Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Thanks for the update.
Indeed, I have noticed that this polygon is on the edge of Sentinel-2 tiles. As
a result, the AOI gets covered with two different tiles on every overpass, but
not completely (bad luck for a 4.5 ha field!). Even the images that display
100% area coverage actually miss a tiny, tiny fraction of it (approximately
4e-10).
catalog <- SearchCatalog(aoi = aoi, from = "2023-06-01", to = "2023-08-31",
collection = "sentinel-2-l2a”, with_geometry = TRUE, client = OAuthClient)
100 - subset(catalog, areaCoverage > 99)$areaCoverage
## [1] 4.085194e-10 4.085194e-10 4.085194e-10 4.085194e-10 4.085194e-10 ...
I'm not sure if this could be the source of the problem, but it's good that you
found a workaround.
Best regards,
Zivan
On 21 Aug 2024, at 18:59, Micha Silver wrote:
Follow up:
After some gnawing of my teeth, I found the problem: Nothing to do with R, sf,
nor the CDSE package. My date range included one date where the Sentinel-2 tile
from Copernicus data space was damaged/clipped/mangled. And my study area was
"hanging over the edge". I found the problem image using the Copernicus
Dataspace browser, and going thru date by date...
I'm not sure why exactly that caused the error, but once I changed the date
range to exclude that problem image, the procedure worked as expected.
Thanks for your help.
On 19/08/2024 21:29, Roger Bivand wrote:
> Adding the output of sessionInfo() and sf_extSoftVersion() might also help.
> The difficulty Zivan points out is that the structure as read is valid, but
> before conversion to text by dput() may have actually had non-identical first
> and last coordinates, because of the number of digits used. Also try putting
> the file created by saveRDS(aoi, ...) on a website with a link here. It would
> be useful to see the code in the workflow at the point of failure (you point
> to Error in MtrxSet, maybe also run traceback() after the failure to give
> more precision in where this is occurring, maybe in stars?
>
> Hop this helps,
>
> Roger
>
> --
> Roger Bivand
> Emeritus Professor
> Norwegian School of Economics
> Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
> roger.biv...@nhh.no <mailto:roger.biv...@nhh.no>
>
>
> From: R-sig-Geo
> <mailto:r-sig-geo-boun...@r-project.org> on behalf of Zivan Karaman
> <mailto:zivan.kara...@gmail.com>
> Sent: 19 August 2024 18:40
> To: Micha Silver
> Cc: R-sig-Geo@r-project.org <mailto:R-sig-Geo@r-project.org>
> Subject: Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
>
> Could you please provide an example of code that actually raises this error?
> Best regards,
> Zivan
>
>
> On 19 Aug 2024, at 16:23, Micha Silver
> <mailto:tsvi...@gmail.com> wrote:
>
> Searching for the error in the subject line returns some discussions from a
> few years ago. But I'm not able to overcome this error.
>
> Here's the polygon in question:
>
>> dput(aoi)
> structure(list(x =
>
> structure(list(structure(list(structure(c(11.0127043, 11.0127061, 11.0134526,
> 11.0134554, 11.0134626, 11.0134692, 11.0134776, 11.0134813, 11.0157343,
> 11.0157373, 11.0157437, 11.0157495, 11.0157546, 11.0157585, 11.015761,
> 11.0157617, 11.0157616, 11.0157613, 11.0153992, 11.0153983, 11.0153956,
> 11.0153922, 11.0153869, 11.0153804, 11.0153729, 11.0153694, 11.0127478,
> 11.0127447, 11.0127379, 11.012732, 11.0127269, 11.0127232, 11.0127212,
> 11.01272, 11.0127197, 11.0126956, 11.0126958, 11.0126965, 11.0126978,
> 11.0127004, 11.0127043, 46.8484069, 46.8484048, 46.8476584, 46.847656,
> 46.8476511, 46.8476481, 46.8476461, 46.8476456, 46.8475213, 46.8475214,
> 46.847522, 46.8475235, 46.8475266, 46.8475311, 46.8475365, 46.8475425,
> 46.8475489, 46.8475519, 46.8495623, 46.8495656, 46.8495729, 46.8495788,
> 46.8495833, 46.8495856, 46.849587, 46.8495874, 46.8496081, 46.8496079,
> 46.8496069, 46.849605, 46.8496014, 46.8495965, 46.8495906, 46.8495839,
> 46.8495808, 46.8484309, 46.8484282, 46.8484218, 46.8484166, 46.848412,
> 46.8484069), dim = c(41L, 2L), dimnames = list( NULL, c("X", "Y", class =
> c("XY", "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision = 0,
> bbox = structure(c(xmin = 11.0126956, ymin = 46.8475213, xmax = 11.0157617,
> ymax = 46.8496081), class = "bbox"), crs = structure(list( input =
> "EPSG:4326", wkt = "GEOGCRS[\"WGS 84\",\n ENSEMBLE[\"World Geodetic System
> 1984 ensemble\",\n MEMBER[\"World Geodetic System 1984 (Transit)\"],\n
> MEMBER[\"World Geodetic System 1984 (G730)\"],\n MEMBER[\"World Ge
Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Follow up:
After some gnawing of my teeth, I found the
problem: Nothing to do with R, sf, nor the CDSE package. My date
range included one date where the Sentinel-2 tile from
Copernicus data space was damaged/clipped/mangled. And my study
area was "hanging over the edge". I found
the problem image using the Copernicus Dataspace browser, and
going thru date by date...
