From efed36eeea43ce1f025a73c8762c12075ff2e239 Mon Sep 17 00:00:00 2001 From: Rupesh Shrestha Date: Tue, 19 Nov 2024 10:24:55 -0500 Subject: [PATCH] running cells --- book/tutorials/EMIT/EMIT_intro.ipynb | 3734 ++++++++++++++++- .../ECOSTRESS_concurrent.ipynb | 1219 +++++- 2 files changed, 4905 insertions(+), 48 deletions(-) diff --git a/book/tutorials/EMIT/EMIT_intro.ipynb b/book/tutorials/EMIT/EMIT_intro.ipynb index 7144454..175117c 100644 --- a/book/tutorials/EMIT/EMIT_intro.ipynb +++ b/book/tutorials/EMIT/EMIT_intro.ipynb @@ -29,12 +29,606 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "d25af780-a4c6-450d-acb5-01b58719d42a", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "data": { + "application/javascript": [ + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + " var py_version = '3.4.0'.replace('rc', '-rc.').replace('.dev', '-dev.');\n", + " var reloading 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(!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", + " */\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 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!== 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" + }, + { + "data": { + "application/vnd.holoviews_exec.v0+json": "", + "text/html": [ + "
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\n", + "
\n", + "" + ] + }, + "metadata": { + "application/vnd.holoviews_exec.v0+json": { + "id": "p1002" + } + }, + "output_type": "display_data" + } + ], "source": [ "#imports\n", "import xarray as xr\n", @@ -73,7 +667,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 2, "id": "96564acb-6375-4e7f-a9a0-69a318d5c28a", "metadata": { "tags": [] @@ -170,10 +764,74 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 3, "id": "70b795dd-84c8-4b8c-8418-eef390510dfd", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Granules found: 2\n", + "Opening 1 granules, approx size: 3.5 GB\n", + "using endpoint: https://data.lpdaac.earthdatacloud.nasa.gov/s3credentials\n" + ] + }, + { + "data": { + "application/vnd.jupyter.widget-view+json": { + "model_id": "2778936f1666460aa7fc97383e7e89c9", + "version_major": 2, + "version_minor": 0 + }, + "text/plain": [ + "QUEUEING TASKS | : 0%| | 0/3 [00:00,\n", + " ,\n", + " ]" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "results = earthaccess.search_data(\n", " short_name='EMITL2ARFL',\n", @@ -195,10 +853,514 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "a73eface-28a5-4fca-899f-0116d321b94f", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset> Size: 2GB\n",
+       "Dimensions:      (downtrack: 1280, crosstrack: 1242, bands: 285)\n",
+       "Dimensions without coordinates: downtrack, crosstrack, bands\n",
+       "Data variables:\n",
+       "    reflectance  (downtrack, crosstrack, bands) float32 2GB dask.array<chunksize=(538, 522, 119), meta=np.ndarray>\n",
+       "Attributes: (12/38)\n",
+       "    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0\n",
+       "    summary:                           The Earth Surface Mineral Dust Source ...\n",
+       "    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...\n",
+       "    Conventions:                       CF-1.63\n",
+       "    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...\n",
+       "    instrument:                        EMIT\n",
+       "    ...                                ...\n",
+       "    southernmost_latitude:             -34.15500797254596\n",
+       "    spatialResolution:                 0.000542232520256367\n",
+       "    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...\n",
+       "    geotransform:                      [ 1.84708746e+01  5.42232520e-04 -0.00...\n",
+       "    day_night_flag:                    Day\n",
+       "    title:                             EMIT L2A Estimated Surface Reflectance...
