[WIP] i.sentinel3.import: New addon to import Sentinel-3 data #612
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| MODULE_TOPDIR = ../.. | ||
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| PGM = i.sentinel3.import | ||
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| include $(MODULE_TOPDIR)/include/Make/Script.make | ||
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| default: script |
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| <h2>DESCRIPTION</h2> | ||
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| The <em>i.sentinel3.import</em> module allows importing Copernicus Sentinel-3 products | ||
| downloaded by the <em><a href="i.sentinel.download.html">i.sentinel.download</a></em> | ||
| module. | ||
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| <p> | ||
| By default <em>i.sentinel3.import</em> imports all Sentinel-3 scene files found | ||
| in the <b>input</b> directory. The number of scene files can be optionally | ||
| reduced by the <b>pattern</b> option or filtered by modification time using the | ||
| <b>modified_after</b> and/or <b>modified_before</b> option. In the <b>pattern</b> | ||
| option, a regular expression for filtering the file names should be given, e.g. | ||
| "0179_076_100_0900_LN2" for importing only specific tiles. | ||
| <p> | ||
| The <em>Sentinel-3</em> format is currently not supported by GDAL and consists | ||
| of several netCDF4 files. Therefore, a GRASS GIS specific import routine is implemented. | ||
| It imports the data pixel-wise after transforming them from WGS84 into the projection | ||
| of the current LOCATION. <em>r.in.xyz<em> is then used to read the coordinates into | ||
| a GRASS GIS raster map. Thus, the the user has to set the computational region extent and | ||
| resolution appropriately, to import the data of interest in the correct resolution. | ||
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| <p> | ||
| By default, ancillary data and quality flag data are imported as well - as artificial | ||
| bands. Import of those additional data layers can be deactivated using the <b>ancillary_bands</b> | ||
| and <b>quality_bands</b> option. | ||
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| <p> | ||
| For each imported band both scene and band specific metadata are written into the map history | ||
| (<em><a href="https://grass.osgeo.org/grass-stable/manuals/r.support.html">r.support</a></em>). | ||
| In addition, the scene name is stored as <em>source1</em> and the imported or linked file name as | ||
| <em>source2</em>. Also, sensing time is written into the timestamp of the | ||
| map. After import, the metadata can be retrieved with <em>r.info -e</em> | ||
| as shown below. | ||
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| <h2>NOTES</h2> | ||
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| <p> | ||
| Currently, only import of SL_2_LST__ products is supported. | ||
| <p> | ||
| By means of the <b>register_file</b> option <em>i.sentinel3.import</em> allows | ||
| creating a file which can be used to register imported imagery data | ||
| into a space-time raster dateset (STRDS) with | ||
| <em><a href="https://grass.osgeo.org/grass-stable/manuals/t.register.html">t.register</a></em>. | ||
| See example below. | ||
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| <p> | ||
| <h3>Metadata storage</h3> | ||
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| By using the <b>-j</b> flag the band metadata are additionally stored | ||
| in JSON format (in the current mapset under <tt>cell_misc</tt>). | ||
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| <h2>EXAMPLES</h2> | ||
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| <h3>List Sentinel bands</h3> | ||
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| At first, print the list of raster files to be imported with <b>-p</b> flag. For | ||
| each file also product content is printed: | ||
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| <div class="code"><pre> | ||
| i.sentinel3.import -p input="data" nprocs=4 modified_before="2021-09-09" product=LST basename=S3_LST | ||
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| ... | ||
|
There was a problem hiding this comment. Why "data"? Are the quotes necessary there? Also, maybe put some of the resulting printed info as example and not only the |
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| </pre></div> | ||
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| <h3>Import Sentinel-3 data</h3> | ||
| Import all Sentinel-3 data found in <i>data</i> directory and store metadata | ||
| as JSON files within the GRASS GIS database directory: | ||
| <div class="code"><pre> | ||
| i.sentinel3.import -a -c -j input="data" nprocs=4 modified_before="2021-09-09" product=LST basename=S3_LST | ||
| </pre></div> | ||
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| <h3>Register imported Sentinel-3 data into STRDS</h3> | ||
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| <div class="code"><pre> | ||
