From 84ea459bc4452f416a00126a03ab2f6d001d3a84 Mon Sep 17 00:00:00 2001 From: ctroupin <charles.troupin@gmail.com> Date: Mon, 24 Dec 2018 22:52:12 +0100 Subject: [PATCH] replies finalised --- latex/Reply_Referee1.tex | 2 +- latex/Reply_Referee2.tex | 102 ++++++++++++++++++++++----------------- latex/Reply_Referee3.tex | 86 +++++++++++++++++++++++++++++++++ 3 files changed, 145 insertions(+), 45 deletions(-) diff --git a/latex/Reply_Referee1.tex b/latex/Reply_Referee1.tex index d0b64e6..a44f050 100644 --- a/latex/Reply_Referee1.tex +++ b/latex/Reply_Referee1.tex @@ -56,7 +56,7 @@ \parskip .2cm \title{Interactive comment on "The AlborEX dataset: sampling of submesoscale features in the Alboran Sea"} -\author{Anonymous Referee \#2} +\author{Anonymous Referee \#1} \date{} \begin{document} diff --git a/latex/Reply_Referee2.tex b/latex/Reply_Referee2.tex index 5f3fc9b..bf82d8a 100644 --- a/latex/Reply_Referee2.tex +++ b/latex/Reply_Referee2.tex @@ -137,19 +137,19 @@ For each platform, we indicated the basic configuration as well as the number of - Figure 2 too small (should take page width) \begin{reply} -$\rightarrow$ Figures 1 and 2 have been enlarged in the new manuscript + Figures 1 and 2 have been enlarged in the new manuscript \end{reply} - Figure 2 caption: there is mention of "flag data equal to 1" while these flag are not introduced in the text. \begin{reply} -$\rightarrow$ SST is not part of the dataset, we just use them to illustrate the situation during the mission, this is why we did not go into details concerning the flag = 1, which is explicitly described in the caption (good data). + SST is not part of the dataset, we just use them to illustrate the situation during the mission, this is why we did not go into details concerning the flag = 1, which is explicitly described in the caption (good data). \end{reply} - p.7, L1: The "total number of valid measurement" is not very useful. I would rather put the number of valid casts (see comment above on a new table with this info). \begin{reply} -$\rightarrow$ We agree. The number of valid measurements (for the gliders) has been removed and replaced by the number of casts, in the new manuscript. + We agree. The number of valid measurements (for the gliders) has been removed and replaced by the number of casts, in the new manuscript. \end{reply} - p.7, L6: "a spatial interpolation is applied on the original data, leading to the so-called Level-2 data, further described in Sec. 3.3." What does 'spatial interpolation' means? Section 3.3 is not very explicit on this. I know you mean that the glider yos have been separated into downward and upward casts and then assigned to a geographical coordinate, but maybe this should be stated explicitly (and I don't think "spatial interpolation" is an accurate description). Moreover, Is there any vertical interpolation done? Because there are still some NaNs in L2 data. @@ -171,7 +171,7 @@ For the spatial and temporal coordinates: the new coordinates of the profiles ar \end{description} \end{newtext} -- p.7, L15: "Interestingly, all the drifters exhibit a trajectory close to the front position" -> Not clear what "trajectory close to the front means". Moreover, is that really surprising that surface drifter would aggregate on a front? +- p.7, L15: "Interestingly, all the drifters exhibit a trajectory close to the front position" $\rightarrow$ Not clear what "trajectory close to the front means". Moreover, is that really surprising that surface drifter would aggregate on a front? \begin{reply} We remove the "Interestingly", as indeed it is expected and rephrased it to: @@ -179,10 +179,10 @@ We remove the "Interestingly", as indeed it is expected and rephrased it to: \end{reply} -- Figure 8 caption: "for the duration of the mission" -> You mean the ship mission? Or the AlborEX campaign? +- Figure 8 caption: "for the duration of the mission" $\rightarrow$ You mean the ship mission? Or the AlborEX campaign? \begin{reply} -$\rightarrow$ We meant for the AlborEX mission; this has been made explicit in the new manuscript. The caption now reads: + We meant for the AlborEX mission; this has been made explicit in the new manuscript. The caption now reads: \end{reply} \begin{newtext} @@ -193,14 +193,14 @@ Surface drifter trajectories. For the sake of simplicity and clarity, the temper - Figure 10: plots on the right column are of little information here (too low resolution to mean something), I would remove. \begin{reply} -$\rightarrow$ We agree that the resolution is not as good as the Arvor-C float, but for completeness we would prefer not to discard them. + We agree that the resolution is not as good as the Arvor-C float, but for completeness we would prefer not to discard them. \end{reply} - Table 1: "Period" should be replaced by "cycle length" as referred to in the text (Section 2.2.4). \begin{reply} -$\rightarrow$ Modified as suggested. + Modified as suggested. \end{reply} @@ -208,36 +208,36 @@ $\rightarrow$ Modified as suggested. 