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])