From 13bc9b34c2054aab9d0c09fe888914cd0dcc56ea Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 13:58:14 +0100 Subject: [PATCH 01/15] Update index.rst Proofreading complete. --- docs/source/cli/index.rst | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/docs/source/cli/index.rst b/docs/source/cli/index.rst index 711d9462ca..2f6cca5149 100644 --- a/docs/source/cli/index.rst +++ b/docs/source/cli/index.rst @@ -1,22 +1,23 @@ -SEPAL environment -================= +CLI utilities and coding tools +============================== +*Use command-line interface (CLI) utilities and coding tools in SEPAL* CLI tools --------- -The SEPAL platform includes a variety of useful command-line interface (CLI) utilities to help resolve specific problems such as: +The SEPAL platform includes a variety of useful command-line interface (CLI) utilities to help resolve specific problems, such as: -- Geospatial Data Abstraction Library (GDAL) -- Google Drive (Drive) -- Google Earth Engine (GEE) -- GuidosToolbox Workbench (GWB) -- Open Foris Geospatial Toolkit (OFGT) -- Orfeo Toolbox (OTB) +- **Geospatial Data Abstraction Library (GDAL)** +- **Google Drive (Drive)** +- **Google Earth Engine (GEE)** +- **GuidosToolbox Workbench (GWB)** +- **Open Foris Geospatial Toolkit (OFGT)** +- **Orfeo Toolbox (OTB)** -These tools can be called directly from the terminal or any programming language sending commands to the kernel, including R and Python (installed by default on any SEPAL account). +These tools can be called directly from the terminal or via any programming language sending commands to the kernel, including R and Python (installed by default on any SEPAL account). .. thumbnail:: ../_images/cli/index/cli_gdalinfo.gif - :title: How to use the gdalinfo command in a SEPAL terminal + :title: How to use the **gdalinfo** command in the SEPAL terminal .. note:: @@ -38,25 +39,24 @@ These tools can be called directly from the terminal or any programming language nohup gdalinfo example.tif - All the console outputs will be redirected to a :code:`nohup.out` in your home directory, but the execution will be running in the background. Thus, you will be able to safely close the terminal or even the browser window without killing your process (for more information about :code:`nohup`, see `here `__. - + All console outputs will be redirected to a :code:`nohup.out` in your home directory, but the execution will be running in the background. Thus, you will be able to safely close the terminal or even the browser window without killing your process (for more information about :code:`nohup`, see `this article `__. Coding tools ------------ -In the **App** section, you'll find three coding tools at the top of the list: +In the **Apps** section, there are three coding tools at the top of the list: - JupyterLab - JupyterNotebook - RStudio .. thumbnail:: ../_images/cli/index/code_editor.png - :title: The three code editor in the SEPAL environment + :title: The three code editors in the SEPAL environment They will allow the user to code wokflows in any of the available languages using the coresponding environment in SEPAL. These environments are fully customizable (select the :code:`Python` or :code:`R` section to know more). .. thumbnail:: ../_images/cli/index/jupyter_example.png - :title: Example of rasterio code running in SEPAL JupyterLab (code extracted from rasterio documentation: https://rasterio.readthedocs.io/en/latest/topics/plotting.html) + :title: Example of **rasterio** code running in SEPAL JupyterLab (code extracted from **rasterio** documentation: https://rasterio.readthedocs.io/en/latest/topics/plotting.html) .. toctree:: :hidden: From 6e2d5f60f6db4265666521d7c1bdbb2e0a48c01c Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 14:14:46 +0100 Subject: [PATCH 02/15] Update gdal.rst Proofreading complete. --- docs/source/cli/gdal.rst | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/source/cli/gdal.rst b/docs/source/cli/gdal.rst index 8730f21033..5d3217d756 100644 --- a/docs/source/cli/gdal.rst +++ b/docs/source/cli/gdal.rst @@ -1,7 +1,13 @@ -Geospatial Data Abstraction Library -=================================== +GDAL +==== -GDAL is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. As a library, it presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. The `News `__ page describes the latest release. +Geospatial Data Abstraction Library (GDAL) is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. + +As a library, GDAL presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. + +It also comes with a variety of useful command-line utilities for data translation and processing. + +The `News `__ page describes the latest release. .. note:: @@ -28,7 +34,7 @@ Raster programmes $ rgb2pct.py # Convert a 24bit RGB image to 8bit paletted. $ pct2rgb.py # Convert an 8bit paletted image to 24bit RGB. $ gdalattachpct.py # Attach a color table to a raster file from an input file. - $ gdal_merge.py # Mosaicks a set of images. + $ gdal_merge.py # Mosaics a set of images. $ gdal2tiles.py # Generates directory with TMS tiles, KMLs and simple web viewers. $ gdal2xyz.py # Translates a raster file into xyz format. $ gdal_rasterize # Burns vector geometries into a raster. @@ -76,5 +82,5 @@ Geographic network programmes .. code-block:: bash - $ gnmmanage # Manages networks - $ gnmanalyse # Analyses networks + $ gnmmanage # Manages networks. + $ gnmanalyse # Analyses networks. From f9299174d03e88bee2e1d0006f573b49dfe2ea4e Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 14:21:26 +0100 Subject: [PATCH 03/15] Update gdal.rst Further proofing. --- docs/source/cli/gdal.rst | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/docs/source/cli/gdal.rst b/docs/source/cli/gdal.rst index 5d3217d756..cf51538bed 100644 --- a/docs/source/cli/gdal.rst +++ b/docs/source/cli/gdal.rst @@ -1,13 +1,11 @@ GDAL ==== -Geospatial Data Abstraction Library (GDAL) is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. +**Geospatial Data Abstraction Library (GDAL)** is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. -As a library, GDAL presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. +As a library, **GDAL** presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. -It also comes with a variety of useful command-line utilities for data translation and processing. - -The `News `__ page describes the latest release. +For information on the newest release of **GDAL**, see `News `__. .. note:: @@ -16,7 +14,7 @@ The `News `__ page descr Available commands ------------------ -The complete documentation of GDAL commands can be found on the `GDAL website `__. +The complete documentation of **GDAL** commands can be found on the `GDAL website `__. Raster programmes ^^^^^^^^^^^^^^^^^ From 248db6b66c7d5f20e3febb46f0cbcd446c641032 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 14:29:04 +0100 Subject: [PATCH 04/15] Update gdrive.rst Proofreading complete. --- docs/source/cli/gdrive.rst | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/source/cli/gdrive.rst b/docs/source/cli/gdrive.rst index cd7cd71547..f243d04744 100644 --- a/docs/source/cli/gdrive.rst +++ b/docs/source/cli/gdrive.rst @@ -1,12 +1,12 @@ -Google Drive -============ +Drive +===== -The **Drive** CLI is a utility that allows managing a Google Drive account from the SEPAL console (for more information, see the Readme file directly in the GitHub repository https://github.com/odeke-em/drive). +The **Google Drive (Drive)** CLI is a utility that allows managing a Google Drive account from the SEPAL console (for more information, see `the Readme file in the GitHub repository `__. Usage ----- -Initialize drive connection +Initialize Drive connection ^^^^^^^^^^^^^^^^^^^^^^^^^^^ Before running any of the **Drive** commands, start a session by running the following line: @@ -15,7 +15,7 @@ Before running any of the **Drive** commands, start a session by running the fol $ drive init -Copy the URL that is displayed in the terminal and paste it into your browser. Log in to your Google account and "trust the connection" by selecting the "allow" button. An authorization code will be displayed; copy and paste it into the SEPAL terminal. You are now ready to use the :code:`Drive` CLI tool. +Copy the URL that is displayed in the terminal and paste it into your browser. Log in to your Google account and "trust the connection" by selecting the **Allow** button. An authorization code will be displayed; copy and paste it into the SEPAL terminal. You are now ready to use the :code:`Drive` CLI tool. .. note:: @@ -37,7 +37,7 @@ You can upload files from your SEPAL environment by using the :code:`Push` comma Download files -------------- -To download files, use the :code:`Pull` command. This command will create files that don't exist locally but do remotely. +To download files, use the :code:`Pull` command, which will create files that don't exist locally (but do remotely). .. code-block:: bash From 1c620b10f2a932516ed16f6db33905a89bc7b4b9 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:05:29 +0100 Subject: [PATCH 05/15] Update gee.rst Proofreading complete. --- docs/source/cli/gee.rst | 38 ++++++++++++++++++++++---------------- 1 file changed, 22 insertions(+), 16 deletions(-) diff --git a/docs/source/cli/gee.rst b/docs/source/cli/gee.rst index ccb8231c6c..626df52b61 100644 --- a/docs/source/cli/gee.rst +++ b/docs/source/cli/gee.rst @@ -1,19 +1,21 @@ -Google Earth Engine -=================== +GEE +=== -The **earthengine** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line. It is installed automatically when you install the Python API. To check whether the tool is installed and functioning correctly, enter the following in a command line: +The **Google Earth Engine (GEE)** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line. + +The tool is installed automatically when you install the Python API. To check whether it is installed and functioning correctly, enter the following in a command line: .. code-block:: console $ earthengine -If the tool is properly installed, it will print out a short summary of available commands. To get help on a specific command, use: +If the tool is properly installed, it will display a short summary of available commands. To get help on a specific command, use: .. code-block:: console $ earthengine command -h -When you first install the Python API, you will need to login using the :code:`Authenticate` command described below. +When you first install the Python API, you will need to log in using the :code:`Authenticate` command, as described below. Available commands ------------------ @@ -40,19 +42,23 @@ More information on the available command can be found on the `Google API websit $ upload_manifest # Uploads an image to GEE using the given manifest file. $ upload_table_manifest # Uploads a table to GEE using the given manifest file. -Use Google Earth Engine in the Jupyter interface ------------------------------------------------- +Use GEE in the Jupyter interface +-------------------------------- + +We highly suggest working directly from the Python interface of GEE, as Python has been extended by the community (gee_tools, geemap, ipygee, sepal_ui, etc.) and is more user-friendly. + +It's also the best way to prototype a script before using it in a SEPAL application, as the translation from Python to Javascript is not always straightforward. -We highly suggest to work directly from the Python interface of Google Earth Engine as the Pythonhas been extended by the community (gee_tools, geemap, ipygee, sepal_ui etc.) and is more user-friendly. -It's also the best way to prototype a script before using it in a SEPAL application as the translation from Python to Javascript is not always straightforward. +The main advantages of the **GEE code editor** are: -The main advantages of the GEE code editor are: - the access to a live map - the value inspector -SEPAL and Jupyter lab can help you bring this to the next level by providing both tools in a Python notebook, allowing you to also access all the Python geospatil tools created by the Eart obseervation community. +SEPAL and JupyterLab can help you bring this to the next level by providing both tools in a Python notebook, allowing you to also access all Python geospatial tools created by the Earth observation community. -First open a JupyterLab instance and start a notebook. In the first cell create a map and place it the sidecar by running the following code: +First, open a JupyterLab instance and start a notebook. + +In the first cell, create a map and place it the sidecar by running the following code: .. code-block:: python @@ -67,15 +73,15 @@ First open a JupyterLab instance and start a notebook. In the first cell create .. thumbnail:: ../_images/cli/gee/create_a_sidecar.png :title: Some code that will be run in the sidecar -As displayed in the previous image, the list of available sidecars is displayed on the right side of the frame. You can create as many sidecars as you want and display any widget in it. We chose to use the sepal_ui mappping widget as it's including key features such as: +As displayed in the previous image, the list of available sidecars is displayed on the right side of the frame. You can create as many sidecars as you want and display any widget in it. We chose to use the **sepal_ui mappping** widget as it includes key features, such as: + - GEE full compatibility - an extended layer manager - a value inspector -From now the map will be displayed in a sidecar next to thenotebook. The map is running live so in any cell you can add extra layers to it. It's more powerful than the Code editor map as you don't need to run all your cells again to get the map updated. +The map will be displayed in a sidecar next to the notebook. It is running live, so you can add extra layers to it in any cell. Also, it is more powerful than the **Code editor map** as you don't need to run all your cells again to update the map. .. thumbnail:: ../_images/cli/gee/sidecar_with_data.png :title: The map displayed in the sidecar -Now you are all set to create your own GEE script. You can use the GEE Python API documentation to get started. - +Now you are all set to create your own **GEE script** – you can use the **GEE Python API documentation** to get started. From b3dc92b99838f8e0d801de96a4468c7afcb026f0 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:11:11 +0100 Subject: [PATCH 06/15] Update gwb.rst Proofreading complete --- docs/source/cli/gwb.rst | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/docs/source/cli/gwb.rst b/docs/source/cli/gwb.rst index 27117952b2..4922ce09a5 100644 --- a/docs/source/cli/gwb.rst +++ b/docs/source/cli/gwb.rst @@ -1,16 +1,18 @@ -GuidosToolbox Workbench -======================= +GWB +=== -The GuidosToolbox Workbench (**GWB**) is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB `_ or `GTB `_). Citation reference: `GuidosToolbox Workbench: Spatial analysis of raster maps for ecological applications `_. +**GuidosToolbox Workbench (GWB)** is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB `_ or `GTB `_). + +Citation reference: `GuidosToolbox Workbench: Spatial analysis of raster maps for ecological applications `_. .. note:: - The current version available on SEPAL is 1.9.0 + The current version available in SEPAL is 1.9.0 Available commands ------------------ -The complete documentation of GWB commands can be found in the `GWB manual `__ +The complete documentation of GWB commands can be found in the `GWB manual `__. .. code-block:: console From bb857ce7a6c8f7a67b85e69309c8e593856d4fa0 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:23:10 +0100 Subject: [PATCH 07/15] Update ofgt.rst Proofreading complete. --- docs/source/cli/ofgt.rst | 26 +++++++++++++++----------- 1 file changed, 15 insertions(+), 11 deletions(-) diff --git a/docs/source/cli/ofgt.rst b/docs/source/cli/ofgt.rst index e2bc68a4bd..7e158e1372 100644 --- a/docs/source/cli/ofgt.rst +++ b/docs/source/cli/ofgt.rst @@ -1,9 +1,13 @@ -Open Foris Geospatial Toolkit -============================= +OFGT +==== -The Open Foris Geospatial Toolkit (OFGT) is a collection of prototype command-line utilities for the processing of geographical data. The tools can be divided into stand-alone programmes and scripts. They have been tested mainly in the Ubuntu Linux environment, although they can be used with other Linux distros, macOS, and MS Windows (Cywgin) as well. Most of the stand-alone programmes use GDAL libraries and many of the scripts rely heavily on GDAL command-line utilities. +The **Open Foris Geospatial Toolkit (OFGT)** is a collection of prototype command-line utilities for processing geographical data. The tools can be divided into stand-alone programmes and scripts. They have been tested mainly in the Ubuntu Linux environment, although they can be used with other Linux distros, macOS, and Microsoft Windows (Cywgin) as well. Most of the stand-alone programmes use **GDAL libraries** and many of the scripts rely heavily on **GDAL command-line utilities**. -The OFGT project started under the Open Foris initiative in an effort to develop, share and support software tools and methods for multipurpose forest assessment, monitoring and reporting (see `Open Foris `__. The initiative develops