Fixed links in markdowns

Former-commit-id: ee79bafaaad816791f302415cd6d59930547119b

Author: vwvbrand

readme.md

@@ -2,18 +2,25 @@
 
 Data4Land tool is developed to enrich various land-use/land-cover (LULC) spatial data with data from another sources to increase the consistency and reliability of LULC datasets for multiple purposes. This software currently includes four separate Jupyter Notebooks:
 
-1. **[Access to historical data from the World Database on Protected Areas (WDPA) and harmonization](1_pas.ipynb)**
+1. **[Access to historical data from the World Database on Protected Areas (WDPA) and harmonization](src/1_pas.ipynb)**
+
 Available only through the authorised credentials (token), as it uses the special API.
-2. **[Access and harmonisation of historical vector data on land-use/land-cover (LULC) - Open Street Map (OSM) data ](2_vector.ipynb)**
+
+2. **[Access and harmonisation of historical vector data on land-use/land-cover (LULC) - Open Street Map (OSM) data ](src/2_vector.ipynb)**
+
 Available without authorised credentials, uses open-access API.
-3. **[Enrichment of land-use/land-cover (LULC) data](3_enrichment.ipynb)**
+
+3. **[Enrichment of land-use/land-cover (LULC) data](src/3_enrichment.ipynb)**
+
 Rectification of commonly produced land-use/land-cover (LULC) raster data with auxiliary data from 1st, 2nd Notebooks or user-defined data.
-4. **[Impedance calculation ('edge effect' of biodiversity stressors)](4_impedance.ipynb)**
+
+4. **[Impedance calculation ('edge effect' of biodiversity stressors)](src/4_impedance.ipynb)**
+
 Calculates 'landscape impedance' datasets based on user-defined biodiversity stressors. This block is useful for researchers to proceed with habitat connectivity studies.
 
 Detailed documentation on each nested workflow is given at the beginnings of Jupyter Notebooks and includes descriptions of all input and output datasets.
-Sample input dataset is extracted from [ESA Sentinel-2](https://collections.sentinel-hub.com/impact-observatory-lulc-map/) remote sensing spatial datasets and located [here](data/input/).
-All configuration to execute Jupyter Notebooks is pre-defined for the sample dataset in the [configuration YAML file](src/config.yaml): paths, filenames, API parameters, user-defined numerical parameters.
+Sample input dataset is extracted from [ESA Sentinel-2](https://collections.sentinel-hub.com/impact-observatory-lulc-map/) remote sensing spatial datasets and located [here](src/data/input/).
+All configuration to execute Jupyter Notebooks is pre-defined for the sample dataset in the [configuration YAML file](src/config/config.yaml): paths, filenames, API parameters, user-defined numerical parameters.
 Data flow within the Data4Land tool can be also explored on the overarching diagram:![diagram](visualisation/workflow.png).
 
 #### Further development
@@ -22,7 +29,7 @@ This tool is mostly completed, but a few improvements are planned to be done:
 - **Design GUI tool (command-line interface) as an addition to separate Notebooks/scripts.**
 - Test [ohsome API](https://docs.ohsome.org/ohsome-api/v1/) again to confirm that not all attributes of OSM features can be fetched and justify the usage of Overpass Turbo API instead of ohsome API or switch to ohsome API if it provides a quicker and more reliable access. See [issue](https://github.com/GIScience/ohsome-api/issues/332).
 - Extend the implementation of [VRT](https://gdal.org/en/latest/drivers/raster/vrt.html) file format to save resource.
-- Implement ingestion of other spatial features which may act opposed to biodiversity stressors, for example, [small woody features](https://land.copernicus.eu/en/products/high-resolution-layer-small-woody-features.)
+- Implement ingestion of other spatial features which may act opposed to biodiversity stressors, for example, [small woody features](https://land.copernicus.eu/en/products/high-resolution-layer-small-woody-features).
 - Implement iterations over multiple LULC files (by year and location) and multiple OSM requests (iterating over the combination of filename-yearname).
 - For use case studies: revisit Catalonian government data and decide on its usage, whether it can support OSM data or not.
 

src/1_pas.ipynb

@@ -35,7 +35,7 @@
    "source": [
     "#### 1. Fetching data through Protected Planet API\n",
     "\n",
-    "Spatial data on protected areas in GeoJSON and GeoPackage formats for countries needed (on our case, Spain, France and Andorra) are obtained through WDPA API using a personal access token and [official docimentation](https://api.protectedplanet.net/documentation). Most meaningful attributes have been chosen (IDs, designation status, IUCN category, year of establishment etc.)"
+    "Spatial data on protected areas in GeoJSON and GeoPackage formats for countries needed (on our case, Spain, France and Andorra) are obtained through Protected Planet API using a personal access token and [official docimentation](https://api.protectedplanet.net/documentation). Most meaningful attributes have been chosen (IDs, designation status, IUCN category, year of establishment etc.)"
    ]
   },
   {
@@ -799,7 +799,7 @@
    "source": [
     "#### 3. Raster recalculation\n",
     "\n",
-    "LULC [enriched](/raster_sum_loop.sh) through the raster calculator (currently, external shell script):\n",
+    "LULC [enriched](raster_sum_loop.sh) through the raster calculator (currently, external shell script):\n",
     "1. Rearranging no data values as they must be considered as 0 to run raster calcualtions.\n",
     "2. To sum initial LULC raster and protected areas (according to the timestamp).\n",
     "3. Writing the new updated LULC map with the doubled amount of LULC codes for each timestamp (loop based on year matching in filenames).\n",
@@ -878,7 +878,7 @@
    "metadata": {},
    "source": [
     "#### 4. Updating landscape impedance\n",
-    "Impedance is reclassified by [CSV table](/reclassification.csv) and compressed (through LZW compression, not Cloud Optimised Geotiff standard to avoid any further issues in processing). Landscape impedance is required by Miramon ICT and Graphab tools both.\n",
+    "Impedance is reclassified by [CSV table](data/input/impedance/lulc_descr_esa.csv) and compressed (through LZW compression, not Cloud Optimised Geotiff standard to avoid any further issues in processing). Landscape impedance is required by Miramon ICT and Graphab tools both.\n",
     "\n",
     "Let's import another set of libraries needed and define the class to update the impedance."
    ]

