time
search_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if search_node is None:
return None
grid_paths = CGU.getAllNodesByTypeSet(search_node, ["GridCoordinates_t"])
if len(grid_paths) == 1:
grid_node = CGU.getNodeByPath(search_node, grid_paths[0])
array_x = CGU.getValueByPath(grid_node, "GridCoordinates/CoordinateX")
array_y = CGU.getValueByPath(grid_node, "GridCoordinates/CoordinateY")
array_z = CGU.getValueByPath(grid_node, "GridCoordinates/CoordinateZ")
if array_z is None:
array = np.concatenate(
(array_x.reshape((-1, 1)), array_y.reshape((-1, 1))), axis=1
)
else:
array = np.concatenate(
(
array_x.reshape((-1, 1)),
array_y.reshape((-1, 1)),
array_z.reshape((-1, 1)),
),
axis=1,
)
return array
elif len(grid_paths) > 1: # pragma: no cover
raise TypeError(
f"Found {len(grid_paths)} <GridCoordinates> nodes, should find only one"
)
[docs]
get_vertices = get_nodes
[docs]
def set_nodes(
self,
nodes: np.ndarray,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> None:
"""Set the coordinates of nodes for a specified base and zone at a given time.
Args:
nodes (np.ndarray): A numpy array containing the new node coordinates.
zone_name (str, optional): The name of the zone where the nodes should be updated. Defaults to None.
base_name (str, optional): The name of the base where the nodes should be updated. Defaults to None.
time (float, optional): The time at which the node coordinates should be updated. If a specific time is not provided, the method will display the tree structure for the default time step.
Raises:
KeyError: Raised if the specified base or zone do not exist. You should first
create the base and zone using the `Sample.init_zone(zone_name,base_name)` method.
Seealso:
This function can also be called using `set_points()` or `set_vertices()`
"""
# get_zone will look for default base_name, zone_name and time
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if zone_node is None:
raise KeyError(
f"there is no base/zone <{base_name}/{zone_name}>, you should first create one with `Sample.init_zone({zone_name=},{base_name=})`"
)
# Check if GridCoordinates_t node exists
gc_nodes = [
child for child in zone_node[2] if child[0] in CGK.GridCoordinates_ts
]
if gc_nodes:
grid_coords_node = gc_nodes[0]
coord_type = [CGK.CoordinateX_s, CGK.CoordinateY_s, CGK.CoordinateZ_s]
for i_dim in range(nodes.shape[-1]):
name = coord_type[i_dim]
# Remove existing coordinate if present
if gc_nodes:
grid_coords_node[2] = [
child for child in grid_coords_node[2] if child[0] != name
]
# Create new coordinate
CGL.newCoordinates(zone_node, name, np.asfortranarray(nodes[..., i_dim]))
[docs]
set_vertices = set_nodes
# -------------------------------------------------------------------------#
[docs]
def get_elements(
self,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> dict[str, np.ndarray]:
"""Retrieve element connectivity data for a specified zone, base, and time.
Args:
zone_name (str, optional): The name of the zone for which element connectivity data is requested. Defaults to None, indicating the default zone.
base_name (str, optional): The name of the base for which element connectivity data is requested. Defaults to None, indicating the default base.
time (float, optional): The time at which element connectivity data is requested. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
dict[str,np.ndarray]: A dictionary where keys are element type names and values are NumPy arrays representing the element connectivity data.
The NumPy arrays have shape (num_elements, num_nodes_per_element), and element indices are 0-based.
"""
# get_zone will look for default base_name, zone_name and time
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if zone_node is None:
return {}
elements = {}
elem_paths = CGU.getAllNodesByTypeSet(zone_node, ["Elements_t"])
for elem in elem_paths:
elem_node = CGU.getNodeByPath(zone_node, elem)
val = CGU.getValue(elem_node)
elem_type = CGNS_ELEMENT_NAMES[val[0]]
elem_size = int(elem_type.split("_")[-1])
# elem_range = CGU.getValueByPath(
# elem_node, "ElementRange"
# ) # TODO elem_range is unused
# -1 is to get back indexes starting at 0
elements[elem_type] = (
CGU.getValueByPath(elem_node, "ElementConnectivity").reshape(
(-1, elem_size)
)
- 1
)
return elements
# -------------------------------------------------------------------------#
[docs]
def get_field_names(
self,
location: str = None,
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> list[str]:
"""Get a set of field names associated with a specified zone, base, location, and/or time.
