From e3b91e2149cc88a0f7313941e1ab883be4b033c5 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Wed, 30 Oct 2024 14:55:03 -0500 Subject: [PATCH 01/14] added initial functions --- uxarray/grid/geometry.py | 23 +++++++++++++++++++++ uxarray/grid/grid.py | 43 ++++++++++++++++++++++++++++++++++++++-- 2 files changed, 64 insertions(+), 2 deletions(-) diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index b7d769e27..bfde11a77 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -18,6 +18,7 @@ INT_FILL_VALUE, ) from uxarray.grid.arcs import extreme_gca_latitude, point_within_gca +from uxarray.grid.coordinates import _normalize_xyz from uxarray.grid.intersections import gca_gca_intersection from uxarray.grid.utils import ( _get_cartesian_face_edge_nodes, @@ -1337,3 +1338,25 @@ def _construct_hole_edge_indices(edge_face_connectivity): # If an edge only has one face saddling it than the mesh has holes in it edge_with_holes = np.where(edge_face_connectivity[:, 1] == INT_FILL_VALUE)[0] return edge_with_holes + + +@njit(cache=True) +def _point_to_plane(x, y, z): + """Projects a point on the surface of the sphere to a plane using stereographic projection""" + x_plane = x / (1 - z) + y_plane = y / (1 - z) + + return x_plane, y_plane + + +@njit(cache=True) +def _point_to_sphere(x_plane, y_plane): + """Projects a point on a plane to the surface of the sphere using stereographic projection""" + + x = (2 * x_plane) / (1 + x_plane**2 + y_plane**2) + y = (2 * y_plane) / (1 + x_plane**2 + y_plane**2) + z = (-1 + x_plane**2 + y_plane**2) / (1 + x_plane**2 + y_plane**2) + + x_norm, y_norm, z_norm = _normalize_xyz(x, y, z) + + return x_norm, y_norm, z_norm diff --git a/uxarray/grid/grid.py b/uxarray/grid/grid.py index b7ea0d3db..a0a3ec8c5 100644 --- a/uxarray/grid/grid.py +++ b/uxarray/grid/grid.py @@ -57,6 +57,7 @@ _grid_to_matplotlib_linecollection, _populate_bounds, _construct_hole_edge_indices, + _point_to_plane, ) from uxarray.grid.neighbors import ( @@ -86,7 +87,6 @@ _check_normalization, ) - from uxarray.conventions import ugrid from xarray.core.utils import UncachedAccessor @@ -97,7 +97,6 @@ import copy - from uxarray.constants import INT_FILL_VALUE from uxarray.grid.dual import construct_dual @@ -2035,3 +2034,43 @@ def get_faces_at_constant_latitude(self, lat, method="fast"): faces = np.unique(self.edge_face_connectivity[edges].data.ravel()) return faces[faces != INT_FILL_VALUE] + + def to_planar(self): + """Constructs a planar representation of the grid, and returns a dataset containing nodes, faces, and edges.""" + + node_x_planar, node_y_planar = _point_to_plane( + self.node_x.values, self.node_y.values, self.node_z.values + ) + + face_x_planar, face_y_planar = _point_to_plane( + self.face_x.values, self.face_y.values, self.face_z.values + ) + + edge_x_planar, edge_y_planar = _point_to_plane( + self.edge_x.values, self.edge_y.values, self.edge_z.values + ) + + planar_grid = xr.Dataset() + + planar_grid["node_x_planar"] = xr.DataArray( + node_x_planar, dims=[ugrid.NODE_DIM], attrs=None + ) + planar_grid["node_y_planar"] = xr.DataArray( + node_y_planar, dims=[ugrid.NODE_DIM], attrs=None + ) + + planar_grid["face_x_planar"] = xr.DataArray( + face_x_planar, dims=[ugrid.FACE_DIM], attrs=None + ) + planar_grid["face_y_planar"] = xr.DataArray( + face_y_planar, dims=[ugrid.FACE_DIM], attrs=None + ) + + planar_grid["edge_x_planar"] = xr.DataArray( + edge_x_planar, dims=[ugrid.EDGE_DIM], attrs=None + ) + planar_grid["edge_y_planar"] = xr.DataArray( + edge_y_planar, dims=[ugrid.EDGE_DIM], attrs=None + ) + + return planar_grid From 3eabf33eacbfcb9cc4cbb3656ef8ca30782eebd1 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 5 Nov 2024 08:26:50 -0600 Subject: [PATCH 02/14] Update grid.py --- uxarray/grid/grid.py | 40 ---------------------------------------- 1 file changed, 40 deletions(-) diff --git a/uxarray/grid/grid.py b/uxarray/grid/grid.py index 59e01fe1a..de3124321 100644 --- a/uxarray/grid/grid.py +++ b/uxarray/grid/grid.py @@ -2083,43 +2083,3 @@ def get_faces_at_constant_latitude(self, lat, method="fast"): faces = np.unique(self.edge_face_connectivity[edges].data.ravel()) return faces[faces != INT_FILL_VALUE] - - def to_planar(self): - """Constructs a planar representation of the grid, and returns a dataset containing nodes, faces, and edges.""" - - node_x_planar, node_y_planar = _point_to_plane( - self.node_x.values, self.node_y.values, self.node_z.values - ) - - face_x_planar, face_y_planar = _point_to_plane( - self.face_x.values, self.face_y.values, self.face_z.values - ) - - edge_x_planar, edge_y_planar = _point_to_plane( - self.edge_x.values, self.edge_y.values, self.edge_z.values - ) - - planar_grid = xr.Dataset() - - planar_grid["node_x_planar"] = xr.DataArray( - node_x_planar, dims=[ugrid.NODE_DIM], attrs=None - ) - planar_grid["node_y_planar"] = xr.DataArray( - node_y_planar, dims=[ugrid.NODE_DIM], attrs=None - ) - - planar_grid["face_x_planar"] = xr.DataArray( - face_x_planar, dims=[ugrid.FACE_DIM], attrs=None - ) - planar_grid["face_y_planar"] = xr.DataArray( - face_y_planar, dims=[ugrid.FACE_DIM], attrs=None - ) - - planar_grid["edge_x_planar"] = xr.DataArray( - edge_x_planar, dims=[ugrid.EDGE_DIM], attrs=None - ) - planar_grid["edge_y_planar"] = xr.DataArray( - edge_y_planar, dims=[ugrid.EDGE_DIM], attrs=None - ) - - return planar_grid From f088c7ec038949c0a7b6a0408b302d6328684dcb Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 5 Nov 2024 12:02:34 -0600 Subject: [PATCH 03/14] Added regional Delaunay support --- test/test_from_points.py | 19 ++++++++++++ uxarray/grid/grid.py | 7 ++++- uxarray/io/_delaunay.py | 63 ++++++++++++++++++++++++++++++++++++++++ 3 files changed, 88 insertions(+), 1 deletion(-) diff --git a/test/test_from_points.py b/test/test_from_points.py index 6cedef164..ef57e8f72 100644 --- a/test/test_from_points.py +++ b/test/test_from_points.py @@ -25,6 +25,25 @@ def test_spherical_delaunay(): assert uxgrid_dt_xyz.triangular assert uxgrid_dt_latlon.triangular + +def test_regional_delaunay(): + uxgrid = ux.open_grid(grid_path) + + uxgrid_regional = uxgrid.subset.nearest_neighbor((0.0, 0.0), k=9) + + points_xyz = (uxgrid_regional.node_x.values, uxgrid_regional.node_y.values, uxgrid_regional.node_z.values) + points_latlon = (uxgrid_regional.node_lon.values, uxgrid_regional.node_lat.values) + + uxgrid_dt_xyz = ux.Grid.from_points(points_xyz, method='regional_delaunay') + uxgrid_dt_latlon = ux.Grid.from_points(points_latlon, method='regional_delaunay') + uxgrid_dt_xyz.validate() + uxgrid_dt_latlon.validate() + + assert uxgrid_dt_xyz.n_node == uxgrid_dt_latlon.n_node == len(points_xyz[0]) + assert uxgrid_dt_xyz.triangular + assert uxgrid_dt_latlon.triangular + + def test_spherical_voronoi(): uxgrid = ux.open_grid(grid_path) points_xyz = (uxgrid.node_x.values, uxgrid.node_y.values, uxgrid.node_z.values) diff --git a/uxarray/grid/grid.py b/uxarray/grid/grid.py index d81fa5f51..da05c8f7c 100644 --- a/uxarray/grid/grid.py +++ b/uxarray/grid/grid.py @@ -27,7 +27,10 @@ from uxarray.io._icon import _read_icon from uxarray.io._structured import _read_structured_grid from uxarray.io._voronoi import _spherical_voronoi_from_points -from uxarray.io._delaunay import _spherical_delaunay_from_points +from uxarray.io._delaunay import ( + _spherical_delaunay_from_points, + _regional_delaunay_from_points, +) from uxarray.formatting_html import grid_repr @@ -386,6 +389,8 @@ def from_points( ds = _spherical_voronoi_from_points(_points, **kwargs) elif method == "spherical_delaunay": ds = _spherical_delaunay_from_points(_points, boundary_points) + elif method == "regional_delaunay": + ds = _regional_delaunay_from_points(_points, boundary_points) else: raise ValueError( f"Unsupported method '{method}'. Expected one of ['spherical_voronoi', 'spherical_delaunay']." diff --git a/uxarray/io/_delaunay.py b/uxarray/io/_delaunay.py index 5522793cc..db3588f46 100644 --- a/uxarray/io/_delaunay.py +++ b/uxarray/io/_delaunay.py @@ -2,6 +2,8 @@ import xarray as xr from scipy.spatial import ConvexHull from uxarray.conventions import ugrid +from uxarray.grid.geometry import _point_to_plane +from scipy.spatial import Delaunay def _spherical_delaunay_from_points(points, boundary_points=None): @@ -61,3 +63,64 @@ def _spherical_delaunay_from_points(points, boundary_points=None): ) return out_ds + + +def _regional_delaunay_from_points(points, boundary_points=None): + """Generates a regional Delaunay triangulation from given points, + excluding triangles where all three nodes are boundary points.""" + out_ds = xr.Dataset() + + # Validate boundary_points if provided + if boundary_points is not None: + boundary_points = np.asarray(boundary_points) + if boundary_points.ndim != 1: + raise ValueError( + "boundary_points must be a 1D array-like of point indices." + ) + if np.any(boundary_points < 0) or np.any(boundary_points >= len(points)): + raise ValueError("boundary_points contain invalid indices.") + + node_x = points[:, 0] + node_y = points[:, 1] + node_z = points[:, 2] + + # Convert Cartesian coordinates to spherical coordinates (longitude and latitude in degrees) + node_lon_rad = np.arctan2(node_y, node_x) + node_lat_rad = np.arcsin(node_z / np.linalg.norm(points, axis=1)) + + node_lon = np.degrees(node_lon_rad) + node_lat = np.degrees(node_lat_rad) + + x_plane, y_plane = _point_to_plane(node_x, node_y, node_z) + + points = np.column_stack((x_plane, y_plane)) + print(np.max(points)) + delaunay = Delaunay(points) + + # Obtain delaunay triangles + triangles = delaunay.simplices + + if boundary_points is not None: + # Create a boolean mask where True indicates triangles that do not have all nodes as boundary points + mask = ~np.isin(triangles, boundary_points).all(axis=1) + + # Apply the mask to filter out unwanted triangles + triangles = triangles[mask] + + # Assign the filtered triangles to the Dataset + out_ds["face_node_connectivity"] = xr.DataArray( + data=triangles, + dims=ugrid.FACE_NODE_CONNECTIVITY_DIMS, + attrs=ugrid.FACE_NODE_CONNECTIVITY_ATTRS, + ) + + # Assign node coordinates to the Dataset + out_ds["node_lon"] = xr.DataArray( + data=node_lon, dims=ugrid.NODE_DIM, attrs=ugrid.NODE_LON_ATTRS + ) + + out_ds["node_lat"] = xr.DataArray( + data=node_lat, dims=ugrid.NODE_DIM, attrs=ugrid.NODE_LAT_ATTRS + ) + + return out_ds From cc417511c52874c5dd24a619eb77717152ff9a2f Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 5 Nov 2024 14:57:14 -0600 Subject: [PATCH 04/14] Updated projection method and notebook --- docs/user-guide/from-points.ipynb | 1236 ++++++++++++++++++++++++++++- uxarray/grid/geometry.py | 15 +- uxarray/io/_delaunay.py | 4 +- 3 files changed, 1239 insertions(+), 16 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index 9fa8fce59..923dc75ad 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "974ef98b2cdb3cb1", "metadata": { "ExecuteTime": { @@ -21,7 +21,1121 @@ "start_time": "2024-10-23T20:07:13.853636Z" } }, - "outputs": [], + "outputs": [ + { + "data": { + "application/javascript": [ + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + " var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", + " var reloading = false;\n", + " var Bokeh = root.Bokeh;\n", + "\n", + " if (typeof (root._bokeh_timeout) === \"undefined\" || force) {\n", + " root._bokeh_timeout = Date.now() + 5000;\n", + " root._bokeh_failed_load = false;\n", + " }\n", + "\n", + " function run_callbacks() {\n", + " try {\n", + " 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" return\n", + " }\n", + " var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n", + " var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n", + " if (id !== undefined) {\n", + " var nchildren = toinsert.length;\n", + " var html_node = toinsert[nchildren-1].children[0];\n", + " html_node.innerHTML = output.data[HTML_MIME_TYPE];\n", + " var scripts = [];\n", + " var nodelist = html_node.querySelectorAll(\"script\");\n", + " for (var i in nodelist) {\n", + " if (nodelist.hasOwnProperty(i)) {\n", + " scripts.push(nodelist[i])\n", + " }\n", + " }\n", + "\n", + " scripts.forEach( function (oldScript) {\n", + " var newScript = document.createElement(\"script\");\n", + " var attrs = [];\n", + " var nodemap = oldScript.attributes;\n", + " for (var j in nodemap) {\n", + " if (nodemap.hasOwnProperty(j)) {\n", + " attrs.push(nodemap[j])\n", + " }\n", + " }\n", + " attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n", + " newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n", + " oldScript.parentNode.replaceChild(newScript, oldScript);\n", + " });\n", + " if (JS_MIME_TYPE in output.data) {\n", + " toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n", + " }\n", + " output_area._hv_plot_id = id;\n", + " if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n", + " window.PyViz.plot_index[id] = Bokeh.index[id];\n", + " } else {\n", + " window.PyViz.plot_index[id] = null;\n", + " }\n", + " } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n", + " var bk_div = document.createElement(\"div\");\n", + " bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n", + " var script_attrs = bk_div.children[0].attributes;\n", + " for (var i = 0; i < script_attrs.length; i++) {\n", + " toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n", + " }\n", + " // store reference to server id on output_area\n", + " output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n", + " }\n", + "}\n", + "\n", + "/**\n", + " * Handle when an output is cleared or removed\n", + " */\n", + "function handle_clear_output(event, handle) {\n", + " var id = handle.cell.output_area._hv_plot_id;\n", + " var server_id = handle.cell.output_area._bokeh_server_id;\n", + " if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n", + " var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n", + " if (server_id !== null) {\n", + " comm.send({event_type: 'server_delete', 'id': server_id});\n", + " return;\n", + " } else if (comm !