and supports innovative, easy-to-use tools needed to produce reliable, up-to-date information on the state of forest resources and their uses. The command-line tools aim to simplify the complex process of transforming raw satellite imagery for automatic image processing to produce valuable information. These tools contain radiometric harmonization, image segmentation and image arithmetic, as well as image statistics, feature extraction, and other image processing analysis. +The **OFGT** project started under the Open Foris initiative in an effort to develop, share and support software tools and methods for multipurpose forest assessment, monitoring and reporting (see `Open Foris `__. + +The Open Foris initiative develops and supports innovative, easy-to-use tools needed to produce reliable, up-to-date information on the state of forest resources and their uses. + +The command-line tools aim to simplify the complex process of transforming raw satellite imagery for automatic image processing to produce valuable information. These tools contain radiometric harmonization, image segmentation and image arithmetic, as well as image statistics, feature extraction and other image processing analysis. .. note:: @@ -12,7 +16,7 @@ The OFGT project started under the Open Foris initiative in an effort to develop Available commands ------------------ -The complete documentation of the OFGT commands can be found in the `OFGT manual `__. +The complete documentation of the **OFGT** commands can be found in the `OFGT manual `__. General tools @@ -23,7 +27,7 @@ General tools $ CsvToPolygon.py # Creates shapefile polygons from a text file. $ genericCsvToPolygon.py # Creates polygons from text files. $ genericGEkml2csv.bash # Converts separate KML files into one CSV file. - $ GExml2csv.bash # Converts XML files from the GEE training data collection tool into one CSV file. + $ GExml2csv.bash # Converts XML files from the GEE training data collection tool into one .csv file. $ oft-addattr.py # Adds one integer attribute in a shape file. $ oft-addpct.py # Adds pseudo color table to an image. $ oft-admin-mask.bash # Prepares a mask of administrative areas within a satellite image. @@ -41,7 +45,7 @@ General tools $ oft-sample-within-polys.bash # Samples pixels within polygons and generates training data for knn. $ oft-shptif.bash # Rasterizes a shapefile to the resolution of a reference image. $ oft-sigshp.bash # Creates a signature file of an image based on training area polygons. - $ PointsToSquares.py # Converts XY-locations into 100 m x 100 m squares in a KML file. + $ PointsToSquares.py # Converts XY-locations into 100 m x 100 m squares in a .kml file. Image manipulation ^^^^^^^^^^^^^^^^^^ @@ -51,7 +55,7 @@ Image manipulation $ multifillerThermal.bash # Utilizes several Landsat scenes to build a multitemporal image composite using the warmest pixel method. $ oft-calc # Raster image calculator. $ oft-chdet.bash # Automated change detection. - $ oft-clip.pl # Subsets an input image using the extent, pixel size, and projection of a reference image. + $ oft-clip.pl # Subsets an input image using the extent, pixel size and projection of a reference image. $ oft-combine-images.bash # Combines two images into one. $ oft-gapfill # Regression-based gap and cloud filler. $ oft-ndvi.bash # Computes NDVI images. @@ -60,16 +64,16 @@ Image manipulation $ oft-shrink # To be combined with oft-trim. $ oft-stack # Creates a multiband image stack. $ oft-trim # Erosion filter producing binary output. - $ oft-trim-maks.bash # Makes a 0/1 mask of a 6 or 7 band Landsat image. + $ oft-trim-maks.bash # Makes a 0/1 mask of a 6- or 7-band Landsat image. Statistics ^^^^^^^^^^ .. code-block:: console - $ oft-ascstat.awk # Computes basic statistics for a space separated text file. + $ oft-ascstat.awk # Computes basic statistics for a space-separated text file. $ oft-avg # Computes zone/segment averages and standard deviations. - $ oft-countpix.pl # Counts number of pixels with, below, or above a specific value. + $ oft-countpix.pl # Counts number of pixels with, below or above a specific value. $ oft-crossvalidate # Computes RMSE and bias estimates for knn via leave-one-out cross-validation. $ oft-extr # Extracts pixel values from an image into a text file. $ oft-his # Computes image histogram by segments. From baf5e8cf1498037fe981fec3903ea827b822b724 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 15:49:19 +0100 Subject: [PATCH 08/15] Update otb.rst Proofreading complete. --- docs/source/cli/otb.rst | 18 ++++++++++-------- 1 file changed, 10 insertions(+), 8 deletions(-) diff --git a/docs/source/cli/otb.rst b/docs/source/cli/otb.rst index 1ac208694d..f2d188bb75 100644 --- a/docs/source/cli/otb.rst +++ b/docs/source/cli/otb.rst @@ -1,13 +1,15 @@ -Orfeo Toolbox -============= +OTB +=== -Orfeo ToolBox (OTB) is an open-source project for state-of-the-art remote sensing. Built upon the foundation of the open-source geospatial community, it can process high-resolution optical, multispectral and radar images on the terabyte scale. A wide variety of applications are available, from ortho-rectification or pansharpening, to classification, SAR processing, and much more. +**Orfeo ToolBox (OTB)** is an open-source project for state-of-the-art remote sensing. Built upon the foundation of the open-source geospatial community, it can process high-resolution optical, multispectral and radar images on the terabyte scale. A wide variety of applications are available, such as ortho-rectification, pansharpening, classification and synthetic-aperture radar (SAR) processing. -OTB is equipped with more than 100 ready-to-use applications for remote sensing tasks. They usually expose existing processing functions from the underlying C++ library, or integrate them into high-level pipelines. OTB applications allow the user to: +**OTB** is equipped with more than 100 ready-to-use applications for remote sensing tasks. They usually expose existing processing functions from the underlying **C++ library**, or integrate them into high-level pipelines. -- combine two or more functions from the Orfeo ToolBox; and -- provide a high-level interface to handle input and output data, definition of parameters, and communication with the user. +**OTB applications** allow the user to: -The complete list of applications is described on the `All Applications page `__. +- combine two or more functions from the OTB; and +- provide a high-level interface to handle input and output data, definition of parameters and communication with the user. -All standard applications share the same implementation and automatically expose generated interfaces. However, they are accessed in a slightly different way: the command-line interface is prefixed by :code:`otbcli\_`. +For a complete list of applications, see `All applications`__. + +All standard applications share the same implementation and automatically expose generated interfaces. However, they are accessed in a slightly different way (the command-line interface is prefixed by :code:`otbcli\_`). From e70c4085415e2c7cb02b3dd96c1d3ecbde4b9a11 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 16:06:16 +0100 Subject: [PATCH 09/15] Update python.rst Proofreading complete. --- docs/source/cli/python.rst | 19 +++++++++---------- 1 file changed, 9 insertions(+), 10 deletions(-) diff --git a/docs/source/cli/python.rst b/docs/source/cli/python.rst index ae9bbff658..7394760915 100644 --- a/docs/source/cli/python.rst +++ b/docs/source/cli/python.rst @@ -4,52 +4,51 @@ Python Usage ----- -SEPAL instances run on :code:`focal` Ubuntu machines and thus provide a fully functional :code:`Python 3.8` environment. This environment is accessible through Jupyter Notebook, JupyterLab or the terminal: +SEPAL instances run on :code:`focal` Ubuntu machines and thus provide a fully functional :code:`Python 3.8` environment, which is accessible through Jupyter Notebook, JupyterLab or the terminal: .. thumbnail:: ../_images/cli/python/jupyter_example.png - :title: A code run in Jupyterlab + :title: A code run in JupyterLab :group: python_environment :width: 32% .. thumbnail:: ../_images/cli/python/notebook_example.png - :title: a code run in Jupyter Notebook + :title: A code run in Jupyter Notebook :group: python_environment :width: 32% .. thumbnail:: ../_images/cli/python/terminal_example.png - :title: A code run in the terminal + :title: A code run in the SEPAL terminal :group: python_environment :width: 32% Description ----------- -The SEPAL Python environment is not empty; there are numerous embedded librairies (see figure below). +The SEPAL Python environment