def test_manip_compress(self):
# one chip 256x256
# factor 16
pattern = np.random.poisson(1000, (256, 256))
dp = DataPattern(pattern_array=pattern)
dp.manip_compress(factor=16, rm_central_pix=0, rm_edge_pix=0)
# factor 22
pattern = np.random.poisson(1000, (256, 256))
dp = DataPattern(pattern_array=pattern)
dp.manip_compress(factor=22, rm_central_pix=0, rm_edge_pix=0)
# one chip 516x516
# factor 22
pattern = np.random.poisson(1000, (512, 512))
dp = DataPattern(pattern_array=pattern)
dp.manip_compress(factor=22, rm_central_pix=0, rm_edge_pix=0)
# two chips
# factor 16
pattern = np.random.poisson(1000, (516, 516))
dp = DataPattern(pattern_array=pattern,
nChipsX=2,
nChipsY=2,
real_size=3)
dp.manip_compress(factor=16, rm_central_pix=0, rm_edge_pix=0)
# factor 22
pattern = np.random.poisson(1000, (516, 516))
dp = DataPattern(pattern_array=pattern,
nChipsX=2,
nChipsY=2,
real_size=3)
dp.manip_compress(factor=22, rm_central_pix=0, rm_edge_pix=0)
def test_init_from_json(self):
filepath = 'data_files/pad_dp_2M.json'
dp_pad = DataPattern(file_path=filepath)
self.assertTrue(dp_pad.pattern_matrix.size >= 0)
filepath = 'data_files/tpx_quad_dp_2M.json'
dp_timepix = DataPattern(file_path=filepath)
self.assertTrue(dp_timepix.pattern_matrix.size >= 0)
def test_init_from_array(self):
pattern = np.random.poisson(1000, (22, 22))
pattern[0, 0] = 0
pattern[0, 1] = 0
pattern[3, 0] = 0
dp = DataPattern(pattern_array=pattern)
self.assertTrue(dp.pattern_matrix.size >= 0)
def test_init_from_txt(self):
filepath = 'data_files/tpx_quad_array_2M.txt'
dp_timepix = DataPattern(file_path=filepath,
nChipsX=2,
nChipsY=2,
real_size=3)
self.assertTrue(dp_timepix.pattern_matrix.size >= 0)
def test_manipulations(self):
# Get a timepix array
filepath = 'data_files/tpx_quad_array_2M.txt'
dp_timepix = DataPattern(file_path=filepath,
nChipsX=2,
nChipsY=2,
real_size=3)
self.assertTrue(dp_timepix.pattern_matrix.size >= 0)
# Manipulation methods
# -Orient
dp_timepix.manip_orient('cw, mh') # TimepixQuad orientation
# -Angular calibration
dp_timepix.manip_create_mesh(pixel_size=0.055, distance=300)
#mm2.manip_create_mesh(pixel_size=1.4, distance=300)
# Zero central pix
dp_timepix.zero_central_pix(0)
# Add extra pixels to account for bigger central pixels
dp_timepix.manip_correct_central_pix()
# -Mask pixels
dp_timepix.mask_std(4, 0)
# -Sum pixels, zero central pixels and remove edge pixels all in one
dp_timepix.manip_compress(factor=2, rm_central_pix=2, rm_edge_pix=4)
# Save and Load previously set mask
dp_timepix.save_mask('test_masksave.txt')
dp_timepix.load_mask('test_masksave.txt')
if os.path.exists("test_masksave.txt"):
os.remove("test_masksave.txt")
# Save
dp_timepix.io_save_ascii('test_ascii_save.txt')
if os.path.exists("test_ascii_save.txt"):
os.remove("test_ascii_save.txt")
# Set angular resolution
dx = -0.1
dy = 0.2
phi = 3
dp_timepix.set_pattern_angular_pos(center=(dx, dy), angle=phi)
# mask array
dp_timepix.set_fit_region(distance=2.5)
def test_basics(self):
lib = Lib2dl('data_files/sb600g05.2dl')
dp_pad = DataPattern('data_files/pad_dp_2M.json')
fm = FitManager(cost_function='chi2', n_sites=2, sub_pixels=8)
fm.set_pattern(dp_pad, lib)
fm.fit_parameters.change_fixed_values(
sigma=0.05) # pad=0.094, tpx=0.064
fm.fit_parameters.change_bounds(phi=(-20, 20))
fm.fit_parameters.change_initial_values(phi=0.5)
fm.set_minimization_settings(profile='fine')
p1 = 1
p2 = 23
fm.run_single_fit(p1, p2, verbose_graphics=False)
self.assertAlmostEqual(fm.df_horizontal['x'][0], -0.1, places=2)
self.assertAlmostEqual(fm.df_horizontal['y'][0], 0.2, places=2)
