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Clean paradigm #316

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merged 3 commits into from Sep 25, 2015
Merged

Clean paradigm #316

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72d8b14
added a test to assess new behaviour
bthirion Apr 7, 2014
eafe22d
Reverted the behavior until future hypothetical release
bthirion May 21, 2014
ca0d09f
Rebased and included Mattews suggestions
bthirion Aug 30, 2015
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10 changes: 2 additions & 8 deletions nipy/modalities/fmri/experimental_paradigm.py
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Expand Up @@ -22,6 +22,7 @@
import numpy as np

from ...utils.compat3 import open4csv
import warnings

##########################################################
# Paradigm handling
Expand All @@ -48,14 +49,7 @@ def __init__(self, con_id=None, onset=None, amplitude=None):
self.amplitude = amplitude
if con_id is not None:
self.n_events = len(con_id)
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No need for this now? Need deprecation warning or informative error?

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I'm still worried by backwards compatibility - I think previous behavior was:

import nipy.modalities.fmri.experimental_paradigm as ep
In [2]: ep.Paradigm([1, 2, 3]).con_id
Out[2]: 
array(['c1', 'c2', 'c3'], 
      dtype='|S2')

where behavior on this branch is:

In [3]: ep.Paradigm([1, 2, 3]).con_id
Out[3]: 
array(['1', '2', '3'], 
      dtype='|S1')

I can see that it's a good idea not to convert strings to ints then back to strings, but maybe preserve c prefix if condition names are integers?

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I think that in general it is a bad idea to decide that the conditions cannot be named '1', '2' etc. and to change this for the user. Now, if you think that backward compatibility is more important, I can revert that one.

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It's OK, I can see arguments both ways...

try:
# this is only for backward compatibility:
#if con_id were integers, they become a string
self.con_id = np.array(['c' + str(int(float(c)))
for c in con_id])
except:
self.con_id = np.ravel(np.array(con_id)).astype('str')

self.con_id = np.ravel(np.array(con_id)).astype('str')
if onset is not None:
if len(onset) != self.n_events:
raise ValueError(
Expand Down
8 changes: 8 additions & 0 deletions nipy/modalities/fmri/tests/test_paradigm.py
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Expand Up @@ -11,6 +11,7 @@

from ..experimental_paradigm import (EventRelatedParadigm, BlockParadigm,
load_paradigm_from_csv_file)
from nose.tools import assert_true


def basic_paradigm():
Expand Down Expand Up @@ -77,6 +78,13 @@ def test_read_paradigm():
assert (read_paradigm.onset == paradigm.onset).all()


def test_paradigm_with_int_condition_ids():
paradigm1 = basic_paradigm()
conditions = [0, 0, 0, 1, 1, 1, 2, 2, 2]
paradigm2 = EventRelatedParadigm(conditions, paradigm1.onset)
assert_true((paradigm2.con_id == np.array(conditions).astype('str')).all())


if __name__ == "__main__":
import nose
nose.run(argv=['', __file__])