ncftools 0.9.2__tar.gz → 0.9.3__tar.gz

{ncftools-0.9.2 → ncftools-0.9.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ncftools
-Version: 0.9.2
+Version: 0.9.3
 Summary: A collection of tools for working with NetCDF files
 Author-email: aaronchh <aaronhsu219@gmail.com>
 License-Expression: MIT

{ncftools-0.9.2 → ncftools-0.9.3}/ncftools/__init__.py

@@ -2,7 +2,7 @@
 NCFTOOLS - A collection of tools for working with NetCDF files.
 """
 
-__version__ = '0.9.2'
+__version__ = '0.9.3'
 
 __all__ = [
     'meshinfo',

ncftools-0.9.3/ncftools/meshinfo.py

@@ -0,0 +1,212 @@
+#!/usr/bin/env python3
+"""
+meshinfo - Display mesh information from FlowFM NetCDF files
+Uses netCDF4 Python bindings
+"""
+
+import argparse
+import os
+import sys
+
+import netCDF4 as nc
+import numpy as np
+
+
+MAX_CELL_NODES = 6  # D-Flow FM only treats closed polygons up to 6 nodes as cells
+
+
+def find_net_cells(x, y, links):
+    """
+    Derive the 2D cells of an old-format net file from its node-link graph.
+
+    Traces every face of the planar graph by walking half-edges with the face
+    kept on the left. Counter-clockwise faces of at most MAX_CELL_NODES nodes
+    are cells; the outer boundary and unmeshed holes are not.
+
+    Args:
+        x, y (ndarray): Node coordinates
+        links (ndarray): (nLinks, 2) zero-based node indices
+
+    Returns:
+        ndarray: Number of nodes of each cell
+    """
+    n_links = len(links)
+    if n_links == 0:
+        return np.array([], dtype=int)
+
+    src = np.concatenate([links[:, 0], links[:, 1]])
+    dst = np.concatenate([links[:, 1], links[:, 0]])
+    twin = np.concatenate([np.arange(n_links, 2 * n_links), np.arange(n_links)])
+
+    # Sort half-edges around each origin node by direction (counter-clockwise)
+    angle = np.arctan2(y[dst] - y[src], x[dst] - x[src])
+    order = np.lexsort((angle, src))
+    rank = np.empty_like(order)
+    rank[order] = np.arange(len(order))
+    degree = np.bincount(src, minlength=len(x))
+    start = np.concatenate([[0], np.cumsum(degree)[:-1]])
+
+    # Next half-edge in the face: the one preceding the twin around the end node
+    s = start[dst]
+    nxt = order[s + (rank[twin] - s - 1) % degree[dst]]
+
+    # Label each face cycle by its smallest half-edge index (pointer jumping)
+    label = np.arange(len(nxt))
+    jump = nxt
+    for _ in range(int(np.ceil(np.log2(len(nxt)))) + 1):
+        label = np.minimum(label, label[jump])
+        jump = jump[jump]
+
+    n_nodes = np.bincount(label, minlength=len(nxt))
+    area2 = np.bincount(label, weights=x[src] * y[dst] - x[dst] * y[src],
+                        minlength=len(nxt))
+    is_cell = (n_nodes >= 3) & (n_nodes <= MAX_CELL_NODES) & (area2 > 0)
+    return n_nodes[is_cell]
+
+
+def _read_ugrid(dataset):
+    """Read counts and coordinates from a UGRID (Mesh2d_*) file."""
+    info = {
+        'nodes': dataset.dimensions['Mesh2d_nNodes'].size,
+        'faces': dataset.dimensions['Mesh2d_nFaces'].size,
+        'edges': dataset.dimensions['Mesh2d_nEdges'].size,
+        'face_sizes': None,
+        'x': None,
+        'y': None,
+    }
+
+    if 'Mesh2d_face_nodes' in dataset.variables:
+        face_nodes = dataset.variables['Mesh2d_face_nodes'][:]
+        fill_value = dataset.variables['Mesh2d_face_nodes']._FillValue
+        info['face_sizes'] = np.sum(face_nodes != fill_value, axis=1)
+
+    if 'Mesh2d_node_x' in dataset.variables and 'Mesh2d_node_y' in dataset.variables:
+        info['x'] = dataset.variables['Mesh2d_node_x'][:]
+        info['y'] = dataset.variables['Mesh2d_node_y'][:]
+
+    return info
+
+
+def _read_net(dataset):
+    """Read counts and coordinates from an old-format (NetNode/NetLink) net file."""
+    x = np.asarray(dataset.variables['NetNode_x'][:], dtype=float)
+    y = np.asarray(dataset.variables['NetNode_y'][:], dtype=float)
+    links = np.asarray(dataset.variables['NetLink'][:], dtype=np.int64)
