# Calculate the angle of the current section:
if parent_section:
joining_vec = new_section.get_distal_npa3(
) - parent_section.get_distal_npa3()
angle = math.radians(math.atan2(joining_vec[1],
joining_vec[0]))
section_angles_dict[new_section] = angle
#Save the section:
section_dict[yaml_id] = new_section
# # TODO: THIS IS A HACK! Ensure the dummy node has no attached regions:
# section_dict[None].regions = []
assert section_dict[0].region == None
if section_dict[0].children == []:
raise ValueError("No segments found")
morphs = MorphologyTree(name=name,
dummysection=section_dict[0],
metadata=metadata)
if len(morphs) < 1:
raise ValueError
return morphs
MorphologyImporter.register('fromDictionary',
DictionaryLoader.load,
allow_override=False,
as_type=MorphologyTree)
from morphforge.morphology.core.morphologyarray import MorphologyArray
from morphforge.morphology.core.morphologytree import MorphologyTree
from morphforge.morphology.ui.mayavirenderer import MayaViRenderer
from morphforge.morphology.ui.matplotlibviewer import MatPlotLibViewer
from morphforge.morphology.importer.morphologyimporter import MorphologyImporter
from morphforge.morphology.exporter.morphologyexporter import MorphologyExporter
from morphforge.morphology.comparison.comparearrays import MorphArrayComparison
from morphforge.morphology.builders.morphologyloader import MorphologyLoader
m = MorphologyImporter.fromSWCFile(filename="/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc", astype=MorphologyTree)
MorphologyExporter.toSWCFile(morphology = m, filename="/home/michael/Desktop/test1.swc")
m2 = MorphologyImporter.fromSWCFile(filename="/home/michael/Desktop/test1.swc", astype=MorphologyTree)
#m2 = MorphologyLoader.fromSWC(src=open("/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc"))
0].getAttribute("y"), pNode[0].getAttribute("z")
p_diamR = pNode[0].getAttribute("diameter")
# I do not understand MorphML to understand why these checks do not fail....
#print (p_xR, p_yR, p_zR)
#print (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
#assert (p_xR, p_yR, p_zR) == (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# In this case, use the diameter just read:
p_x, p_y, p_z = p_xR, p_yR, p_zR
p_diam = p_diamR
else:
assert False
print id, name, cable, parent, (p_x, p_y, p_z,
p_diam), (d_x, d_y, d_z, d_diam)
infTuple = (id, name, cable, parent, (float(p_x), float(p_y),
float(p_z), float(p_diam)),
(float(d_x), float(d_y), float(d_z), float(d_diam)))
assert not id in segmentListInfo
segmentListInfo[id] = infTuple
# Now we have read the file and created the dictionaries:
return (cableIDToRegionName, segmentListInfo)
MorphologyImporter.register(method_name='fromMorphML',
import_functor=MorphMLLoader.load,
as_type=MorphologyTree)
# I do not understand MorphML to understand why these checks do not fail....
# print (p_xR, p_yR, p_zR)
# print (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# assert (p_xR, p_yR, p_zR) == (parent_Dist_Loc[0], parent_Dist_Loc[1], parent_Dist_Loc[2])
# In this case, use the diameter just read:
p_x, p_y, p_z = p_xR, p_yR, p_zR
p_diam = p_diamR
else:
assert False
print id, name, cable, parent, (p_x, p_y, p_z, p_diam), (d_x, d_y, d_z, d_diam)
infTuple = (
id,
name,
cable,
parent,
(float(p_x), float(p_y), float(p_z), float(p_diam)),
(float(d_x), float(d_y), float(d_z), float(d_diam)),
)
assert not id in segmentListInfo
segmentListInfo[id] = infTuple
# Now we have read the file and created the dictionaries:
return (cableIDToRegionName, segmentListInfo)
MorphologyImporter.register(method_name="fromMorphML", import_functor=MorphMLLoader.load, as_type=MorphologyTree)
lines = [line.strip() for line in src.readlines()]
lines = [line for line in lines if line and line[0] != '#']
# Break into sections where we get a new parent:
splits = [[]]
for line in lines:
if int(line.split()[-1]) == -1:
splits.append([])
splits[-1].append(line)
splits = splits[1:]
data_blocks = ['\n'.join(blk) for blk in splits]
file_objs = [StringIO(blk) for blk in data_blocks]
morphs = [cls.load_swc_single(src=fobj) for fobj in file_objs]
return morphs
# To Array:
MorphologyImporter.register('fromSWC', NewSWCLoader.load_swc_single, as_type=MorphologyArray)
# To Tree:
def _load_swc_single_tree(*args, **kwargs):
return NewSWCLoader.load_swc_single(*args, **kwargs).to_tree()
MorphologyImporter.register('fromSWC', _load_swc_single_tree, as_type=MorphologyTree)
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
# ----------------------------------------------------------------------
from morphforge.morphology.core.morphologyarray import MorphologyArray
from morphforge.morphology.core.morphologytree import MorphologyTree
from morphforge.morphology.ui.mayavirenderer import MayaViRenderer
from morphforge.morphology.ui.matplotlibviewer import MatPlotLibViewer
from morphforge.morphology.importer.morphologyimporter import MorphologyImporter
from morphforge.morphology.exporter.morphologyexporter import MorphologyExporter
from morphforge.morphology.comparison.comparearrays import MorphArrayComparison
from morphforge.morphology.builders.morphologyloader import MorphologyLoader
m = MorphologyImporter.fromSWCFile(
filename=
"/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc",
astype=MorphologyTree)
MorphologyExporter.toSWCFile(morphology=m,
filename="/home/michael/Desktop/test1.swc")
m2 = MorphologyImporter.fromSWCFile(filename="/home/michael/Desktop/test1.swc",
astype=MorphologyTree)
#m2 = MorphologyLoader.fromSWC(src=open("/home/michael/workspace/morphforge/src/test_data/swc_srcs/28o_spindle20aFI.CNG.swc"))
are_same = MorphArrayComparison.are_same(m, m2)
print are_same
#m = MorphologyLoader2.loadSWCFile(filename="/home/michael/workspace/morphforge/src/test_data/swc_srcs/05b_pyramidal9aACC.CNG_short.swc", astype=MorphologyTree)
else:
newSection = Section(x=xyz[0], y=xyz[1], z=xyz[2], r=rad, region=None, idTag=sectionIdTag)
sectionDict[None] = newSection
# Calculate the angle of the current section:
if parentSection:
joiningVec = newSection.getDistalNPA3() - parentSection.getDistalNPA3()
angle = math.radians(math.atan2(joiningVec[1], joiningVec[0]))
sectionAnglesDict[newSection] = angle
#Save the section:
sectionDict[yamlID] = newSection
## TODO: THIS IS A HACK! Ensure the dummy node has no attached regions:
#sectionDict[None].regions = []
assert sectionDict[0].region == None
if sectionDict[0].children == []: raise ValueError("No segments found")
c = MorphologyTree(name=name, dummysection=sectionDict[0], metadata=metaData)
if len(c) < 1: raise ValueError
return c
MorphologyImporter.register("fromDictionary", DictionaryLoader.Load, allow_override=False, as_type=MorphologyTree)