is not empty; there are numerous embedded libraries (see figure below). .. literalinclude:: ../_data/python_lib.txt :language: sh -Run :code:`pip show ` to check if it's already installed. +To check if it's already installed, run :code:`pip show `. Customization ------------- -The SEPAL environment can be customized to user needs using any third-party librairies and pip. By default installation will be run in :code:`--user` mode and won't affect other SEPAL users. - +The SEPAL environment can be customized to user needs using any third-party libraries and pip. By default, installation will be run in :code:`--user` mode and won't affect other SEPAL users. .. thumbnail:: ../_images/cli/python/install_sphinx.gif :title: A code run in the terminal .. note:: - If you face compatibility issues when customizing your SEPAL environment, please let us know in the `Github issue tracker `__. + If you face compatibility issues when customizing your SEPAL environment, let us know in the `Github issue tracker `__. Virtual environment ------------------- .. attention:: - SEPAL does not support conda environments. If you need to install compiled libraries, please contact the SEPAL team via the `Github issue tracker `__. + SEPAL does not support conda environments. If you need to install compiled libraries, contact the SEPAL team via the `GitHub issue tracker `__. SEPAL supports Python venv creation. In this section, we'll explain how to create a venv and link it to Jupyter, so you can run your processes on the associated kernel. From 31db33c8f407a5770374858fa8896250197a3bcb Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 16:14:28 +0100 Subject: [PATCH 10/15] Update r.rst Proofreading complete. --- docs/source/cli/r.rst | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/docs/source/cli/r.rst b/docs/source/cli/r.rst index e198ec947f..23e693987e 100644 --- a/docs/source/cli/r.rst +++ b/docs/source/cli/r.rst @@ -4,7 +4,7 @@ R code Usage ----- -SEPAL instances run on :code:`focal` Ubuntu machines, providing a fully functional :code:`R 4.1.2` environment that is accessible in RStudio, Jupyterlab or the terminal. +SEPAL instances run on :code:`focal` Ubuntu machines, providing a fully functional :code:`R 4.1.2` environment that is accessible in RStudio, JupyterLab or the terminal. .. thumbnail:: ../_images/cli/r/rstudio_example.png :title: A code run in RStudio @@ -17,7 +17,7 @@ SEPAL instances run on :code:`focal` Ubuntu machines, providing a fully function :width: 32% .. thumbnail:: ../_images/cli/r/terminal_example.png - :title: A code run in the terminal + :title: A code run in the SEPAL terminal :group: r_environment :width: 32% @@ -32,19 +32,18 @@ The SEPAL :code:`R` environment is not empty; there are numerous embedded packag To check the availability of a specific package: -- Open RStudio. -- Go to :guilabel:`Help` > :guilabel:`R Help` (from the menu above). -- You will see the **Help** panel opened. -- Select :code:`Reference` > :code:`Packages` +# Open RStudio. +# Go to :guilabel:`Help` > :guilabel:`R Help`. +# In the open **Help** pane, select :code:`Reference` > :code:`Packages`. .. thumbnail:: ../_images/cli/r/package_list.png - :title: How to display R packages in **RStudio** + :title: How to display R packages in RStudio :group: r_environment Customization ------------- -The SEPAL environment can be customized to user needs by utilizing third-party packages and CRAN in **RStudio**. +The SEPAL environment can be customized to user needs by utilizing third-party packages and CRAN in RStudio. .. code-block:: r From 5de4d94d85ecf218931277d5a174472cb526c0a1 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 16:26:01 +0100 Subject: [PATCH 11/15] Update index.rst Proofreading complete. --- docs/source/feature/index.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/source/feature/index.rst b/docs/source/feature/index.rst index 7b442ab62c..bd9184b476 100644 --- a/docs/source/feature/index.rst +++ b/docs/source/feature/index.rst @@ -1,7 +1,6 @@ Features ======== - -The SEPAL platform provides useful features to analyse, combine and visualize different types of data. +*Analyse, combine and visualize different types of data with SEPAL Features* Since these features can be accessed across various recipes and modules, they are described extensively in this section of the documentation. From ebf1945e006acb10918139d757ffd5b7aa2c7520 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 17:03:17 +0100 Subject: [PATCH 12/15] Update aoi_selector.rst Proofreading complete. --- docs/source/feature/aoi_selector.rst | 137 ++++++++++++++++++++------- 1 file changed, 101 insertions(+), 36 deletions(-) diff --git a/docs/source/feature/aoi_selector.rst b/docs/source/feature/aoi_selector.rst index f6fe23c1b7..91c4f41e57 100644 --- a/docs/source/feature/aoi_selector.rst +++ b/docs/source/feature/aoi_selector.rst @@ -1,7 +1,7 @@ -Area of interest selection -========================== +AOI selection +============= -In most SEPAL modules, the first mandatory input is the area of interest (AOI), used as a boundary to cut the processes and its outputs. +In most SEPAL modules, the first mandatory input is the area of interest (AOI), which is used as a boundary to cut the processes and its outputs. If you are using the default :btn:`` **Process recipes** or :btn:`` custom **Applications**, you will find different user interfaces. @@ -12,10 +12,14 @@ Recipe AOI Recipes are accessible through the orange :btn:`` globe icon located on the left side of the SEPAL interface. -For many recipes, an AOI has to be selected. Locate the AOI selection button in the lower-right corner. Select the :guilabel:`AOI` button to open the selection window. +For many recipes, an AOI has to be selected. + +Locate the **AOI selection** button in the lower-right corner. + +Select the :guilabel:`AOI` button to open the selection window. .. thumbnail:: ../_images/feature/aoi_selector/no_parameters.png - :title: The five tabs to set up SEPAL optical mosaic parameters + :title: The five tabs to set up SEPAL **Optical mosaic** parameters :group: feature_aoi :align: center :width: 700 @@ -23,7 +27,7 @@ For many recipes, an AOI has to be selected. Locate the AOI selection button in There are multiple methods for selecting AOIs in SEPAL process recipes: - Country/province (administrative boundaries) -- EE Tables (Google Earth Engine [GEE]) +- EE Tables (GEE) - Drawn polygons .. thumbnail:: ../_images/feature/aoi_selector/aoi_landing.png @@ -39,13 +43,17 @@ There are multiple methods for selecting AOIs in SEPAL process recipes: Administrative boundaries """"""""""""""""""""""""" -You can select administrative layers as AOIs. These geometries are extracted from the `FAO GAUL Level 0 `__ dataset available on `GEE `__. To use them, select the :guilabel:`Select country/province` method in the dropdown list. +You can select administrative layers as AOIs. + +These geometries are extracted from the `FAO GAUL Level 0 `__ dataset available on `GEE `__. + +To use them, select the :guilabel:`Select country/province` method in the dropdown list. .. note:: Since GEE does not support non-Latin characters, accents and special characters have been removed from country and province names. -In the first dropdown menu, you will be able to select a country (Administrative layer 0) from the country list. Optionally, you can select a province (Administrative level 1) within the country selected. The dropdown list is updated on the fly with the first administrative level boundaries being based on the country selection. If nothing is selected, the whole country will be considered. +In the first dropdown menu, you will be able to select a country (**Administrative layer 0**) from the country list. Optionally, you can select a province (**Administrative level 1**) within the country selected. The dropdown list is updated on the fly with the first administrative level boundaries being based on the country selection. If nothing is selected, the whole country will be considered. A buffer can be applied to AOI boundaries by defining its size (km) using the provided slider. By default, it is set to 0 and is therefore disabled. @@ -53,7 +61,11 @@ A buffer can be applied to AOI boundaries by defining its size (km) using the pr The AOI and preview will take longer to display when buffering is enabled. -Once all parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. +Once all parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. + +To validate it, select the :btn:` Apply` button. + +Once validated, the map will zoom in on the AOI and draw it in grey on the