Timeseries

[arokem]

Finished first pass of the implementation of this. It runs on the test data, including generating tmp files of the file outputs (csv files and figure files of the resulting calculation). One problem that may exist right now is that the testing opens mpl figures (for testing of aformentioned file generation). We might want to clean up the testing, so that it doesn't do that.

[chrisgorgo]

are you sure you want this into master not maint/0.3?

[arokem]

I am not sure. What is the difference between master and maint/0.3?

I see that the request I issued is to pull into master, but there wasn't much of a thought behind that - I just navigated to my branch and hit "pull request".

So - yes - if you think pulling it into maint/0.3 is more appropriate, please do that

[satra]

hi ariel,

i created a new branch called nitime under nipy/nipype and pulled in all your changes. however nose fails on the following test:

ERROR: Failure: ValueError (Unknown method provided)

Traceback (most recent call last):
File "/software/pythonenvs/devpype/lib/python2.6/site-packages/nose/loader.py", line 224, in generate
for test in g():
File "/software/nipy-repo/masternipype/nipype/interfaces/nitime/tests/test_nitime.py", line 47, in test_coherence_analysis
o = CA.run()
File "/software/nipy-repo/masternipype/nipype/interfaces/base.py", line 750, in run
runtime = self._run_interface(runtime)
File "/software/nipy-repo/masternipype/nipype/interfaces/nitime/analysis.py", line 152, in _run_interface
freq_idx = np.where((A.frequencies>self.inputs.frequency_range[0]) *
File "/software/pythonenvs/devpype/lib/python2.6/site-packages/nitime/descriptors.py", line 137, in get
val = self.getter(obj)
File "/software/pythonenvs/devpype/lib/python2.6/site-packages/nitime/analysis.py", line 323, in frequencies
f,spectrum = tsa.get_spectra(self.input.data,method=self.method)
File "/software/pythonenvs/devpype/lib/python2.6/site-packages/nitime/algorithms.py", line 1339, in get_spectra
raise ValueError("Unknown method provided")
ValueError: Unknown method provided

---

does this require a newer version of nitime. i have 0.1.0 installed?

[arokem]

Hi Satra - thanks for taking a look. I am sorry that it ended so soon and so abruptly.

Indeed - what you stumbled on was a bug in nitime, which is already fixed in 0.2. We are very close to a release of 0.2, which will have a fix for that. Maybe we should wait for the nitime release to move on with this, instead of changing the API back and forth in nipype. What do you think?

Ariel

[satra]

hi ariel,

let's wait till you have 0.2 out. i'll keep the nitime branch alive on nipy/nipype and you can build off of that. in fact i would recommend pulling that into your nipype fork. it's rebased completely off of maint/0.3 (so it has all our bug fixes and bug introductions :) )

[satra]

closing this request for now. will revisit when nitime 0.2 is out.

[arokem]

Hi,

Nitime 0.2 is now out! I pulled in the nitime branch from upstream and ran the nitime tests. They seem to pass now. Could you check?

Cheers,

Ariel

[satra]

pulled in to maint/0.3 and master