Python externals.exists函数代码示例

    def plot(self, label_index=0):
        """

        TODO: make it friendly to labels given by values?
              should we also treat labels_map?
        """
        externals.exists("pylab", raise_=True)
        import pylab as pl

        self._compute()

        labels = self._labels
        # select only rocs for the given label
        rocs = self.rocs[label_index]

        fig = pl.gcf()
        ax = pl.gca()

        pl.plot([0, 1], [0, 1], 'k:')

        for ROC in rocs:
            pl.plot(ROC.fp, ROC.tp, linewidth=1)

        pl.axis((0.0, 1.0, 0.0, 1.0))
        pl.axis('scaled')
        pl.title('Label %s. Mean AUC=%.2f' % (label_index, self.aucs[label_index]))

        pl.xlabel('False positive rate')
        pl.ylabel('True positive rate')

    def _postcall(self, dataset, result):
        """Some postprocessing on the result
        """
        self.raw_result = result
        if not self.__transformer is None:
            if __debug__:
                debug("SA_", "Applying transformer %s" % self.__transformer)
            result = self.__transformer(result)

        # estimate the NULL distribution when functor is given
        if not self.__null_dist is None:
            if __debug__:
                debug("SA_", "Estimating NULL distribution using %s"
                      % self.__null_dist)

            # we need a matching datameasure instance, but we have to disable
            # the estimation of the null distribution in that child to prevent
            # infinite looping.
            measure = copy.copy(self)
            measure.__null_dist = None
            self.__null_dist.fit(measure, dataset)

            if self.states.isEnabled('null_t'):
                # get probability under NULL hyp, but also request
                # either it belong to the right tail
                null_prob, null_right_tail = \
                           self.__null_dist.p(result, return_tails=True)
                self.null_prob = null_prob

                externals.exists('scipy', raiseException=True)
                from scipy.stats import norm

                # TODO: following logic should appear in NullDist,
                #       not here
                tail = self.null_dist.tail
                if tail == 'left':
                    acdf = N.abs(null_prob)
                elif tail == 'right':
                    acdf = 1.0 - N.abs(null_prob)
                elif tail in ['any', 'both']:
                    acdf = 1.0 - N.clip(N.abs(null_prob), 0, 0.5)
                else:
                    raise RuntimeError, 'Unhandled tail %s' % tail
                # We need to clip to avoid non-informative inf's ;-)
                # that happens due to lack of precision in mantissa
                # which is 11 bits in double. We could clip values
                # around 0 at as low as 1e-100 (correspond to z~=21),
                # but for consistency lets clip at 1e-16 which leads
                # to distinguishable value around p=1 and max z=8.2.
                # Should be sufficient range of z-values ;-)
                clip = 1e-16
                null_t = norm.ppf(N.clip(acdf, clip, 1.0 - clip))
                null_t[~null_right_tail] *= -1.0 # revert sign for negatives
                self.null_t = null_t                 # store
            else:
                # get probability of result under NULL hypothesis if available
                # and don't request tail information
                self.null_prob = self.__null_dist.p(result)

        return result

    def __init__(self, sd=0, distribution='rdist', fpp=None, nbins=400, **kwargs):
        """L2-Norm the values, convert them to p-values of a given distribution.

        Parameters
        ----------
        sd : int
          Samples dimension (if len(x.shape)>1) on which to operate
        distribution : string
          Which distribution to use. Known are: 'rdist' (later normal should
          be there as well)
        fpp : float
          At what p-value (both tails) if not None, to control for false
          positives. It would iteratively prune the tails (tentative real positives)
          until empirical p-value becomes less or equal to numerical.
        nbins : int
          Number of bins for the iterative pruning of positives

        WARNING: Highly experimental/slow/etc: no theoretical grounds have been
        presented in any paper, nor proven
        """
        externals.exists('scipy', raise_=True)
        ClassWithCollections.__init__(self, **kwargs)

        self.sd = sd
        if not (distribution in ['rdist']):
            raise ValueError, "Actually only rdist supported at the moment" \
                  " got %s" % distribution
        self.distribution = distribution
        self.fpp = fpp
        self.nbins = nbins

    def __init__(self, source):
        """Reader MEG data from texfiles or file-like objects.