I'm not sure why exactly that caused the error,
but once I changed the date range to exclude that problem image,
the procedure worked as expected.
Thanks for your help.
On 19/08/2024 21:29, Roger Bivand
wrote:
Adding the output of sessionInfo() and sf_extSoftVersion() might also help. The difficulty Zivan points out is that the structure as read is valid, but before conversion to text by dput() may have actually had non-identical first and last coordinates, because of the number of digits used. Also try putting the file created by saveRDS(aoi, ...) on a website with a link here. It would be useful to see the code in the workflow at the point of failure (you point to Error in MtrxSet, maybe also run traceback() after the failure to give more precision in where this is occurring, maybe in stars?
Hop this helps,
Roger
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
roger.biv...@nhh.no
From: R-sig-Geo on behalf of Zivan Karaman
Sent: 19 August 2024 18:40
To: Micha Silver
Cc: R-sig-Geo@r-project.org
Subject: Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Could you please provide an example of code that actually raises this error?
Best regards,
Zivan
On 19 Aug 2024, at 16:23, Micha Silver wrote:
Searching for the error in the subject line returns some discussions from a few years ago. But I'm not able to overcome this error.
Here's the polygon in question:
dput(aoi)
structure(list(x =
structure(list(structure(list(structure(c(11.0127043, 11.0127061, 11.0134526, 11.0134554, 11.0134626, 11.0134692, 11.0134776, 11.0134813, 11.0157343, 11.0157373, 11.0157437, 11.0157495, 11.0157546, 11.0157585, 11.015761, 11.0157617, 11.0157616, 11.0157613, 11.0153992, 11.0153983, 11.0153956, 11.0153922, 11.0153869, 11.0153804, 11.0153729, 11.0153694, 11.0127478, 11.0127447, 11.0127379, 11.012732, 11.0127269, 11.0127232, 11.0127212, 11.01272, 11.0127197, 11.0126956, 11.0126958, 11.0126965, 11.0126978, 11.0127004, 11.0127043, 46.8484069, 46.8484048, 46.8476584, 46.847656, 46.8476511, 46.8476481, 46.8476461, 46.8476456, 46.8475213, 46.8475214, 46.847522, 46.8475235, 46.8475266, 46.8475311, 46.8475365, 46.8475425, 46.8475489, 46.8475519, 46.8495623, 46.8495656, 46.8495729, 46.8495788, 46.8495833, 46.8495856, 46.849587, 46.8495874, 46.8496081, 46.8496079, 46.8496069, 46.849605, 46.8496014, 46.8495965, 46.8495906, 46.8495839, 46.8495808, 46.8484309, 46.8484282, 46.8484218, 46.8484166, 46.848412, 46.8484069), dim = c(41L, 2L), dimnames = list( NULL, c("X", "Y", class = c("XY", "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision = 0, bbox = structure(c(xmin = 11.0126956, ymin = 46.8475213, xmax = 11.0157617, ymax = 46.8496081), class = "bbox"), crs = structure(list( input = "EPSG:4326", wkt = "GEOGCRS[\"WGS 84\",\n ENSEMBLE[\"World Geodetic System 1984 ensemble\",\n MEMBER[\"World Geodetic System 1984 (Transit)\"],\n MEMBER[\"World Geodetic System 1984 (G730)\"],\n MEMBER[\"World Geodetic System 1984 (G873)\"],\n MEMBER[\"World Geodetic System 1984 (G1150)\"],\n MEMBER[\"World Geodetic System 1984 (G1674)\"],\n MEMBER[\"World Geodetic System 1984 (G1762)\"],\n MEMBER[\"World Geodetic System 1984 (G2139)\"],\n ELLIPSOID[\"WGS 84\",6378137,298.257223563,\n LENGTHUNIT[\"metre\",1]],\n ENSEMBLEACCURACY[2.0]],\n PRIMEM[\"Greenwich\",0,\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n CS[ellipsoidal,2],\n AXIS[\"geodetic latitude (Lat)\",north,\n ORDER[1],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n AXIS[\"geodetic longitude (Lon)\",east,\n ORDER[2],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n USAGE[\n SCOPE[\"Horizontal component of 3D system.