Initial import of Chroma from private to public repository.

Apologies for the lack of history, but Chroma's prehistory included
some very large files and possibly proprietary engineering data.
Rather than clutter up the public repository (and panic people), we
are starting fresh.  All development happens here from now on.

3 files changed, 7 insertions, 15 deletions

diff --git a/chroma/__init__.py b/chroma/__init__.py
index 6712470..dd7e323 100644
--- a/chroma/__init__.py
+++ b/chroma/__init__.py
@@ -3,7 +3,6 @@ from chroma import geometry
 from chroma import event
 from chroma.io import root
 from chroma import generator
-from chroma.generator import constant_particle_gun
 from chroma import gpu
 from chroma import itertoolset
 from chroma import likelihood
@@ -12,6 +11,5 @@ from chroma.demo import optics
 from chroma import project
 from chroma import sample
 from chroma.sim import Simulation
-from chroma.likelihood import Likelihood
 from chroma.stl import mesh_from_stl
 from chroma import transform
diff --git a/chroma/camera.py b/chroma/camera.py
index 302bc6f..74ac4ad 100644
--- a/chroma/camera.py
+++ b/chroma/camera.py
@@ -706,14 +706,8 @@ class EventViewer(Camera):
         q = self.ev.channels.q
 
         # Important: Compute range only with HIT channels
-        channel_color = map_to_color(q, range=(q[hit].min(),q[hit].max()))
-        solid_hit = np.zeros(len(self.geometry.mesh.triangles), dtype=np.bool)
-        solid_color = np.zeros(len(self.geometry.mesh.triangles), dtype=np.uint32)
-
-        solid_hit[self.geometry.channel_index_to_solid_id] = hit
-        solid_color[self.geometry.channel_index_to_solid_id] = channel_color
-
-        self.gpu_geometry.color_solids(solid_hit, solid_color)
+        solid_colors = map_to_color(q, range=(q[hit].min(),q[hit].max()))
+        self.gpu_geometry.color_solids(hit, solid_colors)
 
     def process_event(self, event):
         if event.type == KEYDOWN:
diff --git a/chroma/likelihood.py b/chroma/likelihood.py
index 22398e3..93a95c3 100644
--- a/chroma/likelihood.py
+++ b/chroma/likelihood.py
@@ -61,7 +61,7 @@ class Likelihood(object):
                               nreps=nreps,
                               ndaq=ndaq,
                               time_only=self.time_only)
-
+        
         # Normalize probabilities and put a floor to keep the log finite
         hit_prob = hitcount.astype(np.float32) / ntotal
         hit_prob = np.maximum(hit_prob, 0.5 / ntotal)
@@ -79,10 +79,10 @@ class Likelihood(object):
 
         # NLL calculation: note that negation is at the end
         # Start with the probabilties of hitting (or not) the channels
-        hit_channel_prob = np.log(hit_prob[self.event.channels.hit]).sum() + np.log(1.0-hit_prob[~self.event.channels.hit]).sum()
+        hit_channel_prob = np.log(hit_prob[self.event.channels.hit]).sum() + np.log(1.0-hit_prob[~self.event.channels.hit])[1:].sum()
+        hit_channel_prob_uncert = ( (ntotal * hit_prob * (1.0 - hit_prob)) / hit_prob**2 ).sum()**0.5
         log_likelihood = ufloat((hit_channel_prob, 0.0))
-
-        #log_likelihood = ufloat((0.0,0.0)) # FIXME: skipping hit/not hit probabilities for now
+        log_likelihood = ufloat((0.0,0.0)) # FIXME: skipping hit/not hit probabilities for now
 
         # Then include the probability densities of the observed
         # charges and times.
@@ -90,7 +90,7 @@ class Likelihood(object):
                                         pdf_prob_uncert[self.event.channels.hit]))
         log_likelihood += unumpy.log(hit_pdf_ufloat).sum()
         
-        return -log_likelihood
+        return -log_likelihood, pdf_prob
 
     def setup_kernel(self, vertex_generator, nevals, nreps, ndaq, oversample_factor):
         bandwidth_generator = islice(vertex_generator, nevals*oversample_factor)