def segmentation(self):
import segment_dialog as sd
s = sd.current_segmentation()
if s is None and sd.segmentation_map():
d = sd.volume_segmentation_dialog()
s = d.Segment(group=False)
for r in s.regions:
r.set_color(self.ungrouped_color)
v = s.volume_data()
if v:
v.display = False
if s is None:
print 'mouse down: no current segmentation'
return None
return s
def Icos2Map0(self):
dmap = segmentation_map()
if dmap == None:
self.umsg("Select a map in Segment Map dialog")
return
mm = dmap.full_matrix()
#m1 = numpy.zeros_like ( mm )
# transform to index reference frame of ref_map
f1 = dmap.data.ijk_to_xyz_transform
nm = numpy.zeros_like(mm)
minr, maxr = 300, 400
pt = numpy.array([[0, 0, 0]], numpy.float32)
p = pt[0]
im, jm, km = dmap.data.size[0] / 2, dmap.data.size[
1] / 2, dmap.data.size[2] / 2
for i in range(dmap.data.size[0]):
self.status("Masking %s %.1f->%.1f, %d/%d" %
(dmap.name, minr, maxr, i + 1, dmap.data.size[0]))
di = abs(i - im) * dmap.data.step[0]
for j in range(dmap.data.size[1]):
dj = abs(j - jm) * dmap.data.step[1]
for k in range(dmap.data.size[2]):
dk = abs(k - km) * dmap.data.step[2]
r = numpy.sqrt(di * di + dj * dj + dk * dk)
if dk >= minr and dk < maxr:
nm[k, j, i] = mm[k, j, i]
ndata = VolumeData.Array_Grid_Data(nm, dmap.data.origin,
dmap.data.step,
dmap.data.cell_angles)
try:
nvg = VolumeViewer.volume.add_data_set(ndata, None)
except:
nvg = VolumeViewer.volume.volume_from_grid_data(ndata)
nvg.name = dmap.name + "__%.0f--to--%.0f" % (minr, maxr)
def Icos2Map0(self):
smod = self.GetMod("Icosahedron Faces")
if smod == None:
self.umsg("No Icosahedron2 model found")
return
dmap = segmentation_map()
if dmap == None:
self.umsg("Select a map in Segment Map dialog")
return
sepRs = self.segRads.get().split(",")
print "Sep rads:", sepRs
if len(sepRs) != 2:
self.umsg("Enter two radii separated by a comma")
return
try:
start_rad = int(sepRs[0])
except:
self.umsg("Invalid start radius: " + sepRs[0])
return
try:
end_rad = int(sepRs[1])
except:
self.umsg("Invalid end radius: " + sepRs[1])
return
if end_rad <= start_rad:
self.umsg("End rad should be larger than start rad :) ")
return
self.umsg("Mask %s, %d -> %d" % (dmap.name, start_rad, end_rad))
self.MakeTNorms(smod)
import time
start = time.time()
mm = dmap.full_matrix()
#m1 = numpy.zeros_like ( mm )
# transform to index reference frame of ref_map
f1 = dmap.data.ijk_to_xyz_transform
from _contour import affine_transform_vertices as transform_vertices
#f2 = xform_matrix ( mask_map.openState.xform )
#f3 = xform_matrix ( ref_map.openState.xform.inverse() )
#f4 = ref_map.data.xyz_to_ijk_transform
#tf = multiply_matrices( f2, f1 )
#tf = multiply_matrices( f3, tf )
#tf = multiply_matrices( f4, tf )
nm = numpy.zeros_like(mm)
self.updateIcos2(start_rad)
minr, maxr = self.MinRad2(smod), self.MaxRad2(smod)
print " - start rad %d -- min rad %.1f, max rad %.1f" % (
start_rad, numpy.sqrt(minr), numpy.sqrt(maxr))
done = time.time()
elapsed = done - start
print "Took: ", elapsed
pt = numpy.array([[0, 0, 0]], numpy.float32)
p = pt[0]
for i in range(dmap.data.size[0]):
self.status("Masking %s, outside radius %d, %d/%d" %
(dmap.name, start_rad, i + 1, dmap.data.size[0]))
p[0] = i * f1[0][0] + f1[0][3]
for j in range(dmap.data.size[1]):
p[1] = j * f1[1][1] + f1[1][3]
for k in range(dmap.data.size[2]):
#p[2] = k * f1[2][2] + f1[2][3]
#pt = numpy.array ( [[i,j,k]], numpy.float32 )
