junifer 0.0.7.dev132__tar.gz → 0.0.7.dev153__tar.gz

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: junifer
-Version: 0.0.7.dev132
+Version: 0.0.7.dev153
 Summary: JUelich NeuroImaging FEature extractoR
 Author-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
 Maintainer-email: Fede Raimondo <f.raimondo@fz-juelich.de>, Synchon Mandal <s.mandal@fz-juelich.de>
@@ -39,7 +39,7 @@ Requires-Dist: sqlalchemy<=2.1.0,>=2.0.25
 Requires-Dist: ruamel.yaml<0.19,>=0.17
 Requires-Dist: h5py>=3.10
 Requires-Dist: tqdm<4.67.0,>=4.66.1
-Requires-Dist: templateflow>=23.0.0
+Requires-Dist: templateflow<25.0.0,>=23.0.0
 Requires-Dist: lapy<2.0.0,>=1.0.0
 Requires-Dist: lazy_loader==0.4
 Requires-Dist: importlib_metadata; python_version < "3.9"

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/conda-env.yml

@@ -13,7 +13,7 @@ dependencies:
   - ruamel.yaml>=0.17,<0.19
   - h5py>=3.10
   - tqdm>=4.66.1,<4.67.0
-  - templateflow>=23.0.0
+  - templateflow>=23.0.0,<25.0.0
   - lapy>=1.0.0,<2.0.0
   - lazy_loader==0.4
   - importlib_metadata

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/docs/builtin.rst

@@ -743,5 +743,39 @@ Available
    Planned
    ~~~~~~~
 
+
+Maps
+----
+
+..
+    Provide a list of the maps that are implemented or planned.
+
+    Version added: The junifer version in which the maps was added.
+
+Available
+~~~~~~~~~
+
+.. list-table::
+   :widths: auto
+   :header-rows: 1
+
+   * - Name
+     - Options
+     - Keys
+     - Template Spaces
+     - Version Added
+     - Publication
+   * - Smith
+     - ``components``, ``dimension``
+     - | ``Smith_rsn_10``, ``Smith_rsn_20``, ``Smith_rsn_70``,
+       | ``Smith_bm_10``, ``Smith_bm_20``, ``Smith_bm_70``
+     - ``MNI152NLin6Asym``
+     - 0.0.7
+     - | S.M. Smith, P.T. Fox, K.L. Miller et al.
+       | Correspondence of the brain's functional architecture during activation and rest
+       | Proc. Natl. Acad. Sci. U.S.A. 106 (31) 13040-13045 (2009)
+       | https://doi.org/10.1073/pnas.0905267106
+
+
 ..
   helpful site for creating tables: https://rest-sphinx-memo.readthedocs.io/en/latest/ReST.html#tables

junifer-0.0.7.dev153/docs/changes/newsfragments/458.change

@@ -0,0 +1 @@
+:func:`.get_data`, :func:`.load_data`, :func:`.list_data`, :func:`.register_data` and :func:`.deregister_data` now support ``"maps"`` as a valid argument for ``kind`` by `Synchon Mandal`_

junifer-0.0.7.dev153/docs/changes/newsfragments/458.feature

@@ -0,0 +1 @@
+Introduce :class:`.MapsRegistry` to centralise probabilistic atlas (maps) data management by `Synchon Mandal`_

junifer-0.0.7.dev153/docs/changes/newsfragments/458.misc

@@ -0,0 +1 @@
+Constrain ``templateflow`` version to ``>=23.0.0,<25.0.0`` by `Synchon Mandal`_

