Release Junifer 0.0.2 #217
44 changed files with 132 additions and 43 deletions
|
|
@ -1 +0,0 @@
|
||||||
Organize functional connectivity markers in ``junifer.markers.functional_connectivity`` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which relative storage URIs will be computed relative to the CWD and not to the location of the YAML file by `Fede Raimondo`_.
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Expose a :func:`.merge_parcellations` function to merge a list of parcellations by `Leonard Sasse`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add support for HDF5 feature storage via :class:`.HDF5FeatureStorage` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add ``confounds_format`` parameter to :class:`.PatternDataGrabber` constructor for improved handling of confounds specified via ``BOLD_confounds`` data type by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix ``junifer run`` to respect preprocess step specified in the pipeline by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Allow :class:`.PartlyCloudyTestingDataGrabber` to be accessible via ``import junifer.testing.registry`` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add :class:`.TemporalSNRParcels` and :class:`.TemporalSNRSpheres` by `Leonard Sasse`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Update docstrings and fix typo in log message by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add more documentation on registering parcellations, coordinates, and masks by `Leonard Sasse`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add support for ``Power`` coordinates by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add support for nilearn computed masks (``compute_epi_mask``, ``compute_brain_mask``, ``compute_background_mask``, ``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in the aomic sub-package by `Leonard Sasse`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Rename ``store_table()`` to ``store_vector()`` for storage-like objects and adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for storage. Also, improve the logic of storing vectors by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add ``ica_fix`` parameter to :class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers to allow for selecting data processed with ICA+FIX. Default value is ``False`` which changes behaviour since 0.0.1 release. By `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a specific type (e.g.: ``BOLD``) will fail if another non-supported type (e.g.: ``BOLD_confounds``) is present in the data object by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Improved logging output for preprocessing, collecting and pipeline building from YAML by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix :class:`.ALFFParcels`, :class:`.ALFFSpheres`, :class:`.ReHoSpheres` and :class:`.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix several markers that did not properly handle the ``extra_input`` parameter by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Expose ``allow_overlap`` parameter in :class:`.SphereAggregation` and related markers by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Allow for empty spheres in :class:`.JuniferNiftiSpheresMasker`, that will result in NaNs. Also, modify the behaviour of the ``collect`` parameter in HTCondor ``queue`` function to run a collect job even if some of the previous jobs fail. This is useful to collect the results of a pipeline even if some of the jobs fail by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add aggregation function :func:`.count` that returns the number of elements in a given axis. This allows to count the number of voxels per sphere/parcel when used as ``method`` in markers by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which relative paths in the YAML ``with`` directive would be computed relative to the current working directory of the process instead of the location of the YAML file by `Fede Raimondo`_.
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix an issue with datalad cache and locks in which the user-specific configuration might create a conflict in high throughput systems by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which :class:`.ParcelAggregation` could yield duplicated column names if two or more parcels were used and label names were not unique by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Allow for empty parcels in :class:`.ParcelAggregation`, that will result in NaNs by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which :func:`.count` will not be correctly applied across an axis by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Improve metadata and data I/O for :class:`.HDF5FeatureStorage` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix an issue with