Merge pull request #163 from sarahcd/develop

updates to installation, launch, environmental data requests

README.md

@@ -2,13 +2,13 @@
 
 ECODATA-Prepare is a set of Python-based apps to access and process remote sensing and other environmental data products and prepare them for further use along with animal movement data. ECODATA-Prepare is designed to be along with the ECODATA-Animate tool to create movies of animal movement data, and can also be used to create input to resource, habitat and step selection models. Development is supported by MathWorks® and the NASA Earth Science Division, Ecological Forecasting Program, as part of the [Room to Roam: Y2Y Wildlife Movements](https://ceg.osu.edu/Y2Y_Room2Roam) project.
 
-Check out the documentation!
-[Apps documentation](http://ecodata-apps.readthedocs.io/)
-[Package documentation](https://ecodata.readthedocs.io/)
+Check out the documentation!  
+* [Apps documentation](http://ecodata-apps.readthedocs.io/)  
+* [Package documentation](https://ecodata.readthedocs.io/)
 
 **Note**: ECODATA-Prepare is in the early stages of development, and any feedback is welcome! If you have any suggestions or feature requests, enounter any bugs, or come across places where the documentation is unclear, please [submit a GitHub issue](https://github.com/jemissik/ecodata/issues).
 
 
 ## Example data
 
-A test data bundle is available [here](https://drive.google.com/drive/folders/1eAqSKblWpM5kqqEByf6YaiRWywZFMKvJ?usp=sharing)
+A test data bundle is available [here](https://drive.google.com/drive/folders/1eAqSKblWpM5kqqEByf6YaiRWywZFMKvJ?usp=sharing)

docs/apps/environmental_data.md

@@ -14,10 +14,13 @@ You can use a .geojson file from the [Tracks Explorer app](user_guide/tracks_exp
 5. In the Extract Area Sample page, first upload the .geojson file you created in the Tracks Explorer. Alternatively, you can draw a polygon on the page or upload another .geojson or .shp file. It will display a preview of the area for which data will be provided.
 6. Select a date range. You can choose calendar dates for the start and end of the period, or select "Is Date Recurring?" to select a specific range of dates across years.
 7. Select the data layers you want. Type a product name (e.g., "MYD10A2") or description (e.g., "snow") and it will display a list summarizing relevant products. To review all options, available products are listed at <https://appeears.earthdatacloud.nasa.gov/products>. Also see the searchable catalog of many of these products at <https://lpdaac.usgs.gov/product_search/?status=Operational>. Once you have selected a product(s) from the list, click the "+" button on each desired layer. The layers will appear in the "Selected Layers" box to the right.
-8. In "Output options" at the bottom of the page, select "NetCDF-4" as the file format and "Geographic" as the projection.
-9. Select "Submit". Your submission will be added to a queue and you will receive emails from [email protected] confirming the submission and notifying you when the data are ready for download. The time needed to complete the request likely depends on the volume of data requested and the number of other requests their service has recently received. In our tests so far they have come through within a few hours.
-10. When your data are ready for download, click the "Download" link in the email you received from [email protected].
-11. The Appeears website will open in a new tab (log into your account if prompted) and you will see a list of files available to download. Supporting files are listed first, however you will need to download the resulting NetCDF (.nc) file for the next step in the ECODATA-Prepare app (Gridded Data Explorer).
+8. In "Output options" at the bottom of the page, select "NetCDF-4" as the file format and "Geographic" as the projection, like this:
+
+![appeears_output_options](./images/appeears_output_options.png)
+
+9. Select "Submit". Your submission will be added to a queue and you will receive emails from [email protected] confirming the submission and notifying you when the data are ready for download. Keep in mind that notifications could end up in your spam box. The time needed to complete the request likely depends on the volume of data requested and the number of other requests their service has recently received. In our tests so far they have come through within a few hours.
+10. When your data are ready for download, you will receive an email from [email protected]. Click the "Download" link in the email.
+11. The AppEEARS website will open in a new tab (log into your account if prompted) and you will see a list of files available to download. Supporting files are listed first, however you will need to download the resulting NetCDF (.nc) file for the next step in the ECODATA-Prepare app (Gridded Data Explorer).
 12. Check the box to the left of the file name and select Download > Download Files at the right. The downloaded file will appear in your Downloads folder, which you can then move to a local folder. We also recommend downloading at least the README.md file under Supporting files. This will document details of your request and results that you may need to return to later, including data quality information and how to cite your results.
 
