Fix tests

dwi_ml/data/dataset/streamline_containers.py

@@ -106,17 +106,25 @@ def _get_one_streamline(self, idx: int):
 
     def get_array_sequence(self, item=None):
         if item is None:
-            streamlines, dps = _load_all_streamlines_from_hdf(self.hdf_group)
+            streamlines, data_per_streamline = _load_all_streamlines_from_hdf(
+                self.hdf_group)
         else:
             streamlines = ArraySequence()
-            dps_dict = defaultdict(list)
+            data_per_streamline = defaultdict(list)
+
+            # If data_per_streamline is not in the hdf5, use an empty dict
+            # so that we don't add anything to the data_per_streamline in the
+            # following steps.
+            hdf_dps_group = self.hdf_group['data_per_streamline'] if \
+                'data_per_streamline' in self.hdf_group.keys() else {}
 
             if isinstance(item, int):
                 data = self._get_one_streamline(item)
                 streamlines.append(data)
 
-                for dps_key in self.hdf_group['dps_keys']:
-                    dps_dict[dps_key].append(self.hdf_group[dps_key][item])
+                for dps_key in hdf_dps_group.keys():
+                    data_per_streamline[dps_key].append(
+                        hdf_dps_group[dps_key][item])
 
             elif isinstance(item, list) or isinstance(item, np.ndarray):
                 # Getting a list of value from a hdf5: slow. Uses fancy indexing.
@@ -129,8 +137,9 @@ def get_array_sequence(self, item=None):
                     data = self._get_one_streamline(i)
                     streamlines.append(data, cache_build=True)
 
-                    for dps_key in self.hdf_group['dps_keys']:
-                        dps_dict[dps_key].append(self.hdf_group[dps_key][item])
+                    for dps_key in hdf_dps_group.keys():
+                        data_per_streamline[dps_key].append(
+                            hdf_dps_group[dps_key][item])
 
                 streamlines.finalize_append()
 
@@ -141,16 +150,16 @@ def get_array_sequence(self, item=None):
                     streamline = self.hdf_group['data'][offset:offset + length]
                     streamlines.append(streamline, cache_build=True)
 
-                    for dps_key in self.hdf_group['dps_keys']:
-                        dps_dict[dps_key].append(
-                            self.hdf_group[dps_key][offset:offset + length])
+                    for dps_key in hdf_dps_group.keys():
+                        data_per_streamline[dps_key].append(
+                            hdf_dps_group[dps_key][offset:offset + length])
                 streamlines.finalize_append()
 
             else:
                 raise ValueError('Item should be either a int, list, '
                                  'np.ndarray or slice but we received {}'
                                  .format(type(item)))
-        return streamlines, dps
+        return streamlines, data_per_streamline
 
     @property
     def lengths(self):

dwi_ml/models/projects/learn2track_model.py

@@ -227,6 +227,7 @@ def computed_params_for_display(self):
 
     def forward(self, x: List[torch.tensor],
                 input_streamlines: List[torch.tensor] = None,
+                data_per_streamline: List[torch.tensor] = {},
                 hidden_recurrent_states: List = None, return_hidden=False,
                 point_idx: int = None):
         """Run the model on a batch of sequences.
@@ -284,7 +285,8 @@ def forward(self, x: List[torch.tensor],
             unsorted_indices = invert_permutation(sorted_indices)
             x = [x[i] for i in sorted_indices]
             if input_streamlines is not None:
-                input_streamlines = [input_streamlines[i] for i in sorted_indices]
+                input_streamlines = [input_streamlines[i]
+                                     for i in sorted_indices]
 
         # ==== 0. Previous dirs.
         n_prev_dirs = None

dwi_ml/training/trainers_withGV.py

@@ -242,7 +242,7 @@ def gv_phase_one_batch(self, data, compute_all_scores=False):
         seeds and first few segments. Expected results are the batch's
         validation streamlines.
         """
-        real_lines, ids_per_subj = data
+        real_lines, ids_per_subj, data_per_streamline = data
 
         # Possibly sending again to GPU even if done in the local loss
         # computation, but easier with current implementation.

dwi_ml/unit_tests/utils/data_and_models_for_tests.py

@@ -84,7 +84,7 @@ def compute_loss(self, model_outputs, target_streamlines=None,
         else:
             return torch.zeros(n, device=self.device), 1
 
-    def forward(self, inputs: list, streamlines):
+    def forward(self, inputs: list, streamlines, data_per_streamline):
         # Not using streamlines. Pretending to use inputs.
         _ = self.fake_parameter
         regressed_dir = torch.as_tensor([1., 1., 1.])
@@ -143,7 +143,8 @@ def get_tracking_directions(self, regressed_dirs, algo,
             raise ValueError("'algo' should be 'det' or 'prob'.")
 
     def forward(self, inputs: List[torch.tensor],
-                target_streamlines: List[torch.tensor]):
+                target_streamlines: List[torch.tensor],
+                data_per_streamline: List[torch.tensor]):
         # Previous dirs
         if self.nb_previous_dirs > 0:
             target_dirs = compute_directions(target_streamlines)