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/docs/extending/index.rst

@@ -30,6 +30,7 @@ DataGrabbers, Preprocessors, Markers, etc.,  following the *junifer* way.
    parcellations
    coordinates
    masks
+   maps
    plugins
    data_registries
    data_types

junifer-0.0.7.dev153/docs/extending/maps.rst

@@ -0,0 +1,140 @@
+.. include:: ../links.inc
+
+.. _adding_maps:
+
+Adding Maps
+===========
+
+Maps in ``junifer`` are basically probabilistic atlases. They are differentiated
+from parcellations for ease of computation and to handle edge cases in a sane manner.
+Before you start adding your own maps, check whether ``junifer`` has
+the map(s) :ref:`in-built already <builtin>`. Perhaps, what is available
+there will suffice to achieve your goals. However, of course ``junifer`` will not
+have every map(s) available that you may want to use, and if so, it will
+be nice to be able to add it yourself using a format that ``junifer`` understands.
+
+Similarly, you may even be interested in creating your own custom maps
+and then adding them to ``junifer``, so you can use ``junifer`` to obtain
+different Markers to assess and validate your own maps. So, how can you do
+this?
+
+Since both of these use-cases are quite common, and not being able to use your
+favourite map(s) is of course quite a buzzkill, ``junifer`` actually
+provides the easy-to-use :func:`.register_data` function to do just that.
+Let's try to understand the API reference and then use this function to register our
+own map(s).
+
+From the API reference, we can see that it has 3 positional arguments:
+
+* ``kind``
+* ``name``
+* ``space``
+
+as well as one optional keyword argument: ``overwrite``.
+As the ``kind`` needs to be ``"maps"``, we can check
+``MapsRegistry.register`` for keyword arguments to be passed:
+
+* ``maps_path``
+* ``maps_labels``
+
+The ``name`` of the map(s) is up to you and will be the name that
+``junifer`` will use to refer to this particular maps. You can think of
+this as being similar to a key in a Python dictionary, i.e. a key that is used to
+obtain and operate on the actual maps data. This ``name`` must always
+be a string. For example, we could call our map(s)
+``"my_custom_maps"`` (Note, that in a real-world use case this is
+likely not a good name, and you should try to choose a meaningful name that
+conveys as much relevant information about your maps as necessary).
+
+The ``maps_path`` must be a ``str`` or ``Path`` object indicating a
+path to a valid 4D NIfTI image, which contains floating-point labels indicating the
+individual regions-of-interest (ROIs) of your map(s).
+
+We also want to make sure that we can associate each label with
+a human readable name (i.e. the name for each ROI). This serves naming the
+features that maps-based markers produce in an unambiguous way, such
+that a user can easily identify which ROIs were used to produce a specific
+feature (multiple ROIs, because some features consist of information from two
+or more ROIs, as for example in functional connectivity). Therefore, we provide
+junifer with a list of strings, that contains the names for each ROI. In this
+list, the label at the i-th position indicates the i-th index in the 4th dimension
+of the NIfTI image.
+
+Lastly, we specify the ``space`` that the map(s) is in, for example,
+``"MNI152NLin6Asym"`` or ``"native"`` (scanner-native space).
+
+Step 1: Prepare code to register a maps
+---------------------------------------
+
+Now we know everything that we need to know to make sure ``junifer`` can use our
+own map(s) to compute any maps-based Marker. A simple example could
+look like this:
+
+.. code-block:: python
+
+  from pathlib import Path
+
+  import numpy as np
+  from junifer.data import register_data
+
+
+  # these are of course just example paths, replace it with your own:
+  path_to_maps = (
+      Path.cwd() / "my_custom_maps.nii.gz"
+  )
+  path_to_labels = (
+      Path.cwd() / "my_custom_maps_labels.txt"
+  )
+
+  my_labels = list(np.loadtxt(path_to_labels, dtype=str))
+
+  register_data(
+      kind="maps",
+      name="my_custom_maps",
+      maps_path=path_to_maps,
+      maps_labels=my_labels,
+      space="MNI152NLin6Asym",
+  )
+
+We can run this code and it seems to work, however, how can we actually
+include the custom map(s) in a ``junifer`` pipeline using a
+:ref:`code-less YAML configuration <codeless>`?
+
+Step 2: Add maps registration to the YAML file
+----------------------------------------------
+
+In order to use the maps in a ``junifer`` pipeline configured by a YAML
+file, we can save the above code in a Python file, say
+``registering_my_maps.py``. We can then simply add this file using the
+``with`` keyword provided by ``junifer``:
+
+.. code-block:: yaml
+
+  with:
+    - registering_my_maps.py
+
+Afterwards continue configuring the rest of the pipeline in this YAML file, and
+you will be able to use this maps using the name you gave the
+maps when registering it. For example, we can add a
+``MapsAggregation`` Marker to demonstrate how this can be done:
+
+.. code-block:: yaml
+
+  markers:
+    - name: CustomMaps_mean
+      kind: MapsAggregation
+      maps: my_custom_maps
+      method: mean
+
+Now, you can simply use this YAML file to run your pipeline.
+
+.. important::
+
+   It's important to keep in mind that if the paths given in
+   ``registering_my_maps.py`` are relative paths, they will be interpreted
+   by ``junifer`` as relative to the jobs directory (i.e. where ``junifer`` will
+   create submit files, logs directory and so on). For simplicity, you may just
+   want to use absolute paths to avoid confusion, yet using relative paths is
+   likely a better way to make your pipeline directory / repository more portable
+   and therefore more reproducible for others. Really, once you understand how
+   these paths are interpreted by ``junifer``, it is quite easy.