" + ], + "text/plain": [ + " Size: 2GB\n", + "Dimensions: (downtrack: 1280, crosstrack: 1242, bands: 285)\n", + "Dimensions without coordinates: downtrack, crosstrack, bands\n", + "Data variables:\n", + " reflectance (downtrack, crosstrack, bands) float32 2GB dask.array\n", + "Attributes: (12/38)\n", + " ncei_template_version: NCEI_NetCDF_Swath_Template_v2.0\n", + " summary: The Earth Surface Mineral Dust Source ...\n", + " keywords: Imaging Spectroscopy, minerals, EMIT, ...\n", + " Conventions: CF-1.63\n", + " sensor: EMIT (Earth Surface Mineral Dust Sourc...\n", + " instrument: EMIT\n", + " ... ...\n", + " southernmost_latitude: -34.15500797254596\n", + " spatialResolution: 0.000542232520256367\n", + " spatial_ref: GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHER...\n", + " geotransform: [ 1.84708746e+01 5.42232520e-04 -0.00...\n", + " day_night_flag: Day\n", + " title: EMIT L2A Estimated Surface Reflectance..." + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "xr.open_dataset(file_handlers[0].f,engine='h5netcdf',chunks='auto')" ] @@ -214,9 +1376,24 @@ ] }, { - "cell_type": "raw", - "id": "49b67151-bb5c-4bdc-a0e8-89c18d50ddda", + "cell_type": "code", + "execution_count": 5, + "id": "97b766f8-34ee-46d5-9b14-2a5fd648d985", "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Granules found: 2\n", + " Getting 1 granules, approx download size: 3.5 GB\n", + "Accessing cloud dataset using dataset endpoint credentials: https://data.lpdaac.earthdatacloud.nasa.gov/s3credentials\n", + "Downloaded: data/downloads/EMIT_L2A_RFL_001_20230119T114247_2301907_005.nc\n", + "Downloaded: data/downloads/EMIT_L2A_RFLUNCERT_001_20230119T114247_2301907_005.nc\n", + "Downloaded: data/downloads/EMIT_L2A_MASK_001_20230119T114247_2301907_005.nc\n" + ] + } + ], "source": [ "#get the files we want\n", "results = earthaccess.search_data(\n", @@ -230,9 +1407,515 @@ ] }, { - "cell_type": "raw", - "id": "74964b05-ebbd-47a8-ac5e-624c7add01a7", + "cell_type": "code", + "execution_count": 6, + "id": "9a5f0156-330a-45cc-8483-af2c946a205d", "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset> Size: 2GB\n",
+       "Dimensions:      (downtrack: 1280, crosstrack: 1242, bands: 285)\n",
+       "Dimensions without coordinates: downtrack, crosstrack, bands\n",
+       "Data variables:\n",
+       "    reflectance  (downtrack, crosstrack, bands) float32 2GB dask.array<chunksize=(538, 522, 119), meta=np.ndarray>\n",
+       "Attributes: (12/38)\n",
+       "    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0\n",
+       "    summary:                           The Earth Surface Mineral Dust Source ...\n",
+       "    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...\n",
+       "    Conventions:                       CF-1.63\n",
+       "    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...\n",
+       "    instrument:                        EMIT\n",
+       "    ...                                ...\n",
+       "    southernmost_latitude:             -34.15500797254596\n",
+       "    spatialResolution:                 0.000542232520256367\n",
+       "    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...\n",
+       "    geotransform:                      [ 1.84708746e+01  5.42232520e-04 -0.00...\n",
+       "    day_night_flag:                    Day\n",
+       "    title:                             EMIT L2A Estimated Surface Reflectance...
