merge relayout branch

8 files changed, 392 insertions, 0 deletions

diff --git a/chroma/detectors/__init__.py b/chroma/detectors/__init__.py
new file mode 100644
index 0000000..2028300
--- /dev/null
+++ b/chroma/detectors/__init__.py
@@ -0,0 +1,35 @@
+from lbne import build_lbne
+from sno import build_sno as build_sno_detector
+from miniclean import build_miniclean as build_miniclean_detector
+
+# from LBNE document #3951
+radius = 63.30/2
+height = 76.60
+nstrings = 230
+pmts_per_string = 88
+endcap_spacing = 0.86
+
+def lbne_event_view():
+    return build_lbne(radius, height, nstrings, pmts_per_string,
+                      endcap_spacing, physical_model=False)
+
+def lbne():
+    return build_lbne(radius, height, nstrings, pmts_per_string,
+                      endcap_spacing)
+
+def minilbne():
+    return build_lbne(radius/10, height/10, nstrings//10, pmts_per_string//10,
+                      endcap_spacing)
+
+def microlbne():
+    return build_lbne(radius/40, height/40, nstrings//40, pmts_per_string//40,
+                      endcap_spacing)
+
+def sno():
+    return build_sno_detector()
+
+def cad_sno():
+    return build_sno_detector(real_av=True)
+
+def miniclean():
+    return build_miniclean_detector()
diff --git a/chroma/detectors/lbne.py b/chroma/detectors/lbne.py
new file mode 100644
index 0000000..97d09e9
--- /dev/null
+++ b/chroma/detectors/lbne.py
@@ -0,0 +1,49 @@
+import numpy as np
+from chroma.geometry import Solid, Geometry
+import chroma.solids as solids
+from chroma.optics import vacuum, water, water_wcsim, black_surface
+from chroma.transform import rotate, make_rotation_matrix
+from itertools import product
+import chroma.make as make
+
+def build_lbne(radius, height, nstrings, pmts_per_string, endcap_spacing, detector_material=water_wcsim, physical_model=True):
+    if physical_model:
+        pmt = solids.build_12inch_pmt_with_lc(outer_material=detector_material)
+    else:
+        pmt = solids.build_12inch_pmt_shell(outer_material=detector_material)
+
+    lbne = Geometry(detector_material)
+
+    # outer cylinder
+    cylinder_mesh = make.segmented_cylinder(radius, height+height/(pmts_per_string-1), nsteps=16*nstrings, nsegments=1200)
+    cylinder_mesh.vertices = rotate(cylinder_mesh.vertices, np.pi/2, (-1,0,0))
+    lbne.add_solid(Solid(cylinder_mesh, detector_material, vacuum, black_surface, 0xff0000ff))
+
+    lbne.pmtids = []
+
+    # construct the barrel
+    for i in range(pmts_per_string):
+        for j in range(nstrings):
+            rotation = make_rotation_matrix(j*2*np.pi/nstrings, (0,0,1))
+            displacement = rotate((0,-radius,-height/2+i*height/(pmts_per_string-1)), j*2*np.pi/nstrings, (0,0,1))
+            lbne.pmtids.append(lbne.add_solid(pmt, rotation, displacement))
+
+    # construct the top endcap
+    for x, y in np.array(tuple(product(\
+                np.arange(-radius+0.075, radius, endcap_spacing),
+                np.arange(-radius+0.075, radius, endcap_spacing)))):
+        if np.sqrt(x**2 + y**2) < radius - endcap_spacing/2:
+            rotation = make_rotation_matrix(+np.pi/2, (1,0,0))
+            displacement = (x,y,+height/2+height/(pmts_per_string-1)/2)
+            lbne.pmtids.append(lbne.add_solid(pmt, rotation, displacement))
+
+    # construct the bottom endcap
+    for x, y in np.array(tuple(product(\
+                np.arange(-radius+0.075, radius, endcap_spacing),
+                np.arange(-radius+0.075, radius, endcap_spacing)))):
+        if np.sqrt(x**2 + y**2) < radius - endcap_spacing/2:
+            rotation = make_rotation_matrix(-np.pi/2, (1,0,0))
+            displacement = (x,y,-height/2-height/(pmts_per_string-1)/2)
+            lbne.pmtids.append(lbne.add_solid(pmt, rotation, displacement))
+
+    return lbne
