add annotation example #8

DaisukeMiyamoto · Jan 26, 2017 · 774455a · 774455a
1 parent a461afb
commit 774455a
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Showing 2 changed files with 18 additions and 23 deletions.
diff --git a/examples/make_annotation.py b/examples/make_annotation.py
@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+import os
+import swc2vtk
+
+inputfile = 'swc/200000.swc'
+output_dir = '/home/nebula/work/paraview/test_annotation20170126/'
+if not os.path.isdir(output_dir):
+ os.mkdir(output_dir)
+
+vtkgen = swc2vtk.VtkGenerator()
+vtkgen.add_swc(inputfile)
+vtkgen.add_mark((219.430427, 70.454784, 61.439942), size=10)
+vtkgen.write_vtk(os.path.join(output_dir, '200000.vtk'))
+vtkgen.write_annotation_vtk(os.path.join(output_dir, '200000_ano.vtk'))
diff --git a/swc2vtk/vtkgenerator.py b/swc2vtk/vtkgenerator.py
@@ -91,25 +91,6 @@ def add_cylinder(self, pos_x=0, pos_y=0, pos_z=0, radius=1.0, height=1.0, rot_y=
  self.point_list.extend(local_point_list)
  self.cell_list.extend(local_cell_list)
 
- # @staticmethod
- # def add_sphere(x=0, y=0, z=0, size=1.0, data=0.0, point_start=0):
- # # point_start = len(self.point_list)
- #
- # local_cell_list, local_point_list = swc2vtk.GenPrimitives.sphere()
- #
- # for cell in local_cell_list:
- # cell['points'] = [i + point_start for i in cell['points']]
- # cell['data'] = data
- #
- # # scale
- # local_point_list = np.array([ v*[size, size, size] for v in local_point_list])
- # # move
- # local_point_list = np.array([ v+[x, y, z] for v in local_point_list])
- #
- # # self.point_list.extend(local_point_list)
- # # self.cell_list.extend(local_cell_list)
- # return local_cell_list, local_point_list
-
  def add_cylinder_p2p(self, pos1=(0, 0, 0), pos2=(2, 0, 0), size=1.0, data=0, radius_ratio=1.0):
  pos1 = np.array(pos1)
  pos2 = np.array(pos2)
@@ -281,18 +262,18 @@ def add_datafile(self, datafilename):
  def clear_datafile(self):
  self.datafile_list = []
 
- def add_mark(self, pos=(0, 0, 0), data=0.0):
+ def add_mark(self, pos=(0, 0, 0), size=1.0, data=0.0):
  self.annotation_cell_list, self.annotation_point_list = \
- swc2vtk.GenPrimitives.sphere(pos, data, len(self.annotation_cell_list))
+ swc2vtk.GenPrimitives.sphere(pos, size=size, data=data, point_start=len(self.annotation_cell_list))
 
  def add_synapse(self, pre_swc_index, pre_swc_compartment, post_swc_index, post_swc_compartment, diam=0.2):
  pass
 
  def write_annotation_vtk(self, filename):
  with open(filename, 'w') as wfile:
  wfile.write(self.header)
- wfile.write(self.annotation_point_list)
- wfile.write(self.annotation_cell_list)
+ wfile.write(self._point2text(self.annotation_point_list))
+ wfile.write(self._cell2text(self.annotation_cell_list))
 
  def write_swc(self, filename, swc_index=0, comment='swc2vtk'):
  swc = self.swc_list[swc_index]