Merge branch 'enh/dyn_save_uncertainties' into 'master'

ENH: Added uncertainties and mapped parameters to dynamic results save.

See merge request !33

fsl_mrs/tests/test_utils_dynamic_dyn_results.py

@@ -116,6 +116,12 @@ def test_dynRes_newton(fixed_ratio_mrs):
 
     assert np.allclose(res_obj.std_dyn, np.sqrt(np.diagonal(res_obj.cov_dyn)))
 
+    assert isinstance(res_obj.std, pd.DataFrame)
+    assert res_obj.std.shape == (2, 8)
+
+    assert isinstance(res_obj.mapped_params, pd.DataFrame)
+    assert res_obj.mapped_params.shape == (2, 8)
+
 
 def test_dynRes_mcmc(fixed_ratio_mrs):
     """Test mcmc optimiser specific components"""
@@ -133,16 +139,22 @@ def test_dynRes_mcmc(fixed_ratio_mrs):
     res = dyn_obj.fit(method='MH', mh_jumps=20)
 
     res_obj = res['result']
-    assert isinstance(res_obj.cov, pd.DataFrame)
-    assert res_obj.cov.shape == (10, 10)
+    assert isinstance(res_obj.cov_dyn, pd.DataFrame)
+    assert res_obj.cov_dyn.shape == (10, 10)
+
+    assert isinstance(res_obj.corr_dyn, pd.DataFrame)
+    assert res_obj.corr_dyn.shape == (10, 10)
+
+    assert isinstance(res_obj.std_dyn, pd.Series)
+    assert res_obj.std_dyn.shape == (10,)
 
-    assert isinstance(res_obj.corr, pd.DataFrame)
-    assert res_obj.corr.shape == (10, 10)
+    assert np.allclose(res_obj.std_dyn, np.sqrt(np.diagonal(res_obj.cov_dyn)))
 
-    assert isinstance(res_obj.std, pd.Series)
-    assert res_obj.std.shape == (10,)
+    assert isinstance(res_obj.std, pd.DataFrame)
+    assert res_obj.std.shape == (2, 8)
 
-    assert np.allclose(res_obj.std, np.sqrt(np.diagonal(res_obj.cov)))
+    assert isinstance(res_obj.mapped_params, pd.DataFrame)
+    assert res_obj.mapped_params.shape == (2, 8)
 
 
 def test_load_save(fixed_ratio_mrs, tmp_path):
@@ -166,6 +178,10 @@ def test_load_save(fixed_ratio_mrs, tmp_path):
     assert_frame_equal(res._data, res_loaded._data)
     assert_frame_equal(res._init_x, res_loaded._init_x)
 
+    assert (tmp_path / 'res_save_test' / 'dyn_std.csv').is_file()
+    assert (tmp_path / 'res_save_test' / 'mapped_mean.csv').is_file()
+    assert (tmp_path / 'res_save_test' / 'mapped_std.csv').is_file()
+
     res.save(tmp_path / 'res_save_test2', save_dyn_obj=True)
     res_loaded2 = dyn.load_dyn_result(tmp_path / 'res_save_test2')
 

fsl_mrs/utils/dynamic/dyn_results.py

@@ -129,6 +129,11 @@ class dynRes:
         self._data.to_csv(save_dir / 'dyn_results.csv')
         self._init_x.to_csv(save_dir / 'init_results.csv')
 
+        # Save the uncertainties and mapped parameters as well - for ease of results writing
+        self.std_dyn.to_csv(save_dir / 'dyn_std.csv')
+        self.mapped_params.to_csv(save_dir / 'mapped_mean.csv')
+        self.std.to_csv(save_dir / 'mapped_std.csv')
+
         # If selected save the dynamic object to a nested directory
         if save_dyn_obj:
             self._dyn.save(save_dir / 'dynmrs_obj', save_mrs_list=True)
@@ -237,6 +242,48 @@ class dynRes:
         """Free names from stored dynamic object"""
         return self._dyn.free_names
 
+    # Methods implemented in child classes
+    @property
+    def cov_dyn(self):
+        """Implemented in child class
+
+        Returns the covariance matrix of free parameters
+        """
+        pass
+
+    @property
+    def corr_dyn(self):
+        """Implemented in child class
+
+        Returns the correlation matrix of free parameters
+        """
+        pass
+
+    @property
+    def std_dyn(self):
+        """Implemented in child class
+
+        Returns the standard deviations of the free parameters
+        """
+        pass
+
+    @property
+    def std(self):
+        """Implemented in child class
+
+        Returns the standard deviations of the mapped parameters
+        """
+        pass
+
+    # TODO: Do we want to keep this and the similar method in the parent class?
+    @property
+    def mapped_params(self):
+        """Implemented in child class
+
+        Returns mapped parameters as pandas data series
+        """
+        pass
+
     def collected_results(self, to_file=None):
         """Collect the results of dynamic MRS fitting
 
@@ -461,7 +508,7 @@ class dynRes_mcmc(dynRes):
         super().__init__(samples, dyn, init)
 
     @property
-    def cov(self):
+    def cov_dyn(self):
         """Returns the covariance matrix of free parameters
 
         :return: Covariance matrix as a DataFrame
@@ -470,7 +517,7 @@ class dynRes_mcmc(dynRes):
         return self.data_frame.cov()
 
     @property
-    def corr(self):
+    def corr_dyn(self):
         """Returns the correlation matrix of free parameters
 
         :return: Covariance matrix as a DataFrame
@@ -479,7 +526,7 @@ class dynRes_mcmc(dynRes):
         return self.data_frame.corr()
 
     @property
-    def std(self):
+    def std_dyn(self):
         """Returns the standard deviations of the free parameters
 
         :return: Std as data Series
@@ -487,6 +534,20 @@ class dynRes_mcmc(dynRes):
         """
         return self.data_frame.std()
 
+    @property
+    def std(self):
+        """Returns the standard deviations of the mapped parameters
+
+        :return: Std as data Series
+        :rtype: pandas.Series
+        """
+        return pd.DataFrame(self.mapped_parameters.std(axis=0), columns=self.mapped_names)
+
+    # TODO: Do we want to keep this and the similar method in the parent class?
+    @property
+    def mapped_params(self):
+        return pd.DataFrame(self.mapped_parameters.mean(axis=0), columns=self.mapped_names)
+
 
 class dynRes_newton(dynRes):
 
@@ -568,9 +629,9 @@ class dynRes_newton(dynRes):
         :return: Std as data Series
         :rtype: pandas.Series
         """
-        return pd.Series(self._std, self._dyn.vm.mapped_names)
+        return pd.DataFrame(np.hstack(list(self._std.values())), columns=self.mapped_names)
 
     # TODO: Do we want to keep this and the similar method in the parent class?
     @property
     def mapped_params(self):
-        return pd.Series(self._mapped_params, self._dyn.vm.mapped_names)
+        return pd.DataFrame(self.mapped_parameters.mean(axis=0), columns=self.mapped_names)