        Parameters
        ----------
        source : str or file-like
          Strings are assumed to be filenames (with `.gz` suffix
          compressed), while all other object types are treated as file-like
          objects.
        """
        self.ntimepoints = None
        self.timepoints = None
        self.nsamples = None
        self.channelids = []
        self.data = []
        self.samplingrate = None

        # open textfiles
        if isinstance(source, str):
            if source.endswith('.gz'):
                externals.exists('gzip', raise_=True)
                import gzip
                source = gzip.open(source, 'r')
            else:
                source = open(source, 'r')

        # read file
        for line in source:
            # split ID
            colon = line.find(':')

            # ignore lines without id
            if colon == -1:
                continue

            id = line[:colon]
            data = line[colon+1:].strip()
            if id == 'Sample Number':
                timepoints = np.fromstring(data, dtype=int, sep='\t')
                # one more as it starts with zero
                self.ntimepoints = int(timepoints.max()) + 1
                self.nsamples = int(len(timepoints) / self.ntimepoints)
            elif id == 'Time':
                self.timepoints = np.fromstring(data,
                                               dtype=float,
                                               count=self.ntimepoints,
                                               sep='\t')
                self.samplingrate = self.ntimepoints \
                    / (self.timepoints[-1] - self.timepoints[0])
            else:
                # load data
                self.data.append(
                    np.fromstring(data, dtype=float, sep='\t').reshape(
                        self.nsamples, self.ntimepoints))
                # store id
                self.channelids.append(id)

        # reshape data from (channels x samples x timepoints) to
        # (samples x chanels x timepoints)
        self.data = np.swapaxes(np.array(self.data), 0, 1)

def _data2img(data, hdr=None, imgtype=None):
    # input data is t,x,y,z
    if externals.exists("nibabel"):
        # let's try whether we can get it done with nibabel
        import nibabel

        if imgtype is None:
            # default is NIfTI1
            itype = nibabel.Nifti1Image
        else:
            itype = imgtype
        if issubclass(itype, nibabel.spatialimages.SpatialImage) and (hdr is None or hasattr(hdr, "get_data_dtype")):
            # we can handle the desired image type and hdr with nibabel
            # use of `None` for the affine should cause to pull it from
            # the header
            return itype(_get_xyzt_shaped(data), None, hdr)
        # otherwise continue and see if there is hope ....
    if externals.exists("nifti"):
        # maybe pynifti can help
        import nifti

        if imgtype is None:
            itype = nifti.NiftiImage
        else:
            itype = imgtype
        if issubclass(itype, nifti.NiftiImage) and (hdr is None or isinstance(hdr, dict)):
            # pynifti wants it transposed
            return itype(_get_xyzt_shaped(data).T, hdr)

    raise RuntimeError(
        "Cannot convert data to an MRI image "
        "(backends: nibabel(%s), pynifti(%s). Got hdr='%s', "
        "imgtype='%s'." % (externals.exists("nibabel"), externals.exists("nifti"), hdr, imgtype)
    )

    def testExternalsCorrect2ndInvocation(self):
        # always fails
        externals._KNOWN["checker2"] = "raise ImportError"

        self.failUnless(not externals.exists("checker2"), msg="Should be False on 1st invocation")

        self.failUnless(not externals.exists("checker2"), msg="Should be False on 2nd invocation as well")

        externals._KNOWN.pop("checker2")

 def plot(self):
     """Plot correlation coefficients
     """
     externals.exists('pylab', raise_=True)
     import pylab as pl
     pl.plot(self['corrcoef'])
     pl.title('Auto-correlation of the sequence')
     pl.xlabel('Offset')
     pl.ylabel('Correlation Coefficient')
     pl.show()

    def test_externals_correct2nd_invocation(self):
        # always fails
        externals._KNOWN['checker2'] = 'raise ImportError'

        self.failUnless(not externals.exists('checker2'),
                        msg="Should be False on 1st invocation")

        self.failUnless(not externals.exists('checker2'),
                        msg="Should be False on 2nd invocation as well")

        externals._KNOWN.pop('checker2')

    def testExternalsNoDoubleInvocation(self):
        # no external should be checking twice (unless specified
        # explicitely)

        class Checker(object):
            """Helper class to increment count of actual checks"""

            def __init__(self):
                self.checked = 0

            def check(self):
                self.checked += 1

        checker = Checker()

        externals._KNOWN["checker"] = "checker.check()"
        externals.__dict__["checker"] = checker
        externals.exists("checker")
        self.failUnlessEqual(checker.checked, 1)
        externals.exists("checker")
        self.failUnlessEqual(checker.checked, 1)
        externals.exists("checker", force=True)
        self.failUnlessEqual(checker.checked, 2)
        externals.exists("checker")
        self.failUnlessEqual(checker.checked, 2)

        # restore original externals
        externals.__dict__.pop("checker")
        externals._KNOWN.pop("checker")

    def _reverse(self, data):
        if __debug__:
            debug('MAP', "Converting signal back using DWP")

        if self.__level is None:
            raise NotImplementedError
        else:
            if not externals.exists('pywt wp reconstruct'):
                raise NotImplementedError, \
                      "Reconstruction for a single level for versions of " \
                      "pywt < 0.1.7 (revision 103) is not supported"
            if not externals.exists('pywt wp reconstruct fixed'):
                warning("Reconstruction using available version of pywt might "
                        "result in incorrect data in the tails of the signal")
            return self.__reverseSingleLevel(data)

    def test_chi_square_searchlight(self):
        # only do partial to save time

        # Can't yet do this since test_searchlight isn't yet "under nose"
        #skip_if_no_external('scipy')
        if not externals.exists('scipy'):
            return

        from mvpa.misc.stats import chisquare

        transerror = TransferError(sample_clf_lin)
        cv = CrossValidatedTransferError(
                transerror,
                NFoldSplitter(cvtype=1),
                enable_ca=['confusion'])


        def getconfusion(data):
            cv(data)
            return chisquare(cv.ca.confusion.matrix)[0]

        sl = sphere_searchlight(getconfusion, radius=0,
                         center_ids=[3,50])

