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+
+
+
+ 20240716213927-953416e8ef1c8d4dec03f013a8fadf19af2971b6
+ 20240716213927
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 07
+ 2024
+
+
+ 9
+
+ 99
+
+
+
+ scikit-eo: A Python package for Remote Sensing Data
+Analysis
+
+
+
+ Yonatan
+ Tarazona
+ https://orcid.org/0000-0002-5208-1004
+
+
+ Fernando
+ Benitez-Paez
+ https://orcid.org/0000-0002-9884-6471
+
+
+ Jakub
+ Nowosad
+ https://orcid.org/0000-0002-1057-3721
+
+
+ Fabian
+ Drenkhan
+ https://orcid.org/0000-0002-9443-9596
+
+
+ Martín E.
+ Timaná
+ https://orcid.org/0000-0003-1559-4449
+
+
+
+ 07
+ 16
+ 2024
+
+
+ 6692
+
+
+ 10.21105/joss.06692
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.12688708
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6692
+
+
+
+ 10.21105/joss.06692
+ https://joss.theoj.org/papers/10.21105/joss.06692
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06692.pdf
+
+
+
+
+
+ Fusing Landsat and SAR data for mapping
+tropical deforestation through machine learning classification and the
+PVts-β non-seasonal detection approach
+ Tarazona
+ Canadian Journal of Remote
+Sensing
+ 47
+ 10.1080/07038992.2021.1941823
+ 2021
+ Tarazona, Y., Alaitz, Z., Xavier, P.,
+Antoni, B., Jakub, N., & Hamdi A., Z. (2021). Fusing Landsat and SAR
+data for mapping tropical deforestation through machine learning
+classification and the PVts-β non-seasonal detection approach. Canadian
+Journal of Remote Sensing, 47, 677–696.
+https://doi.org/10.1080/07038992.2021.1941823
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+ Monitoring tropical forest degradation using
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+https://doi.org/10.1016/j.rsase.2020.100337
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+ Improving tropical deforestation detection
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+practices for estimating area and assessing accuracy of land change.
+Remote Sensing of Environment, 148, 42–57.
+https://doi.org/10.1016/j.rse.2014.02.015
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+ Satellite-based data fusion crop type
+classification and mapping in Rio Grande do Sul, Brazil
+ Pott
+ ISPRS Journal of Photogrammetry and Remote
+Sensing
+ 176
+ 10.1016/j.isprsjprs.2021.04.015
+ 0924-2716
+ 2021
+ Pott, L. P., Amado, T. J. C.,
+Schwalbert, R. A., Corassa, G. M., & Ciampitti, I. A. (2021).
+Satellite-based data fusion crop type classification and mapping in Rio
+Grande do Sul, Brazil. ISPRS Journal of Photogrammetry and Remote
+Sensing, 176, 196–210.
+https://doi.org/10.1016/j.isprsjprs.2021.04.015
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+ Recent applications of Landsat 8/OLI and
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+& Sanches, I. D. (2020). Recent applications of Landsat 8/OLI and
+Sentinel-2/MSI for land use and land cover mapping: A systematic review.
+Remote Sensing, 12(18).
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+ Geo-spatial Information
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+ 10.1080/10095020.2019.1710438
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+ Trinder, J., & Liu, Q. (2020).
+Assessing environmental impacts of urban growth using remote sensing.
+Geo-Spatial Information Science, 23, 20–39.
+https://doi.org/10.1080/10095020.2019.1710438
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+
+ The role of satellite remote sensing in
+climate change studies
+ Yang
+ Nature Climate Change
+ 3
+ 10.1038/nclimate1908
+ 1758-6798
+ 2013
+ Yang, J., Gong, P., Fu, R., Zhang,
+M., Chen, J., Liang, S., Xu, B., Shi, J., & Dickinson, R. (2013).
+The role of satellite remote sensing in climate change studies. Nature
+Climate Change, 3, 875–883.
+https://doi.org/10.1038/nclimate1908
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+
+ Integrating remote sensing with ecology and
+evolution to advance biodiversity conservation
+ Cavender-Bares
+ Nature Ecology & Evolution 2022
+6:5
+ 6
+ 10.1038/s41559-022-01702-5
+ 2397-334X
+ 2022
+ Cavender-Bares, J., Schneider, F. D.,
+Santos, M. J., Armstrong, A., Carnaval, A., Dahlin, K. M., Fatoyinbo,
+L., Hurtt, G. C., Schimel, D., Townsend, P. A., Ustin, S. L., Wang, Z.,
+& Wilson, A. M. (2022). Integrating remote sensing with ecology and
+evolution to advance biodiversity conservation. Nature Ecology &
+Evolution 2022 6:5, 6, 506–519.