\"],\n AREA[\"World.\"],\n BBOX[-90,-180,90,180]],\n ID[\"EPSG\",4326]]"), class = "crs"), n_empty = 0L)), row.names = 1L, class = c("sf", "data.frame"), sf_column = "x", agr = structure(integer(0), class = "factor", levels = c("constant", "aggregate", "identity"), names = character(0)))
This polygon is used as area o
Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
On 20/08/2024 11:27, Zivan Karaman wrote: Hi Micha, Thank you for sharing the file. I’ve noticed that this polygon has only 5 vertices, while the one in the previous message has 40, so this is not exactly the same object. Both seem OK, and I was able to download and crop satellite images with CDSE without problems. Yes, I used several polygon versions to try to isolate the problem. When I use this polygon as aoi directly in a CDSE::GetImage() call it works fine also for me. So the issue is elsewhere. I'll continue to investigate. Difficult to say more without a reproducible example raising the error. Best, Zivan On 20 Aug 2024, at 09:25, Micha Silver wrote: Hi Zivan, Roger: Thanks for the quick response.Here's the RDS of the polygon: https://filebin.net/pdrazh0e4ej7el9f and sessionInfo, etc: > sessionInfo() R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so <http://libblas.so/>.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so <http://libopenblasp-r0.3.21.so/> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_IL.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_IL.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] tidyr_1.3.1 sf_1.0-16 dplyr_1.1.4 lubridate_1.9.3 [5] RSQLite_2.3.7 CDSE_0.2.0 rOPTRAM_0.3.0.000 ggplot2_3.5.1 [9] knitr_1.47 terra_1.7-78 devtools_2.4.5 usethis_2.2.3 loaded via a namespace (and not attached): [1] pkgload_1.3.4 bit64_4.0.5 jsonlite_1.8.8 here_1.0.1 [5] shiny_1.8.1.1 askpass_1.2.0 blob_1.2.4 remotes_2.5.0 [9] sessioninfo_1.2.2 pillar_1.9.0 glue_1.7.0 digest_0.6.35 [13] promises_1.3.0 colorspace_2.1-0 htmltools_0.5.8.1 httpuv_1.6.15 [17] pkgconfig_2.0.3 s2_1.1.6 purrr_1.0.2 xtable_1.8-4 [21] scales_1.3.0 processx_3.8.4 later_1.3.2 openssl_2.2.0 [25] timechange_0.3.0 tibble_3.2.1 proxy_0.4-27 generics_0.1.3 [29] ellipsis_0.3.2 cachem_1.1.0 withr_3.0.0 cli_3.6.3 [33] lutz_0.3.2 magrittr_2.0.3 mime_0.12 memoise_2.0.1 [37] ps_1.7.6 fs_1.6.4 fansi_1.0.6 class_7.3-22 [41] geojsonsf_2.0.3 pkgbuild_1.4.4 httr2_1.0.1 profvis_0.3.8 [45] tools_4.2.2 lifecycle_1.0.4 stringr_1.5.1 munsell_0.5.1 [49] callr_3.7.6 compiler_4.2.2 e1071_1.7-14 rlang_1.1.4 [53] classInt_0.4-10 units_0.8-5 grid_4.2.2 rstudioapi_0.16.0 [57] rappdirs_0.3.3 htmlwidgets_1.6.4 miniUI_0.1.1.1 wk_0.9.2 [61] gtable_0.3.5 codetools_0.2-20 DBI_1.2.3 curl_5.2.1 [65] R6_2.5.1 fastmap_1.2.0 bit_4.0.5 utf8_1.2.4 [69] rprojroot_2.0.4 KernSmooth_2.23-24 desc_1.4.3 stringi_1.8.4 [73] Rcpp_1.0.12 vctrs_0.6.5 tidyselect_1.2.1 xfun_0.45 [77] urlchecker_1.0.1 > sf_extSoftVersion() GEOS GDAL proj.4 GDAL_with_GEOS USE_PROJ_H "3.11.1" "3.6.2" "9.1.1" "true" "true" PROJ "9.1.1" This error occurs, during a longer analysis, when I begin downloading imagery , and only with the above aoi polygon. So I'm trying to strip out all the steps in the code to