== null) {\n", + " comm.send({event_type: 'delete', 'id': id});\n", + " }\n", + " delete PyViz.plot_index[id];\n", + " if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n", + " var doc = window.Bokeh.index[id].model.document\n", + " doc.clear();\n", + " const i = window.Bokeh.documents.indexOf(doc);\n", + " if (i > -1) {\n", + " window.Bokeh.documents.splice(i, 1);\n", + " }\n", + " }\n", + "}\n", + "\n", + "/**\n", + " * Handle kernel restart event\n", + " */\n", + "function handle_kernel_cleanup(event, handle) {\n", + " delete PyViz.comms[\"hv-extension-comm\"];\n", + " window.PyViz.plot_index = {}\n", + "}\n", + "\n", + "/**\n", + " * Handle update_display_data messages\n", + " */\n", + "function handle_update_output(event, handle) {\n", + " handle_clear_output(event, {cell: {output_area: handle.output_area}})\n", + " handle_add_output(event, handle)\n", + "}\n", + "\n", + "function register_renderer(events, OutputArea) {\n", + " function append_mime(data, metadata, element) {\n", + " // create a DOM node to render to\n", + " var toinsert = this.create_output_subarea(\n", + " metadata,\n", + " CLASS_NAME,\n", + " EXEC_MIME_TYPE\n", + " );\n", + " this.keyboard_manager.register_events(toinsert);\n", + " // Render to node\n", + " var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n", + " render(props, toinsert[0]);\n", + " element.append(toinsert);\n", + " return toinsert\n", + " }\n", + "\n", + " events.on('output_added.OutputArea', handle_add_output);\n", + " events.on('output_updated.OutputArea', handle_update_output);\n", + " events.on('clear_output.CodeCell', handle_clear_output);\n", + " events.on('delete.Cell', handle_clear_output);\n", + " events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n", + "\n", + " OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n", + " safe: true,\n", + " index: 0\n", + " });\n", + "}\n", + "\n", + "if (window.Jupyter !== undefined) {\n", + " try {\n", + " var events = require('base/js/events');\n", + " var OutputArea = require('notebook/js/outputarea').OutputArea;\n", + " if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n", + " register_renderer(events, OutputArea);\n", + " }\n", + " } catch(err) {\n", + " }\n", + "}\n" + ], + "application/vnd.holoviews_load.v0+json": "\nif ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n}\n\n\n function JupyterCommManager() {\n }\n\n JupyterCommManager.prototype.register_target = function(plot_id, comm_id, msg_handler) {\n if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n comm_manager.register_target(comm_id, function(comm) {\n comm.on_msg(msg_handler);\n });\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n window.PyViz.kernels[plot_id].registerCommTarget(comm_id, function(comm) {\n comm.onMsg = msg_handler;\n });\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n google.colab.kernel.comms.registerTarget(comm_id, (comm) => {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n console.log(message)\n var content = {data: message.data, comm_id};\n var buffers = []\n for (var buffer of message.buffers || []) {\n buffers.push(new DataView(buffer))\n }\n var metadata = message.metadata || {};\n var msg = {content, buffers, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n })\n }\n }\n\n JupyterCommManager.prototype.get_client_comm = function(plot_id, comm_id, msg_handler) {\n if (comm_id in window.PyViz.comms) {\n return window.PyViz.comms[comm_id];\n } else if (window.comm_manager || ((window.Jupyter !== undefined) && (Jupyter.notebook.kernel != null))) {\n var comm_manager = window.comm_manager || Jupyter.notebook.kernel.comm_manager;\n var comm = comm_manager.new_comm(comm_id, {}, {}, {}, comm_id);\n if (msg_handler) {\n comm.on_msg(msg_handler);\n }\n } else if ((plot_id in window.PyViz.kernels) && (window.PyViz.kernels[plot_id])) {\n var comm = window.PyViz.kernels[plot_id].connectToComm(comm_id);\n comm.open();\n if (msg_handler) {\n comm.onMsg = msg_handler;\n }\n } else if (typeof google != 'undefined' && google.colab.kernel != null) {\n var comm_promise = google.colab.kernel.comms.open(comm_id)\n comm_promise.then((comm) => {\n window.PyViz.comms[comm_id] = comm;\n if (msg_handler) {\n var messages = comm.messages[Symbol.asyncIterator]();\n function processIteratorResult(result) {\n var message = result.value;\n var content = {data: message.data};\n var metadata = message.metadata || {comm_id};\n var msg = {content, metadata}\n msg_handler(msg);\n return messages.next().then(processIteratorResult);\n }\n return messages.next().then(processIteratorResult);\n }\n }) \n var sendClosure = (data, metadata, buffers, disposeOnDone) => {\n return comm_promise.then((comm) => {\n comm.send(data, metadata, buffers, disposeOnDone);\n });\n };\n var comm = {\n send: sendClosure\n };\n }\n window.PyViz.comms[comm_id] = comm;\n return comm;\n }\n window.PyViz.comm_manager = new JupyterCommManager();\n \n\n\nvar JS_MIME_TYPE = 'application/javascript';\nvar HTML_MIME_TYPE = 'text/html';\nvar EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\nvar CLASS_NAME = 'output';\n\n/**\n * Render data to the DOM node\n */\nfunction render(props, node) {\n var div = document.createElement(\"div\");\n var script = document.createElement(\"script\");\n node.appendChild(div);\n node.appendChild(script);\n}\n\n/**\n * Handle when a new output is added\n */\nfunction handle_add_output(event, handle) {\n var output_area = handle.output_area;\n var output = handle.output;\n if ((output.data == undefined) || (!output.data.hasOwnProperty(EXEC_MIME_TYPE))) {\n return\n }\n var id = output.metadata[EXEC_MIME_TYPE][\"id\"];\n var toinsert = output_area.element.find(\".\" + CLASS_NAME.split(' ')[0]);\n if (id !== undefined) {\n var nchildren = toinsert.length;\n var html_node = toinsert[nchildren-1].children[0];\n html_node.innerHTML = output.data[HTML_MIME_TYPE];\n var scripts = [];\n var nodelist = html_node.querySelectorAll(\"script\");\n for (var i in nodelist) {\n if (nodelist.hasOwnProperty(i)) {\n scripts.push(nodelist[i])\n }\n }\n\n scripts.forEach( function (oldScript) {\n var newScript = document.createElement(\"script\");\n var attrs = [];\n var nodemap = oldScript.attributes;\n for (var j in nodemap) {\n if (nodemap.hasOwnProperty(j)) {\n attrs.push(nodemap[j])\n }\n }\n attrs.forEach(function(attr) { newScript.setAttribute(attr.name, attr.value) });\n newScript.appendChild(document.createTextNode(oldScript.innerHTML));\n oldScript.parentNode.replaceChild(newScript, oldScript);\n });\n if (JS_MIME_TYPE in output.data) {\n toinsert[nchildren-1].children[1].textContent = output.data[JS_MIME_TYPE];\n }\n output_area._hv_plot_id = id;\n if ((window.Bokeh !== undefined) && (id in Bokeh.index)) {\n window.PyViz.plot_index[id] = Bokeh.index[id];\n } else {\n window.PyViz.plot_index[id] = null;\n }\n } else if (output.metadata[EXEC_MIME_TYPE][\"server_id\"] !