def test_stretch():
np.random.seed(2323)
A = np.random.random_integers(12, 120, size=(100,100))
A = stretch(A, 255)
assert A.max() > 250
assert A.min() == 0
A = stretch(A,20)
assert A.max() <= 20
A = stretch(A, 10, 20)
assert A.min() >= 10
A = stretch(A * 0, 10, 20)
assert A.min() >= 10
def preprocessimg(img):
if len(img.shape) > 2:
assert len(img.shape) == 3, "Cannot handle images of more than 3 dimensions."
if options.get('3d.mode','perslice') == 'perslice':
nr_slices=img.shape[0]
out_proc=img.copy()
out_res=img.copy()
for z in xrange(nr_slices):
proc,res=preprocessimg(img[z])
out_proc[z]=proc
out_res[z]=res
return out_proc,out_res
else:
raise Exception('pyslic.preprocessimg: Do not know how to handle 3d.mode: %s' % options['3d.mode'])
if do_bgsub:
regions = image.regions
img = img.copy()
if regions is not None:
rid = (regionid if regionid is not None else 1)
if options.get('bgsub.way','ml') == 'ml':
img *= (regions == rid)
img = bgsub(img, options)
else:
img = bgsub(img, options)
img *= (cropimg == rid)
else:
if regionid:
warn('Selecting a region different from 1 for an image without region information')
img = bgsub(img, options)
imgscaled = stretch(img, 255)
T = thresholdfor(imgscaled,options)
mask = (imgscaled > T)
mask = majority_filter(mask)
residual = img.copy()
img *= mask
residual *= ~mask
return img,residual
def preprocessimg(img):
if len(img.shape) > 2:
assert len(img.shape) == 3, "Cannot handle images of more than 3 dimensions."
if options.get("3d.mode", "perslice") == "perslice":
nr_slices = img.shape[0]
out_proc = img.copy()
out_res = img.copy()
for z in xrange(nr_slices):
proc, res = preprocessimg(img[z])
out_proc[z] = proc
out_res[z] = res
return out_proc, out_res
else:
raise Exception("pyslic.preprocessimg: Do not know how to handle 3d.mode: %s" % options["3d.mode"])
if do_bgsub:
regions = image.regions
img = img.copy()
if regions is not None:
if options.get("bgsub.way", "ml") == "ml":
img *= regions == regionid
img = bgsub(img, options)
else:
img = bgsub(img, options)
img *= cropimg == regionid
else:
if regionid:
warn("Selecting a region different from 1 for an image without region information")
img = bgsub(img, options)
imgscaled = stretch(img, 255)
T = thresholdfor(imgscaled, options)
mask = imgscaled > T
mask = majority_filter(mask)
residual = img.copy()
img *= mask
residual *= ~mask
return img, residual
def test_neg_numbers():
A = np.arange(-10,10)
scaled = stretch(A, 255)
assert scaled.shape == A.shape
assert scaled.min() <= 1
assert scaled.max() >= 254