From b3abb6cbf6ae7d58b1325bf813905c4871a875b9 Mon Sep 17 00:00:00 2001 From: NiPreps Bot Date: Mon, 8 Apr 2024 20:23:04 +0000 Subject: [PATCH] docs(main): Update docs of development line --- main/.buildinfo | 2 +- main/_modules/eddymotion/data/dmri.html | 11 +- main/_modules/eddymotion/data/pet.html | 11 +- main/_modules/eddymotion/data/splitting.html | 11 +- main/_modules/eddymotion/data/utils.html | 11 +- main/_modules/eddymotion/estimator.html | 11 +- main/_modules/eddymotion/model/base.html | 11 +- main/_modules/eddymotion/utils.html | 443 +++++++++++++++++++ main/_modules/eddymotion/viz.html | 11 +- main/_modules/index.html | 12 +- main/_sources/api/eddymotion.utils.rst.txt | 7 + main/_sources/developers.rst.txt | 1 + main/_static/documentation_options.js | 2 +- main/api/eddymotion.data.dmri.html | 11 +- main/api/eddymotion.data.html | 11 +- main/api/eddymotion.data.pet.html | 11 +- main/api/eddymotion.data.splitting.html | 11 +- main/api/eddymotion.data.utils.html | 11 +- main/api/eddymotion.estimator.html | 11 +- main/api/eddymotion.model.base.html | 17 +- main/api/eddymotion.model.html | 11 +- main/api/eddymotion.utils.html | 410 +++++++++++++++++ main/api/eddymotion.viz.html | 17 +- main/changes.html | 11 +- main/developers.html | 18 +- main/genindex.html | 44 +- main/index.html | 12 +- main/installation.html | 11 +- main/links.html | 11 +- main/objects.inv | Bin 1047 -> 1104 bytes main/py-modindex.html | 17 +- main/search.html | 11 +- main/searchindex.js | 2 +- 33 files changed, 1065 insertions(+), 137 deletions(-) create mode 100644 main/_modules/eddymotion/utils.html create mode 100644 main/_sources/api/eddymotion.utils.rst.txt create mode 100644 main/api/eddymotion.utils.html diff --git a/main/.buildinfo b/main/.buildinfo index c73db5de..de2b4410 100644 --- a/main/.buildinfo +++ b/main/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done. -config: b2cea85f3596e30dbcd5b1f0a4c099db +config: 44f68a0e2ab09edafa0073714e68cfe3 tags: 645f666f9bcd5a90fca523b33c5a78b7 diff --git a/main/_modules/eddymotion/data/dmri.html b/main/_modules/eddymotion/data/dmri.html index ed58c9a0..bf7017ac 100644 --- a/main/_modules/eddymotion/data/dmri.html +++ b/main/_modules/eddymotion/data/dmri.html @@ -5,7 +5,7 @@ - eddymotion.data.dmri - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.dmri - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
-
eddymotion 24.0.0.dev218+gecd7ce8 documentation
 +
eddymotion 24.0.0.dev219+g6128b37 documentation
@@ -145,14 +145,14 @@
eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
+
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -520,7 +521,7 @@

    Source code for eddymotion.data.dmri
    -
    +
    diff --git a/main/_modules/eddymotion/data/pet.html b/main/_modules/eddymotion/data/pet.html index 6e2e1a04..429aab24 100644 --- a/main/_modules/eddymotion/data/pet.html +++ b/main/_modules/eddymotion/data/pet.html @@ -5,7 +5,7 @@ - eddymotion.data.pet - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.pet - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -445,7 +446,7 @@

    Source code for eddymotion.data.pet
    -
    +
    diff --git a/main/_modules/eddymotion/data/splitting.html b/main/_modules/eddymotion/data/splitting.html index d1cc2325..9365d554 100644 --- a/main/_modules/eddymotion/data/splitting.html +++ b/main/_modules/eddymotion/data/splitting.html @@ -5,7 +5,7 @@ - eddymotion.data.splitting - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.splitting - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -338,7 +339,7 @@

