def test_get_leaf(self):
d = {}
set_leaf(d, ['b1', 'b2', 'b3.1'], 'theLeaf1')
set_leaf(d, ['b1', 'b2', 'b3.2'], 'theLeaf2')
l1 = get_leaf(d, ['b1', 'b2', 'b3.1'])
l2 = get_leaf(d, ['b1', 'b2', 'b3.2'])
return l2
def test_get_leaf(self):
d = {}
set_leaf(d, ['b1', 'b2', 'b3.1'], 'theLeaf1')
set_leaf(d, ['b1', 'b2', 'b3.2'], 'theLeaf2')
l1 = get_leaf(d, ['b1', 'b2', 'b3.1'])
l2 = get_leaf(d, ['b1', 'b2', 'b3.2'])
return l2
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 test_rearrange(self):
d1 = {}
set_leaf(d1, ['1', '2.1', 'o1'], 'c1')
set_leaf(d1, ['1', '2.1', 'o2'], 'c2')
set_leaf(d1, ['1', '2.2', 'o1'], 'c3')
set_leaf(d1, ['1', '2.2', 'o2'], 'c4')
blabels = ['p1', 'p2', 'outname']
nblabels = ['outname', 'p1', 'p2']
tree_rearrange(d1, blabels, nblabels)
def test_rearrange(self):
d1 = {}
set_leaf(d1, ['1', '2.1', 'o1'], 'c1')
set_leaf(d1, ['1', '2.1', 'o2'], 'c2')
set_leaf(d1, ['1', '2.2', 'o1'], 'c3')
set_leaf(d1, ['1', '2.2', 'o2'], 'c4')
blabels = ['p1', 'p2', 'outname']
nblabels = ['outname', 'p1', 'p2']
tree_rearrange(d1, blabels, nblabels)
def test_tree_to_xndarray(self):
from pyhrf.ndarray import xndarray, tree_to_xndarray
from pyhrf.tools import set_leaf
d1 = {}
set_leaf(d1, ['1', '2.1', '3.1'], xndarray(np.array([1])))
set_leaf(d1, ['1', '2.1', '3.2'], xndarray(np.array([2])))
set_leaf(d1, ['1', '2.2', '3.1'], xndarray(np.array([3])))
set_leaf(d1, ['1', '2.2', '3.2'], xndarray(np.array([3.1])))
d2 = {}
set_leaf(d2, ['1', '2.1', '3.1'], xndarray(np.array([10])))
set_leaf(d2, ['1', '2.1', '3.2'], xndarray(np.array([11])))
set_leaf(d2, ['1', '2.2', '3.1'], xndarray(np.array([12])))
set_leaf(d2, ['1', '2.2', '3.2'], xndarray(np.array([13])))
d = {'d1': d1, 'd2': d2}
labels = ['case', 'p1', 'p2', 'p3']
c = tree_to_xndarray(d, labels)
self.assertEqual(c.data.shape, (2, 1, 2, 2, 1))
npt.assert_array_equal(c.axes_domains['case'], ['d1', 'd2'])
npt.assert_array_equal(c.axes_domains['p1'], ['1'])
npt.assert_array_equal(c.axes_domains['p2'], ['2.1', '2.2'])
npt.assert_array_equal(c.axes_domains['p3'], ['3.1', '3.2'])
def test_stack_trees(self):
d1 = {}
set_leaf(d1, ['b1', 'b2.1', 'b3.1'], 'd1Leaf1')
set_leaf(d1, ['b1', 'b2.1', 'b3.2'], 'd1Leaf2')
set_leaf(d1, ['b1', 'b2.2', 'b3.3'], 'd1Leaf3')
d2 = {}
set_leaf(d2, ['b1', 'b2.1', 'b3.1'], 'd2Leaf1')
set_leaf(d2, ['b1', 'b2.1', 'b3.2'], 'd2Leaf2')
set_leaf(d2, ['b1', 'b2.2', 'b3.3'], 'd2Leaf3')
def test_walk_branches(self):
d = {}
set_leaf(d, ['b1', 'b2.1', 'b3.1'], 'theLeaf1')
set_leaf(d, ['b1', 'b2.1', 'b3.2'], 'theLeaf2')
set_leaf(d, ['b1', 'b2.2', 'b3.3'], 'theLeaf3')
def test_set_leaf(self):
d = {}
set_leaf(d, ['b1', 'b2', 'b3'], 'theLeaf')
def test_stack_trees(self):
d1 = {}
set_leaf(d1, ['b1', 'b2.1', 'b3.1'], 'd1Leaf1')
set_leaf(d1, ['b1', 'b2.1', 'b3.2'], 'd1Leaf2')
set_leaf(d1, ['b1', 'b2.2', 'b3.3'], 'd1Leaf3')
d2 = {}
set_leaf(d2, ['b1', 'b2.1', 'b3.1'], 'd2Leaf1')
set_leaf(d2, ['b1', 'b2.1', 'b3.2'], 'd2Leaf2')
set_leaf(d2, ['b1', 'b2.2', 'b3.3'], 'd2Leaf3')
def test_walk_branches(self):
d = {}
set_leaf(d, ['b1', 'b2.1', 'b3.1'], 'theLeaf1')
set_leaf(d, ['b1', 'b2.1', 'b3.2'], 'theLeaf2')
set_leaf(d, ['b1', 'b2.2', 'b3.3'], 'theLeaf3')