datalad cache and locks in which the overriden settings in Junifer were not propagated to subprocesses, resulting in using the default settings by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase class, because of missing extra_input parameter by `Leonard Sasse`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Force datalad to be non-interactive on *queued* jobs by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Migrate and document changelog creation and maintenance via ``towncrier`` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add copy button to documentation code blocks by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add sections *starting* and *help* in the documentation by `Fede Raimondo`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add missing ``abstractmethod`` decorators for ``get_valid_inputs`` methods of :class:`.BaseMarker` and :class:`.BasePreprocessor` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Fix the output of :class:`.RSSETSMarker` to be 2D by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Rename ``AmplitudeLowFrequencyFluctuationParcels`` and ``AmplitudeLowFrequencyFluctuationSpheres`` to :class:`.ALFFParcels` and :class:`.ALFFSpheres` by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Shorten Sphinx references across code and docs, and add ``black`` shield in README by `Synchon Mandal`_
|
|
||||||
|
|
@ -1 +0,0 @@
|
||||||
Add :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres` by `Leonard Sasse`_
|
|
||||||
|
|
@ -8,6 +8,138 @@ What's new
|
||||||
|
|
||||||
.. towncrier release notes start
|
.. towncrier release notes start
|
||||||
|
|
||||||
|
Junifer 0.0.2 (2023-03-31)
|
||||||
|
--------------------------
|
||||||
|
|
||||||
|
Bugfixes
|
||||||
|
^^^^^^^^
|
||||||
|
|
||||||
|
- Fix a bug in which relative storage URIs will be computed relative to the CWD
|
||||||
|
and not to the location of the YAML file by `Fede Raimondo`_. (:gh:`127`)
|
||||||
|
- Fix ``junifer run`` to respect preprocess step specified in the pipeline by
|
||||||
|
`Synchon Mandal`_ (:gh:`159`)
|
||||||
|
- Fix a bug in which only ``REST1`` and ``REST2`` tasks could be accesed in
|
||||||
|
:class:`.DataladHCP1200` and :class:`.HCP1200` datagrabbers by `Fede
|
||||||
|
Raimondo`_ (:gh:`183`)
|
||||||
|
- Fix a bug in which fitting a marker (e.g. ``SphereAggregation``) on a
|
||||||
|
specific type (e.g.: ``BOLD``) will fail if another non-supported type (e.g.:
|
||||||
|
``BOLD_confounds``) is present in the data object by `Fede Raimondo`_
|
||||||
|
(:gh:`185`)
|
||||||
|
- Fix :class:`.ALFFParcels`, :class:`.ALFFSpheres`, :class:`.ReHoSpheres` and
|
||||||
|
:class:`.ReHoParcels` pass the ``extra_input`` parameter by `Fede Raimondo`_
|
||||||
|
(:gh:`187`)
|
||||||
|
- Fix several markers that did not properly handle the ``extra_input``
|
||||||
|
parameter by `Fede Raimondo`_ (:gh:`189`)
|
||||||
|
- Fix a bug in which relative paths in the YAML ``with`` directive would be
|
||||||
|
computed relative to the current working directory of the process instead of
|
||||||
|
the location of the YAML file by `Fede Raimondo`_. (:gh:`191`)
|
||||||
|
- Fix an issue with datalad cache and locks in which the user-specific
|
||||||
|
configuration might create a conflict in high throughput systems by `Fede
|
||||||
|
Raimondo`_ (:gh:`192`)
|
||||||
|
- Fix a bug in which :class:`.ParcelAggregation` could yield duplicated column
|
||||||
|
names if two or more parcels were used and label names were not unique by
|
||||||
|
`Fede Raimondo`_ (:gh:`194`)
|
||||||
|
- Fix a bug in which :func:`.count` will not be correctly applied across an
|
||||||
|
axis by `Fede Raimondo`_ (:gh:`195`)
|
||||||
|
- Fix an issue with datalad cache and locks in which the overriden settings in
|
||||||
|
Junifer were not propagated to subprocesses, resulting in using the default
|
||||||
|
settings by `Fede Raimondo`_ (:gh:`199`)
|
||||||
|
- Fix a bug in which :func:`.get_mask` fails for FunctionalConnectivityBase
|
||||||
|
class, because of missing extra_input parameter by `Leonard Sasse`_
|
||||||
|
(:gh:`200`)
|
||||||
|
- Fix the output of :class:`.RSSETSMarker` to be 2D by `Synchon Mandal`_
|
||||||
|
(:gh:`215`)
|
||||||
|
|
||||||
|
|
||||||
|
API Changes
|
||||||
|
^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Add ``confounds_format`` parameter to :class:`.PatternDataGrabber`
|
||||||
|
constructor for improved handling of confounds specified via
|
||||||
|
``BOLD_confounds`` data type by `Synchon Mandal`_ (:gh:`158`)
|
||||||
|
- Rename ``store_table()`` to ``store_vector()`` for storage-like objects and
|
||||||
|
adapt marker-like objects to use ``"vector"`` in place of ``"table"`` for
|
||||||
|
storage. Also, improve the logic of storing vectors by `Synchon Mandal`_
|
||||||
|