diff --git a/chroma/detectors/miniclean.py b/chroma/detectors/miniclean.py
new file mode 100644
index 0000000..92dd019
--- /dev/null
+++ b/chroma/detectors/miniclean.py
@@ -0,0 +1,80 @@
+import numpy as np
+import numpy.linalg
+import math
+from chroma.make import linear_extrude, sphere
+from chroma.geometry import *
+from chroma.optics import *
+from chroma.transform import rotate, make_rotation_matrix
+from chroma.itertoolset import grouper
+import os
+
+
+dir = os.path.split(os.path.realpath(__file__))[0]
+
+def read_polygons(filename):
+    polygons = {}
+    with open(filename) as f:
+        for line in f:
+            parts = line.split()
+            idnum = int(parts[0])
+            npoints = int(parts[1])
+            points = np.zeros(shape=(npoints,2), dtype=np.float32)
+            for i, (x,y) in enumerate(grouper(2, parts[2:])):
+                points[i] = [float(x), float(y)]
+            polygons[idnum] = points
+    return polygons
+
+def read_cassettes(filename):
+    cassettes = []
+    with open(filename) as f:
+        for line in f:
+            parts = line.split()
+            cassette_type = int(parts[0])
+            rotation = np.transpose(np.array(map(float, parts[1:10]), dtype=np.float32).reshape((3,3)))
+            displacement = np.array(map(float, parts[10:13]), dtype=np.float32)
+            
+            cassettes.append({'type' : cassette_type, 'rotation' : rotation,
+                              'displacement' : displacement})
+
+    return cassettes
+
+def build_miniclean(real_av=False):
+    geo = Geometry()
+
+    simple_iv = sphere(0.818)
+    geo.add_solid(Solid(simple_iv, liquid_argon, vacuum, color=0xffFF0000))
+
+    polygons = read_polygons(os.path.join(dir, 'miniclean_polygons.txt'))
+
+    height = 0.30
+    polygon_types = {}
+    for polygon_id, polygon_points in polygons.items():
+        mesh = linear_extrude(polygon_points[::-1,0]/1000.0,
+                              polygon_points[::-1,1]/1000.0,
+                              height=height,
+                              center=[0,0,height/2])
+        colors = np.zeros(len(mesh.triangles), dtype=np.uint32)
+        colors.fill(0x03CCCCFF)
+        # Color the faces on one end
+        triangles = mesh.assemble(group=True)
+        triangle_centroids = triangles.mean(axis=1)
+        face = triangle_centroids[:,2] < 0.1
+        colors[face] = 0xffffff
+
+        polygon_types[polygon_id] = (mesh, colors)
+
+    cassettes = read_cassettes(os.path.join(dir, 'miniclean_cassettes.txt'))
+
+    geo.pmtids = []
+    geo.pmt_id_map = {}
+    for i, cassette in enumerate(cassettes):
+        polygon_mesh, polygon_colors = polygon_types[cassette['type']]
+        solid = Solid(polygon_mesh, liquid_argon, liquid_argon, surface=shiny_surface,
+                      color=polygon_colors)
+
+        chroma_id = geo.add_solid(solid, cassette['rotation'], 
+                                  cassette['displacement']/1000.0)
+        geo.pmt_id_map[chroma_id] = i
+        geo.pmtids.append(chroma_id)
+        
+    return geo
diff --git a/chroma/detectors/miniclean_cassettes.txt b/chroma/detectors/miniclean_cassettes.txt
new file mode 100644
index 0000000..a5e59f2
--- /dev/null
+++ b/chroma/detectors/miniclean_cassettes.txt
@@ -0,0 +1,92 @@
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+3	0.032780	-0.552068	0.833155	-0.262865	-0.809017	-0.525731	0.964275	-0.201774	-0.171639	419.459842	-87.771736	-74.663001
+3	-0.436836	0.893264	-0.106079	0.425326	0.309017	0.850651	0.792636	0.326477	-0.514918	344.796720	142.017520	-223.989388
+3	0.714555	-0.691490	-0.106079	-0.425325	-0.309017	-0.850651	0.555436	0.652955	-0.514918	241.614670	284.035427	-223.989346
+3	-0.984535	-0.139422	-0.106079	-0.162460	0.500000	0.850651	-0.065560	0.854729	-0.514918	-28.518594	371.807049	-223.989304