map. .. thumbnail:: ../_images/feature/aoi_selector/aoi_administrative.png :title: Select AOI based on administrative layers @@ -64,7 +76,11 @@ Once all parameters are selected, the AOI will be previewed in the small map at EE table """""""" -You can use custom AOI defined by shapes. These shapes need to be ingested in GEE as a :code:`ee.FeatureCollection` (see `How to upload custom assets to GEE <../setup/gee.html#upload-files-to-gee>`__). To use this method, select :guilabel:`EE table`. +You can use custom AOI defined by shapes. + +These shapes need to be ingested in GEE as a :code:`ee.FeatureCollection` (see `How to upload custom assets to GEE <../setup/gee.html#upload-files-to-gee>`__). + +To use this method, select :guilabel:`EE table`. In the first dropdown list, provide a completely qualified GEE asset name (e.g. :code:`projects/gtfp-fao/assets/aoi_ecowas`). @@ -81,7 +97,11 @@ A buffer can be applied to these boundaries by defining its size (km) using the The AOI and the preview will take longer to display when buffering is enabled. -Once all of the parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. +Once all of the parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. + +To validate it, select the :btn:` Apply` button. + +Once validated, the map will zoom in on the AOI and draw it in grey on the map. .. thumbnail:: ../_images/feature/aoi_selector/aoi_table.png :title: Select AOI based on EE table @@ -92,11 +112,17 @@ Once all of the parameters are selected, the AOI will be previewed in the small Draw polygon """""""""""" -You can use a custom AOI defined by a drawn shape, which will be converted into a :code:`ee.FeatureCollection` on the fly. Select :guilabel:`Draw a polygon` to use this method. +You can use a custom AOI defined by a drawn shape, which will be converted into a :code:`ee.FeatureCollection` on the fly. + +Select :guilabel:`Draw a polygon` to use this method. + +The pointer on the map will be converted into a :icon:`fa-solid fa-plus`. -The pointer on the map will be converted into a :icon:`fa-solid fa-plus`. Click successively on the map to draw a polygon. +Click successively on the map to draw a polygon. -Once the geometric shape is closed, the AOI will be previewed in the small map at the bottom of the frame. To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. +Once the geometric shape is closed, the AOI will be previewed in the small map at the bottom of the frame. + +To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. .. thumbnail:: ../_images/feature/aoi_selector/aoi_polygon.png :title: Select AOI based on drawn polygon @@ -107,9 +133,18 @@ Once the geometric shape is closed, the AOI will be previewed in the small map a Module AOI ^^^^^^^^^^ -The module AOI selector is available in some SEPAL-contributor modules. To access an app, select the purple wrench :btn:`` located on the left side of the SEPAL platform, then use the app's dashboard to search and open a module. +The **Module AOI selector** is available in some contributor modules. + +To access an app, select the purple wrench :btn:``, located on the left side of the SEPAL platform. + +Then, use the app's dashboard to search and open a module. + +A **Module AOI selector** is composed of two main sections: -An AOI selector module is composed of two main sections: (1) the available methods, and (2) the map. Although we will mention all features and methods available, some might not be available in the context of the module you are working on. +1. the available methods; and +2. the map. + +Although we will mention all features and methods available, some might not be available in the context of the module you are working on. .. thumbnail:: ../_images/feature/aoi_selector/module_aoi_overview.png :title: Module AOI selector @@ -119,18 +154,25 @@ An AOI selector module is composed of two main sections: (1) the available metho Available methods """"""""""""""""" -There are two types of processes that require different AOI inputs, depending on the way the module is created and where the core processes are done: directly in a `SEPAL instance <../modules/index.html#start-instance-manually>`__ or in GEE. Although both interfaces appear to be the same, the methods and internal data sources may vary, such as administrative definitions. +There are two types of processes that require different AOI inputs, depending on the way the module is created and where the core processes are done: + +1. directly in a `SEPAL instance <../modules/index.html#start-instance-manually>`__; or +2. in GEE. + +Although both interfaces appear to be the same, the methods and internal data sources may vary, such as administrative definitions. Administrative definitions """""""""""""""""""""""""" -Similar to the previously mentioned :ref:`Recipe AOI selector `, the module AOI uses `FAO GAUL GEE `__ boundaries for GEE and `GADM 3.6 `__ features for local processes. However, in this case, the tool allows you to recurse at a maximum second administrative level. The available sources are the following: +Similar to the previously mentioned :ref:`Recipe AOI selector `, the module AOI uses `FAO GAUL GEE `__ boundaries for GEE and `GADM 3.6 `__ features for local processes. + +However, in this case, the tool allows you to recurse at a maximum second administrative level. The available sources are the following: GEE ### -- Country/province (level 0): Countries or provinces at level 0, available at `FAO GAUL GEE level 0 `__ -- Admin level 1: First administrative level, `FAO GAUL GEE level 1 `__. +- Country/province (level 0): Countries or provinces at level 0, available at `FAO GAUL GEE level 0 `__; +- Admin level 1: First administrative level, `FAO GAUL GEE level 1 `__; and - Admin level 2: Second administrative level, `FAO GAUL GEE level 2 `__. Local @@ -138,7 +180,11 @@ Local - All administrative levels are accessible from the `GADM website `__. -Use the :guilabel:`AOI selection method` dropdown list to select the target administrative level. A new dropdown will load with all corresponding boundaries to the next administrative level that is linked with the base level (i.e. select :code:`Admin level 2` as the method, choose :code:`Colombia` as the country, select the :code:`Amazonas` department as the next level, and finally select the :code:`Leticia` municipality). +Use the :guilabel:`AOI selection method` dropdown list to select the target administrative level. + +A new dropdown list will load with all corresponding boundaries to the next administrative level that is linked with the base level. + +For example, select :code:`Admin level 2` as the method, choose :code:`Colombia` as the country, select the :code:`Amazonas` department as the next level, and finally select the :code:`Leticia` municipality. .. thumbnail:: ../_images/feature/aoi_selector/administrative_selection.png :title: Administrative selection @@ -148,7 +194,7 @@ Use the :guilabel:`AOI selection method` dropdown list to select the target admi Custom geometries """"""""""""""""" -When you are looking for a more specific AOI, the module AOI selector has the following options: +When you are looking for a more specific AOI, the **Module AOI selector** has the following options: - Vector file - Drawn shape @@ -158,14 +204,21 @@ When you are looking for a more specific AOI, the module AOI selector has the fo Vector file ########### -Use this option to upload a custom vector file. Select the :guilabel:`Vector file` method in the dropdown list. A file manager widget (1) will be displayed below, allowing you to search and select a vector file stored in your SEPAL environment (see `How to exchange files with SEPAL `_). The dropdown list, :guilabel:`Column` (2), is useful to filter features of the vector file. The default option is :guilabel:`Use all features`, meaning any filter is used. To filter the collection, select a column and a :guilabel:`Value` (3) in the corresponding dropdown list, then select the :guilabel:`Select AOI` button. +Use this option to upload a custom vector file. + +Select the :guilabel:`Vector file` method in the dropdown list. + +A file manager widget (see **1** in the following figure) will be displayed below, allowing you to search and select a vector file stored in your SEPAL environment (see `How to exchange files with SEPAL `_). + +The dropdown list, :guilabel:`Column` (**2**), is useful to filter features of the vector file. The default option is :guilabel:`Use all features`, meaning any filter is used. + +To filter the collection, select a column and a :guilabel:`Value` (**3**) in the corresponding dropdown list, then select the :guilabel:`Select