More robust lon/lat initialization for imagestack

[Lmoesinger]

The current lon/lat initialization of ImageStack can break if the grid has an unusual row/col arrangement or an unusual shape. E.g. if you create an imagestack with this grid all grid points will have the same lat and lon:

import pygeogrids.grids as grids
from pynetcf.image import ImageStack
import pandas as pd

grid = grids.genreg_grid(0.25, 0.25)
filename = '/path/to/file/filename.nc'
times = pd.date_range('2000', '2001', freq='M').to_pydatetime()
ds = ImageStack(filename, grid=grid, times=times, mode='w')
print ds.dataset.variables['lon'][:]
# all lons are -179.875

The proposed change uses np.unique() to get the lat/lon values, which works independent of the grids orientation.
I ran the tests with the changes and broke none of them, but it still might now screw up some other grid.

[cpaulik]

Just some general thoughts:

The whole image part of pynetcf is used very little and not very well developed. I'm not sure if we should even allow the link of pygeogrids.BasicGrid and an ImageStack since a BasicGrid object can be any discrete grid. The lat2d and lon2d attributes do exist but I think we should probably make a separate class for grids with these limitations.

@sebhahn should decide this PR and the future direction of the image part depending on the needs of TUW.

[Lmoesinger]

@sebhahn as discussed, the np.unique() calls are now moved to the 'ulat' and 'ulon' variables from pygeogrids.basegrid. This push now requires TUW-GEO/pygeogrids#56 to pass first.

Also added lon/lat check (if lon/lat is broken, it will read the wrong gpis)

[cpaulik]

I think this could cause some issues.

Before you where using the lon2d and lat2d attributes which where only set if the grid had a 2D shape. So there was some guarantee that the grid is intended for 2D image use.

Using ulat and ulon which are defined for any grid could easily give a netcdf file which is not correct and where the data that is on the grid is sorted differently from the dimensions that are created.

[sebhahn]

The way I see it is that both approaches are not 100% fail safe. The question is if imagestack is for 2d grids only or can be extended to non-2d grids?

[cpaulik]

There are several options for coordinate systems that we could support (http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#coordinate-system) . A non-2d grid ImageStack would be best represented as an Orthogonal multidimensional array representation with different chunking. For that we already have ArrayStack

[sebhahn]

I can remember we had this discussion some time ago and I wasn't too happy about the naming (ArrayStack and ImageStack). Coming back to this two classes it still confuses me. There seems to me not 1-to-1 relationship to CF coordinate systems, but rather an abstract layer to combine the reader with a grid, right? @cpaulik could you please shortly summarize the distinct differences and use cases of ArrayStack and ImageStack? I have to admit that I haven't been using them a lot, because I'm not an Image user. I hope clarifying the meaning helps to understand if we need two classes here or just a general one.

[cpaulik]

The goal of this package is to write CF conform netCDF files. I think we should completely rewrite the Image part of the package to conform to CF naming and coordinate conventions. As we did with the time series.

The ArrayStack and ImageStack are classes I wrote without thinking too much and I have not used them because they do not really work nicely. The Idea behind ArrayStack was to have a Stack of 1D arrays. Basically Ortho multi but with different chunking to favor image access. The ImageStack was for 2D arrays or images as I called them. I have also never really used this which is the reason why it is so poorly maintained.

What is the current use case for the ImageStack that triggered this pull request? That might help in the decision of how to move forward.

[sebhahn]

@Lmoesinger could you please elaborate on your use case?

[Lmoesinger]

I´m using it to convert time series (stored as GriddedNcContiguousRaggedTs, divided into multiple files by a cellgrid) to to a stack of 2d matrices by iterating over each gpi. All time series have the same time indexes. I know the dates beforehand as they are regularly spaced between a known start- and enddate. I`m only writing one time series per GPI.

Basically it is very similar to Ts2Img from https://github.com/TUW-GEO/repurpose/blob/master/repurpose/ts2img.py .

Also note that it wasn't my goal to make this working with grids that don't have a shape - rather my goal was to make it work with grids that have an unusual shape.

[cpaulik]

I think we can discuss this tomorrow before lunch @sebhahn . @Lmoesinger if you also work at the TU then we might also meet tomorrow.

[Lmoesinger]

Sure, at what time and where?
It might also be an opportunity to discuss TUW-GEO/pytesmo#144