junifer 0.0.5.dev152__tar.gz → 0.0.5.dev164__tar.gz

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev152
+Version: 0.0.5.dev164
 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>

junifer-0.0.5.dev164/docs/changes/newsfragments/136.enh

@@ -0,0 +1 @@
+Add test to be sure that :class:`.JuniferNiftiSpheresMasker` with mean aggregation function behaves exactly as :class:`nilearn.maskers.NiftiSpheresMasker` by `Synchon Mandal`_

junifer-0.0.5.dev164/docs/changes/newsfragments/327.doc

@@ -0,0 +1 @@
+Update "Queueing Jobs (HPC, HTC)" section by `Synchon Mandal`_

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/docs/using/queueing.rst

@@ -10,10 +10,10 @@ computational clusters. This is done by adding the ``queue`` section in the
 :ref:`codeless` file and executing the  ``junifer queue`` command.
 
 While junifer is meant to support `HTCondor`_, `SLURM`_ and local queueing
-using `GNU Parallel`_, only HTCondor is currently supported. This will be
-implemented in future releases of ``junifer``. If you are in immediate need of
-any of these schedulers, please create an issue on the `junifer github`_
-repository.
+using `GNU Parallel`_, only ``HTCondor`` and ``GNU Parallel`` are currently
+supported. This will be implemented in future releases of ``junifer``. If you are
+in immediate need of any of these schedulers, please create an issue on the
+`junifer github`_ repository.
 
 The ``queue`` section of the :ref:`codeless` must start by defining the
 following general parameters:
@@ -22,8 +22,8 @@ following general parameters:
   folder where the job files will be created, as well as any relevant file.
   Depending on the scheduler, it will also be listed in the queueing system
   with this name.
-* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` is
-  supported.
+* ``kind``: The kind of scheduler to be used. Currently, only ``HTCondor`` and
+  ``GNUParallelLocal`` are supported.
 
 Example in YAML:
 
@@ -48,7 +48,9 @@ jobs are finished.
 
 The following parameters are available for HTCondor:
 
-* ``env``: Definition of the Python environment. It must provide two variables:
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
 
   * ``kind``: This is the kind of virtual environment to use:
 
@@ -61,6 +63,9 @@ The following parameters are available for HTCondor:
     the absolute or relative path to the virtualenv when ``venv`` is used.
     If relative path is used then it should be relative to the YAML.
 
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
 * ``mem``: Memory to be used by the job. It must be provided as a string with
   the units (e.g., ``"2GB"``).
 * ``cpus``: Number of CPUs to be used by the job. It must be provided as an
@@ -93,10 +98,78 @@ Example in YAML:
     env:
       kind: conda
       name: junifer
+      shell: zsh
+    mem: 8G
+    disk: 2G
+    collect: "yes"  # wrap it in string to avoid boolean
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestHTCondorQueue
+    kind: HTCondor
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
     mem: 8G
     disk: 2G
     collect: "yes"  # wrap it in string to avoid boolean
 
+.. _queueing_local:
+
+GNUParallelLocal
+----------------
+
+When using GNU Parallel, ``junifer`` will run only in local mode and leverage
+maximum computational power of whatever hardware it is run on.
+
+The following parameters are available for GNUParallelLocal:
+
+* ``pre_run``: Extra shell commands to run before ``junifer run``.
+* ``pre_collect``: Extra shell commands to run before ``junifer collect``.
+* ``env``: Definition of the Python environment. It has the following parameters:
+
+  * ``kind``: This is the kind of virtual environment to use:
+
+    * ``conda``
+    * ``venv``
+    * ``local`` (no virtual environment)
+
+  * ``name``: This is the name of the environment to use in case a virtual
+    environment is used. It should be the name when ``conda`` is used and
+    the absolute or relative path to the virtualenv when ``venv`` is used.
+    If relative path is used then it should be relative to the YAML.
+
+  * ``shell``: This is the shell to use. Only ``bash`` and ``zsh`` are supported
+    as of now.
+
+Example in YAML:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: conda
+      name: junifer
+      shell: zsh
+
+Alternatively, if you use ``venv``, the YAML would look like so:
+
+.. code-block:: yaml
+
+  queue:
+    jobname: TestGNUParallelLocalQueue
+    kind: GNUParallelLocal
+    env:
+      kind: venv
+      name: /home/me/junifer-venv  # should be at the level above `bin/activate`
+      shell: zsh
+
 Once the :ref:`codeless` file is ready, including the ``queue`` section, you can
 queue the jobs by executing the ``junifer queue`` command.
 

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.5.dev152'
-__version_tuple__ = version_tuple = (0, 0, 5, 'dev152')
+__version__ = version = '0.0.5.dev164'
+__version_tuple__ = version_tuple = (0, 0, 5, 'dev164')

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer/external/nilearn/__init__.py

@@ -4,3 +4,6 @@
 # License: AGPL
 
 from .junifer_nifti_spheres_masker import JuniferNiftiSpheresMasker
+
+
+__all__ = ["JuniferNiftiSpheresMasker"]

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer/external/nilearn/junifer_nifti_spheres_masker.py

@@ -29,9 +29,12 @@ if TYPE_CHECKING:
     from pandas import DataFrame
 
 
+__all__ = ["JuniferNiftiSpheresMasker"]
+
+
 # New BSD License
 
-# Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) The nilearn developers.
 # All rights reserved.
 