" + ], + "text/plain": [ + " Size: 2GB\n", + "Dimensions: (downtrack: 1280, crosstrack: 1242, bands: 285)\n", + "Dimensions without coordinates: downtrack, crosstrack, bands\n", + "Data variables:\n", + " reflectance (downtrack, crosstrack, bands) float32 2GB dask.array\n", + "Attributes: (12/38)\n", + " ncei_template_version: NCEI_NetCDF_Swath_Template_v2.0\n", + " summary: The Earth Surface Mineral Dust Source ...\n", + " keywords: Imaging Spectroscopy, minerals, EMIT, ...\n", + " Conventions: CF-1.63\n", + " sensor: EMIT (Earth Surface Mineral Dust Sourc...\n", + " instrument: EMIT\n", + " ... ...\n", + " southernmost_latitude: -34.15500797254596\n", + " spatialResolution: 0.000542232520256367\n", + " spatial_ref: GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHER...\n", + " geotransform: [ 1.84708746e+01 5.42232520e-04 -0.00...\n", + " day_night_flag: Day\n", + " title: EMIT L2A Estimated Surface Reflectance..." + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# Open dataset with xarray\n", "fp = 'data/downloads/EMIT_L2A_RFL_001_20230119T114247_2301907_005.nc'\n", @@ -253,12 +1936,20 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 7, "id": "d52e6825-5f13-4531-9bb2-d2dcffe0d765", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Flags used: ['Aggregate Flag']\n" + ] + } + ], "source": [ "flags=[7]\n", "mask = emit_tools.quality_mask(file_handlers[2].f,flags)" @@ -279,12 +1970,516 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 8, "id": "82145bc0-fa23-47fb-9583-dc14ded063bf", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset> Size: 5GB\n",
+       "Dimensions:           (latitude: 1901, longitude: 2346, wavelengths: 285)\n",
+       "Coordinates:\n",
+       "  * wavelengths       (wavelengths) float32 1kB 381.0 388.4 ... 2.493e+03\n",
+       "    fwhm              (wavelengths) float32 1kB ...\n",
+       "    good_wavelengths  (wavelengths) float32 1kB ...\n",
+       "  * latitude          (latitude) float64 15kB -33.12 -33.13 ... -34.15 -34.15\n",
+       "  * longitude         (longitude) float64 19kB 18.47 18.47 18.47 ... 19.74 19.74\n",
+       "    elev              (latitude, longitude) float32 18MB -9.999e+03 ... -9.99...\n",
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+       "Data variables:\n",
+       "    reflectance       (latitude, longitude, wavelengths) float32 5GB -9.999e+...\n",
+       "Attributes: (12/40)\n",
+       "    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0\n",
+       "    summary:                           The Earth Surface Mineral Dust Source ...\n",
+       "    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...\n",
+       "    Conventions:                       CF-1.63\n",
+       "    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...\n",
+       "    instrument:                        EMIT\n",
+       "    ...                                ...\n",
+       "    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...\n",
+       "    geotransform:                      [ 1.84708746e+01  5.42232520e-04 -0.00...\n",
+       "    day_night_flag:                    Day\n",
+       "    title:                             EMIT L2A Estimated Surface Reflectance...\n",
+       "    granule_id:                        EMIT_L2A_RFL_001_20230119T114247_23019...\n",
+       "    Orthorectified:                    True
" + ], + "text/plain": [ + " Size: 5GB\n", + "Dimensions: (latitude: 1901, longitude: 2346, wavelengths: 285)\n", + "Coordinates:\n", + " * wavelengths (wavelengths) float32 1kB 381.0 388.4 ... 2.493e+03\n", + " fwhm (wavelengths) float32 1kB ...\n", + " good_wavelengths (wavelengths) float32 1kB ...\n", + " * latitude (latitude) float64 15kB -33.12 -33.13 ... -34.15 -34.15\n", + " * longitude (longitude) float64 19kB 18.47 18.47 18.47 ... 19.74 19.74\n", + " elev (latitude, longitude) float32 18MB -9.999e+03 ... -9.99...\n", + " spatial_ref int64 8B 0\n", + "Data variables:\n", + " reflectance (latitude, longitude, wavelengths) float32 5GB -9.999e+...