| i.sentinel3.import -a -c -j input="data" register_output=data/reg.txt nprocs=4 modified_before="2021-09-09" product=LST basename=S3_LST | ||
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| # register imported data into existing STRDS | ||
| t.register input=Sentinel_3 file=data/reg.txt | ||
| </pre></div> | ||
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| A register file typically contains two columns: imported raster map | ||
| name and timestamp separated by <tt>|</tt>. In the case of current | ||
| development version of GRASS GIS which supports band references concept | ||
| (see <em><a href="https://grass.osgeo.org/grass-devel/manuals/g.bands.html">g.bands</a></em> module for details) a | ||
| register file is extended by a third column containg band reference | ||
| information, see the examples below. | ||
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| <div class="code"><pre> | ||
| # register file produced by stable GRASS GIS 7.8 version | ||
| S3_imp_surface_temperature_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00 | ||
| S3_imp_surface_temperature_standard_error_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00 | ||
| S3_imp_confidence_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00 | ||
| ... | ||
| # register file produced by development GRASS GIS 7.9 version | ||
| S3_imp_surface_temperature_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00|S3_surface_temperature | ||
| S3_imp_surface_temperature_standard_error_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00|S3_surface_temperature_standard_error | ||
| S3_imp_confidence_20210907T205026|2021-09-07T20:50:26.285902+00:00|2021-09-07T20:53:25.977846+00:00|S3_confidence | ||
| </pre></div> | ||
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| <h2>REQUIREMENTS</h2> | ||
| The following Python libraries are required | ||
| <ul> | ||
| <li>GDAL (install through system software management)</li> | ||
| <li>numpy</li> | ||
| <li>netcdf4</li> | ||
| <li>cf-units (for unit conversion)</li> | ||
| </ul> | ||
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| <h2>SEE ALSO</h2> | ||
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| <em> | ||
| <a href="i.sentinel.html">Overview of i.sentinel toolset</a> | ||
| </em> | ||
| <p> | ||
| <em> | ||
| <a href="i.sentinel.download.html">i.sentinel.download</a>, | ||
| <a href="https://grass.osgeo.org/grass-stable/manuals/r.in.xyz.html">r.in.xyz</a>, | ||
| <a href="https://grass.osgeo.org/grass-stable/manuals/t.register.html">t.register</a> | ||
| </em> | ||
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| <h2>AUTHOR</h2> | ||
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| Stefan Blumentrath, <a href="https://www.nina.no/">NINA</a>, Norway | ||
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| <!-- | ||
| <p> | ||
| <i>Last changed: $Date$</i> | ||
| --> | ||
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What does QGIS uses then to open the nc files within the S3 zip files? I tested with a S3SY2VG1 product. A double click just opens the ndvi layer in QGIS and
r.importworks just fine for that layer as well. Maybe, this statement is a bit too strong or only valid for S3 LST products...?There was a problem hiding this comment.
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Do you mean the semi automated classification plugin? That one has a similar (but not the same) workaround for the S3-format...
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No, plain QGIS opens the
.ncmentioned file just fine, I do not use the semi automated classification pluginThere was a problem hiding this comment.
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OK, thanks for clarifying.
Yes, QGIS does open the
.ncbut - at least the QGIS 3.16 version I am running does not resolve the geometrical information correctly. The image is flipped and distorted....The sentinel-3 format is pretty peculiar and one needs to combine the geometry and data nc files in order to get a reasonble geographical representation of the data....
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NDVI products look just fine
LST is flipped
This is what I meant originally with my comment, some of the S3 products are read just fine (NDVI from the S3A_SY_2_VG1 above). Hence, it's not completely true that none of the S3 formats is supported by GDAL as stated.
I use GDAL 3.2.2 and QGIS 3.20
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Thanks for clarifying and bearing with me. My focus has been on SLSTR. So, the different products seem to come in different formats / packaging also across processing levels...
So a "final"
i.sentinel3.importmodule should support the formats for the different instrumentsfor level 1 and 2.
Not sure if I find the time to investigate and implement all of them (can be as simple as
r.import/r.in.gdal/r.external).In any case this should be made clear in the documentation, as you correctly point out...