def export_cb(self):
def save(okay, dialog, self=self):
if okay:
paths = dialog.getPaths()
if paths:
self.write_comma_separated_values(paths[0])
from segment_dialog import current_segmentation
seg = current_segmentation()
if seg is None:
idir = ifile = None
elif hasattr(seg, 'path'):
import os.path
idir, ifile = os.path.split(seg.path)
ifile = os.path.splitext(ifile)[0] + '.csv'
else:
import os.path
idir = None
ifile = os.path.splitext(seg.name)[0] + '.csv'
from OpenSave import SaveModeless
SaveModeless(title='Export Comma Separated Values',
initialdir=idir,
initialfile=ifile,
command=save)
def Update(self):
from segment_dialog import current_segmentation
s = current_segmentation()
if s is None:
return
rlist = self.filter_regions(s.regions)
if rlist is None:
return
self.status('Table has %d regions from %s' % (len(rlist), s.name))
self.add_columns()
self.attribute_table.setData(rlist)
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 add_columns(self):
from segment_dialog import current_segmentation
s = current_segmentation()
if s is None:
return
k = set(self.computed_attributes.keys())
for r in s.regions:
k.update(r.attributes().keys())
knew = list(k.difference(self.keys))
kgone = self.keys.difference(k)
if knew or kgone:
t = self.attribute_table
mreg = t.middleRow()
knew.sort()
for key in knew:
self.add_column(key, refresh=False)
for key in kgone:
t.removeColumn(key, refresh=False)
self.keys = k
t.refresh(rebuild=True)
t.showRow(mreg) # TODO: Adding column loses scroll position.
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)