Fixed notebooks links that were broken due to my previous changes (#1162

) * Added the sensor name Oli Tirs to the end of the Landsat 9 product URLs to make it consistent * Changing case of 'Tools' in links to fix broken links * Fixing some miscellaneous broken links * Fixing one link (casing) * Fixing 3 links * Fixed a waterbodies link * Reverted data_tools source (.py) links back to relative links so that they will open in a tab in the Jupyter Notebook * Reverted another data tools Python link * Reverted some remaining links to be .py links * Fixed one Scalable machine learning relative link * Fixed several more links - 19 Dec --------- Co-authored-by: Benjamin Glitsos <[email protected]>
GeoscienceAustralia · Dec 19, 2023 · b911735 · b911735
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diff --git a/Beginners_guide/01_Jupyter_notebooks.ipynb b/Beginners_guide/01_Jupyter_notebooks.ipynb
@@ -208,7 +208,7 @@
     "\n",
     "To rename this notebook to something more useful, right-click on it in the file browser and select \"Rename\".\n",
     "\n",
-    "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](../../DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
+    "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](https://github.com/GeoscienceAustralia/dea-notebooks/blob/develop/DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
    ]
   },
   {

diff --git a/Beginners_guide/05_Plotting.ipynb b/Beginners_guide/05_Plotting.ipynb
@@ -33,7 +33,7 @@
    "source": [
     "## Description\n",
     "This introductory notebook demonstrates how to visualise DEA satellite data returned from running a datacube query.\n",
-    "The notebook demonstrates commonly used `xarray` plotting methods, as well as custom functions provided in the [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module.\n",
+    "The notebook demonstrates commonly used `xarray` plotting methods, as well as custom functions provided in the [dea_tools.plotting](../Tools/dea_tools/plotting.py) module.\n",
     "\n",
     "Topics covered in this notebook include:\n",
     "\n",
@@ -65,7 +65,7 @@
    "source": [
     "### Load packages\n",
     "The first step is to run `%matplotlib inline`, which ensures figures plot correctly in the Jupyter notebook.\n",
-    "Next, load the `datacube` package to enable loading data, and a selection of custom DEA functions from the [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module."
+    "Next, load the `datacube` package to enable loading data, and a selection of custom DEA functions from the [dea_tools.plotting](../Tools/dea_tools/plotting.py) module."
    ]
   },
   {
@@ -2763,7 +2763,7 @@
     "\n",
     "For advanced plotting and visualisation options, see:\n",
     "\n",
-    "* The [dea_tools.plotting](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.plotting/) module containing functions used for plotting and visualising DEA data.\n",
+    "* The [dea_tools.plotting](../Tools/dea_tools/temporal.py) module containing functions used for plotting and visualising DEA data.\n",
     "\n",
     "Once you have you have completed the beginner tutorials, join advanced users in exploring:\n",
     "\n",

diff --git a/DEA_notebooks_template.ipynb b/DEA_notebooks_template.ipynb
@@ -23,8 +23,8 @@
     "* Use the [PEP8 standard](https://www.python.org/dev/peps/pep-0008/) for code. To make sure all code in the notebook is consistent, you can use the `jupyterlab_code_formatter` tool: select each code cell, then click `Edit` and then one of the `Apply X Formatter` options (`YAPF` or `Black` are recommended). This will reformat the code in the cell to a consistent style.\n",
     "* For additional guidance, refer to the style conventions and layouts in approved `develop` branch notebooks. Examples include:\n",
     "    * [How_to_guides/Using_load_ard.ipynb](../How_to_guides/Using_load_ard.ipynb)\n",
-    "    * [Real_world_examples/Coastal_erosion.ipynb](./Real_world_examples/Coastal_erosion.ipynb)\n",
-    "    * [Tools/dea_tools/datahandling.py](./Tools/dea_tools/datahandling.py)\n",
+    "    * [Real_world_examples/Coastal_erosion.ipynb](../Real_world_examples/Coastal_erosion.ipynb)\n",
+    "    * [Tools/dea_tools/datahandling.py](../Tools/dea_tools/datahandling.py)\n",
     "* In the final notebook cell, include a set of relevant tags which are used to build the DEA User Guide's [Tag Index](https://docs.dea.ga.gov.au/genindex/). \n",
     "Use all lower-case (unless the tag is an acronym), separate words with spaces (unless it is the name of an imported module), and [re-use existing tags](https://github.com/GeoscienceAustralia/dea-notebooks/wiki/List-of-tags).\n",
     "Ensure the tags cell below is in `Raw` format, rather than `Markdown` or `Code`.\n",