    Source code for eddymotion.data.splitting
    -
    +
    diff --git a/main/_modules/eddymotion/data/utils.html b/main/_modules/eddymotion/data/utils.html index cf6841f5..c16e7691 100644 --- a/main/_modules/eddymotion/data/utils.html +++ b/main/_modules/eddymotion/data/utils.html @@ -5,7 +5,7 @@ - eddymotion.data.utils - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.utils - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -294,7 +295,7 @@

    Source code for eddymotion.data.utils
    -
    +
    diff --git a/main/_modules/eddymotion/estimator.html b/main/_modules/eddymotion/estimator.html index 7722d9de..d4dec776 100644 --- a/main/_modules/eddymotion/estimator.html +++ b/main/_modules/eddymotion/estimator.html @@ -5,7 +5,7 @@ - eddymotion.estimator - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.estimator - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -712,7 +713,7 @@

    Source code for eddymotion.estimator
    -
    +
    diff --git a/main/_modules/eddymotion/model/base.html b/main/_modules/eddymotion/model/base.html index a8c606d0..912a21e5 100644 --- a/main/_modules/eddymotion/model/base.html +++ b/main/_modules/eddymotion/model/base.html @@ -5,7 +5,7 @@ - eddymotion.model.base - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.model.base - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -724,7 +725,7 @@

    Source code for eddymotion.model.base
    -
    +
    diff --git a/main/_modules/eddymotion/utils.html b/main/_modules/eddymotion/utils.html new file mode 100644 index 00000000..b59b24d2 --- /dev/null +++ b/main/_modules/eddymotion/utils.html @@ -0,0 +1,443 @@ + + + + + + + + eddymotion.utils - eddymotion 24.0.0.dev219+g6128b37 documentation + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    eddymotion 24.0.0.dev219+g6128b37 documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    +
    + +
    + +
    +
    +

    Source code for eddymotion.utils

    +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright 2024 The NiPreps Developers <nipreps@gmail.com>
+#
+# 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/
+#
+"""Iterators to traverse the volumes in a 4D image."""
+
+import random
+from itertools import chain, zip_longest
+from typing import Iterator
+
+
+
    
+[docs]
+def linear_iterator(size: int = None, **kwargs) -> Iterator[int]:
+    """
+    Traverse the dataset volumes in ascending order.
+
+    Parameters
+    ----------
+    size : :obj:`int`
+        Number of volumes in the dataset
+        (for instance, the number of orientations in a DWI)
+
+    Returns
+    -------
+    :obj:`~typing.Iterator`
+        The sorted index order.
+
+    Examples
+    --------
+    >>> list(linear_iterator(10))
+    [0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+
+    """
+    if size is None and "bvals" in kwargs:
+        size = len(kwargs["bvals"])
+    if size is None:
+        raise TypeError("Cannot build iterator without size")
+
+    return range(size)
    
+
+
+
+
    
+[docs]
+def random_iterator(size: int = None, **kwargs) -> Iterator[int]:
+    """
+    Traverse the dataset volumes randomly.
+
+    Parameters
+    ----------
+    size : :obj:`int`
+        Number of volumes in the dataset
+        (for instance, the number of orientations in a DWI)
+    seed : :obj:`int` or :obj:`bool` or :obj:`bool` or ``None``
+        If :obj:`int` or :obj:`str` or ``None``, initializes the seed of Python's random generator
+        with the given value.
+        If ``False``, the random generator is passed ``None``.
+        If ``True``, a default seed value is set.
+
+    Returns
+    -------
+    :obj:`~typing.Iterator`
+        The sorted index order.
+
+    Examples
+    --------
+    >>> list(random_iterator(15, seed=0))  # seed is 0
+    [1, 10, 9, 5, 11, 2, 3, 7, 8, 4, 0, 14, 12, 6, 13]
+    >>>  # seed is True -> the default value 20210324 is set
+    >>> list(random_iterator(15, seed=True))
+    [1, 12, 14, 5, 0, 11, 10, 9, 7, 8, 3, 13, 2, 6, 4]
+    >>> list(random_iterator(15, seed=20210324))
+    [1, 12, 14, 5, 0, 11, 10, 9, 7, 8, 3, 13, 2, 6, 4]
+    >>> list(random_iterator(15, seed=42))  # seed is 42
+    [8, 13, 7, 6, 14, 12, 5, 2, 9, 3, 4, 11, 0, 1, 10]
+
+    """
+
+    if size is None and "bvals" in kwargs:
+        size = len(kwargs["bvals"])
+    if size is None:
+        raise TypeError("Cannot build iterator without size")
+
+    _seed = kwargs.get("seed", None)
+    _seed = 20210324 if _seed is True else _seed
+
+    random.seed(None if _seed is False else _seed)
+
+    index_order = list(range(size))
+    random.shuffle(index_order)
+    return (x for x in index_order)
    