+https://doi.org/10.1038/s41559-022-01702-5
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+ Remote sensing of natural hazard-related
+disasters with small drones: Global trends, biases, and research
+opportunities
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+ Remote Sensing of Environment
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+ 10.1016/J.RSE.2021.112577
+ 0034-4257
+ 2021
+ Kucharczyk, M., & Hugenholtz, C.
+H. (2021). Remote sensing of natural hazard-related disasters with small
+drones: Global trends, biases, and research opportunities. Remote
+Sensing of Environment, 264, 112577.
+https://doi.org/10.1016/J.RSE.2021.112577
+
+
+ The Turing Way: A handbook for reproducible
+data science
+ The Turing Way Community
+ 10.5281/ZENODO.3233986
+ 2019
+ The Turing Way Community, Arnold, B.,
+Bowler, L., Gibson, S., Herterich, P., Higman, R., Krystalli, A.,
+Morley, A., O’Reilly, M., & Whitaker, K. (2019). The Turing Way: A
+handbook for reproducible data science.
+https://doi.org/10.5281/ZENODO.3233986
+
+
+ Global-scale hydrological response to future
+glacier mass loss
+ Huss
+ Nature Climate Change
+ 8
+ 10.1038/s41558-017-0049-x
+ 2018
+ Huss, M., & Hock, R. (2018).
+Global-scale hydrological response to future glacier mass loss. Nature
+Climate Change, 8, 135–140.
+https://doi.org/10.1038/s41558-017-0049-x
+
+
+ Accelerated global glacier mass loss in the
+early twenty-first century
+ Hugonnet
+ Nature
+ 592
+ 10.1038/s41586-021-03436-z
+ 2018
+ Hugonnet, R., McNabb, R., Berthier,
+E., Menounos, B., Nuth, C., Girod, L., Farinotti, D., Huss, M.,
+Dussaillant, I., Brun, F., & Kääb, A. (2018). Accelerated global
+glacier mass loss in the early twenty-first century. Nature, 592,
+726–731.
+https://doi.org/10.1038/s41586-021-03436-z
+
+
+
+
+
+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6692
+10.21105/joss.06692
+
+scikit-eo: A Python package for Remote Sensing Data
+Analysis
+
+
+
+https://orcid.org/0000-0002-5208-1004
+
+Tarazona
+Yonatan
+
+
+
+
+https://orcid.org/0000-0002-9884-6471
+
+Benitez-Paez
+Fernando
+
+
+
+
+https://orcid.org/0000-0002-1057-3721
+
+Nowosad
+Jakub
+
+
+
+
+https://orcid.org/0000-0002-9443-9596
+
+Drenkhan
+Fabian
+
+
+
+
+https://orcid.org/0000-0003-1559-4449
+
+Timaná
+Martín E.
+
+
+
+
+
+Department of Earth Sciences, Center for Earth and Space
+Research (CITEUC), University of Coimbra, Portugal
+
+
+
+
+The School of Geography and Sustainable Development,
+University of St Andrews, The UK
+
+
+
+
+Adam Mickiewicz University in Poznań
+
+
+
+
+Geography and the Environment, Department of Humanities,
+Pontificia Universidad Católica del Perú, Lima, Peru
+
+
+
+
+Applied Geography Research Center, Pontificia Universidad
+Católica del Perú, Lima, Peru
+
+
+
+
+29
+3
+2024
+
+9
+99
+6692
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+Python
+Remote Sensing
+Earth Observation
+Machine Learning
+Deep Learning
+Spatial Analysis
+
+
+
+
+
+ Summary
+
In recent years, a growing body of space-borne and drone imagery
+ has become available with increasing spatial and temporal resolutions.
+ This remotely sensed data has enabled researchers to address and
+ tackle a broader range of challenges effectively by using novel tools
+ and data. However, analysts spend an important amount of time finding
+ the adequate libraries to read and process remotely sensed data.