diff --git a/DEA_products/DEA_Land_Cover.ipynb b/DEA_products/DEA_Land_Cover.ipynb
@@ -1367,7 +1367,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "In the following sections, we will plot data using the `plot_land_cover()` function. More details about the function can be found in [land_cover.py](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.landcover/)."
+    "In the following sections, we will plot data using the `plot_land_cover()` function. More details about the function can be found in [landcover.py](../Tools/dea_tools/landcover.py)."
    ]
   },
   {

diff --git a/DEA_products/DEA_Landsat_Surface_Reflectance.ipynb b/DEA_products/DEA_Landsat_Surface_Reflectance.ipynb
@@ -24,9 +24,9 @@
     "\n",
     "It contains three sub-products that provide corrections or attribution information:\n",
     "\n",
-    "* Surface Reflectance NBAR ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-9))\n",
-    "* Surface Reflectance NBART ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-9))\n",
-    "* Surface Reflectance Observation Attributes (OA) ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-9))\n",
+    "* Surface Reflectance NBAR ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbar-landsat-9-oli-tirs/))\n",
+    "* Surface Reflectance NBART ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-nbart-landsat-9-oli-tirs/))\n",
+    "* Surface Reflectance Observation Attributes (OA) ([Landsat 5 TM](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-5-tm), [Landsat 7 ETM+](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-7-etm), [Landsat 8 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-8-oli-tirs), [Landsat 9 OLI-TIRS](https://docs.dea.ga.gov.au/data/product/dea-surface-reflectance-oa-landsat-9-oli-tirs/))\n",
     "\n",
     "The resolution is a 30 m grid based on the USGS Landsat Collection 1 archive.\n",
     "\n",

diff --git a/DEA_products/DEA_Wetlands_Insight_Tool.ipynb b/DEA_products/DEA_Wetlands_Insight_Tool.ipynb
@@ -69,9 +69,9 @@
     "Licencing information is provided at the bottom of this notebook, and requires attribution.** \n",
     "\n",
     "## Related products\n",
-    "* [DEA Fractional Cover (Landsat)](https://docs.dea.ga.gov.au/notebooks/DEA_products/DEA_Fractional_Cover.ipynb)\n",
+    "* [DEA Fractional Cover (Landsat)](../DEA_products/DEA_Fractional_Cover.ipynb)\n",
     "* [DEA Tasseled Cap Indices Percentiles Calendar Year (Landsat)](https://docs.dea.ga.gov.au/data/product/dea-wetness-percentiles-landsat)\n",
-    "* [DEA Water Observations (Landsat)](https://docs.dea.ga.gov.au/notebooks/DEA_products/DEA_Water_Observations/)"
+    "* [DEA Water Observations (Landsat)](../DEA_products/DEA_Water_Observations.ipynb)"
    ]
   },
   {
@@ -436,7 +436,7 @@
     "Loading 8 time steps\n",
     "```\n",
     "\n",
-    "For further information on the functions used here, go to the [function documentation](https://github.com/GeoscienceAustralia/dea-notebooks/blob/b13f020f8a41c30bc1bb4120ce492098a25a2bfa/Tools/dea_tools/datahandling.py)."
+    "For further information on the functions used here, go to the [function documentation](../Tools/dea_tools/datahandling.py)."
    ]
   },
   {
@@ -2126,7 +2126,7 @@
     "\n",
     "1. Mask pixels not in the polygon\n",
     "\n",
-    "2. Use the [Water Observations bit flags](https://github.com/GeoscienceAustralia/dea-notebooks/blob/develop/DEA_products/DEA_Water_Observations.ipynb) to mask noncontiguous data, low solar incidence angle, cloud, and water out of the `wet` category. We distinguish `open water` from `wet` as mutually exclusive categories. \n",
+    "2. Use the [Water Observations bit flags](../DEA_products/DEA_Water_Observations.ipynb) to mask noncontiguous data, low solar incidence angle, cloud, and water out of the `wet` category. We distinguish `open water` from `wet` as mutually exclusive categories. \n",
     "\n",
     "## Thresholding\n",
     "\n",