+
+
+
+
    
+[docs]
+def bvalue_iterator(size: int = None, **kwargs) -> Iterator[int]:
+    """
+    Traverse the volumes in a DWI dataset by growing b-value.
+
+    Parameters
+    ----------
+    bvalues : :obj:`list`
+        List of b-values corresponding to all orientations of the dataset.
+
+    Returns
+    -------
+    :obj:`~typing.Iterator`
+        The sorted index order.
+
+    Examples
+    --------
+    >>> list(bvalue_iterator(bvals=[0.0, 0.0, 1000.0, 1000.0, 700.0, 700.0, 2000.0, 2000.0, 0.0]))
+    [0, 1, 8, 4, 5, 2, 3, 6, 7]
+
+    """
+    bvals = kwargs.get("bvals", None)
+    if bvals is None:
+        raise TypeError("Keyword argument bvals is required")
+    indexed_bvals = sorted([(round(b, 2), i) for i, b in enumerate(bvals)])
+    return (index[1] for index in indexed_bvals)
    
+
+
+
+
    
+[docs]
+def centralsym_iterator(size: int = None, **kwargs) -> Iterator[int]:
+    """
+    Traverse the dataset starting from the center and alternatingly progressing to the sides.
+
+    Parameters
+    ----------
+    size : :obj:`int`
+        Number of volumes in the dataset
+        (for instance, the number of orientations in a DWI)
+
+    Returns
+    -------
+    :obj:`~typing.Iterator`
+        The sorted index order.
+
+    Examples
+    --------
+    >>> list(centralsym_iterator(10))
+    [5, 4, 6, 3, 7, 2, 8, 1, 9, 0]
+    >>> list(centralsym_iterator(11))
+    [5, 4, 6, 3, 7, 2, 8, 1, 9, 0, 10]
+
+    """
+    if size is None and "bvals" in kwargs:
+        size = len(kwargs["bvals"])
+    if size is None:
+        raise TypeError("Cannot build iterator without size")
+    linear = list(range(size))
+    return (
+        x
+        for x in chain.from_iterable(
+            zip_longest(
+                linear[size // 2 :],
+                reversed(linear[: size // 2]),
+            )
+        )
+        if x is not None
+    )
    
+
+
    +
    +
    +
    + +
    + + +
    +
    +
    +
    + Copyright © Copyright 2021, The eddymotion developers +
    + Made with Sphinx and @pradyunsg's + + Furo + +
    +
    + +
    +
    + +
    +
    + +
    +
    + + + + + + \ No newline at end of file diff --git a/main/_modules/eddymotion/viz.html b/main/_modules/eddymotion/viz.html index e8180364..0922bf82 100644 --- a/main/_modules/eddymotion/viz.html +++ b/main/_modules/eddymotion/viz.html @@ -5,7 +5,7 @@ - eddymotion.viz - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.viz - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -680,7 +681,7 @@

    Source code for eddymotion.viz
    -
    +
    diff --git a/main/_modules/index.html b/main/_modules/index.html index 8f5e0be5..cb523b97 100644 --- a/main/_modules/index.html +++ b/main/_modules/index.html @@ -5,7 +5,7 @@ - Overview: module code - eddymotion 24.0.0.dev218+gecd7ce8 documentation + Overview: module code - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -123,7 +123,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -145,14 +145,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -223,6 +224,7 @@

    All modules for which code is available

  • eddymotion.data.utils
  • eddymotion.estimator
  • eddymotion.model.base
    • +
  • eddymotion.utils
  • eddymotion.viz
    • @@ -256,7 +258,7 @@

