CF lat lon and Panoply display

[Claudio2574]

Question

Hello. I'm new to CF conventions.
Starting from a non-CF-compliant NetCDF file, I tried to create a new one which seems to be ok, according to CFchecker web page. It uses a geostationary projection and looks good in Panoply x-y .
However, asking for georeferenced longitude-latitude I get an empty plot.
I can add two more variables with MATLAB, lat and lon, the file of course becomes much bigger, but the longitude-latitude is still empty.
The metadata of the "small" file are:

dimensions:
t = 2;
y = 3712;
x = 3712;
variables:
short acc_rr(x=3712, y=3712, t=2);
:valid_min = 0S; // short
:valid_max = 10000S; // short
:long_name = "Hourly accumulated rain amount";
:units = "mm";
:add_offset = 0.0; // double
:scale_factor = 0.1; // double
:missing_value = -990S; // short
:grid_mapping = "geostationary_projection";
:_ChunkSizes = 1238U, 1238U, 1U; // uint

byte qind(x=3712, y=3712, t=2);
  :valid_min = 0B; // byte
  :valid_max = 100B; // byte
  :long_name = "pixel quality index";
  :units = "percent";
  :missing_value = -99B; // byte
  :grid_mapping = "geostationary_projection";
  :_ChunkSizes = 1856U, 1856U, 1U; // uint

short t(t=2);
  :units = "s since 2025-04-10 15:00:00";
  :standard_name = "time";
  :long_name = "seconds offset from filename time";
  :calendar = "standard";
  :_ChunkSizes = 2U; // uint

int y(y=3712);
  :units = "m";
  :standard_name = "projection_y_coordinate";
  :long_name = "y coordinate of projection";
  :_ChunkSizes = 3712U; // uint

byte geostationary_projection;
  :grid_mapping_name = "geostationary";
  :latitude_of_projection_origin = 0.0; // double
  :longitude_of_projection_origin = 0.0; // double
  :perspective_point_height = 35785831; // int
  :semi_major_axis = 6378169; // int
  :semi_minor_axis = 6356584; // int
  :sweep_angle_axis = "y";
  :long_name = "satellite view parameters";

int x(x=3712);
  :units = "m";
  :standard_name = "projection_x_coordinate";
  :long_name = "x coordinate of projection";
  :_ChunkSizes = 3712U; // uint

The "extended" file has the following metadata:

dimensions:
t = 2;
y = 3712;
x = 3712;
variables:
short acc_rr(x=3712, y=3712, t=2);
:valid_min = 0S; // short
:valid_max = 10000S; // short
:long_name = "Hourly accumulated rain amount";
:units = "mm";
:add_offset = 0.0; // double
:scale_factor = 0.1; // double
:missing_value = -990S; // short
:grid_mapping = "geostationary_projection";
:coordinates = "lon lat";
:_ChunkSizes = 1238U, 1238U, 1U; // uint

byte qind(x=3712, y=3712, t=2);
  :coordinates = "lon lat";
  :valid_min = 0B; // byte
  :valid_max = 100B; // byte
  :long_name = "pixel quality index";
  :units = "percent";
  :missing_value = -99B; // byte
  :grid_mapping = "geostationary_projection";
  :_ChunkSizes = 1856U, 1856U, 1U; // uint

short t(t=2);
  :units = "s since 2025-04-10 15:00:00";
  :standard_name = "time";
  :long_name = "seconds offset from filename time";
  :calendar = "standard";
  :_ChunkSizes = 2U; // uint

double lat(x=3712, y=3712);
  :long_name = "Latitude at the center of each pixel";
  :units = "degrees_north";
  :standard_name = "latitude";
  :valid_range = "-90.0f, 90.0f";
  :_ChunkSizes = 619U, 619U; // uint

int y(y=3712);
  :units = "m";
  :standard_name = "projection_y_coordinate";
  :long_name = "y coordinate of projection";
  :_ChunkSizes = 3712U; // uint

byte geostationary_projection;
  :grid_mapping_name = "geostationary";
  :latitude_of_projection_origin = 0.0; // double
  :longitude_of_projection_origin = 0.0; // double
  :perspective_point_height = 35785831; // int
  :semi_major_axis = 6378169; // int
  :semi_minor_axis = 6356584; // int
  :sweep_angle_axis = "y";
  :long_name = "satellite view parameters";

int x(x=3712);
  :units = "m";
  :standard_name = "projection_x_coordinate";
  :long_name = "x coordinate of projection";
  :_ChunkSizes = 3712U; // uint

double lon(x=3712, y=3712);
  :long_name = "Longitude at the center of each pixel";
  :units = "degrees_east";
  :standard_name = "longitude";
  :valid_range = "-180.0f, 180.0f";
  :_ChunkSizes = 619U, 619U; // uint

Any suggestion will be appreciated.

[Armin-RS]

Could it be the order of the dimensions which are troubling Panoply ?

I have a similar kind of file which I can view with Panoply as Geo2D Plot, but it has
"short acc(t=2, y=3712, x=3712)"

And it also has an additional attribut
acc:coordinates = "x y"

HTH,
Armin

[Claudio2574]

Thanks.
1: while defining the dimensions in matlab I wrote:

var='acc_rr';
nccreate(filename3, var, 'Dimensions', {'t' 'y' 'x'}, 'Datatype', 'int16', 'Format', 'netcdf4', 'DeflateLevel', 5);

I did expect that the same order t-y-x appears into the metadata. It doesn't, don't know why.
2: the coordinates attribute is not set. I actually place it in the form:

ncwriteatt(filename3, var, 'coordinates', 'lon lat');

but I can do this ONLY when the two variables lat and lon (3712x3712) are defined. And anyway the lat lon plot is full blue

I'm lost

[Armin-RS]

Here is an explanation of the order of dimensions in Matlab netCDF files: https://de.mathworks.com/matlabcentral/answers/64018-creating-netcdf-files-how-can-i-set-the-order-of-the-dimensions-in-a-field
It seems the behaviour you observe is related to differences between column-major and row-major storage of data arrays in Matlab and netCDF.

I would think that the correct order of dimensions could fix your display problems as Geo2D Plot in Matlab.

I think you can also have
acc: coordinates = "x y"
in case there are no "lon" and "lat" coordinates in your file (although this is probably implicitely assumed anyway in that case).