diff --git a/How_to_guides/Detecting_seasonality.ipynb b/How_to_guides/Detecting_seasonality.ipynb
@@ -9,7 +9,7 @@
     "* **[Sign up to the DEA Sandbox](https://app.sandbox.dea.ga.gov.au/)** to run this notebook interactively from a browser\n",
     "* **Compatibility:** Notebook currently compatible with both the `NCI` and `DEA Sandbox` environments\n",
     "* **Products used:** \n",
-    "[DEA Waterbodies](https://docs.dea.ga.gov.au/data/product/waterboards)\n"
+    "[DEA Waterbodies](https://docs.dea.ga.gov.au/data/product/dea-waterbodies-landsat)\n"
    ]
   },
   {

diff --git a/How_to_guides/Downloading_data_with_STAC.ipynb b/How_to_guides/Downloading_data_with_STAC.ipynb
@@ -17,7 +17,7 @@
    "metadata": {},
    "source": [
     "## Background\n",
-    "Digital Earth Australia (DEA) stores a range of data products on [Amazon Web Service's Simple Cloud Storage (S3)](https://docs.dea.ga.gov.au/guides/setup/aws/data_and_metadata/) with free public access. These products can be browsed on the interactive [DEA Sandbox Explorer](https://explorer.sandbox.dea.ga.gov.au/products). To make it easier to find data in the DEA archive, the DEA Sandbox Explorer also provides a [SpatioTemporal Asset Catalog (STAC)](https://stacspec.org/) endpoint for listing or searching metadata (https://explorer.sandbox.dea.ga.gov.au/stac/).\n",
+    "Digital Earth Australia (DEA) stores a range of data products on [Amazon Web Service's Simple Cloud Storage (S3)](https://docs.dea.ga.gov.au/guides/setup/AWS/data_and_metadata/) with free public access. These products can be browsed on the interactive [DEA Sandbox Explorer](https://explorer.sandbox.dea.ga.gov.au/products). To make it easier to find data in the DEA archive, the DEA Sandbox Explorer also provides a [SpatioTemporal Asset Catalog (STAC)](https://stacspec.org/) endpoint for listing or searching metadata (https://explorer.sandbox.dea.ga.gov.au/stac/).\n",
     "\n",
     "STAC is a recently developed specification that provides a common language to describe geospatial information so it can more easily be indexed and discovered. \n",
     "DEA's STAC metadata can be used to quickly identify all available data for a given product, location or time period. \n",

diff --git a/How_to_guides/Generating_composites.ipynb b/How_to_guides/Generating_composites.ipynb
@@ -1131,7 +1131,7 @@
    "source": [
     "To get an image at a certain time, often there is missing data, due to clouds and other masking.  We can fill in these gaps by using data from surrounding times.\n",
     "\n",
-    "To generate these images, we can use the custom functions `first`, `last` and `nearest` from the [dea_datahandling](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.datahandling/) script.\n",
+    "To generate these images, we can use the custom functions `first`, `last` and `nearest` from the [datahandling](../Tools/dea_tools/datahandling.py) script.\n",
     "\n",
     "You can also use the in-built `.first()` and `.last()` methods when doing `groupby` and `resample` as described above. They are described in the [xarray documentation](http://xarray.pydata.org/en/stable/groupby.html#first-and-last) on grouped data."
    ]