identify what the cause is. No luck yet... Note: I don't think that the CDSE package is the cause. Best regards, Micha On 19/08/2024 21:29, Roger Bivand wrote: Adding the output of sessionInfo() and sf_extSoftVersion() might also help. The difficulty Zivan points out is that the structure as read is valid, but before conversion to text by dput() may have actually had non-identical first and last coordinates, because of the number of digits used. Also try putting the file created by saveRDS(aoi, ...) on a website with a link here. It would be useful to see the code in the workflow at the point of failure (you point to Error in MtrxSet, maybe also run traceback() after the failure to give more precision in where this is occurring, maybe in stars? Hop this helps, Roger -- Roger Bivand Emeritus Professor Norwegian School of Economics Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway roger.biv...@nhh.no From: R-sig-Geo on behalf of Zivan Karaman Sent: 19 August 2024 18:40 To: Micha Silver Cc:R-sig-Geo@r-project.org Subject: Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed Could you please provide an example of code that actually raises this error? Best regards, Zivan On 19 Aug 2024, at 16:23, Micha Silver wrote: Searching
Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Hi Micha, Thank you for sharing the file. I’ve noticed that this polygon has only 5 vertices, while the one in the previous message has 40, so this is not exactly the same object. Both seem OK, and I was able to download and crop satellite images with CDSE without problems. Difficult to say more without a reproducible example raising the error. Best, Zivan On 20 Aug 2024, at 09:25, Micha Silver wrote: Hi Zivan, Roger: Thanks for the quick response.Here's the RDS of the polygon: https://filebin.net/pdrazh0e4ej7el9f and sessionInfo, etc: > sessionInfo() R version 4.2.2 Patched (2022-11-10 r83330) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Debian GNU/Linux 12 (bookworm) Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so <http://libblas.so/>.3 LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.21.so <http://libopenblasp-r0.3.21.so/> locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_IL.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_IL.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] tidyr_1.3.1 sf_1.0-16 dplyr_1.1.4 lubridate_1.9.3 [5] RSQLite_2.3.7 CDSE_0.2.0rOPTRAM_0.3.0.000 ggplot2_3.5.1 [9] knitr_1.47terra_1.7-78 devtools_2.4.5usethis_2.2.3 loaded via a namespace (and not attached): [1] pkgload_1.3.4 bit64_4.0.5jsonlite_1.8.8 here_1.0.1 [5] shiny_1.8.1.1 askpass_1.2.0 blob_1.2.4 remotes_2.5.0 [9] sessioninfo_1.2.2 pillar_1.9.0 glue_1.7.0 digest_0.6.35 [13] promises_1.3.0 colorspace_2.1-0 htmltools_0.5.8.1 httpuv_1.6.15 [17] pkgconfig_2.0.3s2_1.1.6 purrr_1.0.2xtable_1.8-4 [21] scales_1.3.0 processx_3.8.4 later_1.3.2openssl_2.2.0 [25] timechange_0.3.0 tibble_3.2.1 proxy_0.4-27 generics_0.1.3 [29] ellipsis_0.3.2 cachem_1.1.0 withr_3.0.0cli_3.6.3 [33] lutz_0.3.2 magrittr_2.0.3 mime_0.12 memoise_2.0.1 [37] ps_1.7.6 fs_1.6.4 fansi_1.0.6class_7.3-22 [41] geojsonsf_2.0.3pkgbuild_1.4.4 httr2_1.0.1profvis_0.3.8 [45] tools_4.2.2lifecycle_1.0.4stringr_1.5.1 munsell_0.5.1 [49] callr_3.7.6compiler_4.2.2 e1071_1.7-14 rlang_1.1.4 [53] classInt_0.4-10units_0.8-5grid_4.2.2 rstudioapi_0.16.0 [57] rappdirs_0.3.3 htmlwidgets_1.6.4 