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/junifer/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.7.dev132'
-__version_tuple__ = version_tuple = (0, 0, 7, 'dev132')
+__version__ = version = '0.0.7.dev153'
+__version_tuple__ = version_tuple = (0, 0, 7, 'dev153')
 
-__commit_id__ = commit_id = 'gb32daf1f6'
+__commit_id__ = commit_id = 'g42a09b3a7'

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/junifer/data/__init__.pyi

@@ -3,6 +3,7 @@ __all__ = [
     "CoordinatesRegistry",
     "DataDispatcher",
     "ParcellationRegistry",
+    "MapsRegistry",
     "MaskRegistry",
     "get_data",
     "list_data",
@@ -17,6 +18,7 @@ __all__ = [
 from .pipeline_data_registry_base import BasePipelineDataRegistry
 from .coordinates import CoordinatesRegistry
 from .parcellations import ParcellationRegistry
+from .maps import MapsRegistry
 from .masks import MaskRegistry
 
 from ._dispatch import (

{junifer-0.0.7.dev132 → junifer-0.0.7.dev153}/junifer/data/_dispatch.py

@@ -17,6 +17,7 @@ from numpy.typing import ArrayLike
 
 from ..utils import raise_error
 from .coordinates import CoordinatesRegistry
+from .maps import MapsRegistry
 from .masks import MaskRegistry
 from .parcellations import ParcellationRegistry
 from .pipeline_data_registry_base import BasePipelineDataRegistry
@@ -52,6 +53,7 @@ class DataDispatcher(MutableMapping):
                 {
                     "coordinates": CoordinatesRegistry,
                     "parcellation": ParcellationRegistry,
+                    "maps": MapsRegistry,
                     "mask": MaskRegistry,
                 }
             )
@@ -118,14 +120,14 @@ def get_data(
     extra_input: Optional[dict[str, Any]] = None,
 ) -> Union[
     tuple[ArrayLike, list[str]],  # coordinates
-    tuple["Nifti1Image", list[str]],  # parcellation
+    tuple["Nifti1Image", list[str]],  # parcellation / maps
     "Nifti1Image",  # mask
 ]:
     """Get tailored ``kind`` for ``target_data``.
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to fetch and apply.
     names : str or dict or list of str / dict
         The registered name(s) of the data.
@@ -166,7 +168,7 @@ def list_data(kind: str) -> list[str]:
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data registry to list.
 
