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What are the bare minimum required files to run Fmask, version 4, on a Sentinel 2 tile? Is the entire SAFE structure necessary?

I've got this error when I used the GUI v.4.3 for Landsat8. Can anyone help?

Can the GLOBAL AUXILIARY DATA provide the download link of Baidu online disk? thank you！

PS：Does python-fask also need the auxiliary data？

Can Fmask be run on the ARD tiles available from USGS? The folder structure appears to be different.

For example, these are the top-of-atmosphere files I downloaded:

We have been running Fmask in northern europe over the past few years and have noticed that if often fails on very cloudy imagery. It mostly happens in the Autumn and Winter, but occasionally in Summer. The latest example here, but there are many:

S2B_MSIL1C_20210918T101639_N0301_R065_T33UWB_20210918T122319.SAFE

Its a fully clouded scene:

When Fmask 4.3 is run we get this result (black has value == 0 and should be clear land pixels)

When the Sentinel-2 image is masked using Fmask we get this result, with lots of cloud not masked.

Hello Fmask team @prs021 @qsly09 ,

I installed Fmask 4.6 for windows, but when I open the application the following message appears. On the other hand, version 4.5 runs correctly.

Thank you

I noticed that FMask 4.0 standalone fails on some S2 scenes with the error

Cell contents reference from a non-cell array object.

Error in ReadSunViewGeometryMSI (line 171)


Error in nd2toarbt_msi2 (line 44)


Error in LoadData (line 105)


Error in autoFmask (line 96)


Error in Fmask_4_0 (line 10)

MATLAB:cellRefFromNonCell

All of the offending scenes are from orbits only partially covering the tile, like this one:

List of failing scenes:

S2B_MSIL1C_20180801T104019_N0206_R008_T32UPF_20180801T161339
S2A_MSIL1C_20180727T104021_N0206_R008_T32UPF_20180727T125155
S2B_MSIL1C_20180807T105619_N0206_R094_T32VMJ_20180807T150742
S2A_MSIL1C_20180707T104021_N0206_R008_T32UPF_20180707T125205
S2B_MSIL1C_20180628T105619_N0206_R094_T32VMJ_20180629T091005
S2B_MSIL1C_20180718T110039_N0206_R094_T32VMJ_20180718T145209
S2B_MSIL1C_20180811T104019_N0206_R008_T32UPF_20180811T143244
S2A_MSIL1C_20180703T105621_N0206_R094_T32VMJ_20180703T130749
S2A_MSIL1C_20180713T105621_N0206_R094_T32VMJ_20180713T130920
S2A_MSIL1C_20180723T105621_N0206_R094_T32VMJ_20180723T130754
S2A_MSIL1C_20180816T104021_N0206_R008_T33VUC_20180816T164132
S2B_MSIL1C_20180801T104019_N0206_R008_T32UPF_20180801T161339
S2A_MSIL1C_20180816T104021_N0206_R008_T32UPF_20180816T164132
S2B_MSIL1C_20180821T104019_N0206_R008_T33VUC_20180821T144801
S2B_MSIL1C_20180728T105619_N0206_R094_T32VMJ_20180728T131913
S2A_MSIL1C_20180826T104021_N0206_R008_T33VUC_20180826T125219
S2A_MSIL1C_20180806T104021_N0206_R008_T33VUC_20180806T130931
S2A_MSIL1C_20180617T104021_N0206_R008_T33VUC_20180617T125156
S2A_MSIL1C_20180627T104021_N0206_R008_T32UPF_20180627T125110
S2B_MSIL1C_20180702T104019_N0206_R008_T33VUC_20180702T142357
S2B_MSIL1C_20180722T104019_N0206_R008_T33VUC_20180722T142325
S2B_MSIL1C_20180817T105619_N0206_R094_T32VMJ_20180817T131751
S2B_MSIL1C_20180801T104019_N0206_R008_T33VUC_20180801T161339
S2A_MSIL1C_20180812T105621_N0206_R094_T32VMJ_20180812T131737
S2B_MSIL1C_20180622T104019_N0206_R008_T32UPF_20180622T124339
S2A_MSIL1C_20180727T104021_N0206_R008_T33VUC_20180727T125155
S2A_MSIL1C_20180802T105621_N0206_R094_T32VMJ_20180802T132133
S2A_MSIL1C_20180617T104021_N0206_R008_T32UPF_20180617T125156
S2B_MSIL1C_20180827T110029_N0206_R094_T32VMJ_20180827T150823
S2B_MSIL1C_20180712T104019_N0206_R008_T33VUC_20180712T143102
S2B_MSIL1C_20180821T104019_N0206_R008_T32UPF_20180821T144801
S2B_MSIL1C_20180622T104019_N0206_R008_T33VUC_20180622T124339
S2B_MSIL1C_20180708T105619_N0206_R094_T32VMJ_20180708T134424
S2B_MSIL1C_20180811T104019_N0206_R008_T33VUC_20180811T143244
S2A_MSIL1C_20180627T104021_N0206_R008_T33VUC_20180627T125110
S2B_MSIL1C_20180702T104019_N0206_R008_T32UPF_20180702T142357
S2A_MSIL1C_20180822T105621_N0206_R094_T32VMJ_20180822T132540
S2A_MSIL1C_20180623T105621_N0206_R094_T32VMJ_20180623T130607
S2A_MSIL1C_20180806T104021_N0206_R008_T32UPF_20180806T130931
S2A_MSIL1C_20180826T104021_N0206_R008_T32UPF_20180826T125219
S2B_MSIL1C_20180722T104019_N0206_R008_T32UPF_20180722T142325
S2B_MSIL1C_20180618T105619_N0206_R094_T32VMJ_20180618T131745
S2A_MSIL1C_20180717T104021_N0206_R008_T32UPF_20180717T160515
S2B_MSIL1C_20180712T104019_N0206_R008_T32UPF_20180712T143102
S2A_MSIL1C_20180717T104021_N0206_R008_T33VUC_20180717T160515
S2A_MSIL1C_20180707T104021_N0206_R008_T33VUC_20180707T124148