#p[0],p[1],p[2] = ti,tj,tk
#transform_vertices ( pt, f1 )
p[2] = k * f1[2][2] + f1[2][3]
ptr = numpy.sum(p * p)
if ptr < minr:
pass
elif ptr > maxr:
nm[k, j, i] = mm[k, j, i]
elif self.PIsOutside(pt[0], smod):
nm[k, j, i] = mm[k, j, i]
self.updateIcos2(end_rad)
minr, maxr = self.MinRad2(smod), self.MaxRad2(smod)
print " - end rad %d -- min rad %.1f, max rad %.1f" % (
start_rad, numpy.sqrt(minr), numpy.sqrt(maxr))
for i in range(dmap.data.size[0]):
self.status("Masking %s, inside radius %d, %d/%d" %
(dmap.name, end_rad, i + 1, dmap.data.size[0]))
p[0] = i * f1[0][0] + f1[0][3]
for j in range(dmap.data.size[1]):
p[1] = j * f1[1][1] + f1[1][3]
for k in range(dmap.data.size[2]):
#pt = numpy.array ( [[i,j,k]], numpy.float32 )
#p[0],p[1],p[2] = ti,tj,tk
#transform_vertices ( pt, f1 )
p[2] = k * f1[2][2] + f1[2][3]
ptr = numpy.sum(p * p)
if ptr < minr:
continue
elif ptr > maxr:
nm[k, j, i] = 0.0
elif self.PIsOutside(p, smod):
nm[k, j, i] = 0.0
ndata = VolumeData.Array_Grid_Data(nm, dmap.data.origin,
dmap.data.step,
dmap.data.cell_angles)
try:
nvg = VolumeViewer.volume.add_data_set(ndata, None)
except:
nvg = VolumeViewer.volume.volume_from_grid_data(ndata)
nvg.name = dmap.name + "__%d--to--%d_fast" % (start_rad, end_rad)
done = time.time()
elapsed = done - start
print "Took: ", elapsed
def Icos2CC(self):
smod = self.GetMod("Icosahedron Faces")
if smod == None:
self.umsg("No Icos2 found")
return
dmap = segmentation_map()
if dmap == None:
self.umsg("No map selected")
return
start_rad, end_rad = 0, 0
try:
start_rad = int(self.startRad.get())
except:
self.umsg("Invalid start radius: " + self.startRad.get())
return
try:
end_rad = int(self.endRad.get())
except:
self.umsg("Invalid end radius: " + self.endRad.get())
return
if end_rad <= start_rad:
self.umsg("End rad should be larger than start rad :) ")
return
self.umsg("CC in %s" % dmap.name)
fname = "IcosCC.txt"
if hasattr(self, 'fi'):
fname = "IcosCC_%d.txt" % self.fi
p1 = smod.icosVerts[smod.icosTris[0][0]]
rS = numpy.sqrt(numpy.sum(p1 * p1))
print " - rad before: ", rS
ccs = []
#fp = open ( fname, "w" )
for rad in range(start_rad, end_rad + 1):
self.updateIcos2(rad)
cc = self.IcosCC(smod, dmap)
self.status("Rad: %d, CC: %.4f" % (rad, cc))
#fp.write ( "%d\t%f\n" % (rad, cc) )
ccs.append([rad, cc])
#fp.close ()
self.updateIcos2(rS)
def save(okay, dialog):
if okay:
paths = dialog.getPaths()
if paths:
path = paths[0]
self.umsg("Saved CCs to: " + path)
f = open(path, "w")
for rad, cc in ccs:
f.write("%d\t%f\n" % (rad, cc))
f.close()
from OpenSave import SaveModeless
SaveModeless(title='Save Cross Correlations',
filters=[('TXT', '*.txt', '.txt')],
initialfile="rad_cc.txt",
command=save)
def LineCC(self):
dmap = segmentation_map()
if dmap == None:
umsg("No map selected")
return
from chimera import Molecule
mlist = OML(modelTypes=[Molecule])
if len(mlist) == 0:
umsg("No molecule found")
return
mol = mlist[0]
print "Doing line CC in " + dmap.name + " using mol " + mol.name
print dmap.openState.xform
print mol.openState.xform
rccs = []
rmap = None
rmap_pos = None
rpoints, rpoint_weights = None, None
xf = None
resolution = 10.0
for ri, res in enumerate(mol.residues):
try:
cat = res.atomsMap["CA"][0]
except:
continue
if rmap == None:
rmap = makeMap("#%d:%d@CA" % (mol.id, res.id.position),
resolution, 1, (.5, .5, .5, 1.0), "resmap")
rmap_pos = cat.coord().toVector()
print " - sphere map pos ", rmap_pos