+3	0.878456	0.465900	-0.106079	0.162460	-0.500000	-0.850651	-0.449358	0.730026	-0.514918	-195.470612	317.561131	-223.989214
+3	-0.171639	-0.979432	-0.106079	-0.525731	-0.000000	0.850651	-0.833155	0.201774	-0.514918	-362.422317	87.771667	-223.989282
+3	-0.171639	0.979432	-0.106079	0.525731	-0.000000	-0.850651	-0.833155	-0.201774	-0.514918	-362.422317	-87.771667	-223.989282
+3	0.878456	-0.465900	-0.106079	-0.162460	-0.500000	0.850651	-0.449358	-0.730026	-0.514918	-195.470612	-317.561131	-223.989214
+3	-0.984535	0.139422	-0.106079	0.162460	0.500000	-0.850651	-0.065560	-0.854729	-0.514918	-28.518594	-371.807049	-223.989304
+3	0.714555	0.691490	-0.106079	0.425325	-0.309017	0.850651	0.555436	-0.652955	-0.514918	241.614670	-284.035427	-223.989346
+3	-0.436836	-0.893264	-0.106079	-0.425326	0.309017	-0.850651	0.792636	-0.326477	-0.514918	344.796720	-142.017520	-223.989388
+3	-0.727076	0.000000	-0.686557	0.000000	1.000000	-0.000000	0.686557	-0.000000	-0.727076	298.652292	0.000000	-316.278056
+3	-0.224679	-0.691490	-0.686557	-0.951056	0.309017	-0.000000	0.212158	0.652955	-0.727076	92.288693	284.035318	-316.277940
+3	0.588217	-0.427365	-0.686557	-0.587785	-0.809017	-0.000000	-0.555436	0.403548	-0.727076	-241.614708	175.543411	-316.278111
+3	0.588217	0.427365	-0.686557	0.587785	-0.809017	-0.000000	-0.555436	-0.403548	-0.727076	-241.614708	-175.543411	-316.278111
+3	-0.224679	0.691490	-0.686557	0.951056	0.309017	-0.000000	0.212158	-0.652955	-0.727076	92.288693	-284.035318	-316.277940
+3	0.939234	0.000000	0.343279	0.000000	-1.000000	-0.000000	0.343279	0.000000	-0.939234	149.326291	0.000000	-408.566590
+3	0.290240	0.893264	0.343278	0.951056	-0.309018	-0.000000	0.106079	0.326477	-0.939234	46.144352	142.017454	-408.566692
+3	-0.759856	0.552068	0.343278	0.587785	0.809017	-0.000000	-0.277718	0.201774	-0.939234	-120.807298	87.771665	-408.566679
+3	-0.759856	-0.552068	0.343278	-0.587785	0.809017	-0.000000	-0.277718	-0.201774	-0.939234	-120.807298	-87.771665	-408.566679
+3	0.290240	-0.893264	0.343278	-0.951056	-0.309018	-0.000000	0.106079	-0.326477	-0.939234	46.144352	-142.017454	-408.566692
diff --git a/chroma/detectors/miniclean_polygons.txt b/chroma/detectors/miniclean_polygons.txt
new file mode 100644
index 0000000..594ed7d
--- /dev/null
+++ b/chroma/detectors/miniclean_polygons.txt
@@ -0,0 +1,3 @@
+1	5	-66.925194	48.624001	25.563150	78.675285	82.724091	0.000000	25.563150	-78.675285	-66.925194	-48.624001
+3	6	-84.296997	48.624001	1.690830	107.301506	87.678658	61.878311	87.678658	-61.878311	1.690830	-107.301506	-84.296997	-48.624001
+2	6	-97.248001	0.000000	-48.624001	84.219238	48.624001	84.219238	97.248001	0.000000	48.624001	-84.219238	-48.624001	-84.219238
diff --git a/chroma/detectors/sno.py b/chroma/detectors/sno.py
new file mode 100644
index 0000000..d5c9ce9
--- /dev/null
+++ b/chroma/detectors/sno.py
@@ -0,0 +1,133 @@
+import numpy as np
+import numpy.linalg
+import math
+from chroma.make import rotate_extrude
+from chroma.stl import mesh_from_stl
+from chroma.geometry import *
+from chroma.optics import *
+from chroma.solids import build_8inch_pmt_with_lc
+from chroma.transform import rotate, make_rotation_matrix
+import os
+
+def sno_vessel(sphere_radius, neck_radius, neck_top, nsteps=40):
+    '''Compute the 2D coordinates of the profile of one side of a 
+    SNO-style acrylic vessel.  The center of the sphere is at (0,0), with
+    the neck extending along the positive y direction.
+    
+       sphere_radius: Radius of spherical part of profile
+       neck_radius: Radius of neck part
+       neck_top: y coordinate of top of neck
+       nsteps: number of points around the circumference of the sphere
+
+       Returns: Tuple of x and y coordinate numpy arrays.