In preparation for ESA's planned January 25 update of the Sentinel 2 processing baseline to 4.0.0. We are testing our processing pipeline for Harmonized Landsat Sentinel against the sample products they have provided.

When attempting to process any of these Baseline 4 sample products with Fmask 4.3 we receive the following error

Error using xmlread
--
Java exception occurred:
org.xml.sax.SAXParseException; systemId: file:/var/scratch/d529375f-d9c1-495b-8bb2-ff85568178f6/S2B_MSIL1C_20211010T105859_N7990_R094_T30SVG_20211117T185835/S2B_MSIL1C_20211010T105859_N7990_R094_T30SVG_20211117T185835.SAFE/GRANULE/L1C_T30SVG_A024001_20211010T110917/QI_DATA/MSK_DETFOO_B04.jp2; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:205)
Error in xml2struct (line 53)
Error in ReadSunViewGeometryMSI (line 159)
Error in nd2toarbt_msi (line 44)
Error in LoadData (line 48)
Error in autoFmask (line 114)
Error in Fmask_4_3 (line 10)
MATLAB:Java:GenericException

Given the time sensitivity of this upcoming baseline release (January 25, 2022), Fmask will no longer work with granules produced after that date, nor reprocessed granules in the archive. @qsly09 Would it be possible for your team to review these Baseline 4 updates and release an updated version of Fmask which can accommodate them? cc @junchangju.

We've begun some initial testing of Fmask with the new Landsat Collection 2 data in anticipation of its release later this year.

There are some structural and metadata changes at the product level which are detailed here. When running Fmask 4.1 with one of the Collection 2 samples we are receiving the following error.

Error using GRIDobj (line 295)
GRIDobj cannot read the TIF-file because it does not have a tfw-file.
Error in nd2toarbt (line 575)
Error in LoadData (line 101)
Error in autoFmask (line 114)
Error in Fmask_4_1 (line 10)
TopoToolbox:GRIDobj:read

Which indicates an error at the geotiffread level. As a note, the geotiffread method is listed as not recommended in the official Matlab documentation.

