update imports in old scripts

conmorph/connections.py

@@ -3,7 +3,7 @@ import graph_tool as gt
 import itertools
 import numpy as np
 
-from conmorph.volume import get_distance_from_to
+from interneuron_polarity.model.morphology.volume import get_distance_from_to
 
 
 class RecurrentInhibition:

conmorph/neurons.py

@@ -2,7 +2,7 @@ import numpy as np
 from tqdm import tqdm
 
 from conmorph.connections import OverlapMatrix
-from conmorph.shapes import get_overlap, distance
+from interneuron_polarity.model.morphology.shapes import get_overlap, distance
 
 
 class NeuronType:

conmorph/test_volume.py

@@ -1,7 +1,7 @@
 from unittest import TestCase
 import numpy as np
 
-from conmorph.volume import get_second_order_distance_cube, mask_invalid_entries
+from interneuron_polarity.model.morphology.volume import get_second_order_distance_cube, mask_invalid_entries
 
 
 class TestVolume(TestCase):

scripts/distance_dependence_first_order_connectivity_recurrent_inhibition.py

@@ -1,9 +1,8 @@
 from conmorph.connections import RecurrentInhibition
 import numpy as np
-import matplotlib.pyplot as plt
 
 from conmorph.util import load_spec
-from conmorph.volume import get_distance_from_to
+from interneuron_polarity.model.morphology.volume import get_distance_from_to
 
 labels=["polar", "circular"]
 

scripts/distance_dependence_second_order_connectivity_recurrent_inhibition.py

@@ -2,7 +2,7 @@ import numpy as np
 
 from conmorph.connections import RecurrentInhibition
 from conmorph.util import load_spec
-from conmorph.volume import get_distance_from_to
+from interneuron_polarity.model.morphology.volume import get_distance_from_to
 
 labels=["polar", "circular"]
 

scripts/generate_overlap_matrices.py

@@ -2,9 +2,9 @@ import numpy as np
 
 from conmorph.connections import save_overlap
 from conmorph.neurons import NeuronType, NeuralTissue
-from conmorph.positions import Uniform, Deterministic, UniformOrientation
-from conmorph.shapes import Ellipsoid, NeuralProcess
-from conmorph.volume import NeuralVolume
+from interneuron_polarity.model.morphology.positions import Uniform, Deterministic, UniformOrientation
+from interneuron_polarity.model.morphology.shapes import Ellipsoid, NeuralProcess
+from interneuron_polarity.model.morphology.volume import NeuralVolume
 
 ### Define the neural volume
 voxel_size = 10

scripts/generate_recurrent_inhibition_connectivity.py

@@ -1,10 +1,9 @@
 import numpy as np
 
 from conmorph.connections import RecurrentInhibition
-from conmorph.positions import Uniform, UniformOrientation
-from conmorph.shapes import Ellipsoid
-from conmorph.volume import NeuralVolume
-import matplotlib.pyplot as plt
+from interneuron_polarity.model.morphology.positions import Uniform, UniformOrientation
+from interneuron_polarity.model.morphology.shapes import Ellipsoid
+from interneuron_polarity.model.morphology.volume import NeuralVolume
 
 ### Define the neural volume
 voxel_size = 10