diff --git a/book/_toc.yml b/book/_toc.yml index bb65dbf..859e8ae 100644 --- a/book/_toc.yml +++ b/book/_toc.yml @@ -9,6 +9,10 @@ parts: chapters: - file: tutorials/NotebookBasics/NotebookBasics.ipynb - file: tutorials/PRISM/PRISM_explore.ipynb + - file: tutorials/ANG_FieldData/ConcurrentEMIT.ipynb + - file: tutorials/ANG_FieldData/Field_AVNG_Explore.ipynb + - file: tutorials/ANG_FieldData/plotspectra_2csv_3x3.ipynb + - file: tutorials/LVIS/lvis.ipynb # - caption: Tutorials - Day 2 numbered: false diff --git a/book/tutorials/ANG_FieldData/ConcurrentEMIT.ipynb b/book/tutorials/ANG_FieldData/ConcurrentEMIT.ipynb index 5d1d4f6..746cdcb 100644 --- a/book/tutorials/ANG_FieldData/ConcurrentEMIT.ipynb +++ b/book/tutorials/ANG_FieldData/ConcurrentEMIT.ipynb @@ -13,7 +13,7 @@ "id": "74791378-5713-42cf-a30d-71b16cc79b05", "metadata": {}, "source": [ - "##
BioSCape Data Skills Workshop: From the Field to the Image
\n", + "## BioSCape Data Skills Workshop: From the Field to the Image\n", "![Bioscape](images/121229-87.png)\n", "\n", "[**BioSCape**](https://www.bioscape.io/), the Biodiversity Survey of the Cape, is NASA’s first biodiversity-focused airborne and field campaign that was conducted in South Africa in 2023. BioSCape’s primary objective is to study the structure, function, and composition of the region’s ecosystems, and how and why they are changing. \n", @@ -30,9 +30,7 @@ "- In-person contributors: Anabelle Cardoso, Erin Hestir, Phil Townsend, Henry Frye, Glenn Moncrieff, Jasper Slingsby, Michele Thornton, Rupesh Shrestha\n", "- Virtual contributors: Kerry Cawse-Nicholson, Nico Stork, Kyle Kovach\n", "\n", - "**Audience:** This training is primarily intended for government natural resource management agency representatives and field technicians in South Africa, as well as local academics and students, especially those connected to the BioSCape Team. \n", - "\n", - "----" + "**Audience:** This training is primarily intended for government natural resource management agency representatives and field technicians in South Africa, as well as local academics and students, especially those connected to the BioSCape Team. " ] }, { @@ -41,7 +39,6 @@ "metadata": {}, "source": [ "## Overview \n", - "----\n", "This tutorial will demonstrate how to discover EMIT Reflectance data that is available from NASA Earthdata that are concurrent with the temporal range of the BioSCape Campaign. \n", "\n", "### Learning Objectives\n", @@ -64,491 +61,16 @@ "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", - " 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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", + "application/vnd.holoviews_load.v0+json": "" }, "metadata": {}, "output_type": "display_data" diff --git a/book/tutorials/ANG_FieldData/Field_AVNG_Explore.ipynb b/book/tutorials/ANG_FieldData/Field_AVNG_Explore.ipynb index f122421..dd3548b 100644 --- a/book/tutorials/ANG_FieldData/Field_AVNG_Explore.ipynb +++ b/book/tutorials/ANG_FieldData/Field_AVNG_Explore.ipynb @@ -6,7 +6,7 @@ "metadata": {}, "source": [ "# Exploring, Visualizing, and Plotting BioSCape Field and AVIRIS-NG Data\n", - "##
BioSCape Data Skills Workshop: From the Field to the Image
