Hi Patrick,
Fiji currently ships with Jython 2.5.3. And I am guessing you are using at
least Python 2.7 with your iPython notebook setup?
It seems that you aren't the only one experiencing trouble mixing and
matching Python versions with pickle:
http://stackoverflow.com/q/9313050/1207769Probably you need to use a serialization format that is more stable, such
as JSON, as suggested in the SO post.
Regards,
Curtis
P.S. We want to update ImageJ2 & Fiji to Jython 2.7, but that entails an
upgrade to Java 7 or 8. It's in the works:
http://imagej.net/2015-06-15_-_Major_updates_in_the_worksOn Fri, Nov 20, 2015 at 12:20 PM, Patrick Page-McCaw <
[hidden email]>
wrote:
> I have a dictionary in a python script with many x,y pixel coordinates.
> When the dict is serialized by pickle and then opened into an
> iPython-notebook so that I can use numpy and pyplot, the data is corrupted.
> The structure of the data is maintained, but the data which comes from the
> results table, is mangled.
>
> For example, in fiji the dictionary looks like this
> {u'a': [[array('f', [252.0, 371.0, 273.0, 326.0, 346.0,...
> but unpickled this looks like
> {u'a': [[array('f', [1.180597739699512e-38, 1.1806694861808855e-38,
>
> I'm guessing there is something about the java array 'f' type that does
> not serialize with pickle? The keys are ok and other text
>
> I could write it all out to text, then back in, but surely there is a way
> to do the serializing more readily?
>
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