def test_jump_by_cluster(setup_NGC6440E):
"""
Compare selection by MJD with selection by cluster (which by default selects TOAs by 2h gaps)
"""
m_copy = copy.deepcopy(setup_NGC6440E.m)
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
par = p.maskParameter(name="JUMP",
key="mjd",
value=0.2,
key_value=[54099, 54100],
units=u.s)
# this should be the last group of any TOAs
cp.add_param(par, setup=True)
# add clusters to the TOAs
clusters = setup_NGC6440E.t.get_clusters(2 * u.hr, add_column=False)
for i, v in zip(np.arange(len(setup_NGC6440E.t)), clusters):
setup_NGC6440E.t.table[i]["flags"]["toacluster"] = str(v)
m_copy.add_component(PhaseJump(), validate=False)
cp_copy = m_copy.components["PhaseJump"]
par_copy = p.maskParameter(name="JUMP",
key="-toacluster",
value=0.2,
key_value=41,
units=u.s)
# this should be identical to the cluster above
cp_copy.add_param(par_copy, setup=True)
assert set(cp.JUMP1.select_toa_mask(setup_NGC6440E.t)) == set(
cp_copy.JUMP1.select_toa_mask(setup_NGC6440E.t))
def test_remove_jump_and_flags(setup_NGC6440E):
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
selected_toa_ind = [1, 2, 3]
selected_toa_ind2 = [10, 11, 12]
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind])
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind2])
# test delete_jump_and_flags
setup_NGC6440E.m.delete_jump_and_flags(setup_NGC6440E.t.table["flags"], 1)
for dict in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert "jump" not in dict
assert "gui_jump" not in dict
# check that other flags at higher indeces adjust
for dict in setup_NGC6440E.t.table["flags"][selected_toa_ind2]:
assert dict["jump"] == ["1"]
assert dict["gui_jump"] == "1"
assert len(cp.jumps) == 1
assert "JUMP1" in cp.jumps
# delete last jump
setup_NGC6440E.m.delete_jump_and_flags(setup_NGC6440E.t.table["flags"], 1)
for dict in setup_NGC6440E.t.table["flags"][selected_toa_ind2]:
assert "jump" not in dict
assert "gui_jump" not in dict
assert "PhaseJump" not in setup_NGC6440E.m.components
def test_remove_jump_and_flags(setup_NGC6440E):
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
selected_toa_ind = [1, 2, 3]
selected_toa_ind2 = [10, 11, 12]
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind])
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind2])
# test delete_jump_and_flags
setup_NGC6440E.m.delete_jump_and_flags(setup_NGC6440E.t.table["flags"], 1)
assert len(cp.jumps) == 1
# delete last jump
setup_NGC6440E.m.delete_jump_and_flags(setup_NGC6440E.t.table["flags"], 2)
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind2]:
assert "jump" not in d
assert "PhaseJump" not in setup_NGC6440E.m.components
def test_jump_params_to_flags(setup_NGC6440E):
""" Check jump_params_to_flags function. """
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
par = p.maskParameter(
name="JUMP", key="freq", value=0.2, key_value=[1440, 1700], units=u.s
) # TOAs indexed 48, 49, 54 in NGC6440E are within this frequency range
cp.add_param(par, setup=True)
# sanity check - ensure no jump flags from initialization
for i in range(setup_NGC6440E.t.ntoas):
assert "jump" not in setup_NGC6440E.t.table["flags"][i]
# add flags based off jumps added to model
setup_NGC6440E.m.jump_params_to_flags(setup_NGC6440E.t)
# index to affected TOAs and ensure appropriate flags set
toa_indeces = [48, 49, 54]
for i in toa_indeces:
assert "jump" in setup_NGC6440E.t.table["flags"][i]
assert setup_NGC6440E.t.table["flags"][i]["jump"][0] == "1"
# ensure no extraneous flags added to unaffected TOAs
for i in range(setup_NGC6440E.t.ntoas):
if i not in toa_indeces:
assert "jump" not in setup_NGC6440E.t.table["flags"][i]
# check case where multiple calls are performed (no-ops)
old_table = setup_NGC6440E.t.table
setup_NGC6440E.m.jump_params_to_flags(setup_NGC6440E.t)
assert all(old_table) == all(setup_NGC6440E.t.table)
# check that adding overlapping jump works
par2 = p.maskParameter(
name="JUMP", key="freq", value=0.2, key_value=[1600, 1900], units=u.s
) # frequency range overlaps with par, 2nd jump will have common TOAs w/ 1st
cp.add_param(par2, setup=True)
# add flags based off jumps added to model
setup_NGC6440E.m.jump_params_to_flags(setup_NGC6440E.t)
mask2 = par2.select_toa_mask(setup_NGC6440E.t)
intersect = np.intersect1d(toa_indeces, mask2)
assert intersect is not []
for i in mask2:
assert "2" in setup_NGC6440E.t.table["flags"][i]["jump"]
for i in toa_indeces:
assert "1" in setup_NGC6440E.t.table["flags"][i]["jump"]
def test_add_overlapping_jump(setup_NGC6440E):
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
selected_toa_ind = [1, 2, 3]
selected_toa_ind2 = [10, 11, 12]
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind])
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind2])
# attempt to add overlapping jump - should not add jump
selected_toa_ind3 = [9, 10, 11]
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind3])
# check previous jump flags unaltered
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert d["gui_jump"] == "1"
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind2]:
assert d["gui_jump"] == "2"
# check that no flag added to index 9
assert "jump" not in setup_NGC6440E.t.table[9].colnames
assert "gui_jump" not in setup_NGC6440E.t.table[9].colnames
def test_add_jumps_and_flags(setup_NGC6440E):
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
# simulate selecting TOAs in pintk and jumping them
selected_toa_ind = [1, 2, 3] # arbitrary set of TOAs
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind])
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert d["gui_jump"] == "1"
# add second jump to different set of TOAs
selected_toa_ind2 = [10, 11, 12]
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind2])
# check previous jump flags unaltered
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert d["gui_jump"] == "1"
# check appropriate flags added
for d in setup_NGC6440E.t.table["flags"][selected_toa_ind2]:
assert d["gui_jump"] == "2"
def test_multijump_toa(setup_NGC6440E):
setup_NGC6440E.m.add_component(PhaseJump(), validate=False)
cp = setup_NGC6440E.m.components["PhaseJump"]
par = p.maskParameter(
name="JUMP", key="freq", value=0.2, key_value=[1440, 1700], units=u.s
) # TOAs indexed 48, 49, 54 in NGC6440E are within this frequency range
selected_toa_ind = [48, 49, 54]
cp.add_param(par, setup=True)
# check that one can still add "gui jumps" to model-jumped TOAs
cp.add_jump_and_flags(setup_NGC6440E.t.table["flags"][selected_toa_ind])
# add flags based off jumps added to model
setup_NGC6440E.m.jump_params_to_flags(setup_NGC6440E.t)
for dict in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert dict["jump"] in ["1,2", "2,1"]
assert dict["gui_jump"] == "2"
assert len(cp.jumps) == 2
setup_NGC6440E.m.delete_jump_and_flags(setup_NGC6440E.t.table["flags"], 2)
for dict in setup_NGC6440E.t.table["flags"][selected_toa_ind]:
assert "jump" in dict
assert len(cp.jumps) == 1
assert "JUMP1" in cp.jumps