major update

- new module: b3d - added nblast all-by-all to rmaid - improved neuron objects in core - updated docs - bugfixes (morpho, igraph and elsewhere) - made all code pep8-compliant: all 4 space indents now, trailing whitespaces removed, etc.
navis-org · Jul 30, 2017 · f689e1c · f689e1c
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diff --git a/.gitignore b/.gitignore
diff --git a/LICENSE b/LICENSE
diff --git a/MANIFEST b/MANIFEST
@@ -1,6 +1,7 @@
 # file GENERATED by distutils, do NOT edit
 setup.py
 pymaid/__init__.py
+pymaid/b3d.py
 pymaid/cluster.py
 pymaid/core.py
 pymaid/igraph_catmaid.py

diff --git a/README.md b/README.md
@@ -22,6 +22,8 @@ PyMaid is on [ReadTheDocs](http://pymaid.readthedocs.io/ "PyMaid ReadTheDocs").
 
 `pymaid.user_stats` contains functions for user stats and contributions
 
+`pymaid.b3d` interface with [Blender 3D](https://www.blender.org). This can only be used from within Blender. See [ReadTheDocs](http://pymaid.readthedocs.io/ "PyMaid ReadTheDocs") on how to setup PyMaid for Blender.
+
 `pymaid.rmaid` provides an interface with R libraries ([nat](https://github.com/jefferis/nat), [rcatmaid](https://github.com/jefferis/rcatmaid), [elmr](https://github.com/jefferis/elmr), [catnat](https://github.com/alexanderbates/catnat) ) using [rpy2](https://rpy2.readthedocs.io/en/version_2.8.x/). *Attention*: rpy2 is not installed as dependency as it requires R to be installed. In order to use this module you must setup R and install rpy2 manually.
 
 ## Installation

diff --git a/dist/pymaid-0.1.tar.gz b/dist/pymaid-0.1.tar.gz
diff --git a/dist/pymaid-0.11.tar.gz b/dist/pymaid-0.11.tar.gz
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diff --git a/dist/pymaid-0.44.tar.gz b/dist/pymaid-0.44.tar.gz
diff --git a/dist/pymaid-0.45.tar.gz b/dist/pymaid-0.45.tar.gz
diff --git a/dist/pymaid-0.46.tar.gz b/dist/pymaid-0.46.tar.gz
diff --git a/docs/Makefile b/docs/Makefile
diff --git a/docs/conf.py b/docs/conf.py
diff --git a/docs/index.rst b/docs/index.rst
@@ -12,6 +12,7 @@ PyMaid documentation
    source/overview
    source/rmaid_doc
    source/plotting
+   source/blender
    source/pymaid
    source/core
    source/cluster
@@ -20,6 +21,7 @@ PyMaid documentation
    source/plot
    source/user_stats
    source/rmaid
+   source/b3d
 