\n", + "Attributes: (12/40)\n", + " ncei_template_version: NCEI_NetCDF_Swath_Template_v2.0\n", + " summary: The Earth Surface Mineral Dust Source ...\n", + " keywords: Imaging Spectroscopy, minerals, EMIT, ...\n", + " Conventions: CF-1.63\n", + " sensor: EMIT (Earth Surface Mineral Dust Sourc...\n", + " instrument: EMIT\n", + " ... ...\n", + " spatial_ref: GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHER...\n", + " geotransform: [ 1.84708746e+01 5.42232520e-04 -0.00...\n", + " day_night_flag: Day\n", + " title: EMIT L2A Estimated Surface Reflectance...\n", + " granule_id: EMIT_L2A_RFL_001_20230119T114247_23019...\n", + " Orthorectified: True" + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "ds = emit_tools.emit_xarray(file_handlers[0].f, ortho=True, qmask=mask)\n", "ds" @@ -300,7 +2495,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 9, "id": "e6728d81-0c70-490e-9eff-e7461dc5975e", "metadata": {}, "outputs": [], @@ -318,7 +2513,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 10, "id": "5efff08c-f7dd-41ff-883e-c5ac0e27dd68", "metadata": { "tags": [] @@ -339,7 +2534,7 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 11, "id": "0ed2f601-4f1d-41b4-92b9-5bf56c228299", "metadata": { "tags": [] @@ -362,12 +2557,101 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 12, "id": "290d1299-3e46-4573-9f4e-6d2b598ff623", "metadata": { "tags": [] }, - "outputs": [], + "outputs": [ + { + "data": {}, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.holoviews_exec.v0+json": "", + "text/html": [ + "
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Make this Notebook Trusted to load map: File -> Trust Notebook
" + ], + "text/plain": [ + "" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "#load points\n", "gdf = gpd.read_file(\"/shared/users/gmoncrieff/emit_unmix.gpkg\")\n", @@ -464,13 +3201,696 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 16, "id": "ec5a64bc-b69a-44d8-ba5c-c4cf66506066", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.Dataset> Size: 113kB\n",
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+       "    fwhm              (wavelengths) float32 976B 8.415 8.415 ... 8.807 8.809\n",
+       "    good_wavelengths  (wavelengths) float32 976B 1.0 1.0 1.0 1.0 ... 1.0 1.0 1.0\n",
+       "    elev              (geometry) float32 444B dask.array<chunksize=(111,), meta=np.ndarray>\n",
+       "    spatial_ref       int64 8B 0\n",
+       "  * geometry          (geometry) object 888B POINT (19.2194 -33.9549) ... POI...\n",
+       "    index             (geometry) int64 888B 0 1 2 3 4 5 ... 106 107 108 109 110\n",
+       "Data variables:\n",
+       "    reflectance       (geometry, wavelengths) float32 108kB dask.array<chunksize=(111, 10), meta=np.ndarray>\n",
+       "Indexes:\n",
+       "    geometry  GeometryIndex (crs=EPSG:4326)\n",
+       "Attributes: (12/40)\n",
+       "    ncei_template_version:             NCEI_NetCDF_Swath_Template_v2.0\n",
+       "    summary:                           The Earth Surface Mineral Dust Source ...\n",
+       "    keywords:                          Imaging Spectroscopy, minerals, EMIT, ...\n",
+       "    Conventions:                       CF-1.63\n",
+       "    sensor:                            EMIT (Earth Surface Mineral Dust Sourc...\n",
+       "    instrument:                        EMIT\n",
+       "    ...                                ...\n",
+       "    spatial_ref:                       GEOGCS["WGS 84",DATUM["WGS_1984",SPHER...\n",
+       "    geotransform:                      [ 1.84708746e+01  5.42232520e-04 -0.00...\n",
+       "    day_night_flag:                    Day\n",
+       "    title:                             EMIT L2A Estimated Surface Reflectance...\n",
+       "    granule_id:                        EMIT_L2A_RFL_001_20230119T114247_23019...\n",
+       "    Orthorectified:                    True
