[GRASS-user] Example project for a GRASS GIS module on GitHub
Dear users and contributors, I've created an example project (repository) on GitHub. It is a GRASS GIS module written in Python which simply adds two raster maps together. It uses GitHub Actions to build the module and publish its documentation as a website (using GitHub Pages). https://github.com/wenzeslaus/r.example.plus This is based on my earlier work on an example project on GitLab [1] and includes several improvements and changes: * There is a test suite included with couple of test functions. * It uses Black for code formatting (assuming author runs it manually). * Repository is marked as a template (see the big "Use this template" button). * GitHub Actions are used for: * compiling the module and running tests, * checking code quality with Flake8 and Pylint, and * checking code style with Black. * GitHub Actions are now used for publishing documentation (done by GitLab CI before). * Option names now follow GRASS GIS standards more. * More documentation in the code and on how to use the code. * Badges are now in the README file (GitLab had those as project properties). Otherwise, I hope the project should describe itself and if something is missing or is not documented enough, please open an issue or a pull request. Best, Vaclav PS: We can discuss on grass-dev if this should go under some organization and how to improve the "what's next" part [2]. [1] https://lists.osgeo.org/pipermail/grass-dev/2018-November/090438.html [2] https://github.com/wenzeslaus/r.example.plus#what-is-next ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] error in i.sentinel.mask: nan values in xml file
Hi Robi, So I found that i.sentinel.import fails for latlong locations. I moved to UTM as in the original data and all fine. I reached the cloud masking step, and I find a different problem now. Here's the command and an extract of the output: GRASS 7.9.dev (dengue_cba):~/webgis > i.sentinel.mask -s \ > blue=$blue \ > green=$green \ > red=$red \ > swir11=$swir11 \ > nir=$nir \ > swir12=$swir12 \ > nir8a=$nir8a \ > cloud_raster=cloud \ > shadow_raster=shadow \ > mtd_file=`find $out_dir -name 'MTD_TL.xml'` \ > scale_fac=1 WARNING: All subsequent operations will be limited to the current computational region --- Start rescaling bands --- T21JYM_20200126T134201_B02_10m 100% T21JYM_20200126T134201_B03_10m 100% T21JYM_20200126T134201_B04_10m 100% T21JYM_20200126T134201_B08_10m 100% T21JYM_20200126T134201_B8A_20m 100% T21JYM_20200126T134201_B11_20m 100% T21JYM_20200126T134201_B12_20m 100% T21JYM_20200126T134201_B02_10m_double,T21JYM_20200126T134201_B03_10m_double,T21JYM_20200126T134201_B04_10m_double,T21JYM_20200126T134201_B08_10m_double,T21JYM_20200126T134201_B8A_20m_double,T21JYM_20200126T134201_B11_20m_double,T21JYM_20200126T134201_B12_20m_double --- All bands have been rescaled --- --- Start computing maximum values of bands --- T21JYM_20200126T134201_B02_10m_double T21JYM_20200126T134201_B03_10m_double T21JYM_20200126T134201_B04_10m_double T21JYM_20200126T134201_B08_10m_double T21JYM_20200126T134201_B8A_20m_double T21JYM_20200126T134201_B11_20m_double T21JYM_20200126T134201_B12_20m_double --- Computed maximum value: dict_values([0.9352, 1.168, 1.1056, 1.0704, 0.7023, 0.9381, 1.3597]) --- --- Statistics have been computed! --- --- Start clouds detection procedure --- --- Computing cloud mask... --- 100% --- Converting raster cloud mask into vector map --- Extracting areas... 100% Writing areas... 100% Building topology for vector map ... Registering primitives... Building areas... 100% Attaching islands... 100% Attaching centroids... 