Merge pull request #248 from EmmaRenauld/dps_in_config_file

Dps management

dwi_ml/data/dataset/streamline_containers.py

@@ -8,9 +8,10 @@
 import h5py
 from nibabel.streamlines import ArraySequence
 import numpy as np
+from collections import defaultdict
 
 
-def _load_space_attributes_from_hdf(hdf_group: h5py.Group):
+def _load_streamlines_attributes_from_hdf(hdf_group: h5py.Group):
     a = np.array(hdf_group.attrs['affine'])
     d = np.array(hdf_group.attrs['dimensions'])
     vs = np.array(hdf_group.attrs['voxel_sizes'])
@@ -43,7 +44,13 @@ def _load_all_streamlines_from_hdf(hdf_group: h5py.Group):
     streamlines._offsets = np.array(hdf_group['offsets'])
     streamlines._lengths = np.array(hdf_group['lengths'])
 
-    return streamlines
+    # DPS
+    hdf_dps_group = hdf_group['data_per_streamline']
+    dps_dict = {}
+    for dps_key in hdf_dps_group.keys():
+        dps_dict[dps_key] = hdf_dps_group[dps_key][:]
+
+    return streamlines, dps_dict
 
 
 def _load_connectivity_info(hdf_group: h5py.Group):
@@ -79,40 +86,85 @@ def _get_one_streamline(self, idx: int):
 
         return data
 
+    def _assert_dps(self, dps_dict, n_streamlines):
+        for key, value in dps_dict.items():
+            if len(value) != n_streamlines:
+                raise ValueError(
+                    f"Length of data_per_streamline {key} is {len(value)} "
+                    f"but should be {n_streamlines}.")
+            elif not isinstance(value, np.ndarray):
+                raise ValueError(
+                    f"Data_per_streamline {key} should be a numpy array, "
+                    f"not a {type(value)}.")
+
     def get_array_sequence(self, item=None):
         if item is None:
-            streamlines = _load_all_streamlines_from_hdf(self.hdf_group)
+            streamlines, data_per_streamline = _load_all_streamlines_from_hdf(
+                self.hdf_group)
         else:
             streamlines = ArraySequence()
+            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):
-                streamlines.append(self._get_one_streamline(item))
+                data = self._get_one_streamline(item)
+                streamlines.append(data)
+
+                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.
-                # But possible. See here:
+                # Getting a list of value from a hdf5: slow. Uses fancy
+                # indexing. But possible. See here:
                 # https://stackoverflow.com/questions/21766145/h5py-correct-way-to-slice-array-datasets
                 # Looping and accessing ourselves.
                 # Good also load the whole data and access the indexes after.
                 # toDo Test speed for the three options.
                 for i in item:
-                    streamlines.append(self._get_one_streamline(i),
-                                       cache_build=True)
+                    data = self._get_one_streamline(i)
+                    streamlines.append(data, cache_build=True)
+
+                    for dps_key in hdf_dps_group.keys():
+                        data_per_streamline[dps_key].append(
+                            hdf_dps_group[dps_key][item])
+
                 streamlines.finalize_append()
 
             elif isinstance(item, slice):
                 offsets = self.hdf_group['offsets'][item]
                 lengths = self.hdf_group['lengths'][item]
-                for offset, length in zip(offsets, lengths):
+                indices = np.arange(item.start, item.stop, item.step)
+                for offset, length, idx in zip(offsets, lengths, indices):
                     streamline = self.hdf_group['data'][offset:offset + length]
                     streamlines.append(streamline, cache_build=True)
+
+                    for dps_key in hdf_dps_group.keys():
+                        # Indexing with a list (e.g. [idx]) will preserve the
+                        # shape of the array. Crucial for concatenation below.
+                        dps_data = hdf_dps_group[dps_key][[idx]]
+                        data_per_streamline[dps_key].append(dps_data)
                 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
+
+            # The accumulated data_per_streamline is a list of numpy arrays.
+            # We need to merge them into a single numpy array so it can be
+            # reused in the StatefulTractogram.
+            for key in data_per_streamline.keys():
+                data_per_streamline[key] = \
+                    np.concatenate(data_per_streamline[key])
+
+        self._assert_dps(data_per_streamline, len(streamlines))
+        return streamlines, data_per_streamline
 