#rpoints, rpoint_weights = fit_points (rmap)
rpoints, rpoint_weights = fit_points_old(rmap)
xf = rmap.openState.xform
break
for radi in range(0, 1300, 1):
#d = cat.coord() - rmap_pos
d = chimera.Vector(0, 0, radi) - rmap_pos
#print chimera.Vector(0,0,radi)
trx = chimera.Xform.translation(d)
#xf = dmap.openState.xform.inverse
xf2 = xf.__copy__()
xf2.multiply(trx)
rmap.openState.xform = xf2
break
if 1:
rmap_values = dmap.interpolated_values(rpoints, xf2)
olap, corr = overlap_and_correlation(rpoint_weights,
rmap_values)
if radi % 100 == 0:
print " %d - overlap: %f, cross-correlation: %f" % (
radi, olap, corr)
rccs.append([radi, corr])
#print corr,
#chimera.openModels.close ( rmap )
fp = open("lineCC.txt", "w")
for rad, cc in rccs:
fp.write("%d\t%f\n" % (rad, cc))
fp.close()
def Segment2(self):
dmap = segmentation_map()
if dmap == None:
self.umsg("Please select a map in the Segment Map Dialog")
return
smod = current_segmentation()
if smod == None:
self.umsg(
"Please select a Current Segmentation in the Segment Map dialog"
)
return
print "Seg has %d regions" % (len(smod.regions))
imod2 = self.GetMod("Icosahedron Faces")
if imod2 == None:
self.umsg("No Icosahedron2 model found")
return
sepRs = []
for rstr in self.segRads.get().split(","):
try:
radv = float(rstr)
except:
self.umsg(
"Error parsing distances; enter only numbers and commas")
return
sepRs.append(radv)
print "Sep rads:", sepRs
regs = list(smod.regions)
sregs = []
f1 = dmap.data.ijk_to_xyz_transform
from _contour import affine_transform_vertices as transform_vertices
self.MakeTNorms(imod2)
for i, srad in enumerate(sepRs):
self.umsg("Segmenting using %s - rad %.1f - %d regs" %
(imod2.name, srad, len(regs)))
self.updateIcos2(srad)
gregs, left_regs = [], []
for ri, r in enumerate(regs):
p = r.max_point
#pt = numpy.array ( [ [ p[2],p[1],p[0] ] ], numpy.float32 )
pt = numpy.array([[p[2], p[1], p[0]]], numpy.float32)
transform_vertices(pt, f1)
c = r.center_of_points()
ptc = numpy.array([c], numpy.float32)
#print ri, p, c, pt[0]
#return
if self.PIsOutside(ptc[0], imod2):
#print " - outside"
left_regs.append(r)
else:
#print " - inside"
gregs.append(r)
if ri % 1000 == 0:
self.status("Segmenting using %s - rad %.1f - %s/%s regs" %
(imod2.name, srad, "{:,}".format(ri),
"{:,}".format(len(regs))))
sregs.append(gregs)
regs = left_regs
print " - rad %.1f - %d regions inside" % (srad, len(gregs))
print " - remaining %d regions" % (len(regs))
sregs.append(regs)
for i, regs in enumerate(sregs):
self.status("Segmenting, layer %d - %d regs" % (i, len(regs)))
if len(regs) > 1:
try:
smod.join_regions(regs)
except:
self.umsg(
"An error occurred - regions may have changed - please start again."
)
smod.display_regions()
return
smod.display_regions()
self.umsg("Done, created %d groups based on radial distances" %
len(sregs))
from segment_dialog import volume_segmentation_dialog
volume_segmentation_dialog().ReportRegionCount(smod)
def Segment(self):
segMap = segmentation_map()
if segMap == None:
self.umsg("Please select a map in the Segment Map Dialog")
return
smod = current_segmentation()
if smod == None:
self.umsg(
"Please select a Current Segmentation in the Segment Map dialog"
)
return
print "Seg has %d regions" % (len(smod.regions))
print "Seg rads:", self.segRads.get()
if hasattr(self, 'distByReg'):
print "Found distByReg"
else:
self.umsg("Make Histogram first.")
