def test_isolate_type(self):
test_file = pyswc.Swc('test_file.swc')
isolated = pyswc.isolate_type(test_file, [2])
self.assertEqual(isolated.num_nodes, 3)
def test_scale_function(self):
test_file = pyswc.Swc('test_file.swc')
test_file.scale(0.1)
self.assertEqual(round(test_file.data[0][2], 2), -15.39)
def test_surface_area_calculation(self):
test_file = pyswc.Swc('test_file.swc')
isolated = pyswc.isolate_type(test_file, [4])
target = 114.06
self.assertEqual(round(isolated.surface_area, 2), target)
def isolate_type(swc, isolated_labels):
"""
Returns a new swc file that is a copy of the input file with the selected
node isolated and the rest deleted
"""
if not isinstance(swc, pyswc.Swc):
raise TypeError('Must be an instance of the Swc class')
node_number = 0
node_label = 1
node_parent = 6
isolated_nodes = []
# Find all nodes to keep in the output file
for node in range(0, swc.num_nodes):
if swc.data[node, node_label] in isolated_labels:
isolated_nodes.append(swc.data[node, :])
if len(isolated_nodes) == 0:
#print('There are no nodes of type ' + str(isolated_labels))
return 0
old_id = []
new_id = []
# Create two lists, one with the old IDs of the reminaing nodes and one
# with the new IDs, this will be used to reference changes in node ID
for i, node in enumerate(isolated_nodes):
old_id.append(node[0])
new_id.append(i + 1)
# If the node's parent had its ID changed then change the parent number
# If the node's parent was deleted then make it origin (-1)
for i, node in enumerate(isolated_nodes):
node[node_number] = i + 1
if node[node_parent] == -1:
node[node_parent] == -1
elif node[node_parent] in old_id:
node[node_parent] = new_id[old_id.index(node[node_parent])]
else:
node[node_parent] = -1
new_file = 'temp.swc'
f = open(new_file, "w")
new_swc = pyswc.Swc(new_file)
new_swc.data = np.asarray(isolated_nodes)
new_swc.num_nodes = new_swc.data.shape[0]
new_swc.surface_area = new_swc.find_surface_area()
f.close()
os.remove(new_file)
return new_swc
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 11 15:51:00 2020
@author: Owner
"""
import pyswc
swc = pyswc.Swc(
'C:/Users/Owner/Desktop/pySWC-isolate_dendrite/test_files/VCN_c02_Full.swc'
)
swc.rotate(0, 90, 0)
new_swc = pyswc.isolate_type(swc, [
0,
])
new_swc.save_file('rotated_2swc')