def test_set_leaf(self):
d = {}
set_leaf(d, ['b1', 'b2', 'b3'], 'theLeaf')
def test_tree_to_xndarray(self):
from pyhrf.ndarray import xndarray, tree_to_xndarray
from pyhrf.tools import set_leaf
d1 = {}
set_leaf(d1, ['1', '2.1', '3.1'], xndarray(np.array([1])))
set_leaf(d1, ['1', '2.1', '3.2'], xndarray(np.array([2])))
set_leaf(d1, ['1', '2.2', '3.1'], xndarray(np.array([3])))
set_leaf(d1, ['1', '2.2', '3.2'], xndarray(np.array([3.1])))
d2 = {}
set_leaf(d2, ['1', '2.1', '3.1'], xndarray(np.array([10])))
set_leaf(d2, ['1', '2.1', '3.2'], xndarray(np.array([11])))
set_leaf(d2, ['1', '2.2', '3.1'], xndarray(np.array([12])))
set_leaf(d2, ['1', '2.2', '3.2'], xndarray(np.array([13])))
d = {'d1': d1, 'd2': d2}
labels = ['case', 'p1', 'p2', 'p3']
c = tree_to_xndarray(d, labels)
self.assertEqual(c.data.shape, (2, 1, 2, 2, 1))
npt.assert_array_equal(c.axes_domains['case'], ['d1', 'd2'])
npt.assert_array_equal(c.axes_domains['p1'], ['1'])
npt.assert_array_equal(c.axes_domains['p2'], ['2.1', '2.2'])
npt.assert_array_equal(c.axes_domains['p3'], ['3.1', '3.2'])
def set_option(self, option_def, option_value):
set_leaf(self.options, option_def, option_value)
if option_def == ('view_mode',):
self.switch_color_dialog()
self.on_draw()
def outputResults_old(self, results, output_dir, filter='.\A',
historyFlag=False):
""" Return a dictionnary mapping output names to cuboid objects
"""
from pyhrf.boldsynth.spatialconfig import xndarrayMapper1D
filter = re.compile(filter)
pyhrf.verbose(1,'Building outputs ...')
pyhrf.verbose(6, 'results :')
pyhrf.verbose.printDict(6, results, exclude=['xmlHandler'])
for i,r in enumerate(results):
# print 'i:', i
# print 'r:', r
if r[1] is None:
results.pop(i)
nbROI = len(results)
if nbROI == 0: #Nothing ...
print 'No result found, everything crashed?'
return None
pyhrf.verbose(1, '%s ROI(s)' %(nbROI))
resultTree = {}
roiMapperTree = {}
target_shape = results[0][0].spatial_shape
meta_data = results[0][0].meta_obj
if len(target_shape) == 3: #Volumic data:
targetAxes = MRI3Daxes#['axial','coronal', 'sagittal']
else: #surfacic
targetAxes = ['voxel']
pyhrf.verbose(1,'Get each ROI output ...')
for roiData,result,report in results:
roiId = roiData.get_roi_id()
roiMapper = xndarrayMapper1D(maskToMapping(roiData.roiMask==roiId),
target_shape, targetAxes, 'voxel')
if report == 'ok':
if not isinstance(result, dict):
outs = result.getOutputs()
else:
outs = result
set_leaf(resultTree,[roiId], outs)
set_leaf(roiMapperTree,[roiId], roiMapper)
else:
pyhrf.verbose(1, '-> Sampling crashed, roi %d!' %roiId)
pyhrf.verbose(2, report)
if len(resultTree) == 0:
return None
pyhrf.verbose(1,'Joining outputs ...')
outputs = {}
outputs = stack_trees(resultTree.values())
roiList = resultTree.keys()
topop = []
for on, cubList in outputs.iteritems():
pyhrf.verbose(4, "Treating output: " + on + "...")
if not filter.match(on):
try:
outputs[on] = self.joinOutputs(cubList, roiList,
roiMapperTree)
except Exception, e:
print 'Could not join outputs for', on
print 'Exception was:'
print e
topop.append(on)
else:
print on, 'filtered!'
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