    All modules for which code is available

    -
    +
    diff --git a/main/_sources/api/eddymotion.utils.rst.txt b/main/_sources/api/eddymotion.utils.rst.txt new file mode 100644 index 00000000..558e90ec --- /dev/null +++ b/main/_sources/api/eddymotion.utils.rst.txt @@ -0,0 +1,7 @@ +eddymotion.utils module +======================= + +.. automodule:: eddymotion.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/main/_sources/developers.rst.txt b/main/_sources/developers.rst.txt index 0d44320b..8cd62d50 100644 --- a/main/_sources/developers.rst.txt +++ b/main/_sources/developers.rst.txt @@ -32,4 +32,5 @@ Information on specific functions, classes, and methods. api/eddymotion.data.dmri api/eddymotion.estimator api/eddymotion.model + api/eddymotion.utils api/eddymotion.viz diff --git a/main/_static/documentation_options.js b/main/_static/documentation_options.js index ca25d89f..7cfb8afd 100644 --- a/main/_static/documentation_options.js +++ b/main/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '24.0.0.dev218+gecd7ce8', + VERSION: '24.0.0.dev219+g6128b37', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/main/api/eddymotion.data.dmri.html b/main/api/eddymotion.data.dmri.html index b8bccc5b..a3d51150 100644 --- a/main/api/eddymotion.data.dmri.html +++ b/main/api/eddymotion.data.dmri.html @@ -6,7 +6,7 @@ - eddymotion.data.dmri module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.dmri module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -408,7 +409,7 @@
    -
    +
    diff --git a/main/api/eddymotion.data.html b/main/api/eddymotion.data.html index 7f8097ec..df04d234 100644 --- a/main/api/eddymotion.data.html +++ b/main/api/eddymotion.data.html @@ -6,7 +6,7 @@ - eddymotion.data package - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data package - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -301,7 +302,7 @@

    Submodules +

    diff --git a/main/api/eddymotion.data.pet.html b/main/api/eddymotion.data.pet.html index ea03e105..e90c53cf 100644 --- a/main/api/eddymotion.data.pet.html +++ b/main/api/eddymotion.data.pet.html @@ -6,7 +6,7 @@ - eddymotion.data.pet module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.pet module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -378,7 +379,7 @@
    -
    +
    diff --git a/main/api/eddymotion.data.splitting.html b/main/api/eddymotion.data.splitting.html index 7a47099a..922ce6c9 100644 --- a/main/api/eddymotion.data.splitting.html +++ b/main/api/eddymotion.data.splitting.html @@ -6,7 +6,7 @@ - eddymotion.data.splitting module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.splitting module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -314,7 +315,7 @@
    -
    +
    diff --git a/main/api/eddymotion.data.utils.html b/main/api/eddymotion.data.utils.html index 545e36a9..45cf0673 100644 --- a/main/api/eddymotion.data.utils.html +++ b/main/api/eddymotion.data.utils.html @@ -6,7 +6,7 @@ - eddymotion.data.utils module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.data.utils module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -311,7 +312,7 @@
    -
    +
    diff --git a/main/api/eddymotion.estimator.html b/main/api/eddymotion.estimator.html index 071cf182..b747cf11 100644 --- a/main/api/eddymotion.estimator.html +++ b/main/api/eddymotion.estimator.html @@ -6,7 +6,7 @@ - eddymotion.estimator module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.estimator module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -334,7 +335,7 @@
    -
    +
    diff --git a/main/api/eddymotion.model.base.html b/main/api/eddymotion.model.base.html index 2909ffc9..00e93136 100644 --- a/main/api/eddymotion.model.base.html +++ b/main/api/eddymotion.model.base.html @@ -3,10 +3,10 @@ - + - eddymotion.model.base module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.model.base module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -347,12 +348,12 @@
    +
    diff --git a/main/api/eddymotion.model.html b/main/api/eddymotion.model.html index 5bc355f2..5b8e2d70 100644 --- a/main/api/eddymotion.model.html +++ b/main/api/eddymotion.model.html @@ -6,7 +6,7 @@ - eddymotion.model package - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.model package - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -416,7 +417,7 @@

