Cloud masking

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= Sentinel-2 cloud mask =
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= Inspect Sentinel-2 quality indicator data =
 
The exclusion of clouds and cloud shadow is an important processing step which is usually done in an early pre-processing stage.
 
The exclusion of clouds and cloud shadow is an important processing step which is usually done in an early pre-processing stage.
−
The Sentinel-2 products are annotated with Quality Indicators (QI_DATA). In the Level 2A product you may find a file in the folder '''QI_DATA''' with the extension '''_CLD_20m.jp2''' (data type: 8bit unsigned integer, spatial resolution 20m) which might be used for masking clouds. The data range is from 0 for high confidence clear sky to 100 for high confidence cloudy (for more details see [https://earth.esa.int/documents/247904/685211/S2+L2A+Product+Definition+Document/2c0f6d5f-60b5-48de-bc0d-e0f45ca06304 L2A Product Definition Document]).
+
The Sentinel-2 products are annotated with Quality Indicators (QI_DATA).
 +
 +
If you use a Sentinel-2 Level 1C product, you'll find a rough dense cloud and cirrus mask (GML vector format) in the folder '''QI_DATA''' with the file name '''MSK_CLOUDS_B00.gml'''. The vector attribute column ''masktype'' distinguishes two classes: OPAQUE (dense clouds) and CIRRUS.
  
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If you downloaded a Level 1C product, you'll find a rough dense cloud and cirrus mask (GML vector format) in the folder '''QI_DATA''' with the file name '''MSK_CLOUDS_B00.gml''' and a spatial resolution of 60m. In the vector attribute column ''masktype'' distinguishes two classes: OPAQUE (dense clouds) and CIRRUS.
+
In case of a Sentinel-2 Level 2A product you may find a file in the folder '''QI_DATA''' with the extension '''_CLD_20m.jp2''' (data type: 8bit unsigned integer, spatial resolution 20m) which might be used for masking clouds. Data range is from 0 for high confidence clear sky to 100 for high confidence cloudy (for more details see [https://earth.esa.int/documents/247904/685211/S2+L2A+Product+Definition+Document/2c0f6d5f-60b5-48de-bc0d-e0f45ca06304 L2A Product Definition Document]).
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* Load a multiband Sentinel-2 satellite image (Level 2-A product) [[Changing Raster Layer Style]] to display a true color and a false color composite.
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 +
* Load a multiband Sentinel-2 satellite image (Level 2-A product) [[Changing Raster Layer Style]] to display a true color (RGB = B4,B3,B2) and a standard false color composite (RGB = B8,B4,B3)
 
* Zoom in to a cloudy part of the image and compare the extent of cloud and cloud shadow in both composites. Which composite is better for displaying clouds?
 
* Zoom in to a cloudy part of the image and compare the extent of cloud and cloud shadow in both composites. Which composite is better for displaying clouds?
 
[[File:Qgis_cloud_tcc.png|400px]] [[File:Qgis_cloud_fcc.png|400px]]
 
[[File:Qgis_cloud_tcc.png|400px]] [[File:Qgis_cloud_fcc.png|400px]]
 
* Overlay the QI Cloud band on top of the color composites. Use the {{tool|text=Identify Feature Tool}} for requesting pixel values of the QI band file inside a cloud. Which values represent clouds?
 
* Overlay the QI Cloud band on top of the color composites. Use the {{tool|text=Identify Feature Tool}} for requesting pixel values of the QI band file inside a cloud. Which values represent clouds?
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* First, {{mitem|text=Layer Properties --> Style --> Min/max value settings}} of the QI layer. Tick Min / max and click  {{button|text=Apply}}. Then change the ''Render type''' from Singleband grey to  Singelband pseudocolor with interpolation '''discrete''' and mode '''equal''' with 10 interval classes as shown in the screenshot.  
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* Change '''Render type''' {{button|text=Singelband pseudocolor}}
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* Double click on a color field of some classes {{mitem|text=Layer --> Properties --> Style) to open the change color window. Change the opacity from 100% to 0%. Find the best threshold for clouds.
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* '''Interpolation''' is {{button|text=discrete}}'''.
 +
* Choose '''Color ramp''' {{button|text=spectral}}
 +
* '''Mode''' is {{button|text=equal}} with
 +
* Interval '''Classes''' is {{typed|text=10}} as shown in the screenshot.  
 +
* Double click on a color field of some classes {{mitem|text=Layer --> Properties --> Style) to open the change color window. Change the opacity from 100% to 0%. Find the threshold for clouds.
 