+
With an increasing amount of open access data, there is a growing
+ need to account for effective open source tools to read, process and
+ execute analysis that contributes to underpin patterns, changes and
+ trends that are critical for environmental studies. Applications that
+ integrate spatial-temporal data are used to study a variety of complex
+ environmental processes, such as monitoring and assessment of land
+ cover changes
+ (Chaves
+ et al., 2020), crop classifications
+ (Pott
+ et al., 2021), deforestation
+ (Tarazona
+ et al., 2018), impact on urbanization level
+ (Trinder
+ & Liu, 2020) and climate change impacts
+ (Yang
+ et al., 2013). Other complex environmental processes that are
+ monitored by integrating spatial-temporal data are assessments of
+ glacier retreat
+ (Hugonnet
+ et al., 2018), related hydrological change
+ (Huss
+ & Hock, 2018), biodiversity conservation
+ (Cavender-Bares
+ et al., 2022) and disaster management
+ (Kucharczyk
+ & Hugenholtz, 2021).
+
To bridge the gaps in remotely sensed data processing tools, we
+ here introduce scikit-eo, a brand-new Python package for
+ satellite remote sensing analysis. Unlike other tools, it is a
+ centralized, scalable, and open-source toolkit due to its flexibility
+ in being adapted into large dataset processing pipelines. It provides
+ central access to the most commonly used Python functions in remote
+ sensing analysis for environmental studies, including machine learning
+ methods. scikit-eo stands out with its ability to be used
+ in various settings, from a lecturer room to a crucial part of any
+ Python environment in a research project. The majority of the tools
+ included in scikit-eo are derived from peer-reviewed
+ scientific publications, ensuring their reliability and accuracy.
+
By integrating this diverse set of tools, scikit-eo
+ allows to focus on analyzing the results of data rather than being
+ bogged down by complex lines of code. With its centralized structure,
+ integrated use cases, and example data, scikit-eo
+ empowers to optimize resources and dedicate more attention to the
+ meaningful interpretation of findings in a more efficient way.
+
+
+ Statement of Need
+
As remote sensing data and sophisticated processing tools become
+ increasingly available, there is a growing need for scalable and
+ customized toolkits to help environmental researchers classify
+ satellite and drone imagery quickly and accurately. Our goal is to
+ simplify the identification of patterns, changes, and trends that are
+ crucial for environmental research and analysis.
+
In this paper, we introduce scikit-eo, a specialized
+ library with tailored analysis capabilities designed to meet the
+ unique demands of environmental studies. From statistical methods to
+ machine learning algorithms, scikit-eo assists
+ researchers in uncovering intricate spatial patterns, relationships,
+ and trends, while also simplifying the evaluation and calibration of
+ generated outputs.
+
+
Workflow of main functionalities of the
+ scikit-eo python package as well as outputs that
+ can be obtained by using the tools developed.
+
+
+
+
scikit-eo is an open-source package built entirely in
+ Python through Object-Oriented Programming and Structured Programming
+ that provides a helpful variety of remote sensing tools (see
+ [fig:workflow]),
+ from primary and exploratory functions to more advanced methods to
+ classify, calibrate, or fuse satellite imagery. Depending on the
+ users’ needs, scikit-eo can provide the basic but
+ essential land cover characterization mapping, including the confusion
+ matrix and the required metrics such as user’s accuracy, producer’s
+ accuracy, omission and commission errors. These required metrics can
+ be combined as a pandas DataFrame object.
+ Furthermore, a class prediction map is a result of land cover mapping,
+ i.e., a land cover map, which represents the output of the
+ classification algorithm or the output of the segmentation algorithm.
+ These two outcomes must include uncertainties with a confidence level
+ (e.g., at
+
+ 95%
+ or
+
+ 90%).
+ All required metrics from the confusion matrix can be easily computed
+ and included confidence levels with scikit-eo following
+ guidance proposed by Olofsson et al.
+ (2014).
+ Other useful tools for remote sensing analysis can be found in this
+ package; and for more information about the full list of the supported
+ functions, tutorials as well as how to install and execute the package
+ within a Python setting, visit the
+ scikit-eo
+ website.
+
+
+ Audience
+
scikit-eo is an adaptable Python package that covers
+ multiple users, including students, remote sensing professionals,
+ environmental analysis researchers, and organizations looking for
+ satellite image analysis. Its tools and algorithms implemented make it
+ well-suited for various applications, such as university teaching,
+ that includes technical and practical sessions and cutting-edge
+ research using the most recent machine learning and deep learning
+ techniques applied to remote sensing.
+
This python package provides key tools for both students seeking
+ insights from a satellite image analysis or an experienced researcher
+ looking for advanced tools. scikit-eo offers a valuable
+ resource to support the most valuable methods for environmental
+ studies.