miniUI_0.1.1.1 wk_0.9.2 [61] gtable_0.3.5 codetools_0.2-20 DBI_1.2.3 curl_5.2.1 [65] R6_2.5.1 fastmap_1.2.0 bit_4.0.5 utf8_1.2.4 [69] rprojroot_2.0.4KernSmooth_2.23-24 desc_1.4.3 stringi_1.8.4 [73] Rcpp_1.0.12vctrs_0.6.5tidyselect_1.2.1 xfun_0.45 [77] urlchecker_1.0.1 > sf_extSoftVersion() GEOS GDAL proj.4 GDAL_with_GEOS USE_PROJ_H "3.11.1""3.6.2""9.1.1" "true" "true" PROJ "9.1.1" This error occurs, during a longer analysis, when I begin downloading imagery , and only with the above aoi polygon. So I'm trying to strip out all the steps in the code to identify what the cause is. No luck yet... Note: I don't think that the CDSE package is the cause. Best regards, Micha On 19/08/2024 21:29, Roger Bivand wrote: > Adding the output of sessionInfo() and sf_extSoftVersion() might also help. > The difficulty Zivan points out is that the structure as read is valid, but > before conversion to text by dput() may have actually had non-identical first > and last coordinates, because of the number of digits used. Also try putting > the file created by saveRDS(aoi, ...) on a website with a link here. It would > be useful to see the code in the workflow at the point of failure (you point > to Error in MtrxSet, maybe also run traceback() after the failure to give > more precision in where this is occurring, maybe in stars? > > Hop this helps, > > Roger > > -- > Roger Bivand > Emeritus Professor > Norwegian School of Economics > Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway > roger.biv...@nhh.no <mailto:roger.biv...@nhh.no> > > > From: R-sig-Geo > <mailto:r-sig-geo-boun...@r-project.org> on behalf of Zivan Karaman > <mailto:zivan.kara...@gmail.com> > Sent: 19 August 20
Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
40
To: Micha Silver
Cc: R-sig-Geo@r-project.org
Subject: Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Could you please provide an example of code that actually raises this error?
Best regards,
Zivan
On 19 Aug 2024, at 16:23, Micha Silver wrote:
Searching for the error in the subject line returns some discussions from a few years ago. But I'm not able to overcome this error.
Here's the polygon in question:
dput(aoi)
structure(list(x =
structure(list(structure(list(structure(c(11.0127043, 11.0127061, 11.0134526, 11.0134554, 11.0134626, 11.0134692, 11.0134776, 11.0134813, 11.0157343, 11.0157373, 11.0157437, 11.0157495, 11.0157546, 11.0157585, 11.015761, 11.0157617, 11.0157616, 11.0157613, 11.0153992, 11.0153983, 11.0153956, 11.0153922, 11.0153869, 11.0153804, 11.0153729, 11.0153694, 11.0127478, 11.0127447, 11.0127379, 11.012732, 11.0127269, 11.0127232, 11.0127212, 11.01272, 11.0127197, 11.0126956, 11.0126958, 11.0126965, 11.0126978, 11.0127004, 11.0127043, 46.8484069, 46.8484048, 46.8476584, 46.847656, 46.8476511, 46.8476481, 46.8476461, 46.8476456, 46.8475213, 46.8475214, 46.847522, 46.8475235, 46.8475266, 46.8475311, 46.8475365, 46.8475425, 46.8475489, 46.8475519, 46.8495623, 46.8495656, 46.8495729, 46.8495788, 46.8495833, 46.8495856, 46.849587, 46.8495874, 46.8496081, 46.8496079, 46.8496069, 46.849605, 46.8496014, 46.8495965, 46.8495906, 46.8495839, 46.8495808, 46.8484309, 46.8484282, 46.8484218, 46.8484166, 46.848412, 46.8484069), dim = c(41L, 2L), dimnames = list( NULL, c("X", "Y", class = c("XY", "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision = 0, bbox = structure(c(xmin = 11.0126956, ymin = 