[[File:Qgis_cloud_qi_pseudo.png|400px]] [[File:Qgis_cloud_qi_opacity.png|300px]]
 
[[File:Qgis_cloud_qi_pseudo.png|400px]] [[File:Qgis_cloud_qi_opacity.png|300px]]
  
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= Refining cloud mask =
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= Convert quality indicator band to a binary cloud mask =
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* Create a binary cloud mask (bitmask) where clouds = 1 and non-clouds = 0. Use the Processing tool {{mitem|text= OTB --> Miscellaneous --> Band Math}}. Tick the single band QI layer in the '''Input Image list''' list. You may write a conditional ''ifelse expression'' using lazy operators. Type into the '''Expression''' field: {{typed|text=(im1b1>30)?1:0}} If pixel values of band 1 of multiband image 1 are larger than 30 then replace with 1 otherwise replace with 0. The output pixel type is '''uint8'''.
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* Create a binary cloud mask (bitmask) where clouds = 1 and non-clouds = 0. Use the Processing tool {{mitem|text= OTB --> Image Manipulation --> Band Math}}. Tick the single band QI layer ('''_CLD''') in the '''Input Image list''' list. In the Parameter tab write a conditional ''ifelse expression'' using lazy operators.  
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[[File:Qgis_cloud_bandmath.png|300px]]]
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Type into the '''Expression''' field: {{typed|text=(im1b1>30)?1:0}}
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* Apply a circular majority filter with a radius of 7 pixels. Open the Processing tool {{mitem|text= SAGA --> Raster filter --> Majority filter}}. The input Grid is the Output image of the band math operation step. Change the '''Search mode''' to Circle with an radius of 5 pixels. Mark the '''Filtered Grid''' in the [[TOC]] and click [[File:Qgis_local_hist.png]] to stretch the histogram to view extents.
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If pixel values of band 1 of multiband image 1 are larger than 30 then replace with 1 otherwise replace with 0. Adjusot labels for NoData {{typed|text=3}} and undecided {{typed|text=2}} he output pixel type is '''uint8'''.
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[[File:Qgis_cloud_majority.png|300px]]
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* (This Processing Module does currently not work) Open the Processing tool {{mitem|text= OTB --> Feature Extraction --> BinaryMorphologicalOperation (dilate)}}. Choose the '''Filtered Grid''' as input image. The structuring element type is '''ball''' with a radius of 7 pixels. Mark the '''Feature Output Image''' in the [[TOC]] and click [[File:Qgis_local_hist.png]] to stretch the histogram to view extents.
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[[File:Qgis_cloud_bandmath.png|400px]]]
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[[File:Qgis_cloud_dilate.png|300px]]
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* Convert the Feature Output Imge from raster to vector format. {{mitem|text= Raster --> Conversion --> Polygonize}}. Select an output file name for vector polygons.
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* Apply a circular majority filter with a radius of 16 pixels. Open the Processing tool {{mitem|text=OTB --> Learning --> ClassificationMapRegularization}}. The input classifcation image is the Output Image of the band math operation step. Adjust the Label for NoData {{typed|text=3}} and Undecided  {{typed|text=2}} class. Structuring element radius is 16 pixels. Output pixel type is '''uint8'''.
 +
 