 
 Indices and tables

diff --git a/docs/make.bat b/docs/make.bat
diff --git a/docs/requirements.txt b/docs/requirements.txt
diff --git a/docs/source/b3d.rst b/docs/source/b3d.rst
@@ -0,0 +1,7 @@
+The b3d module
+---------------
+
+.. automodule:: pymaid.b3d
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/source/blender.rst b/docs/source/blender.rst
@@ -0,0 +1,65 @@
+Blender interface
+*****************
+
+Pymaid comes with an interface to import neurons into Blender: :mod:`pymaid.b3d`
+
+.. note::
+   Blender's Python console does not show all outputs. Please check the terminal
+   if you experience issues. In Windows simply go to `Help` >> `Toggle System 
+   Console`. In MacOS, right-click Blender in Finder >> `Show Package Contents` 
+   >> `MacOS` >> `blender`.
+
+Installation
+============
+
+Blender comes with its own Python 3.5, so you need to install PyMaid for this distribution in order to use it from within Blender.
+
+There are several ways to install additional packages for Blender's built-in Python. The easiest way is probably this:
+
+1. Download `PIPs <https://pip.pypa.io/en/stable/installing/>`_ get-pip.py and save e.g. in your downloads directory
+2. run get-pip.py from Blender Python console:
+
+>>>	with open('/Users/YOURNAME/Downloads/get-pip.py') as source_file:
+...  exec(source_file.read())
+
+3. Then use pip to install any given package. Here, we install as Scipy an example:
+
+>>> import pip
+>>> pip.main(['install','git+git://github.com/schlegelp/pymaid@master'])
+
+Alternatively run Blender's Python from a Terminal. In MacOS do:
+1. Make sure Blender is in your Applications folder
+2. Right click on Blender icon -> **Show Package Contents**
+3. Navigate to **Contents/Resources/2.XX/python/bin** and run **python3.5m** by drag&dropping it into a Terminal
+4. Try above steps from the Terminal 
+
+Quickstart
+==========
+
+:mod:`pymaid.b3d` provides a simple handler that let's you add, select and manipulate neurons from within the Blender terminal. Try this from within Blender's console:
+
+>>> from pymaid import pymaid, b3d
+>>> rm = pymaid.CatmaidInstance('server_url', 'http_user', 'http_pw', 'token')
+>>> pymaid.remote_instance = rm
+>>> # Fetch a bunch of neurons
+>>> nl = pymaid.get_3D_skeleton( 'annotation: glomerulus DA1' )
+>>> # Initialise handler
+>>> handler = b3d.handler()
+>>> # Load neurons into scene
+>>> handler.add( nl )
+>>> # Colorise neurons
+>>> handler.colorize()
+>>> # Change thickness of all neurons
+>>> handler.neurons.bevel( .02 )
+>>> # Select subset
+>>> subset = handle.select( nl[:10] )
+>>> # Make subset red
+>>> subset.color(1,0,0)
+>>> # Change color of presynapses to green
+>>> handle.presynapses.color(0,1,0)
+>>> # Show only connectors
+>>> handle.connectors.hide_others()
+>>> #Clear all objects
+>>> handler.clear()
+
+
diff --git a/docs/source/cluster.rst b/docs/source/cluster.rst
diff --git a/docs/source/core.rst b/docs/source/core.rst
diff --git a/docs/source/igraph.rst b/docs/source/igraph.rst
diff --git a/docs/source/install.rst b/docs/source/install.rst
diff --git a/docs/source/intro.rst b/docs/source/intro.rst
@@ -125,6 +125,7 @@ The project ID is part of the CatmaidInstance and defaults to 1. You can change
 ...                         http_pw = 'HTTP_PASSWORD', 
 ...                         auth_token = 'TOKEN' )
 
+
 CatmaidNeuron and CatmaidNeuronList objects
 -------------------------------------------
 

diff --git a/docs/source/morpho.rst b/docs/source/morpho.rst
diff --git a/docs/source/overview.rst b/docs/source/overview.rst
diff --git a/docs/source/plot.rst b/docs/source/plot.rst
diff --git a/docs/source/plotting.rst b/docs/source/plotting.rst
diff --git a/docs/source/pymaid.rst b/docs/source/pymaid.rst
diff --git a/docs/source/rmaid.rst b/docs/source/rmaid.rst
diff --git a/docs/source/rmaid_doc.rst b/docs/source/rmaid_doc.rst
@@ -8,6 +8,7 @@ On a fundamental level, you can use every single R function from within Python.
    The :mod:`pymaid.rmaid` module requires `rpy2 <https://rpy2.readthedocs.io>`_.
    As `rpy2` installation fails if no R is installed, it is not a default 
    dependency and has to be installed manually *after* R has been set up.
+   Also: the latest R version supported by `rpy2` appears to be 3.3.3 (Jul/2017).
 
 Quickstart
 ==========

diff --git a/docs/source/user_stats.rst b/docs/source/user_stats.rst
diff --git a/examples/example_retrieving_connectors.ipynb b/examples/example_retrieving_connectors.ipynb
diff --git a/examples/nblasting.ipynb b/examples/nblasting.ipynb
diff --git a/examples/plot_neurons.ipynb b/examples/plot_neurons.ipynb
diff --git a/examples/using_R_functions.ipynb b/examples/using_R_functions.ipynb
diff --git a/pymaid/__init__.py b/pymaid/__init__.py
@@ -1 +1 @@
-__version__ = "0.45"
+__version__ = "0.46"