Unfortunately we do not have access to a Matlab installation to try and diagnose and debug these lower level read issues.

The Landsat 9 metadata package is functionally the same as Landsat 8. Can we extend Fmask to support Landsat 9 products? Currently running Fmask against a Landsat 9 granule reports

Error using autoFmask (line 81)
Fmask 4.5 works only for Landsats 4-7, Landsat 8, and Sentinel 2 images.
Error in Fmask_4_5 (line 72)

A reference Landsat 9 granule is available at s3://usgs-landsat/collection02/level-1/standard/oli-tirs/2022/225/084/LC09_L1TP_225084_20220131_20220131_02_T1/ for testing purposes.

When we are trying to run current FMask tool on current LANDSAT 8 images we are getting the following error:

Error

Dimensions of arrays being concatenated are not consistent.
Error in => Fmask_4_6.m at line 57

OK

Also FMask puts the following messages into the console:

Fmask 4.6 start ...
Cloud/cloud shadow/snow dilated by 2/5/0 pixels.
Cloud probability threshold of 22.50%.
Load or calculate TOA reflectances.
Error using horzcat
Dimensions of arrays being concatenated are not consistent.

Error in lndhdrread (line 287)

Error in nd2toarbt (line 33)

Error in LoadData (line 113)

Error in autoFmask (line 122)

Error in Fmask_4_6 (line 57)

MATLAB:catenate:dimensionMismatch

It's pretty simple to reproduce this issue even without any METRIC involving. Here are the steps:

1. Download any images bundle we need to use in METRIC (Collection 2 Level 2). It can be done manually in USGS EarthExplorer (https://earthexplorer.usgs.gov/). Also it can be done using the API Url directly, for example https://landsatlook.usgs.gov/gen-bundle?landsat_product_id=LC08_L2SP_039037_20220305_20220314_02_T1&requestSignature=eyJjb250YWN0SWQiOjE3MTQyNTgsImRvd25sb2FkSWQiOjE0Mjg1MjgxNywiZGF0ZUdlbmVyYXRlZCI6IjIwMjItMDMtMThUMTE6MzY6NTYtMDU6MDAiLCJzaWduYXR1cmUiOiIkNSQkVGFMMjgwTy5qVzBoMHgwemtQWGZFQlRRSnJBUlRiT0FuSXFwdTNvTUdsOSJ9.

2. Extract all the files from the downloaded archive into the separate folder.

3. Launch FMask tool in this folder. It can be launched without parameters or with the following parameters: "C:\Program Files\GERS\Fmask_4_6\application\Fmask_4_6.exe" 2 5 0 22.5

We have investigated the FMask code and it looks like it cannot find some files. For example it could seek for band 9 image, but there is no such image in these bundles.

Hi! When I open this Fmask_4_6.exe file in windows, it shows the following errors, and the same in Linux.
Btw, Fmask_4_5 runs sucessfully on my computer.

Hi @qsly09 ,

Based on README, there should be an installer of Fmask 4.2 for Mac in the google drive. However, I didn't find any in the drive. Is there an update or something?

Please help to check about this. Thanks a lot.

Best,
Lei

Dear Fmask developer,

I am now using Fmask 4.0 in the Command Prompt, I want to change the default parameters according to Fmask 3.3:

Fmask_4_0 4 6 1 50

first parameter (4) is the number of pixels dilated for cloud (default is 3)
the second parameter (6) is the number of pixels dilated for cloud shadow (default is 3)
the third parameter (1) is the number of pixels dilated for snow (default is 0),
and the last parameter (50) is the cloud probability threshold with default value of 22.5

Then it appeared that Cloud/cloud shadow/snow dileted by 52/54/49 pixels, cloud probability threshold of 53.00%

I would like to ask what is the correct way to set up these parameters.

