Merge branch 'devel'

DaisukeMiyamoto · Jan 29, 2017 · aa6089b · aa6089b
2 parents 0a3fd6b + 77bc7ff
commit aa6089b
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Showing 44 changed files with 691 additions and 104 deletions.
diff --git a/_docs/annotations.rst b/_docs/annotations.rst
@@ -0,0 +1,53 @@
+Draw Annotations
+================
+
+draw annotations like stimulation points, samplings point or synapses.
+
+- :download:`simple.swc<../tests/simple.swc>`
+
+
+Draw marks
+----------
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_mark((1.0, 1.0, 1.0), size=0.5)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_mark.vtk')
+
+
+.. image:: _static/simple_annotation1.png
+
+Draw SWC compartment marks
+--------------------------
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_swc_mark(0, 2, size=0.5)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_swc_mark.vtk')
+
+
+.. image:: _static/simple_annotation2.png
+
+
+Draw Synapses
+-------------
+
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_swc('simple.swc', shift_y=30)
+    vtkgen.add_swc_connection(0, 2, 1, 1, size=0.5, data=2)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_connection.vtk')
+
+
+.. image:: _static/simple_annotation3.png
+
diff --git a/_docs/drawmode.rst b/_docs/drawmode.rst
@@ -11,20 +11,19 @@ Sample Program
 .. code-block:: python
 
     import os
-    from swc2vtk.vtkgenerator import VtkGenerator
+    import swc2vtk
 
     filename = 'simple'
     outputpos = ''
 
-    vtkgen = VtkGenerator()
+    vtkgen = swc2vtk.VtkGenerator()
     vtkgen.add_swc(os.path.join('swc', filename + '.swc'))
 
     for i in range(4):
         vtkgen.set_draw_mode(i)
         vtkgen.write_vtk(os.path.join(outputpos, filename + '_draw'+str(i)+'.vtk'))
 
 
-
 ``draw_mode = 0``
 -----------------
 

diff --git a/_docs/index.rst b/_docs/index.rst
@@ -13,6 +13,7 @@ Welcome to swc2vtk's documentation!
    examples
    drawmode
    volume
+   annotations
    gallery
    apis/modules
 

diff --git a/_docs/volume.rst b/_docs/volume.rst
@@ -15,7 +15,7 @@ Sample Code
 .. code-block:: python
 
     import swc2vtk
-    vtkgen = VtkGenerator()
+    vtkgen = swc2vtk.VtkGenerator()
     vtkgen.add_swc('simple.swc'))
     vtkgen.write_volume_vtk('simple.vtk', origin=(-10.0, -10.0, -10.0), ratio=(1, 1, 1), div=(20, 20, 20))
 

diff --git a/docs/.doctrees/annotations.doctree b/docs/.doctrees/annotations.doctree
diff --git a/docs/.doctrees/apis/swc2vtk.doctree b/docs/.doctrees/apis/swc2vtk.doctree
diff --git a/docs/.doctrees/drawmode.doctree b/docs/.doctrees/drawmode.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/gallery.doctree b/docs/.doctrees/gallery.doctree
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/readme.doctree b/docs/.doctrees/readme.doctree
diff --git a/docs/.doctrees/volume.doctree b/docs/.doctrees/volume.doctree
diff --git a/docs/_images/simple_annotation1.png b/docs/_images/simple_annotation1.png
diff --git a/docs/_images/simple_annotation2.png b/docs/_images/simple_annotation2.png
diff --git a/docs/_images/simple_annotation3.png b/docs/_images/simple_annotation3.png
diff --git a/docs/_sources/annotations.rst.txt b/docs/_sources/annotations.rst.txt
@@ -0,0 +1,53 @@
+Draw Annotations
+================
+
+draw annotations like stimulation points, samplings point or synapses.
+
+- :download:`simple.swc<../tests/simple.swc>`
+
+
+Draw marks
+----------
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_mark((1.0, 1.0, 1.0), size=0.5)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_mark.vtk')
+
+
+.. image:: _static/simple_annotation1.png
+
+Draw SWC compartment marks
+--------------------------
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_swc_mark(0, 2, size=0.5)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_swc_mark.vtk')
+
+
+.. image:: _static/simple_annotation2.png
+
+
+Draw Synapses
+-------------
+
+.. code-block:: python
+
+    import swc2vtk
+    vtkgen = swc2vtk.VtkGenerator()
+    vtkgen.add_swc('simple.swc')
+    vtkgen.add_swc('simple.swc', shift_y=30)
+    vtkgen.add_swc_connection(0, 2, 1, 1, size=0.5, data=2)
+    vtkgen.write_vtk('simple.vtk')
+    vtkgen.write_annotation_vtk('simple_connection.vtk')
+
+
+.. image:: _static/simple_annotation3.png
+
diff --git a/docs/_sources/drawmode.rst.txt b/docs/_sources/drawmode.rst.txt
@@ -11,20 +11,19 @@ Sample Program
 .. code-block:: python
 
     import os
-    from swc2vtk.vtkgenerator import VtkGenerator
+    import swc2vtk
 
     filename = 'simple'
     outputpos = ''
 
-    vtkgen = VtkGenerator()
+    vtkgen = swc2vtk.VtkGenerator()
     vtkgen.add_swc(os.path.join('swc', filename + '.swc'))
 
     for i in range(4):
         vtkgen.set_draw_mode(i)
         vtkgen.write_vtk(os.path.join(outputpos, filename + '_draw'+str(i)+'.vtk'))
 
 
-
 ``draw_mode = 0``
 -----------------
 

diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -13,6 +13,7 @@ Welcome to swc2vtk's documentation!
    examples
    drawmode
    volume
+   annotations
    gallery
    apis/modules
 

diff --git a/docs/_sources/readme.rst.txt b/docs/_sources/readme.rst.txt
@@ -27,5 +27,8 @@ Quick example
 .. image:: _static/simple.0003.png
 
 
-Citation
+Reference
 ---------
+
+Citation
+--------
diff --git a/docs/_sources/volume.rst.txt b/docs/_sources/volume.rst.txt
@@ -15,7 +15,7 @@ Sample Code
 .. code-block:: python
 
     import swc2vtk
-    vtkgen = VtkGenerator()
+    vtkgen = swc2vtk.VtkGenerator()
     vtkgen.add_swc('simple.swc'))
     vtkgen.write_volume_vtk('simple.vtk', origin=(-10.0, -10.0, -10.0), ratio=(1, 1, 1), div=(20, 20, 20))
 

diff --git a/docs/_static/annotation1.png b/docs/_static/annotation1.png
diff --git a/docs/_static/simple_annotation1.png b/docs/_static/simple_annotation1.png
diff --git a/docs/_static/simple_annotation2.png b/docs/_static/simple_annotation2.png
diff --git a/docs/_static/simple_annotation3.png b/docs/_static/simple_annotation3.png