46.8475213, xmax = 11.0157617, ymax = 46.8496081), class = "bbox"), crs = structure(list( input = "EPSG:4326", wkt = "GEOGCRS[\"WGS 84\",\n ENSEMBLE[\"World Geodetic System 1984 ensemble\",\n MEMBER[\"World Geodetic System 1984 (Transit)\"],\n MEMBER[\"World Geodetic System 1984 (G730)\"],\n MEMBER[\"World Geodetic System 1984 (G873)\"],\n MEMBER[\"World Geodetic System 1984 (G1150)\"],\n MEMBER[\"World Geodetic System 1984 (G1674)\"],\n MEMBER[\"World Geodetic System 1984 (G1762)\"],\n MEMBER[\"World Geodetic System 1984 (G2139)\"],\n ELLIPSOID[\"WGS 84\",6378137,298.257223563,\n LENGTHUNIT[\"metre\",1]],\n ENSEMBLEACCURACY[2.0]],\n PRIMEM[\"Greenwich\",0,\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n CS[ellipsoidal,2],\n AXIS[\"geodetic latitude (Lat)\",north,\n ORDER[1],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n AXIS[\"geodetic longitude (Lon)\",east,\n ORDER[2],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n USAGE[\n SCOPE[\"Horizontal component of 3D system.\"],\n AREA[\"World.\"],\n BBOX[-90,-180,90,180]],\n ID[\"EPSG\",4326]]"), class = "crs"), n_empty = 0L)), row.names = 1L, class = c("sf", "data.frame"), sf_column = "x", agr = structure(integer(0), class = "factor", levels = c("constant", "aggregate", "identity"), names = character(0)))
This polygon is used as area of interest to crop Copernicus imagery that I am downloading using the {CDSE} package. (I have run this workflow successfully many times with several other aoi polygons)
I have tried:
1- sf::st_make_valid()
2- transforming to a UTM CRS
3- extracting coordinates and recreating the polygon (i.e.:
aoi_p <- st_polygon(list(st_coordinates(aoi)[,1:2]))
aoi3 <- aoi_p |>
st_sfc() |>
st_as_sf()
st_crs(aoi3) <- "EPSG:4326"
4- buffering by a small amount
The above error recurs in all cases (only with this problem polygon). Any suggestions?
Thanks
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
https://orcid.org/-0002-1128-1325
--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
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--
Micha Silver
Remote Sensing Lab, Sde Boker
Ben Gurion University
+972-523-665918
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Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Adding the output of sessionInfo() and sf_extSoftVersion() might also help. The
difficulty Zivan points out is that the structure as read is valid, but before
conversion to text by dput() may have actually had non-identical first and last
coordinates, because of the number of digits used. Also try putting the file
created by saveRDS(aoi, ...) on a website with a link here. It would be useful
to see the code in the workflow at the point of failure (you point to Error in
MtrxSet, maybe also run traceback() after the failure to give more precision in
where this is occurring, maybe in stars?
Hop this helps,
Roger
--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
roger.biv...@nhh.no
From: R-sig-Geo on behalf of Zivan Karaman
Sent: 19 August 2024 18:40
To: Micha Silver
Cc: R-sig-Geo@r-project.org
Subject: Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Could you please provide an example of code that actually raises this error?
Best regards,
Zivan
On 19 Aug 2024, at 16:23, Micha Silver wrote:
Searching for the error in the subject line returns some discussions from a few
years ago. But I'm not able to overcome this error.