Thanks and with regards,
Zhongyang

When trying the non-gui Fmask with Sentinel-2 data, following error is always showing up. It works fine with Landsat-7. Tried with two Sentinel-2 images, one recent, one 2016, downloaded from the ESA/Copernicus Scihub. Just changed directory to the subdirectory of GRANULE (S2A_MSIL1C_20201231T100411_N0209_R122_T33UWR_20201231T110732.SAFE/GRANULE/L1C_T33UWR_A028862_20201231T100414, per instructions in handbook) and ran the program without any parameters. Full console output including prompt showing folder location:

tom@uozp46:/media/Data/GISdata/DPZ/Chlorofyl-vzorkovani/2020-12-31_R122_S2A_ns/L1C/S2A_MSIL1C_20201231T100411_N0209_R122_T33UWR_20201231T110732.SAFE/GRANULE/L1C_T33UWR_A028862_20201231T100414$ /usr/local/GERS/Fmask_4_3/application/Fmask_4_3
Fmask 4.3 start ...
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 20.00%.
Load or calculate TOA reflectances.
Error using ReadSunViewGeometryMSI (line 29)
The metadata was wrongly loaded. Please input Sentinel-2 TOA data.

Error in nd2toarbt_msi (line 44)

Error in LoadData (line 48)

Error in autoFmask (line 114)

Error in Fmask_4_3 (line 10)

The most recent patched release of Fmask_4_4 includes this commit commenting about the referencing of auxiliary data. We (and I believe the majority of people) using the standalone executable are doing so through the run_Fmask_4_4.sh shell entrypoint which is included with the installer (but not shown in the source Matlab repository here). Is it possible for you to modify this as part of the installer package so that it includes the ${exe_dir}/AuxiData reference in the Fmask_4_4 call.

Additionally, I believe the majority of the community has been running Fmask without referencing the auxiliary data (as this has been silently failing with no notification). Can you describe the implications of the resulting output being created without the auxiliary data?

I'm cc'ing @j08lue here as well as I know they are standalone users via https://github.com/DHI-GRAS/fmaskilicious.

We use Fmask to process multiple adjacent Sentinel 2 tiles. When there are shadows that would go outside of the tile boundary, we get edges at the tile boundary, like you can see below (white=clouds, grey=shadows, low Sun angle from south-south-east).

An ideal solution would be that Fmask had an option to extend the bounds of the output mask, such that all shadows are included. So the southern tile in the scene below would extend north and overlap with the northern tile. Then, when merging the tiles, we could take care of the shadows nicely.

If I had access to the code, I'd be happy to help implementing this.

Hi,
I'm able to run Fmas using Matlab source code, however not standalone versions (neither on Linux - WSL2/Docker nor Windows). I have the same error as below, on different versions of Fmask 4.x. Do you have an idea if this is a problem with Fmask or rather runtime?

Fmask 4.5 start ...
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 20.00%.
Load or calculate TOA reflectances.
Error using xmlread (line 116)
Java exception occurred:
org.xml.sax.SAXParseException; systemId: file:/work/a.SAFE/; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
        at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
        at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
        at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
        at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
        at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
        at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
        at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
        at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:205)

Error in xml2struct (line 53)

Error in ReadS2RadiometricOffset (line 10)

Error in LoadData (line 52)

Error in autoFmask (line 122)

Error in Fmask_4_5 (line 72)

MATLAB:Java:GenericException

Thanks!

错误使用 GRIDobj (line 299)
GRIDobj cannot read the TIF-file because it does not have a tfw-file.

出错 nd2toarbt (line 575)
trgt = GRIDobj(fullfile(path_top,n_B3.name)); clear n_B3;

出错 LoadData (line 101)
[Temp,data,trgt,dim,ul,bbox,zen,azi,zc,satu_B1,satu_B2,satu_B3,resolu]=nd2toarbt(path_data,main_meta.name);

出错 autoFmask (line 117)
[data_meta,data_toabt,angles_view,trgt] = LoadData(path_data,sensor,InputFile,main_meta);

Hello,
Thank you for releasing Fmask 4.2 version. When I run autoFmask.m on a Landsat 8 Level 1 collection 1 product (sceneid = LC08_L1TP_034037_20160520_20170223_01_T1), I get the following error:

Fmask 4.2 start ...
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 17.50%.
Load or calculate TOA reflectances.
Error using GRIDobj (line 299)
GRIDobj cannot read the TIF-file because it does not have a tfw-file.