+
+ scikit-eo as a research tool:
+
In environmental studies, particularly in land cover
+ classification, the availability of scalable but user-friendly
+ software tools is crucial for facilitating research, analysis, and
+ modelling. With the widespread adoption of Python as one of the most
+ popular programming languages, particularly in the GIScience and
+ remote sensing fields, developing specialized packages has massively
+ enhanced the effectiveness of environmental research.
+ scikit-eo is a dedicated piece of software tailored to
+ address unique challenges encountered in land cover mapping, forest
+ or land degradation
+ (Tarazona
+ & Miyasiro-López, 2020), and the fusion of multiple
+ satellite imagery from several formats
+ (Tarazona
+ et al., 2021). scikit-eo provides the assessment
+ and calibration metrics to evaluate the provided outputs. The
+ current version scikit-eo requires that users provide
+ the dataset to process. However, we expect to provide a wide range
+ of functionalities for acquiring environmental data from diverse
+ sources and file formats, enabling researchers to access satellite
+ imagery.
+
One of scikit-eo’s key strengths is its advanced
+ analysis capabilities. It provides a rich suite of algorithms
+ specifically designed for environmental studies, including
+ statistical analysis, deep learning, data fusion, and spatial
+ analysis. Researchers can leverage these tools to explore patterns,
+ relationships, and trends within their datasets, uncover complex
+ land or forest degradation or mapping, classify the land cover, and
+ generate insightful visualizations.
+
As a particular example of these advanced analysis capabilities,
+ we have integrated the
+ deepLearning function, which
+ includes the Fully connected layers (FC), also
+ known as dense layers model. This is one of the
+ most straightforward yet functional neural networks we can apply to
+ remote sensing analysis. The term “fully connected” comes from the
+ fact that each neuron in one layer is connected to every neuron in
+ the preceding layer, creating a highly interconnected network known
+ as the Multi-Layer Perceptron (MLP). The model is trained using a
+ specified dataset, with the bands as input_shape,
+ including input features and corresponding class labels. The weights
+ W are initialized and then adjusted during training
+ to ensure the neural network’s output is consistent with the class
+ labels. The training process involves minimizing the error function
+ using Gradient Descent and
+ backpropagation algorithms. The activation
+ functions used in this model are ReLU (Rectified Linear
+ Unit) for the neurons in each hidden layer and
+ Softmax for the final classification layer. For
+ more details, see tutorial No
+ 11
+ In future version, u-net architectures will be implemented within
+ scikit-eo.
+
It’s important to note that ReLU introduces
+ non-linearity to the model, enabling it to learn complex patterns,
+ while Softmax is used for multi-class
+ classification, transforming the output into a probability
+ distribution over multiple classes and better suited for more than
+ two land covers. Unlike traditional machine learning models, such as
+ support vector machine or decision tree, which typically are simpler
+ and don’t involve multiple layers, the FC model uses multiple hidden
+ layers, allowing it to learn hierarchical representations of the
+ input data. Deep learning models like this one can automatically
+ learn and extract complex features from the raw input, making them
+ exceptionally powerful for tasks such as land cover
+ classification.
+
To run an example of how to use the function
+ deepLearning find a detailed
+ notebook in tutorial No 11
+ Deep
+ Learning Classification.
+
+
+ scikit-eo in the lecture room:
+
scikit-eo can be part of a classroom as part of the
+ set of tools for environmental studies where a quantitative approach
+ and computer labs are required. Therefore, first of all an
+ appropriate introduction of Python, the basics of remote sensing,
+ and the relevance of environmental studies to address climate change
+ challenges or impacts of anthropogenic activity are needed. Lectures
+ can use the simplicity of scikit-eo routines to execute
+ supervised classification methods,
+ Principal Components Analysis,
+ Spectral Mixture Analysis,
+ Mapping forest or
+ land degradation and more types of analysis.
+ By reducing the number of required lines of code, students can focus
+ on the analysis and how the methods work rather than dealing with
+ complex and unnecessary programming tasks. Lecturers can structure
+ their computer labs using open data sources and integrate
+ scikit-eo to allow students to understand the
+ importance of the calibration and assessment metrics, get insights
+ about the classification mapping using satellite imagery, and
+ provide an introduction to more advanced methods that include
+ machine learning techniques.
+
+
+ scikit-eo as open source tool:
+
As open-source software keeps transforming the landscape of
+ scientific research
+ (The
+ Turing Way Community et al., 2019), enabling collaboration,
+ reproducibility and transparency, scikit-eo was
+ explicitly developed as an open-source tool. scikit-eo
+ integrates most of the popular open source python libraries from the
+ so-called geo-python stack for remote sensing (e.g.,.
