Merge branch 'master' of https://github.com/NeuralEnsemble/python-neo into spikegadgets_implementation

Author: samuelgarcia

doc/source/authors.rst

@@ -55,6 +55,7 @@ and may not be the current affiliation of a contributor.
 * Peter N Steinmetz [22]
 * Shashwat Sridhar
 * Alessio Buccino [23]
+* Regimantas Jurkus [13]
 
 1. Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292 - INSERM U1028 - Universite Claude Bernard Lyon 1
 2. Unité de Neuroscience, Information et Complexité, CNRS UPR 3293, Gif-sur-Yvette, France

doc/source/core.rst

@@ -191,7 +191,7 @@ Relationship:
 
 :download:`Click here for a better quality SVG diagram <./images/simple_generated_diagram.svg>`
 
-.. note:: This figure has not yet been updated to include :class:`ImageSequence` and :class:`RegionOfInterest`.
+.. note:: This figure do not include :class:`ChannelView` and :class:`RegionOfInterest`.
 
 For more details, see the :doc:`api_reference`.
 

doc/source/developers_guide.rst

@@ -45,7 +45,7 @@ Requirements
     * Sphinx_ (for building documentation)
     * (optional) coverage_ >= 2.85 (for measuring test coverage)
     * (optional) scipy >= 0.12 (for MatlabIO)
-    * (optional) h5py >= 2.5 (for KwikIO, NeoHdf5IO)
+    * (optional) h5py >= 2.5 (for KwikIO)
     * (optional) nixio (for NixIO)
     * (optional) pillow (for TiffIO)
 

doc/source/images/generate_diagram.py

@@ -29,7 +29,6 @@ def get_rect_height(name, obj):
     nlines += len(getattr(obj, '_all_attrs', []))
     nlines += len(getattr(obj, '_single_child_objects', []))
     nlines += len(getattr(obj, '_multi_child_objects', []))
-    nlines += len(getattr(obj, '_multi_parent_objects', []))
     return nlines * line_heigth
 
 
@@ -58,7 +57,7 @@ def calc_coordinates(pos, height):
     return pos[0], y
 
 
-def generate_diagram(filename, rect_pos, rect_width, figsize):
+def generate_diagram(rect_pos, rect_width, figsize):
     rw = rect_width
 
     fig = pyplot.figure(figsize=figsize)
@@ -67,7 +66,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
     all_h = {}
     objs = {}
     for name in rect_pos:
-        objs[name] = fake_neo(name)
+        objs[name] = fake_neo(name, cascade=False)
         all_h[name] = get_rect_height(name, objs[name])
 
     # draw connections
@@ -81,6 +80,8 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
 
         for r in range(3):
             for ch_name in relationships[r]:
+                if ch_name not in rect_pos:
+                    continue
                 x1, y1 = calc_coordinates(rect_pos[ch_name], all_h[ch_name])
                 x2, y2 = calc_coordinates(pos, all_h[name])
 
@@ -100,8 +101,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
     for name, pos in rect_pos.items():
         htotal = all_h[name]
         obj = objs[name]
-        allrelationship = (list(getattr(obj, '_child_containers', []))
-                           + list(getattr(obj, '_multi_parent_containers', [])))
+        allrelationship = list(getattr(obj, '_child_containers', []))
 
         rect = Rectangle(pos, rect_width, htotal,
                          facecolor='w', edgecolor='k', linewidth=2.)
@@ -123,8 +123,7 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
         ax.add_patch(rect)
 
         # multi relationship
-        relationship = (list(getattr(obj, '_multi_child_objects', []))
-                        + list(getattr(obj, '_multi_parent_containers', [])))
+        relationship = list(getattr(obj, '_multi_child_objects', []))
         pos2 = (pos[1] + htotal - line_heigth * (1.5 + len(relationship))
                 - rect_height)
         rect_height = len(relationship) * line_heigth
@@ -196,28 +195,38 @@ def generate_diagram(filename, rect_pos, rect_width, figsize):
 
     ax.set_xticks([])
     ax.set_yticks([])
-    fig.savefig(filename, dpi=dpi)
+
+    return fig
 
 
 def generate_diagram_simple():
     figsize = (18, 12)
     rw = rect_width = 3.
     bf = blank_fact = 1.2
-    rect_pos = {'Block': (.5 + rw * bf * 0, 4),
+    rect_pos = {
+                #  col 0
+                'Block': (.5 + rw * bf * 0, 4),
+                #  col 1
                 'Segment': (.5 + rw * bf * 1, .5),
+                'Group': (.5 + rw * bf * 1, 6.5),
+                #  col 2 : not do for now too complicated with our object generator
+                # 'ChannelView': (.5 + rw * bf * 2, 5),
+
+                # col 2.5
+                'ImageSequence': (.5 + rw * bf * 2.5, 3.0),
+                'SpikeTrain': (.5 + rw * bf * 2.5, 0.5),
+                #  col 3
+                'IrregularlySampledSignal': (.5 + rw * bf * 3, 9),
+                'AnalogSignal': (.5 + rw * bf * 3, 7.),
+                #  col 3
                 'Event': (.5 + rw * bf * 4, 3.0),
                 'Epoch': (.5 + rw * bf * 4, 1.0),
-                'Group': (.5 + rw * bf * 1, 7.5),
-                'ChannelView': (.5 + rw * bf * 2., 9.9),
-                'SpikeTrain': (.5 + rw * bf * 3, 7.5),
-                'IrregularlySampledSignal': (.5 + rw * bf * 3, 0.5),
-                'AnalogSignal': (.5 + rw * bf * 3, 4.9),
+
                 }
     # todo: add ImageSequence, RegionOfInterest
-    generate_diagram('simple_generated_diagram.svg',
-                     rect_pos, rect_width, figsize)
-    generate_diagram('simple_generated_diagram.png',
-                     rect_pos, rect_width, figsize)
+    fig = generate_diagram(rect_pos, rect_width, figsize)
+    fig.savefig('simple_generated_diagram.png', dpi=dpi)
+    fig.savefig('simple_generated_diagram.svg', dpi=dpi)
 
 
 if __name__ == '__main__':