Here's the polygon in question:
> dput(aoi)
structure(list(x =
structure(list(structure(list(structure(c(11.0127043, 11.0127061, 11.0134526,
11.0134554, 11.0134626, 11.0134692, 11.0134776, 11.0134813, 11.0157343,
11.0157373, 11.0157437, 11.0157495, 11.0157546, 11.0157585, 11.015761,
11.0157617, 11.0157616, 11.0157613, 11.0153992, 11.0153983, 11.0153956,
11.0153922, 11.0153869, 11.0153804, 11.0153729, 11.0153694, 11.0127478,
11.0127447, 11.0127379, 11.012732, 11.0127269, 11.0127232, 11.0127212,
11.01272, 11.0127197, 11.0126956, 11.0126958, 11.0126965, 11.0126978,
11.0127004, 11.0127043, 46.8484069, 46.8484048, 46.8476584, 46.847656,
46.8476511, 46.8476481, 46.8476461, 46.8476456, 46.8475213, 46.8475214,
46.847522, 46.8475235, 46.8475266, 46.8475311, 46.8475365, 46.8475425,
46.8475489, 46.8475519, 46.8495623, 46.8495656, 46.8495729, 46.8495788,
46.8495833, 46.8495856, 46.849587, 46.8495874, 46.8496081, 46.8496079,
46.8496069, 46.849605, 46.8496014, 46.8495965, 46.8495906, 46.8495839,
46.8495808, 46.8484309, 46.8484282, 46.8484218, 46.8484166, 46.8
48412, 46.8484069), dim = c(41L, 2L), dimnames = list( NULL, c("X", "Y",
class = c("XY", "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision
= 0, bbox = structure(c(xmin = 11.0126956, ymin = 46.8475213, xmax =
11.0157617, ymax = 46.8496081), class = "bbox"), crs = structure(list( input =
"EPSG:4326", wkt = "GEOGCRS[\"WGS 84\",\n ENSEMBLE[\"World Geodetic System 1984
ensemble\",\n MEMBER[\"World Geodetic System 1984 (Transit)\"],\n
MEMBER[\"World Geodetic System 1984 (G730)\"],\n MEMBER[\"World Geodetic System
1984 (G873)\"],\n MEMBER[\"World Geodetic System 1984 (G1150)\"],\n
MEMBER[\"World Geodetic System 1984 (G1674)\"],\n MEMBER[\"World Geodetic
System 1984 (G1762)\"],\n MEMBER[\"World Geodetic System 1984 (G2139)\"],\n
ELLIPSOID[\"WGS 84\",6378137,298.257223563,\n LENGTHUNIT[\"metre\",1]],\n
ENSEMBLEACCURACY[2.0]],\n PRIMEM[\"Greenwich\",0,\n
ANGLEUNIT[\"degree\",0.0174532925199433]],\n CS[ellipsoidal,2],\n
AXIS[\"geodetic latitude (Lat)\",north,\n ORDER[1],\n AN
GLEUNIT[\"degree\",0.0174532925199433]],\n AXIS[\"geodetic longitude
(Lon)\",east,\n ORDER[2],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n
USAGE[\n SCOPE[\"Horizontal component of 3D system.\"],\n AREA[\"World.\"],\n
BBOX[-90,-180,90,180]],\n ID[\"EPSG\",4326]]"), class = "crs"), n_empty = 0L)),
row.names = 1L, class = c("sf", "data.frame"), sf_column = "x", agr =
structure(integer(0), class = "factor", levels = c("constant", "aggregate",
"identity"), names = character(0)))
This polygon is used as area of interest to crop Copernicus imagery that I am
downloading using the {CDSE} package. (I have run this workflow successfully
many times with several other aoi polygons)
I have tried:
1- sf::st_make_valid()
2- transforming to a UTM CRS
3- extracting coordinates and recreating the polygon (i.e.:
aoi_p <- st_polygon(list(st_coordinates(aoi)[,1:2]))
aoi3 <- aoi_p |>
st_sfc() |>
st_as_sf()
st_crs(aoi3) <- "EPSG:4326"
4- buffering by a small amount
The above error recurs in all cases (only with this problem polygon). Any
suggestions?
Thanks
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-
Re: [R-sig-Geo] Error in MtrxSet ... polygons not (all) closed
Could you please provide an example of code that actually raises this error?
Best regards,
Zivan
On 19 Aug 2024, at 16:23, Micha Silver wrote:
Searching for the error in the subject line returns some discussions from a few
years ago. But I'm not able to overcome this error.