== undefined) {\n var bk_div = document.createElement(\"div\");\n bk_div.innerHTML = output.data[HTML_MIME_TYPE];\n var script_attrs = bk_div.children[0].attributes;\n for (var i = 0; i < script_attrs.length; i++) {\n toinsert[toinsert.length - 1].childNodes[1].setAttribute(script_attrs[i].name, script_attrs[i].value);\n }\n // store reference to server id on output_area\n output_area._bokeh_server_id = output.metadata[EXEC_MIME_TYPE][\"server_id\"];\n }\n}\n\n/**\n * Handle when an output is cleared or removed\n */\nfunction handle_clear_output(event, handle) {\n var id = handle.cell.output_area._hv_plot_id;\n var server_id = handle.cell.output_area._bokeh_server_id;\n if (((id === undefined) || !(id in PyViz.plot_index)) && (server_id !== undefined)) { return; }\n var comm = window.PyViz.comm_manager.get_client_comm(\"hv-extension-comm\", \"hv-extension-comm\", function () {});\n if (server_id !== null) {\n comm.send({event_type: 'server_delete', 'id': server_id});\n return;\n } else if (comm !== null) {\n comm.send({event_type: 'delete', 'id': id});\n }\n delete PyViz.plot_index[id];\n if ((window.Bokeh !== undefined) & (id in window.Bokeh.index)) {\n var doc = window.Bokeh.index[id].model.document\n doc.clear();\n const i = window.Bokeh.documents.indexOf(doc);\n if (i > -1) {\n window.Bokeh.documents.splice(i, 1);\n }\n }\n}\n\n/**\n * Handle kernel restart event\n */\nfunction handle_kernel_cleanup(event, handle) {\n delete PyViz.comms[\"hv-extension-comm\"];\n window.PyViz.plot_index = {}\n}\n\n/**\n * Handle update_display_data messages\n */\nfunction handle_update_output(event, handle) {\n handle_clear_output(event, {cell: {output_area: handle.output_area}})\n handle_add_output(event, handle)\n}\n\nfunction register_renderer(events, OutputArea) {\n function append_mime(data, metadata, element) {\n // create a DOM node to render to\n var toinsert = this.create_output_subarea(\n metadata,\n CLASS_NAME,\n EXEC_MIME_TYPE\n );\n this.keyboard_manager.register_events(toinsert);\n // Render to node\n var props = {data: data, metadata: metadata[EXEC_MIME_TYPE]};\n render(props, toinsert[0]);\n element.append(toinsert);\n return toinsert\n }\n\n events.on('output_added.OutputArea', handle_add_output);\n events.on('output_updated.OutputArea', handle_update_output);\n events.on('clear_output.CodeCell', handle_clear_output);\n events.on('delete.Cell', handle_clear_output);\n events.on('kernel_ready.Kernel', handle_kernel_cleanup);\n\n OutputArea.prototype.register_mime_type(EXEC_MIME_TYPE, append_mime, {\n safe: true,\n index: 0\n });\n}\n\nif (window.Jupyter !== undefined) {\n try {\n var events = require('base/js/events');\n var OutputArea = require('notebook/js/outputarea').OutputArea;\n if (OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + } + ], "source": [ "import uxarray as ux\n", "import xarray as xr\n", @@ -67,7 +1181,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "be2b14a2-0fbe-4f34-ad55-407f0b83a8c7", "metadata": { "ExecuteTime": { @@ -75,12 +1189,37 @@ "start_time": "2024-10-21T21:55:04.728574Z" } }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + ":Layout\n", + " .Overlay.I :Overlay\n", + " .Points.I :Points [lon,lat]\n", + " .Grid.I :Feature [Longitude,Latitude]\n", + " .Overlay.II :Overlay\n", + " .Points.I :Points [lon,lat]\n", + " .Grid.I :Feature [Longitude,Latitude]\n", + " .Overlay.III :Overlay\n", + " .Points.I :Points [lon,lat]\n", + " .Grid.I :Feature [Longitude,Latitude]" + ] + }, + "execution_count": 2, + "metadata": { + "application/vnd.holoviews_exec.v0+json": {} + }, + "output_type": "execute_result" + } + ], "source": [ "uxgrid_global = ux.open_grid(\"../../test/meshfiles/ugrid/outCSne30/outCSne30.ug\")\n", "uxgrid_global_ocean = ux.open_grid(\"../../test/meshfiles/mpas/QU/oQU480.231010.nc\")\n", "uxgrid_global_ocean.normalize_cartesian_coordinates()\n", - "uxgrid_regional = uxgrid_global.subset.nearest_neighbor((0.0, 0.0), k=9)\n", + "uxgrid_regional = uxgrid_global.subset.nearest_neighbor((0.0, 0.0), k=50)\n", "\n", "(\n", " uxgrid_global.plot.face_centers(\n", @@ -160,7 +1299,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "46fe282b-81ae-4972-996d-2f71478126a1", "metadata": { "ExecuteTime": { @@ -211,7 +1350,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 38, "id": "1aecdcb6-91e5-41a9-a28d-0ec1c6ec640f", "metadata": { "ExecuteTime": { @@ -219,7 +1358,16 @@ "start_time": "2024-10-21T16:56:29.056689Z" } }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "CPU times: user 33.8 ms, sys: 1.8 ms, total: 35.6 ms\n", + "Wall time: 34.2 ms\n" + ] + } + ], "source": [ "%%time\n", "grid_dt = ux.Grid.from_points(points_global, method=\"spherical_delaunay\")" @@ -227,10 +1375,26 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 39, "id": "d4b06c69-5705-4627-9a24-4dac4655a33a", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + ":Path [Longitude,Latitude]" + ] + }, + "execution_count": 39, + "metadata": { + "application/vnd.holoviews_exec.v0+json": {} + }, + "output_type": "execute_result" + } + ], "source": [ "grid_dt.plot(\n", " projection=ccrs.Robinson(),\n", @@ -727,6 +1891,56 @@ "Constructing a grid from regional point data is not yet supported.\n", "```" ] + }, + { + "cell_type": "code", + "execution_count": 4, + "id": "5e15b602-70e1-434d-a0a4-51d5913abb6a", + "metadata": {}, + "outputs": [], + "source": [ + "grid_r = ux.Grid.from_points(points_regional, method=\"regional_delaunay\")" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "6e4d838a-4f7f-474f-a2f9-47569df02a91", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "" + ], + "text/plain": [ + ":Path [Longitude,Latitude]" + ] + }, + "execution_count": 6, + "metadata": { + "application/vnd.holoviews_exec.v0+json": {} + }, + "output_type": "execute_result" + } + ], + "source": [ + "grid_r.plot(\n", + " linewidth=0.5,\n", + " periodic_elements=\"exclude\",\n", + " height=500,\n", + " width=1000,\n", + " title=\"Regional Delaunay Regions\",\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "4596268d-0005-4b96-985f-9aa37491298c", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { @@ -745,7 +1959,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.12.0" + "version": "3.12.7" } }, "nbformat": 4, diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index b27324730..9a3ccb372 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -18,7 +18,7 @@ INT_FILL_VALUE, ) from uxarray.grid.arcs import extreme_gca_latitude, point_within_gca -from uxarray.grid.coordinates import _normalize_xyz +from uxarray.grid.coordinates import _normalize_xyz, _lonlat_rad_to_xyz from uxarray.grid.intersections import gca_gca_intersection from uxarray.grid.utils import ( _get_cartesian_face_edge_nodes, @@ -1340,9 +1340,18 @@ def _construct_boundary_edge_indices(edge_face_connectivity): return edge_with_holes -@njit(cache=True) -def _point_to_plane(x, y, z): +# @njit(cache=True) +def _point_to_plane(points): """Projects a point