" + ], + "text/plain": [ + " Size: 113kB\n", + "Dimensions: (geometry: 111, wavelengths: 244)\n", + "Coordinates:\n", + " * wavelengths (wavelengths) float32 976B 381.0 388.4 ... 2.493e+03\n", + " fwhm (wavelengths) float32 976B 8.415 8.415 ... 8.807 8.809\n", + " good_wavelengths (wavelengths) float32 976B 1.0 1.0 1.0 1.0 ... 1.0 1.0 1.0\n", + " elev (geometry) float32 444B dask.array\n", + " spatial_ref int64 8B 0\n", + " * geometry (geometry) object 888B POINT (19.2194 -33.9549) ... POI...\n", + " index (geometry) int64 888B 0 1 2 3 4 5 ... 106 107 108 109 110\n", + "Data variables:\n", + " reflectance (geometry, wavelengths) float32 108kB dask.array\n", + "Indexes:\n", + " geometry GeometryIndex (crs=EPSG:4326)\n", + "Attributes: (12/40)\n", + " ncei_template_version: NCEI_NetCDF_Swath_Template_v2.0\n", + " summary: The Earth Surface Mineral Dust Source ...\n", + " keywords: Imaging Spectroscopy, minerals, EMIT, ...\n", + " Conventions: CF-1.63\n", + " sensor: EMIT (Earth Surface Mineral Dust Sourc...\n", + " instrument: EMIT\n", + " ... ...\n", + " spatial_ref: GEOGCS[\"WGS 84\",DATUM[\"WGS_1984\",SPHER...\n", + " geotransform: [ 1.84708746e+01 5.42232520e-04 -0.00...\n", + " day_night_flag: Day\n", + " title: EMIT L2A Estimated Surface Reflectance...\n", + " granule_id: EMIT_L2A_RFL_001_20230119T114247_23019...\n", + " Orthorectified: True" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "extracted = ds.xvec.extract_points(gdf['geometry'], x_coords=\"longitude\", y_coords=\"latitude\",index=True)\n", - "extracted\n" + "extracted" ] }, { @@ -483,10 +3903,167 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 17, "id": "ebdca302-8ad2-42b2-be35-dafcd66ad1b9", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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wavelengthsreflectancegeometry_xCategoryindex
0381.0055850.017709POINT (19.2194 -33.9549)PINE0
1388.4092100.018134POINT (19.2194 -33.9549)PINE0
2395.8158260.018555POINT (19.2194 -33.9549)PINE0
3403.2254030.018993POINT (19.2194 -33.9549)PINE0
4410.6380000.019613POINT (19.2194 -33.9549)PINE0
..................
270792463.3815920.044974POINT (19.38343349154113 -33.445019637266505)FYNBOS110
270802470.7678220.045954POINT (19.38343349154113 -33.445019637266505)FYNBOS110
270812478.1530760.044455POINT (19.38343349154113 -33.445019637266505)FYNBOS110
270822485.5385740.042368POINT (19.38343349154113 -33.445019637266505)FYNBOS110
270832492.9238280.041585POINT (19.38343349154113 -33.445019637266505)FYNBOS110
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27084 rows × 5 columns

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" + ], + "text/plain": [ + " wavelengths reflectance \\\n", + "0 381.005585 0.017709 \n", + "1 388.409210 0.018134 \n", + "2 395.815826 0.018555 \n", + "3 403.225403 0.018993 \n", + "4 410.638000 0.019613 \n", + "... ... ... \n", + "27079 2463.381592 0.044974 \n", + "27080 2470.767822 0.045954 \n", + "27081 2478.153076 0.044455 \n", + "27082 2485.538574 0.042368 \n", + "27083 2492.923828 0.041585 \n", + "\n", + " geometry_x Category index \n", + "0 POINT (19.2194 -33.9549) PINE 0 \n", + "1 POINT (19.2194 -33.9549) PINE 0 \n", + "2 POINT (19.2194 -33.9549) PINE 0 \n", + "3 POINT (19.2194 -33.9549) PINE 0 \n", + "4 POINT (19.2194 -33.9549) PINE 0 \n", + "... ... ... ... \n", + "27079 POINT (19.38343349154113 -33.445019637266505) FYNBOS 110 \n", + "27080 POINT (19.38343349154113 -33.445019637266505) FYNBOS 110 \n", + "27081 POINT (19.38343349154113 -33.445019637266505) FYNBOS 110 \n", + "27082 POINT (19.38343349154113 -33.445019637266505) FYNBOS 110 \n", + "27083 POINT (19.38343349154113 -33.445019637266505) FYNBOS 110 \n", + "\n", + "[27084 rows x 5 columns]" + ] + }, + "execution_count": 17, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "extracted = (extracted\n", " .to_dataframe() #turn into a dataframe\n", @@ -509,10 +4086,99 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 18, "id": "b6f82184-bfb5-43c9-9286-ce1bc0916e0a", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": {}, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/vnd.holoviews_exec.v0+json": "", + "text/html": [ + "
