def subvol_list(structType, model):
#use dictionaries to store voxels corresponding to regions, region_classes (e.g. head) or regions/structures
region_list = decode(model['regions'])
region_dict = OrderedDict()
region_struct_dict = OrderedDict()
#create dictionary of voxels and volumes for each region
reg_voxel = omdict((zip(model['grid'][:]['region'],
range(len(model['grid'])))))
reg_voxel_vol = omdict((zip(model['grid'][:]['region'],
model['grid'][:]['volume'])))
for regnum in reg_voxel.keys():
region_dict[region_list[regnum]] = {
'vox': reg_voxel.allvalues(regnum),
'vol': sum(reg_voxel_vol.allvalues(regnum))
}
# for regions of more than one type, create dictionary of voxels and volumes for each type of each region
if len(np.unique(
model['grid'][reg_voxel.allvalues(regnum)]['type'])) > 1:
types = decode(model['grid'][reg_voxel.allvalues(regnum)]['type'])
struct_voxels = omdict((zip(types, reg_voxel.allvalues(regnum))))
struct_vox_vol = omdict((zip(types,
reg_voxel_vol.allvalues(regnum))))
for struct in struct_voxels.keys():
depth = model['grid'][struct_voxels.allvalues(
struct)]['y0'] - model['grid'][struct_voxels.allvalues(
struct)]['y2']
#Depth is an array. For submemb, only a single value, for cyt - different values. Presently only storing one of the values
key = region_list[regnum] + struct[0:3]
region_struct_dict[key] = {
'vox': struct_voxels.allvalues(struct),
'depth': depth[0],
'vol': sum(struct_vox_vol.allvalues(struct))
}
return region_list, region_dict, region_struct_dict
def _load_one_model(filepath):
lineNo = 0
top_def = None
cur_def = None
with open(filepath, 'r+t') as strm:
for line in strm:
lineNo += 1
# Strip out any comment
pos = line.find('#')
if pos >= 0:
line = line[:pos]
line = line.strip()
if not line: # empty line, ignore!
continue
m = re.match('^[-]*\s*(?P<key>\w+)\s*:\s*(?P<value>.+)$', line)
if not m:
print(f'Failed to parse {filepath}:{lineNo}')
continue # TODO(HS): Should this be an error?
key = m.group('key').strip()
value = m.group('value').strip()
if key in [ 'obj_def', 'class_def', 'group_def' ]:
top_def = orderedmultidict.omdict([
('type', key),
('name', value),
('extends', None),
('subclasses', set()),
])
cur_def = top_def
elif key in ['name']:
cur_def['vpiname'] = value
elif key in ['extends']:
top_def[key] = value
elif key in ['property', 'class_ref', 'obj_ref', 'group_ref', 'class']:
cur_def = orderedmultidict.omdict([
('type', key),
('name', value),
])
top_def.add(key, cur_def)
elif key in ['type', 'card', 'vpi', 'vpi_obj']:
cur_def[key] = value
else:
print(f'Found unknown key "{key}" at {filepath}:{lineNo}')
return top_def
def __init__(self, type): # @ReservedAssignment
super(NamedObjectMap, self).__init__()
self.type = type
self._data = omdict()
if not issubclass(type, NamedObject):
raise TypeError("type must be a NamedObject")
def __init__(self, file):
self.file = file
# Start processing the file at line 2, ie. the first
# non-header line.
self.linenr = 2
# Maintain a backlog of Lines that we know we will need later
# on from some file
self.backlog = omdict()
def multi_spines(model):
spine_dict=OrderedDict()
#create list of spine voxels
#first identify all spine voxels and spine labels
groups=model['grid'][:]['group']
newgroups=list()
for n,i in enumerate(groups):
#in python3 must explicitly decode from byte to string
if type(i) is np.bytes_:
groups[n]=i.decode('UTF-8')
newgroups.append(i.decode('UTF-8'))
if newgroups[n] =='':
newgroups[n]='nonspine'
groups=newgroups
spine_voxel=omdict((zip(groups,range(len(model['grid'])) ) ))
spine_voxel_vol=omdict(( zip(groups,model['grid'][:]['volume']) ))
#create a unique set of spine labels
newspinelist=spine_voxel.keys()
for spinenum,spine in enumerate(newspinelist):
spine_dict[spine]={'vox':spine_voxel.allvalues(spine), 'vol': sum(spine_voxel_vol.allvalues(spine))}
return newspinelist,spine_dict
def _parse_query(self):
# type: () -> URI
query = self.query if self.query is not None else ""
query_dict = omdict()
queries = query.split("&")
query_items = []
for q in queries:
key, _, val = q.partition("=")
val = unquote_plus(val.replace("+", " "))
query_items.append((key, val))
query_dict.load(query_items)
return attr.evolve(self, query_dict=query_dict, query=query)
def test_normalize_params_omdict():
"""
Order is guaranteed for omdicts.
