TypeError: Package infodynamics.measures.continuous.gaussian.ConditionalMutualInfoCalculatorMultiVariateGaussian is not Callable

[nickvandewiele]

Any idea what I am doing wrong?

I'm running the example shown in the wiki. I installed JPype1 via pip, although the package via the conda-forge channel runs into the same issue.

ubuntu 12.04, python 3.5 run from within a conda env. some more info below.

(idt) vagrant@precise64:/vagrant_data$ python first.py
Adding data with properties: 5 processes, 1000 samples, 5 replications
overwriting existing data

####### analysing target with index 0 from list [0, 1, 2, 3, 4]
Traceback (most recent call last):
  File "first.py", line 17, in <module>
    results = network_analysis.analyse_network(settings=settings, data=data)
  File "/vagrant_data/IDTxl/idtxl/multivariate_te.py", line 163, in analyse_network
    sources[t])
  File "/vagrant_data/IDTxl/idtxl/multivariate_te.py", line 273, in analyse_single_target
    self._initialise(settings, data, sources, target)
  File "/vagrant_data/IDTxl/idtxl/network_inference.py", line 51, in _initialise
    self._cmi_estimator = EstimatorClass(settings)
  File "/vagrant_data/IDTxl/idtxl/estimators_jidt.py", line 1230, in __init__
    super().__init__(CalcClass, settings)
  File "/vagrant_data/IDTxl/idtxl/estimators_jidt.py", line 306, in __init__
    self.calc = CalcClass()
  File "/home/vagrant/anaconda/envs/idt/lib/python3.5/site-packages/jpype/_jpackage.py", line 60, in __call__
    raise TypeError("Package {0} is not Callable".format(self.__name))
TypeError: Package infodynamics.measures.continuous.gaussian.ConditionalMutualInfoCalculatorMultiVariateGaussian is not Callable

(idt) vagrant@precise64:/vagrant_data$ pip freeze
certifi==2016.2.28
cffi==1.10.0
cycler==0.10.0
decorator==4.1.2
h5py==2.7.0
-e git+https://github.com/pwollstadt/IDTxl.git@4ddb995bc5fa15587cbb95d8b876bee26795ea96#egg=idtxl
JPype1==0.6.2
matplotlib==2.0.2
networkx==1.11
numpy==1.13.1
pycparser==2.18
pyparsing==2.2.0
python-dateutil==2.6.1
pytz==2017.2
scipy==0.19.1
six==1.10.0

(idt) vagrant@precise64:/vagrant_data$ conda list
# packages in environment at /home/vagrant/anaconda/envs/idt:
#
certifi                   2016.2.28                py35_0
cffi                      1.10.0                   py35_0
cycler                    0.10.0                   py35_0
dbus                      1.10.20                       0
decorator                 4.1.2                    py35_0
expat                     2.1.0                         0
fontconfig                2.12.1                        3
freetype                  2.5.5                         2
glib                      2.50.2                        1
gst-plugins-base          1.8.0                         0
gstreamer                 1.8.0                         0
h5py                      2.7.0               np113py35_0
hdf5                      1.8.17                        2
icu                       54.1                          0
jpeg                      9b                            0
JPype1                    0.6.2                     <pip>
libffi                    3.2.1                         1
libgcc                    5.2.0                         0
libgfortran               3.0.0                         1
libiconv                  1.14                          0
libpng                    1.6.30                        1
libxcb                    1.12                          1
libxml2                   2.9.4                         0
matplotlib                2.0.2               np113py35_0
mkl                       2017.0.3                      0
networkx                  1.11                     py35_0
numpy                     1.13.1                   py35_0
openssl                   1.0.2l                        0
pcre                      8.39                          1
pip                       9.0.1                    py35_1
pycparser                 2.18                     py35_0
pyparsing                 2.2.0                    py35_0
pyqt                      5.6.0                    py35_2
python                    3.5.4                         0
python-dateutil           2.6.1                    py35_0
pytz                      2017.2                   py35_0
qt                        5.6.2                         5
readline                  6.2                           2
scipy                     0.19.1              np113py35_0
setuptools                36.4.0                   py35_1
sip                       4.18                     py35_0
six                       1.10.0                   py35_0
sqlite                    3.13.0                        0
tk                        8.5.18                        0
wheel                     0.29.0                   py35_0
xz                        5.2.3                         0
zlib                      1.2.11                        0