    Submodules +

    diff --git a/main/api/eddymotion.utils.html b/main/api/eddymotion.utils.html new file mode 100644 index 00000000..ccd6a2af --- /dev/null +++ b/main/api/eddymotion.utils.html @@ -0,0 +1,410 @@ + + + + + + + + + eddymotion.utils module - eddymotion 24.0.0.dev219+g6128b37 documentation + + + + + + + + + + + + + + + + + Contents + + + + + + Menu + + + + + + + + Expand + + + + + + Light mode + + + + + + + + + + + + + + Dark mode + + + + + + + Auto light/dark mode + + + + + + + + + + + + + + + + + + + +
    +
    +
    + +
    +
    +
    eddymotion 24.0.0.dev219+g6128b37 documentation
     +
    +
    +
    + +
    + +
    +
    + +
    +
    +
    + + + + + Back to top + +
    + +
    + +
    + +
    +
    +
    +

    eddymotion.utils module#

    +

    Iterators to traverse the volumes in a 4D image.

    +
    +
    +eddymotion.utils.bvalue_iterator(size: int | None = None, **kwargs) → Iterator[int][source]#
    +

    Traverse the volumes in a DWI dataset by growing b-value.

    +
    +
    Parameters:
    +

    bvalues (list) – List of b-values corresponding to all orientations of the dataset.

    +
    +
    Returns:
    +

    The sorted index order.

    +
    +
    Return type:
    +

    Iterator

    +
    +
    +

    Examples

    +
    >>> list(bvalue_iterator(bvals=[0.0, 0.0, 1000.0, 1000.0, 700.0, 700.0, 2000.0, 2000.0, 0.0]))
+[0, 1, 8, 4, 5, 2, 3, 6, 7]
+
    +
    +
    + +
    +
    +eddymotion.utils.centralsym_iterator(size: int | None = None, **kwargs) → Iterator[int][source]#
    +

    Traverse the dataset starting from the center and alternatingly progressing to the sides.

    +
    +
    Parameters:
    +

    size (int) – Number of volumes in the dataset +(for instance, the number of orientations in a DWI)

    +
    +
    Returns:
    +

    The sorted index order.

    +
    +
    Return type:
    +

    Iterator

    +
    +
    +

    Examples

    +
    >>> list(centralsym_iterator(10))
+[5, 4, 6, 3, 7, 2, 8, 1, 9, 0]
+>>> list(centralsym_iterator(11))
+[5, 4, 6, 3, 7, 2, 8, 1, 9, 0, 10]
+
    +
    +
    + +
    +
    +eddymotion.utils.linear_iterator(size: int | None = None, **kwargs) → Iterator[int][source]#
    +

    Traverse the dataset volumes in ascending order.

    +
    +
    Parameters:
    +

    size (int) – Number of volumes in the dataset +(for instance, the number of orientations in a DWI)

    +
    +
    Returns:
    +

    The sorted index order.

    +
    +
    Return type:
    +

    Iterator

    +
    +
    +

    Examples

    +
    >>> list(linear_iterator(10))
+[0, 1, 2, 3, 4, 5, 6, 7, 8, 9]
+
    +
    +
    + +
    +
    +eddymotion.utils.random_iterator(size: int | None = None, **kwargs) → Iterator[int][source]#
    +

    Traverse the dataset volumes randomly.

    +
    +
    Parameters:
    +
      +

    • size (int) – Number of volumes in the dataset +(for instance, the number of orientations in a DWI)

      • +

    • seed (int or bool or bool or None) – If int or str or None, initializes the seed of Python’s random generator +with the given value. +If False, the random generator is passed None. +If True, a default seed value is set.

      • +
    +
    +
    Returns:
    +

    The sorted index order.