+    '''
+    if neck_radius >= sphere_radius:
+        raise ValueError('neck_radius must be less than sphere_radius')
+
+    intersect_height = (sphere_radius**2 - neck_radius**2)**0.5
+    max_angle = math.atan2(intersect_height, neck_radius)
+
+    if neck_top < intersect_height:
+        raise ValueError('neck_top must be greater than the y-value where the sphere and cylinder intersect')
+
+    # Start with point at bottom
+    angles = np.linspace(-math.pi/2, max_angle, nsteps)
+    x = list(np.cos(angles) * sphere_radius)
+    y = list(np.sin(angles) * sphere_radius)
+    x[0] = 0.0 # Round-off error might make cos(-pi/2) not exactly zero
+    
+    # Neck intersection point
+    x.append(neck_radius)
+    y.append(intersect_height)
+
+    # Top of neck
+    x.append(neck_radius)
+    y.append(neck_top)
+    
+    # Top of neck on axis
+    x.append(0.0)
+    y.append(neck_top)
+    
+    return x, y
+
+##### SNO Parts
+
+nsteps = 40
+av_outside_profile = sno_vessel(sphere_radius=6.0604, neck_radius=0.79375, 
+                                neck_top=10.50, nsteps=nsteps)
+# For simplicity, cap the top of the AV with acrylic
+av_inside_profile  = sno_vessel(sphere_radius=6.0053, neck_radius=0.72898,
+                                neck_top=10.00, nsteps=nsteps)
+
+av_outside_mesh = rotate_extrude(av_outside_profile[0], av_outside_profile[1],
+                                 nsteps)
+av_outside_mesh.vertices = rotate(av_outside_mesh.vertices, np.pi/2, (-1,0,0))
+
+av_inside_mesh = rotate_extrude(av_inside_profile[0], av_inside_profile[1],
+                                 nsteps)
+av_inside_mesh.vertices = rotate(av_inside_mesh.vertices, np.pi/2, (-1,0,0))
+
+dir = os.path.split(os.path.realpath(__file__))[0]
+
+def build_sno(real_av=False):
+    import h5py
+    pmtinfo = h5py.File(dir+'/sno_pmt_info.hdf5')
+
+    pmt = build_8inch_pmt_with_lc()
+
+
+    if real_av:
+        geo = Geometry(water)
+        real_av_mesh = mesh_from_stl(dir+'/sno_av_ascii.stl.bz2')
+        real_av_mesh.vertices *= 0.0254 # inch -> meter
+        geo.add_solid(Solid(real_av_mesh, glass, water, color=0xBBAAAAFF))
+    else:
+        geo = Geometry(water)
+        geo.add_solid(Solid(av_outside_mesh, acrylic_sno, water, 
+                            color=0xBBFFFFFF))
+        geo.add_solid(Solid(av_inside_mesh, water, acrylic_sno, 
+                            color=0xBB0000FF))
+    geo.pmtids = []
+
+    snoman_id_dict = {}
+
+    pmt_offset = 122.0 - 2 * 0.01# max bucket height - 2 * facegap (mm)
+
+    for position, direction, idnum, pmt_type in zip(pmtinfo['pos'], pmtinfo['dir'],
+                                          pmtinfo['snoman_id'],
+                                          pmtinfo['pmt_type']):
+
+        # PMT type codes:
+        #        1 = normal; 2 = OWL; 3 = Low Gain; 4 = BUTT; 5 = Neck
+        #        6 = Calib channel;  10 = spare;  11 = invalid
+        if pmt_type != 1:  # All the other PMTs have nonsense directions
+            continue
+
+        
+        # Flip and renormalize
+        direction *= -1.0/numpy.linalg.norm(direction)
+
+        # Orient PMT that starts facing Y axis
+        y_axis = np.array((0.0,1.0,0.0))
+        axis = np.cross(direction, y_axis)
+        angle = np.arccos(np.dot(y_axis, direction))
+        rotation = make_rotation_matrix(angle, axis)
+
+        # Values in database are for front face of concentrator.
+        # need to shift so position is for equator of PMT
+        if pmt_type == 1:
+            displacement = position - direction * pmt_offset
+        displacement /= 1000.0 # mm -> m
+        chroma_id = geo.add_solid(pmt, rotation, displacement)
+        snoman_id_dict[chroma_id] = idnum
+        geo.pmtids.append(chroma_id)
+
+    # Convert dict to numpy array for fast array remapping later
+    chroma_ids = np.array(snoman_id_dict.keys())
+    snoman_ids = np.array(snoman_id_dict.values())
+    snoman_id_map = np.zeros(max(chroma_ids)+1) - 1 # Fill with -1 everywhere
+    snoman_id_map[chroma_ids] = snoman_ids
+
+    geo.snoman_id_map = snoman_id_map
+        
+    return geo
diff --git a/chroma/detectors/sno_av_ascii.stl.bz2 b/chroma/detectors/sno_av_ascii.stl.bz2
new file mode 100644
index 0000000..1298a60
--- /dev/null
+++ b/chroma/detectors/sno_av_ascii.stl.bz2
diff --git a/chroma/detectors/sno_pmt_info.hdf5 b/chroma/detectors/sno_pmt_info.hdf5
new file mode 100644
index 0000000..1358189
--- /dev/null
+++ b/chroma/detectors/sno_pmt_info.hdf5