     @property
     def lengths(self):
@@ -160,6 +212,7 @@ class SFTDataAbstract(object):
     all information necessary to treat with streamlines: the data itself and
     _offset, _lengths, space attributes, etc.
     """
+
     def __init__(self, space_attributes: Tuple, space: Space, origin: Origin,
                  contains_connectivity: bool,
                  connectivity_nb_blocs: List = None,
@@ -256,17 +309,19 @@ def as_sft(self,
         streamline_ids: Union[List[int], int, slice, None]
             List of chosen ids. If None, use all streamlines.
         """
-        streamlines = self._get_streamlines_as_list(streamline_ids)
+        streamlines, dps = self._get_streamlines_as_list(streamline_ids)
 
         sft = StatefulTractogram(streamlines, self.space_attributes,
-                                 self.space, self.origin)
+                                 self.space, self.origin,
+                                 data_per_streamline=dps)
 
         return sft
 
 
 class SFTData(SFTDataAbstract):
     def __init__(self, streamlines: ArraySequence,
                  lengths_mm: List, connectivity_matrix: np.ndarray,
+                 data_per_streamline: np.ndarray = None,
                  **kwargs):
         """
         streamlines: ArraySequence or LazyStreamlinesGetter
@@ -279,6 +334,7 @@ def __init__(self, streamlines: ArraySequence,
         self._lengths_mm = lengths_mm
         self._connectivity_matrix = connectivity_matrix
         self.is_lazy = False
+        self.data_per_streamline = data_per_streamline
 
     def __len__(self):
         return len(self.streamlines)
@@ -306,7 +362,7 @@ def init_sft_data_from_hdf_info(cls, hdf_group: h5py.Group):
         Creating class instance from the hdf in cases where data is not
         loaded yet. Non-lazy = loading the data here.
         """
-        streamlines = _load_all_streamlines_from_hdf(hdf_group)
+        streamlines, dps_dict = _load_all_streamlines_from_hdf(hdf_group)
         # Adding non-hidden parameters for nicer later access
         lengths_mm = hdf_group['euclidean_lengths']
 
@@ -318,7 +374,8 @@ def init_sft_data_from_hdf_info(cls, hdf_group: h5py.Group):
         else:
             connectivity_matrix = None
 
-        space_attributes, space, origin = _load_space_attributes_from_hdf(hdf_group)
+        space_attributes, space, origin = _load_streamlines_attributes_from_hdf(
+            hdf_group)
 
         # Return an instance of SubjectMRIData instantiated through __init__
         # with this loaded data:
@@ -328,13 +385,18 @@ def init_sft_data_from_hdf_info(cls, hdf_group: h5py.Group):
                    space=space, origin=origin,
                    contains_connectivity=contains_connectivity,
                    connectivity_nb_blocs=connectivity_nb_blocs,
-                   connectivity_labels=connectivity_labels)
+                   connectivity_labels=connectivity_labels,
+                   data_per_streamline=dps_dict)
 
     def _get_streamlines_as_list(self, streamline_ids):
         if streamline_ids is not None:
-            return self.streamlines.__getitem__(streamline_ids)
+            dps_indexed = {}
+            for key, value in self.data_per_streamline.items():
+                dps_indexed[key] = value[streamline_ids]
+
+            return self.streamlines.__getitem__(streamline_ids), dps_indexed
         else:
-            return self.streamlines
+            return self.streamlines, self.data_per_streamline
 
 
 class LazySFTData(SFTDataAbstract):
@@ -368,7 +430,7 @@ def _access_connectivity_matrix(self, indxyz: Tuple = None):
 
