some features visibility changed

connectivipy/__init__.py

@@ -2,7 +2,8 @@
 #! /usr/bin/env python
 
 from data import Data
-from conn import ConnectAR, spectrum, spectrumft, DTF
+from conn import conn_estim_dc
 from mvarmodel import Mvar
+from mvar.fitting import mvar_gen, mvar_gen_inst
 
-__version__ = '0.31'
+__version__ = '0.34'

connectivipy/data.py

@@ -338,7 +338,7 @@ def plot_conn(self, name='', ylim=None, xlim=None, signi=True, show=True):
         if show:
             plt.show()
 
-    def plot_short_time_conn(self, name='',signi=True, show=True):
+    def plot_short_time_conn(self, name='', signi=True, percmax=1., show=True):
         '''
         Plot short-time version of estimation results.
         
@@ -348,6 +348,8 @@ def plot_short_time_conn(self, name='',signi=True, show=True):
           *signi* = True : boolean
             reset irrelevant values; it works only after short time
             significance calculation using *short_time_significance*
+          *percmax* = 1. : float (0,1)
+            percent of maximal value which is maximum on the color map
           *show* = True : boolean
             show the plot or not            
         '''
@@ -365,7 +367,7 @@ def plot_short_time_conn(self, name='',signi=True, show=True):
         for i in xrange(self.__chans):
             mask[:,:,i,i] = 1
         masked_shtimest = np.ma.array(shtvalues, mask=mask)
-        dtmax = np.max(masked_shtimest)
+        dtmax = np.max(masked_shtimest)*percmax
         dtmin = np.min(masked_shtimest)
         for i in xrange(self.__chans):
             for j in xrange(self.__chans):

connectivipy/mvarmodel.py

@@ -11,17 +11,17 @@ class Mvar(object):
     acronym of algorithm and value is a function from *mvar.fitting*.
     """
 
-    _fit_dict = {'yw': yulewalker,
-                 'ns': nutallstrand,
-                 'vm': vieiramorf}
+    fit_dict = {'yw': yulewalker,
+                'ns': nutallstrand,
+                'vm': vieiramorf}
 
     @classmethod
     def fit(cls, data, order=None, method='yw'):
         """
         Mvar model fitting.
         Args:
           *data* : numpy.array
-              array with data (kXN, k - channels nr, N - data points)
+              array with data shaped (k, N), k - channels nr, N - data points)
           *order*=None : int
               model order, when default None it estimates order using
               akaike order criteria.
@@ -34,11 +34,11 @@ def fit(cls, data, order=None, method='yw'):
               reflection matrix (kXk)
         """
         if order == None:
-            order, crit_val = cls._order_hq(data, p_max=None, method=method)        
-        return cls._fit_dict[method](data,order)
+            order, crit_val = cls.order_hq(data, p_max=None, method=method)        
+        return cls.fit_dict[method](data,order)
 
     @classmethod
-    def _order_akaike(cls, data, p_max=None, method='yw'):
+    def order_akaike(cls, data, p_max=None, method='yw'):
         """
         Akaike criterion of MVAR order estimation.
 
@@ -73,7 +73,7 @@ def _order_akaike(cls, data, p_max=None, method='yw'):
         return np.argmin(crit)+1, crit 
 
     @classmethod
-    def _order_hq(cls, data, p_max=None, method='yw'):
+    def order_hq(cls, data, p_max=None, method='yw'):
         """
         Hannan-Quin criterion of MVAR order estimation.
 
@@ -108,7 +108,7 @@ def _order_hq(cls, data, p_max=None, method='yw'):
         return np.argmin(crit)+1, crit
 
     @classmethod
-    def _order_schwartz(cls, data, p_max=None, method='yw'):
+    def order_schwartz(cls, data, p_max=None, method='yw'):
         """
         Schwartz criterion of MVAR order estimation.
 
@@ -143,7 +143,7 @@ def _order_schwartz(cls, data, p_max=None, method='yw'):
         return np.argmin(crit)+1, crit
 
     @classmethod
-    def _order_fpe(cls, data, p_max=None, method='yw'):
+    def order_fpe(cls, data, p_max=None, method='yw'):
         """
         Final Prediction Error criterion of MVAR order estimation.
         (not recommended)

doc/conf.py

@@ -36,6 +36,9 @@
     'sphinx.ext.viewcode',
 ]
 
+#Autodoc
+autodoc_member_order = 'bysource'
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -57,9 +60,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '0.32'
+version = '0.34'
 # The full version, including alpha/beta/rc tags.
-release = '0.32a'
+release = '0.34a'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -124,7 +127,7 @@
 #html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+html_short_title = 'ConnPy'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -158,7 +161,9 @@
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+html_additional_pages = {
+    'Download': 'https://github.com/dokato/connectivipy',
+}
 
 # If false, no module index is generated.
 #html_domain_indices = True