24T12:02:59+00:00, which is different from this table. \begin{reply} -$\rightarrow$ The correct date is indeed 2015-04-24T12:02:59+00:00. The table has been modified accordingly. + The correct date is indeed 2015-04-24T12:02:59+00:00. The table has been modified accordingly. \end{reply} - Figure 11 caption: "quality flag" not defined. \begin{reply} -$\rightarrow$ Quality flag with a value of 1 (meaning "good data") is specified in the caption. We added a complete description in the text concerning this part. + Quality flag with a value of 1 (meaning "good data") is specified in the caption. We added a complete description in the text concerning this part. \end{reply} - Section 3.3.1: A Section on processing levels, but they are not all provided. Why? I think all levels should be provided. This is related to a previous comment. \begin{reply} -$\rightarrow$ The origin of the initial decision of not providing the L0 data for all the files is twofold: + The origin of the initial decision of not providing the L0 data for all the files is twofold: For some platforms (gliders), the L0 files are rather large and contain many variables related to the platform engineering, no to oceanography. Even if the files were not provided through the Zenodo platform, they are still publicly available using the SOCIB thredds server. In the new version of the manuscript, we adopted a new way to distribute the data (the data catalog), in which the data files corresponding to all the processing levels are made available. \end{reply} -- p.14, Level 2 (L2): "obtained by interpolating the L1 data" -> How L2 is obtained by "interpolating" L1? Isn't L1 cut into casts that makes L2? +- p.14, Level 2 (L2): "obtained by interpolating the L1 data" $\rightarrow$ How L2 is obtained by "interpolating" L1? Isn't L1 cut into casts that makes L2? \begin{reply} -$\rightarrow$ Correct. It is not an interpolating but a gridding. The explanation of how this gridding is performed has been added to the manuscript. + Correct. It is not an interpolating but a gridding. The explanation of how this gridding is performed has been added to the manuscript. \end{reply} -- p.14, Level 2 (L2): "It is only provided for gliders, mostly for visualization and post-processing purposes: specific tools designed to read and display profiler data can then be used the same way for gliders." -> Is there a problem with this sentence? I don't understand it. +- p.14, Level 2 (L2): "It is only provided for gliders, mostly for visualization and post-processing purposes: specific tools designed to read and display profiler data can then be used the same way for gliders." $\rightarrow$ Is there a problem with this sentence? I don't understand it. \begin{reply} -$\rightarrow$ We removed the part of the sentence starting with "post-processing purposes" + We removed the part of the sentence starting with "post-processing purposes" \end{reply} - Section 3.3.1 / Table 3: Is L1 level for float equivalent to L2 level for glider? For consistency, I think profiling float should have L1 and L2 data as well since these instruments have similarities on the way they profile the water column\ldots @@ -250,19 +250,19 @@ The L1 glider data consists of a 3-dimensional trajectories, which means that bo \end{figure} \end{reply} -- p.12, L1: "This type of current measurements requires a careful processing in order to get meaningful velocities from the raw signal" -> Why? What are the limitations that makes this instrument more sensitive compare to other ones? +- p.12, L1: "This type of current measurements requires a careful processing in order to get meaningful velocities from the raw signal" $\rightarrow$ Why? What are the limitations that makes this instrument more sensitive compare to other ones? \begin{reply} -$\rightarrow$ The main reason for this sensitivity is the fact that the vessel's velocity is one or two order or magnitudes greater than the currents that have to be measured. It is thus critical to have good measurements of the vessel heading and velocity. + The main reason for this sensitivity is the fact that the vessel's velocity is one or two order or magnitudes greater than the currents that have