Re: [Matplotlib-users] filled contours, and missing data

[Perry G. <pe...@st...>]

On Feb 19, 2005, at 9:23 PM, Eric Firing wrote:

> John et al.,
>
> I would like to phase in matplotlib to replace Matlab ASAP for 
> plotting physical oceanographic observations, primarily current 
> profile measurements.  I (and many other physical oceanographers) 
> primarily use contourf to plot filled contours; I only rarely use line 
> contours.  It looks to me like gcntr.c has the necessary 
> functionality--the ability to output polygons enclosing regions 
> between a pair of specified levels. Is someone already working on 
> exposing that functionality in matplotlib, or is it planned?
>
No one (as far as I know :-) is working on it right now. It is in our 
plans to add this capability. As you correctly note, the underlying C 
code can handle this capability. I'm not sure how long it will be; 
right now the priority is to finish contour labeling capability, and 
the person working on that also has other work that competes with her 
time to do this. I'm guessing that she could start looking at it in a 
couple weeks. Of course, if someone wants to help now, that would be 
great.

> It appears that gcntr.c also has the ability to handle missing data 
> via setting elements of the reg array to zero, and that this could be 
> exposed fairly easily in the contour method in axes.py by adding "reg" 
> to the set of kwargs.  Correct?  If so, is this also planned?
>
Correct. Yes (it is planned).

> The question of missing data handling in contour plotting brings up 
> the more general issue of how to handle data gaps in plots.  For 
> example, the ocean current profiles that I measure using a Doppler 
> profiler extend to varying depths, and sometimes have holes in the 
> middle where there are not enough acoustic scatterers to give a 
> signal.  This sort of thing--data gaps--is universal in physical 
> oceanography.  One of Matlab's major strengths is the way it handles 
> them, using nan as a bad value flag.  Plotting a line with the plot 
> command, the line is broken at each nan; so if there is a hole in the 
> data, the plot shows exactly that.  The same for contouring: nans are 
> automatically used as a mask.
>
> Obviously, not everyone needs this kind of automatic handling of data 
> gaps, but I think it would be very useful for many applications, so I 
> hope it can be considered as a possible goal.  At the plotting level, 
> collections may make it easier to implement than would have been the 
> case in the early days of matplotlib.  At the array manipulation 
> level, the implementation could involve either masked arrays or nans.  
> I would greatly prefer the Matlab-style nan approach, but I don't know 
> whether this would work with Numeric.  Maybe in Numeric3?  Numarray 
> appears better equipped, with its ieeespecial.py module.
>
I think you touch on the key issue. I think we'd have to figure out how 
to handle this between Numeric and numarray (and Numeric3 potentially). 
Would a mask array be a suitable substitute as an interim solution?

Perry