100% r.to.vect complete. --- Cleaning geometries --- [...] --- Start removing misclassification from the shadow mask --- --- Data preparation... --- WARNING: Values in column will be overwritten WARNING: Number of centroids exceeds number of areas: 24 > 22 WARNING: Number of duplicate centroids: 2 WARNING: Values in column will be overwritten WARNING: Values in column will be overwritten --- Reading mean sun zenith and azimuth from metadata file to compute clouds shift --- --- the mean sun Zenith is: 28.732 deg --- --- the mean sun Azimuth is: 82.028 deg --- --- Start computing the east and north clouds shift at steps of 100m of clouds height--- Traceback (most recent call last): File "/home/veroandreo/.grass7/addons/scripts/i.sentinel.mask", line 638, in main() File "/home/veroandreo/.grass7/addons/scripts/i.sentinel.mask", line 561, in main quiet=True, stderr=subprocess.DEVNULL) File "/home/veroandreo/software/grass79-dev/dist.x86_64-pc-linux-gnu/etc/python/grass/script/core.py", line 499, in run_command return handle_errors(returncode, result=None, args=args, kwargs=kwargs) File "/home/veroandreo/software/grass79-dev/dist.x86_64-pc-linux-gnu/etc/python/grass/script/core.py", line 392, in handle_errors returncode=returncode) grass.exceptions.CalledModuleError: Module run v.overlay v.overlay --o --q ainput=addcat_5922 binput=cl_shift_5922 operator=and output=overlay_5922 ended with error Process ended with non-zero return code 1. See errors in the (error) output. Where is this error output to inspect? This is the UUID in case you want to test: 541021f8-63f5-4e9d-ba28-425c4c8451df Thanks much in advance Vero ps: I use grass-dev with python 3.7.4 (because of the ctypes issue) El mié., 29 ene. 2020 a las 14:53, Veronica Andreo () escribió: > Hi Robi, > > My bad, region was wrong... anyway, trying to replicate from the beginning > I see that i.sentinel.import with -r is importing empty maps. However, the > jp2 files have data. I can visualize them in QGIS. I'll report in a > different thread. Once I can figure it out and reach this point again, I'll > report back to you. Thanks for the clarification! > > Cheers > Vero > > El mié., 29 ene. 2020 a las 9:08, roberta fagandini (< > robifagand...@hotmail.it>) escribió: > >> Hi Vero, >> i.sentinel.mask doesn't retrieve the maximum from the xml file but >> computes the value from the image using r.univar. The error could be due to >> the computational region..has the region been set correctly? >> Can you send the MTD_TL.xml file? I can download the image and make some >> tests. >> >> Roberta >> >> -- >> *Da:* grass-user per conto di >> Veronica Andreo >> *Inviato:* martedì 28 gennaio 2020 19:57 >> *A:* grass-user >> *Oggetto:* [GRASS-user] error in i.sentinel.mask: nan values in xml file >> >> Hello >> >> I try to use i.sentinel.mask but I get the following error: >> >> i.sentinel.mask blue=$blue green=$green red=$red
Re: [GRASS-user] i.sentinel.import imports empty maps
Hi Vero, On Wed, Jan 29, 2020 at 3:20 PM Veronica Andreo wrote: ... > BTW, I noted that grass-addons repo does not have the issues activated. With > trac closed for new tickets, I think it is necessary to activate issues in > grass-addons too Sorry for that, I have activated it now. Please open a ticket at https://github.com/OSGeo/grass-addons/issues Best Markus ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] i.sentinel.import imports empty maps
Same issue! Cumprimentos, *Valter Albino -* Geógrafo Físico, M.Sc. Modelação H / Riscos ambientais / OT www.valteralbino.wixsite.com/hydrodynamics Veronica Andreo escreveu no dia quarta, 29/01/2020 à(s) 14:31: > Suspicion confirmed, this was a map imported with i.sentinel.import in > latlong location. It forces a resolution of 20 degrees, instead of the > equivalent of 20m in degrees > > GRASS 7.9.dev (latlong_wgs84):~ > r.info T21JYM_20200126T134201_B11_20m > > > ++ > | Map: T21JYM_20200126T134201_B11_20 Date: Wed Jan 29 11:09:18 2020 >| > | Mapset: sentinel2 Login of Creator: vandreo > | > | Location: latlong_wgs84 >| > | DataBase: /home/vandreo/grassdata >| > | Title: > | > | Timestamp: 26 Jan 2020 13:49:32.751425 > | > > > || > | >| > | Type of Map: raster Number of Categories: 0 > | > | Data Type:FCELL >| > | Rows: 1 >| > | Columns: 1 >| > | Total Cells: 1 >| > |Projection: Latitud - Longitud. > | > |N:20SS:40S Res:20 > | > |E:40WW:60W Res:20 > | > | Range of data:min = NULL max = NULL > | > | >| > | Data Description: >| > |generado por r.proj > | > | >| > | Comments: >| > |r.proj --quiet location="temp_import_location_97485" > mapset="PERMANE\ | > |NT" input="T21JYM_20200126T134201_B11_20m" method="bilinear" > memory=\ | > |500 resolution=20.0 > | > | >| > > > ++ > > El mié., 29 ene. 2020 a las 11:20, Veronica Andreo () > escribió: > >> Hi all, >> >> I'm using i.sentinel.import with -r flag to import sentinel scenes into a >> latlong location. No matter if I use, extent=region or extent=input, I get >> empty maps imported. >> >> Estimated target resolution for input band >> : 0.00018570053194443554 >> Using given resolution for input band : >> 20.0 >> Reprojecting ... >> ERROR: The reprojected raster is empty >> >> Meanwhile a normal r.import with input and output, imports the map >> properly. Is it possible that i.sentinel.import tries to set a 20 >> resolution also in a lat long location???That would be degrees then, and >> hence the empty maps... >> >> BTW, I noted that grass-addons repo does not have the issues activated. >> With trac closed for new tickets, I think it is necessary to activate >> issues in grass-addons too >> >> Thanks much in advance >> >> Vero >> > ___ > grass-user mailing list > grass-user@lists.osgeo.org > https://lists.osgeo.org/mailman/listinfo/grass-user ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] i.sentinel.import imports empty maps
Suspicion confirmed, this was a map imported with i.sentinel.import in latlong location. It forces a resolution of 20 degrees, instead of the equivalent of 20m in degrees GRASS 7.9.dev (latlong_wgs84):~ > r.info T21JYM_20200126T134201_B11_20m ++ | Map: T21JYM_20200126T134201_B11_20 Date: Wed Jan 29 11:09:18 2020 | | Mapset: sentinel2 Login of Creator: vandreo | | Location: latlong_wgs84 | | DataBase: /home/vandreo/grassdata | | Title: | | Timestamp: 26 Jan 2020 13:49:32.751425 | || | | | Type of Map: raster Number of Categories: 0 | | Data Type:FCELL | | Rows: 1 | | Columns: 1 | | Total Cells: 1 | |Projection: Latitud - Longitud. | |N:20SS:40S Res:20 | |E:40WW:60W Res:20 | | Range of data:min = NULL max = NULL | | | | Data Description: | |generado por r.proj | | | | Comments: | |r.proj --quiet location="temp_import_location_97485" mapset="PERMANE\ | |NT" input="T21JYM_20200126T134201_B11_20m" method="bilinear" memory=\ | |500 resolution=20.0 | | | ++ El mié., 29 ene. 2020 a las 11:20, Veronica Andreo () escribió: > Hi all, > > I'm using i.sentinel.import with -r flag to import sentinel scenes into a > latlong location. No matter if I use, extent=region or extent=input, I get > empty maps imported. > > Estimated target resolution for input band > : 0.00018570053194443554 > Using given resolution for input band : > 20.0 > Reprojecting ... > ERROR: The reprojected raster is empty > > Meanwhile a normal r.import with input and output, imports the map > properly. Is it possible that i.sentinel.import tries to set a 20 > resolution also in a lat long location???That would be degrees then, and > hence the empty maps... > > BTW, I noted that grass-addons repo does not have the issues activated. > With trac closed for new tickets, I think it is necessary to activate > issues in grass-addons too > > Thanks much in advance > > Vero > ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] i.sentinel.import imports empty maps