to be measured. It is thus critical to have good measurements of the vessel heading and velocity. A sentence has been inserted at the beginning of that paragraph and we removed the sentence "\textit{hence it is relevant to have a quality flag (QF) assigned to each measurement}". \end{reply} -- p.12, L4: "Figure 12 shows the QF during the whole mission." -> How QF are calculated? +- p.12, L4: "Figure 12 shows the QF during the whole mission." $\rightarrow$ How QF are calculated? \begin{reply} -$\rightarrow$ The QC procedure for the VM-ADCP is complex as it involves tests on a large number of variables such as: + The QC procedure for the VM-ADCP is complex as it involves tests on a large number of variables such as: \begin{itemize} \item[] Bottom Track Direction \item[]Bottom Track Velocity @@ -297,17 +297,17 @@ The vessel's velocity is one or two order or magnitudes greater than the current - Figure 12: Too small. \begin{reply} -$\rightarrow$ the figure has been enlarged in the new manuscript. + the figure has been enlarged in the new manuscript. \end{reply} - Figure 12 and text below: 9 different quality flag are presented without any introduction on how they are calculated. \begin{reply} -$\rightarrow$ The new paragraph in the same section (see comment before) now explains how the quality flag are assigned. + The new paragraph in the same section (see comment before) now explains how the quality flag are assigned. \end{reply} - Section 3.3.2 is very short. Should be re-worked following comments above. \begin{reply} -$\rightarrow$ We agree that the section dedicated to the Quality Control was too short. The QC are now described as follows: + We agree that the section dedicated to the Quality Control was too short. The QC are now described as follows: A general description in Section "2.5.2 QC tests" and Specific explanations of the tests performed for each platform, making that part more self-contained. \end{reply} @@ -324,13 +324,13 @@ Here are some comments: - There are very large spikes in deep glider turbidity \begin{reply} -$\rightarrow$ yes, as the provided datasets for gliders have not undergone the quality checks (yet), there are still spikes and bad values for some of the variables. The text has been modified accordingly. + yes, as the provided datasets for gliders have not undergone the quality checks (yet), there are still spikes and bad values for some of the variables. The text has been modified accordingly. \end{reply} - There are missing data for about 10h in deep glider data between May 25-26. Unless I missed it, no explanation for this are provided. \begin{reply} -$\rightarrow$ The referee is right, some data are missing because the glider payload suffered an issue with the data logging software, resulting in no data acquisition during a few hours, during which the problem was being fixed. After that the data acquisition could be resumed. + The referee is right, some data are missing because the glider payload suffered an issue with the data logging software, resulting in no data acquisition during a few hours, during which the problem was being fixed. After that the data acquisition could be resumed. This explanation has been added to the corresponding section in the new manuscript. \end{reply} @@ -343,15 +343,27 @@ On May 25 at 19:24 (UTC), the deep glider payload suffered an issue with the dat - Oxygen data for both glider seems to suffer from thermal lag problems \begin{reply} -$\rightarrow$ yes it is true, we have reached the same conclusion when plotting the oxygen data. It is planned to improve the complement the glider toolbox with new functionalities to address that issue. We now mention this issue in the new manuscript. +Yes it is true, we have reached the same conclusion when checking the oxygen data. The issue comes from the sensitivity of the optode to the temperature and the time response of the temperature sensor. + +Comparing the temperature obtained with the glider CTD and the temperature of the oxygen sensor (next Figure) also highlights the lag existing between the 2. + +\begin{figure} +\centering +\includegraphics[width=.75\textwidth]{temperatures_glider.png} +\end{figure} + +To the extent of our knowledge, there is not yet an agreement from the community on how to correct this lag. \citet{NICHOLSON2017} proposed a calibration based on the measurements made with the glider optode of the oxygen partial pressure of the atmosphere. Such a procedure can be contemplated in the near future. \end{reply} \begin{newtext} -"Finally, oxygen data (not shown here) seem to exhibit a lag in the