Merge pull request pyhrf#136 from thperret/ubuntu1404install

[Fixes pyhrf#134, Closes pyhrf#135] 0.4.1.post1 release

CHANGELOG.rst

@@ -21,6 +21,31 @@ Current development
 
 -----------------------------------
 
+Release 0.4.1.post1
++++++++++++++++++++
+
+Fixes:
+------
+
+- missing function (#135)
+- nipy version required for installation (#134)
+
+Release 0.4.1
++++++++++++++
+
+Fixes:
+------
+
+- logging level not set by command line (#113)
+- error with VEM algorithm (#115)
+
+Enhancements:
+-------------
+
+- clean and update setup.py (#84)
+- update travis configuration file (#123)
+
+
 Release 0.4
 +++++++++++
 

python/pyhrf/vbjde/vem_tools.py

@@ -12,6 +12,7 @@
 
 from numpy.matlib import *
 from scipy.linalg import toeplitz
+from scipy.optimize import fmin_slsqp
 
 import pyhrf
 import pyhrf.vbjde.UtilsC as UtilsC
@@ -32,7 +33,7 @@
 # Tools
 ##############################################################
 
-eps = 1e-6
+eps = np.spacing(1)
 
 
 def mult_old(v1, v2):
@@ -269,6 +270,61 @@ def roc_curve(dvals, labels, rocN=None, normalize=True):
 
     return fpc, tpc, area
 
+
+def norm1_constraint(function, variance):
+    """Returns the function constrained with optimization strategy.
+
+    Parameters
+    ----------
+    function : array_like
+        function to optimize under norm1 constraint
+    variance : array_like
+        variance of the `function`, must be the same size
+
+    Returns
+    -------
+    optimized_function : numpy array
+
+    Raises
+    ------
+    ValueError
+        If `len(variance) != len(function)`
+
+    """
+
+    variance_inv = np.linalg.inv(variance)
+
+    current_level = logger.getEffectiveLevel()
+    if current_level >= logging.WARNING:
+        disp = 0
+    elif current_level >= logging.INFO:
+        disp = 1
+    else:
+        disp = 2
+
+    def minimized_function(fct):
+        """Function to minimize"""
+        return np.dot(np.dot((fct - function).T, variance_inv), (fct - function))
+
+    def norm1_constraint_equation(fct):
+        """Norm2(fct) == 1"""
+        return np.linalg.norm(fct, 2) - 1
+
+    def first_element_constraint(fct):
+        """fct[0] == 0"""
+        return fct[0]
+
+    def last_element_constraint(fct):
+        """fct[-1] == 0"""
+        return fct[-1]
+
+    return fmin_slsqp(minimized_function, function,
+                      eqcons=[norm1_constraint_equation,
+                              first_element_constraint,
+                              last_element_constraint],
+                      bounds=[(None, None)] * (len(function)), disp=disp)
+
+
 # Expectation functions
 ##############################################################
 

setup.py

@@ -51,7 +51,7 @@
 
 setup(
     name = "pyhrf",
-    version = "0.4.1",
+    version = "0.4.1.post1",
     description = ("PyHRF is a set of tools to analyze fMRI data and "
                    "specifically study hemodynamics."),
     long_description = open("README.rst").read(),
@@ -73,7 +73,7 @@
                         "matplotlib>=1.1,<1.4",
                         "nibabel>=1.1",
                         "sympy>=0.7",
-                        "nipy==0.3.0"],
+                        "nipy>=0.3.0"],
     extras_require = {"Ward": ["scikit-learn>=0.10"],
                       "parallel": ["joblib>=0.5"],
                       "cluster": ["soma-workflow"],