def appendParametersToDOMTree(self, doc, node):
if self.cuboid is not None:
if 0:
print ""
print "Appending to DOM tree:"
print "- parameters :"
print self.parameters
print "- cuboid descrip:"
print self.cuboid.descrip()
lu = max([self.longest_underscore(an) for an in self.cuboid.getAxesNames()])
lud = 0
for d in self.cuboid.getAxesDomains():
if "str" in d.dtype.name:
lud = max([self.longest_underscore(v) for v in d])
sep = "_" * (max([lud, lu]) + 1)
if self.cuboid.is_nii_writable():
fn0 = op.join(self.outDir, self.parameters["name"] + ".nii")
eaxes, fns = writexndarrayToNiftii(self.cuboid, fn0, sep=sep)
fns = fns.values()
elif self.cuboid.getNbDims() <= 2:
eaxes = []
fns = [op.join(self.outDir, self.parameters["name"] + ".csv")]
self.cuboid.save(fns[0])
else:
eaxes = []
fns = [op.join(self.outDir, self.parameters["name"] + ".h5")]
self.cuboid.save(fns[0])
self.parameters["dataFiles"] = fns
self.parameters["explodedAxes"] = eaxes
# print 'eaxes:', eaxes
XMLParamDrivenClass.appendParametersToDOMTree(self, doc, node)
def __init__(self, parameters=None, xmlHandler=NumpyXMLHandler(), xmlLabel=None, xmlComment=None):
XMLParamDrivenClass.__init__(self, parameters, xmlHandler, xmlLabel, xmlComment)
clabel = self.parameters["name"]
ad = self.parameters["domains"]
an = self.parameters["orientation"]
vlab = self.parameters["value_label"]
fl = self.parameters["dataFiles"]
eaxes = self.parameters["explodedAxes"]
self.outDir = "./"
# print ''
# print 'clabel:', clabel
# print 'eaxes :', eaxes
# print 'an:', an
if len(fl) > 0:
ed = dict(zip(eaxes, [ad[ea] for ea in eaxes]))
if len(eaxes) > 0:
iaxes = list(set(an).difference(eaxes))
else:
iaxes = an
idomains = dict(zip(iaxes, [ad[ia] for ia in iaxes]))
ctree = {}
if 0:
print "fl:", fl
print "id:", idomains
print "iaxes:", iaxes
print "ad:", ad
print "ed:", ed
print "eaxes:", eaxes
if len(eaxes) > 0:
for fn in fl:
n = os.path.splitext(os.path.basename(fn))[0]
blabels, bvals = self.slice_idx_from_filename(n, clabel)
if 0:
print "blabels:", blabels
print "bvals:", bvals
print "fn:", fn
cdata = self.load_cuboid(fn, iaxes, vlab, idomains)
# print 'ctree:'
# print ctree
# print 'cdata:', cdata
set_leaf(ctree, bvals, cdata)
self.cuboid = tree_to_cuboid(ctree, branchLabels=blabels)
else:
self.cuboid = self.load_cuboid(fl[0], iaxes, vlab, idomains)
self.cuboid.set_orientation(an)
else:
self.cuboid = None
def appendParametersToDOMTree(self, doc, node):
if self.savexndarray:
if self.cuboid is not None:
if 0:
print ""
print "Appending to DOM tree:"
print "- parameters :"
print self.parameters
print "- cuboid descrip:"
print self.cuboid.descrip()
sep = "_"
if self.cuboid.is_nii_writable():
fn0 = op.join(self.outDir, self.parameters["name"] + ".nii")
pyhrf.verbose(3, "Writing cuboid for %s ..." % self.parameters["name"])
eaxes, slicefns = writexndarrayToNiftii(self.cuboid, fn0, sep=sep, meta_data=self.meta_data)
pyhrf.verbose(3, "Written cuboid for %s" % self.parameters["name"])
elif self.cuboid.getNbDims() <= 2:
eaxes = []
fn = op.join(self.outDir, self.parameters["name"] + ".csv")
# slicefns = { ('_','_') : fn }
slicefns = {None: fn}
self.cuboid.save(fn)
else:
eaxes = []
fn = op.join(self.outDir, self.parameters["name"] + ".h5")
# slicefns = { ('_','_') : fn }
slicefns = {None: fn}
self.cuboid.save(fn)
for s, f in slicefns.iteritems():
if self.useRelativePath:
slicefns[s] = op.join("./", op.basename(f))
else:
slicefns[s] = op.abspath(f)
self.parameters["dataFiles"] = slicefns
self.parameters["explodedAxes"] = eaxes
# print 'eaxes:', eaxes
XMLParamDrivenClass.appendParametersToDOMTree(self, doc, node)
else:
raise Exception("No cuboid to save")
else:
XMLParamDrivenClass.appendParametersToDOMTree(self, doc, node)
def __init__(self, parameters=None, xmlHandler=NumpyXMLHandler(), xmlLabel=None, xmlComment=None):
if 0:
print "xndarrayXml2.__init__ ..."
XMLParamDrivenClass.__init__(self, parameters, xmlHandler, xmlLabel, xmlComment)
clabel = self.parameters["name"]
ad = self.parameters["domains"]
an = self.parameters["orientation"]
vlab = self.parameters["value_label"]
fl = self.parameters["dataFiles"]
eaxes = self.parameters["explodedAxes"]
self.outDir = "./"
self.meta_data = None
# print ''
# print 'clabel:', clabel
# print 'eaxes :', eaxes
# print 'an:', an
if len(fl) > 0 and self.loadxndarray:
ed = dict(zip(eaxes, [ad[ea] for ea in eaxes]))
if len(eaxes) > 0:
iaxes = []
for a in an:
if a not in eaxes:
iaxes.append(a)
# iaxes = list(set(an).difference(eaxes))
else:
iaxes = an
idomains = dict(zip(iaxes, [ad[ia] for ia in iaxes]))
ctree = {}
if 0:
print "fl:", fl
print "id:", idomains
print "iaxes:", iaxes
print "ad:", ad
print "ed:", ed
print "eaxes:", eaxes
if len(eaxes) > 0:
for slice, fn in fl.iteritems():
slice = list(slice)
if 0:
print "slice:", slice
print "fn:", fn
if slice is not None:
if "_" in slice:
slice.remove("_")
if "_" in slice:
slice.remove("_")
cdata = self.load_cuboid(fn, iaxes, vlab, idomains)
# print 'ctree:'
# print ctree
# print 'cdata:', cdata
set_leaf(ctree, list(slice), cdata)
self.cuboid = tree_to_cuboid(ctree, branchLabels=eaxes)
else:
self.cuboid = self.load_cuboid(fl.values()[0], iaxes, vlab, idomains)
self.cuboid.set_orientation(an)
else:
self.cuboid = None
self.useRelativePath = False