 +
[[File:Qgis_cloud_majority.png|400px]]
 +
 
 +
* Open the Processing tool {{mitem|text= OTB --> Feature Extraction --> BinaryMorphologicalOperation}}. Choose the '''Regularized image''' as input image. The structuring element type is '''ball''' with a X and Y radius of 21 pixels. The morphological operation is {{button|text=dilate}}. Output pixel type is {{button|text=uin8}}.
 +
 
 +
[[File:Qgis_cloud_dilate.png|400px]]
 +
 
 +
* Convert the Feature Output Imge from raster to vector format. {{mitem|text= Raster --> Conversion --> Polygonize}}. Select an output file name for vector polygons in format GPKG.
 +
 
 
[[File:Qgis_cloud_polygonize.png|400px]]
 
[[File:Qgis_cloud_polygonize.png|400px]]
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* Change the display of the output vector polygon layer {{mitem|text= Layer properties --> Style --> Single Symbol --> Simple Fill --> Fill Style}} from ''Solid'' to ''No Brush''. Change the '''Outline color''' to bright green and increase the '''Outline width'''. As background layer use a False Color Composite of the Sentinel-2 image.
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* Toggle editing [[File:Qgis_vector_edit.png]] of the resulting vector polygon layer. Activate {{tool|text=Select polygons by dragging a box or by single click}} [[File:Qgis_vector_select.png]], select all polygons with attribute '''DN''' = 0 or which are misclassified as clouds and delete them by pressing {{button|text=Del}} on your keyboard. Save your edits [[File:Qgis_vector_save.png]].
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* Change the display of the output vector polygon layer {{mitem|text= Layer properties --> Symbology --> Single Symbol --> Simple Fill --> Fill Style}} from ''Solid'' to ''No Brush''. Change the '''Outline color''' to bright green and increase the '''Outline width'''. As background layer use a Standard False Color Composite (RGB = B8,B$,B3) of the Sentinel-2 image.
 +
 
 +
* Toggle editing [[File:Qgis_vector_edit.png]] of the resulting vector polygon layer. Activate {{tool|text=Select polygons by dragging a box or by single click}} [[File:Qgis_vector_select.png]]. select all polygons with attribute '''DN''' = 0 and delete them by pressing {{button|text=Del}} on your keyboard. Save your edits [[File:Qgis_vector_save.png]].
  
 
= Creating cloud shadow mask =
 
= Creating cloud shadow mask =
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* Prepare a False color composite of the Sentinel-2 image as background layer in the canvas.
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* Prepare a False color composite (RGB = B8,B4,B3) of the Sentinel-2 image as background layer in the canvas.
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* Right click on the edited polygon layer in the [[TOC]]. Choose {{button|text= Export --> Save features as...}}. Fill the form as shown below.
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* Right click on the cloud polygon layer in the [[TOC]]. Choose {{button|text= Export --> Save features as...}}. Fill the form as shown below.
 
[[File:Qgis_vector_saveas.png|400px]]
 
[[File:Qgis_vector_saveas.png|400px]]
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* Mark the new created polygon layer in the [[TOC]] and toggle editing [[File:Qgis_vector_edit.png]] of the vector file. Select all polygons using [[File:Qgis_vector_select_all.png|200px]] or press {{button|text=Ctrl + A}}. Activate {{mitem|text=Edit --> Move feature(s)}} [[File:Qgis_vector_move.png]]. Left click on the canvas and move the cloud polygons that shadows on the background false color composite are completely covered. Save your edits [[File:Qgis_vector_save.png]]and stop editing [[File:Qgis_vector_edit.png]].
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* Mark the new created polygon layer in the [[TOC]] and toggle editing [[File:Qgis_vector_edit.png]] of the vector file. Select all polygons using [[File:Qgis_vector_select_all.png|200px]] or press {{button|text=Ctrl + A}}. Activate {{mitem|text=Edit --> Move feature(s)}} [[File:Qgis_vector_move.png]]. Left click on a selected yellow polygon, move the polygon that shadows are completely covered, and confirm with left click. Save your edits and [[File:Qgis_vector_save.png]]and stop editing [[File:Qgis_vector_edit.png]].
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* Select polygons [[File:Qgis_vector_select.png]] outside the image extent of the false color composite and delete them by pressing {{button|text=Del}} on your keyboard. Save your edits and stop editing [[File:Qgis_vector_edit.png]].
+
  
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= Applying cloud and cloud shadow mask =
+
= Merge cloud and cloud shadow mask =
 
* {{mitem|text= Vector --> Data management tools --> Merge vector layers}}. as '''Layer to merge''' select the ''cloud'' and ''cloud_shadow'' polygon layers. {{button|text=Run}}.
 