measurements. According to \citep{}, this issue is also related to the time response of oxygen optodes. +Finally, oxygen concentration measurements (not shown here) seem to exhibit a lag. According to \citet{BITTIG2014}, this issue is also related to the time response of oxygen optodes. As far as we know, there is not yet an agreement from the community on how to correct this lag, this is why the data are kept as they are in the present version, though we don't discard an improvement of the glider toolbox to address this specific issue. \end{newtext} - Provor-bio datafile contains levels down to over 7000 m. Some problems are found: 1. Why such long level dimension? + + +\begin{reply} The 7000 comes is the depth dimension, as shown by the "\texttt{ncdump -h}" output: \begin{verbatim} dimensions: @@ -368,10 +380,11 @@ The profiles from PROVBIO are shown in the next 2 figures. \includegraphics[width=.75\textwidth]{provbio_profiles_zoom.png} \caption{Salinity profiles acquired by the PROVBIO float. The 2nd panel depicts the profile in the 500--1000~m layer.} \end{figure} - +\end{reply} 2. No good data is found below \~325m, although Table 1 suggest that the float is profiling to 1000m +\begin{reply} We confirm that the float acquired data up to approx. 2000~m, even though the vertical resolution is not as high as near the surface. We reproduce (see below) the Figure 10 from the manuscript, this time without limiting the depth range, in order to confirm the availability of data at that depth. \begin{figure} @@ -379,7 +392,7 @@ We confirm that the float acquired data up to approx. 2000~m, even though the ve \includegraphics[width=\textwidth]{fig10_new.png} \caption{Adapted figure 10 of the manuscript, with the maximal depth of the profiles displayed.} \end{figure} - +\end{reply} - Arvor A3 data file suffers from similar problem: file contains data only down to 115m while Table 1 says 2000m @@ -389,58 +402,59 @@ For the Arvor A3 we confirm that profiles are available up to approx. 2000 m. Th - Arvor-C data file (only L0 provided) do not contain metadata (no file attributes, etc.). In addition, missing data (at least for temperature) appears to me as very large numbers (9.969210e+36) that makes them difficult to manipulate. -$\rightarrow$ The L0 file with the metadata and the L1 file have been prepared and are now available. The link to the thredds catalog are provided below: +\begin{reply} + The L0 file with the metadata and the L1 file have been prepared and are now available. The link to the thredds catalog are provided below: L0: \url{http://thredds.socib.es/thredds/catalog/drifter/profiler_drifter/profiler_drifter_arvorc001-ime_arvorc001/L0/2014/catalog.html?dataset=drifter/profiler_drifter/profiler_drifter_arvorc001-ime_arvorc001/L0/2014/dep0001_profiler-drifter-arvorc001_ime-arvorc001_L0_2014-05-25.nc} L1: \url{http://thredds.socib.es/thredds/catalog/drifter/profiler_drifter/profiler_drifter_arvorc001-ime_arvorc001/L1/2014/catalog.html?dataset=drifter/profiler_drifter/profiler_drifter_arvorc001-ime_arvorc001/L1/2014/dep0001_profiler-drifter-arvorc001_ime-arvorc001_L1_2014-05-25.nc} - +\end{reply} R/V Socib CTD and thermosalinograph files say that units of temperature are "C". I prefer the convention from glider files which uses "Celsius". \begin{reply} -$\rightarrow$ We take note of the suggestion and will perform the modification in a new release of the data files, as it involves a re-processing of several files from other missions). The referee is totally right, as the Unidata documentation (\url{https://www.unidata.ucar.edu/software/netcdf/netcdf/Units.html}) states that "Celsius" should be used, "C" meaning "Coulomb". + We take note of the suggestion and will perform the modification in a new release of the data files, as it involves a re-processing of several files from other missions). The referee is totally right, as the Unidata documentation (\url{https://www.unidata.ucar.edu/software/netcdf/netcdf/Units.html}) states that "Celsius" should be used, "C" meaning "Coulomb". \end{reply} \subsection*{Minor comments} -- p.2; L23: "makes it possible" -> makes possible +- p.2; L23: "makes it possible" $\rightarrow$ makes possible \begin{reply} -$\rightarrow$ corrected + corrected \end{reply} -- p.2; L23: "creation and publication of aggregated datasets covering the Mediterranean Sea" -> SeaDataNet is not only about the Mediterranean +- p.2; L23: "creation and publication of aggregated datasets covering the Mediterranean Sea" $\rightarrow$ SeaDataNet is not only about the Mediterranean \begin{reply} -$\rightarrow$ replaced by "covering different European regional seas, including the Mediterranean Sea" + replaced by "covering different European regional seas, including the Mediterranean Sea" \end{reply} -- p.2; L32: "thanks due to" -> thanks to +- p.2; L32: "thanks due to" $\rightarrow$ thanks to \begin{reply} -$\rightarrow$ corrected (removed "due") + corrected (removed "due") \end{reply} - Section 2.2.1: "CTD surveys" or CTD legs? \begin{reply} -$\rightarrow$ corrected (legs) + corrected (legs) \end{reply} - Glider L1 files (e.g. \texttt{dep0012\_ideep00\_ime-sldeep000\_L1\_2014-05-25\_data\_dt.nc}) say that the project is "PERSEUS". Is that right? There is no mention of the AlborEX project in the file header. \begin{reply} -$\rightarrow$ Correct, AlborEx was the Subtask 3.3.4 of PERSEUS project, but in this case AlborEx was not explicitly mentioned in the file header. This will be added during the next re-processing of the data files. + Correct, AlborEx was the Subtask 3.3.4 of PERSEUS project, but in this case AlborEx was not explicitly mentioned in the file header. This will be added during the next re-processing of the data files. \end{reply} - p.10, L1: problems with latitude longitude degree symbol. \begin{reply} -$\rightarrow$ corrected + corrected \end{reply} - p.10, L5: temperature, salinity and T,S is use on the same line. Please homogenize. \begin{reply} -$\rightarrow$ replaced by "In addition to these variables" + replaced by "In addition to these variables" \end{reply} - p.12, L17: "Network Common Data Form @@ -448,19 +462,19 @@ $\rightarrow$ replaced by "In addition to these variables" 3, 2018)" Is there a mis-placed parenthesis? \begin{reply} -$\rightarrow$ Corrected, the "(" after {\tt .org} has been removed. + Corrected, the "(" after {\tt .org} has been removed. \end{reply} - p.13, L2: problem with file name (too long for page) \begin{reply} -$\rightarrow$ Corrected (new line added). + Corrected (new line added). \end{reply} - p.16, L25: How stable in time the python codes made available on Github will be? \begin{reply} -$\rightarrow$ Generally, reading netCDF files with Python is an easy task, as it is with other languages (MATLAB, Julia, R), so we do not expect any difficulties for the data users. Here what we did is to provide a set of the Python codes written to show how to read the data and reproduce the plots of the papers, as we think it might save time if somebody wants to create something similar, or even reproduce the paper plot. + Generally, reading netCDF files with Python is an easy task, as it is with other languages (MATLAB, Julia, R), so we do not expect any difficulties for the data users. Here what we did is to provide a set of the Python codes written to show how to read the data and reproduce the plots of the papers, as we think it might save time if somebody wants to create something similar, or even reproduce the paper plot. With Python it is relatively straightforward to use virtual environment, which allows one to work with specific version python modules. If a user works with a virtual environment which has the same packages versions as those specified on GitHub (file \texttt{requirements.txt}), then the code will run (since the netCDF files will be the same). diff --git a/latex/Reply_Referee3.tex b/latex/Reply_Referee3.tex index 38ed7c6..cafcf4a 100644 --- a/latex/Reply_Referee3.tex +++ b/latex/Reply_Referee3.tex @@ -63,4 +63,90 @@ \noindent +\subsection*{Major comments} +- What are the instruments specifications? A list of the parameters measured by each platform along with the corresponding sensor name must be provided for the CTD, glider and profiling floats. + +\begin{reply} +The instrument specifications have been added in the manuscript: for each platform, a subsection "\textit{Configuration}", containing the information about the platform and variables, has been added. +\end{reply} + +- Were they any water sample taken during the cruise in order to calibrate the CTD, or chlorophyll-a fluorescence? More than four years after the experiment, I expect this calibration to be done. These are mentioned p16 l22. Along the same lines, a list of future QC to be applied is advocated p15. I would be reluctant to use such a data set. My conception of publishing a data set in such a journal is that final QC should be performed beforehand, and future users should not worry about it. + +\begin{reply} +You are right, water samples were collected. + +The CTD data calibrated using the bottle data are available as a new processing level called \texttt{L1\_corr}, and now described in the