{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "bb6ec0fd-cb13-42c5-a457-f21e4c6da0a5", "metadata": {}, "outputs": [ { "data": { "text/html": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "(function(root) {\n", " function now() {\n", " return new Date();\n", " }\n", "\n", " const force = true;\n", " const py_version = '3.6.3'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", " const reloading = false;\n", " const Bokeh = root.Bokeh;\n", "\n", " // Set a timeout for this load but only if we are not already initializing\n", " if (typeof (root._bokeh_timeout) === \"undefined\" || (force || !root._bokeh_is_initializing)) {\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_failed_load = false;\n", " }\n", "\n", " function run_callbacks() {\n", " try {\n", " root._bokeh_onload_callbacks.forEach(function(callback) {\n", " if (callback != null)\n", " callback();\n", " });\n", " } finally {\n", " delete 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versions are fully initialized.\n", " if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n", " // If the timeout and bokeh was not successfully loaded we reset\n", " // everything and try loading again\n", " root._bokeh_timeout = Date.now() + 5000;\n", " root._bokeh_is_initializing = false;\n", " root._bokeh_onload_callbacks = undefined;\n", " root._bokeh_is_loading = 0\n", " console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n", " load_or_wait();\n", " } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n", " setTimeout(load_or_wait, 100);\n", " } else {\n", " root._bokeh_is_initializing = true\n", " root._bokeh_onload_callbacks = []\n", " const bokeh_loaded = root.Bokeh != null && (root.Bokeh.version === py_version || (root.Bokeh.versions !== undefined && root.Bokeh.versions.has(py_version)));\n", " if (!reloading && 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!root._bokeh_is_initializing)) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n // Don't load bokeh if it is still initializing\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n } else if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n // There is nothing to load\n 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element.async = false;\n element.src = url;\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (let i = 0; i < js_modules.length; i++) {\n const url = js_modules[i];\n const escaped = encodeURI(url)\n if (skip.indexOf(escaped) !== -1 || existing_scripts.indexOf(escaped) !== -1) {\n if (!window.requirejs) {\n on_load();\n }\n continue;\n }\n var element = document.createElement('script');\n element.onload = on_load;\n element.onerror = on_error;\n element.async = false;\n element.src = url;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n document.head.appendChild(element);\n }\n for (const name in js_exports) {\n const url = js_exports[name];\n const escaped = encodeURI(url)\n if (skip.indexOf(escaped) >= 0 || root[name] != null) {\n if (!window.requirejs) {\n on_load();\n }\n continue;\n }\n var element = document.createElement('script');\n element.onerror = on_error;\n element.async = false;\n element.type = \"module\";\n console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n element.textContent = `\n import ${name} from \"${url}\"\n window.${name} = ${name}\n window._bokeh_on_load()\n `\n document.head.appendChild(element);\n }\n if (!js_urls.length && !js_modules.length) {\n on_load()\n }\n };\n\n function inject_raw_css(css) {\n const element = document.createElement(\"style\");\n element.appendChild(document.createTextNode(css));\n document.body.appendChild(element);\n }\n\n const js_urls = [\"https://cdn.holoviz.org/panel/1.6.1/dist/bundled/reactiveesm/es-module-shims@^1.10.0/dist/es-module-shims.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.6.3.