(:gh:`181`)
|
||||||
|
- Add ``ica_fix`` parameter to :class:`.DataladHCP1200` and :class:`.HCP1200`
|
||||||
|
datagrabbers to allow for selecting data processed with ICA+FIX. Default
|
||||||
|
value is ``False`` which changes behaviour since 0.0.1 release. By `Fede
|
||||||
|
Raimondo`_ (:gh:`183`)
|
||||||
|
- Add ``pre_run`` parameter to ``_queue_condor`` by `Fede Raimondo`_
|
||||||
|
(:gh:`188`)
|
||||||
|
- Expose ``allow_overlap`` parameter in :class:`.SphereAggregation` and
|
||||||
|
related markers by `Fede Raimondo`_ (:gh:`190`)
|
||||||
|
- Rename ``AmplitudeLowFrequencyFluctuationParcels`` and
|
||||||
|
``AmplitudeLowFrequencyFluctuationSpheres`` to :class:`.ALFFParcels` and
|
||||||
|
:class:`.ALFFSpheres` by `Synchon Mandal`_ (:gh:`216`)
|
||||||
|
|
||||||
|
|
||||||
|
Improved Documentation
|
||||||
|
^^^^^^^^^^^^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Add more documentation on registering parcellations, coordinates, and masks
|
||||||
|
by `Leonard Sasse`_ (:gh:`166`)
|
||||||
|
- Migrate and document changelog creation and maintenance via ``towncrier`` by
|
||||||
|
`Synchon Mandal`_ (:gh:`203`)
|
||||||
|
- Add copy button to documentation code blocks by `Synchon Mandal`_ (:gh:`205`)
|
||||||
|
- Add sections *starting* and *help* in the documentation by `Fede Raimondo`_
|
||||||
|
(:gh:`210`)
|
||||||
|
- Shorten Sphinx references across code and docs, and add ``black`` shield in
|
||||||
|
README by `Synchon Mandal`_ (:gh:`218`)
|
||||||
|
|
||||||
|
|
||||||
|
Enhancements
|
||||||
|
^^^^^^^^^^^^
|
||||||
|
|
||||||
|
- Organize functional connectivity markers in
|
||||||
|
``junifer.markers.functional_connectivity`` by `Synchon Mandal`_ (:gh:`107`)
|
||||||
|
- Change HCP datagrabber tests to decrease CI running time by `Fede Raimondo`_
|
||||||
|
(:gh:`155`)
|
||||||
|
- Allow :class:`.PartlyCloudyTestingDataGrabber` to be accessible via ``import
|
||||||
|
junifer.testing.registry`` by `Synchon Mandal`_ (:gh:`160`)
|
||||||
|
- Update docstrings and fix typo in log message by `Synchon Mandal`_
|
||||||
|
(:gh:`165`)
|
||||||
|
- Add fMRIPrep brain masks to the datagrabber patterns for all datagrabbers in
|
||||||
|
the aomic sub-package by `Leonard Sasse`_ (:gh:`177`)
|
||||||
|
- Improved logging output for preprocessing, collecting and pipeline building
|
||||||
|
from YAML by `Fede Raimondo`_ (:gh:`185`)
|
||||||
|
- Allow for empty spheres in :class:`.JuniferNiftiSpheresMasker`, that will
|
||||||
|
result in NaNs. Also, modify the behaviour of the ``collect`` parameter in
|
||||||
|
HTCondor ``queue`` function to run a collect job even if some of the previous
|
||||||
|
jobs fail. This is useful to collect the results of a pipeline even if some
|
||||||
|
of the jobs fail by `Fede Raimondo`_ (:gh:`190`)
|
||||||
|
- Allow for empty parcels in :class:`.ParcelAggregation`, that will result in
|
||||||
|
NaNs by `Fede Raimondo`_ (:gh:`194`)
|
||||||
|
- Improve metadata and data I/O for :class:`.HDF5FeatureStorage` by `Synchon
|
||||||
|
Mandal`_ (:gh:`196`)
|
||||||
|
- Force datalad to be non-interactive on *queued* jobs by `Fede Raimondo`_
|
||||||
|
(:gh:`201`)
|
||||||
|
- Add missing ``abstractmethod`` decorators for ``get_valid_inputs`` methods of
|
||||||
|
:class:`.BaseMarker` and :class:`.BasePreprocessor` by `Synchon Mandal`_
|
||||||
|
(:gh:`214`)
|
||||||
|
|
||||||
|
|
||||||
|
Features
|
||||||
|
^^^^^^^^
|
||||||
|
|
||||||
|
- Add :class:`.EdgeCentricFCParcels` and :class:`.EdgeCentricFCSpheres` by
|
||||||
|
`Leonard Sasse`_ (:gh:`64`)
|
||||||
|
- Expose a :func:`.merge_parcellations` function to merge a list of
|
||||||
|
parcellations by `Leonard Sasse`_ (:gh:`146`)
|
||||||
|
- Add support for HDF5 feature storage via :class:`.HDF5FeatureStorage` by
|
||||||
|
`Synchon Mandal`_ (:gh:`147`)
|
||||||
|
- Add :class:`.TemporalSNRParcels` and :class:`.TemporalSNRSpheres` by `Leonard
|
||||||
|
Sasse`_ (:gh:`163`)
|
||||||
|
- Add support for ``Power`` coordinates by `Synchon Mandal`_ (:gh:`167`)
|
||||||
|
- Add support for ``Dosenbach`` coordinates by `Synchon Mandal`_ (:gh:`168`)
|
||||||
|
- Add support for nilearn computed masks (``compute_epi_mask``,
|
||||||
|
``compute_brain_mask``, ``compute_background_mask``,
|
||||||
|
``fetch_icbm152_brain_gm_mask``) by `Fede Raimondo`_ (:gh:`175`)
|
||||||
|
- Add aggregation function :func:`.count` that returns the number of elements
|
||||||
|
in a given axis. This allows to count the number of voxels per sphere/parcel
|
||||||
|
when used as ``method`` in markers by `Fede Raimondo`_ (:gh:`190`)
|
||||||
|
|
||||||
|
|
||||||
junifer 0.0.1 (2022-12-20)
|
junifer 0.0.1 (2022-12-20)
|
||||||
--------------------------
|
--------------------------
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Reference in a new issue