        # run searchlight
        results = sl(self.dataset)
        self.failUnless(results.nfeatures == 2)

def skip_if_no_external(dep, ver_dep=None, min_version=None, max_version=None):
    """Raise SkipTest if external is missing

    Parameters
    ----------
    dep : string
      Name of the external
    ver_dep : string, optional
      If for version checking use some different key, e.g. shogun:rev.
      If not specified, `dep` will be used.
    min_version : None or string or tuple
      Minimal required version
    max_version : None or string or tuple
      Maximal required version
    """

    if not externals.exists(dep):
        raise SkipTest, \
              "External %s is not present thus tests battery skipped" % dep

    if ver_dep is None:
        ver_dep = dep

    if min_version is not None and externals.versions[ver_dep] < min_version:
        raise SkipTest, \
              "Minimal version %s of %s is required. Present version is %s" \
              ". Test was skipped." \
              % (min_version, ver_dep, externals.versions[ver_dep])

    if max_version is not None and externals.versions[ver_dep] > max_version:
        raise SkipTest, \
              "Maximal version %s of %s is required. Present version is %s" \
              ". Test was skipped." \
              % (min_version, ver_dep, externals.versions[ver_dep])

    def testResampling(self):
        ds = EEPDataset(os.path.join(pymvpa_dataroot, 'eep.bin'),
                        labels=[1, 2], labels_map={1:100, 2:101})
        channelids = N.array(ds.channelids).copy()
        self.failUnless(N.round(ds.samplingrate) == 500.0)

        if not externals.exists('scipy'):
            return

        # should puke when called with nothing
        self.failUnlessRaises(ValueError, ds.resample)

        # now for real -- should divide nsamples into half
        rds = ds.resample(sr=250, inplace=False)
        # We should have not changed anything
        self.failUnless(N.round(ds.samplingrate) == 500.0)

        # by default do 'inplace' resampling
        ds.resample(sr=250)
        for d in [rds, ds]:
            self.failUnless(N.round(d.samplingrate) == 250)
            self.failUnless(d.nsamples == 2)
            self.failUnless(N.abs((d.dt - 1.0/250)/d.dt)<1e-5)
            self.failUnless(N.all(d.channelids == channelids))
            # lets now see if we still have a mapper
            self.failUnless(d.O.shape == (2, len(channelids), 2))
            # and labels_map
            self.failUnlessEqual(d.labels_map, {1:100, 2:101})

    def test_dist_p_value(self):
        """Basic testing of DistPValue"""
        if not externals.exists('scipy'):
            return
        ndb = 200
        ndu = 20
        nperd = 2
        pthr = 0.05
        Nbins = 400

        # Lets generate already normed data (on sphere) and add some nonbogus features
        datau = (np.random.normal(size=(nperd, ndb)))
        dist = np.sqrt((datau * datau).sum(axis=1))

        datas = (datau.T / dist.T).T
        tn = datax = datas[0, :]
        dataxmax = np.max(np.abs(datax))

        # now lets add true positive features
        tp = [-dataxmax * 1.1] * (ndu/2) + [dataxmax * 1.1] * (ndu/2)
        x = np.hstack((datax, tp))

        # lets add just pure normal to it
        x = np.vstack((x, np.random.normal(size=x.shape))).T
        for distPValue in (DistPValue(), DistPValue(fpp=0.05)):
            result = distPValue(x)
            self.failUnless((result>=0).all)
            self.failUnless((result<=1).all)

        if cfg.getboolean('tests', 'labile', default='yes'):
            self.failUnless(distPValue.ca.positives_recovered[0] > 10)
            self.failUnless((np.array(distPValue.ca.positives_recovered) +
                             np.array(distPValue.ca.nulldist_number) == ndb + ndu).all())
            self.failUnlessEqual(distPValue.ca.positives_recovered[1], 0)

    def testChiSquareSearchlight(self):
        # only do partial to save time
        if not externals.exists('scipy'):
            return

        from mvpa.misc.stats import chisquare

        transerror = TransferError(sample_clf_lin)
        cv = CrossValidatedTransferError(
                transerror,
                NFoldSplitter(cvtype=1),
                enable_states=['confusion'])


        def getconfusion(data):
            cv(data)
            return chisquare(cv.confusion.matrix)[0]

        # contruct radius 1 searchlight
        sl = Searchlight(getconfusion, radius=1.0,
                         center_ids=[3,50])

        # run searchlight
        results = sl(self.dataset)

        self.failUnless(len(results) == 2)