return
sepRs = []
for rstr in self.segRads.get().split(","):
try:
radv = float(rstr)
except:
self.umsg(
"Error parsing distances; enter only numbers and commas")
return
sepRs.append(radv)
sepRs.append(1e99)
self.umsg("Segmenting...")
print "Sep rads:", sepRs
sregs = []
for r in sepRs:
sregs.append([])
for reg, rad in self.distByReg.iteritems():
#if reg.surface_piece != None :
# if reg.surface_piece.display == False :
# continue
minRad = 0.0
for i, maxRad in enumerate(sepRs):
if rad > minRad and rad <= maxRad:
sregs[i].append(reg)
break
for i, regs in enumerate(sregs):
print "%d - %d regs" % (i, len(regs))
if len(regs) > 1:
try:
smod.join_regions(regs)
except:
self.umsg(
"An error occurred - regions may have changed - please start again."
)
smod.display_regions()
return
smod.display_regions()
self.umsg("Done, created %d groups based on radial distances" %
len(sregs))
from segment_dialog import volume_segmentation_dialog
volume_segmentation_dialog().ReportRegionCount(smod)
def MakeHist(self):
segMap = segmentation_map()
if segMap == None:
self.umsg("Please select a map in the Segment Map Dialog")
return
import axes
reload(axes)
pts, weights = axes.map_points(segMap)
print len(pts)
COM, U, S, V = prAxes(pts)
print " - COM : ", COM
smod = current_segmentation()
if smod == None:
self.umsg(
"Please select a Current Segmentation in the Segment Map dialog"
)
return
print "Seg has %d regions" % (len(smod.regions))
if hasattr(self, 'icos_vecs'):
self.umsg("Making (icosahedrally corrected) histogram...")
else:
self.umsg("Making histogram...")
nregs, last = len(smod.regions), 0
regs = list(smod.regions)
distByReg = {}
for ri, r in enumerate(regs):
if 0 and r.surface_piece != None:
if r.surface_piece.display == False:
print "i" + ri,
continue
try:
p = r.center_of_points()
except:
print "+"
continue
rvec = chimera.Vector(p[0], p[1], p[2]) - chimera.Vector(
COM[0], COM[1], COM[2])
rad = 0.0
if hasattr(self, 'icos_vecs'):
for ivec in self.icos_vecs:
irad = ivec * rvec
if irad > rad:
rad = irad
else:
rad = rvec.length
distByReg[r] = rad
at = int(numpy.floor(10.0 * (ri + 1) / nregs))
if at > last:
#print at,
if hasattr(self, 'icos_vecs'):
self.status(
"Making (icosahedrally corrected) histogram %d regions, at %d"
% (len(regs), ri + 1))
else:
self.status("Making histogram %d regions, at %d" %
(len(regs), ri + 1))
last = at
at += 1
print ""
dists = distByReg.values()
maxDist = max(dists) + 0.01
minDist = min(dists)
nbins = int(self.numBins.get())
dr = (maxDist - minDist) / float(nbins)
print "%d dists - max %.2f, min %.2f, nb %d, dr %.2f" % (
len(dists), maxDist, minDist, nbins, dr)
bins = []
for i in range(nbins):
bins.append([])
print "bad bins: ",
for regm, rad in distByReg.iteritems():
bini = int(numpy.floor((rad - minDist) / dr))
if bini >= len(bins):
print bini,
bini = len(bins) - 1
bins[bini].append(regm)
print ""
if 0:
f = open("rads.txt", "w")
for k, regs in enumerate(bins):
v = len(regs)
vmin = minDist + k * dr
vmax = minDist + (k + 1) * dr
rm = .5 * (vmin + vmax)
vn = v / (4 * 3.14 * rm * rm)
f.write("%d\t%.2f\t%.2f\t%d\t%f\n" % (k, vmin, vmax, v, vn))
f.close()
self.distByReg = distByReg
#print self.distByReg
def save(okay, dialog):
if okay:
paths = dialog.getPaths()
if paths:
path = paths[0]
self.umsg("Saved plot to: " + path)
f = open(path, "w")
for k, regs in enumerate(bins):
v = len(regs)
vmin = minDist + k * dr
vmax = minDist + (k + 1) * dr
rm = .5 * (vmin + vmax)
vn = v / (4 * 3.14 * rm * rm)
f.write("%.2f,%d\n" % (vmin, v))
f.close()
from OpenSave import SaveModeless
SaveModeless(title='Save Histogram',
filters=[('TXT', '*.txt', '.txt')],
initialfile="dist_hist.txt",
command=save)