\n", + "## BioSCape Data Skills Workshop: From the Field to the Image\n", "![Bioscape](images/121229-87.png)\n", "\n", "[**BioSCape**](https://www.bioscape.io/), the Biodiversity Survey of the Cape, is NASA’s first biodiversity-focused airborne and field campaign that was conducted in South Africa in 2023. BioSCape’s primary objective is to study the structure, function, and composition of the region’s ecosystems, and how and why they are changing. \n", @@ -23,9 +23,7 @@ "- In-person contributors: Anabelle Cardoso, Erin Hestir, Phil Townsend, Henry Frye, Glenn Moncrieff, Jasper Slingsby, Michele Thornton, Rupesh Shrestha\n", "- Virtual contributors: Kerry Cawse-Nicholson, Nico Stork, Kyle Kovach\n", "\n", - "**Audience:** This training is primarily intended for government natural resource management agency representatives and field technicians in South Africa, as well as local academics and students, especially those connected to the BioSCape Team. \n", - "\n", - "----" + "**Audience:** This training is primarily intended for government natural resource management agency representatives and field technicians in South Africa, as well as local academics and students, especially those connected to the BioSCape Team. " ] }, { @@ -34,7 +32,6 @@ "metadata": {}, "source": [ "## Overview \n", - "----\n", "This tutorial will explore BioSCape Campaign `airborne data` currently available on the BioSCape SMCE S3 storage as well as preliminary `vegetation plot data`. Participants will learn to access cloud-based storage and explore files. Analysis will occur with combinations of data available on S3 storage as well as vector plot and polygon data brought to the Hub. Demonstrations will provide methods to locate AVIRIS-NG scenes associated with vegetation plot data. Vegetation spectral profiles will be extracted and graphed from projected plot locations. \n", "\n", "### Learning Objectives\n", @@ -127,8 +124,8 @@ "id": "bdb845f1-f771-49f5-ae94-63d09a042942", "metadata": {}, "source": [ - "#### Let's look deeper into each airborne folder on the SMCE\n", - "#### **AVIRIS-Next Generation (AVNG)**\n", + "### Let's look deeper into each airborne folder on the SMCE\n", + "### **AVIRIS-Next Generation (AVNG)**\n", "- We'll spend a little more time looking into the AVIRIS-NG files as these data are a focus of this Notebook\n" ] }, @@ -183,7 +180,7 @@ "id": "d450f15c-e075-493d-b6a7-bf88612dc94a", "metadata": {}, "source": [ - "#### File **Naming Conventions** provide information about each flight line, scene, and data type.\n", + "### File **Naming Conventions** provide information about each flight line, scene, and data type.\n", "\n", "- **`L1B`** are AVIRIS-NG Surface Radiance\n", "- **`L2A`** are AVIRIS-NG Surface Reflectance\n", @@ -202,7 +199,7 @@ "id": "b90843fb-4cad-4ba9-9143-08b41a773a52", "metadata": {}, "source": [ - "#### **Portable Remote Imaging Spectrometer (PRISM)**" + "### **Portable Remote Imaging Spectrometer (PRISM)**" ] }, { @@ -249,7 +246,7 @@ "id": "972597ae-21f2-4685-b6ba-cef78cd95dcf", "metadata": {}, "source": [ - "#### **Land, Vegetation, and Ice Sensor (LVIS)**" + "### **Land, Vegetation, and Ice Sensor (LVIS)**" ] }, { @@ -295,7 +292,7 @@ "id": "6c55337c-7ce8-4aeb-a326-21521bddda3d", "metadata": {}, "source": [ - "#### **Hyperspectral Thermal Emissions Spectrometer (HyTES)**\n", + "### **Hyperspectral Thermal Emissions Spectrometer (HyTES)**\n", "- BioSCape HyTES data is currently available from [**NASA JPL HyTES**](https://hytes.jpl.nasa.gov/order!) distribution site" ] }, @@ -304,7 +301,6 @@ "id": "b4855ac8-198d-4a14-abd8-e621ea351971", "metadata": {}, "source": [ - "----\n", "## Examine Field Data Sites: Vegetation Site Data " ] }, @@ -320,7 +316,7 @@ "\n", "On the BioSCape SMCE Hub, you can easily upload those files into your working area. Simply click the `Upload Files` button at the top of the folder/file listing panel. You can also drag and drop folders into the file listing panel. \n", "\n", - "