+ numpy,
+ pandas,
+ rasterio
+ and few more) to extent and create a centralised package for
+ advanced spatial analysis of remotely sensed data. The package
+ provides researchers and developers with a free, scalable, and
+ community-driven platform to process, analyse, and visualise
+ satellite imagery, specifically, centralising multiple functions’
+ use for classification and mapping land cover.
+
+
+
+ Functionalities
+
+ Main tools
+
Scikit-eo includes several algorithms to process
+ satellite images to assess complex environmental processes and
+ impacts. These include functions such as atmospheric correction,
+ machine learning and deep learning techniques, estimating area and
+ uncertainty, linear trend analysis, combination of optical and radar
+ images, and classification sub-pixel, and more. The main functions
+ are listed below:
+
+
+
Main tools available for scikit-eo package.
+
+
+
+
+
+
+
+
+
+
Name of functions/classes
+
Description
+
+
+
+
+
mla
+
Supervised Classification in Remote Sensing
+
+
+
calmla
+
Calibrating Supervised Classification in Remote
+ Sensing
+
+
+
confintervalML
+
Information of Confusion Matrix by proportions of area,
+ overall accuracy, user’s accuracy with confidence interval
+ and estimated area with confidence interval as well.
+
+
+
deepLearning
+
Deep Learning algorithms
+
+
+
atmosCorr
+
Radiometric and Atmospheric Correction (currently
+ supporting Landsat)
+
+
+
rkmeans
+
K-means classification
+
+
+
calkmeans
+
This function allows to calibrate the kmeans algorithm.
+ It is possible to obtain the best k value and the best
+ embedded algorithm in kmeans.
+
+
+
pca
+
Principal Components Analysis
+
+
+
linearTrend
+
Linear trend is useful for mapping forest degradation or
+ land degradation
+
+
+
fusionrs
+
This algorithm allows to fuse images coming from
+ different spectral sensors (e.g., optical-optical, optical
+ and SAR or SAR-SAR). Among many of the qualities of this
+ function, it is possible to obtain the contribution (%) of
+ each variable in the fused image
For more information the reader is referred to the
+ scikit-eo
+ website.
+
+
+
+ State of the field:
+
Scikit-eo is built upon well-known packages and
+ libraries that support remote sensing analysis in python, but is
+ designed specifically to study land cover classification, and
+ providing tailored functionalities for environmental studies. It aims
+ to simplify the identification of patterns, changes, and trends for
+ environmental research. Like many other Python packages,
+ Scikit-eo makes use of Rasterio and
+ GDAL, which are essential for geospatial data
+ handling. Additionally, Scikit-eo is based on
+ Scikit-learn and tensorflow, a widely-used
+ machine learning libraries in Python that includes several algorithms
+ for classification, regression, clustering, and dimensionality
+ reduction. However, Scikit-eo includes machine learning
+ tools to remote sensing analysis. Another well-known library,
+ Geemap that provides interactive mapping capabilities
+ using Google Earth Engine and focuses more on visualization and data
+ exploration, while Scikit-eo is designed for deeper
+ analytical tasks using remote sensing data for land cover analysis.
+ The SITS package is particularly useful for time
+ series, while Scikit-eo provides functionalities for land
+ cover studies. torchgeo a popular Python library that
+ provides comprehensive deep learning functions for geospatial data.
+ However Scikit-eo integrates machine learning methods
+ that are particularly useful for analysing satellite imagery with
+ multiple bands for environmental studies. Lastly,
+ EO-learn can be considered the most aligned package
+ with Scikit-eo providing efficient processing and
+ analysis of satellite imagery capabilities but lacking the deep
+ learning and tailored functions specifically included for land cover
+ analysis.
+
+
+ Acknowledgments
+
The authors would like to thank to David Montero Loaiza for the
+ idea of the package name and Qiusheng Wu for the suggestions that
+ helped to improve the package.
+
+
+
+
+
+
+
+
+ TarazonaYonatan
+ AlaitzZabala
+ XavierPons
+ AntoniBroquetas
+ JakubNowosad
+ Hamdi A.Zurqani
+
+ Fusing Landsat and SAR data for mapping tropical deforestation through machine learning classification and the PVts-β non-seasonal detection approach
+
+ Taylor & Francis Online
+ 2021
+ 47
+ 10.1080/07038992.2021.1941823
+ 677
+ 696
+
+
+
+
+
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