     @classmethod
     def init_sft_data_from_hdf_info(cls, hdf_group: h5py.Group):
-        space_attributes, space, origin = _load_space_attributes_from_hdf(
+        space_attributes, space, origin = _load_streamlines_attributes_from_hdf(
             hdf_group)
 
         contains_connectivity, connectivity_nb_blocs, connectivity_labels = \
@@ -384,6 +446,6 @@ def init_sft_data_from_hdf_info(cls, hdf_group: h5py.Group):
                    connectivity_labels=connectivity_labels)
 
     def _get_streamlines_as_list(self, streamline_ids):
-        streamlines = self.streamlines_getter.get_array_sequence(
+        streamlines, dps = self.streamlines_getter.get_array_sequence(
             streamline_ids)
-        return streamlines
+        return streamlines, dps

dwi_ml/data/hdf5/hdf5_creation.py

@@ -136,7 +136,6 @@ class HDF5Creator:
     def __init__(self, root_folder: Path, out_hdf_filename: Path,
                  training_subjs: List[str], validation_subjs: List[str],
                  testing_subjs: List[str], groups_config: dict,
-                 dps_keys: List[str] = [],
                  step_size: float = None,
                  nb_points: int = None,
                  compress: float = None,
@@ -160,8 +159,6 @@ def __init__(self, root_folder: Path, out_hdf_filename: Path,
             List of subject names for each data set.
         groups_config: dict
             Information from json file loaded as a dict.
-        dps_keys: List[str]
-            List of keys to keep in data_per_streamline. Default: [].
         step_size: float
             Step size to resample streamlines. Default: None.
         nb_points: int
@@ -186,7 +183,6 @@ def __init__(self, root_folder: Path, out_hdf_filename: Path,
         self.validation_subjs = validation_subjs
         self.testing_subjs = testing_subjs
         self.groups_config = groups_config
-        self.dps_keys = dps_keys
         self.step_size = step_size
         self.nb_points = nb_points
         self.compress = compress
@@ -596,7 +592,7 @@ def _create_streamline_groups(self, ref, subj_input_dir, subj_id,
                     "in the config_file. If all files are .trk, we can use "
                     "ref 'same' but if some files were .tck, we need a ref!"
                     "Hint: Create a volume group 'ref' in the config file.")
-            sft, lengths, connectivity_matrix, conn_info = (
+            sft, lengths, connectivity_matrix, conn_info, dps_keys = (
                 self._process_one_streamline_group(
                     subj_input_dir, group, subj_id, ref))
 
@@ -614,6 +610,8 @@ def _create_streamline_groups(self, ref, subj_input_dir, subj_id,
             streamlines_group.attrs['dimensions'] = d
             streamlines_group.attrs['voxel_sizes'] = vs
             streamlines_group.attrs['voxel_order'] = vo
+
+            # This streamline's group connectivity info
             if connectivity_matrix is not None:
                 streamlines_group.attrs[
                     'connectivity_matrix_type'] = conn_info[0]
@@ -626,18 +624,17 @@ def _create_streamline_groups(self, ref, subj_input_dir, subj_id,
                     streamlines_group.attrs['connectivity_nb_blocs'] = \
                         conn_info[1]
 
+            # DPP not managed yet!
             if len(sft.data_per_point) > 0:
                 logging.debug('sft contained data_per_point. Data not kept.')
+                logging.debug("    Including dps \"{}\" in the HDF5."
+                              .format(dps_keys))
 
-            for dps_key in self.dps_keys:
-                if dps_key not in sft.data_per_streamline:
-                    raise ValueError(
-                        "The data_per_streamline key '{}' was not found in "
-                        "the sft. Check your tractogram file.".format(dps_key))
-
-                logging.debug("    Include dps \"{}\" in the HDF5.".format(dps_key))
-                streamlines_group.create_dataset('dps_' + dps_key,
-                                                 data=sft.data_per_streamline[dps_key])
+            # This streamline's group dps info
+            dps_group = streamlines_group.create_group('data_per_streamline')
+            for dps_key in dps_keys:
+                dps_group.create_dataset(
+                    dps_key, data=sft.data_per_streamline[dps_key])
 
             # Accessing private Dipy values, but necessary.
             # We need to deconstruct the streamlines into arrays with
@@ -678,6 +675,11 @@ def _process_one_streamline_group(
             The Euclidean length of each streamline
         """
         tractograms = self.groups_config[group]['files']
+        dps_keys = []
+        if 'dps_keys' in self.groups_config[group]:
+            dps_keys = self.groups_config[group]['dps_keys']
+            if isinstance(dps_keys, str):
+                dps_keys = [dps_keys]
 