Here's the polygon in question:
> dput(aoi)
structure(list(x =
structure(list(structure(list(structure(c(11.0127043, 11.0127061, 11.0134526,
11.0134554, 11.0134626, 11.0134692, 11.0134776, 11.0134813, 11.0157343,
11.0157373, 11.0157437, 11.0157495, 11.0157546, 11.0157585, 11.015761,
11.0157617, 11.0157616, 11.0157613, 11.0153992, 11.0153983, 11.0153956,
11.0153922, 11.0153869, 11.0153804, 11.0153729, 11.0153694, 11.0127478,
11.0127447, 11.0127379, 11.012732, 11.0127269, 11.0127232, 11.0127212,
11.01272, 11.0127197, 11.0126956, 11.0126958, 11.0126965, 11.0126978,
11.0127004, 11.0127043, 46.8484069, 46.8484048, 46.8476584, 46.847656,
46.8476511, 46.8476481, 46.8476461, 46.8476456, 46.8475213, 46.8475214,
46.847522, 46.8475235, 46.8475266, 46.8475311, 46.8475365, 46.8475425,
46.8475489, 46.8475519, 46.8495623, 46.8495656, 46.8495729, 46.8495788,
46.8495833, 46.8495856, 46.849587, 46.8495874, 46.8496081, 46.8496079,
46.8496069, 46.849605, 46.8496014, 46.8495965, 46.8495906, 46.8495839,
46.8495808, 46.8484309, 46.8484282, 46.8484218, 46.8484166, 46.848412,
46.8484069), dim = c(41L, 2L), dimnames = list( NULL, c("X", "Y", class =
c("XY", "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision = 0,
bbox = structure(c(xmin = 11.0126956, ymin = 46.8475213, xmax = 11.0157617,
ymax = 46.8496081), class = "bbox"), crs = structure(list( input = "EPSG:4326",
wkt = "GEOGCRS[\"WGS 84\",\n ENSEMBLE[\"World Geodetic System 1984
ensemble\",\n MEMBER[\"World Geodetic System 1984 (Transit)\"],\n
MEMBER[\"World Geodetic System 1984 (G730)\"],\n MEMBER[\"World Geodetic System
1984 (G873)\"],\n MEMBER[\"World Geodetic System 1984 (G1150)\"],\n
MEMBER[\"World Geodetic System 1984 (G1674)\"],\n MEMBER[\"World Geodetic
System 1984 (G1762)\"],\n MEMBER[\"World Geodetic System 1984 (G2139)\"],\n
ELLIPSOID[\"WGS 84\",6378137,298.257223563,\n LENGTHUNIT[\"metre\",1]],\n
ENSEMBLEACCURACY[2.0]],\n PRIMEM[\"Greenwich\",0,\n
ANGLEUNIT[\"degree\",0.0174532925199433]],\n CS[ellipsoidal,2],\n
AXIS[\"geodetic latitude (Lat)\",north,\n ORDER[1],\n
ANGLEUNIT[\"degree\",0.0174532925199433]],\n AXIS[\"geodetic longitude
(Lon)\",east,\n ORDER[2],\n ANGLEUNIT[\"degree\",0.0174532925199433]],\n
USAGE[\n SCOPE[\"Horizontal component of 3D system.\"],\n AREA[\"World.\"],\n
BBOX[-90,-180,90,180]],\n ID[\"EPSG\",4326]]"), class = "crs"), n_empty = 0L)),
row.names = 1L, class = c("sf", "data.frame"), sf_column = "x", agr =
structure(integer(0), class = "factor", levels = c("constant", "aggregate",
"identity"), names = character(0)))
This polygon is used as area of interest to crop Copernicus imagery that I am
downloading using the {CDSE} package. (I have run this workflow successfully
many times with several other aoi polygons)
I have tried:
1- sf::st_make_valid()
2- transforming to a UTM CRS
3- extracting coordinates and recreating the polygon (i.e.:
aoi_p <- st_polygon(list(st_coordinates(aoi)[,1:2]))
aoi3 <- aoi_p |>
st_sfc() |>
st_as_sf()
st_crs(aoi3) <- "EPSG:4326"
4- buffering by a small amount
The above error recurs in all cases (only with this problem polygon). Any
suggestions?
Thanks
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
https://orcid.org/-0002-1128-1325
--
Micha Silver
Ben Gurion Univ.
Sde Boker, Remote Sensing Lab
cell: +972-523-665918
___
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R-sig-Geo@r-project.org
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