Added plottools from BBP

.gitignore

@@ -35,3 +35,6 @@ pip-log.txt
 *.xml
 *.ipynb_checkpoints
 *.dat
+
+x86_64
+temp_data/

README.md

@@ -1,24 +1,11 @@
-[![Build Status](https://travis-ci.org/scidash/neuronunit.svg?branch=master)](https://travis-ci.org/scidash/neuronunit)
-
-NeuronUnit: A SciUnit repository for neuroscience-related tests, capabilities and so on.
-
-![NeuronUnit Logo](https://raw.githubusercontent.com/scidash/assets/master/logos/neuronunit.png)
-
-# Concept:  
-
-https://github.com/rgerkin/papers/blob/master/neuronunit_frontiers/Paper.pdf
-
 # Documentation:
 (See SciUnit documentation [here](http://github.com/scidash/sciunit/blob/master/docs/chapter1.ipynb) first)
 - [Chapter 1](http://github.com/scidash/neuronunit/blob/master/docs/chapter1.ipynb)
 - [Chapter 2](http://github.com/scidash/neuronunit/blob/master/docs/chapter2.ipynb)
 - [Chapter 3](http://github.com/scidash/neuronunit/blob/master/docs/chapter3.ipynb)
 
 # Presentations:  
-
-INCF Meeting (August, 2014) (Less code)
-https://github.com/scidash/assets/blob/master/presentations/SciUnit%20INCF%20Talk.pdf?raw=true
-
+=======
 OpenWorm Journal Club (August, 2014) (More code)
 https://github.com/scidash/assets/blob/master/presentations/SciUnit%20OpenWorm%20Journal%20Club.pdf?raw=true
 
@@ -275,3 +262,10 @@ score.describe()
 The score was computed according to 'the difference of the predicted and observed means divided by the observed standard deviation' with raw value 1.0
 '''
 ```
+
+NeuronUnit: A SciUnit repository for neuroscience-related tests, capabilities and so on.
+
+![NeuronUnit Logo](https://raw.githubusercontent.com/scidash/assets/master/logos/neuronunit.png)
+
+https://github.com/rgerkin/papers/blob/master/neuronunit_frontiers/Paper.pdf
+

neuronunit/plottools.py

@@ -0,0 +1,142 @@
+#!/usr/bin/env python
+"""DocString"""
+
+from itertools import cycle
+import matplotlib
+import matplotlib.colors as mplcol
+import matplotlib.pyplot as plt
+import colorsys
+import numpy
+import collections
+
+
+def adjust_spines(ax, spines, color='k', d_out=10, d_down=[]):
+
+    if d_down == []:
+        d_down = d_out
+
+    ax.set_frame_on(True)
+    ax.patch.set_visible(False)
+
+    for loc, spine in ax.spines.items():
+        if loc in spines:
+            if loc == 'bottom':
+                spine.set_position(('outward', d_down))  # outward by 10 points
+            else:
+                spine.set_position(('outward', d_out))  # outward by 10 points
+            #spine.set_smart_bounds(True)
+        else:
+            spine.set_visible(False) # set_color('none') # don't draw spine
+
+    # turn off ticks where there is no spine
+    if 'left' in spines:
+        ax.yaxis.set_ticks_position('left')
+
+        if color is not 'k':
+
+            ax.spines['left'].set_color(color)
+            ax.yaxis.label.set_color(color)
+            ax.tick_params(axis='y', colors=color)
+
+
+    elif 'right' not in spines:
+        # no yaxis ticks
+        ax.yaxis.set_ticks([])
+
+    if 'right' in spines:
+        ax.yaxis.set_ticks_position('right')
+
+        if color is not 'k':
+
+            ax.spines['right'].set_color(color)
+            ax.yaxis.label.set_color(color)
+            ax.tick_params(axis='y', colors=color)
+
+    if 'bottom' in spines:
+        pass
+        ax.xaxis.set_ticks_position('bottom')
+        #ax.axes.get_xaxis().set_visible(True)
+
+    else:
+        # no xaxis ticks
+        ax.xaxis.set_ticks([])
+        ax.axes.get_xaxis().set_visible(False)
+
+
+def light_palette(color, n_colors=6, reverse=False, lumlight=0.8, light=None):
+
+    rgb = mplcol.colorConverter.to_rgb(color)
+
+    if light is not None:
+        light = mplcol.colorConverter.to_rgb(light)
+    else:
+        vals = list(colorsys.rgb_to_hls(*rgb))
+        vals[1] = lumlight
+        light = colorsys.hls_to_rgb(*vals)
+
+    colors = [color, light] if reverse else [light, color]
+    pal = mplcol.LinearSegmentedColormap.from_list("blend", colors)
+
+    palette = pal(numpy.linspace(0, 1, n_colors))
+
+    return palette
+
+
+def tiled_figure(figname='', frames=1, columns=2, figs=collections.OrderedDict(), axs=None, orientation='page', width_ratios=None, height_ratios=None, top=0.97, bottom=0.05, left=0.07, right=0.97, hspace=0.6, wspace=0.2, dirname=''):
+
+    if figname not in figs:
+
+        if axs == None:
+            axs = []
+
+        if orientation == 'landscape':
+            figsize=(297/25.4, 210/25.4)
+        elif orientation == 'page':
+            figsize=(210/25.4, 297/25.4)
+
+        # Some of these are not valid params in the current version
+        # of matplotlib so I've commented them out.   
+        params = {'backend': 'ps',
+                  'axes.labelsize': 6,
+                  'axes.linewidth' : 0.5,
+                  #'title.fontsize': 8,
+                  #'text.fontsize': 8,
+                  'font.size': 8,
+                  'axes.titlesize': 8,
+                  'legend.fontsize': 8,
+                  'xtick.labelsize': 6,
+                  'ytick.labelsize': 6,
+                  'legend.borderpad': 0.2,
+                  #'legend.linewidth': 0.1, 
+                  'legend.loc': 'best',
+                  #'legend.ncol': 4, 
+                  'text.usetex': False,
+                  'pdf.fonttype': 42,
+                  'figure.figsize': figsize}
+        matplotlib.rcParams.update(params)
+
+        fig = plt.figure(figname, facecolor='white')
+        figs[figname] = {}
+        figs[figname]['fig'] = fig
+        figs[figname]['dirname'] = dirname
+
+        if width_ratios is None:
+            width_ratios=[1]*columns
+
+        rows = int(numpy.ceil(frames/float(columns)))
+        if height_ratios is None:
+            height_ratios=[1]*rows
+
+        gs = matplotlib.gridspec.GridSpec(rows, columns, height_ratios=height_ratios, width_ratios=width_ratios)
+        gs.update(top=top, bottom=bottom, left=left, right=right, hspace=hspace, wspace=wspace)
+
+        for fi in range(frames):
+            axs.append(fig.add_subplot(gs[int(fi/columns), int(fi%columns)]))
+            adjust_spines(axs[-1], ['left', 'bottom'], d_out=0)
+
+        figs[figname]['axs'] = axs
+
+    else:
+        axs = figs[figname]['axs']
+
+    return axs