Error in nd2toarbt (line 575)
    trgt = GRIDobj(fullfile(path_top,n_B3.name)); clear n_B3;

Error in LoadData (line 101)
        [Temp,data,trgt,dim,ul,bbox,zen,azi,zc,satu_B1,satu_B2,satu_B3,resolu]=nd2toarbt(path_data,main_meta.name);

Error in autoFmask (line 114)
    [data_meta,data_toabt,angles_view,trgt] = LoadData(path_data,sensor,InputFile,main_meta);

Error in autoFmaskBatch (line 11)
        autoFmask();% 4.0

I followed the lines of code and finally got to this point that the problem is that the code cannot read *.TIF files for generating tgrt properly using mapping toolbox and instead tries to read tfw files, which do not exist. I guess the main problem is at line

Would you please help me to fix this error?

Also, it would be great if you could explain a bit more on how to use AuxiData folder as axuilary inputs of Fmask 4.2.
Thanks

Hi all,
I encounter an issue in using Fmask 4.5 for cloud masking Landsat 8 data. Anyone have any idea how to resolve this problem? Thanks

(1/1) LC08_L1TP_121059_20220608_20220608_02_RT:
Cloud/cloud shadow/snow dilated by 3/3/0 pixels
Cloud probability threshold of 17.50%
Load input data (TOA reflectances, DEM, slope, aspect, and GSWO)
Detect potential clouds, cloud shadows, snow, and water
Error: Arrays have incompatible sizes for this operation.

I'm a student studying remote sensing in estimating crop yield. Recently I want to using Fmask to remove clouds and shadow in Sentinel2 images.

I carefully install Fmask4.6 following the guide.
1.Install version 9.10 (R2021a) of the MATLAB Runtime
2.Run Fmask_4_6_Linux_mcr.install

with the issue#22 in Github, I modify the
eval "\"${exe_dir}/Fmask_4_6\"" $args
to
eval "\"${exe_dir}/Fmask_4_6\"" "${exe_dir}/AuxiData" $args

However, when I try to run Fmask, mycommad is

(base) shenzhou@shenzhou-CN15S:~/S2A_MSIL2A_20210721T021611_N0301_R003_T52TFT_20210721T050130.SAFE/GRANULE/L2A_T52TFT_A031746_20210721T022210$ /home/shenzhou/GERS/Fmask_4_6/application/Fmask_4_6 
Fmask 4.6 start ...
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 20.00%.
Load or calculate TOA reflectances.
Error using xmlread (line 116)
Java exception occurred: 
org.xml.sax.SAXParseException; systemId: file:/home/shenzhou/S2A_MSIL2A_20210721T021611_N0301_R003_T52TFT_20210721T050130.SAFE/; lineNumber: 1; columnNumber: 1; Content is not allowed in prolog.
	at org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown Source)
	at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
	at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
	at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
	at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
	at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:205)

Error in xml2struct (line 53)

Error in ReadS2RadiometricOffset (line 10)

Error in LoadData (line 52)

Error in autoFmask (line 122)

Error in Fmask_4_6 (line 44)

MATLAB:Java:GenericException

Could you please help me fix it?

Fmask4 appears to run indefinitely with some Sentinel 2 scenes. The initial processing start is logged

------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/v95/runtime/glnxa64:/usr/local/MATLAB/v95/bin/glnxa64:/usr/local/MATLAB/v95/sys/os/glnxa64:/usr/local/MATLAB/v95/sys/opengl/lib/glnxa64
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 20.00%.
Load or calculate TOA reflectances, Detect potential clouds, cloud shadows, snow, and water.
Match cloud shadows with clouds.

But the process continues to run (we terminate the container process after 90 minutes). Here is a list of problem scenes we have encountered.