For each argument that is not specified, the method will search for fields in all available values for this argument.
Args:
location (str, optional): The desired grid location where to search for. Defaults to None.
Possible values : :py:const:`plaid.constants.CGNS_FIELD_LOCATIONS`
zone_name (str, optional): The name of the zone to search for. Defaults to None.
base_name (str, optional): The name of the base to search for. Defaults to None.
time (float, optional): The specific time at which to search for. Defaults to None.
Returns:
set[str]: A set containing the names of the fields that match the specified criteria.
"""
def get_field_names_one_time_base_zone_location(
location: str, zone_name: str, base_name: str, time: float
) -> list[str]:
# get_zone will look for default zone_name, base_name, time
search_node = self.get_zone(
zone_name=zone_name, base_name=base_name, time=time
)
if search_node is None: # pragma: no cover
return []
names = []
solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t])
for f_path in solution_paths:
if (
CGU.getValueByPath(search_node, f_path + "/GridLocation")
.tobytes()
.decode()
!= location
):
continue
f_node = CGU.getNodeByPath(search_node, f_path)
for path in CGU.getPathByTypeFilter(f_node, CGK.DataArray_t):
field_name = path.split("/")[-1]
if not (field_name == "GridLocation"):
names.append(field_name)
return names
field_names = []
times = [time] if time is not None else self.get_all_mesh_times()
for time in times:
base_names = (
[base_name] if base_name is not None else self.get_base_names(time=time)
)
for base_name in base_names:
zone_names = (
[zone_name]
if zone_name is not None
else self.get_zone_names(base_name=base_name, time=time)
)
for zone_name in zone_names:
locations = (
[location] if location is not None else CGNS_FIELD_LOCATIONS
)
for location in locations:
field_names += get_field_names_one_time_base_zone_location(
location=location,
zone_name=zone_name,
base_name=base_name,
time=time,
)
field_names = sorted(set(field_names))
return field_names
[docs]
def get_field(
self,
name: str,
location: str = "Vertex",
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> Field:
"""Retrieve a field with a specified name from a given zone, base, location, and time.
Args:
name (str): The name of the field to retrieve.
location (str, optional): The location at which to retrieve the field. Defaults to 'Vertex'.
Possible values : :py:const:`plaid.constants.CGNS_FIELD_LOCATIONS`
zone_name (str, optional): The name of the zone to search for. Defaults to None.
base_name (str, optional): The name of the base to search for. Defaults to None.
time (float, optional): The time value to consider when searching for the field. If a specific time is not provided, the method will display the tree structure for the default time step.
Returns:
Field: A set containing the names of the fields that match the specified criteria.
"""
# get_zone will look for default time
search_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if search_node is None:
return None
is_empty = True
full_field = []
solution_paths = CGU.getPathsByTypeSet(search_node, [CGK.FlowSolution_t])
for f_path in solution_paths:
if (
CGU.getValueByPath(search_node, f_path + "/GridLocation")
.tobytes()
.decode()
== location
):
field = CGU.getValueByPath(search_node, f_path + "/" + name)
if field is None:
field = np.empty((0,))
else:
is_empty = False
full_field.append(field)
if is_empty:
return None
else:
return np.concatenate(full_field)
[docs]
def add_field(
self,
name: str,
field: Field,
location: str = "Vertex",
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
warning_overwrite: bool = True,
) -> None:
"""Add a field to a specified zone in the grid.
Args:
name (str): The name of the field to be added.
field (Field): The field data to be added.
location (str, optional): The grid location where the field will be stored. Defaults to 'Vertex'.
Possible values : :py:const:`plaid.constants.CGNS_FIELD_LOCATIONS`
zone_name (str, optional): The name of the zone where the field will be added. Defaults to None.
base_name (str, optional): The name of the base where the zone is located. Defaults to None.
time (float, optional): The time associated with the field. Defaults to 0.
warning_overwrite (bool, optional): Show warning if a preexisting field is being overwritten. Defaults to True.