 
@@ -99,6 +102,17 @@ def _apply_mask_and_get_affinity(
         Contains the boolean indices for each sphere.
         shape: (number of seeds, number of voxels)
 
+    Raises
+    ------
+    ValueError
+        If ``niimg`` and ``mask_img`` are both provided or
+        if overlap is detected between spheres.
+
+    Warns
+    -----
+    RuntimeWarning
+        If the provided images contain NaN, they will be converted to zeroes.
+
     """
     seeds = list(seeds)
 
@@ -210,7 +224,7 @@ def _iter_signals_from_spheres(
     X, A = _apply_mask_and_get_affinity(
         seeds, niimg, radius, allow_overlap, mask_img=mask_img
     )
-    for _, row in enumerate(A.rows):
+    for row in A.rows:
         yield X[:, row]
 
 

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer/external/nilearn/tests/test_junifer_nifti_spheres_masker.py

@@ -4,12 +4,14 @@
 # License: AGPL
 
 import warnings
+from typing import List, Tuple
 
 import nibabel
 import numpy as np
 import pytest
 from nilearn._utils import data_gen
 from nilearn.image import get_data
+from nilearn.maskers import NiftiSpheresMasker
 from numpy.testing import assert_array_equal
 
 from junifer.external.nilearn import JuniferNiftiSpheresMasker
@@ -17,7 +19,7 @@ from junifer.external.nilearn import JuniferNiftiSpheresMasker
 
 # New BSD License
 
-# Copyright (c) 2007 - 2022 The nilearn developers.
+# Copyright (c) The nilearn developers.
 # All rights reserved.
 
 
@@ -331,3 +333,76 @@ def test_nifti_spheres_masker_io_shapes() -> None:
         )
         test_data = masker.transform(img_4d)
         assert test_data.shape == (n_volumes, n_regions)
+
+
+@pytest.mark.parametrize(
+    "shape",
+    [
+        (10, 11, 12),
+        (10, 11, 12, 5),
+    ],
+)
+@pytest.mark.parametrize(
+    "radius, allow_overlap",
+    [
+        (2.0, True),
+        (2.0, False),
+        (3.0, True),
+        (4.0, True),
+        (5.0, True),
+    ],
+)
+@pytest.mark.parametrize(
+    "coords",
+    [
+        [(1, 1, 1)],
+        [(1, 1, 1), (4, 4, 4)],
+        [(1, 1, 1), (4, 4, 4), (10, 10, 10)],
+    ],
+)
+def test_junifer_and_nilearn_mean_agg_are_equal(
+    shape: Tuple[int, ...],
+    radius: float,
+    allow_overlap: bool,
+    coords: List[Tuple[int, int, int]],
+) -> None:
+    """Test junifer's masker behaves same as nilearn's when agg is mean.
+
+    Parameters
+    ----------
+    shape : tuple of int
+        The parametrized shape of the input image.
+    radius : float
+        The parametrized radius of the spheres.
+    allow_overlap : bool
+        The parametrized option to overlap spheres or not.
+    coords : list of tuple of int, int and int
+        The parametrized seeds.
+
+    """
+    # Set affine
+    affine = np.eye(4)
+    # Generate random image
+    input_img, mask_img = data_gen.generate_random_img(
+        shape=shape,
+        affine=affine,
+    )
+    # Compute junifer's version
+    junifer_masker = JuniferNiftiSpheresMasker(
+        seeds=coords,
+        radius=radius,
+        allow_overlap=allow_overlap,
+        mask_img=mask_img,
+    )
+    junifer_output = junifer_masker.fit_transform(input_img)
+    # Compute nilearn's version
+    nilearn_masker = NiftiSpheresMasker(
+        seeds=coords,
+        radius=radius,
+        allow_overlap=allow_overlap,
+        mask_img=mask_img,
+    )
+    nilearn_output = nilearn_masker.fit_transform(input_img)
+    # Checks
+    assert junifer_output.shape == nilearn_output.shape
+    np.testing.assert_almost_equal(junifer_output, nilearn_output)

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.5.dev152
+Version: 0.0.5.dev164
 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>

{junifer-0.0.5.dev152 → junifer-0.0.5.dev164}/junifer.egg-info/SOURCES.txt

@@ -58,10 +58,12 @@ docs/api/utils.rst
 docs/changes/contributors.inc
 docs/changes/newsfragments/.gitignore
 docs/changes/newsfragments/115.doc
+docs/changes/newsfragments/136.enh
 docs/changes/newsfragments/161.feature
 docs/changes/newsfragments/273.feature
 docs/changes/newsfragments/323.feature
 docs/changes/newsfragments/324.bugfix
+docs/changes/newsfragments/327.doc
 docs/changes/newsfragments/330.doc
 docs/changes/newsfragments/331.bugfix
 docs/changes/newsfragments/332.bugfix