src/3_enrichment.ipynb

@@ -29,7 +29,7 @@
     "The following types of input data are exploited:\n",
     "1. Raster land-use/land-cover (LULC) data, GeoTIFF format. Cloud Optimised GeoTiff (COG) is preferable (COG with LZW compression is used to optimise storaging data). ***MANDATORY***\n",
     "2. Vector data (GPKG) to enrich and refine LULC data (currently, roads, railways, water bodies and waterways are processed) derived either from OSM or user-specified data. ***MANDATORY***\n",
-    "3. Tabular (CSV) data mapping LULC types to their specifications: (1) whether concrete LULC type should be refined by vector data or not (***MANDATORY***) and (2) whether negative \"edge effect\" of concrete LULC type should be considered, for instance, roads affect suitability of habitats alongside roads (***OPTIONAL***). This reclassification table is being used in the [first block](1_protected_areas/1_preprocessing_pas.ipynb) of the Data4Land tool."
+    "3. Tabular (CSV) data mapping LULC types to their specifications: (1) whether concrete LULC type should be refined by vector data or not (***MANDATORY***) and (2) whether negative \"edge effect\" of concrete LULC type should be considered, for instance, roads affect suitability of habitats alongside roads (***OPTIONAL***). This reclassification table is being used in the [first block](1_pas.ipynb) of the Data4Land tool."
    ]
   },
   {

src/4_impedance.ipynb

@@ -24,7 +24,7 @@
     "- LULC raster dataset and its derivatives from the previous Notebook - stressors (GeoTIFF)\n",
     "- OSM raster datasets with rasterised spatial features (GeoTIFF)\n",
     "- configuration of edge effect from user: which LULC categories cause edge effect (0...\\*,) which OSM spatial features can cause edge effect (0...\\*), defined in [CSV](data/input/impedance/lulc_descr_esa.csv)\n",
-    "- parameters of edge effect from stressors [(YAML configuration file)](config_impedance.yaml)\n",
+    "- parameters of edge effect from stressors [(YAML configuration file)](config/config_impedance.yaml)\n",
     "\n",
     "**OUTPUT**\n",
     "- enriched impedance raster dataset with applied edge effect (GeoTIFF)\n",
@@ -423,7 +423,7 @@
    "metadata": {},
    "source": [
     "### Populating impedance configuration with stressors from OSM\n",
-    "Another portion of stressors comes from another source - rasterised vector features (being produced in the [3rd Notebook](3_preprocessing.ipynb)), recommended to be fetched from Open Street Map. For the sample dataset, two types of stressors are being used - railways and roads. Moreover, it is implemented to define a different parameters for subtypes of vector features, in this case, for roads - it is justified by the fact that roads vary by width and traffic frequency."
+    "Another portion of stressors comes from another source - rasterised vector features (being produced in the [3rd Notebook](3_enrichment.ipynb)), recommended to be fetched from Open Street Map. For the sample dataset, two types of stressors are being used - railways and roads. Moreover, it is implemented to define a different parameters for subtypes of vector features, in this case, for roads - it is justified by the fact that roads vary by width and traffic frequency."
    ]
   },
   {
@@ -565,7 +565,7 @@
    "source": [
     "# Impedance Configuration Processor\n",
     "\n",
-    "This is a wrapper class to populate the [config_impedance.yaml](config_impedance.yaml) file with the lulc and osm stressors. This configuration is a temporary file that will be used for impedance recalculation. "
+    "This is a wrapper class to populate the [config_impedance.yaml](config/config_impedance.yaml) file with the lulc and osm stressors. This configuration is a temporary file that will be used for impedance recalculation. "
    ]
   },
   {

src/config/config.yaml

@@ -31,7 +31,7 @@ output_dir: 'data/output'
 
 ## 1st NOTEBOOK
 # Protected Planet API
-token: "968cef6f0c37b925225fb60ac8deaca6" # replace with your token
+token: "your_token" # replace with your token
 marine: false # 'false' by default to bring marine protected areas or not. warning: being transformed into 'False' in URI, but recognised as a boolean value. Does not cause issues.
 api_countries: true # 'true' by default. Brings codes of countries intersecting with input raster dataset. Otherwise, user must specify list of countries as ISO3 codes.
 # Parameters to update the impedance datasets