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\n", + "" + ], + "text/plain": [ + ":NdOverlay [index]\n", + " :Curve [wavelengths] (reflectance)" + ] + }, + "execution_count": 18, + "metadata": { + "application/vnd.holoviews_exec.v0+json": { + "id": "p1286" + } + }, + "output_type": "execute_result" + } + ], "source": [ "extracted_plot = extracted.query('Category == \"FYNBOS\"')\n", "extracted_plot.hvplot.line(y='reflectance',x='wavelengths',by='index',\n", diff --git a/book/tutorials/TIR_HyTES_ECOSTRESS/ECOSTRESS_concurrent.ipynb b/book/tutorials/TIR_HyTES_ECOSTRESS/ECOSTRESS_concurrent.ipynb index 6b8abdc..2b42186 100644 --- a/book/tutorials/TIR_HyTES_ECOSTRESS/ECOSTRESS_concurrent.ipynb +++ b/book/tutorials/TIR_HyTES_ECOSTRESS/ECOSTRESS_concurrent.ipynb @@ -55,10 +55,604 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 1, "id": "62b21a7d-c903-45e9-b83d-882657b9d4cc", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "application/javascript": [ + "(function(root) {\n", + " function now() {\n", + " return new Date();\n", + " }\n", + "\n", + " var force = true;\n", + " var py_version = '3.4.0'.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", + " 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", + " console.debug(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", + " return null;\n", + " }\n", + " if (js_urls.length === 0 && js_modules.length === 0 && Object.keys(js_exports).length === 0) {\n", + " run_callbacks();\n", + " return null;\n", + " }\n", + " if (!reloading) {\n", + " console.debug(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", + " }\n", + "\n", + " function on_load() {\n", + " root._bokeh_is_loading--;\n", + " if (root._bokeh_is_loading === 0) {\n", + " console.debug(\"Bokeh: all BokehJS libraries/stylesheets loaded\");\n", + " run_callbacks()\n", + " }\n", + " }\n", + " window._bokeh_on_load = on_load\n", + "\n", + " function on_error() {\n", + " console.error(\"failed to load \" + url);\n", + " }\n", + "\n", + " var skip = [];\n", + " if (window.requirejs) {\n", + " window.requirejs.config({'packages': {}, 'paths': {}, 'shim': {}});\n", + " root._bokeh_is_loading = css_urls.length + 0;\n", + " } else {\n", + " root._bokeh_is_loading = css_urls.length + js_urls.length + js_modules.length + Object.keys(js_exports).length;\n", + " }\n", + "\n", + " var existing_stylesheets = []\n", + " var links = document.getElementsByTagName('link')\n", + " for (var i = 0; i < links.length; i++) {\n", + " var link = links[i]\n", + " if (link.href != null) {\n", + "\texisting_stylesheets.push(link.href)\n", + " }\n", + " }\n", + " for (var i = 0; i < css_urls.length; i++) {\n", + " var url = css_urls[i];\n", + " if (existing_stylesheets.indexOf(url) !== -1) {\n", + "\ton_load()\n", + "\tcontinue;\n", + " }\n", + " const element = document.createElement(\"link\");\n", + " element.onload = on_load;\n", + " element.onerror = on_error;\n", + " element.rel = \"stylesheet\";\n", + " element.type = \"text/css\";\n", + " element.href = url;\n", + " console.debug(\"Bokeh: injecting link tag for BokehJS stylesheet: \", url);\n", + " document.body.appendChild(element);\n", + " } var existing_scripts = []\n", + " var scripts = document.getElementsByTagName('script')\n", + " for (var i = 0; i < scripts.length; i++) {\n", + " var script = scripts[i]\n", + " if (script.src != null) {\n", + "\texisting_scripts.push(script.src)\n", + " }\n", + " }\n", + " for (var i = 0; i < js_urls.length; i++) {\n", + " var url = js_urls[i];\n", + " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", + "\tif (!window.requirejs) {\n", + "\t on_load();\n", + "\t}\n", + "\tcontinue;\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", + " console.debug(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", + " document.head.appendChild(element);\n", + " }\n", + " for (var i = 0; i < js_modules.length; i++) {\n", + " var url = js_modules[i];\n", + " if (skip.indexOf(url) !== -1 || existing_scripts.indexOf(url) !