def load_roifile(self):
"""Load ROI definitions from self.roifile.
"""
# Check if file exists
if not os.path.exists(self.roifile):
print("ROI file %s doesn't exist.." % self.roifile)
return
# Create basic VertexData to avoid expensive initialization..
empty = VertexData(None, self.subject)
# Load ROIs from file
if self.roifile.endswith("npz"):
roidata = np.load(self.roifile)
for roi in roidata.keys():
self.rois[roi] = empty.copy(roidata[roi])
roidata.close()
elif self.roifile.endswith("svg"):
pts, polys = surfs.getSurf(self.subject, "flat", merge=True, nudge=True)
npts = len(pts)
svgroipack = get_roipack(self.roifile, pts, polys)
for name in svgroipack.names:
roimask = np.zeros((npts,))
roimask[svgroipack.get_roi(name)] = 1
self.rois[name] = empty.copy(roimask)
elif self.roifile.endswith("hf5"):
raise NotImplementedError
else:
raise ValueError("Don't understand ROI filetype: %s" % self.roifile)
def load_roifile(self):
"""Load ROI definitions from self.roifile.
"""
# Check if file exists
if not os.path.exists(self.roifile):
print("ROI file %s doesn't exist.." % self.roifile)
return
# Create basic VertexData to avoid expensive initialization..
empty = VertexData(None, self.subject)
# Load ROIs from file
if self.roifile.endswith("npz"):
roidata = np.load(self.roifile)
for roi in roidata.keys():
self.rois[roi] = empty.copy(roidata[roi])
roidata.close()
elif self.roifile.endswith("svg"):
pts, polys = surfs.getSurf(self.subject,
"flat",
merge=True,
nudge=True)
npts = len(pts)
svgroipack = get_roipack(self.roifile, pts, polys)
for name in svgroipack.names:
roimask = np.zeros((npts, ))
roimask[svgroipack.get_roi(name)] = 1
self.rois[name] = empty.copy(roimask)
elif self.roifile.endswith("hf5"):
raise NotImplementedError
else:
raise ValueError("Don't understand ROI filetype: %s" %
self.roifile)
def to_svg(self, open_inkscape=False, filename=None):
"""Generate SVG file from vertex ROI masks.
"""
# Generate temp filename if not provided
if filename is None:
filename = tempfile.mktemp(suffix=".svg",
prefix=self.subject + "-rois-")
mpts, mpolys = surfs.getSurf(self.subject,
"flat",
merge=True,
nudge=True)
svgmpts = mpts[:, :2].copy()
svgmpts -= svgmpts.min(0)
svgmpts *= 1024 / svgmpts.max(0)[1]
svgmpts[:, 1] = 1024 - svgmpts[:, 1]
npts = len(mpts)
svgroipack = get_roipack(filename, mpts, mpolys)
# Add default layers
# Add curvature
from matplotlib import cm
curv = VertexData(np.hstack(get_curvature(self.subject)), self.subject)
fp = cStringIO.StringIO()
curvim = quickflat.make_png(fp,
curv,
height=1024,
with_rois=False,
with_labels=False,
with_colorbar=False,
cmap=cm.gray,
recache=True)
fp.seek(0)
svgroipack.add_roi("curvature",
binascii.b2a_base64(fp.read()),
add_path=False)
# Add thickness
# Add ROI boundaries
svg = etree.parse(svgroipack.svgfile, parser=parser)
# Find boundary vertices for each ROI
lsurf, rsurf = [
Surface(*pp) for pp in surfs.getSurf(self.subject, "fiducial")
]
flsurf, frsurf = [
Surface(*pp) for pp in surfs.getSurf(self.subject, "flat")
]
valids = [set(np.unique(flsurf.polys)), set(np.unique(frsurf.polys))]
# Construct polygon adjacency graph for each surface
polygraphs = [lsurf.poly_graph, rsurf.poly_graph]
for roi in self.rois.keys():
print("Adding %s.." % roi)
masks = self.rois[roi].left, self.rois[roi].right
mmpts = svgmpts[:len(masks[0])], svgmpts[len(masks[0]):]
roilayer = _make_layer(_find_layer(svg, "rois"), roi)
for valid, pgraph, surf, mask, mmp in zip(valids, polygraphs,
[lsurf, rsurf], masks,
mmpts):
if mask.sum() == 0:
continue
# Find bounds
inbound, exbound = surf.get_boundary(np.nonzero(mask)[0])
# Find polys
allbpolys = np.unique(surf.connected[inbound +
exbound].indices)
selbpolys = surf.polys[allbpolys]
inpolys = np.in1d(selbpolys, inbound).reshape(selbpolys.shape)
expolys = np.in1d(selbpolys, exbound).reshape(selbpolys.shape)
badpolys = np.logical_or(inpolys.all(1), expolys.all(1))
boundpolys = np.logical_and(
np.logical_or(inpolys, expolys).all(1), ~badpolys)
# Walk around boundary
boundpolyinds = set(allbpolys[np.nonzero(boundpolys)[0]])
bgraph = nx.Graph()
pos = dict()
for pa in boundpolyinds:
for pb in set(pgraph[pa]) & boundpolyinds:
edge = pgraph[pa][pb]["verts"]
validverts = list(valid & edge)
pos[edge] = mmp[validverts].mean(0)
bgraph.add_edge(*edge)
cc = nx.cycles.cycle_basis(bgraph)
if len(cc) > 1:
edges = reduce(set.symmetric_difference, [
set(
map(lambda l: tuple(sorted(l)),
zip(c, c[1:] + [c[0]]))) for c in cc
])
eg = nx.from_edgelist(edges)
cycles = nx.cycles.cycle_basis(eg)
longest = np.argmax(map(len, cycles))
path_order = cycles[longest]
else:
path_order = cc[0]
path_points = [
tuple(pos[frozenset(p)])
for p in zip(path_order[:-1], path_order[1:])
]
# Store poly
path = "M %f %f L" % tuple(path_points[0])
path += ", ".join(["%f %f" % p for p in path_points[1:]])
path += "Z "
# Insert into SVG
svgpath = etree.SubElement(roilayer, "path")
svgpath.attrib[
"style"] = "fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opactiy:1"
svgpath.attrib["d"] = path
#svgpath.attrib["sodipodi:nodetypes"] = "c" * len(pts)
with open(svgroipack.svgfile, "w") as xml:
xml.write(etree.tostring(svg, pretty_print=True))
def to_svg(self, open_inkscape=False, filename=None):
"""Generate SVG file from vertex ROI masks.