AOI` button. .. thumbnail:: ../_images/feature/aoi_selector/method_vector_file.png :title: Module vector file :align: center :width: 600 - .. note:: Available vector formats include: [:code:`.shp`, :code:`.geojson`, :code:`.gpkg`, :code:`.kml`]. Once selected, the module will transform its original coordinate system into :code:`EPSG:4326`. @@ -175,7 +228,11 @@ Use this option to upload a custom vector file. Select the :guilabel:`Vector fil Drawn shape ########### -Use this option to manually draw geometric shapes on the map. Select the :guilabel:`Drawn shapes` method in the dropdown list, and create a name for your drawing, if desired (if not provided, the tool will assign a unique name containing the following structure: +Use this option to manually draw geometric shapes on the map. + +Select the :guilabel:`Drawn shapes` method in the dropdown list. + +Then, create a name for your drawing, if desired. If not provided, the tool will assign a unique name containing the following structure: :code:`Manual_aoi_YYYY-MM-DD_HH-MM-SS` @@ -190,7 +247,7 @@ Three geometric shapes will appear in the upper-left corner of the map: :btn:`` and :btn:`` buttons located in the upper-right corner. + To draw, zoom in on your AOI by using the mouse wheel button, or the :btn:`` and :btn:`` buttons located in the upper-right corner. - :btn:`` (polygon): Draw your custom polygon by clicking the vertices of the geometry on the map. To close and finish your geometry, click the first vertex or select the :guilabel:`finish` button. Note that once you select the polygon geometric shape, three new buttons will be available at the top of the map: :guilabel:`Finish`, :guilabel:`Delete last point` and :guilabel:`Cancel`. @@ -201,19 +258,21 @@ Three geometric shapes will appear in the upper-left corner of the map: :btn:` Date: Thu, 16 Nov 2023 17:05:41 +0100 Subject: [PATCH 13/15] Update vizualisation.rst Proofreading complete. --- docs/source/feature/vizualisation.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/source/feature/vizualisation.rst b/docs/source/feature/vizualisation.rst index 6a9568b645..bed199f11d 100644 --- a/docs/source/feature/vizualisation.rst +++ b/docs/source/feature/vizualisation.rst @@ -1,4 +1,4 @@ -Vizualisation +Visualization ============= .. include:: ../_templates/no_feature.rst From d3722c3241282332f64a76f306711fb272ff8997 Mon Sep 17 00:00:00 2001 From: Alex Gregor <111502950+alexryangregor@users.noreply.github.com> Date: Thu, 16 Nov 2023 17:37:59 +0100 Subject: [PATCH 14/15] Update project.rst Proofreading complete. --- docs/source/feature/project.rst | 30 ++++++++++++++++++------------ 1 file changed, 18 insertions(+), 12 deletions(-) diff --git a/docs/source/feature/project.rst b/docs/source/feature/project.rst index eed2fcd909..9d6c83e04b 100644 --- a/docs/source/feature/project.rst +++ b/docs/source/feature/project.rst @@ -1,12 +1,16 @@ -SEPAL recipe projects -===================== +Recipe projects +=============== -When interacting with SEPAL processes, a user creates *recipes*, which can work together and be interconnected inside a single project (e.g. :code:`Mosaics` used in a :code:`Classification`). To help with these interconnections, the SEPAL platform provides a :code:`Project` system to organize users' work. +When interacting with SEPAL processes, a user creates **Recipes**, which can work together and be interconnected inside a single project (e.g. :code:`Mosaics` used in a :code:`Classification`). + +To help with these interconnections, the SEPAL platform provides a :code:`Project` system to organize users' work. Overview -------- -Go to the **Processes** interface of SEPAL (:btn:``) (you should see the following; if you've already created recipes in previous releases, you will see a list of existing recipes). +Go to the **Processes** interface of SEPAL (:btn:``). + +(You should see the following. If you've already created recipes in previous releases, you will see a list of existing recipes). .. thumbnail:: ../_images/feature/project/project-landing.png :title: Landing page for **Processes** showing the project interface @@ -34,7 +38,7 @@ Project For every user, a :code:`[no project]` project is created during registration. This project will be the fallback for every recipe that was created before the publication of the feature. It cannot be deleted or renamed. -To create a project, select :btn:` Projects`, which opens the following interface (see figure below). +To create a project, select :btn:` Projects`, which opens the interface (see figure below). Then, select :btn:` Add` to create a new project. Enter the name and select :btn:` Apply`. @@ -50,7 +54,7 @@ The newly created project will now apear in the list. :group: recipe-process :width: 49% -To remove a project, select the :btn:`` icon (located beside its name). (Note: all recipes included in the process will be destroyed as well.) +To remove a project, select the :btn:`` icon (located beside its name), which will destroy all recipes included in the process as well. .. thumbnail:: ../_images/feature/project/project-list.png :title: The list of projects available in your SEPAL account @@ -60,7 +64,7 @@ To remove a project, select the :btn:`` icon (located beside Recipes ------- -When entering the **Process** interface, no projects are selected by default, meaning that users will see all of the recipes available in their SEPAL accounts. All recipes are displayed using the following prototype: :code:` / `. +When entering the **Process** interface, no projects are selected by default, meaning that users will see all recipes available in their SEPAL accounts. All recipes are displayed using the following prototype: :code:` / `. .. thumbnail:: ../_images/feature/project/all-recipes.png :title: All recipes available in one account @@ -72,17 +76,17 @@ From this page, the user can customize and manage recipes. Filter recipes ^^^^^^^^^^^^^^ -Select (3) to filter recipes according to your project. Once selected, only the recipes included in the project will be displayed. The field is "clearable", meaning you can go back to the unfiltered state and select another project. Also, :code:`[no project]` can be selected. +Select (3) to filter recipes according to your project. Once selected, only the recipes included in the project will be displayed. The field is clearable (i.e. you can go back to the unfiltered state and select another project). Also, :code:`[no project]` can be selected. .. thumbnail:: ../_images/feature/project/filtered-recipes.png :title: The filtered recipes included in the "foo 2" project :group: recipe-process :align: center -Once a project is selected, it will appear as "current project" in the project list (see figure below). +Once a project is selected, it will appear as **Current project** in the project list (see figure below). .. thumbnail:: ../_images/feature/project/change-project.png - :title: The list of projects, showing the currently selected project + :title: List of projects, showing currently selected project :group: recipe-process :align: center @@ -98,7 +102,7 @@ Edit recipes Recipe behaviour can be edited directly from this view. Select the :btn:` Edit` button to open the **Editing** interface. .. thumbnail:: ../_images/feature/project/edit-recipes.png - :title: The recipe editing interface + :title: The **Recipe editing** interface :group: recipe-process :align: center @@ -115,7 +119,9 @@ From this interface, you can: Connect recipes ^^^^^^^^^^^^^^^ -When creating recipes such as :code:`Classification`, users can use other recipes as inputs for the process. To avoid flooding the dropdown list with too many values, only the recipes from the same projet will be displayed (see following figure on the left). If one still wants to see all of the recipes in the dropdown list, select :btn:`All` and all of the recipes will be displayed using project names as headers (see following figure on right). +When creating recipes such as :code:`Classification`, users can use other recipes as inputs for the process. To avoid flooding the dropdown list with too many values, only the recipes from the same projet will be displayed (see following figure on the left). + +If one still wants to see all of the recipes in the dropdown list, select :btn:`All` and all recipes will be displayed using project names as headers (see following figure on right). .. thumbnail:: ../_images/feature/project/connected-project-only.png :title: Dropdown list that only shows recipes from the same project From 1932b7d5d63fd28b2859677c4f5e033a06f3bb51 Mon Sep 17 00:00:00 2001 From: dfguerrerom Date: Fri, 17 Nov 2023 09:45:53 +0100 Subject: [PATCH 15/15] style: lint trailing --- docs/source/cli/gdal.rst | 4 +- docs/source/cli/gee.rst | 4 +- docs/source/cli/gwb.rst | 2 +- docs/source/cli/ofgt.rst | 4 +- docs/source/cli/otb.rst | 4 +- docs/source/feature/aoi_selector.rst | 68 ++++++++++++++-------------- docs/source/feature/project.rst | 4 +- 7 files changed, 45 insertions(+), 45 deletions(-) diff --git a/docs/source/cli/gdal.rst b/docs/source/cli/gdal.rst index cf51538bed..4157a37cf3 100644 --- a/docs/source/cli/gdal.rst +++ b/docs/source/cli/gdal.rst @@ -1,9 +1,9 @@ GDAL ==== -**Geospatial Data Abstraction Library (GDAL)** is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. +**Geospatial Data Abstraction Library (GDAL)** is a translator library for raster and vector geospatial data formats that is released under an `MIT style license `__ by the `Open Source Geospatial Foundation `__. -As a library, **GDAL** presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. +As a library, **GDAL** presents a single raster abstract data model and single vector abstract data model to the calling application for all supported formats. It also comes with a variety of useful command-line utilities for data translation and processing. For information on the newest release of **GDAL**, see `News `__. diff --git a/docs/source/cli/gee.rst b/docs/source/cli/gee.rst index 626df52b61..46e1cb6188 100644 --- a/docs/source/cli/gee.rst +++ b/docs/source/cli/gee.rst @@ -1,7 +1,7 @@ GEE === -The **Google Earth Engine (GEE)** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line. +The **Google Earth Engine (GEE)** tool is a utility program that allows you to manage Google Earth Engine (GEE) assets and tasks from the command line. The tool is installed automatically when you install the Python API. To check whether it is installed and functioning correctly, enter the following in a command line: @@ -56,7 +56,7 @@ The main advantages of the **GEE code editor** are: SEPAL and JupyterLab can help you bring this to the next level by providing both tools in a Python notebook, allowing you to also access all Python geospatial tools created by the Earth observation community. -First, open a JupyterLab instance and start a notebook. +First, open a JupyterLab instance and start a notebook. In the first cell, create a map and place it the sidecar by running the following code: diff --git a/docs/source/cli/gwb.rst b/docs/source/cli/gwb.rst index 4922ce09a5..1182953163 100644 --- a/docs/source/cli/gwb.rst +++ b/docs/source/cli/gwb.rst @@ -1,7 +1,7 @@ GWB === -**GuidosToolbox Workbench (GWB)** is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB `_ or `GTB `_). +**GuidosToolbox Workbench (GWB)** is a subset of the desktop software package GuidosToolbox (GTB), designed as a command-line application for Linux 64bit servers (see `GWB `_ or `GTB `_). Citation reference: `GuidosToolbox Workbench: Spatial analysis of raster maps for ecological applications `_. diff --git a/docs/source/cli/ofgt.rst b/docs/source/cli/ofgt.rst index 7e158e1372..eb32ff5980 100644 --- a/docs/source/cli/ofgt.rst +++ b/docs/source/cli/ofgt.rst @@ -3,9 +3,9 @@ OFGT The **Open Foris Geospatial Toolkit (OFGT)** is a collection of prototype command-line utilities for processing geographical data. The tools can be divided into stand-alone programmes and scripts. They have been tested mainly in the Ubuntu Linux environment, although they can be used with other Linux distros, macOS, and Microsoft Windows (Cywgin) as well. Most of the stand-alone programmes use **GDAL libraries** and many of the scripts rely heavily on **GDAL command-line utilities**. -The **OFGT** project started under the Open Foris initiative in an effort to develop, share and support software tools and methods for multipurpose forest assessment, monitoring and reporting (see `Open Foris `__. +The **OFGT** project started under the Open Foris initiative in an effort to develop, share and support software tools and methods for multipurpose forest assessment, monitoring and reporting (see `Open Foris `__. -The Open Foris initiative develops and supports innovative, easy-to-use tools needed to produce reliable, up-to-date information on the state of forest resources and their uses. +The Open Foris initiative develops and supports innovative, easy-to-use tools needed to produce reliable, up-to-date information on the state of forest resources and their uses. The command-line tools aim to simplify the complex process of transforming raw satellite imagery for automatic image processing to produce valuable information. These tools contain radiometric harmonization, image segmentation and image arithmetic, as well as image statistics, feature extraction and other image processing analysis. diff --git a/docs/source/cli/otb.rst b/docs/source/cli/otb.rst index f2d188bb75..84ea25b3df 100644 --- a/docs/source/cli/otb.rst +++ b/docs/source/cli/otb.rst @@ -3,13 +3,13 @@ OTB **Orfeo ToolBox (OTB)** is an open-source project for state-of-the-art remote sensing. Built upon the foundation of the open-source geospatial community, it can process high-resolution optical, multispectral and radar images on the terabyte scale. A wide variety of applications are available, such as ortho-rectification, pansharpening, classification and synthetic-aperture radar (SAR) processing. -**OTB** is equipped with more than 100 ready-to-use applications for remote sensing tasks. They usually expose existing processing functions from the underlying **C++ library**, or integrate them into high-level pipelines. +**OTB** is equipped with more than 100 ready-to-use applications for remote sensing tasks. They usually expose existing processing functions from the underlying **C++ library**, or integrate them into high-level pipelines. **OTB applications** allow the user to: - combine two or more functions from the OTB; and - provide a high-level interface to handle input and output data, definition of parameters and communication with the user. -For a complete list of applications, see `All applications`__. +For a complete list of applications, see `All applications `__. All standard applications share the same implementation and automatically expose generated interfaces. However, they are accessed in a slightly different way (the command-line interface is prefixed by :code:`otbcli\_`). diff --git a/docs/source/feature/aoi_selector.rst b/docs/source/feature/aoi_selector.rst index 91c4f41e57..ae1de64077 100644 --- a/docs/source/feature/aoi_selector.rst +++ b/docs/source/feature/aoi_selector.rst @@ -12,9 +12,9 @@ Recipe AOI Recipes are accessible through the orange :btn:`` globe icon located on the left side of the SEPAL interface. -For many recipes, an AOI has to be selected. +For many recipes, an AOI has to be selected. -Locate the **AOI selection** button in the lower-right corner. +Locate the **AOI selection** button in the lower-right corner. Select the :guilabel:`AOI` button to open the selection window. @@ -43,9 +43,9 @@ There are multiple methods for selecting AOIs in SEPAL process recipes: Administrative boundaries """"""""""""""""""""""""" -You can select administrative layers as AOIs. +You can select administrative layers as AOIs. -These geometries are extracted from the `FAO GAUL Level 0 `__ dataset available on `GEE `__. +These geometries are extracted from the `FAO GAUL Level 0 `__ dataset available on `GEE `__. To use them, select the :guilabel:`Select country/province` method in the dropdown list. @@ -61,9 +61,9 @@ A buffer can be applied to AOI boundaries by defining its size (km) using the pr The AOI and preview will take longer to display when buffering is enabled. -Once all parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. +Once all parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. -To validate it, select the :btn:` Apply` button. +To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. @@ -76,9 +76,9 @@ Once validated, the map will zoom in on the AOI and draw it in grey on the map. EE table """""""" -You can use custom AOI defined by shapes. +You can use custom AOI defined by shapes. -These shapes need to be ingested in GEE as a :code:`ee.FeatureCollection` (see `How to upload custom assets to GEE <../setup/gee.html#upload-files-to-gee>`__). +These shapes need to be ingested in GEE as a :code:`ee.FeatureCollection` (see `How to upload custom assets to GEE <../setup/gee.html#upload-files-to-gee>`__). To use this method, select :guilabel:`EE table`. @@ -97,9 +97,9 @@ A buffer can be applied to these boundaries by defining its size (km) using the The AOI and the preview will take longer to display when buffering is enabled. -Once all of the parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. +Once