    +
    +
    Return type:
    +

    Iterator

    +
    +
    +

    Examples

    +
    >>> list(random_iterator(15, seed=0))  # seed is 0
+[1, 10, 9, 5, 11, 2, 3, 7, 8, 4, 0, 14, 12, 6, 13]
+>>>  # seed is True -> the default value 20210324 is set
+>>> list(random_iterator(15, seed=True))
+[1, 12, 14, 5, 0, 11, 10, 9, 7, 8, 3, 13, 2, 6, 4]
+>>> list(random_iterator(15, seed=20210324))
+[1, 12, 14, 5, 0, 11, 10, 9, 7, 8, 3, 13, 2, 6, 4]
+>>> list(random_iterator(15, seed=42))  # seed is 42
+[8, 13, 7, 6, 14, 12, 5, 2, 9, 3, 4, 11, 0, 1, 10]
+
    +
    +
    + +
    + +
    +
    + +
    + +
    +
    + + + + + + \ No newline at end of file diff --git a/main/api/eddymotion.viz.html b/main/api/eddymotion.viz.html index f9efe691..d43bd01b 100644 --- a/main/api/eddymotion.viz.html +++ b/main/api/eddymotion.viz.html @@ -3,10 +3,10 @@ - + - eddymotion.viz module - eddymotion 24.0.0.dev218+gecd7ce8 documentation + eddymotion.viz module - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -403,14 +404,14 @@
    - +
    Previous
    -
    eddymotion.model.base module
    +
    eddymotion.utils module
     @@ -463,7 +464,7 @@
    -
    +
    diff --git a/main/changes.html b/main/changes.html index 578bfb4f..792cc3f3 100644 --- a/main/changes.html +++ b/main/changes.html @@ -6,7 +6,7 @@ - What’s new? - eddymotion 24.0.0.dev218+gecd7ce8 documentation + What’s new? - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -294,7 +295,7 @@

    0.1.4 (April 12, 2021) +

    diff --git a/main/developers.html b/main/developers.html index 6afb6d71..706baf80 100644 --- a/main/developers.html +++ b/main/developers.html @@ -6,7 +6,7 @@ - For developers - eddymotion 24.0.0.dev218+gecd7ce8 documentation + For developers - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -146,14 +146,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -382,6 +383,13 @@

    Library API (application program interface)eddymotion.utils module +
  • eddymotion.viz module

    • diff --git a/main/genindex.html b/main/genindex.html index db1184b0..7ed88347 100644 --- a/main/genindex.html +++ b/main/genindex.html @@ -4,7 +4,7 @@ - Index - eddymotion 24.0.0.dev218+gecd7ce8 documentation + Index - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -122,7 +122,7 @@
    -
    eddymotion 24.0.0.dev218+gecd7ce8 documentation
     +
    eddymotion 24.0.0.dev219+g6128b37 documentation
    @@ -144,14 +144,14 @@
    eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
    +
  • eddymotion.utils module
  • eddymotion.viz module
    • @@ -218,7 +219,7 @@

    Index

    -
    A | B | D | E | F | G | I | L | M | P | R | S | T
    +
    A | B | C | D | E | F | G | I | L | M | P | R | S | T

    A

    @@ -258,12 +259,24 @@

    B

    +
    +

    C

    + + +
    +
    +

    D

    @@ -337,8 +350,6 @@

    E

  • module
    • - - +
    • eddymotion.estimator @@ -346,6 +357,8 @@

      E

    • module
    +
    • eddymotion.model @@ -358,6 +371,13 @@

      E

      • +
    • + eddymotion.utils + +
    • @@ -451,6 +471,8 @@

      I

      L

        +
      • linear_iterator() (in module eddymotion.utils) +
      • load() (in module eddymotion.data.dmri)
          @@ -494,6 +516,8 @@

          M

        • eddymotion.model
        • eddymotion.model.base +
          • +
        • eddymotion.utils
        • eddymotion.viz
          • @@ -551,6 +575,10 @@

          P

          R

          + + + + +
          @@ -283,6 +284,7 @@

          Contents
        • eddymotion.data.dmri module
        • eddymotion.estimator module
        • eddymotion.model package
          • +
        • eddymotion.utils module
        • eddymotion.viz module
          • @@ -355,7 +357,7 @@

