diff --git a/pylock.toml b/pylock.toml index ea23052..949a93a 100644 --- a/pylock.toml +++ b/pylock.toml @@ -5,11 +5,24 @@ requires-python = ">=3.10" environments = [ "python_version >= \"3.10\"", ] -extras = ["dev", "docs", "full", "opt", "tests"] +extras = ["dev", "docs", "full", "opt", "tests", "types", "vtk"] dependency-groups = ["default"] default-groups = ["default"] created-by = "pdm" +[[packages]] +name = "pygments" +version = "2.19.2" +requires-python = ">=3.8" +sdist = {name = "pygments-2.19.2.tar.gz", url = "https://files.pythonhosted.org/packages/b0/77/a5b8c569bf593b0140bde72ea885a803b82086995367bf2037de0159d924/pygments-2.19.2.tar.gz", hashes = {sha256 = "636cb2477cec7f8952536970bc533bc43743542f70392ae026374600add5b887"}} +wheels = [ + {name = "pygments-2.19.2-py3-none-any.whl",url = "https://files.pythonhosted.org/packages/c7/21/705964c7812476f378728bdf590ca4b771ec72385c533964653c68e86bdc/pygments-2.19.2-py3-none-any.whl",hashes = {sha256 = 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a/src/pymech/dataset.py b/src/pymech/dataset.py index 70cc958..4866918 100644 --- a/src/pymech/dataset.py +++ b/src/pymech/dataset.py @@ -1,9 +1,15 @@ +import enum import re from functools import partial from pathlib import Path +import matplotlib as mp +import netCDF4 as nc import numpy as np +import uxarray as uxr import xarray as xr +from matplotlib.collections import PatchCollection +from matplotlib.patches import Polygon from xarray.core.utils import Frozen from .neksuite import readnek @@ -24,6 +30,15 @@ re.VERBOSE, ) +exo_ext_pattern = re.compile( + r""" + .* # one or more characters + \. # character "." + (exo|e) # "exo" or 'e' +""", + re.VERBOSE, +) + def can_open_nek_dataset(path): """A regular expression check of the file extension. @@ -31,10 +46,11 @@ def can_open_nek_dataset(path): .. hint:: - Would not match: .f90 .f .fort .f0000 - - Would match: .fld .f00001 .f12345 + - Would match: .fld .f00001 .f12345, .exo, .e """ - return nek_ext_pattern.match(str(path)) + + return nek_ext_pattern.match(str(path)) or exo_ext_pattern.match(str(path)) def open_dataset(path, **kwargs): @@ -43,10 +59,10 @@ def open_dataset(path, **kwargs): Parameters ---------- path : str - Path to a field file (only Nek files are supported at the moment.) + Path to a field file (only Nek files are supported at the moment.) kwargs : dict - Keyword arguments passed on to the compatible open function. + Keyword arguments passed on to the compatible open function. """ if can_open_nek_dataset(path): @@ -65,15 +81,42 @@ def open_dataset(path, **kwargs): parameters.""" -def _open_nek_dataset(path, drop_variables=None): +class MeshType(enum.Enum): + CARTESIAN = enum.auto() + UNSTRUCT = enum.auto() + + +def _open_nek_dataset( + path: str | Path, drop_variables=None, mesh_type: str = "CARTESIAN" +): """Interface for converting Nek field files into xarray_ datasets. + Parameters + ---------- + path : str + Path to a Nek field file. + + drop_variables: str or collection of str + Names of data variables to drop. + + See: https://docs.xarray.dev/en/stable/generated/xarray.Dataset.drop_vars.html#xarray.Dataset.drop_vars + + mesh_type: str + + .. _xarray: https://docs.xarray.dev/en/stable/ """ - field = readnek(path) - if isinstance(field, int): - raise OSError(f"Failed to load {path}") + known_mesh_type = getattr(MeshType, mesh_type.upper()) + if known_mesh_type == MeshType.CARTESIAN: + return _open_nek_dataset_struct(path, drop_variables) + elif known_mesh_type == MeshType.UNSTRUCT: + return _open_nek_dataset_unstruct(path) + else: + raise ValueError("Unknown