Hi all, I'm using i.sentinel.import with -r flag to import sentinel scenes into a latlong location. No matter if I use, extent=region or extent=input, I get empty maps imported. Estimated target resolution for input band : 0.00018570053194443554 Using given resolution for input band : 20.0 Reprojecting ... ERROR: The reprojected raster is empty Meanwhile a normal r.import with input and output, imports the map properly. Is it possible that i.sentinel.import tries to set a 20 resolution also in a lat long location???That would be degrees then, and hence the empty maps... BTW, I noted that grass-addons repo does not have the issues activated. With trac closed for new tickets, I think it is necessary to activate issues in grass-addons too Thanks much in advance Vero ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] error in i.sentinel.mask: nan values in xml file
Hi Robi, My bad, region was wrong... anyway, trying to replicate from the beginning I see that i.sentinel.import with -r is importing empty maps. However, the jp2 files have data. I can visualize them in QGIS. I'll report in a different thread. Once I can figure it out and reach this point again, I'll report back to you. Thanks for the clarification! Cheers Vero El mié., 29 ene. 2020 a las 9:08, roberta fagandini (< robifagand...@hotmail.it>) escribió: > Hi Vero, > i.sentinel.mask doesn't retrieve the maximum from the xml file but > computes the value from the image using r.univar. The error could be due to > the computational region..has the region been set correctly? > Can you send the MTD_TL.xml file? I can download the image and make some > tests. > > Roberta > > -- > *Da:* grass-user per conto di > Veronica Andreo > *Inviato:* martedì 28 gennaio 2020 19:57 > *A:* grass-user > *Oggetto:* [GRASS-user] error in i.sentinel.mask: nan values in xml file > > Hello > > I try to use i.sentinel.mask but I get the following error: > > i.sentinel.mask blue=$blue green=$green red=$red swir11=$swir11 nir=$nir > swir12=$swir12 nir8a=$nir8a cloud_mask=cloud shadow_mask=shadow > mtd_file=`find $out_dir -name 'MTD_TL.xml'` > > ADVERTENCIA: All subsequent operations will be limited to the current > computational region > ADVERTENCIA: Any rescale factor has been applied > --- Start computing maximum values of bands --- > T21JYM_20200126T134201_B02_10m > T21JYM_20200126T134201_B03_10m > T21JYM_20200126T134201_B04_10m > T21JYM_20200126T134201_B08_10m > T21JYM_20200126T134201_B8A_20m > T21JYM_20200126T134201_B11_20m > T21JYM_20200126T134201_B12_20m > --- Computed maximum value: dict_values([nan, nan, nan, nan, nan, nan, > nan]) --- > --- Statistics have been computed! --- > --- Start clouds detection procedure --- > --- Computing cloud mask... --- > Mapa no válido > Parse error > ERROR: error al parsear > ERROR: An error occurred while running r.mapcalc with expression: >cloud_def82115 = ifT21JYM_20200126T134201_B02_10m > (0.08*nan)) >&& (T21JYM_20200126T134201_B03_10m > (0.08*nan)) && >(T21JYM_20200126T134201_B04_10m > (0.08*nan))) == 1) && >(((T21JYM_20200126T134201_B04_10m < ((0.08*nan)*1.5)) && >(T21JYM_20200126T134201_B04_10m > >T21JYM_20200126T134201_B12_20m*1.3)) == 0) && >(((T21JYM_20200126T134201_B11_20m < (0.1*nan)) && >(T21JYM_20200126T134201_B12_20m < (0.1*nan))) == 0) && >((if(T21JYM_20200126T134201_B8A_20m == >max(T21JYM_20200126T134201_B8A_20m, 2 * >T21JYM_20200126T134201_B02_10m, 2 * T21JYM_20200126T134201_B03_10m, >2 * T21JYM_20200126T134201_B04_10m))) == 0) && >((T21JYM_20200126T134201_B02_10m > 0.2) == 1), 0, null()) > > I checked the xml file and there are a lot of nan's yes, but there are > also real values. Why doesn't the max function in this part: > https://github.com/OSGeo/grass-addons/blob/master/grass7/imagery/i.sentinel/i.sentinel.mask/i.sentinel.mask.py#L321 > recognize them? Isn't there a way to avoid nan while computing max? > > Thanks much in advance > Vero > > ps: I can provide the xml if needed. > ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.sim.water simulation considering dams