* {{mitem|text= Vector --> Data management tools --> Merge vector layers}}. as '''Layer to merge''' select the ''cloud'' and ''cloud_shadow'' polygon layers. {{button|text=Run}}.
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[[File:Qgis_vector_merge.png|400px]]
+
[[File:Qgis_vector_merge.png|400px]]
 +
= Apply the cloud and cloud shadow mask to a Sentinel-2 multiband file =
 
* Create a polygon with the extent of the Sentinel-2 image: [[Create image extent polygon]].  
 
* Create a polygon with the extent of the Sentinel-2 image: [[Create image extent polygon]].  
 
* {{mitem|text= Vector --> Geoprocessing Tools --> Symmetrical difference}}. Input layers are the image extent and the merged cloud and cloud_shadow polygons.
 
* {{mitem|text= Vector --> Geoprocessing Tools --> Symmetrical difference}}. Input layers are the image extent and the merged cloud and cloud_shadow polygons.
 
[[File:Qgis_vector_symdiff.png|400px]]
 
[[File:Qgis_vector_symdiff.png|400px]]
−
* Apply the output vector layer '''Cleaned''' as mask to the multiband Sentinel-2 image file. {{mitem|text= Raster --> Extraction --> Clip Raster by Mask Layer layers}}.
+
* Apply the output vector layer '''cloud_cloudshadow''' as mask to the multiband Sentinel-2 image file. {{mitem|text= Raster --> Extraction --> Clip Raster by Mask Layer}}.
  
 
=Graphical Processing Tool Model=
 
=Graphical Processing Tool Model=
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You can use a prepared graphical processing toolbox model. Download the file from Stud.IP:{{typed|text=S2cloudDetection.model3}}.  
+
Use a prepared graphical processing toolbox model. Download the file from Stud.IP: {{typed|text=S2cloudDetection.model3}}.  
−
# Open QGIS and go to the Processing Toolbox; if the Toolbox is not opened click {{mitem|text= Processing --> Toolbox}} to activate it. Once the Toolbox is opened go to [[File:qgis-processing_model_iconExample.png]] {{mitem|text= Models --> Open existing models}} and load the previously downloaded model.  
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# Open QGIS and go to the Processing Toolbox; if the Toolbox is not opened click {{mitem|text= Processing --> Toolbox}} to activate it. Once the Toolbox is opened go to [[File:qgis-processing_model_iconExample.png]] {{mitem|text= Models --> Add model to Toolbox...}}. Open the downloaded model.  
−
# The model should appear in the Models tab. Double click on it to execute.
+
# The model should appear in the Toolbox under {{mitem|text=Models --> S2 --> S2 Cloud Detection}}. Double click to execute.
 
# A window showing the different input and outputs should appear, just as if you were using any other geo-algorithm of the Processing Toolbox.  
 
# A window showing the different input and outputs should appear, just as if you were using any other geo-algorithm of the Processing Toolbox.  
−
# You will just need to provide a multispectral Sentinel-2 image file with 10 ordered bands (B2, B3, B4, B5, B6, B7, B8, B8A, B11, B12).
+
# Just provide a multispectral Sentinel-2 image file with 10 bands with the rank (B2, B3, B4, B5, B6, B7, B8, B8A, B11, B12). Click {{button|text=Run}}.
 +
# {{mitem|text=Models --> S2 --> S2 Cloud Detection}} . Right click {{button|text=Edit Model}}. In the Model Designer double click on the graphical objects to display parameters of processing components. It is easy to change parameter settings of input, output or processing steps. Save changes in the Model Designer {{mitem|text=Model --> Save Model as...}}.
 +
 
 
[[File:Qgis_s2_cloud_detection_model.png|700px]]
 
[[File:Qgis_s2_cloud_detection_model.png|700px]]
  
 +
Find out how to use the [https://docs.qgis.org/3.16/en/docs/user_manual/processing/modeler.html?highlight=graphical%20model graphical modeler] to program your own workflow.
  