\n", + "![upload_button](images/upload_button.PNG)\n", "\n", "For the purpose of this Notebook, we're using a polygon shape file of Vegetation Polygons as well as point locations of the Vegetation Polygon Center for a few specific polygons in the Cape Peninsula.\n", "\n", @@ -548,7 +544,8 @@ "\n", "#### A geoJSON of the AVIRIS-NG Flight Line's Scenes are available from the JPL BioSCape Data Portal \n", "- This file has been exported and is available in the BioSCape hub.\n", - "
" + "\n", + "![AVIRISFlightLines](images/AVNG_flightlinedownload.PNG)" ] }, { @@ -732,7 +729,6 @@ "id": "a0228866-faf2-4e07-8882-bf66cbb43ea5", "metadata": {}, "source": [ - "----\n", "## Examine BioSCape AVIRIS-NG Files that have Vegetation Plot of Interest" ] }, @@ -741,7 +737,7 @@ "id": "a6828913-1e50-4e76-b978-35e8dcc7b347", "metadata": {}, "source": [ - "#### The ang20231109t131923_019 scene is a segment of a larger flight line, ang20231109t131923" + "### The ang20231109t131923_019 scene is a segment of a larger flight line, ang20231109t131923" ] }, { @@ -806,7 +802,7 @@ "id": "197ae49b-e0a8-456c-b5ea-b54fa910a8b1", "metadata": {}, "source": [ - "#### Examine the Quicklook file with GDAL" + "### Examine the Quicklook file with GDAL" ] }, { @@ -864,7 +860,7 @@ "id": "143a7aea-32cd-4f83-9015-3f7846ed53aa", "metadata": {}, "source": [ - "#### Using GDAL to read the AVIRIS-NG raster file as a numerical array\n", + "### Using GDAL to read the AVIRIS-NG raster file as a numerical array\n", "- convert an existing **`Gdal Dataset`** or a Band into a numpy array with the `ReadAsArray()` function" ] }, @@ -1056,7 +1052,6 @@ "id": "6c80f448-6530-4c28-8a56-350d5b0d45f6", "metadata": {}, "source": [ - "----\n", "## Plot a Spectral Profile from a Point of Interest" ] }, diff --git a/book/tutorials/ANG_FieldData/plotspectra_2csv_3x3.ipynb b/book/tutorials/ANG_FieldData/plotspectra_2csv_3x3.ipynb index 7cb1231..10cf817 100644 --- a/book/tutorials/ANG_FieldData/plotspectra_2csv_3x3.ipynb +++ b/book/tutorials/ANG_FieldData/plotspectra_2csv_3x3.ipynb @@ -13,7 +13,7 @@ "id": "de2586e7-8467-4d15-b457-c2618ac2715b", "metadata": {}, "source": [ - "##
BioSCape Data Skills Workshop: From the Field to the Image
\n", + "## BioSCape Data Skills Workshop: From the Field to the Image\n", "![Bioscape](images/121229-87.png)\n", "\n", "[**BioSCape**](https://www.bioscape.io/), the Biodiversity Survey of the Cape, is NASA’s first biodiversity-focused airborne and field campaign that was conducted in South Africa in 2023. BioSCape’s primary objective is to study the structure, function, and composition of the region’s ecosystems, and how and why they are changing. \n", @@ -39,7 +39,6 @@ "metadata": {}, "source": [ "## Overview \n", - "----\n", "This tutorial will explore BioSCape Campaign discover, plot, and export to csv AVIRIS-NG spectral data for vegetation plot locations. In addition, for each plot location, a 3x3 pixel block of spectral data will be extracted and graphed by mean and standard deviation. \n", "\n", "### Learning Objectives\n", diff --git a/book/tutorials/LVIS/lvis.ipynb b/book/tutorials/LVIS/lvis.ipynb index 7de11f1..9f83f3b 100644 --- a/book/tutorials/LVIS/lvis.ipynb +++ b/book/tutorials/LVIS/lvis.ipynb @@ -7,7 +7,7 @@ "source": [ "# Exploring and Visualizing BioSCape LVIS Data\n", "## BioSCape Data Skills Workshop: From the Field to the Image\n", - "![Bioscape](images/121229-87.png)\n", + "![Bioscape](../PRISM/images/121229-87.png)\n", "\n", "[**BioSCape**](https://www.bioscape.io/), the Biodiversity Survey of the Cape, is NASA’s first biodiversity-focused airborne and field campaign that was conducted in South Africa in 2023. BioSCape’s primary objective is to study the structure, function, and composition of the region’s ecosystems, and how and why they are changing. \n", "\n",