         # Silencing SFT's logger if our logging is in DEBUG mode, because it
         # typically produces a lot of outputs!
@@ -690,7 +692,7 @@ def _process_one_streamline_group(
         tractograms = format_filelist(tractograms, self.enforce_files_presence,
                                       folder=subj_dir)
         for tractogram_file in tractograms:
-            sft = self._load_and_process_sft(tractogram_file, header)
+            sft = self._load_and_process_sft(tractogram_file, header, dps_keys)
 
             if sft is not None:
                 # Compute euclidean lengths (rasmm space)
@@ -750,9 +752,9 @@ def _process_one_streamline_group(
             conn_matrix = np.load(conn_file)
             conn_matrix = conn_matrix > 0
 
-        return final_sft, output_lengths, conn_matrix, conn_info
+        return final_sft, output_lengths, conn_matrix, conn_info, dps_keys
 
-    def _load_and_process_sft(self, tractogram_file, header):
+    def _load_and_process_sft(self, tractogram_file, header, dps_keys):
         # Check file extension
         _, file_extension = os.path.splitext(str(tractogram_file))
         if file_extension not in ['.trk', '.tck']:
@@ -773,6 +775,19 @@ def _load_and_process_sft(self, tractogram_file, header):
                      .format(os.path.basename(tractogram_file)))
         sft = load_tractogram(str(tractogram_file), header)
 
+        # Check for required dps_keys
+        for dps_key in dps_keys:
+            if dps_key not in sft.data_per_streamline.keys():
+                raise ValueError("DPS key {} is not present in file {}. Only "
+                                 "found the following keys: {}"
+                                 .format(dps_key, tractogram_file,
+                                         list(sft.data_per_streamline.keys())))
+
+        # Remove non-required dps_keys
+        for dps_key in list(sft.data_per_streamline.keys()):
+            if dps_key not in dps_keys:
+                del sft.data_per_streamline[dps_key]
+
         # Resample or compress streamlines
         sft = resample_or_compress(sft, self.step_size,
                                    self.nb_points,

dwi_ml/data/hdf5/utils.py

@@ -78,9 +78,6 @@ def add_hdf5_creation_args(p: ArgumentParser):
                         "(Final concatenated standardized volumes and \n"
                         "final concatenated resampled/compressed "
                         "streamlines.)")
-    p.add_argument('--dps_keys', type=str, nargs='+', default=[],
-                   help="List of keys to keep in data_per_streamline. "
-                        "Default: Empty.")
 
 
 def add_streamline_processing_args(p: ArgumentParser):

dwi_ml/data/processing/streamlines/data_augmentation.py

@@ -81,6 +81,12 @@ def split_streamlines(sft: StatefulTractogram, rng: np.random.RandomState,
     for i in range(len(sft.streamlines)):
         old_streamline = sft.streamlines[i]
         old_dpp = sft.data_per_point[i]
+
+        # Note: This getter gets lists of numpy arrays of shape
+        # (n_features, n_streamlines) for some reason. This is why we need to
+        # transpose the all_dps arrays at the end. Not sure why this is
+        # happening as the arrays are stored within the PerArrayDict as
+        # numpy arrays of shape (n_streamlines, n_features).
         old_dps = sft.data_per_streamline[i]
 
         # Cut if at least min_nb_points
@@ -103,6 +109,19 @@ def split_streamlines(sft: StatefulTractogram, rng: np.random.RandomState,
             all_dpp = _extend_dict(all_dpp, old_dpp)
             all_dps = _extend_dict(all_dps, old_dps)
 
+    # Since _extend_dict appends many numpy arrays into a list,
+    # we need to merge them into a single array that can be fed
+    # to StatefulTractogram at data_per_streamlines.
+    #
+    # Note: at this point, all_dps is a dict of lists of numpy arrays
+    # of shape (n_features, n_streamlines). The StatefulTractogram
+    # expects a dict of numpy arrays of shape (n_streamlines, n_features).
+    # We need to concat along the second axis and transpose to get the
+    # correct shape.
+
+    for key in sft.data_per_streamline.keys():
+        all_dps[key] = np.concatenate(all_dps[key], axis=1).transpose()
+
     new_sft = StatefulTractogram.from_sft(all_streamlines, sft,
                                           data_per_point=all_dpp,
                                           data_per_streamline=all_dps)