+    start_index = getattr(dataset.variables['NetLink'], 'start_index', 1)
+    face_sizes = find_net_cells(x, y, links - start_index)
+
+    return {
+        'nodes': len(x),
+        'faces': len(face_sizes),
+        'edges': len(links),
+        'face_sizes': face_sizes,
+        'x': x,
+        'y': y,
+    }
+
+
+def show_mesh_info(nc_file):
+    """
+    Display mesh information from a FlowFM NetCDF file.
+
+    Supports both UGRID map/net files (Mesh2d_* variables) and old-format
+    net files (NetNode_x/NetNode_y/NetLink), whose cells are derived from
+    the links.
+
+    Args:
+        nc_file (str): Path to the FlowFM NetCDF mesh file
+    """
+    with nc.Dataset(nc_file, 'r') as dataset:
+        if 'Mesh2d_nNodes' in dataset.dimensions:
+            info = _read_ugrid(dataset)
+            derived = False
+        elif all(v in dataset.variables for v in ('NetNode_x', 'NetNode_y', 'NetLink')):
+            info = _read_net(dataset)
+            derived = True
+        else:
+            raise ValueError('no Mesh2d_* or NetNode/NetLink variables found')
+
+    print(f"FlowFM Mesh Information from: {nc_file}")
+    print("=" * 60)
+
+    nodes, faces, edges = info['nodes'], info['faces'], info['edges']
+    suffix = "  (derived from NetLink)" if derived else ""
+
+    print(f"Number of mesh nodes:     {nodes:,}")
+    print(f"Number of mesh faces:     {faces:,}{suffix}")
+    print(f"Number of mesh edges:     {edges:,}")
+
+    if info['face_sizes'] is not None:
+        valid_nodes = info['face_sizes']
+
+        triangles = int(np.sum(valid_nodes == 3))
+        quads = int(np.sum(valid_nodes == 4))
+        others = int(np.sum(valid_nodes > 4))
+
+        print("\nElement Types:")
+        print(f"  Triangular elements:    {triangles:,}")
+        print(f"  Quadrilateral elements: {quads:,}")
+        if others:
+            print(f"  5-6 sided elements:     {others:,}")
+        print(f"  Total elements:         {triangles + quads + others:,}")
+
+    if info['x'] is not None and len(info['x']):
+        x_coords, y_coords = info['x'], info['y']
+
+        print("\nSpatial extent:")
+        print(f"  X range: {np.min(x_coords):.1f} to {np.max(x_coords):.1f}")
+        print(f"  Y range: {np.min(y_coords):.1f} to {np.max(y_coords):.1f}")
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        prog='meshinfo',
+        description='Display mesh information from FlowFM NetCDF files',
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  meshinfo                         # Use default FlowFM_net.nc
+  meshinfo grid.nc                 # Use any FlowFM mesh file
+  meshinfo -i grid.nc              # Same, with the -i flag
+  meshinfo -h                      # Show this help message
+
+The tool displays:
+  - Number of nodes, faces, and edges
+  - Element type distribution (triangles vs quadrilaterals)
+  - Spatial extent (X and Y coordinate ranges)
+        """,
+    )
+
+    parser.add_argument(
+        'file',
+        nargs='?',
+        metavar='FILE',
+        help='Path to the FlowFM NetCDF mesh file (default: FlowFM_net.nc)',
+    )
+    parser.add_argument(
+        '-i', '--input',
+        metavar='FILE',
+        help='Same as FILE (kept for backward compatibility)',
+    )
+
+    args = parser.parse_args()
+
+    if args.file and args.input:
+        parser.error('give the mesh file either as FILE or with -i, not both')
+    args.input = args.file or args.input or 'FlowFM_net.nc'
+
+    if not os.path.isfile(args.input):
+        print(f"Error: File '{args.input}' not found.")
+        print(f"Current directory: {os.getcwd()}")
+        print("Please check the file path and try again.")
+        sys.exit(1)
+
+    try:
+        show_mesh_info(args.input)
+    except Exception as e:
+        print(f"Error reading NetCDF file: {e}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