== -1) {\n", + "\tif (!window.requirejs) {\n", + "\t on_load();\n", + "\t}\n", + "\tcontinue;\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", + " var url = js_exports[name];\n", + " if (skip.indexOf(url) >= 0 || root[name] != null) {\n", + "\tif (!window.requirejs) {\n", + "\t on_load();\n", + "\t}\n", + "\tcontinue;\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", + " var js_urls = [\"https://cdn.bokeh.org/bokeh/release/bokeh-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-gl-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-widgets-3.4.0.min.js\", \"https://cdn.bokeh.org/bokeh/release/bokeh-tables-3.4.0.min.js\", \"https://cdn.holoviz.org/panel/1.4.1/dist/panel.min.js\"];\n", + " var js_modules = [];\n", + " var js_exports = {};\n", + " var css_urls = [];\n", + " var inline_js = [ function(Bokeh) {\n", + " Bokeh.set_log_level(\"info\");\n", + " },\n", + "function(Bokeh) {} // ensure no trailing comma for IE\n", + " ];\n", + "\n", + " function run_inline_js() {\n", + " if ((root.Bokeh !== undefined) || (force === true)) {\n", + " for (var i = 0; i < inline_js.length; i++) {\n", + "\ttry {\n", + " inline_js[i].call(root, root.Bokeh);\n", + "\t} catch(e) {\n", + "\t if (!reloading) {\n", + "\t throw e;\n", + "\t }\n", + "\t}\n", + " }\n", + " // Cache old bokeh versions\n", + " if (Bokeh != undefined && !reloading) {\n", + "\tvar NewBokeh = root.Bokeh;\n", + "\tif (Bokeh.versions === undefined) {\n", + "\t Bokeh.versions = new Map();\n", + "\t}\n", + "\tif (NewBokeh.version !== Bokeh.version) {\n", + "\t Bokeh.versions.set(NewBokeh.version, NewBokeh)\n", + "\t}\n", + "\troot.Bokeh = Bokeh;\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", + " root._bokeh_is_initializing = false;\n", + " root._bokeh_onload_callbacks = undefined;\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", + " var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n", + " if (!reloading && !bokeh_loaded) {\n", + "\troot.Bokeh = undefined;\n", + " }\n", + " load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n", + "\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n", + "\trun_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));" + ], + "application/vnd.holoviews_load.v0+json": "(function(root) {\n function now() {\n return new Date();\n }\n\n var force = true;\n var py_version = '3.4.0'.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 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 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undefined)) {\n setTimeout(load_or_wait, 100);\n } else {\n root._bokeh_is_initializing = true\n root._bokeh_onload_callbacks = []\n var bokeh_loaded = Bokeh != null && (Bokeh.version === py_version || (Bokeh.versions !== undefined && Bokeh.versions.has(py_version)));\n if (!reloading && !bokeh_loaded) {\n\troot.Bokeh = undefined;\n }\n load_libs(css_urls, js_urls, js_modules, js_exports, function() {\n\tconsole.debug(\"Bokeh: BokehJS plotting callback run at\", now());\n\trun_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", + "\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", + " 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}\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", + "\n", + "var JS_MIME_TYPE = 'application/javascript';\n", + "var HTML_MIME_TYPE = 'text/html';\n", + "var EXEC_MIME_TYPE = 'application/vnd.holoviews_exec.v0+json';\n", + "var CLASS_NAME = 'output';\n", + "\n", + "/**\n", + " * Render data to the DOM node\n", + " */\n", + "function 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", + " 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< 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 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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" + }, + { + "data": { + "application/vnd.holoviews_exec.v0+json": "", + "text/html": [ + "
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Data: ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_water.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_cloud.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_view_zenith.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_height.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_QC.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST_err.tifECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_EmisWB.tif