 
{| class="wikitable"
 
{| class="wikitable"
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| style="border: 0pt" | [[file:Qgis_cloud_fcc_masked.png|thumb|left|400px|'''Figure B:''' False color composite RGB=8,4,3 masked with cloud and cloud shadow]]
 
| style="border: 0pt" | [[file:Qgis_cloud_fcc_masked.png|thumb|left|400px|'''Figure B:''' False color composite RGB=8,4,3 masked with cloud and cloud shadow]]
 
|}
 
|}
 +
 +
 
[[Category:QGIS Tutorial]]
 
[[Category:QGIS Tutorial]]

Latest revision as of 12:05, 19 November 2020

Contents

[edit] Inspect Sentinel-2 quality indicator data

The exclusion of clouds and cloud shadow is an important processing step which is usually done in an early pre-processing stage. The Sentinel-2 products are annotated with Quality Indicators (QI_DATA).

If you use a Sentinel-2 Level 1C product, you'll find a rough dense cloud and cirrus mask (GML vector format) in the folder QI_DATA with the file name MSK_CLOUDS_B00.gml. The vector attribute column masktype distinguishes two classes: OPAQUE (dense clouds) and CIRRUS.

In case of a Sentinel-2 Level 2A product you may find a file in the folder QI_DATA with the extension _CLD_20m.jp2 (data type: 8bit unsigned integer, spatial resolution 20m) which might be used for masking clouds. Data range is from 0 for high confidence clear sky to 100 for high confidence cloudy (for more details see L2A Product Definition Document).

  • Load a multiband Sentinel-2 satellite image (Level 2-A product) Changing Raster Layer Style to display a true color (RGB = B4,B3,B2) and a standard false color composite (RGB = B8,B4,B3)
  • Zoom in to a cloudy part of the image and compare the extent of cloud and cloud shadow in both composites. Which composite is better for displaying clouds?

Qgis cloud tcc.png Qgis cloud fcc.png

  • Overlay the QI Cloud band on top of the color composites. Use the Identify Feature Tool for requesting pixel values of the QI band file inside a cloud. Which values represent clouds?
  • Change Render type Singelband pseudocolor
  • Interpolation is discrete.
  • Choose Color ramp spectral
  • Mode is equal with
  • Interval Classes is 10 as shown in the screenshot.
  • Double click on a color field of some classes {{mitem|text=Layer --> Properties --> Style) to open the change color window. Change the opacity from 100% to 0%. Find the threshold for clouds.

Qgis cloud qi pseudo.png Qgis cloud qi opacity.png

[edit] Convert quality indicator band to a binary cloud mask

  • Create a binary cloud mask (bitmask) where clouds = 1 and non-clouds = 0. Use the Processing tool OTB --> Image Manipulation --> Band Math. Tick the single band QI layer (_CLD) in the Input Image list list. In the Parameter tab write a conditional ifelse expression using lazy operators.

Type into the Expression field: (im1b1>30)?1:0 If pixel values of band 1 of multiband image 1 are larger than 30 then replace with 1 otherwise replace with 0. Adjusot labels for NoData 3 and undecided 2 he output pixel type is uint8.

Qgis cloud bandmath.png]

  • Apply a circular majority filter with a radius of 16 pixels. Open the Processing tool OTB --> Learning --> ClassificationMapRegularization. The input classifcation image is the Output Image of the band math operation step. Adjust the Label for NoData 3 and Undecided 2 class. Structuring element radius is 16 pixels. Output pixel type is uint8.