{ncftools-0.9.2 → ncftools-0.9.3}/ncftools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ncftools
-Version: 0.9.2
+Version: 0.9.3
 Summary: A collection of tools for working with NetCDF files
 Author-email: aaronchh <aaronhsu219@gmail.com>
 License-Expression: MIT

{ncftools-0.9.2 → ncftools-0.9.3}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ncftools"
-version = "0.9.2"
+version = "0.9.3"
 authors = [
     { name = "aaronchh", email = "aaronhsu219@gmail.com" },
 ]

ncftools-0.9.2/ncftools/meshinfo.py

@@ -1,110 +0,0 @@
-#!/usr/bin/env python3
-"""
-meshinfo - Display mesh information from FlowFM NetCDF files
-Uses netCDF4 Python bindings
-"""
-
-import argparse
-import os
-import sys
-
-import netCDF4 as nc
-import numpy as np
-
-
-def show_mesh_info(nc_file):
-    """
-    Display mesh information from a FlowFM NetCDF file.
-
-    Args:
-        nc_file (str): Path to the FlowFM NetCDF mesh file
-    """
-    dataset = nc.Dataset(nc_file, 'r')
-
-    print(f"FlowFM Mesh Information from: {nc_file}")
-    print("=" * 60)
-
-    nodes = dataset.dimensions['Mesh2d_nNodes'].size
-    faces = dataset.dimensions['Mesh2d_nFaces'].size
-    edges = dataset.dimensions['Mesh2d_nEdges'].size
-
-    print(f"Number of mesh nodes:     {nodes:,}")
-    print(f"Number of mesh faces:     {faces:,}")
-    print(f"Number of mesh edges:     {edges:,}")
-
-    if 'Mesh2d_face_nodes' in dataset.variables:
-        face_nodes = dataset.variables['Mesh2d_face_nodes'][:]
-        fill_value = dataset.variables['Mesh2d_face_nodes']._FillValue
-        valid_nodes = np.sum(face_nodes != fill_value, axis=1)
-
-        triangles = int(np.sum(valid_nodes == 3))
-        quads = int(np.sum(valid_nodes == 4))
-
-        print("\nElement Types:")
-        print(f"  Triangular elements:    {triangles:,}")
-        print(f"  Quadrilateral elements: {quads:,}")
-        print(f"  Total elements:         {triangles + quads:,}")
-
-    if 'Mesh2d_node_x' in dataset.variables and 'Mesh2d_node_y' in dataset.variables:
-        x_coords = dataset.variables['Mesh2d_node_x'][:]
-        y_coords = dataset.variables['Mesh2d_node_y'][:]
-
-        print("\nSpatial extent:")
-        print(f"  X range: {np.min(x_coords):.1f} to {np.max(x_coords):.1f}")
-        print(f"  Y range: {np.min(y_coords):.1f} to {np.max(y_coords):.1f}")
-
-    dataset.close()
-
-
-def main():
-    parser = argparse.ArgumentParser(
-        prog='meshinfo',
-        description='Display mesh information from FlowFM NetCDF files',
-        formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog="""
-Examples:
-  meshinfo                         # Use default FlowFM_net.nc
-  meshinfo grid.nc                 # Use any FlowFM mesh file
-  meshinfo -i grid.nc              # Same, with the -i flag
-  meshinfo -h                      # Show this help message
-
-The tool displays:
-  - Number of nodes, faces, and edges
-  - Element type distribution (triangles vs quadrilaterals)
-  - Spatial extent (X and Y coordinate ranges)
-        """,
-    )
-
-    parser.add_argument(
-        'file',
-        nargs='?',
-        metavar='FILE',
-        help='Path to the FlowFM NetCDF mesh file (default: FlowFM_net.nc)',
-    )
-    parser.add_argument(
-        '-i', '--input',
-        metavar='FILE',
-        help='Same as FILE (kept for backward compatibility)',
-    )
-
-    args = parser.parse_args()
-
-    if args.file and args.input:
-        parser.error('give the mesh file either as FILE or with -i, not both')
-    args.input = args.file or args.input or 'FlowFM_net.nc'
-
-    if not os.path.isfile(args.input):
-        print(f"Error: File '{args.input}' not found.")
-        print(f"Current directory: {os.getcwd()}")
-        print("Please check the file path and try again.")
-        sys.exit(1)
-
-    try:
-        show_mesh_info(args.input)
-    except Exception as e:
-        print(f"Error reading NetCDF file: {e}")
-        sys.exit(1)
-
-
-if __name__ == "__main__":
-    main()