diff --git a/How_to_guides/Generating_geomedian_composites.ipynb b/How_to_guides/Generating_geomedian_composites.ipynb
@@ -148,7 +148,7 @@
    "source": [
     "## Load Landsat 8 from the datacube\n",
     "\n",
-    "Here we are loading in a timeseries of cloud-masked Landsat 8 satellite images through the datacube API using the [load_ard](https://github.com/GeoscienceAustralia/dea-notebooks/blob/develop/How_to_guides/Using_load_ard.ipynb) function. \n",
+    "Here we are loading in a timeseries of cloud-masked Landsat 8 satellite images through the datacube API using the [load_ard](../How_to_guides/Using_load_ard.ipynb) function. \n",
     "This will provide us with some data to work with. To limit computation and memory this example uses only three optical bands (red, green, blue)."
    ]
   },

diff --git a/How_to_guides/Image_segmentation.ipynb b/How_to_guides/Image_segmentation.ipynb
@@ -110,7 +110,7 @@
    "source": [
     "## Load Sentinel 2 data from the datacube\n",
     "\n",
-    "Here we are loading in a timeseries of `Sentinel 2` satellite images through the datacube API using the [load_ard](https://github.com/GeoscienceAustralia/dea-notebooks/blob/develop/How_to_guides/Using_load_ard.ipynb) function. This will provide us with some data to work with."
+    "Here we are loading in a timeseries of `Sentinel 2` satellite images through the datacube API using the [load_ard](../How_to_guides/Using_load_ard.ipynb) function. This will provide us with some data to work with."
    ]
   },
   {

diff --git a/How_to_guides/Land_cover_animated_plots.ipynb b/How_to_guides/Land_cover_animated_plots.ipynb
@@ -926,7 +926,7 @@
     "## Modifying `lc_animation()`\n",
     "`lc_animation()` contains many optional parameters allowing customisation of the appearance of the land cover animations. \n",
     "Below are examples of how some of them operate. \n",
-    "For the full details of the parameters please refer to the [land_cover.py](https://docs.dea.ga.gov.au/notebooks/tools/gen/dea_tools.landcover/) file.\n"
+    "For the full details of the parameters please refer to the [landcover.py](../Tools/dea_tools/landcover.py) file.\n"
    ]
   },
   {

diff --git a/How_to_guides/Machine_learning_with_ODC.ipynb b/How_to_guides/Machine_learning_with_ODC.ipynb
@@ -23,7 +23,7 @@
    "source": [
     "## Description\n",
     "\n",
-    "This notebook demonstrates a potential workflow using functions from the [dea_tools.classification](../Tools/gen/dea_tools.classification.ipynb) script to implement a supervised learning landcover classifier within the [ODC (Open Data Cube)](https://www.opendatacube.org.ipynb) framework. \n",
+    "This notebook demonstrates a potential workflow using functions from the [dea_tools.classification](../Tools/dea_tools/classification.py) script to implement a supervised learning landcover classifier within the [ODC (Open Data Cube)](https://www.opendatacube.org.ipynb) framework. \n",
     "\n",
     "For larger model training and prediction implementations this notebook can be adapted into a Python file and run in a distributed fashion.\n",
     "\n",
@@ -694,7 +694,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Once the data has been loaded, we can classify it using DEA [predict_xr](../Tools/gen/dea_tools.classification.ipynb) function:"
+    "Once the data has been loaded, we can classify it using DEA [predict_xr](../Tools/dea_tools/classification.py) function:"
    ]
   },
   {
-Original file line number
+Diff line change
@@ Expand Up / @@ -208,7 +208,7 @@ @@
         "\n",
         "To rename this notebook to something more useful, right-click on it in the file browser and select \"Rename\".\n",
         "\n",
-        "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](../../DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
+        "> **Note:** The `dea-notebooks` repository provides a **template notebook** containing a consistent structure and style that is recommended for all DEA Jupyter notebooks. To use this template rather than start a notebook from scratch, click [this link to open the \"DEA_notebooks_template.ipynb\"](https://github.com/GeoscienceAustralia/dea-notebooks/blob/develop/DEA_notebooks_template.ipynb) notebook, then click \"File\" and \"Save Notebook As...\" to create a copy of the template in your desired location."
        ]
       },
       {
@@ Expand Down @@