mesh type.") + +def _open_nek_dataset_struct(path, drop_variables): + field = readnek(path) elements = field.elem elem_stores = [_NekDataStore(elem) for elem in elements] try: @@ -99,6 +142,54 @@ def _open_nek_dataset(path, drop_variables=None): return ds +def extract_elem_data(elem_array): + # Use lists to accumulate data + x_list, y_list, z_list = [], [], [] + ux_list, uy_list, uz_list, p_list = [], [], [], [] + + # Loop through the elements in the array + for elem in elem_array: + # Append data to respective lists + x_list.append(np.ravel(elem.pos[0])) + y_list.append(np.ravel(elem.pos[1])) + z_list.append(np.ravel(elem.pos[2])) + + ux_list.append(np.ravel(elem.vel[0])) + uy_list.append(np.ravel(elem.vel[1])) + uz_list.append(np.ravel(elem.vel[2])) + + p_list.append(np.ravel(elem.pres)) + + # Convert lists to NumPy arrays after the loop + x = np.concatenate(x_list) + y = np.concatenate(y_list) + z = np.concatenate(z_list) + ux = np.concatenate(ux_list) + uy = np.concatenate(uy_list) + uz = np.concatenate(uz_list) + p = np.concatenate(p_list) + + # Create an xarray dataset + data = xr.Dataset( + { + "ux": (["points"], ux), + "uy": (["points"], uy), + "uz": (["points"], uz), # Correctly assign uz + "p": (["points"], p), # Correctly assign p + }, + coords={ + "x": (["points"], x), + "y": (["points"], y), + "z": (["points"], z), + }, + ) + + # Wrap the xarray dataset in a uxarray grid (optional) + ux_ds = uxr.Grid.from_dataset(data) + + return ux_ds + + class PymechXarrayBackend(xr.backends.BackendEntrypoint): def guess_can_open(self, filename_or_obj): return can_open_nek_dataset(filename_or_obj) @@ -184,3 +275,48 @@ def get_variables(self): ) return Frozen(data_vars) + + +def _open_nek_dataset_unstruct(path): + # Proposed Methodology + # Step 1: Read the exodus data and plot it. + # Step 2: Find the polynomial order data automatically from the visualization file. + # Step 3: Implement a method to estimate the GLL nodes on each edge, find them in the nodes data and arrange them. + # Step 4: Create a connectivity data from them. + # Step 5: Create a ugrid from this for further use. + + # Step 1: Read the exodus data and plot it. + + mesh = nc.Dataset(path) + X = mesh.variables["coordx"] + Y = mesh.variables["coordy"] + connect = mesh.variables["connect1"] + xy = np.array([X[:], Y[:]]).T + patches = [] + for coords in xy[connect[:] - 1]: + quad = Polygon(coords[:4], closed=False) + patches.append(quad) + + fig, ax = mp.pyplot.subplots() + colors = 100 * np.random.rand(len(patches)) + p = PatchCollection(patches, cmap=mp.cm.coolwarm, alpha=0.4) + p.set_array(np.array(colors)) + ax.add_collection(p) + ax.set_xlim([-4, 4]) + ax.set_ylim([-2, 2]) + ax.set_aspect("equal") + mp.pyplot.show() + + # QUAD8 Connectivity Order: + # Corner Nodes: Top-Left to Top-Right in CW + # Middle Nodes: Left Side to Top Side in CW + + # field = readnek(path) + # if isinstance(field, int): + # raise OSError(f"Failed to load {path}") + + # elements = field.elem + + # Method: Manually create array of x, y, z and variables and use it to + # make a uxarray dataset along with manually created connectivity data. + # ds = extract_elem_data(elements) diff --git a/tests/test_dataset_unstruct.py b/tests/test_dataset_unstruct.py new file mode 100644 index 0000000..a3f8bea --- /dev/null +++ b/tests/test_dataset_unstruct.py @@ -0,0 +1,10 @@ +import pymech as pm + + +def test_unstruct_dataset(test_data_dir): + pm.open_dataset( + test_data_dir + "/nek" + "/naca" + "/naca(10x4).e", mesh_type="UNSTRUCT" + ) + + +test_unstruct_dataset("C:/Users/gaura/Desktop/pymech-test-data")