          Contents - + diff --git a/main/installation.html b/main/installation.html index b291d650..2b8dff4f 100644 --- a/main/installation.html +++ b/main/installation.html @@ -6,7 +6,7 @@ - Installation - eddymotion 24.0.0.dev218+gecd7ce8 documentation + Installation - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
          -
          eddymotion 24.0.0.dev218+gecd7ce8 documentation
           +
          eddymotion 24.0.0.dev219+g6128b37 documentation
          @@ -146,14 +146,14 @@
          eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
          +
        • eddymotion.utils module
        • eddymotion.viz module
          • @@ -304,7 +305,7 @@

          External Dependencies

          -
          +
          diff --git a/main/links.html b/main/links.html index 8d056cb8..491c00c7 100644 --- a/main/links.html +++ b/main/links.html @@ -6,7 +6,7 @@ - <no title> - eddymotion 24.0.0.dev218+gecd7ce8 documentation + <no title> - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -124,7 +124,7 @@
          -
          eddymotion 24.0.0.dev218+gecd7ce8 documentation
           +
          eddymotion 24.0.0.dev219+g6128b37 documentation
          @@ -146,14 +146,14 @@
          eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
          +
        • eddymotion.utils module
        • eddymotion.viz module
          • @@ -250,7 +251,7 @@
          -
          +
          diff --git a/main/objects.inv b/main/objects.inv index 4babfda91db0b779cf7106f3ccedcb952f992eb6..71974b67351e1c77bcfb7fa8e3f71f0c12df0bf7 100644 GIT binary patch delta 989 zcmV<310wvF2+#5ORa2!(i_}YtnB#;M zg9RjQdbQWs>+MN~O=8EHZ6M~Rs^Of^hXeeE6CmVJ2u%f_6Ra^R4|jziI|k?m;gWuW zZvT9%3--ZU%s!%7a@kJ`Nu7|&$cr>zJU>*ljA5nFtphejnd3aC94dbp)>_i_PQx_d zT4KrztX^U=-$9Cqyy{7;e?=rhk=jhEh|rt@BLyyFBBdzOoHF3JsAs(Zy%l5{bOSm* zQ({7a>zMg0nb2tm93#@2S_p+{77M9NLbb$PH|<(purNWQX%j=m_$ReE|h!HXYVNj>Xp)jfH>L8ZAxZW8Jtsrw<72 z1w4dm4p4e*osXlyEYgbvNia&2Z=YZcz!$q2S$3v^8mR97f3555SmRQE`B^r z9pYj&8BzP+6gPRxZc_HVShJ&;$@(r#T$H!j5=;_rSyWWBEo{yGZg5l zqdr(~MGb+)TQ}h<>q8CH+i+yO1YE1ZgKXy^*?B&;2J1a$J4mTEs&+hh4j+z(&&9SU z18(knOdX0yKxPi?SVn@Gn}BiqyWvAmn^v8-3!MB;zfG@~+OuG>fh8={ng9!q!E zL8?-vf=yv2E@gNPYyzt;{AE}ki%t_Dh-n@G#RKSxZtOP1M2e~LASLC#|yfZ0yNAS zd6`v7$BTd3t&aNr`(MzO0*3kB8#U_n?x)+^_At3UqND%s=>6;F?CkF1HlH2T@82J@ zE8G2v9?Nm1wZpvArb8DVM^?7Qd;^_;j!o9hekR6A%)%x6< z32WPu4RFc{ywxtXepXJWR_pRm{hPFANAj7)vI$Y&m?@1Jv*p8%b=!Wzwk?VIPQG;F zt{bf3XD*PYn!%UEB&H|a@-RDfSdT~hX|sW!^*Y?14(24oyWYxtzO!xD(Y9HipSJ(0 LTCV>9k(>X%SSjS_ delta 932 zcmV;V16%yi2$u+uN&z^LOFMs<&5qk35XbL+3Z(X$boaWdTD3}6T2(8p)JS`@h#4nz zF<3ydn?3b4`g(nmVw2c$Y8!~TL@~_#Jj2J|3_!@C5Sj`;Cs<=t9_|W3b_~!B!X^C# z-TwJj7wm(zn0-XEk~$%kkr!#ccz&p88N*7UTL)~6GRJvNIaGfzthJ=;orY<^ zwZxPcSiQt#zJnAIdDW9x|B6V2BDEu_B0_Ttj1;(xiIk#9bIO3@qMr2v^j45*&<*JL zOo<5vu49g8$%IZj;24qC)Iumsvsg%F22@MTRW4)^3#vu*Nis-Ib4_FLn82jsphx2?C<6$-Uu|bc*(cOsCj!Ur59`!5f-GLp+HX^ z^}%{8Y6vXex(QcVA8Mf9h9lz*z_l7Y$llZUF$Ff=W71o76Nz8bjLM9;&cqFDh*AoA zyg<4RQeBuS*c8BZ%J3T41Xg|hlwomqvU*6(!Cca}08me1 zgOnzBL}X}oJ9ul4E`3Uzy_gSPGIaaof;Kl)sMp&r&}5*db-_<%FY5ChLAMpL;|1M% z6%BJnUSJNwf8Cs&AYI%>{7}Dt zf6SFK4wHXRTLfKr99h{G^9^(+>)2$yp0`;4{ryKF4zFJm0()Sh1le(DTdmK%8Q!)n z*#M`Uz+3H7t6k-EYPBv8)!(EwJCe^VmQDD^Oli!Ry>jYUx9ulv+mbNKUpjHu4c728 z7f4gh;7ei#rYGF;FgtZvk4O68yWR@0%(h)e+h%=!+Wx0%as30; Ga8zQxAj?bu diff --git a/main/py-modindex.html b/main/py-modindex.html index 34182f87..9efff4fa 100644 --- a/main/py-modindex.html +++ b/main/py-modindex.html @@ -4,7 +4,7 @@ - Python Module Index - eddymotion 24.0.0.dev218+gecd7ce8 documentation + Python Module Index - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -122,7 +122,7 @@
          -
          eddymotion 24.0.0.dev218+gecd7ce8 documentation
           +
          eddymotion 24.0.0.dev219+g6128b37 documentation
          @@ -144,14 +144,14 @@
          eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
          +
        • eddymotion.utils module
        • eddymotion.viz module
          • @@ -282,6 +283,12 @@