Raises:
KeyError: Raised if the specified zone does not exist in the given base.
"""
_check_names([name])
# init_tree will look for default time
self.init_tree(time)
# get_zone will look for default zone_name, base_name and time
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
if zone_node is None:
raise KeyError(
f"there is no Zone with name {zone_name} in base {base_name}. Did you check topological and physical dimensions ?"
)
# solution_paths = CGU.getPathsByTypeOrNameList(self._tree, '/.*/.*/FlowSolution_t')
solution_paths = CGU.getPathsByTypeSet(zone_node, "FlowSolution_t")
has_FlowSolution_with_location = False
if len(solution_paths) > 0:
for s_path in solution_paths:
val_location = (
CGU.getValueByPath(zone_node, f"{s_path}/GridLocation")
.tobytes()
.decode()
)
if val_location == location:
has_FlowSolution_with_location = True
if not (has_FlowSolution_with_location):
CGL.newFlowSolution(zone_node, f"{location}Fields", gridlocation=location)
solution_paths = CGU.getPathsByTypeSet(zone_node, "FlowSolution_t")
assert len(solution_paths) > 0
for s_path in solution_paths:
val_location = (
CGU.getValueByPath(zone_node, f"{s_path}/GridLocation")
.tobytes()
.decode()
)
if val_location != location:
continue
field_node = CGU.getNodeByPath(zone_node, f"{s_path}/{name}")
if field_node is None:
flow_solution_node = CGU.getNodeByPath(zone_node, s_path)
# CGL.newDataArray(flow_solution_node, name, np.asfortranarray(np.copy(field), dtype=np.float64))
CGL.newDataArray(flow_solution_node, name, np.asfortranarray(field))
# res = [name, np.asfortranarray(field, dtype=np.float32), [], 'DataArray_t']
# print(field.shape)
# flow_solution_node[2].append(res)
else:
if warning_overwrite:
logger.warning(
f"field node with name {name} already exists -> data will be replaced"
)
CGU.setValue(field_node, np.asfortranarray(field))
[docs]
def del_field(
self,
name: str,
location: str = "Vertex",
zone_name: Optional[str] = None,
base_name: Optional[str] = None,
time: Optional[float] = None,
) -> CGNSTree:
"""Delete a field with specified name in the mesh.
Args:
name (str): The name of the field to be deleted.
location (str, optional): The grid location where the field is stored. Defaults to 'Vertex'.
Possible values : :py:const:`plaid.constants.CGNS_FIELD_LOCATIONS`
zone_name (str, optional): The name of the zone from which the field will be deleted. Defaults to None.
base_name (str, optional): The name of the base where the zone is located. Defaults to None.
time (float, optional): The time associated with the field. Defaults to None.
Raises:
KeyError: Raised if the specified zone or field does not exist in the given base.
Returns:
CGNSTree: The tree at the provided time (without the deleted node)
"""
# get_zone will look for default zone_name, base_name, and time
zone_node = self.get_zone(zone_name=zone_name, base_name=base_name, time=time)
time = self.get_time_assignment(time)
mesh_tree = self.data[time]
if zone_node is None:
raise KeyError(
f"There is no Zone with name {zone_name} in base {base_name}."
)
solution_paths = CGU.getPathsByTypeSet(zone_node, [CGK.FlowSolution_t])
updated_tree = None
for s_path in solution_paths:
if (
CGU.getValueByPath(zone_node, f"{s_path}/GridLocation")
.tobytes()
.decode()
== location
):
field_node = CGU.getNodeByPath(zone_node, f"{s_path}/{name}")
if field_node is not None:
updated_tree = CGU.nodeDelete(mesh_tree, field_node)
# If the function reaches here, the field was not found
if updated_tree is None:
raise KeyError(f"There is no field with name {name} in the specified zone.")
return updated_tree
[docs]
def show_tree(self, time: Optional[float] = None) -> None:
"""Display the structure of the CGNS tree for a specified time.
Args:
time (float, optional): The time step for which you want to display the CGNS tree structure. Defaults to None. If a specific time is not provided, the method will display the tree structure for the default time step.
"""
time = self.get_time_assignment(time)
if self.data is not None:
CGH.show_cgns_tree(self.data.get(time))