def screen_data_dirnme(in4d, outdir): """uses nipy diagnostic code to screen the data for outlier values and saves results to three images mean, std, pca, in same dir as original file(s)""" img = nipy.load_image(in4d) result = diag.screen(img) # save mean, std, pca pth, nme = os.path.split(in4d) stripnme = nme.split('.')[0] pcafile = os.path.join(outdir, 'QA-PCA_%s.nii.gz' % (nme)) meanfile = os.path.join(outdir, 'QA-MEAN_%s.nii.gz' % (nme)) stdfile = os.path.join(outdir, 'QA-STD_%s.nii.gz' % (nme)) nipy.save_image(result['mean'], meanfile) nipy.save_image(result['std'], stdfile) nipy.save_image(result['pca'], pcafile) print 'saved: %s\n \t%s\n \t%s\n' % (pcafile, meanfile, stdfile)
def screen_data_dirnme(in4d, outdir): """uses nipy diagnostic code to screen the data for outlier values and saves results to three images mean, std, pca, in same dir as original file(s)""" img = nipy.load_image(in4d) result = diag.screen(img) # save mean, std, pca pth, nme = os.path.split(in4d) stripnme = nme.split('.')[0] pcafile = os.path.join(outdir, 'QA-PCA_%s.nii.gz'%(nme)) meanfile = os.path.join(outdir, 'QA-MEAN_%s.nii.gz'%(nme)) stdfile = os.path.join(outdir, 'QA-STD_%s.nii.gz'%(nme)) nipy.save_image(result['mean'], meanfile) nipy.save_image(result['std'], stdfile) nipy.save_image(result['pca'], pcafile) print 'saved: %s\n \t%s\n \t%s\n'%(pcafile, meanfile, stdfile)
def test_screen(): img = ni.load_image(funcfile) res = nad.screen(img) yield assert_equal(res['mean'].ndim, 3) yield assert_equal(res['pca'].ndim, 4) yield assert_equal(sorted(res.keys()), ['max', 'mean', 'min', 'pca', 'pca_res', 'std', 'ts_res']) data = np.asarray(img) yield assert_array_equal(np.max(data, axis=-1), res['max']) yield assert_array_equal(np.mean(data, axis=-1), res['mean']) yield assert_array_equal(np.min(data, axis=-1), res['min']) yield assert_array_equal(np.std(data, axis=-1), res['std']) pca_res = nad.pca.pca(data, axis=-1, standardize=False, ncomp=10) for key in pca_res: yield assert_array_equal(pca_res[key], res['pca_res'][key]) ts_res = nad.time_slice_diffs(data) for key in ts_res: yield assert_array_equal(ts_res[key], res['ts_res'][key])