manuscript. +Concerning the chlorophyll-a fluorescence calibration: it is correct that the calibration has not yet been performed. The decision to publish the data in the present state comes from a balance between: +\begin{itemize} +\item The will to share as soon as possible that dataset with the research community interested in the submesoscale, knowing that articles using the dataset have already been published. +\item The need to have the best quality for the dataset. +\end{itemize} +Even if there may still be room for improvement in terms of quality control, for instance by creating new quality checks, our conviction is that the dataset in its current state is mature enough to be employed by other researchers +\end{reply} + +- Section 2.2.2: It is never specified that the gliders were set to surface every 3 (deep) and 10 (shallow) dives. Estimates of depth-average currents by gliders between consecutive surfacing should be mentioned. Those are essential to infer geostrophic velocities. The sampling strategy unfortunately divides by 3 and 10 the number of current estimations. What was the aim of this sampling strategy? Moreover, when the glider does not spend equally distributed time at each depth level, depth-average currents can not be treated as such anymore. How does the QC deal with this issue? To my mind, this is a real weakness of the glider dataset, especially in an experiment dedicated to submesoscale. I discovered this point by looking at the glider data. Readers should be made aware of this in the manuscript. + +\begin{reply} +Thanks for mentioning this issue. It is indeed something that was not properly addressed in the initial manuscript. + +We also believe that it is essential \begin{itemize} +\item to have measurements near the surface to tackle oceanic processes and +\item the highest frequency of profiles near the surface in order to properly estimate the depth-integrated velocity. +\end{itemize} + +The reason why the gliders did not go to the surface for every profile arises from safety concerns: the intense marine traffic (see for example the density maps of MarineTraffic) and the existence of a Traffic Separation Scheme (TSS) near the sampling area were taken into account for the decision to limit the glider surfacing. + +We added a paragraph in the subsection "\textit{Configuration}" with the "\textit{Gliders}" section: +\end{reply} + +\begin{newtext} +Due to safety concerns, both the deep and coastal gliders had their surfacing limited: the deep glider came to the surface one in every 3 profiles, while the coastal gliders came out one in every 10 profiles. While this strategy does not appear optimal in a scientific point of view (loss of measurements near the surface, meaning of the depth-average currents), the priority was set on the glider integrity. +\end{newtext} + + +- Section 3.3.2: How in-house QC differ from international standard for profiling floats and gliders? + +\begin{reply} +In-house quality control are in fact based on international standards. The idea is not to reinvent the wheel but to use what already exists and add other contributions whenever possible. +All the QC are detailed in: +\begin{SimpleBox}{QUID\_DCF\_SOCIB-QC-procedures.pdf} +SOCIB Quality Control Procedures\\ +Data Center Facility\\ +September 2018\\ +DOI: \doi{10.25704/q4zs-tspv} +\end{SimpleBox} + +and the quality control is re-organised as follows: +\begin{enumerate} +\item A general section explaining the approach for the quality control. +\item For each platform, a sub-section describing the specificities in terms of QC. +\end{enumerate} +As all the procedures are explained in the aforementioned document, for the sake of conciseness, we prefer to keep a summarised version in the manuscript. +\end{reply} + +\subsection*{Specific comments} +p2 l32 "thanks due" + +\begin{reply} +corrected +\end{reply} + +p6 l2: Specify the glider type and sensors + +\begin{reply} +\begin{description} +\item[Coastal:] Teledyne Webb Research Corp. Slocum, 1st generation, shallow version (200~m) +\item[Deep:] Teledyne Webb Research Corp., Slocum, 1st generation, deep version (1000~m) +\end{description} +This information is now included in Table~3 in the subsection "\textit{3.2.1 Configuration}" related to the Gliders, along with the sensors and other technical data. + +Overall, the descriptions of all the instruments and sensors have been extended and improved. +\end{reply} + +p10 l1: wrong degree symbol, please also correct other instances. + +\begin{reply} +Corrected +\end{reply} + \end{document} \ No newline at end of file -- GitLab