the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
A global daily gap-filled chlorophyll-a dataset in open oceans during 2001–2021 from multisource information using convolutional neural networks
Zhongkun Hong
Xingdong Li
Yiming Wang
Jianmin Zhang
Hamouda Abdelmoghny Mohamed
Mohamed Mostafa Ahmed Mohamed
Abstract. Ocean color data are essential for developing our understanding of biological and ecological phenomena and processes, and also important sources of input for physical and biogeochemical ocean models. Chlorophyll-a (Chl-a) is a critical variable of ocean color in the marine environment. Quantitative retrieval from satellite remote sensing is a main way to obtain large-scale oceanic Chl-a. However, data missing is a major limitation in satellite remote sensing-based Chl-a products, due mostly to the influence of cloud, sun glint contamination, and high satellite viewing angles. The common methods to reconstruct (gap filling) missing data often consider spatiotemporal information of initial images alone, such as data interpolation empirical orthogonal function, optimal interpolation, Kriging interpolation, and extended Kalman filter. However, these methods do not perform well in the presence of large-scale missing values in the image and ignore the potential of other information on missing pixels in the data reconstruction. Here we developed a convolutional neural network (CNN) named OCNET for Chl-a concentration data reconstruction in open ocean areas, considering environmental variables that are associated with ocean phytoplankton growth and distribution. Sea surface temperature (SST), salinity (SAL), photosynthetically active radiation (PAR), and sea surface pressure (SSP) from reanalysis data and satellite observations were selected as the input of OCNET to correlate with the environment and phytoplankton mass. The developed OCNET model achieves good performance in the reconstruction of global ocean Chl-a concentration data, and captures temporal variations of these features. This study also shows the potential of machine learning in large-scale ocean color data reconstruction and offers the possibility to predict Chl-a concentration trends under a changing environment.
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Zhongkun Hong et al.
Status: final response (author comments only)
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RC1: 'Comment on essd-2023-257', Anonymous Referee #1, 05 Aug 2023
The variation of Chl-a concentration in the global ocean surface is influenced by various complex factors, which poses challenges to accurately retrieve Chl-a concentration. In this manuscript, the authors selected Chl-a data products retrieved from satellite data as a reference, supplemented by reanalysis data to provide environmental factor information. By combining the advantages of machine learning in big data analysis and simulation, they ultimately reconstructed a global-scale, long-term time series of Chl-a concentration dataset. The results show that the OCNET model performs very well in reconstructing Chl-a concentrations, accurately capturing the temporal variations of these features. This suggests that the model has strong potential for use in large-scale ocean color data reconstruction, and may even be able to predict Chl-a concentration trends in response to changes in the environment.
The dataset is extremely valuable for a wide range of researchers, policymakers, and managers involved in the monitoring and management of aquatic ecosystems. This study and its results are really novel and impressive to me.
Some suggestions are given as follows:
Pg. 3, Lines 65-66: Please provide an explanation for the difference between OCNET and the CNNs used in previous studies (Cao et al., 2020; Jin et al., 2021; Cen et al., 2022; Yussof et al., 2021). Clarifying this distinction would enhance the reader's understanding of the novelty of the OCNET model.
Pg. 6, Lines 125-126: The authors state that "We have selected three environmental variables, i.e., sea surface temperature (SST), salinity (SAL), and photosynthetically active radiation (PAR) as the input data for the OCNET model." However, it appears that the input data also contain SSP. Please address this discrepancy and provide clarity on whether SSP is included in the input data or not.
Overall, I find this study and its results to be highly promising and valuable for the scientific community. With the suggested clarifications and improvements, this manuscript has the potential to make a significant contribution to the field of Chl-a concentration retrieval and ocean color data reconstruction.
Citation: https://doi.org/10.5194/essd-2023-257-RC1 -
CC2: 'Reply on RC1', Zhongkun Hong, 18 Aug 2023
Thank you very much for your valuable suggestions. OCNET, a modified U-Net architecture, deviates from the Convolutional Neural Network (CNN) in terms of network structure. We will further elaborate on the distinctive features of OCNET in the revised manuscript. Regarding the selection of model input data, the three variables – sea surface temperature (SST), salinity (SAL), and photosynthetically active radiation (PAR) – are expounded upon in the subsequent sentence: "These variables play a significant role in influencing the growth of marine phytoplankton." Additionally, SSP is certainly one of the model's input data, but it affects the transport of nutrients and the spatial distribution of phytoplankton. We will provide further clarification in the revised manuscript to avoid ambiguity. Once again, we sincerely appreciate your suggestions!
Citation: https://doi.org/10.5194/essd-2023-257-CC2
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CC2: 'Reply on RC1', Zhongkun Hong, 18 Aug 2023
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CC1: 'Comment on essd-2023-257', Andrew C. Ross, 17 Aug 2023
I agree with reviewer #1 that this dataset has the potential to be extremely valuable (I found it while searching for a gapless daily chl dataset to test an idea on), and I thank the authors for making their data publicly available. However, I'm leaving this comment to suggest that the authors provide the data as netCDF files, perhaps one for each year, which would meet this journal's request that the data be provided in a non-proprietary community-established format that is findable, accessible, interoperable, and reusable. In the repository linked in the manuscript, the data are provided as 74 .rar files, each containing a number of ascii files. Every interested user (including myself, right now) will have to download and extract all 74 rar files, then write their own code to read the non-standard format and take a guess at some of the missing metadata (e.g., units).
Citation: https://doi.org/10.5194/essd-2023-257-CC1 -
CC3: 'Reply on CC1', Zhongkun Hong, 18 Aug 2023
Thank you very much for your suggestions! Previously, due to unstable data website transmission, the dataset was divided into numerous smaller files for uploading, which indeed caused inconvenience. The second version of the dataset has been re-uploaded. Please refer to https://doi.org/10.5281/zenodo.8262779. This version of the dataset consists of one NetCDF file per year, with unit information specified. Due to the 50GB total data upload limit on the ZENODO website, we have compressed and uploaded the NetCDF files for every two years. Subsequent updates to the dataset index will be provided in the manuscript. Thank you once again for your valuable suggestions!
Citation: https://doi.org/10.5194/essd-2023-257-CC3
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CC3: 'Reply on CC1', Zhongkun Hong, 18 Aug 2023
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RC2: 'Comment on essd-2023-257', Anonymous Referee #2, 26 Sep 2023
This manuscript describes a large dataset from 2001-2021 for global daily gap filled chlorophyll-a. The authors developed a convolutional neural network called OCNET to reconstruct global chlorophyll-a concentration in open oceans. This dataset is very useful and important for the scientific community. The manuscript in general is well written, but would benefit from some minor clarifications, and adjustments before publication.
Kindly check the attached pdf document to see my comments
Zhongkun Hong et al.
Data sets
OCNET global daily Chlorophyll-a products Zhongkun Hong, Di Long, Xingdong Li, Yiming Wang, Jianmin Zhang, Mohamed A. Hamouda, and Mohamed M. Mohamed https://doi.org/10.5281/zenodo.8105194
Zhongkun Hong et al.
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