Fix circuilar imports

vascpy/conversion.py

@@ -21,9 +21,9 @@
 import numpy as np
 import pandas as pd
 
+import vascpy.point_vasculature
+import vascpy.section_vasculature
 from vascpy import specs
-from vascpy.point_vasculature import PointVasculature
-from vascpy.section_vasculature import SectionVasculature
 from vascpy.utils.geometry import unique_points
 
 # from vascpy.section_graph.io import save_section_graph_data
@@ -83,7 +83,7 @@ def convert_section_to_point_vasculature(section_vasculature):
  columns=[t.name for t in SPEC.EDGE_PROPERTIES],
  )
 
- return PointVasculature(node_properties, edge_properties)
+ return vascpy.point_vasculature.PointVasculature(node_properties, edge_properties)
 
 
 def convert_point_to_section_vasculature(point_vasculature): # pylint: disable=R0914,R0915
@@ -169,7 +169,7 @@ def _section_point_indices(edge_list):
  h5f.create_dataset("structure", data=structure, dtype=SPEC.STRUCTURE)
  h5f.create_dataset("connectivity", data=chain_connectivity, dtype=SPEC.CONNECTIVITY)
 
- section_vasculature = SectionVasculature.load(filename)
+ section_vasculature = vascpy.section_vasculature.SectionVasculature.load(filename)
 
  return section_vasculature
 

vascpy/point_vasculature.py

@@ -21,6 +21,7 @@
 import numpy as np
 import pandas as pd
 
+import vascpy.conversion
 from vascpy.exceptions import VasculatureAPIError
 from vascpy.point_graph import features, io
 from vascpy.utils.adjacency import AdjacencyMatrix
@@ -130,11 +131,12 @@ def n_edges(self):
  @property
  def adjacency_matrix(self):
  """Returns sparse adjacency matrix of the nodes"""
-
  return AdjacencyMatrix(self.edges, n_vertices=self.n_nodes)
 
  def remove(
- self, node_indices: Optional[np.ndarray] = None, edge_indices: Optional[np.ndarray] = None
+ self,
+ node_indices: Optional[np.ndarray] = None,
+ edge_indices: Optional[np.ndarray] = None,
  ):
  """
  Remove node and edge indices from the point graph.
@@ -291,10 +293,7 @@ def volume(self):
 
  def as_section_graph(self):
  """Converts the point graph to a section graph"""
- # pylint: disable=import-outside-toplevel
- from vascpy.conversion import convert_point_to_section_vasculature
-
- return convert_point_to_section_vasculature(self)
+ return vascpy.conversion.convert_point_to_section_vasculature(self)
 
 
 def add_section_annotation(point_vasculature, annotation_name, section_ids, segment_ids):
@@ -329,7 +328,10 @@ def add_section_annotation(point_vasculature, annotation_name, section_ids, segm
  old_index = edge_properties.index
 
  edge_properties.index = pd.MultiIndex.from_arrays(
- (edge_properties["section_id"].to_numpy(), edge_properties["segment_id"].to_numpy())
+ (
+ edge_properties["section_id"].to_numpy(),
+ edge_properties["segment_id"].to_numpy(),
+ )
  )
 
  # initialze with -1 if the column doesn't exist

vascpy/section_vasculature.py

@@ -13,16 +13,17 @@
 See the License for the specific language governing permissions and
 limitations under the License.
 """
-from morphio.vasculature import Vasculature
+import morphio.vasculature
 
-from vascpy.section_graph import io
+import vascpy.conversion
+import vascpy.section_graph.io
 
 
 class SectionVasculature:
  """Section representation of graphs"""
 
  def __init__(self, filepath):
- self._graph = Vasculature(filepath)
+ self._graph = morphio.vasculature.Vasculature(filepath)
 
  @classmethod
  def load(cls, filepath):
@@ -56,11 +57,8 @@ def as_point_graph(self):
  Returns:
  Point graph
  """
- # pylint: disable=import-outside-toplevel
- from vascpy.conversion import convert_section_to_point_vasculature
-
- return convert_section_to_point_vasculature(self)
+ return vascpy.conversion.convert_section_to_point_vasculature(self)
 
  def save(self, filepath):
  """Write morphology to file"""
- io.HDF5.write(filepath, self.points, self.diameters, self.sections)
+ vascpy.section_graph.io.HDF5.write(filepath, self.points, self.diameters, self.sections)