Hi, I don't have any experience with that parameter, but I think if you don't need permeable structures, you don't need that parameter. I would try to represent the structures in the elevation, that should work. But keep in mind that it's a shallow water flow model, so it's not ideal for filling large and deep depressions. In that case you can also consider Itzi model. Anna On Thu, Jan 23, 2020 at 5:16 AM Johannes Radinger < johannesradin...@gmail.com> wrote: > Dear GRASS users, > > maybe someone of you has already worked with r.sim.water while considering > dams as impermeable structures that retain water, i.e. create > impoundments/reservoirs. > > I am wondering how to best specify dams within r.sim.water: There is the > parameter flow_control which is a raster map that indicates the > permeability of the landscape. The manual mentions here a permeability > ratio (0-1) and I guess this should be 0 for all cells that represent a dam > and 1 for all other cells of the computational region?! > But what about the elevation data then; Do I need to provide an > elevation raster that includes the dam height or should this be the > elevation as without dams? > I'd like to know whether I need to provide a flow_control map or an > elevation map that includes dams or both? I couldn't find any example of > r.sim.water that uses the flow_control parameter so far... any > ideas/experiences from your side? > > cheers, > Johannes > > ___ > grass-user mailing list > grass-user@lists.osgeo.org > https://lists.osgeo.org/mailman/listinfo/grass-user ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] R: error in i.sentinel.mask: nan values in xml file
Hi Vero, i.sentinel.mask doesn't retrieve the maximum from the xml file but computes the value from the image using r.univar. The error could be due to the computational region..has the region been set correctly? Can you send the MTD_TL.xml file? I can download the image and make some tests. Roberta Da: grass-user per conto di Veronica Andreo Inviato: martedì 28 gennaio 2020 19:57 A: grass-user Oggetto: [GRASS-user] error in i.sentinel.mask: nan values in xml file Hello I try to use i.sentinel.mask but I get the following error: i.sentinel.mask blue=$blue green=$green red=$red swir11=$swir11 nir=$nir swir12=$swir12 nir8a=$nir8a cloud_mask=cloud shadow_mask=shadow mtd_file=`find $out_dir -name 'MTD_TL.xml'` ADVERTENCIA: All subsequent operations will be limited to the current computational region ADVERTENCIA: Any rescale factor has been applied --- Start computing maximum values of bands --- T21JYM_20200126T134201_B02_10m T21JYM_20200126T134201_B03_10m T21JYM_20200126T134201_B04_10m T21JYM_20200126T134201_B08_10m T21JYM_20200126T134201_B8A_20m T21JYM_20200126T134201_B11_20m T21JYM_20200126T134201_B12_20m --- Computed maximum value: dict_values([nan, nan, nan, nan, nan, nan, nan]) --- --- Statistics have been computed! --- --- Start clouds detection procedure --- --- Computing cloud mask... --- Mapa no válido Parse error ERROR: error al parsear ERROR: An error occurred while running r.mapcalc with expression: cloud_def82115 = ifT21JYM_20200126T134201_B02_10m > (0.08*nan)) && (T21JYM_20200126T134201_B03_10m > (0.08*nan)) && (T21JYM_20200126T134201_B04_10m > (0.08*nan))) == 1) && (((T21JYM_20200126T134201_B04_10m < ((0.08*nan)*1.5)) && (T21JYM_20200126T134201_B04_10m > T21JYM_20200126T134201_B12_20m*1.3)) == 0) && (((T21JYM_20200126T134201_B11_20m < (0.1*nan)) && (T21JYM_20200126T134201_B12_20m < (0.1*nan))) == 0) && ((if(T21JYM_20200126T134201_B8A_20m == max(T21JYM_20200126T134201_B8A_20m, 2 * T21JYM_20200126T134201_B02_10m, 2 * T21JYM_20200126T134201_B03_10m, 2 * T21JYM_20200126T134201_B04_10m))) == 0) && ((T21JYM_20200126T134201_B02_10m > 0.2) == 1), 0, null()) I checked the xml file and there are a lot of nan's yes, but there are also real values. Why doesn't the max function in this part: https://github.com/OSGeo/grass-addons/blob/master/grass7/imagery/i.sentinel/i.sentinel.mask/i.sentinel.mask.py#L321 recognize them? Isn't there a way to avoid nan while computing max? Thanks much in advance Vero ps: I can provide the xml if needed. ___ grass-user mailing list grass-user@lists.osgeo.org https://lists.osgeo.org/mailman/listinfo/grass-user