S2B_MSIL1C_20200224T214859_N0209_R043_T02KMG_20200224T230359
S2B_MSIL1C_20200224T214859_N0209_R043_T02LNL_20200224T230359
S2B_MSIL1C_20200224T214859_N0209_R043_T02LMJ_20200224T230359
S2B_MSIL1C_20200224T214859_N0209_R043_T02LMK_20200224T230359
S2B_MSIL1C_20200224T214859_N0209_R043_T02LMH_20200224T230359

I'll track these failures during testing and continue to add failing scenes here in the comments for tracking purposes.

Hi all,

When I try to run Fmask_4_3_Linux_mcr.install in Linux using chmod +x, it does not work and I could not get the file end with '.sh'. Could you help me to figure out what the problem is? Is it correct for my procedure?

Thank you so much and best,
Ming

Hi,
I have download the 4.0 version of fmask and i was able to mask the clouds etc using the GUI. I wanted to understand how do i automate using command line. I have gone through the tutorials which was written for 3.3. version and for windows. But didn't understand.
Moreover, I have one more question what does " Number of dilated pixels for XYZ" means ? Does it mean you take 33 matrix and replace the whole 33 matrix with one value?

Hello
Could you please help me.
I applied Fmask to my Landsat-8 L1 data, but it seems like masking is incorrect (the coverage of cloud masking is not full (white pixels) .How can I solve this problem?

Also have problems with cloud shadows over open water (fmask don’t mask shadows)

Hello,
I somehow have troubel to run fmask 4 on windows from the cmd-line without the GUI.
Running the exe FMask.exe from the cmd-line after I changed to the granule dir of a S2 scene always fires up the GUI. When I specify some additional parameter like "FMask.exe 3 3 0 20" I get a messagebox with the info "to many parameter" ?
What am I doing wrong

Hello. We noticed some rectangular artifacts in the masks producted by Fmask 4.4, for example:

(S2B_MSIL2A_20200112T111329_N0213_R137_T30TUN_20200112T122412.SAFE)

The thresholds in the command line were 3 3 0 10.

Fmask 4.4 start ...
Cloud/cloud shadow/snow dilated by 3/3/0 pixels.
Cloud probability threshold of 10.00%.
Load or calculate TOA reflectances.
Detect potential clouds, cloud shadows, snow, and water.
Match cloud shadows with clouds.
Fmask 4.4 finished (31.75 minutes)
for L1C_T30TUN_A014892_20200112T111437 with 41.29% clear pixels

I haven't looked too closely, but I suspect we don't have the auxiliary data installed correctly. Still, filing this now for future reference and in case anyone else runs into the same problem.

Hi,

I have installed the Fmask4.0 Standalone on Ubuntu 14.04.

However, when trying to run the Software I receive the following error:

error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory.

This appears to be a common error across other applications like in the below link:

https://stackoverflow.com/questions/24004240/matlab-2014a-8-3-compiler-runtime-errors-libmwlaunchermain-so

However, following these instructions, I haven't solved the issue. I'd be really grateful for some help in configuring everything correctly!

Thanks!

Hi Everyone,

I believe I set everything correctly but when I try to run Fmask I get the following error:
Fmask_4_0: error while loading shared libraries: libmwlaunchermain.so: cannot open shared object file: No such file or directory

I added the following lines to .profile (also tried .bashrc):

LD_LIBRARY_PATH=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/sys/java/jre/glnxa64/jre/lib/amd64
XAPPLRESDIR=/usr/local/MATLAB/MATLAB_Compiler_Runtime/v95/X11/app-defaults

PATH=$PATH:$LD_LIBRARY_PATH
PATH=$PATH:$XAPPLRESDIR
PATH=$PATH:/usr/GERS/Fmask_4_0/application

Dear developers.
I need to run fmask_4_0 with clipped images. Do you have anyway?

Thanks and regards,

Mateus

Dear Dr. Qiu,

I only found the Fmask 4.0 of Windows in the shared fold of google drive, and I would like to get the version of Linux or MacOS, could you provide them for me?

Best Regards,
Zhigang Cao