ENH: Indexes sorting options

src/eddymotion/data/splitting.py

@@ -21,9 +21,11 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Data splitting helpers."""
+
 from pathlib import Path
-import numpy as np
+
 import h5py
+import numpy as np
 
 
 def lovo_split(dataset, index, with_b0=False):

src/eddymotion/estimator.py

@@ -36,6 +36,7 @@
 
 from eddymotion.data.splitting import lovo_split
 from eddymotion.model import ModelFactory
+from eddymotion.utils import SortingStrategy, sort_dwdata_indices
 
 
 class EddyMotionEstimator:
@@ -88,22 +89,15 @@ def fit(
 
         align_kwargs = align_kwargs or {}
 
-        index_order = _sort_dwdata_indices(seed, len(dwdata))
+        index_order = sort_dwdata_indices(dwdata, SortingStrategy.RANDOM, seed=None)
 
         if "num_threads" not in align_kwargs and omp_nthreads is not None:
             align_kwargs["num_threads"] = omp_nthreads
 
         n_iter = len(models)
         for i_iter, model in enumerate(models):
-            reg_target_type = (
-                "dwi" if model.lower() not in ("b0", "s0", "avg", "average", "mean") else "b0"
-            )
-
-            # When downsampling these need to be set per-level
             bmask_img = _prepare_brainmask_data(dwdata.brainmask, dwdata.affine)
 
-            _prepare_kwargs(dwdata, kwargs)
-
             single_model = model.lower() in (
                 "b0",
                 "s0",
@@ -241,35 +235,6 @@ def _to_nifti(data, affine, filename, clip=True):
     nii.to_filename(filename)
 
 
-def _sort_dwdata_indices(seed, dwi_vol_count):
-    """Sort the DWI data volume indices.
-
-    Parameters
-    ----------
-    seed : :obj:`int` or :obj:`bool`
-        Seed the random number generator. If an integer, the value is used to initialize the
-        generator; if ``True``, the arbitrary value of ``20210324`` is used to initialize it.
-    dwi_vol_count : :obj:`int`
-        Number of DWI volumes.
-
-    Returns
-    -------
-    index_order : :obj:`numpy.ndarray`
-        Index order.
-    """
-
-    _seed = None
-    if seed or seed == 0:
-        _seed = 20210324 if seed is True else seed
-
-    rng = np.random.default_rng(_seed)
-
-    index_order = np.arange(dwi_vol_count)
-    rng.shuffle(index_order)
-
-    return index_order
-
-
 def _prepare_brainmask_data(brainmask, affine):
     """Prepare the brainmask data: save the data to disk.
 

