new version 0.0.4: added densitygraph and fixed bugs

LICENSE.txt

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+TODO

build/lib/clarityviz/atlasregiongraph.py

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+#!/usr/bin/env python
+#-*- coding:utf-8 -*-
+from __future__ import print_function
+
+__author__ = 'seelviz'
+
+from plotly.offline import download_plotlyjs
+from plotly.graph_objs import *
+from plotly import tools
+import plotly
+
+import os
+#os.chdir('C:/Users/L/Documents/Homework/BME/Neuro Data I/Data/')
+
+import csv,gc  # garbage memory collection :)
+
+import numpy as np
+import matplotlib.pyplot as plt
+from mpl_toolkits.mplot3d import axes3d
+
+from mpl_toolkits.mplot3d import axes3d
+from collections import namedtuple
+
+import csv
+import re
+import matplotlib
+import time
+import seaborn as sns
+
+from collections import OrderedDict
+
+class atlasregiongraph(object):
+    """Class for generating the color coded atlas region graphs"""
+
+    def __init(self, token):
+        self._token = token
+        self._data = np.genfromtxt(token + '/' + token + '.csv', delimiter=',', dtype='int', usecols = (0,1,2,4), names=['x','y','z','region'])
+
+    def generate_atlas_region_graph(self):
+        font = {'weight' : 'bold',
+            'size'   : 18}
+
+        matplotlib.rc('font', **font)
+
+        ### load data
+        thedata = np.genfromtxt(self._token + '/' + self._token + '.csv', delimiter=',', dtype='int', usecols = (0,1,2,4), names=['x','y','z','region'])
+
+        region_dict = OrderedDict()
+        for l in thedata:
+            trace = 'trace' + str(l[3])
+            if trace not in region_dict:
+                region_dict[trace] = np.array([[l[0], l[1], l[2], l[3]]])
+            else:
+                tmp = np.array([[l[0], l[1], l[2], l[3]]])
+                region_dict[trace] = np.concatenate((region_dict.get(trace, np.zeros((1,4))), tmp), axis=0)
+
+        current_palette = sns.color_palette("husl", 396)
+        # print current_palette
+
+        data = []
+        for i, key in enumerate(region_dict):
+            trace = region_dict[key]
+            tmp_col = current_palette[i]
+            tmp_col_lit = 'rgb' + str(tmp_col)
+            trace_scatter = Scatter3d(
+                x = trace[:,0], 
+                y = trace[:,1],
+                z = trace[:,2],
+                mode='markers',
+                marker=dict(
+                    size=1.2,
+                    color=tmp_col_lit, #'purple',                # set color to an array/list of desired values
+                    colorscale='Viridis',   # choose a colorscale
+                    opacity=0.15
+                )
+            )
+
+            data.append(trace_scatter)
+
+
+        layout = Layout(
+            margin=dict(
+                l=0,
+                r=0,
+                b=0,
+                t=0
+            ),
+            paper_bgcolor='rgb(0,0,0)',
+            plot_bgcolor='rgb(0,0,0)'
+        )
+
+        fig = Figure(data=data, layout=layout)
+        plotly.offline.plot(fig, filename= self._token + '/' + self._token + "_region_color.html")
+