 ![appeears_download](./images/appeears_download.png)
@@ -29,7 +32,13 @@ You can use a .geojson file from the [Tracks Explorer app](user_guide/tracks_exp
 
 To request data:
 1. Go to the [data request page](https://cds.climate.copernicus.eu/cdsapp#!/dataset/reanalysis-era5-single-levels?tab=form).
-2. In the "Variable" section, select the variables you wish to download.
+2. In the "Variable" section, select the variables you wish to download, for example as shown here:
+
+![ecmwf_variables](./images/ecmwf_variables.png)
+
 3. Select the times of interest.
-4. Under "Geographical area", select "Sub-region extraction" and enter the bounding box coordinates for the area of interest (max and min longitude and latitude)
-5. Under "Format", select "NetCDF (experimental)"
+4. Under "Geographical area", select "Sub-region extraction" and enter the bounding box coordinates for the area of interest (max and min longitude and latitude).
+5. Under "Format", select "NetCDF (experimental)".
+6. If you have entered all required information and are logged in, you will have the option to "Submit Form" and send the request. An example of selections and options for steps 4-6 is shown here:
+
+![ecmwf_area_format](./images/ecmwf_area_format.png)

docs/apps/index.md

@@ -2,7 +2,7 @@
 
 ## Overview
 
-ECODATA-Prepare is a set of Python-based apps to access and process remote sensing and other environmental data products and prepare them for further use along with animal movement data. ECODATA-Prepare is designed to be along with the [ECODATA-Animate](https://ecodata-animate.readthedocs.io/en/latest/) tool to create movies of animal movement data, and can also be used to create input to resource, habitat and step selection models. Development is supported by MathWorks® and the NASA Earth Science Division, Ecological Forecasting Program, as part of [Room to Roam: Y2Y Wildlife Movements](https://ceg.osu.edu/Y2Y_Room2Roam) project.
+ECODATA-Prepare is a set of Python-based apps to access and process remote sensing and other environmental data products and prepare them for further use along with animal movement data. ECODATA-Prepare is designed to be used along with the [ECODATA-Animate](https://ecodata-animate.readthedocs.io/en/latest/) tool to create customized movies of animal movement data, and can also be used to prepare input to resource, habitat and step selection models. Development is supported by MathWorks® and the NASA Earth Science Division, Ecological Forecasting Program, as part of [Room to Roam: Y2Y Wildlife Movements](https://ceg.osu.edu/Y2Y_Room2Roam) project.
 
 Within ECODATA-Prepare,
 
@@ -14,16 +14,12 @@ Within ECODATA-Prepare,
 
 - The [**Movie Maker App**](user_guide/movie_maker) produces an animation file out of a stack of static maps which were produced by the ECODATA-Animate program.
 
-We recommend the following workflow (you can skip any steps you don't need):
-1. Use the [Tracks Explorer App](user_guide/tracks_explorer) to create a .geojson file that defines the area of interest based on your tracking data.
-2. Use this file to [request environmental data from NASA AppEEARS](request-nasa-data) to use in subsequent animations or analysis.
-3. Use the [Gridded Data Explorer App](user_guide/gridded_data_explorer) to review and further process the environmental data received from NASA AppEEARS.
-4. Use the [Subsetter App](user_guide/subsetter) to extract relevant features from very large datasets (for example, global vector GIS data products for features like roads, water bodies or protected areas) to use in subsequent animations or analysis.
-5. Use [ECODATA-Animate](https://ecodata-animate.readthedocs.io/en/latest/) to combine your tracking data, environmental data, subsetted vector layers, and other information, configure viewing options, and create a set of images to use as frames for an animation or for further exploration and analysis.
-6. Use the [Movie Maker App](user_guide/movie_maker) to create an animation from the output of ECODATA-Animate.
+[Read our overview](https://www.movebank.org/cms/movebank-content/ecodata#how_to_use_ecodata) of how to use Movebank, MoveApps, ECODATA-Animate and ECODATA-Prepare to discover and process tracking data, remote sensing data, shapefiles and other layers to create custom visualizations and input for ecological analysis. To try the software before working with your own data, see [our example](https://www.movebank.org/cms/movebank-content/ecodata#example_ecodata_animation) based on publicly-available data sources.
 
 For help, [submit a GitHub issue](https://ecodata-apps.readthedocs.io/en/latest/support.html) or contact [email protected].
 
+![ecodata_workflow](https://www.movebank.org/cms/serve/images/ecodata_workflow.png)
+
 ## Python package
 
 The functions underlying the ECODATA-Prepare apps can also be used directly as a python package (i.e. without the GUI inferface). The package documentation is [here](https://ecodata.readthedocs.io).