src/eddymotion/utils.py

@@ -0,0 +1,176 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2022 The NiPreps Developers <[email protected]>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""Utils to sort the DWI data volume indices"""
+
+from enum import Enum
+
+import numpy as np
+
+
+class SortingStrategy(Enum):
+    """
+    Enum class representing different sorting strategies.
+
+    Available sorting strategies:
+    - LINEAR: Sorts the items in a linear order.
+    - RANDOM: Sorts the items in a random order.
+    - BVALUE: Sorts the items based on their b-value.
+    - CENTRALSYM: Sorts the items based on their central symmetry.
+    """
+
+    LINEAR = "linear"
+    RANDOM = "random"
+    BVALUE = "bvalue"
+    CENTRALSYM = "centralsym"
+
+
+def sort_dwdata_indices(dwdata, strategy, seed=None):
+    """Sort the DWI data volume indices following the given strategy.
+
+    Parameters
+    ----------
+    dwdata : :obj:`~eddymotion.dmri.DWI`
+        DWI dataset, represented by this tool's internal type.
+    strategy : :obj:`~eddymotion.utils.SortingStrategy`
+        The sorting strategy to be used. Available options are:
+        - SortingStrategy.LINEAR: Sort the indices linearly.
+        - SortingStrategy.RANDOM: Sort the indices randomly.
+        - SortingStrategy.BVALUE: Sort the indices based on the last column of gradients in ascending order.
+        - SortingStrategy.CENTRALSYM: Sort the indices in a central symmetric manner.
+    seed : :obj:`int` or :obj:`bool`, optional
+        Seed the random number generator. If an integer, the value is used to
+        initialize the generator; if ``True``, the arbitrary value
+        of ``20210324`` is used to initialize it.
+
+    Returns
+    -------
+    index_order : :obj:`numpy.ndarray`
+        The sorted index order.
+    """
+    if strategy == SortingStrategy.LINEAR:
+        return linear_action(dwdata)
+    elif strategy == SortingStrategy.RANDOM:
+        return random_action(dwdata, seed)
+    elif strategy == SortingStrategy.BVALUE:
+        return bvalue_action(dwdata)
+    elif strategy == SortingStrategy.CENTRALSYM:
+        return centralsym_action(dwdata)
+    else:
+        raise ValueError("Invalid sorting strategy")
+
+
+def linear_action(dwdata):
+    """
+    Sort the DWI data volume indices linearly
+
+    Parameters
+    ----------
+    dwdata : :obj:`~eddymotion.dmri.DWI` DWI dataset, represented by this tool's internal type.
+
+    Returns
+    -------
+    index_order : :obj:`numpy.ndarray`
+    The sorted index order.
+    """
+    index_order = np.arange(len(dwdata))
+
+    return index_order
+
+
+def random_action(dwdata, seed=None):
+    """Sort the DWI data volume indices.
+
+    Parameters
+    ----------
+    dwdata : :obj:`~eddymotion.dmri.DWI` DWI dataset, represented by this tool's internal type.
+    seed : :obj:`int` or :obj:`bool`, optional
+        Seed the random number generator. If an integer, the value is used to
+        initialize the generator; if ``True``, the arbitrary value
+        of ``20210324`` is used to initialize it.
+
+    Returns
+    -------
+    index_order : :obj:`numpy.ndarray`
+        The sorted index order.
+    """
+
+    _seed = None
+    if seed or seed == 0:
+        _seed = 20210324 if seed is True else seed
+
+    rng = np.random.default_rng(_seed)
+
+    index_order = np.arange(len(dwdata))
+    rng.shuffle(index_order)
+
+    return index_order
+
+
+def bvalue_action(dwdata):
+    """
+    Sort the DWI data volume indices in ascending order based on the last column of gradients.
+
+    Parameters
+    ----------
+    dwdata : :obj:`~eddymotion.dmri.DWI` DWI dataset, represented by this tool's internal type.
+
+    Returns
+    -------
+    numpy.ndarray: The sorted index order.
+    """
+    last_column = dwdata.gradients[:, -1]
+    index_order = np.argsort(last_column)
+    return index_order
+
+
+def centralsym_action(dwdata):
+    """
+    Sort the DWI data volume indices in a central symmetric manner.
+
+    Parameters
+    ----------
+    dwdata : :obj:`~eddymotion.dmri.DWI` DWI dataset, represented by this tool's internal type.
+
+    Returns
+    -------
+    numpy.ndarray: The sorted index order.
+
+    """
+    old_index = np.arange(len(dwdata))
+
+    index_order = old_index.copy()
+    if len(old_index) % 2 == 0:
+        middle_point = int(len(old_index) / 2 - 1)
+        index_order[0] = old_index[middle_point]
+
+        for i in np.arange(1, middle_point+1):
+            index_order[2 * i - 1] = old_index[middle_point + i]
+            index_order[2 * i] = old_index[middle_point - i]
+    else:
+        middle_point = int(len(old_index) / 2)
+        index_order[0] = old_index[middle_point]
+        for i in np.arange(1, middle_point + 1):
+            index_order[2 * i - 1] = old_index[middle_point + i]
+            index_order[2 * i] = old_index[middle_point - i]
+
+    return index_order

test/test_model.py

@@ -26,8 +26,8 @@
 import pytest
 
 from eddymotion import model
-from eddymotion.data.splitting import lovo_split
 from eddymotion.data.dmri import DWI
+from eddymotion.data.splitting import lovo_split
 
 
 def test_trivial_model():

test/test_splitting.py

@@ -21,7 +21,9 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Unit test testing the lovo_split function."""
+
 import numpy as np
+
 from eddymotion.data.dmri import DWI
 from eddymotion.data.splitting import lovo_split
 
@@ -50,13 +52,11 @@ def test_lovo_split(datadir):
     data.gradients[..., index] = 1
 
     # Apply the lovo_split function at the specified index
-    (train_data, train_gradients), \
-        (test_data, test_gradients) = lovo_split(data, index)
+    (train_data, train_gradients), (test_data, test_gradients) = lovo_split(data, index)
 
     # Check if the test data contains only 1s
     # and the train data contains only 0s after the split
     assert np.all(test_data == 1)
     assert np.all(train_data == 0)
     assert np.all(test_gradients == 1)
     assert np.all(train_gradients == 0)
-