Use PEtab parameter prior for starting point sampling (#194)

* make parPE use startpoint sampling from PEtab * Update PEtab requirement to provide code for prior handling
ICB-DCM · Dec 13, 2019 · 1d3c76c · 1d3c76c
1 parent 0acbc8d
commit 1d3c76c
Show file tree

Hide file tree

Showing 2 changed files with 10 additions and 10 deletions.
diff --git a/misc/generateHDF5DataFileFromText.py b/misc/generateHDF5DataFileFromText.py
@@ -1135,22 +1135,22 @@ def write_bounds(self):
 
     def write_starting_points(self):
         """
-        Write a list of random starting points uniformly sampled from the
-        parameter bounds.
-        Parameter bounds need to be written beforehand.
+        Write a list of random starting points sampled as specified in PEtab
+        file.
         """
         num_params = self.f['/parameters/parameterNames'].shape[0]
         num_starting_points = 100
         np.random.seed(0)
+
         starting_points = self.f.require_dataset(
             '/optimizationOptions/randomStarts',
             [num_params, num_starting_points], 'f8')
-        lower = self.f['/parameters/lowerBound'][:]
-        upper = self.f['/parameters/upperBound'][:]
-        starting_points[:] = np.transpose(
-            np.random.rand(num_starting_points, num_params) * (
-                    upper - lower) + lower)
 
+        starting_points[:] = \
+            self.petab_problem.sample_parameter_startpoints(
+                num_starting_points)
+
+        # Write nominal values for testing purposes
         if 'nominalValue' in self.parameter_df:
             self.f['/parameters/nominalValues'] = \
                 self.parameter_df.nominalValue[

diff --git a/python/setup.py b/python/setup.py
@@ -11,8 +11,8 @@
     install_requires=['numpy',
                       'termcolor',
                       'colorama',
-                      'petab>=0.0.0a14',
-                      'amici>=0.10.13',
+                      'petab>=0.0.0a17',
+                      'amici>=0.10.16',
                       'h5py',
                       'python-libsbml>=5.17.0',
                       'jinja2',