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New upper bound for inter1d objects #205

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4 changes: 3 additions & 1 deletion treetime/config.py
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Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
VERBOSE = 3
import sys

VERBOSE = 3
BIG_NUMBER = 1e10
BIGGEST_NUMBER = sys.float_info.max
TINY_NUMBER = 1e-12
SUPERTINY_NUMBER = 1e-24
MIN_LOG = -1e8 # minimal log value
Expand Down
14 changes: 7 additions & 7 deletions treetime/merger_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,14 +65,14 @@ def set_Tc(self, Tc, T=None):
'''
if isinstance(Tc, Iterable):
if len(Tc)==len(T):
x = np.concatenate(([ttconf.BIG_NUMBER], T, [-ttconf.BIG_NUMBER]))
x = np.concatenate(([ttconf.BIGGEST_NUMBER], T, [-ttconf.BIGGEST_NUMBER]))
y = np.concatenate(([Tc[0]], Tc, [Tc[-1]]))
self.Tc = interp1d(x,y)
else:
self.logger("need Tc values and Timepoints of equal length",2,warn=True)
self.Tc = interp1d([-ttconf.BIG_NUMBER, ttconf.BIG_NUMBER], [1e-5, 1e-5])
self.Tc = interp1d([-ttconf.BIGGEST_NUMBER, ttconf.BIGGEST_NUMBER], [1e-5, 1e-5])
else:
self.Tc = interp1d([-ttconf.BIG_NUMBER, ttconf.BIG_NUMBER],
self.Tc = interp1d([-ttconf.BIGGEST_NUMBER, ttconf.BIGGEST_NUMBER],
[Tc+ttconf.TINY_NUMBER, Tc+ttconf.TINY_NUMBER])
self.calc_integral_merger_rate()

Expand Down Expand Up @@ -117,7 +117,7 @@ def calc_branch_count(self, posterior=False):
cdf_function=n.joint_inverse_cdf

if cdf_function is not None:
x_vals = np.concatenate([[-ttconf.BIG_NUMBER], cdf_function(y_points), [ttconf.BIG_NUMBER]])
x_vals = np.concatenate([[-ttconf.BIGGEST_NUMBER], cdf_function(y_points), [ttconf.BIGGEST_NUMBER]])
y_vals = np.concatenate([ [(len(n.clades)-1),(len(n.clades)-1)], (1-y_points[1:-1]), [0,0]])
tree_smooth_events += [interp1d(x_vals, y_vals, kind="linear")]
else:
Expand All @@ -134,7 +134,7 @@ def calc_branch_count(self, posterior=False):
unique_mergers = np.array(sorted(dn_branch.items(), key = lambda x:-x[0]))

# calculate the branch count at each point summing the delta branch counts
nbranches_discrete = [[ttconf.BIG_NUMBER, 1], [unique_mergers[0,0]+ttconf.TINY_NUMBER, 1]]
nbranches_discrete = [[ttconf.BIGGEST_NUMBER, 1], [unique_mergers[0,0]+ttconf.TINY_NUMBER, 1]]
for ti, (t, dn) in enumerate(unique_mergers[:-1]):
new_n = nbranches_discrete[-1][1]+dn
next_t = unique_mergers[ti+1,0]+ttconf.TINY_NUMBER
Expand All @@ -143,7 +143,7 @@ def calc_branch_count(self, posterior=False):

new_n += unique_mergers[-1,1]
nbranches_discrete.append([unique_mergers[ti+1,0], new_n])
nbranches_discrete.append([-ttconf.BIG_NUMBER, new_n])
nbranches_discrete.append([-ttconf.BIGGEST_NUMBER, new_n])
nbranches_discrete=np.array(nbranches_discrete)
nbranches_discrete = interp1d(nbranches_discrete[:,0], nbranches_discrete[:,1], kind='linear')

Expand Down Expand Up @@ -180,7 +180,7 @@ def calc_integral_merger_rate(self):
# the latter is scaled by 0.5/Tc
# need to add extra point at very large time before present to
# prevent 'out of interpolation range' errors
self.integral_merger_rate = interp1d(np.concatenate(([-ttconf.BIG_NUMBER], tvals,[ttconf.BIG_NUMBER])),
self.integral_merger_rate = interp1d(np.concatenate(([-ttconf.BIGGEST_NUMBER], tvals,[ttconf.BIGGEST_NUMBER])),
np.concatenate(([cost[0]], cost,[cost[-1]])), kind='linear')

def branch_merger_rate(self, t):
Expand Down