def parse_rsml_(organ: ET, polylines: list, properties: dict, functions: dict,
parent: int) -> (list, dict, dict):
""" Recursivly parses the rsml file, used by read_rsml """
for poly in organ.iterfind('geometry'): # only one
polyline = []
for p in poly[0]: # 0 is the polyline
n = p.attrib
newnode = [float(n['x']), float(n['y']), float(n['z'])]
polyline.append(newnode)
polylines.append(polyline)
properties.setdefault("parent-poly", []).append(parent)
for prop in organ.iterfind('properties'):
for p in prop: # i.e legnth, type, etc..
properties.setdefault(str(p.tag),
[]).append(float(p.attrib['value']))
for funcs in organ.iterfind('functions'):
for fun in funcs:
samples = []
for sample in fun.iterfind('sample'):
samples.append(float(sample.attrib['value']))
functions.setdefault(str(fun.attrib['name']), []).append(samples)
pi = len(polylines) - 1
for elem in organ.iterfind('root'): # and all laterals
polylines, properties, functions = parse_rsml_(elem, polylines,
properties, functions,
pi)
return polylines, properties, functions
def parse_rsml_(organ: ET, polylines: list, properties: dict, functions: dict,
parent: int) -> (list, dict, dict):
""" Recursivly parses the rsml file, used by read_rsml """
for poly in organ.iterfind('geometry'): # only one
polyline = []
for p in poly[0]: # 0 is the polyline
n = p.attrib
if len(n) == 3: # RSML is 3D
newnode = [float(n['x']), float(n['y']), float(n['z'])]
else: # RSML is 2D
newnode = [
float(n['x']) / 116.93, 0.0,
-1 * float(n['y']) / 116.93 + 10
] # 116.93 is resolution in pixel/cm TODO: get this info out of RSML if possible
polyline.append(newnode)
polylines.append(polyline)
properties.setdefault("parent-poly", []).append(parent)
for prop in organ.iterfind('properties'):
if len(
list(prop)
) == 2: # special fix for broken .rsml # TODO <--------- Remove after repairs...
properties.setdefault('parent-node', []).append(-1)
for p in prop: # i.e length, type, etc..
if 'value' in p.attrib: # no value defined
try:
properties.setdefault(str(p.tag),
[]).append(float(p.attrib['value']))
except:
properties.setdefault(str(p.tag), []).append(float(np.nan))
else:
try:
properties.setdefault(str(p.tag), []).append(float(p.text))
except:
properties.setdefault(str(p.tag), []).append(float(np.nan))
for funcs in organ.iterfind('functions'):
for fun in funcs:
samples = []
for sample in fun.iterfind('sample'):
if 'value' in sample.attrib:
samples.append(float(sample.attrib['value']))
else:
try:
samples.append(float(sample.text))
except:
samples.append(float(np.nan))
functions.setdefault(str(fun.attrib['name']), []).append(samples)
pi = len(polylines) - 1
for elem in organ.iterfind('root'): # and all laterals
polylines, properties, functions = parse_rsml_(elem, polylines,
properties, functions,
pi)
return polylines, properties, functions
def recipe_etree_to_triples(source, etree):
for recipe in etree.iterfind("recipe"):
key = recipe.attrib['name']
uri_label = el_uri_label(source, recipe)
if uri_label:
uri, label = uri_label
item_uri = tag_uri(ITEMS_SOURCE, key)
# give it a type
yield (uri, RDF.type, source.rdf_type)
# link the item to it's recipe
yield (item_uri, source.ns['recipe'], uri)
for triple in parent_label(uri, source, label):
yield triple
for triple in attrib_to_triples(source, uri, recipe.attrib):
yield triple
for ingredient in recipe.iterfind("ingredient"):
name = ingredient.attrib['name']
ingredient_uri = uri_join(uri, u"ingredient/{name}".format(name=name))
yield (uri, source.ns['ingredient'], ingredient_uri)
item_uri = source_uri(ITEMS_SOURCE, name)
yield (ingredient_uri, SEVEN_NS['Item'], item_uri)
yield (ingredient_uri, SEVEN_NS['count'], Literal(int(ingredient.attrib['count'])))
def parse_rsml_(organ: ET, polylines: list, properties: dict, functions: dict,
parent: int) -> (list, dict, dict):
""" Recursivly parses the rsml file, used by read_rsml """
for poly in organ.iterfind('geometry'): # only one
polyline = []
for p in poly[0]: # 0 is the polyline
n = p.attrib
if len(n) == 3: # RSML is 3D
newnode = [float(n['x']), float(n['y']), float(n['z'])]
else: # RSML is 2D
newnode = [
float(n['x']) / 116.93, 0.0,
-1 * float(n['y']) / 116.93 + 10
] # 116.93 is resolution in pixel/cm TODO: get this info out of RSML if possible
polyline.append(newnode)
polylines.append(polyline)
properties.setdefault("parent-poly", []).append(parent)
for prop in organ.iterfind('properties'):
for p in prop: # i.e legnth, type, etc..
if not p.attrib['value']: # no value defined
properties.setdefault(str(p.tag), []).append(-99)
elif any(c.isalpha() for c in p.attrib['value']):
properties.setdefault(str(p.tag), []).append(-99)
else:
properties.setdefault(str(p.tag),
[]).append(float(p.attrib['value']))
for funcs in organ.iterfind('functions'):
for fun in funcs:
samples = []
for sample in fun.iterfind('sample'):
samples.append(float(sample.attrib['value']))
functions.setdefault(str(fun.attrib['name']), []).append(samples)
pi = len(polylines) - 1
for elem in organ.iterfind('root'): # and all laterals
polylines, properties, functions = parse_rsml_(elem, polylines,
properties, functions,
pi)
return polylines, properties, functions
def etree_to_triples(parent_source, source, etree):
for parent in etree.iterfind('./*/property/..'):
for prop in parent.iterfind('property'):
for triple in prop_to_triples(parent_source, source, parent, prop):
yield triple