"""
# Generate temp filename if not provided
if filename is None:
filename = tempfile.mktemp(suffix=".svg", prefix=self.subject+"-rois-")
mpts, mpolys = surfs.getSurf(self.subject, "flat", merge=True, nudge=True)
svgmpts = mpts[:,:2].copy()
svgmpts -= svgmpts.min(0)
svgmpts *= 1024 / svgmpts.max(0)[1]
svgmpts[:,1] = 1024 - svgmpts[:,1]
npts = len(mpts)
svgroipack = get_roipack(filename, mpts, mpolys)
# Add default layers
# Add curvature
from matplotlib import cm
curv = VertexData(np.hstack(get_curvature(self.subject)), self.subject)
fp = io.BytesIO()
curvim = quickflat.make_png(fp, curv, height=1024, with_rois=False, with_labels=False,
with_colorbar=False, cmap=cm.gray,recache=True)
fp.seek(0)
svgroipack.add_roi("curvature", binascii.b2a_base64(fp.read()), add_path=False)
# Add thickness
# Add ROI boundaries
svg = etree.parse(svgroipack.svgfile, parser=parser)
# Find boundary vertices for each ROI
lsurf, rsurf = [Surface(*pp) for pp in surfs.getSurf(self.subject, "fiducial")]
flsurf, frsurf = [Surface(*pp) for pp in surfs.getSurf(self.subject, "flat")]
valids = [set(np.unique(flsurf.polys)), set(np.unique(frsurf.polys))]
# Construct polygon adjacency graph for each surface
polygraphs = [lsurf.poly_graph, rsurf.poly_graph]
for roi in self.rois.keys():
print("Adding %s.." % roi)
masks = self.rois[roi].left, self.rois[roi].right
mmpts = svgmpts[:len(masks[0])], svgmpts[len(masks[0]):]
roilayer = _make_layer(_find_layer(svg, "rois"), roi)
for valid, pgraph, surf, mask, mmp in zip(valids, polygraphs,
[lsurf, rsurf], masks, mmpts):
if mask.sum() == 0:
continue
# Find bounds
inbound, exbound = surf.get_boundary(np.nonzero(mask)[0])
# Find polys
allbpolys = np.unique(surf.connected[inbound+exbound].indices)
selbpolys = surf.polys[allbpolys]
inpolys = np.in1d(selbpolys, inbound).reshape(selbpolys.shape)
expolys = np.in1d(selbpolys, exbound).reshape(selbpolys.shape)
badpolys = np.logical_or(inpolys.all(1), expolys.all(1))
boundpolys = np.logical_and(np.logical_or(inpolys, expolys).all(1), ~badpolys)
# Walk around boundary
boundpolyinds = set(allbpolys[np.nonzero(boundpolys)[0]])
bgraph = nx.Graph()
pos = dict()
for pa in boundpolyinds:
for pb in set(pgraph[pa]) & boundpolyinds:
edge = pgraph[pa][pb]["verts"]
validverts = list(valid & edge)
pos[edge] = mmp[validverts].mean(0)
bgraph.add_edge(*edge)
cc = nx.cycles.cycle_basis(bgraph)
if len(cc) > 1:
# Need to deal with this later: map/reduce calls not python3 compatible
edges = reduce(set.symmetric_difference,
[set(map(lambda l:tuple(sorted(l)), zip(c, c[1:]+[c[0]]))) for c in cc])
eg = nx.from_edgelist(edges)
cycles = nx.cycles.cycle_basis(eg)
#longest = np.argmax(map(len, cycles))
longest = np.argmax([len(x) for x in cycles]) # python3 compatible
path_order = cycles[longest]
else:
path_order = cc[0]
path_points = [tuple(pos[frozenset(p)]) for p in zip(path_order[:-1],
path_order[1:])]
# Store poly
path = "M %f %f L" % tuple(path_points[0])
path += ", ".join(["%f %f"%p for p in path_points[1:]])
path += "Z "
# Insert into SVG
svgpath = etree.SubElement(roilayer, "path")
svgpath.attrib["style"] = "fill:none;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opactiy:1"
svgpath.attrib["d"] = path
#svgpath.attrib["sodipodi:nodetypes"] = "c" * len(pts)
with open(svgroipack.svgfile, "w") as xml:
xml.write(etree.tostring(svg, pretty_print=True))