WIP: Slicereg

stpt_pipeline/bead_model.py

+import numpy as np
+from scipy.special import factorial
+#
+# Bead fitting procedures
+#
+
+
+def print_theta(theta):
+    s = ''
+    for i in theta:
+        s += '{0:.3f} '.format(i)
+    return s
+#
+
+
+def sigmoid(r, rt, c):
+    return (1.0 - 1.0 / (1.0 + np.exp(-c * (r**2 - rt**2))))
+#
+
+
+def bead_profile_sigmoid(x, y, x0, y0, rt, p, a, c):
+    #
+    r = np.sqrt((x - x0)**2 + (y - y0)**2)
+    return np.abs(p - a * r**2) * sigmoid(r, rt, c)
+    # return (p-a*r**2)*(r<=rt)
+#
+
+
+def bead_profile_supergaussian(x, y, x0, y0, p, s, c):
+    #
+    r = np.sqrt((x - x0)**2 + (y - y0)**2)
+    return p * np.exp(-((r / s)**2)**c)
+
+
+def neg_log_like(theta, xx, yy, zz, do_full, do_print):
+    #
+    # x0,y0,rt,p,a=theta
+    x0, y0, p, s, c = theta
+    if x0 < -10:
+        return np.inf
+    if y0 < -10:
+        return np.inf
+    if c < 1:
+        return np.inf
+    if s < 0.0:
+        return np.inf
+    if p < 0.0:
+        return np.inf
+    # model=1.+bead_profile_2d(xx,yy,x0,y0,rt,p,a,c)
+    model = 1. + bead_profile_supergaussian(xx, yy, x0, y0, p, s, c)
+    ll = -model + (1. + zz) * np.log(model)
+    if do_full:
+        ll -= np.log(factorial(1. + zz))
+    #
+    if do_print:
+        print(print_theta(theta), ll.sum())
+    return -1.0 * ll.sum()
+#
+
+
+def neg_log_like_conf(theta, xx, yy, zz, conf, do_full, do_print):
+    #
+    # x0,y0,rt,p,a=theta
+    x0, y0, p, s, c = theta
+    if x0 < -10:
+        return np.inf
+    if y0 < -10:
+        return np.inf
+    if c < 1:
+        return np.inf
+    if s < 0.0:
+        return np.inf
+    if p < 0.0:
+        return np.inf
+    # model=1.+bead_profile_2d(xx,yy,x0,y0,rt,p,a,c)
+    model = 1. + bead_profile_supergaussian(xx, yy, x0, y0, p, s, c)
+    ll = (-model + (1. + zz) * np.log(model)) * conf
+    if do_full:
+        ll -= np.log(factorial(1. + zz))
+    #
+    if do_print:
+        print(print_theta(theta), np.nansum(ll))
+    return -1.0 * np.nansum(ll)

[Eduardo Gonzalez Solares]

to remove or convert to log.debug

By Eduardo Gonzalez Solares on 2020-06-01T08:50:56 (imported from GitLab)

[Eduardo Gonzalez Solares]

remove or convert to log.debug

By Eduardo Gonzalez Solares on 2020-06-01T08:51:14 (imported from GitLab)

[Eduardo Gonzalez Solares]

remove or log.debug

By Eduardo Gonzalez Solares on 2020-06-01T08:51:34 (imported from GitLab)