Qgis cloud majority.png

  • Open the Processing tool OTB --> Feature Extraction --> BinaryMorphologicalOperation. Choose the Regularized image as input image. The structuring element type is ball with a X and Y radius of 21 pixels. The morphological operation is dilate. Output pixel type is uin8.

Qgis cloud dilate.png

  • Convert the Feature Output Imge from raster to vector format. Raster --> Conversion --> Polygonize. Select an output file name for vector polygons in format GPKG.

Qgis cloud polygonize.png

  • Change the display of the output vector polygon layer Layer properties --> Symbology --> Single Symbol --> Simple Fill --> Fill Style from Solid to No Brush. Change the Outline color to bright green and increase the Outline width. As background layer use a Standard False Color Composite (RGB = B8,B$,B3) of the Sentinel-2 image.
  • Toggle editing Qgis vector edit.png of the resulting vector polygon layer. Activate Select polygons by dragging a box or by single click Qgis vector select.png. select all polygons with attribute DN = 0 and delete them by pressing Del on your keyboard. Save your edits Qgis vector save.png.

[edit] Creating cloud shadow mask

  • Prepare a False color composite (RGB = B8,B4,B3) of the Sentinel-2 image as background layer in the canvas.
  • Right click on the cloud polygon layer in the TOC. Choose Export --> Save features as.... Fill the form as shown below.

Qgis vector saveas.png

  • Mark the new created polygon layer in the TOC and toggle editing Qgis vector edit.png of the vector file. Select all polygons using Qgis vector select all.png or press Ctrl + A. Activate Edit --> Move feature(s) Qgis vector move.png. Left click on a selected yellow polygon, move the polygon that shadows are completely covered, and confirm with left click. Save your edits and Qgis vector save.pngand stop editing Qgis vector edit.png.

[edit] Merge cloud and cloud shadow mask

  • Vector --> Data management tools --> Merge vector layers. as Layer to merge select the cloud and cloud_shadow polygon layers. Run.

Qgis vector merge.png

[edit] Apply the cloud and cloud shadow mask to a Sentinel-2 multiband file

  • Create a polygon with the extent of the Sentinel-2 image: Create image extent polygon.
  • Vector --> Geoprocessing Tools --> Symmetrical difference. Input layers are the image extent and the merged cloud and cloud_shadow polygons.

Qgis vector symdiff.png

  • Apply the output vector layer cloud_cloudshadow as mask to the multiband Sentinel-2 image file. Raster --> Extraction --> Clip Raster by Mask Layer.

[edit] Graphical Processing Tool Model

Use a prepared graphical processing toolbox model. Download the file from Stud.IP: S2cloudDetection.model3.

  1. Open QGIS and go to the Processing Toolbox; if the Toolbox is not opened click Processing --> Toolbox to activate it. Once the Toolbox is opened go to Qgis-processing model iconExample.png Models --> Add model to Toolbox.... Open the downloaded model.
  2. The model should appear in the Toolbox under Models --> S2 --> S2 Cloud Detection. Double click to execute.
  3. A window showing the different input and outputs should appear, just as if you were using any other geo-algorithm of the Processing Toolbox.
  4. Just provide a multispectral Sentinel-2 image file with 10 bands with the rank (B2, B3, B4, B5, B6, B7, B8, B8A, B11, B12). Click Run.
  5. Models --> S2 --> S2 Cloud Detection . Right click Edit Model. In the Model Designer double click on the graphical objects to display parameters of processing components. It is easy to change parameter settings of input, output or processing steps. Save changes in the Model Designer Model --> Save Model as....

Qgis s2 cloud detection model.png

Find out how to use the graphical modeler to program your own workflow.

Figure A: False color composite RGB=8,4,3
Figure B: False color composite RGB=8,4,3 masked with cloud and cloud shadow
Retrieved from "http://wiki.awf.forst.uni-goettingen.de/wiki/index.php?title=Cloud_masking&oldid=16064"
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