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Size: 17.45 MB

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Cloud Hosted: True

\n", + "
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\n", + " " + ], + "text/plain": [ + "Collection: {'ShortName': 'ECO_L2T_LSTE', 'Version': '002'}\n", + "Spatial coverage: {'HorizontalSpatialDomain': {'Geometry': {'BoundingRectangles': [{'WestBoundingCoordinate': 17.737026086961954, 'EastBoundingCoordinate': 18.953671378813702, 'NorthBoundingCoordinate': -33.397079450234656, 'SouthBoundingCoordinate': -34.41143932610581}]}}}\n", + "Temporal coverage: {'RangeDateTime': {'BeginningDateTime': '2023-11-13T13:44:54.439Z', 'EndingDateTime': '2023-11-13T13:45:46.408Z'}}\n", + "Size(MB): 17.45\n", + "Data: ['https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_water.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_cloud.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_view_zenith.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_height.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_QC.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST_err.tif', 'https://data.lpdaac.earthdatacloud.nasa.gov/lp-prod-protected/ECO_L2T_LSTE.002/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_EmisWB.tif']" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# print one granule\n", "granules[4]" @@ -135,10 +788,44 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 4, "id": "0da52a3c-da6e-4ab8-bc0a-41d0f9da53a1", "metadata": {}, - "outputs": [], + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + " Getting 1 granules, approx download size: 0.02 GB\n", + "Accessing cloud dataset using dataset endpoint credentials: https://data.lpdaac.earthdatacloud.nasa.gov/s3credentials\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_water.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_cloud.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_view_zenith.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_height.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_QC.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST_err.tif\n", + "Downloaded: downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_EmisWB.tif\n" + ] + }, + { + "data": { + "text/plain": [ + "[PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_water.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_cloud.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_view_zenith.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_height.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_QC.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST_err.tif'),\n", + " PosixPath('downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_EmisWB.tif')]" + ] + }, + "execution_count": 4, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# earthaccess login\n", "earthaccess.login(strategy=\"interactive\", persist=True)\n", @@ -148,10 +835,21 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 5, "id": "0b6643ee-014b-4b2f-883a-9bdfc98f0112", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "'downloads/ECOv002_L2T_LSTE_30360_029_34HBH_20231113T134454_0712_02_LST.tif'" + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# finding LST file\n", "LST_f = glob(\"downloads/ECO*LST.tif\")[0]\n", @@ -160,10 +858,415 @@ }, { "cell_type": "code", - "execution_count": null, + "execution_count": 6, "id": "a3062a42-a604-4e88-9166-34a282755cf8", "metadata": {}, - "outputs": [], + "outputs": [ + { + "data": { + "text/html": [ + "
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<xarray.DataArray (y: 1568, x: 1568)> Size: 10MB\n",
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+       "Coordinates:\n",
+       "  * x            (x) float64 13kB 2e+05 2.001e+05 ... 3.096e+05 3.097e+05\n",
+       "  * y            (y) float64 13kB 6.3e+06 6.3e+06 6.3e+06 ... 6.19e+06 6.19e+06\n",
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