          Python Module Index

          eddymotion.model.base
              + eddymotion.utils +
              @@ -321,7 +328,7 @@

          Python Module Index

          - + diff --git a/main/search.html b/main/search.html index 66ff7d52..79996892 100644 --- a/main/search.html +++ b/main/search.html @@ -4,7 +4,7 @@ - Search - eddymotion 24.0.0.dev218+gecd7ce8 documentation + Search - eddymotion 24.0.0.dev219+g6128b37 documentation @@ -121,7 +121,7 @@
          -
          eddymotion 24.0.0.dev218+gecd7ce8 documentation
           +
          eddymotion 24.0.0.dev219+g6128b37 documentation
          @@ -143,14 +143,14 @@
          eddymotion - 24.0.0.dev218 (dev) + 24.0.0.dev219 (dev)
          +
        • eddymotion.utils module
        • eddymotion.viz module
          • @@ -257,7 +258,7 @@
          -
          +
          diff --git a/main/searchindex.js b/main/searchindex.js index 467e4afd..102c5622 100644 --- a/main/searchindex.js +++ b/main/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["api/eddymotion.data", "api/eddymotion.data.dmri", "api/eddymotion.data.pet", "api/eddymotion.data.splitting", "api/eddymotion.data.utils", "api/eddymotion.estimator", "api/eddymotion.model", "api/eddymotion.model.base", "api/eddymotion.viz", "changes", "developers", "index", "installation", "links"], "filenames": ["api/eddymotion.data.rst", "api/eddymotion.data.dmri.rst", "api/eddymotion.data.pet.rst", "api/eddymotion.data.splitting.rst", "api/eddymotion.data.utils.rst", "api/eddymotion.estimator.rst", "api/eddymotion.model.rst", "api/eddymotion.model.base.rst", "api/eddymotion.viz.rst", "changes.rst", "developers.rst", "index.rst", "installation.rst", "links.rst"], "titles": ["eddymotion.data package", "eddymotion.data.dmri module", "eddymotion.data.pet module", "eddymotion.data.splitting 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