def main():
testSrcsPath = LocMgr().get_test_srcs_path()
srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc")
srcSWCFile = "/home/michael/Desktop/ply/forPly/aIN 471 nrn + ns 100325.transl.invX.scaled.straightened.swc"
morphs = NewSWCLoader.load_swc_set(src=open(srcSWCFile))
m = morphs[0]
m = m.to_tree()
mesh = MeshFromGTS.build(m)
def include_file(self, filename, options):
src_obj = self.global_scope.getFileObjRead(filename)
morphs = NewSWCLoader.load_swc_set(src=src_obj)
# Hack: only first:
# morphs = [morphs[0]]
for m in morphs:
m = m.to_tree()
# Create the color LUT:
bi_dict = m.region_number_to_name_bidict
rgn_colors = {}
for rgn in m.get_regions():
rgn_name = rgn.name
rgn_int = bi_dict.region_name_to_int(rgn_name)
rgn_color = self.get_region_color(rgn_int)
print '%s -> %s' % (rgn_name, rgn_int), rgn_color
rgn_colors[rgn_name] = rgn_color
# Check for ignored Region:
if None in rgn_colors.values():
for v in rgn_colors.values():
if v is not None:
print 'Partly ignoring Structure:',
for (k, v) in rgn_colors.iteritems():
print k, v
assert False, 'Partly ignored structure!'
continue
# Apply the options:
if 'trim' in options:
m = AxonTrimmer.trim_axon_from_morphology(
m, max_dist_to_parent=options['trim'])
if 'offset' in options:
m = MorphologyTranslator.translate(morphology=m,
offset=options['offset'])
if self.global_scope.has_option_set(
MeshGenerationOptions.minimum_diameter):
m = MorphologyMinimumDiameter.ensure(
m,
min_diameter=self.global_scope.get_option(
MeshGenerationOptions.minimum_diameter))
mesh = MeshFromGTS.build(m,
plot=False,
region_color_map=rgn_colors)
self.meshes.append(mesh)
def include_file(self, filename, options):
src_obj = self.global_scope.getFileObjRead(filename)
morphs = NewSWCLoader.load_swc_set(src=src_obj)
# Hack: only first:
# morphs = [morphs[0]]
for m in morphs:
m = m.to_tree()
# Create the color LUT:
bi_dict = m.region_number_to_name_bidict
rgn_colors = {}
for rgn in m.get_regions():
rgn_name = rgn.name
rgn_int = bi_dict.region_name_to_int(rgn_name)
rgn_color = self.get_region_color(rgn_int)
print '%s -> %s' % (rgn_name, rgn_int), rgn_color
rgn_colors[rgn_name] = rgn_color
# Check for ignored Region:
if None in rgn_colors.values():
for v in rgn_colors.values():
if v is not None:
print 'Partly ignoring Structure:',
for (k, v) in rgn_colors.iteritems():
print k, v
assert False, 'Partly ignored structure!'
continue
# Apply the options:
if 'trim' in options:
m = AxonTrimmer.trim_axon_from_morphology(m,
max_dist_to_parent=options['trim'])
if 'offset' in options:
m = MorphologyTranslator.translate(morphology=m,
offset=options['offset'])
if self.global_scope.has_option_set(MeshGenerationOptions.minimum_diameter):
m = MorphologyMinimumDiameter.ensure(m,
min_diameter=self.global_scope.get_option(MeshGenerationOptions.minimum_diameter))
mesh = MeshFromGTS.build(m, plot=False,
region_color_map=rgn_colors)
self.meshes.append(mesh)
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (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.core import LocMgr, Join from morphforge.morphology.ui import MatPlotLibViewer from morphforge.morphology.core import MorphologyTree from morphforgecontrib.indev.highqualitymesh.create_mesh import MeshFromGTS from morphforge.morphology.importer.import_array_swc import NewSWCLoader testSrcsPath = LocMgr().get_test_srcs_path() srcSWCFile = Join(testSrcsPath, "swc_srcs/28o_spindle20aFI.CNG.swc") srcSWCFile = "/home/michael/Desktop/ply/forPly/aIN 471 nrn + ns 100325.transl.invX.scaled.straightened.swc" morphs = NewSWCLoader.load_swc_set(src=open(srcSWCFile)) m = morphs[0] m = m.to_tree() mesh = MeshFromGTS.build(m) # MatPlotLibViewer(m, use_pca=False)
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (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.core import LocMgr, Join from morphforge.morphology.ui import MatPlotLibViewer from morphforge.morphology.core import MorphologyTree from morphforgecontrib.indev.highqualitymesh.create_mesh import MeshFromGTS from morphforge.morphology.importer.import_array_swc import NewSWCLoader testSrcsPath = LocMgr().get_test_srcs_path() srcSWCFile = Join(testSrcsPath, 'swc_srcs/28o_spindle20aFI.CNG.swc') srcSWCFile = '/home/michael/Desktop/ply/forPly/aIN 471 nrn + ns 100325.transl.invX.scaled.straightened.swc' morphs = NewSWCLoader.load_swc_set(src=open(srcSWCFile)) m = morphs[0] m = m.to_tree() mesh = MeshFromGTS.build(m) # MatPlotLibViewer(m, use_pca=False)