"""
from orderedmultidict import omdict
dct = omdict()
dct['q'] = 'office'
dct['facet'] = 'on'
dct.add('facet.field', 'network')
dct.add('facet.field', 'runtime')
tuples = normalize_params(dct)
assert tuples == [('q', 'office'), ('facet', 'on'),
('facet.field', 'network'), ('facet.field', 'runtime')]
def __setitem__(self, key, value):
if not isinstance(value, self.type):
raise TypeError("can only add " + self.type.__name__ + " objects")
if isinstance(key, six.integer_types):
self._data = omdict([
(value.name, value) if i == key else (k, v)
for i, (k, v) in enumerate(six.iteritems(self._data))
])
else:
if value.name != key:
raise ValueError("key does not match name of " +
self.type.__name__)
self._data[key] = value
def test_normalize_params_omdict():
"""
Order is guaranteed for omdicts.
"""
from orderedmultidict import omdict
dct = omdict()
dct['q'] = 'office'
dct['facet'] = 'on'
dct.add('facet.field', 'network')
dct.add('facet.field', 'runtime')
tuples = normalize_params(dct)
assert tuples == [('q', 'office'),
('facet', 'on'),
('facet.field', 'network'),
('facet.field', 'runtime')]
def _parse_query(self):
# type: () -> URI
query = self.query if self.query is not None else ""
query_dict = omdict()
queries = query.split("&")
query_items = []
subdirectory = self.subdirectory if self.subdirectory else None
for q in queries:
key, _, val = q.partition("=")
val = unquote_plus(val.replace("+", " "))
if key == "subdirectory" and not subdirectory:
subdirectory = val
else:
query_items.append((key, val))
query_dict.load(query_items)
return attr.evolve(
self, query_dict=query_dict, subdirectory=subdirectory, query=query
)
def test_update_updateall(self):
data, omd1, omd2 = omdict(), OneDimensionalOrderedMultidict(), OneDimensionalOrderedMultidict()
# All permutations of (self.keys, self.values) and (self.keys,
# self.valuelists).
allitems = chain(product(self.keys, self.values),
product(self.keys, self.valuelists))
# All updates of length one item, two items, and three items.
iterators = [permutations(allitems, 1),
permutations(allitems, 2),
permutations(allitems, 3),
permutations(allitems, 4),
]
for iterator in iterators:
for update in iterator:
data.update(update)
omd1.update(update)
omd2.updateall(update)
for key in omd1.iterkeys():
if isinstance(data[key], list):
assert omd1[key] == data[key][-1]
else:
assert omd1[key] == data[key]
for key in omd2.iterkeys():
data_values_unpacked = []
for value in data.getlist(key):
if isinstance(value, list):
data_values_unpacked.extend(value)
else:
data_values_unpacked.append(value)