def try__update_compress_factors_tpx_quad(self, factor, rm_central_pix,
rm_edge_pix):
# Get a timepix array
filepath = 'data_files/tpx_quad_array_2M.txt'
dp_timepix = DataPattern(file_path=filepath,
nChipsX=2,
nChipsY=2,
real_size=3)
dp_timepix.manip_correct_central_pix()
rm_central_pix, rm_edge_pix = \
dp_timepix._update_compress_factors_tpx_quad(factor, rm_central_pix, rm_edge_pix)
# verify if the rest is zero
nx, ny = dp_timepix.nx, dp_timepix.ny
div_rest = (nx - 2 * rm_edge_pix) % factor
self.assertEqual(div_rest, 0)
div_rest = (ny - 2 * rm_edge_pix) % factor
self.assertEqual(div_rest, 0)
return rm_central_pix, rm_edge_pix
def setUp(self) -> None:
# Runs before each test
dp_pad = DataPattern('data_files/pad_dp_2M.json')
self.xmesh = dp_pad.xmesh
self.ymesh = dp_pad.ymesh
self.patt = dp_pad.pattern_matrix
def test_manip_orient(self):
# Square pattern
# 0 1
# 2 3
pattern_sq = np.arange(4).reshape((2, 2))
xmesh = np.array([[-1, 1], [-1, 1]])
ymesh = np.array([[1, 1], [-1, -1]])
# No rotation
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('')
self.assertTrue(np.alltrue(dp.pattern_matrix == pattern_sq))
self.assertTrue(np.alltrue(dp.xmesh == xmesh))
self.assertTrue(np.alltrue(dp.ymesh == ymesh))
# Rotate clockwise
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('cw')
result = np.array([[2, 0], [3, 1]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh))
self.assertTrue(np.alltrue(dp.ymesh == ymesh))
# Rotate counterclockwise
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('cc')
result = np.array([[1, 3], [0, 2]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh))
self.assertTrue(np.alltrue(dp.ymesh == ymesh))
# Mirror horizontaly
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('mh')
result = np.array([[1, 0], [3, 2]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh))
self.assertTrue(np.alltrue(dp.ymesh == ymesh))
# Mirror verticaly
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('mv')
result = np.array([[2, 3], [0, 1]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh))
self.assertTrue(np.alltrue(dp.ymesh == ymesh))
# Rectangular pattern
# 0 1
# 2 3
# 4 5
pattern_sq = np.arange(6).reshape((3, 2))
xmesh = np.array([[-1, 1], [-1, 1], [-1, 1]])
ymesh = np.array([[1, 1], [0, 0], [-1, -1]])
# Rotate clockwise
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('cw')
result = np.array([[4, 2, 0], [5, 3, 1]])
xmesh_res = np.array([[-1, 0, 1], [-1, 0, 1]])
ymesh_res = np.array([[1, 1, 1], [-1, -1, -1]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh_res))
self.assertTrue(np.alltrue(dp.ymesh == ymesh_res))
# Rotate counterclockwise
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('cc')
result = np.array([[1, 3, 5], [0, 2, 4]])
xmesh_res = np.array([[-1, 0, 1], [-1, 0, 1]])
ymesh_res = np.array([[1, 1, 1], [-1, -1, -1]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh_res))
self.assertTrue(np.alltrue(dp.ymesh == ymesh_res))
# Multiple rotations (same results as counterclockwise)
dp = DataPattern(pattern_array=pattern_sq)
dp.set_xymesh(xmesh, ymesh)
dp.manip_orient('cw, cw, cw, cw, cc')
result = np.array([[1, 3, 5], [0, 2, 4]])
xmesh_res = np.array([[-1, 0, 1], [-1, 0, 1]])
ymesh_res = np.array([[1, 1, 1], [-1, -1, -1]])
self.assertTrue(np.alltrue(dp.pattern_matrix == result))
self.assertTrue(np.alltrue(dp.xmesh == xmesh_res))
self.assertTrue(np.alltrue(dp.ymesh == ymesh_res))
def make_mock_pad(self):
dp = DataPattern(file_path=self.pad_path)
return dp
def make_mock_tpx(self):
dp = DataPattern(file_path=self.tpx_path)
return dp