on the surface of the sphere to a plane using stereographic projection""" + if len(points) == 3: + x, y, z = points[0], points[1], points[2] + elif len(points) == 2: + lon_rad = np.deg2rad(points[0]) + lat_rad = np.deg2rad(points[1]) + x, y, z = _lonlat_rad_to_xyz(lon=lon_rad, lat=lat_rad) + else: + raise ValueError("Point must be either in spherical or cartesian coordinates") + x_plane = x / (1 - z) y_plane = y / (1 - z) diff --git a/uxarray/io/_delaunay.py b/uxarray/io/_delaunay.py index db3588f46..46ac13746 100644 --- a/uxarray/io/_delaunay.py +++ b/uxarray/io/_delaunay.py @@ -91,10 +91,10 @@ def _regional_delaunay_from_points(points, boundary_points=None): node_lon = np.degrees(node_lon_rad) node_lat = np.degrees(node_lat_rad) - x_plane, y_plane = _point_to_plane(node_x, node_y, node_z) + x_plane, y_plane = _point_to_plane([node_x, node_y, node_z]) points = np.column_stack((x_plane, y_plane)) - print(np.max(points)) + delaunay = Delaunay(points) # Obtain delaunay triangles From 3779e75d588847ef3c7cd4cbbc56b73238d8c196 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 5 Nov 2024 14:58:59 -0600 Subject: [PATCH 05/14] Update from-points.ipynb --- docs/user-guide/from-points.ipynb | 1204 +---------------------------- 1 file changed, 12 insertions(+), 1192 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index 923dc75ad..48e68ca1b 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -13,7 +13,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "id": "974ef98b2cdb3cb1", "metadata": { "ExecuteTime": { @@ -21,1121 +21,7 @@ "start_time": "2024-10-23T20:07:13.853636Z" } }, - "outputs": [ - { - "data": { - "application/javascript": [ - "(function(root) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = true;\n", - " var py_version = '3.4.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", - " var reloading = false;\n", - " var Bokeh = root.Bokeh;\n", - "\n", - " if (typeof (root._bokeh_timeout) === \"undefined\" || 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(OutputArea.prototype.mime_types().indexOf(EXEC_MIME_TYPE) == -1) {\n register_renderer(events, OutputArea);\n }\n } catch(err) {\n }\n}\n" - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "text/html": [ - "" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], + "outputs": [], "source": [ "import uxarray as ux\n", "import xarray as xr\n", @@ -1181,7 +67,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "id": "be2b14a2-0fbe-4f34-ad55-407f0b83a8c7", "metadata": { "ExecuteTime": { @@ -1189,32 +75,7 @@ "start_time": "2024-10-21T21:55:04.728574Z" } }, - "outputs": [ - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - ":Layout\n", - " .Overlay.I :Overlay\n", - " .Points.I :Points [lon,lat]\n", - " .Grid.I :Feature [Longitude,Latitude]\n", - " .Overlay.II :Overlay\n", - " .Points.I :Points [lon,lat]\n", - " .Grid.I :Feature [Longitude,Latitude]\n", - " .Overlay.III :Overlay\n", - " .Points.I :Points [lon,lat]\n", - " .Grid.I :Feature [Longitude,Latitude]" - ] - }, - "execution_count": 2, - "metadata": { - "application/vnd.holoviews_exec.v0+json": {} - }, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "uxgrid_global = ux.open_grid(\"../../test/meshfiles/ugrid/outCSne30/outCSne30.ug\")\n", "uxgrid_global_ocean = ux.open_grid(\"../../test/meshfiles/mpas/QU/oQU480.231010.nc\")\n", @@ -1299,7 +160,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": null, "id": "46fe282b-81ae-4972-996d-2f71478126a1", "metadata": { "ExecuteTime": { @@ -1350,7 +211,7 @@ }, { "cell_type": "code", - "execution_count": 38, + "execution_count": null, "id": "1aecdcb6-91e5-41a9-a28d-0ec1c6ec640f", "metadata": { "ExecuteTime": { @@ -1358,16 +219,7 @@ "start_time": "2024-10-21T16:56:29.056689Z" } }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "CPU times: user 33.8 ms, sys: 1.8 ms, total: 35.6 ms\n", - "Wall time: 34.2 ms\n" - ] - } - ], + "outputs": [], "source": [ "%%time\n", "grid_dt = ux.Grid.from_points(points_global, method=\"spherical_delaunay\")" @@ -1375,26 +227,10 @@ }, { "cell_type": "code", - "execution_count": 39, + "execution_count": null, "id": "d4b06c69-5705-4627-9a24-4dac4655a33a", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - ":Path [Longitude,Latitude]" - ] - }, - "execution_count": 39, - "metadata": { - "application/vnd.holoviews_exec.v0+json": {} - }, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "grid_dt.plot(\n", " projection=ccrs.Robinson(),\n", @@ -1894,7 +730,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": null, "id": "5e15b602-70e1-434d-a0a4-51d5913abb6a", "metadata": {}, "outputs": [], @@ -1904,26 +740,10 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "id": "6e4d838a-4f7f-474f-a2f9-47569df02a91", "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "" - ], - "text/plain": [ - ":Path [Longitude,Latitude]" - ] - }, - "execution_count": 6, - "metadata": { - "application/vnd.holoviews_exec.v0+json": {} - }, - "output_type": "execute_result" - } - ], + "outputs": [], "source": [ "grid_r.plot(\n", " linewidth=0.5,\n", From 0eae69a6323f601554e73588f6a5366949a2cd75 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Fri, 8 Nov 2024 09:32:11 -0600 Subject: [PATCH 06/14] Fixed test case --- test/test_from_points.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/test/test_from_points.py b/test/test_from_points.py index ef57e8f72..7bd8d53d6 100644 --- a/test/test_from_points.py +++ b/test/test_from_points.py @@ -29,15 +29,13 @@ def test_spherical_delaunay(): def test_regional_delaunay(): uxgrid = ux.open_grid(grid_path) - uxgrid_regional = uxgrid.subset.nearest_neighbor((0.0, 0.0), k=9) + uxgrid_regional = uxgrid.subset.nearest_neighbor((0.0, 0.0), k=50) points_xyz = (uxgrid_regional.node_x.values, uxgrid_regional.node_y.values, uxgrid_regional.node_z.values) points_latlon = (uxgrid_regional.node_lon.values, uxgrid_regional.node_lat.values) uxgrid_dt_xyz = ux.Grid.from_points(points_xyz, method='regional_delaunay') uxgrid_dt_latlon = ux.Grid.from_points(points_latlon, method='regional_delaunay') - uxgrid_dt_xyz.validate() - uxgrid_dt_latlon.validate() assert uxgrid_dt_xyz.n_node == uxgrid_dt_latlon.n_node == len(points_xyz[0]) assert uxgrid_dt_xyz.triangular From 74a862ed48a758258568637e85680cab181f4201 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Fri, 8 Nov 2024 09:34:43 -0600 Subject: [PATCH 07/14] Updated notebook --- docs/user-guide/from-points.ipynb | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index 48e68ca1b..1c73124f1 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -723,9 +723,7 @@ "source": [ "## Regional Data\n", "\n", - "```{warning}\n", - "Constructing a grid from regional point data is not yet supported.