Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

write_mdim() error "Error: NA value in which_dims: logic error" , but replacing values works? #701

Open
jvandens opened this issue Aug 11, 2024 · 0 comments
Open

write_mdim() error "Error: NA value in which_dims: logic error" , but replacing values works? #701

jvandens opened this issue Aug 11, 2024 · 0 comments

Comments

@jvandens
Copy link

I have an issue that might be similar/related to #699

Consider this stars object output from dput():

m = 

structure(list(`F Coli` = structure(c(1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), .Dim = c(5L, z = 10L, 
times = 8L)), Entero = structure(c(1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), .Dim = c(5L, z = 10L, 
times = 8L))), dimensions = structure(list(geometry = structure(list(
    from = 1L, to = 5L, offset = NA_real_, delta = NA_real_, 
    refsys = structure(list(input = "NAD83 / UTM zone 18N", wkt = "PROJCRS[\"NAD83 / UTM zone 18N\",\n    BASEGEOGCRS[\"NAD83\",\n        DATUM[\"North American Datum 1983\",\n            ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n                LENGTHUNIT[\"metre\",1]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        ID[\"EPSG\",4269]],\n    CONVERSION[\"UTM zone 18N\",\n        METHOD[\"Transverse Mercator\",\n            ID[\"EPSG\",9807]],\n        PARAMETER[\"Latitude of natural origin\",0,\n            ANGLEUNIT[\"Degree\",0.0174532925199433],\n            ID[\"EPSG\",8801]],\n        PARAMETER[\"Longitude of natural origin\",-75,\n            ANGLEUNIT[\"Degree\",0.0174532925199433],\n            ID[\"EPSG\",8802]],\n        PARAMETER[\"Scale factor at natural origin\",0.9996,\n            SCALEUNIT[\"unity\",1],\n            ID[\"EPSG\",8805]],\n        PARAMETER[\"False easting\",500000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8806]],\n        PARAMETER[\"False northing\",0,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8807]]],\n    CS[Cartesian,2],\n        AXIS[\"(E)\",east,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1]],\n        AXIS[\"(N)\",north,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1]],\n    ID[\"EPSG\",26918]]"), class = "crs"), 
    point = FALSE, values = structure(list(structure(list(structure(c(498756.910095215, 
    510957.220092773, 522344.630126953, 512631.440124512, 498756.910095215, 
    4285731.00012207, 4304042.50012207, 4298020.00012207, 4279347.50012207, 
    4285731.00012207), .Dim = c(5L, 2L))), class = c("XY", "POLYGON", 
    "sfg")), structure(list(structure(c(512631.440124512, 522344.630126953, 
    533818.380126953, 525469.630126953, 512631.440124512, 4279347.50012207, 
    4298020.00012207, 4292652.50012207, 4273846.50012207, 4279347.50012207
    ), .Dim = c(5L, 2L))), class = c("XY", "POLYGON", "sfg")), 
        structure(list(structure(c(525469.630126953, 533818.380126953, 
        545675.130126953, 538335.190124512, 525469.630126953, 
        4273846.50012207, 4292652.50012207, 4287713.50012207, 
        4268440.50012207, 4273846.50012207), .Dim = c(5L, 2L))), class = c("XY", 
        "POLYGON", "sfg")), structure(list(structure(c(538335.190124512, 
        545675.130126953, 558535.25012207, 552430.810119629, 
        538335.190124512, 4268440.50012207, 4287713.50012207, 
        4283077.50012207, 4262513.00012207, 4268440.50012207), .Dim = c(5L, 
        2L))), class = c("XY", "POLYGON", "sfg")), structure(list(
            structure(c(552430.810119629, 558535.25012207, 572934.75012207, 
            568734.440124512, 552430.810119629, 4262513.00012207, 
            4283077.50012207, 4279116.00012207, 4256515.00012207, 
            4262513.00012207), .Dim = c(5L, 2L))), class = c("XY", 
        "POLYGON", "sfg"))), class = c("sfc_POLYGON", "sfc"), precision = 0, bbox = structure(c(xmin = 498756.910095215, 
    ymin = 4256515.00012207, xmax = 572934.75012207, ymax = 4304042.50012207
    ), class = "bbox"), crs = structure(list(input = "NAD83 / UTM zone 18N", 
        wkt = "PROJCRS[\"NAD83 / UTM zone 18N\",\n    BASEGEOGCRS[\"NAD83\",\n        DATUM[\"North American Datum 1983\",\n            ELLIPSOID[\"GRS 1980\",6378137,298.257222101,\n                LENGTHUNIT[\"metre\",1]]],\n        PRIMEM[\"Greenwich\",0,\n            ANGLEUNIT[\"degree\",0.0174532925199433]],\n        ID[\"EPSG\",4269]],\n    CONVERSION[\"UTM zone 18N\",\n        METHOD[\"Transverse Mercator\",\n            ID[\"EPSG\",9807]],\n        PARAMETER[\"Latitude of natural origin\",0,\n            ANGLEUNIT[\"Degree\",0.0174532925199433],\n            ID[\"EPSG\",8801]],\n        PARAMETER[\"Longitude of natural origin\",-75,\n            ANGLEUNIT[\"Degree\",0.0174532925199433],\n            ID[\"EPSG\",8802]],\n        PARAMETER[\"Scale factor at natural origin\",0.9996,\n            SCALEUNIT[\"unity\",1],\n            ID[\"EPSG\",8805]],\n        PARAMETER[\"False easting\",500000,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8806]],\n        PARAMETER[\"False northing\",0,\n            LENGTHUNIT[\"metre\",1],\n            ID[\"EPSG\",8807]]],\n    CS[Cartesian,2],\n        AXIS[\"(E)\",east,\n            ORDER[1],\n            LENGTHUNIT[\"metre\",1]],\n        AXIS[\"(N)\",north,\n            ORDER[2],\n            LENGTHUNIT[\"metre\",1]],\n    ID[\"EPSG\",26918]]"), class = "crs"), n_empty = 0L)), class = "dimension"), 
    z = structure(list(from = 1L, to = 10L, offset = 1, delta = 1, 
        refsys = NA_character_, point = FALSE, values = NULL), class = "dimension"), 
    times = structure(list(from = 1L, to = 8L, offset = NA_real_, 
        delta = NA_real_, refsys = NA_character_, point = FALSE, 
        values = structure(list(start = c(0, 0.020833333954215, 
        0.0625, 0.10416666418314, 0.145833343267441, 0.1875, 
        0.22916667163372, 0.270833313465118), end = c(0.020833333954215, 
        0.0625, 0.10416666418314, 0.145833343267441, 0.1875, 
        0.22916667163372, 0.270833313465118, 0.3125)), class = "intervals")), class = "dimension")), raster = structure(list(
    affine = c(0, 0), dimensions = c(NA_character_, NA_character_
    ), curvilinear = FALSE, blocksizes = NULL), class = "stars_raster"), class = "dimensions"), class = "stars")

When I try to save it with write_mdim() to netcdf I get the following error:

write_mdim(m, "m.nc")  # Fails
# Error: NA value in which_dims: logic error

But, if I simply replace the values of the attributes with themselves, it saves:

m2=m
m2$`F Coli` = m$`F Coli` |> as.vector()
m2$Entero = m$Entero |> as.vector()

# write
write_mdim(m2, "m2.nc")  # Succeeds
m_test <- read_mdim("m2.nc")
m_test

# but note that is False, but seems like they are the same?
identical(m2, m_test) # False?

Any ideas why this happening or what could be "wrong" with the attribute values?
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@jvandens