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.6.3.min.js\", \"https://cdn.holoviz.org/panel/1.6.1/dist/panel.min.js\"];\n const js_modules = [];\n const js_exports = {};\n const css_urls = [];\n const inline_js = [ function(Bokeh) {\n Bokeh.set_log_level(\"info\");\n },\nfunction(Bokeh) {} // ensure no trailing comma for IE\n ];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (let i = 0; i < inline_js.length; i++) {\n try {\n inline_js[i].call(root, root.Bokeh);\n } catch(e) {\n if (!reloading) {\n throw e;\n }\n }\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n var NewBokeh = root.Bokeh;\n if (Bokeh.versions === undefined) {\n Bokeh.versions = new Map();\n }\n if (NewBokeh.version !== Bokeh.version) {\n Bokeh.versions.set(NewBokeh.version, NewBokeh)\n }\n root.Bokeh = Bokeh;\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n // If the timeout and bokeh was not successfully loaded we reset\n // everything and try loading again\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n root._bokeh_is_loading = 0\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n const bokeh_loaded = root.Bokeh != null && (root.Bokeh.version === py_version || (root.Bokeh.versions !== undefined && root.Bokeh.versions.has(py_version)));\n if (!reloading && !bokeh_loaded) {\n if (root.Bokeh) {\n root.Bokeh = undefined;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n }\n // Give older versions of the autoload script a head-start to ensure\n // they initialize before we start loading newer version.\n setTimeout(load_or_wait, 100)\n}(window));" }, 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not already initializing\n if (typeof (root._bokeh_timeout) === \"undefined\" || (force || !root._bokeh_is_initializing)) {\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_failed_load = false;\n }\n\n function run_callbacks() {\n try {\n root._bokeh_onload_callbacks.forEach(function(callback) {\n if (callback != null)\n callback();\n });\n } finally {\n delete root._bokeh_onload_callbacks;\n }\n console.debug(\"Bokeh: all callbacks have finished\");\n }\n\n function load_libs(css_urls, js_urls, js_modules, js_exports, callback) {\n if (css_urls == null) css_urls = [];\n if (js_urls == null) js_urls = [];\n if (js_modules == null) js_modules = [];\n if (js_exports == null) js_exports = {};\n\n root._bokeh_onload_callbacks.push(callback);\n\n if (root._bokeh_is_loading > 0) {\n // Don't load bokeh if it is still initializing\n console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n return null;\n } else if (js_urls.length === 0 && js_modules.length 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];\n\n function run_inline_js() {\n if ((root.Bokeh !== undefined) || (force === true)) {\n for (let i = 0; i < inline_js.length; i++) {\n try {\n inline_js[i].call(root, root.Bokeh);\n } catch(e) {\n if (!reloading) {\n throw e;\n }\n }\n }\n // Cache old bokeh versions\n if (Bokeh != undefined && !reloading) {\n var NewBokeh = root.Bokeh;\n if (Bokeh.versions === undefined) {\n Bokeh.versions = new Map();\n }\n if (NewBokeh.version !== Bokeh.version) {\n Bokeh.versions.set(NewBokeh.version, NewBokeh)\n }\n root.Bokeh = Bokeh;\n }\n } else if (Date.now() < root._bokeh_timeout) {\n setTimeout(run_inline_js, 100);\n } else if (!root._bokeh_failed_load) {\n console.log(\"Bokeh: BokehJS failed to load within specified timeout.\");\n root._bokeh_failed_load = true;\n }\n root._bokeh_is_initializing = false\n }\n\n function load_or_wait() {\n // Implement a backoff loop that tries to ensure we do not load multiple\n // versions of Bokeh and its dependencies at the same time.\n // In recent versions we use the root._bokeh_is_initializing flag\n // to determine whether there is an ongoing attempt to initialize\n // bokeh, however for backward compatibility we also try to ensure\n // that we do not start loading a newer (Panel>=1.0 and Bokeh>3) version\n // before older versions are fully initialized.