all of the parameters are selected, the AOI will be previewed in the small map at the bottom of the frame. -To validate it, select the :btn:` Apply` button. +To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. @@ -112,15 +112,15 @@ Once validated, the map will zoom in on the AOI and draw it in grey on the map. Draw polygon """""""""""" -You can use a custom AOI defined by a drawn shape, which will be converted into a :code:`ee.FeatureCollection` on the fly. +You can use a custom AOI defined by a drawn shape, which will be converted into a :code:`ee.FeatureCollection` on the fly. Select :guilabel:`Draw a polygon` to use this method. -The pointer on the map will be converted into a :icon:`fa-solid fa-plus`. +The pointer on the map will be converted into a :icon:`fa-solid fa-plus`. Click successively on the map to draw a polygon. -Once the geometric shape is closed, the AOI will be previewed in the small map at the bottom of the frame. +Once the geometric shape is closed, the AOI will be previewed in the small map at the bottom of the frame. To validate it, select the :btn:` Apply` button. Once validated, the map will zoom in on the AOI and draw it in grey on the map. @@ -133,16 +133,16 @@ To validate it, select the :btn:` Apply` button. Once validat Module AOI ^^^^^^^^^^ -The **Module AOI selector** is available in some contributor modules. +The **Module AOI selector** is available in some contributor modules. -To access an app, select the purple wrench :btn:``, located on the left side of the SEPAL platform. +To access an app, select the purple wrench :btn:``, located on the left side of the SEPAL platform. Then, use the app's dashboard to search and open a module. -A **Module AOI selector** is composed of two main sections: +A **Module AOI selector** is composed of two main sections: -1. the available methods; and -2. the map. +1. the available methods; and +2. the map. Although we will mention all features and methods available, some might not be available in the context of the module you are working on. @@ -154,17 +154,17 @@ Although we will mention all features and methods available, some might not be a Available methods """"""""""""""""" -There are two types of processes that require different AOI inputs, depending on the way the module is created and where the core processes are done: +There are two types of processes that require different AOI inputs, depending on the way the module is created and where the core processes are done: -1. directly in a `SEPAL instance <../modules/index.html#start-instance-manually>`__; or -2. in GEE. +1. directly in a `SEPAL instance <../modules/index.html#start-instance-manually>`__; or +2. in GEE. Although both interfaces appear to be the same, the methods and internal data sources may vary, such as administrative definitions. Administrative definitions """""""""""""""""""""""""" -Similar to the previously mentioned :ref:`Recipe AOI selector `, the module AOI uses `FAO GAUL GEE `__ boundaries for GEE and `GADM 3.6 `__ features for local processes. +Similar to the previously mentioned :ref:`Recipe AOI selector `, the module AOI uses `FAO GAUL GEE `__ boundaries for GEE and `GADM 3.6 `__ features for local processes. However, in this case, the tool allows you to recurse at a maximum second administrative level. The available sources are the following: @@ -180,9 +180,9 @@ Local - All administrative levels are accessible from the `GADM website `__. -Use the :guilabel:`AOI selection method` dropdown list to select the target administrative level. +Use the :guilabel:`AOI selection method` dropdown list to select the target administrative level. -A new dropdown list will load with all corresponding boundaries to the next administrative level that is linked with the base level. +A new dropdown list will load with all corresponding boundaries to the next administrative level that is linked with the base level. For example, select :code:`Admin level 2` as the method, choose :code:`Colombia` as the country, select the :code:`Amazonas` department as the next level, and finally select the :code:`Leticia` municipality. @@ -204,13 +204,13 @@ When you are looking for a more specific AOI, the **Module AOI selector** has th Vector file ########### -Use this option to upload a custom vector file. +Use this option to upload a custom vector file. -Select the :guilabel:`Vector file` method in the dropdown list. +Select the :guilabel:`Vector file` method in the dropdown list. -A file manager widget (see **1** in the following figure) will be displayed below, allowing you to search and select a vector file stored in your SEPAL environment (see `How to exchange files with SEPAL `_). +A file manager widget (see **1** in the following figure) will be displayed below, allowing you to search and select a vector file stored in your SEPAL environment (see `How to exchange files with SEPAL `_). -The dropdown list, :guilabel:`Column` (**2**), is useful to filter features of the vector file. The default option is :guilabel:`Use all features`, meaning any filter is used. +The dropdown list, :guilabel:`Column` (**2**), is useful to filter features of the vector file. The default option is :guilabel:`Use all features`, meaning any filter is used. To filter the collection, select a column and a :guilabel:`Value` (**3**) in the corresponding dropdown list, then select the :guilabel:`Select AOI` button. @@ -228,9 +228,9 @@ To filter the collection, select a column and a :guilabel:`Value` (**3**) in the Drawn shape ########### -Use this option to manually draw geometric shapes on the map. +Use this option to manually draw geometric shapes on the map. -Select the :guilabel:`Drawn shapes` method in the dropdown list. +Select the :guilabel:`Drawn shapes` method in the dropdown list. Then, create a name for your drawing, if desired. If not provided, the tool will assign a unique name containing the following structure: @@ -265,7 +265,7 @@ Use this method to load a single point or multipoint datasets. Select :guilabel: :align: center :width: 600 -Use the file selector widget to navigate through your SEPAL environment and search for a table file (:code:`.csv` or :code:`.txt`) containing the coordinates of your points. +Use the file selector widget to navigate through your SEPAL environment and search for a table file (:code:`.csv` or :code:`.txt`) containing the coordinates of your points. Make sure the file uses the following structure: @@ -299,12 +299,12 @@ GEE asset Use this method to load a custom feature collection available as an asset in GEE. -Select :guilabel:`GEE asset name` in the **Method** dropdown list. +Select :guilabel:`GEE asset name` in the **Method** dropdown list. -The following widgets will appear by default: +The following widgets will appear by default: - an asset selector (**1**); -- a dropdown list containing the columns of the selected asset (**2**); and +- a dropdown list containing the columns of the selected asset (**2**); and - unique column fields, which are optional (**3**). .. thumbnail:: ../_images/feature/aoi_selector/method_asset.png diff --git a/docs/source/feature/project.rst b/docs/source/feature/project.rst index 9d6c83e04b..7d5b626493 100644 --- a/docs/source/feature/project.rst +++ b/docs/source/feature/project.rst @@ -1,7 +1,7 @@ Recipe projects =============== -When interacting with SEPAL processes, a user creates **Recipes**, which can work together and be interconnected inside a single project (e.g. :code:`Mosaics` used in a :code:`Classification`). +When interacting with SEPAL processes, a user creates **Recipes**, which can work together and be interconnected inside a single project (e.g. :code:`Mosaics` used in a :code:`Classification`). To help with these interconnections, the SEPAL platform provides a :code:`Project` system to organize users' work. @@ -119,7 +119,7 @@ From this interface, you can: Connect recipes ^^^^^^^^^^^^^^^ -When creating recipes such as :code:`Classification`, users can use other recipes as inputs for the process. To avoid flooding the dropdown list with too many values, only the recipes from the same projet will be displayed (see following figure on the left). +When creating recipes such as :code:`Classification`, users can use other recipes as inputs for the process. To avoid flooding the dropdown list with too many values, only the recipes from the same projet will be displayed (see following figure on the left). If one still wants to see all of the recipes in the dropdown list, select :btn:`All` and all recipes will be displayed using project names as headers (see following figure on right).