     Returns
@@ -195,7 +197,9 @@ def load_data(
     **kwargs,
 ) -> Union[
     tuple[ArrayLike, list[str], str],  # coordinates
-    tuple[Optional["Nifti1Image"], list[str], Path, str],  # parcellation
+    tuple[
+        Optional["Nifti1Image"], list[str], Path, str
+    ],  # parcellation / maps
     tuple[
         Optional[Union["Nifti1Image", Callable]], Optional[Path], str
     ],  # mask
@@ -204,7 +208,7 @@ def load_data(
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to load.
     name : str
         The registered name of the data.
@@ -244,7 +248,7 @@ def register_data(
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to register.
     name : str
         The name to register.
@@ -277,7 +281,7 @@ def deregister_data(kind: str, name: str) -> None:
 
     Parameters
     ----------
-    kind : {"coordinates", "parcellation", "mask"}
+    kind : {"coordinates", "parcellation", "mask", "maps"}
         Kind of data to register.
     name : str
         The name to de-register.

junifer-0.0.7.dev153/junifer/data/maps/__init__.py

@@ -0,0 +1,9 @@
+"""Maps."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import lazy_loader as lazy
+
+
+__getattr__, __dir__, __all__ = lazy.attach_stub(__name__, __file__)

junifer-0.0.7.dev153/junifer/data/maps/__init__.pyi

@@ -0,0 +1,5 @@
+__all__ = [
+    "MapsRegistry",
+]
+
+from ._maps import MapsRegistry

junifer-0.0.7.dev153/junifer/data/maps/_ants_maps_warper.py

@@ -0,0 +1,156 @@
+"""Provide class for maps space warping via ANTs."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any, Optional
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, raise_error, run_ext_cmd
+from ..template_spaces import get_template, get_xfm
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["ANTsMapsWarper"]
+
+
+class ANTsMapsWarper:
+    """Class for maps space warping via ANTs.
+
+    This class uses ANTs ``antsApplyTransforms`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        maps_name: str,
+        maps_img: "Nifti1Image",
+        src: str,
+        dst: str,
+        target_data: dict[str, Any],
+        warp_data: Optional[dict[str, Any]],
+    ) -> "Nifti1Image":
+        """Warp ``maps_img`` to correct space.
+
+        Parameters
+        ----------
+        maps_name : str
+            The name of the maps.
+        maps_img : nibabel.nifti1.Nifti1Image
+            The maps image to transform.
+        src : str
+            The data type or template space to warp from.
+            It should be empty string if ``dst="T1w"``.
+        dst : str
+            The data type or template space to warp to.
+            `"T1w"` is the only allowed data type and it uses the resampled T1w
+            found in ``target_data.reference``. The ``"reference"``
+            key is added if the :class:`.SpaceWarper` is used or if the
+            data is provided in native space.
+        target_data : dict
+            The corresponding item of the data object to which the maps
+            will be applied.
+        warp_data : dict or None
+            The warp data item of the data object. The value is unused if
+            ``dst!="T1w"``.
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed maps image.
+
+        Raises
+        ------
+        ValueError
+            If ``warp_data`` is None when ``dst="T1w"``.
+
+        """
+        # Create element-scoped tempdir so that warped maps is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        prefix = (
+            f"ants_maps_warper_{maps_name}"
+            f"{'' if not src else f'_from_{src}'}_to_{dst}_"
+            f"{uuid.uuid1()}"
+        )
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix=prefix,
+        )
+
+        # Native space warping
+        if dst == "native":  # pragma: no cover
+            # Warp data check
+            if warp_data is None:
+                raise_error("No `warp_data` provided")
+            if "reference" not in target_data:
+                raise_error("No `reference` provided")
+            if "path" not in target_data["reference"]:
+                raise_error("No `path` provided in `reference`")
+
+            logger.debug("Using ANTs for maps transformation")
+
+            # Save existing maps image to a tempfile
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            nib.save(maps_img, prewarp_maps_path)
+
+            # Create a tempfile for warped output
+            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {prewarp_maps_path.resolve()}",
+                # use resampled reference
+                f"-r {target_data['reference']['path'].resolve()}",
+                f"-t {warp_data['path'].resolve()}",
+                f"-o {warped_maps_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Template space warping
+        else:
+            logger.debug(f"Using ANTs to warp maps from {src} to {dst}")
+
+            # Get xfm file
+            xfm_file_path = get_xfm(src=src, dst=dst)
+            # Get template space image
+            template_space_img = get_template(
+                space=dst,
+                target_img=maps_img,
+                extra_input=None,
+            )
+            # Save template to a tempfile
+            template_space_img_path = element_tempdir / f"{dst}_T1w.nii.gz"
+            nib.save(template_space_img, template_space_img_path)
+
+            # Save existing maps image to a tempfile
+            prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+            nib.save(maps_img, prewarp_maps_path)
+
+            # Create a tempfile for warped output
+            warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+            # Set antsApplyTransforms command
+            apply_transforms_cmd = [
+                "antsApplyTransforms",
+                "-d 3",
+                "-e 3",
+                "-n LanczosWindowedSinc",
+                f"-i {prewarp_maps_path.resolve()}",
+                f"-r {template_space_img_path.resolve()}",
+                f"-t {xfm_file_path.resolve()}",
+                f"-o {warped_maps_path.resolve()}",
+            ]
+            # Call antsApplyTransforms
+            run_ext_cmd(name="antsApplyTransforms", cmd=apply_transforms_cmd)
+
+        # Load nifti
+        return nib.load(warped_maps_path)

