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pik-copan / pyunicorn

Unified Complex Network and Recurrence Analysis Toolbox
http://pik-potsdam.de/~donges/pyunicorn/
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Using twin_surrogates #111

Closed manmeet3591 closed 4 years ago

manmeet3591 commented 6 years ago

Dear Sir

I am trying to test the twin_surrogates function using the test dataset ts and am getting the following error

Traceback (most recent call last): File "gen_twin_surrogate.py", line 34, in surrogates = Surrogates.SmallTestData().twin_surrogates(ts, 10, 1, 0.5, 7) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/pyunicorn/timeseries/surrogates.py", line 625, in twin_surrogates twins = self.twins(embedding, threshold, min_dist) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/pyunicorn/timeseries/surrogates.py", line 359, in twins weave.inline(code, arg_names=args, type_converters=weave.converters.blitz, compiler='gcc',extra_compile_args=['-O3']) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/inline_tools.py", line 366, in inline **kw) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/inline_tools.py", line 473, in compile_function type_converters=type_converters) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/ext_tools.py", line 182, in init auto_downcast, type_converters) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/ext_tools.py", line 432, in assign_variable_types raise TypeError(format_error_msg(errors)) TypeError: {'dimension': "The type and dimensionality specificationsfor variable 'dimension' are missing."}

I am unable to undestand the error as to why its coming The statement throwing up this is

surrogates = Surrogates.SmallTestData().twin_surrogates(ts, 10, 1, 0.5, 7)

where ts is the test data set obtained by

ts = Surrogates.SmallTestData().original_data

jdonges commented 6 years ago

Dear Manmeet,

please try to use the latest version of pyunicorn (dev version on github) where this should be fixed. Note that the current dev version, which is to be released soon, runs only on Python 3.x.

Best regards, Jonathan

Am 08.06.2018 um 15:09 schrieb Manmeet Singh notifications@github.com:

Dear Sir

I am trying to test the twin_surrogates function using the test dataset ts and am getting the following error

Traceback (most recent call last): File "gen_twin_surrogate.py", line 34, in surrogates = Surrogates.SmallTestData().twin_surrogates(ts, 10, 1, 0.5, 7) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/pyunicorn/timeseries/surrogates.py", line 625, in twin_surrogates twins = self.twins(embedding, threshold, min_dist) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/pyunicorn/timeseries/surrogates.py", line 359, in twins weave.inline(code, arg_names=args, type_converters=weave.converters.blitz, compiler='gcc',extra_compile_args=['-O3']) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/inline_tools.py", line 366, in inline **kw) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/inline_tools.py", line 473, in compile_function type_converters=type_converters) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/ext_tools.py", line 182, in init auto_downcast, type_converters) File "/iitm2/cccr-res/msingh/anaconda3/envs/python_2_7/lib/python2.7/site-packages/weave/ext_tools.py", line 432, in assign_variable_types raise TypeError(format_error_msg(errors)) TypeError: {'dimension': "The type and dimensionality specificationsfor variable 'dimension' are missing."}

I am unable to undestand the error as to why its coming The statement throwing up this is

surrogates = Surrogates.SmallTestData().twin_surrogates(ts, 10, 1, 0.5, 7)

where ts is the test data set obtained by

ts = Surrogates.SmallTestData().original_data

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manmeet3591 commented 6 years ago

Thanks Jonathan. I'll try using the dev version. Please help me with the installation if possible, I guess I tried the github version installation previously.

Warm Regards Manmeet

manmeet3591 commented 6 years ago

Hi Jonathan

I tried installing and using the dev version on github, but there is a lot of python 2.7 code in it due to which it doesnt work with python 3.5, like you can see below error

import pyunicorn Traceback (most recent call last): File "", line 1, in File "/iitm2/cccr-res/msingh/Libraries/sources/pyunicorn/build/lib.linux-x86_64-3.5/pyunicorn/init.py", line 34, in from .utils import mpi File "/iitm2/cccr-res/msingh/Libraries/sources/pyunicorn/build/lib.linux-x86_64-3.5/pyunicorn/utils/mpi.py", line 249 print "MPI master : assigning call with id", id, "to slave", \ ^ SyntaxError: Missing parentheses in call to 'print'

jdonges commented 6 years ago

Hi,

we need to merge some pull requests fixing this. Please stay tuned for the next release of pyunicorn in a few weeks. This will be fully Python 3 compatible. Please excuse the inconvenience right now.

Best, Jonathan

Am 10.06.2018 um 16:10 schrieb Manmeet Singh notifications@github.com:

Hi Jonathan

I tried installing and using the dev version on github, but there is a lot of python 2.7 code in it due to which it doesnt work with python 3.5, like you can see below error

import pyunicorn Traceback (most recent call last): File "", line 1, in File "/iitm2/cccr-res/msingh/Libraries/sources/pyunicorn/build/lib.linux-x86_64-3.5/pyunicorn/init.py", line 34, in from .utils import mpi File "/iitm2/cccr-res/msingh/Libraries/sources/pyunicorn/build/lib.linux-x86_64-3.5/pyunicorn/utils/mpi.py", line 249 print "MPI master : assigning call with id", id, "to slave", ^ SyntaxError: Missing parentheses in call to 'print'

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manmeet3591 commented 6 years ago

Hi Jonathan

I am able to resolve the issue in the older version itself. The issue was that in the file surrogate.py, the function twins did not have dimension argument, which I added and its working now, Am I allowed to push the change to the github master, as I see the same thing there as well.