[jlizier]

Hi Nick,

This seems to match a known issue (not formally listed here as an issue) that I haven't addressed yet, being that the jar for the underlying JIDT computation engine was targetted for Java 1.7 but I think you're using an earlier Java version. You can verify this by running:

jsys = JPackage("java.lang").System
print("%s\n" % jsys.getProperty("java.version"))

somewhere in your code.

The targetting of Java 1.7 should have been brought back to 1.6 earlier, but I just haven't gotten to this yet; it depends on a fix coming through from JIDT. We'll get you to retest when that comes through.

Can I also confirm you are running from the master branch?

Thanks,
--joe

[nickvandewiele]

Thanks for the quick reply! You are right, I was using JDK 6 (default JDK for Ubuntu 12.04).

(idt) vagrant@precise64:~$ java -version
java version "1.6.0_41"
OpenJDK Runtime Environment (IcedTea6 1.13.13) (6b41-1.13.13-0ubuntu0.12.04.1)
OpenJDK 64-Bit Server VM (build 23.41-b41, mixed mode)

I was indeed using the master branch.

vagrant@precise64:/vagrant_data/IDTxl$ git branch
* master

(idt) vagrant@precise64:/vagrant_data/IDTxl$ git log -1
commit 4ddb995bc5fa15587cbb95d8b876bee26795ea96
Author: pwollstadt <patricia.wollstadt@gmx.de>
Date:   Mon Sep 11 12:34:09 2017 +0200

    Remove unnecessary line from examples

...
Upon upgrading to JDK7 (sudo apt-get install openjdk-7-jdk)

Upon testing again, it seems to go through, but at the end, I get the following:

creating surrogate table with 500 permutations:
        cand.   (3, 1) -- significant


---------------------------- (4) final statistics
[(4, 1), (4, 4), (4, 2), (4, 3), (4, 5), (3, 1)]
no. target sources: 5, no. sources: 1
omnibus test, n_perm: 500
 -- significant

final source samples: [(3, 1)]
final target samples: [(4, 1), (4, 4), (4, 2), (4, 3), (4, 5)]
Traceback (most recent call last):
  File "first.py", line 20, in <module>
    print_res_to_console(data=data, results=results)
TypeError: print_res_to_console() got an unexpected keyword argument 'results'

Should I close this issue, and create a new issue?

[nickvandewiele]

the last error is because the keyword args used by print_res_to_console, plot_network in first.py should be changed from results to res with 4ddb995. Not a big deal, though. Thanks!

[jlizier]

Thanks Nick, Don't close the issue, I still need to deal with the java 7 dependence. Re the 2nd problem - thanks for identifying it. I'll leave it to Patricia re whether she wants do deal with it here or separately.

…

--joe

On 3 Oct 2017 5:18 am, "NICK VANDEWIELE" ***@***.***> wrote: the last error is because the keyword args used by print_res_to_console, plot_network in first.py should be changed from results to res with 4ddb995 <4ddb995>. Not a big deal, though. Thanks! — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#9 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABirw5DdkaSzEN0TVYRYqYIFEwm3BfZdks5soSkLgaJpZM4Pnzqy> .

[pwollstadt]

Hi Nick,
thanks for pointing that out, I corrected the example script in the wiki.
Best, Patricia

[Dirivian]

I get the same error and my Java version is 11

[pwollstadt]

Hi @Dirivian, for debugging could you try running example code after a new install in a conda environment (see my answer to #26) and let me know if this works for you? Thanks!