\n if (root._bokeh_is_initializing && Date.now() > root._bokeh_timeout) {\n // If the timeout and bokeh was not successfully loaded we reset\n // everything and try loading again\n root._bokeh_timeout = Date.now() + 5000;\n root._bokeh_is_initializing = false;\n root._bokeh_onload_callbacks = undefined;\n root._bokeh_is_loading = 0\n console.log(\"Bokeh: BokehJS was loaded multiple times but one version failed to initialize.\");\n load_or_wait();\n } else if (root._bokeh_is_initializing || (typeof root._bokeh_is_initializing === \"undefined\" && root._bokeh_onload_callbacks !== undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n const bokeh_loaded = root.Bokeh != null && (root.Bokeh.version === py_version || (root.Bokeh.versions !== undefined && root.Bokeh.versions.has(py_version)));\n if (!reloading && !bokeh_loaded) {\n if (root.Bokeh) {\n root.Bokeh = undefined;\n }\n console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n console.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n run_inline_js();\n });\n }\n }\n // Give older versions of the autoload script a head-start to ensure\n // they initialize before we start loading newer version.\n setTimeout(load_or_wait, 100)\n}(window));" }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "if ((window.PyViz === undefined) || (window.PyViz instanceof HTMLElement)) {\n", " window.PyViz = {comms: {}, comm_status:{}, kernels:{}, receivers: {}, plot_index: []}\n", "}\n", 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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:{}, 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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" } ], "source": [ "import argparse, time, os\n", "import random\n", "\n", "from tqdm import tqdm\n", "import copy, math\n", "import numpy as np\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import geopandas as gpd\n", "from pyproj import Proj, Transformer, Geod\n", "import xarray\n", "import xrspatial.slope\n", "from bokeh.models import PrintfTickFormatter, FixedTicker\n", "import datashader as ds\n", "import holoviews as hv\n", "from holoviews import opts\n", "from holoviews.operation.datashader import datashade, rasterize, inspect_points\n", "import hvplot.xarray\n", "import hvplot.pandas\n", "import rioxarray\n", "\n", "hv.extension('bokeh')" ] }, { "cell_type": "code", "execution_count": 2, "id": "d8256c70-e154-4e28-a6b4-3687bf50ed90", "metadata": {}, "outputs": [], "source": [ "from bokeh.themes.theme import Theme\n", "# Custom Bokeh theme for improved colorbar title styling\n", "theme = Theme(json={\n", " 'attrs': {\n", " 'Title': {'align': 'center', 'text_font_size': '15px'}, # Larger and centered title\n", " 'Axis': {'axis_label_text_font_style': 'normal'}, # No italic labels\n", " 'Legend': {'title_text_font_style': 'normal'},\n", " 'ColorBar': {'title_text_font_size': '16pt', # Larger colorbar title\n", " 'title_text_font_style': 'normal',\n", " 'major_label_text_font_size': '13pt'}\n", " }\n", "})\n", "\n", "hv.renderer('bokeh').theme = theme" ] }, { "cell_type": "code", "execution_count": 3, "id": "64db87ff-0a69-4515-a06a-385e7a95b5a7", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "We are dealing with 151 files from BedMap\n" ] } ], "source": [ "bedmap_folder = f\"/media/maffe/nvme/polar_ice_thickness_data/bedmap\"\n", "\n", "# Find all .csv files in the directory\n", "files_bedmap = [\n", " os.path.join(root, file)\n", " for root, _, files in os.walk(bedmap_folder)\n", " for file in files if file.endswith(\".csv\")\n", "]\n", "\n", "# Process each file\n", "total_files = len(files_bedmap)\n", "print(f\"We are dealing with {total_files} files from BedMap\")" ] }, { "cell_type": "code", "execution_count": 4, "id": "90c36e12-75eb-47a5-8cb5-4487fc3d0cb2", "metadata": {}, "outputs": [], "source": [ "# Columns to check for. Also let's rename the column names to values on the right\n", "required_columns_bedmap = {\n", " 'longitude (degree_east)': 'LON',\n", " 'latitude (degree_north)': 'LAT',\n", " 'date': 'date',\n", " 'surface_altitude (m)': 'surface_altitude (m)',\n", " 'land_ice_thickness (m)': 'THICK',\n", " 'bedrock_altitude (m)': 'bedrock_altitude (m)'\n", "}" ] }, { "cell_type": "code", "execution_count": 5, "id": "be631f5f-b25d-4804-ab3f-8f46d8d7164e", "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "100%|█████████████████████████████████████████| 151/151 [01:15<00:00, 2.00it/s]\n" ] } ], "source": [ "# List to store dataframes\n", "bedmap_list_csv = []\n", " \n", "for i, file in tqdm(enumerate(files_bedmap), total=total_files, leave=True):\n", "\n", " try: \n", " # Read the CSV file, skipping the header\n", " df_file_csv = pd.read_csv(file, skiprows=18, low_memory=False, dtype={'date': 'string'})\n", "\n", " # Check if required columns exist\n", " missing_columns = [col for col in required_columns_bedmap.keys() if col not in df_file_csv.columns]\n", " if missing_columns:\n", " raise ValueError(f\"Missing columns: {missing_columns}\")\n", "\n", " # Select only the required columns\n", " #df_file_csv = df_file_csv[required_columns_bedmap]\n", " df_file_csv = df_file_csv[required_columns_bedmap.keys()].rename(columns=required_columns_bedmap)\n", " \n", " # Append to the list of dataframes\n", " bedmap_list_csv.append(df_file_csv)\n", "\n", " except Exception as e:\n", " print(f\"Error processing file '{file}': {e}\")" ] }, { "cell_type": "code", "execution_count": 6, "id": "c5c23f97-bbe0-44f8-bec0-8c9365e09d74", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Original BedMap no. points: 95892117.\n" ] } ], "source": [ "# Concatenate all dataframes into one\n", "combined_bedmap_df = pd.concat(bedmap_list_csv, axis=0, ignore_index=True)\n", "print(f\"Original BedMap no. points: {len(combined_bedmap_df)}.\")" ] }, { "cell_type": "code", "execution_count": 7, "id": "1691c896-0f29-41e0-a851-bfd44d938547", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "no. points: 81087281.\n" ] } ], "source": [ "# Data cleaning\n", "\n", "# NOTE: this could be further refined. In particular, some crossing tracks sometimes appear not consistent\n", "\n", "# 1) remove rows where THICK is -9999\n", "combined_bedmap_df = combined_bedmap_df[~combined_bedmap_df[['THICK']].isin([-9999]).any(axis=1)\n", "]\n", "# 2) Remove too small ice thickness data\n", "combined_bedmap_df = combined_bedmap_df[combined_bedmap_df['THICK'] > 0.5]\n", "print(f\"no. points: {len(combined_bedmap_df)}.\")" ] }, { "cell_type": "code", "execution_count": 8, "id": "486aaf09-5772-42b6-96a4-ae63b66d0598", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " LON LAT date surface_altitude (m) THICK \\\n", "0 76.889142 -69.876749 -9999 -9999.0 1046.6 \n", "1 76.893603 -69.876762 -9999 -9999.0 1058.5 \n", "2 76.899026 -69.876753 -9999 -9999.0 1061.1 \n", "3 76.904100 -69.876424 -9999 -9999.0 1063.7 \n", "4 76.909194 -69.876374 -9999 -9999.0 1069.8 \n", "\n", " bedrock_altitude (m) \n", "0 -9999.0 \n", "1 -9999.0 \n", "2 -9999.0 \n", "3 -9999.0 \n", "4 -9999.0 \n" ] } ], "source": [ "print(combined_bedmap_df.head(5))" ] }, { "cell_type": "code", "execution_count": 9, "id": "6c755d44-9743-4c1a-81b0-d168cc050083", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " LON LAT THICK geometry EAST \\\n", "0 76.889142 -69.876749 1046.6 POINT (2150724.686 500918.979) 2.150725e+06 \n", "1 76.893603 -69.876762 1058.5 POINT (2150762.268 500751.208) 2.150762e+06 \n", "2 76.899026 -69.876753 1061.1 POINT (2150810.656 500547.878) 2.150811e+06 \n", "3 76.904100 -69.876424 1063.7 POINT (2150890.832 500365.723) 2.150891e+06 \n", "4 76.909194 -69.876374 1069.8 POINT (2150940.759 500175.761) 2.150941e+06 \n", "\n", " NORTH \n", "0 500918.979443 \n", "1 500751.208165 \n", "2 500547.878047 \n", "3 500365.723321 \n", "4 500175.761230 \n", "EPSG:3031\n" ] } ], "source": [ "bedmap = combined_bedmap_df[['LON', 'LAT', 'THICK']]\n", "bedmap_gdf = gpd.GeoDataFrame(\n", " bedmap,\n", " geometry=gpd.points_from_xy(bedmap['LON'], bedmap['LAT']), crs=\"EPSG:4326\").to_crs(\"EPSG:3031\")\n", "bedmap_gdf['EAST'] = bedmap_gdf.geometry.x.values\n", "bedmap_gdf['NORTH'] = bedmap_gdf.geometry.y.values\n", "print(bedmap_gdf.head(5))\n", "print(bedmap_gdf.crs)" ] }, { "cell_type": "code", "execution_count": 10, "id": "f5789a54-d990-4fbb-a9ba-74271a9c02d0", "metadata": {}, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "
\n", "
\n", "
\n", "" ], "text/plain": [ ":DynamicMap []\n", " :Image [EAST,NORTH] (EAST_NORTH THICK)" ] }, "metadata": { "application/vnd.holoviews_exec.v0+json": { "id": "p1006" } }, "output_type": "display_data" } ], "source": [ "points_bedmap = hv.Points(bedmap_gdf, ['EAST', 'NORTH'], 'THICK') # HoloViews Points object\n", "\n", "formatter = PrintfTickFormatter(format='%i')\n", "\n", "# Rasterize the points\n", "rasterized_bedmap = rasterize(points_bedmap,aggregator=ds.mean('THICK')).opts(\n", " cmap=plt.colormaps['turbo'],\n", " cnorm='eq_hist',\n", " width=700,\n", " height=700,\n", " colorbar=True,\n", " xaxis=None, # Remove x-axis\n", " yaxis=None, # Remove y-axis\n", " colorbar_opts={\n", " 'title': 'Ice Thickness measurements [m]',\n", " 'formatter': formatter, # Apply custom formatter to the colorbar,\n", " \"ticker\": FixedTicker(ticks=[500, 1000, 1500, 2000, 2500, 3000, 4500])\n", " },\n", " colorbar_position='bottom',\n", ")\n", "\n", "\n", "# Display the plot\n", "hv.output(rasterized_bedmap)" ] }, { "cell_type": "code", "execution_count": 11, "id": "94501df0-faa1-4d8e-9353-6b9ac5fad59e", "metadata": {}, "outputs": [], "source": [ "FOLDER_AN_VELOCITY = f\"/media/maffe/nvme/Antarctica_NSIDC/velocity/NSIDC-0754/\"\n", "FOLDER_AN_THICKNESS = f\"/media/maffe/nvme/Antarctica_NSIDC/thickness/NSIDC-0756/\"\n", "FOLDER_AN_RACMO = f\"/media/maffe/nvme/racmo/antarctica_racmo2.3p2/2km/\"\n", "\n", "file_an_v = f\"{FOLDER_AN_VELOCITY}antarctic_ice_vel_phase_map_v01.nc\"\n", "file_an_smb = f\"{FOLDER_AN_RACMO}smb_antarctica_mean_1979_2021_RACMO23p2_gf.nc\"\n", "file_an_bedmac = f\"{FOLDER_AN_THICKNESS}BedMachineAntarctica-v3.nc\"" ] }, { "cell_type": "code", "execution_count": 12, "id": "ad50fecf-a2b1-4a42-a3c3-2811bc612997", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "(450.0, -450.0)\n", "(450.0, -450.0)\n", "(500.0, -500.0)\n", "(500.0, -500.0)\n", "(2000.0, -2000.0)\n" ] } ], "source": [ "# Open Antarctica arrays\n", "an_v = rioxarray.open_rasterio(file_an_v)\n", "an_smb = rioxarray.open_rasterio(file_an_smb)\n", "an_bedmac = rioxarray.open_rasterio(file_an_bedmac)\n", "\n", "print(an_v['VX'].rio.resolution())\n", "print(an_v['VY'].rio.resolution())\n", "print(an_bedmac['thickness'].rio.resolution())\n", "print(an_bedmac['surface'].rio.resolution())\n", "print(an_smb.rio.resolution())\n", "\n", "an_bedmac['thickness'] = an_bedmac['thickness'].where(an_bedmac['thickness'] != 0.0)\n", "\n", "# Calculate the slope\n", "res_elevation = an_bedmac['surface'].rio.resolution()[0] # 500 m\n", "#an_bedmac['slope'] = xrspatial.slope(an_bedmac['surface'].squeeze())\n", "dz_dy, dz_dx = np.gradient(an_bedmac['surface'].squeeze(), res_elevation, res_elevation)\n", "slope_raw = np.sqrt(dz_dx**2 + dz_dy**2)\n", "an_bedmac['slope'] = (('y', 'x'), slope_raw)\n", "\n", "nodata_v = an_v['VX'].rio.nodata\n", "\n", "an_vx = an_v['VX']\n", "an_vy = an_v['VY']\n", "\n", "an_vx.values = np.where(an_vx.values == nodata_v, np.nan, an_vx.values)\n", "an_vy.values = np.where(an_vy.values == nodata_v, np.nan, an_vy.values)\n", "\n", "an_v['V'] = (an_vx**2 + an_vy**2)**0.5\n", "\n", "assert an_vx.rio.crs == an_vy.rio.crs == an_smb.rio.crs == an_bedmac.rio.crs, 'Different crs.'" ] }, { "cell_type": "code", "execution_count": 13, "id": "b2780631-db1b-4743-aade-36ee80ab1fdd", "metadata": {}, "outputs": [], "source": [ "# Interpolate arrays linearly\n", "eastings_ar = xarray.DataArray(bedmap_gdf['EAST'])\n", "northings_ar = xarray.DataArray(bedmap_gdf['NORTH'])\n", "\n", "elev_interp_data = an_bedmac['surface'].interp(y=northings_ar, x=eastings_ar, method='linear').data.squeeze()\n", "ith_interp_data = an_bedmac['thickness'].interp(y=northings_ar, x=eastings_ar, method='linear').data.squeeze()\n", "slope_interp_data = an_bedmac['slope'].interp(y=northings_ar, x=eastings_ar, method='linear').data.squeeze()\n", "v_interp_data = an_v['V'].interp(y=northings_ar, x=eastings_ar, method='linear').data.squeeze()\n", "smb_interp_data = an_smb.interp(y=northings_ar, x=eastings_ar, method='linear').data.squeeze()" ] }, { "cell_type": "code", "execution_count": 14, "id": "77979e91-f940-4b6c-80de-b63429b6832e", "metadata": {}, "outputs": [], "source": [ "# Plug in dataset\n", "\n", "bedmap_gdf['v'] = v_interp_data\n", "bedmap_gdf['ith_bm'] = ith_interp_data\n", "bedmap_gdf['smb'] = smb_interp_data\n", "bedmap_gdf['z'] = elev_interp_data\n", "bedmap_gdf['s'] = slope_interp_data" ] }, { "cell_type": "code", "execution_count": 15, "id": "fbed5871-84c1-4a9e-8860-5eb10c7caece", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Before dropping nans: 81087281 points\n", "After dropping nans: 79890423 points\n" ] } ], "source": [ "print(f\"Before dropping nans: {len(bedmap_gdf)} points\")\n", "bedmap_gdf = bedmap_gdf.dropna()\n", "print(f\"After dropping nans: {len(bedmap_gdf)} points\")" ] }, { "cell_type": "code", "execution_count": 16, "id": "60179777-85be-44e0-9e45-e1ad6f91087a", "metadata": {}, "outputs": [], "source": [ "# Check no invalid points\n", "invalid_count = (~bedmap_gdf.geometry.is_valid).sum()\n", "assert invalid_count==0, f\"Invalid geometries: {invalid_count}\"" ] }, { "cell_type": "code", "execution_count": 17, "id": "a7ca8fce-e01c-4509-93a0-900fd552422d", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " THICK smb z s v\n", "THICK 1.000000 -0.364856 0.742594 -0.346988 -0.240941\n", "smb -0.364856 1.000000 -0.454212 0.368349 0.228904\n", "z 0.742594 -0.454212 1.000000 -0.207117 -0.359341\n", "s -0.346988 0.368349 -0.207117 1.000000 0.006415\n", "v -0.240941 0.228904 -0.359341 0.006415 1.000000\n" ] } ], "source": [ "cols = ['THICK', 'smb', 'z', 's', 'v']\n", "corr_matrix = bedmap_gdf[cols].corr()\n", "print(corr_matrix)" ] }, { "cell_type": "code", "execution_count": 22, "id": "1e0e4b26-26e7-4c02-ad7a-0c03f61c9203", "metadata": {}, "outputs": [], "source": [ "# Save\n", "save = False\n", "if save:\n", " bedmap_gdf.to_parquet(f\"{bedmap_folder}/bedmap_train.parquet\", engine='pyarrow', index=False)\n", " print(f\"Combined BedMap dataframe saved as parquet: {len(bedmap_gdf)} points.\")" ] }, { "cell_type": "code", "execution_count": 18, "id": "61e4a0f9-6602-4b08-9b38-6548f769ea1f", "metadata": {}, "outputs": [ { "data": {}, "metadata": {}, "output_type": "display_data" }, { "data": { "application/vnd.holoviews_exec.v0+json": "", "text/html": [ "
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\n", "" ], "text/plain": [ ":DynamicMap []\n", " :Image [x,y] (slope)" ] }, "execution_count": 18, "metadata": { "application/vnd.holoviews_exec.v0+json": { "id": "p1077" } }, "output_type": "execute_result" } ], "source": [ "# Plot\n", "\n", "x = an_bedmac['slope'].hvplot.image(\n", " x='x', y='y',\n", " rasterize=True,\n", " dynamic=True,\n", " #logz=True,\n", " clim=(0, .3),\n", ").opts(\n", " cmap='binary',\n", " width=700,\n", " height=700,\n", " xaxis=None,\n", " yaxis=None,\n", " title=\"\",\n", " colorbar_opts={\n", " 'title': 'Surface slope [unitless]',\n", " },\n", " colorbar_position='bottom',\n", " tools=[]\n", ")\n", "\n", "# HoloViews Points object\n", "points = hv.Points(bedmap_gdf, ['EAST', 'NORTH'], 's')\n", "\n", "# Rasterize the points\n", "#rasterized_points = rasterize(points,aggregator=ds.mean('s')).opts(\n", "# cmap=plt.colormaps['turbo'],\n", "# #logz=True,\n", "# clim=(0, 2.5),\n", "# colorbar=False,\n", "# tools=['hover'],\n", "#)\n", "\n", "\n", "x #* rasterized_points" ] }, { "cell_type": "code", "execution_count": null, "id": "5adf4199-0970-444b-a714-421ed5cda0da", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.12.7" } }, "nbformat": 4, "nbformat_minor": 5 }