def run(args): from mvpa2.base.hdf5 import h5save ds = None if not args.txt_data is None: verbose(1, "Load data from TXT file '%s'" % args.txt_data) samples = _load_from_txt(args.txt_data) ds = Dataset(samples) elif not args.npy_data is None: verbose(1, "Load data from NPY file '%s'" % args.npy_data) samples = _load_from_npy(args.npy_data) ds = Dataset(samples) elif not args.mri_data is None: verbose(1, "Load data from MRI image(s) %s" % args.mri_data) from mvpa2.datasets.mri import fmri_dataset vol_attr = dict() if not args.add_vol_attr is None: # XXX add a way to use the mapper of an existing dataset to # add a volume attribute without having to load the entire # mri data again vol_attr = dict(args.add_vol_attr) if not len(args.add_vol_attr) == len(vol_attr): warning("--vol-attr option with duplicate attribute name: " "check arguments!") verbose(2, "Add volumetric feature attributes: %s" % vol_attr) ds = fmri_dataset(args.mri_data, mask=args.mask, add_fa=vol_attr) if ds is None: if args.data is None: raise RuntimeError('no data source specific') else: ds = hdf2ds(args.data)[0] else: if args.data is not None: verbose( 1, 'ignoring dataset input in favor of other data source -- remove either one to disambiguate' ) # act on all attribute options ds = process_common_dsattr_opts(ds, args) if not args.add_fsl_mcpar is None: from mvpa2.misc.fsl.base import McFlirtParams mc_par = McFlirtParams(args.add_fsl_mcpar) for param in mc_par: verbose( 2, "Add motion regressor as sample attribute '%s'" % ('mc_' + param)) ds.sa['mc_' + param] = mc_par[param] verbose(3, "Dataset summary %s" % (ds.summary())) # and store outfilename = args.output if not outfilename.endswith('.hdf5'): outfilename += '.hdf5' verbose(1, "Save dataset to '%s'" % outfilename) h5save(outfilename, ds, mkdir=True, compression=args.hdf5_compression)
def test_zscore_withoutchunks(): # just a smoke test to see if all issues of # https://github.com/PyMVPA/PyMVPA/issues/26 # are fixed from mvpa2.datasets import Dataset ds = Dataset(np.arange(32).reshape((8,-1)), sa=dict(targets=range(8))) zscore(ds, chunks_attr=None) assert(np.any(ds.samples != np.arange(32).reshape((8,-1)))) ds_summary = ds.summary() assert(ds_summary is not None)
def test_zscore_withoutchunks(): # just a smoke test to see if all issues of # https://github.com/PyMVPA/PyMVPA/issues/26 # are fixed from mvpa2.datasets import Dataset ds = Dataset(np.arange(32).reshape((8, -1)), sa=dict(targets=range(8))) zscore(ds, chunks_attr=None) assert (np.any(ds.samples != np.arange(32).reshape((8, -1)))) ds_summary = ds.summary() assert (ds_summary is not None)
def run(args): from mvpa2.base.hdf5 import h5save ds = None if not args.txt_data is None: verbose(1, "Load data from TXT file '%s'" % args.txt_data) samples = _load_from_txt(args.txt_data) ds = Dataset(samples) elif not args.npy_data is None: verbose(1, "Load data from NPY file '%s'" % args.npy_data) samples = _load_from_npy(args.npy_data) ds = Dataset(samples) elif not args.mri_data is None: verbose(1, "Load data from MRI image(s) %s" % args.mri_data) from mvpa2.datasets.mri import fmri_dataset vol_attr = dict() if not args.add_vol_attr is None: # XXX add a way to use the mapper of an existing dataset to # add a volume attribute without having to load the entire # mri data again vol_attr = dict(args.add_vol_attr) if not len(args.add_vol_attr) == len(vol_attr): warning("--vol-attr option with duplicate attribute name: " "check arguments!") verbose(2, "Add volumetric feature attributes: %s" % vol_attr) ds = fmri_dataset(args.mri_data, mask=args.mask, add_fa=vol_attr) if ds is None: if args.data is None: raise RuntimeError('no data source specific') else: ds = hdf2ds(args.data)[0] else: if args.data is not None: verbose(1, 'ignoring dataset input in favor of other data source -- remove either one to disambiguate') # act on all attribute options ds = process_common_dsattr_opts(ds, args) if not args.add_fsl_mcpar is None: from mvpa2.misc.fsl.base import McFlirtParams mc_par = McFlirtParams(args.add_fsl_mcpar) for param in mc_par: verbose(2, "Add motion regressor as sample attribute '%s'" % ('mc_' + param)) ds.sa['mc_' + param] = mc_par[param] verbose(3, "Dataset summary %s" % (ds.summary())) # and store outfilename = args.output if not outfilename.endswith('.hdf5'): outfilename += '.hdf5' verbose(1, "Save dataset to '%s'" % outfilename) h5save(outfilename, ds, mkdir=True, compression=args.hdf5_compression)