From f57aa9762e5c28a9bd27f91d22eddd5a7dd3ec1d Mon Sep 17 00:00:00 2001
From: airwarriorg91 <gauravxpgupta@gmail.com>
Date: Mon, 14 Oct 2024 11:24:56 +0530
Subject: [PATCH 1/2] unstructured-array-attempt
---
src/pymech/dataset.py | 84 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 84 insertions(+)
diff --git a/src/pymech/dataset.py b/src/pymech/dataset.py
index 70cc958..08878fd 100644
--- a/src/pymech/dataset.py
+++ b/src/pymech/dataset.py
@@ -4,6 +4,7 @@
import numpy as np
import xarray as xr
+import uxarray as uxr
from xarray.core.utils import Frozen
from .neksuite import readnek
@@ -98,6 +99,53 @@ 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):
@@ -184,3 +232,39 @@ def get_variables(self):
)
return Frozen(data_vars)
+
+
+def open_unstruc_dataset(path):
+
+ # Proposed Methodology
+ # Step 1: Use readnek to import the data
+ # Step 2: Create an array of nodes, elements, and fields
+ # Step 3: Create a grid and xarray dataset from the data array
+ # Step 4: Create a uxarray dataset and return it
+
+ field = readnek(path)
+ if isinstance(field, int):
+ raise OSError(f"Failed to load {path}")
+
+ elements = field.elem
+
+ # Method 1 : adapt the existing method used for xarray
+
+ #elem_stores = [_NekDataStore(elem) for elem in elements]
+ #
+ # try:
+ # elem_dsets = [
+ # uxr.UxDataset.load_store(store).set_coords(store.axes) for store in elem_stores
+ # ]
+ # except Exception as error:
+ # print("uxarray failure")
+ # print(error)
+ # print(elem_stores[0].axes)
+
+ # Method 2 : manually create array of x, y, z and variables and use it to
+ # make a uxarray dataset
+ ds = extract_elem_data(elements)
+
+
+
+
\ No newline at end of file
From ef0360f9ea23f454afb79a23eac5d6eebb07c462 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
<66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 14 Oct 2024 06:15:19 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks
for more information, see https://pre-commit.ci
---
src/pymech/dataset.py | 23 ++++++++++-------------
1 file changed, 10 insertions(+), 13 deletions(-)
diff --git a/src/pymech/dataset.py b/src/pymech/dataset.py
index 08878fd..9e43d06 100644
--- a/src/pymech/dataset.py
+++ b/src/pymech/dataset.py
@@ -3,8 +3,8 @@
from pathlib import Path
import numpy as np
-import xarray as xr
import uxarray as uxr
+import xarray as xr
from xarray.core.utils import Frozen
from .neksuite import readnek
@@ -99,6 +99,7 @@ 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 = [], [], []
@@ -110,11 +111,11 @@ def extract_elem_data(elem_array):
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
@@ -132,13 +133,13 @@ def extract_elem_data(elem_array):
"ux": (["points"], ux),
"uy": (["points"], uy),
"uz": (["points"], uz), # Correctly assign uz
- "p": (["points"], p) # Correctly assign p
+ "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)
@@ -235,7 +236,7 @@ def get_variables(self):
def open_unstruc_dataset(path):
-
+
# Proposed Methodology
# Step 1: Use readnek to import the data
# Step 2: Create an array of nodes, elements, and fields
@@ -247,10 +248,10 @@ def open_unstruc_dataset(path):
raise OSError(f"Failed to load {path}")
elements = field.elem
-
+
# Method 1 : adapt the existing method used for xarray
- #elem_stores = [_NekDataStore(elem) for elem in elements]
+ # elem_stores = [_NekDataStore(elem) for elem in elements]
#
# try:
# elem_dsets = [
@@ -261,10 +262,6 @@ def open_unstruc_dataset(path):
# print(error)
# print(elem_stores[0].axes)
- # Method 2 : manually create array of x, y, z and variables and use it to
+ # Method 2 : manually create array of x, y, z and variables and use it to
# make a uxarray dataset
ds = extract_elem_data(elements)
-
-
-
-
\ No newline at end of file