def test_write_center(self):
dpath = os.path.join('test', 'tmp')
cen_range = (5, 7, 0.5)
cen = np.arange(*cen_range)
write_center(
read_file('proj.npy'),
read_file('angle.npy'),
dpath, cen_range=cen_range,
algorithm='gridrec', filter_name='shepp')
for m in range(cen.size):
assert_equals(
os.path.isfile(
os.path.join(
os.path.join('test', 'tmp'),
str('{0:.2f}'.format(cen[m]) + '.tiff'))), True)
shutil.rmtree(dpath)
def check_rpc_consistency(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale1 = nmtransform.nm_rescale(q.shape[0], n)
rescale2 = nmtransform.nm_rescale(n, q.shape[0])
beads_n = rescale1.b1tob2(q)
beads_1 = rescale1.b2tob1(beads_n)
beads_2 = rescale2.b1tob2(beads_n)
assert_equals(beads_1, beads_2)
def check_rpc_consistency(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale1 = nmtransform.nm_rescale(q.shape[0], n)
rescale2 = nmtransform.nm_rescale(n, q.shape[0])
beads_n = rescale1.b1tob2(q)
beads_1 = rescale1.b2tob1(beads_n)
beads_2 = rescale2.b1tob2(beads_n)
assert_equals(beads_1, beads_2)
def test_write_center(self):
dpath = os.path.join('test', 'tmp')
cen_range = (5, 7, 0.5)
cen = np.arange(*cen_range)
write_center(read_file('proj.npy'),
read_file('angle.npy'),
dpath,
cen_range=cen_range,
algorithm='gridrec',
filter_name='shepp')
for m in range(cen.size):
assert_equals(
os.path.isfile(
os.path.join(os.path.join('test', 'tmp'),
str('{0:.2f}'.format(cen[m]) + '.tiff'))),
True)
shutil.rmtree(dpath)
def check_centroid_pos(n, q):
"""Check if expanding and then contracting a ring polymer
maintains the centroid.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
beads_big = check_up_and_down_scaling(n, q)
rescale_big = nmtransform.mk_rs_matrix(n, 1)
rescale_q = nmtransform.mk_rs_matrix(q.shape[0], 1)
centroid_big = np.dot(rescale_big, beads_big)
centroid_q = np.dot(rescale_q, q)
assert_equals(centroid_q, centroid_big)
def check_centroid_pos(n, q):
"""Check if expanding and then contracting a ring polymer
maintains the centroid.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
beads_big = check_up_and_down_scaling(n, q)
rescale_big = nmtransform.mk_rs_matrix(n, 1)
rescale_q = nmtransform.mk_rs_matrix(q.shape[0], 1)
centroid_big = np.dot(rescale_big, beads_big)
centroid_q = np.dot(rescale_q, q)
assert_equals(centroid_q, centroid_big)
def check_up_and_down_scaling(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale = nmtransform.nm_rescale(q.shape[0], n)
print "Initial position of the beads:"
print q, q.shape, (q.shape[0], n)
# rescale up to the n beads
beads_n = rescale.b1tob2(q)
print "Upscaled to %d beads:" % n
print beads_n, beads_n.shape
beads_final = rescale.b2tob1(beads_n)
print "Final position of the beads:"
print beads_final
assert_equals(q, beads_final)
return beads_n
def check_up_and_down_scaling(n, q):
"""Check if q expanding and then contracting a ring polymer is a no-op.
Args:
n: The number of beads in the scaled ring polymer.
q: The original position array.
"""
rescale = nmtransform.nm_rescale(q.shape[0], n)
print "Initial position of the beads:"
print q, q.shape, (q.shape[0], n)
# rescale up to the n beads
beads_n = rescale.b1tob2(q)
print "Upscaled to %d beads:" % n
print beads_n, beads_n.shape
beads_final = rescale.b2tob1(beads_n)
print "Final position of the beads:"
print beads_final
assert_equals(q, beads_final)
return beads_n
def test_shepp2d(self):
assert_equals(shepp2d().dtype, 'float32')
assert_equals(shepp2d().shape, (1, 512, 512))
assert_equals(shepp2d(size=(128, 256)).shape, (1, 128, 256))
assert_equals(shepp2d(size=64).shape, (1, 64, 64))
def test_checkerboard(self):
assert_equals(checkerboard().dtype, 'float32')
assert_equals(checkerboard().shape, (1, 512, 512))
assert_equals(checkerboard(size=(128, 256)).shape, (1, 128, 256))
assert_equals(checkerboard(size=64).shape, (1, 64, 64))
def test_cameraman(self):
assert_equals(cameraman().dtype, 'float32')
assert_equals(cameraman().shape, (1, 512, 512))
assert_equals(cameraman(size=(128, 256)).shape, (1, 128, 256))
assert_equals(cameraman(size=64).shape, (1, 64, 64))
def test_barbara(self):
assert_equals(barbara().dtype, 'float32')
assert_equals(barbara().shape, (1, 512, 512))
assert_equals(barbara(size=(128, 256)).shape, (1, 128, 256))
assert_equals(barbara(size=64).shape, (1, 64, 64))
def test_shepp3d(self):
assert_equals(shepp3d(size=(6, 8, 10)).dtype, 'float32')
assert_equals(shepp3d(size=(6, 8, 10)).shape, (6, 8, 10))
assert_equals(shepp3d(size=(6, 8, 10)).min(), 0)
assert_equals(shepp3d(size=6).shape, (6, 6, 6))