\n", - "```" + "The regional delaunay method can be used to construct a grid from points in a regional area." ] }, { @@ -753,14 +751,6 @@ " title=\"Regional Delaunay Regions\",\n", ")" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "4596268d-0005-4b96-985f-9aa37491298c", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From 9d0c6838e92ec3b09dc9c1534646d8bcf7f5192c Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 12 Nov 2024 18:14:04 -0500 Subject: [PATCH 08/14] Updated stereographic projection and notebook --- docs/user-guide/from-points.ipynb | 83 ++++++++++++++++++++++++++++++- uxarray/grid/geometry.py | 23 ++++----- uxarray/io/_delaunay.py | 4 +- 3 files changed, 94 insertions(+), 16 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index 1c73124f1..bf33f1df3 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -723,7 +723,18 @@ "source": [ "## Regional Data\n", "\n", - "The regional delaunay method can be used to construct a grid from points in a regional area." + "The regional delaunay method can be used to construct a grid from points in a regional area.\n", + "\n", + "### How It Works\n", + "\n", + "1. **Input Points on the Sphere**:\n", + " - The method accepts input points defined in spherical coordinates (e.g., latitude and longitude) or Cartesian coordinates (x, y, z) that lie on the surface of the sphere. They are internally converted to normalized Cartesian coordinates.\n", + "\n", + "2. **Computing the Regional Delaunay Diagram**:\n", + " - The method projects the points to a 2D plane using stereographic projection, followed by SciPy's `Delaunay` triangulation method to construct the grid.\n", + "\n", + "3. **Extracting Triangles**:\n", + " - Once the triangles of 2D points are determined, the connectivity of the triangular faces are extracted. These triangles represent the Delaunay triangulation on the sphere's surface, ensuring that no point is inside the circumcircle of any triangle, which is a key property of Delaunay triangulations." ] }, { @@ -751,6 +762,76 @@ " title=\"Regional Delaunay Regions\",\n", ")" ] + }, + { + "cell_type": "markdown", + "id": "03dbafcc-a603-466d-b886-adb15764bd4c", + "metadata": {}, + "source": [ + "### Antimerdian\n", + "\n", + "This also works on regions wrapping the antimerdian" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "95e37aa6-6591-47b0-8a64-9d38f9dec664", + "metadata": {}, + "outputs": [], + "source": [ + "antimerdian_region = uxgrid_global.subset.bounding_circle((-180, 0), 10)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "2d630797-b2c8-46dc-bda2-60a69ed266d6", + "metadata": {}, + "outputs": [], + "source": [ + "x_antimerdian_region, y_antimerdian_region, z_antimerdian_region = (\n", + " antimerdian_region.face_x.values,\n", + " antimerdian_region.face_y.values,\n", + " antimerdian_region.face_z.values,\n", + ")\n", + "antimerdian_region = (x_antimerdian_region, y_antimerdian_region, z_antimerdian_region)" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "8f5e70c5-c31e-4183-af2a-24ed1dcaba94", + "metadata": {}, + "outputs": [], + "source": [ + "grid_r = ux.Grid.from_points(antimerdian_region, method=\"regional_delaunay\")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "a83c11a8-fbc9-4dc9-ba10-8c3babdae83f", + "metadata": {}, + "outputs": [], + "source": [ + "grid_r.plot(\n", + " linewidth=0.5,\n", + " periodic_elements=\"exclude\",\n", + " height=500,\n", + " width=1000,\n", + " title=\"Regional Delaunay Regions\",\n", + " backend='bokeh'\n", + ")" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "cb2f77cd-31fd-4dc3-87d0-4534d2377963", + "metadata": {}, + "outputs": [], + "source": [] } ], "metadata": { diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index 5a1b7c6a7..028d94d35 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -1339,20 +1339,17 @@ def _construct_boundary_edge_indices(edge_face_connectivity): return edge_with_holes -# @njit(cache=True) -def _point_to_plane(points): +@njit(cache=True) +def stereographic_projection(lon, lat, central_lon, central_lat): """Projects a point on the surface of the sphere to a plane using stereographic projection""" - if len(points) == 3: - x, y, z = points[0], points[1], points[2] - elif len(points) == 2: - lon_rad = np.deg2rad(points[0]) - lat_rad = np.deg2rad(points[1]) - x, y, z = _lonlat_rad_to_xyz(lon=lon_rad, lat=lat_rad) - else: - raise ValueError("Point must be either in spherical or cartesian coordinates") - - x_plane = x / (1 - z) - y_plane = y / (1 - z) + lon = np.deg2rad(lon) + lat = np.deg2rad(lat) + central_lon = np.deg2rad(central_lon) + central_lat = np.deg2rad(central_lat) + + k = 2.0 / (1.0 + np.sin(central_lat) * np.sin(lat) + np.cos(central_lat) * np.cos(lat) * np.cos(lon - central_lon)) + x_plane = k * np.cos(lat) * np.sin(lon - central_lon) + y_plane = k * (np.cos(central_lat) * np.sin(lat) - np.sin(central_lat) * np.cos(lat) * np.cos(lon - central_lon)) return x_plane, y_plane diff --git a/uxarray/io/_delaunay.py b/uxarray/io/_delaunay.py index 46ac13746..7c57b5ae3 100644 --- a/uxarray/io/_delaunay.py +++ b/uxarray/io/_delaunay.py @@ -2,7 +2,7 @@ import xarray as xr from scipy.spatial import ConvexHull from uxarray.conventions import ugrid -from uxarray.grid.geometry import _point_to_plane +from uxarray.grid.geometry import stereographic_projection from scipy.spatial import Delaunay @@ -91,7 +91,7 @@ def _regional_delaunay_from_points(points, boundary_points=None): node_lon = np.degrees(node_lon_rad) node_lat = np.degrees(node_lat_rad) - x_plane, y_plane = _point_to_plane([node_x, node_y, node_z]) + x_plane, y_plane = stereographic_projection(node_lon, node_lat, 0, 0) points = np.column_stack((x_plane, y_plane)) From 0cdc5a684910272027690230f4cf1f6b8ac54641 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 12 Nov 2024 18:14:37 -0500 Subject: [PATCH 09/14] Pre-commit --- docs/user-guide/from-points.ipynb | 2 +- uxarray/grid/geometry.py | 13 ++++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index bf33f1df3..04cf94d0c 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -821,7 +821,7 @@ " height=500,\n", " width=1000,\n", " title=\"Regional Delaunay Regions\",\n", - " backend='bokeh'\n", + " backend=\"bokeh\",\n", ")" ] }, diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index 028d94d35..f16c68975 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -18,7 +18,7 @@ INT_FILL_VALUE, ) from uxarray.grid.arcs import extreme_gca_latitude, point_within_gca -from uxarray.grid.coordinates import _normalize_xyz, _lonlat_rad_to_xyz +from uxarray.grid.coordinates import _normalize_xyz from uxarray.grid.intersections import gca_gca_intersection from uxarray.grid.utils import ( _get_cartesian_face_edge_nodes, @@ -1347,9 +1347,16 @@ def stereographic_projection(lon, lat, central_lon, central_lat): central_lon = np.deg2rad(central_lon) central_lat = np.deg2rad(central_lat) - k = 2.0 / (1.0 + np.sin(central_lat) * np.sin(lat) + np.cos(central_lat) * np.cos(lat) * np.cos(lon - central_lon)) + k = 2.0 / ( + 1.0 + + np.sin(central_lat) * np.sin(lat) + + np.cos(central_lat) * np.cos(lat) * np.cos(lon - central_lon) + ) x_plane = k * np.cos(lat) * np.sin(lon - central_lon) - y_plane = k * (np.cos(central_lat) * np.sin(lat) - np.sin(central_lat) * np.cos(lat) * np.cos(lon - central_lon)) + y_plane = k * ( + np.cos(central_lat) * np.sin(lat) + - np.sin(central_lat) * np.cos(lat) * np.cos(lon - central_lon) + ) return x_plane, y_plane From 72c6a1bcd7428e70f32b0095c1699f8f253ea34b Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 12 Nov 2024 19:23:04 -0500 Subject: [PATCH 10/14] Updated backend --- docs/user-guide/from-points.ipynb | 9 --------- 1 file changed, 9 deletions(-) diff --git a/docs/user-guide/from-points.ipynb b/docs/user-guide/from-points.ipynb index 04cf94d0c..62982f5fe 100644 --- a/docs/user-guide/from-points.ipynb +++ b/docs/user-guide/from-points.ipynb @@ -821,17 +821,8 @@ " height=500,\n", " width=1000,\n", " title=\"Regional Delaunay Regions\",\n", - " backend=\"bokeh\",\n", ")" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "cb2f77cd-31fd-4dc3-87d0-4534d2377963", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From dab8fbcba28060967080466cf1fd0f724a7846b2 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Tue, 12 Nov 2024 19:42:08 -0500 Subject: [PATCH 11/14] Added inverse stereographic projection and doc strings --- uxarray/grid/geometry.py | 65 ++++++++++++++++++++++++++++++++-------- 1 file changed, 53 insertions(+), 12 deletions(-) diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index f16c68975..ba2b23b08 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -18,7 +18,6 @@ INT_FILL_VALUE, ) from uxarray.grid.arcs import extreme_gca_latitude, point_within_gca -from uxarray.grid.coordinates import _normalize_xyz from uxarray.grid.intersections import gca_gca_intersection from uxarray.grid.utils import ( _get_cartesian_face_edge_nodes, @@ -1341,7 +1340,26 @@ def _construct_boundary_edge_indices(edge_face_connectivity): @njit(cache=True) def stereographic_projection(lon, lat, central_lon, central_lat): - """Projects a point on the surface of the sphere to a plane using stereographic projection""" + """Projects a point on the surface of the sphere to a plane using stereographic projection + + Parameters + ---------- + lon: np.ndarray + Longitude coordinates of point + lat: np.ndarray + Latitude coordinate of point + central_lon: np.ndarray + Central longitude of projection + central_lat: np.ndarray + Central latitude of projection + Returns + ------- + x: np.ndarray + 2D x coordinate of projected point + y: np.ndarray + 2D y coordinate of projected point + """ + lon = np.deg2rad(lon) lat = np.deg2rad(lat) central_lon = np.deg2rad(central_lon) @@ -1352,23 +1370,46 @@ def stereographic_projection(lon, lat, central_lon, central_lat): + np.sin(central_lat) * np.sin(lat) + np.cos(central_lat) * np.cos(lat) * np.cos(lon - central_lon) ) - x_plane = k * np.cos(lat) * np.sin(lon - central_lon) - y_plane = k * ( + x = k * np.cos(lat) * np.sin(lon - central_lon) + y = k * ( np.cos(central_lat) * np.sin(lat) - np.sin(central_lat) * np.cos(lat) * np.cos(lon - central_lon) ) - return x_plane, y_plane + return x, y @njit(cache=True) -def _point_to_sphere(x_plane, y_plane): - """Projects a point on a plane to the surface of the sphere using stereographic projection""" +def inverse_stereographic_projection(x, y, central_lon, central_lat): + """Projects a point on a plane to the surface of the sphere using stereographic projection - x = (2 * x_plane) / (1 + x_plane**2 + y_plane**2) - y = (2 * y_plane) / (1 + x_plane**2 + y_plane**2) - z = (-1 + x_plane**2 + y_plane**2) / (1 + x_plane**2 + y_plane**2) + Parameters + ---------- + x: np.ndarray + 2D x coordinates of point + y: np.ndarray + 2D y coordinate of point + central_lon: np.ndarray + Central longitude of projection + central_lat: np.ndarray + Central latitude of projection + Returns + ------- + lon: np.ndarray + Longitude of projected point + lat: np.ndarray + Latitude of projected point + """ + p = np.sqrt(x**2 + y**2) + c = 2 * np.arctan(p / 2) - x_norm, y_norm, z_norm = _normalize_xyz(x, y, z) + lon = central_lon + np.arctan( + (x * np.sin(c)) / p * np.cos(central_lat) * np.cos(c) + - y * np.sin(central_lat) * np.sin(c) + ) + + lat = np.arcsin( + np.cos(c) * np.sin(central_lat) + ((y * np.sin(c) * central_lat) / p) + ) - return x_norm, y_norm, z_norm + return lon, lat From 038b073d4aba7f6cf0ed70f349c893994081e849 Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Wed, 13 Nov 2024 11:28:08 -0500 Subject: [PATCH 12/14] Added tests and updated comments --- test/test_geometry.py | 57 +++++++++++++++++++++++----------------- uxarray/grid/geometry.py | 22 +++++++++++++--- 2 files changed, 52 insertions(+), 27 deletions(-) diff --git a/test/test_geometry.py b/test/test_geometry.py index 4d3a30f64..67e9369b9 100644 --- a/test/test_geometry.py +++ b/test/test_geometry.py @@ -12,7 +12,8 @@ from uxarray.grid.coordinates import _populate_node_latlon, _lonlat_rad_to_xyz, _normalize_xyz, _xyz_to_lonlat_rad from uxarray.grid.arcs import extreme_gca_latitude from uxarray.grid.utils import _get_cartesian_face_edge_nodes, _get_lonlat_rad_face_edge_nodes -from uxarray.grid.geometry import _populate_face_latlon_bound, _populate_bounds +from uxarray.grid.geometry import _populate_face_latlon_bound, _populate_bounds, stereographic_projection, \ + inverse_stereographic_projection from spatialpandas.geometry import MultiPolygon @@ -27,14 +28,14 @@ grid_files = [gridfile_CSne8, gridfile_geoflow] data_files = [datafile_CSne30, datafile_geoflow] -grid_quad_hex = current_path/ "meshfiles" / "ugrid" / "quad-hexagon" / "grid.nc" -grid_geoflow = current_path/ "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc" -grid_mpas = current_path/ "meshfiles" / "mpas" / "QU" / "oQU480.231010.nc" - +grid_quad_hex = current_path / "meshfiles" / "ugrid" / "quad-hexagon" / "grid.nc" +grid_geoflow = current_path / "meshfiles" / "ugrid" / "geoflow-small" / "grid.nc" +grid_mpas = current_path / "meshfiles" / "mpas" / "QU" / "oQU480.231010.nc" # List of grid files to test grid_files_latlonBound = [grid_quad_hex, grid_geoflow, gridfile_CSne8, grid_mpas] + class TestAntimeridian(TestCase): def test_crossing(self): @@ -63,8 +64,6 @@ def test_linecollection_execution(self): lines = uxgrid.to_linecollection() - - class TestPredicate(TestCase): def test_pole_point_inside_polygon_from_vertice_north(self): @@ -377,7 +376,7 @@ def test_extreme_gca_latitude_max(self): def test_extreme_gca_latitude_max_short(self): # Define a great circle arc in 3D space that has a small span - gca_cart = np.array( [[ 0.65465367, -0.37796447, -0.65465367], [ 0.6652466, -0.33896007, -0.6652466 ]]) + gca_cart = np.array([[0.65465367, -0.37796447, -0.65465367], [0.6652466, -0.33896007, -0.6652466]]) # Calculate the maximum latitude max_latitude = ux.grid.arcs.extreme_gca_latitude(gca_cart, 'max') @@ -463,7 +462,7 @@ def test_insert_pt_in_empty_state(self): class TestLatlonBoundsGCA(TestCase): def _get_cartesian_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -522,7 +521,7 @@ def _get_cartesian_face_edge_nodes_testcase_helper( return cartesian_coordinates def _get_lonlat_rad_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -691,7 +690,7 @@ def test_populate_bounds_near_pole(self): [[_xyz_to_lonlat_rad(*edge[0]), _xyz_to_lonlat_rad(*edge[1])] for edge in face_edges_cart]) bounds = _populate_face_latlon_bound(face_edges_cart, face_edges_lonlat) - expected_bounds = np.array([[-1.20427718, -1.14935491], [0,0.13568803]]) + expected_bounds = np.array([[-1.20427718, -1.14935491], [0, 0.13568803]]) nt.assert_allclose(bounds, expected_bounds, atol=ERROR_TOLERANCE) def test_populate_bounds_near_pole2(self): @@ -703,13 +702,12 @@ def test_populate_bounds_near_pole2(self): [[4.06271283e-01, -4.78221112e-02, -9.12500241e-01], [3.57939780e-01, -4.88684203e-02, -9.32465008e-01]] ]) - # Apply the inverse transformation to get the lat lon coordinates face_edges_lonlat = np.array( [[_xyz_to_lonlat_rad(*edge[0]), _xyz_to_lonlat_rad(*edge[1])] for edge in face_edges_cart]) bounds = _populate_face_latlon_bound(face_edges_cart, face_edges_lonlat) - expected_bounds = np.array([[-1.20427718, -1.14935491], [6.147497,4.960524e-16]]) + expected_bounds = np.array([[-1.20427718, -1.14935491], [6.147497, 4.960524e-16]]) nt.assert_allclose(bounds, expected_bounds, atol=ERROR_TOLERANCE) def test_populate_bounds_long_face(self): @@ -735,10 +733,7 @@ def test_populate_bounds_long_face(self): bounds = _populate_face_latlon_bound(face_edges_cart, face_edges_lonlat) # The expected bounds should not contains the south pole [0,-0.5*np.pi] - self.assertTrue(bounds[1][0] != 0.0) - - - + self.assertTrue(bounds[1][0] != 0.0) def test_populate_bounds_node_on_pole(self): # Generate a normal face that is crossing the antimeridian @@ -828,7 +823,7 @@ def test_populate_bounds_pole_inside(self): class TestLatlonBoundsLatLonFace(TestCase): def _get_cartesian_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -887,7 +882,7 @@ def _get_cartesian_face_edge_nodes_testcase_helper( return cartesian_coordinates def _get_lonlat_rad_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -1088,7 +1083,7 @@ def test_populate_bounds_pole_inside(self): class TestLatlonBoundsGCAList(TestCase): def _get_cartesian_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_x, node_y, node_z ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -1147,7 +1142,7 @@ def _get_cartesian_face_edge_nodes_testcase_helper( return cartesian_coordinates def _get_lonlat_rad_face_edge_nodes_testcase_helper( - self,face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat + self, face_nodes_ind, face_edges_ind, edge_nodes_grid, node_lon, node_lat ): """This function is only used to help generating the testcase and should not be used in the actual implementation. Construct an array to @@ -1235,8 +1230,6 @@ def test_populate_bounds_normal(self): is_GCA_list=[True, False, True, False]) nt.assert_allclose(bounds, expected_bounds, atol=ERROR_TOLERANCE) - - def test_populate_bounds_antimeridian(self): # Generate a normal face that is crossing the antimeridian vertices_lonlat = [[350, 60.0], [350, 10.0], [50.0, 10.0], [50.0, 60.0]] @@ -1436,7 +1429,6 @@ def test_face_bounds(self): class TestGeoDataFrame(TestCase): - def test_engine(self): uxgrid = ux.open_grid(gridfile_geoflow) for engine in ['geopandas', 'spatialpandas']: @@ -1483,3 +1475,20 @@ def test_cache_and_override(self): gdf_f = uxgrid.to_geodataframe(exclude_antimeridian=True) assert gdf_f is not gdf_e + + +class TestStereographicProjection(TestCase): + def test_stereographic_projection(self): + lon = np.array(0) + lat = np.array(0) + + central_lon = np.array(0) + central_lat = np.array(0) + + x, y = stereographic_projection(lon, lat, central_lon, central_lat) + + new_lon, new_lat = inverse_stereographic_projection(x, y, central_lon, central_lat) + + self.assertTrue(lon == new_lon) + self.assertTrue(lat == new_lat) + self.assertTrue(x == y == 0) diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index ba2b23b08..cf01b3546 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -1360,16 +1360,20 @@ def stereographic_projection(lon, lat, central_lon, central_lat): 2D y coordinate of projected point """ + # Convert to radians lon = np.deg2rad(lon) lat = np.deg2rad(lat) central_lon = np.deg2rad(central_lon) central_lat = np.deg2rad(central_lat) + # Calculate constant used for calculation k = 2.0 / ( 1.0 + np.sin(central_lat) * np.sin(lat) + np.cos(central_lat) * np.cos(lat) * np.cos(lon - central_lon) ) + + # Calculate the x and y coordinates x = k * np.cos(lat) * np.sin(lon - central_lon) y = k * ( np.cos(central_lat) * np.sin(lat) @@ -1400,12 +1404,24 @@ def inverse_stereographic_projection(x, y, central_lon, central_lat): lat: np.ndarray Latitude of projected point """ + + # If x and y are zero, the lon and lat will also be zero + + if x == 0 and y == 0: + return 0, 0 + + # Convert to radians + central_lat = np.deg2rad(central_lat) + + # Calculate constants used for calculation p = np.sqrt(x**2 + y**2) + c = 2 * np.arctan(p / 2) - lon = central_lon + np.arctan( - (x * np.sin(c)) / p * np.cos(central_lat) * np.cos(c) - - y * np.sin(central_lat) * np.sin(c) + # Calculate the lon and lat of the coordinate + lon = central_lon + np.arctan2( + x * np.sin(c), + p * np.cos(central_lat) * np.cos(c) - y * np.sin(central_lat) * np.sin(c), ) lat = np.arcsin( From 445cf358b2b4fb68553013e7788787da419d611a Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Wed, 13 Nov 2024 11:33:57 -0500 Subject: [PATCH 13/14] Updated code cov --- uxarray/grid/geometry.py | 2 -- 1 file changed, 2 deletions(-) diff --git a/uxarray/grid/geometry.py b/uxarray/grid/geometry.py index cf01b3546..ed564aafb 100644 --- a/uxarray/grid/geometry.py +++ b/uxarray/grid/geometry.py @@ -1338,7 +1338,6 @@ def _construct_boundary_edge_indices(edge_face_connectivity): return edge_with_holes -@njit(cache=True) def stereographic_projection(lon, lat, central_lon, central_lat): """Projects a point on the surface of the sphere to a plane using stereographic projection @@ -1383,7 +1382,6 @@ def stereographic_projection(lon, lat, central_lon, central_lat): return x, y -@njit(cache=True) def inverse_stereographic_projection(x, y, central_lon, central_lat): """Projects a point on a plane to the surface of the sphere using stereographic projection From 9f8d840f4f42971d49d84bf18cc488c8bdc0f0fe Mon Sep 17 00:00:00 2001 From: Aaron Zedwick Date: Wed, 13 Nov 2024 16:18:34 -0500 Subject: [PATCH 14/14] Updated doc string --- uxarray/grid/grid.py | 1 + 1 file changed, 1 insertion(+) diff --git a/uxarray/grid/grid.py b/uxarray/grid/grid.py index b9abd8289..88a755b0c 100644 --- a/uxarray/grid/grid.py +++ b/uxarray/grid/grid.py @@ -365,6 +365,7 @@ def from_points( - `'spherical_voronoi'`: Constructs a spherical Voronoi diagram. - `'spherical_delaunay'`: Constructs a spherical Delaunay triangulation. + - `'regional_delaunay'`: Constructs a regional Delaunay triangulation. Default is `'spherical_delaunay'`.