junifer-0.0.7.dev153/junifer/data/maps/_fsl_maps_warper.py

@@ -0,0 +1,85 @@
+"""Provide class for maps space warping via FSL FLIRT."""
+
+# Authors: Synchon Mandal <s.mandal@fz-juelich.de>
+# License: AGPL
+
+import uuid
+from typing import TYPE_CHECKING, Any
+
+import nibabel as nib
+
+from ...pipeline import WorkDirManager
+from ...utils import logger, run_ext_cmd
+
+
+if TYPE_CHECKING:
+    from nibabel.nifti1 import Nifti1Image
+
+
+__all__ = ["FSLMapsWarper"]
+
+
+class FSLMapsWarper:
+    """Class for maps space warping via FSL FLIRT.
+
+    This class uses FSL FLIRT's ``applywarp`` for transformation.
+
+    """
+
+    def warp(
+        self,
+        maps_name: str,
+        maps_img: "Nifti1Image",
+        target_data: dict[str, Any],
+        warp_data: dict[str, Any],
+    ) -> "Nifti1Image":  # pragma: no cover
+        """Warp ``maps_img`` to correct space.
+
+        Parameters
+        ----------
+        maps_name : str
+            The name of the maps.
+        maps_img : nibabel.nifti1.Nifti1Image
+            The maps image to transform.
+        target_data : dict
+            The corresponding item of the data object to which the maps
+            will be applied.
+        warp_data : dict
+            The warp data item of the data object.
+
+        Returns
+        -------
+        nibabel.nifti1.Nifti1Image
+            The transformed maps image.
+
+        """
+        logger.debug("Using FSL for maps transformation")
+
+        # Create element-scoped tempdir so that warped maps is
+        # available later as nibabel stores file path reference for
+        # loading on computation
+        element_tempdir = WorkDirManager().get_element_tempdir(
+            prefix=f"fsl_maps_warper_{maps_name}_{uuid.uuid1()}"
+        )
+
+        # Save existing maps image to a tempfile
+        prewarp_maps_path = element_tempdir / "prewarp_maps.nii.gz"
+        nib.save(maps_img, prewarp_maps_path)
+
+        # Create a tempfile for warped output
+        warped_maps_path = element_tempdir / "maps_warped.nii.gz"
+        # Set applywarp command
+        applywarp_cmd = [
+            "applywarp",
+            "--interp=spline",
+            f"-i {prewarp_maps_path.resolve()}",
+            # use resampled reference
+            f"-r {target_data['reference']['path'].resolve()}",
+            f"-w {warp_data['path'].resolve()}",
+            f"-o {warped_maps_path.resolve()}",
+        ]
+        # Call applywarp
+        run_ext_cmd(name="applywarp", cmd=applywarp_cmd)
+
+        # Load nifti
+        return nib.load(warped_maps_path)