assert omd2.getlist(key) == data_values_unpacked
# Test different empty list value locations.
update_tests = [([(1, None), (2, None)],
[(1, [1, 11]), (2, [2, 22])],
[(1, 11), (2, 22)]),
([(1, None), (2, None)],
[(1, []), (1, 1), (1, 11)],
[(1, 11), (2, None)]),
([(1, None), (2, None)],
[(1, 1), (1, []), (1, 11)],
[(1, 11), (2, None)]),
([(1, None), (2, None)],
[(1, 1), (1, 11), (1, [])],
[(2, None)]),
]
for init, update, result in update_tests:
omd = OneDimensionalOrderedMultidict(init)
omd.update(update)
assert omd.allitems() == result
updateall_tests = [([(1, None), (2, None)],
[(1, [1, 11]), (2, [2, 22])],
[(1, 1), (2, 2), (1, 11), (2, 22)]),
([(1, None), (2, None)],
[(1, []), (1, 1), (1, 11)],
[(1, 1), (2, None), (1, 11)]),
([(1, None), (2, None)],
[(1, 1), (1, []), (1, 11)],
[(1, 11), (2, None)]),
([(1, None), (2, None)],
[(1, 1), (1, 11), (1, [])],
[(2, None)]),
]
for init, update, result in updateall_tests:
omd = OneDimensionalOrderedMultidict(init)
omd.updateall(update)
assert omd.allitems() == result
def __init__(self, groupdb):
self.groupdb = groupdb
self.initial_groups = omdict()
self.new_groups = omdict()
def test_update_updateall(self):
data, omd1, omd2 = omdict(), omdict1D(), omdict1D()
# All permutations of (self.keys, self.values) and (self.keys,
# self.valuelists).
allitems = chain(product(self.keys, self.values),
product(self.keys, self.valuelists))
# All updates of length one item, two items, and three items.
iterators = [
permutations(allitems, 1),
permutations(allitems, 2),
permutations(allitems, 3),
permutations(allitems, 4),
]
for iterator in iterators:
for update in iterator:
data.update(update)
omd1.update(update)
omd2.updateall(update)
for key in omd1.iterkeys():
if isinstance(data[key], list):
assert omd1[key] == data[key][-1]
else:
assert omd1[key] == data[key]
for key in omd2.iterkeys():
data_values_unpacked = []
for value in data.getlist(key):
if isinstance(value, list):
data_values_unpacked.extend(value)
else:
data_values_unpacked.append(value)
assert omd2.getlist(key) == data_values_unpacked
# Test different empty list value locations.
update_tests = [
([(1, None), (2, None)], [(1, [1, 11]), (2, [2, 22])], [(1, 11),
(2, 22)]),
([(1, None), (2, None)], [(1, []), (1, 1), (1, 11)], [(1, 11),
(2, None)]),
([(1, None), (2, None)], [(1, 1), (1, []), (1, 11)], [(1, 11),
(2, None)]),
([(1, None), (2, None)], [(1, 1), (1, 11), (1, [])], [(2, None)]),
]
for init, update, result in update_tests:
omd = omdict1D(init)
omd.update(update)
assert omd.allitems() == result
updateall_tests = [
([(1, None), (2, None)], [(1, [1, 11]), (2, [2, 22])], [(1, 1),
(2, 2),
(1, 11),
(2, 22)]),
([(1, None), (2, None)], [(1, []), (1, 1), (1, 11)], [(1, 1),
(2, None),
(1, 11)]),
([(1, None), (2, None)], [(1, 1), (1, []), (1, 11)], [(1, 11),
(2, None)]),
([(1, None), (2, None)], [(1, 1), (1, 11), (1, [])], [(2, None)]),
]
for init, update, result in updateall_tests:
omd = omdict1D(init)
omd.updateall(update)
assert omd.allitems() == result
def clear(self):
self._data = omdict()
def __init__(self, groupdb):
self.groupdb = groupdb
self.initial_groups = omdict()
self.new_groups = omdict()
#---------------------------------------- Preprocess test file sentences
preprocessed_sentences = []
test_trees = []
for sentence in test_sentences:
processed = preprocess(sentence.split())
preprocessed_sentences.append(processed)
test_trees.append(cp.parse(processed))
#------------------------------ Create annotated test sentences both ways
dictionary_parsed_sentences = []
i = 0
spec_case = 0
for sentence, tree in zip(preprocessed_sentences, test_trees):
sentence_dict = omdict()
neural_sentence = ""
for word_tuple in sentence:
sentence_dict.add(word_tuple[0], "O")
neural_sentence = neural_sentence + " " + word_tuple[0]
for subtree in tree.subtrees(lambda t: t.label() == "NP"):
probab = {
"per": 0,
"event": 0,
"geo": 0,
"org": 0,
"obj": 0,
"gpe": 0,
"time": 0
}
