junifer 0.0.6.dev16__tar.gz → 0.0.6.dev23__tar.gz

{junifer-0.0.6.dev16 → junifer-0.0.6.dev23}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev16
+Version: 0.0.6.dev23
 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-0.0.6.dev23/docs/changes/newsfragments/359.doc

@@ -0,0 +1 @@
+Add documentation on analysing extracted features by `Synchon Mandal`_

junifer-0.0.6.dev23/docs/changes/newsfragments/360.bugfix

@@ -0,0 +1 @@
+Enable ``spike`` mapping from ``adhoc`` to ``fmriprep`` for :class:`.fMRIPrepConfoundRemover` by `Leonard Sasse`_ and `Synchon Mandal`_

junifer-0.0.6.dev23/docs/using/running.rst

@@ -0,0 +1,285 @@
+.. include:: ../links.inc
+
+.. _running:
+
+Running Jobs
+============
+
+Once we have the :ref:`code-less configuration file <codeless>`, we can use the
+command line interface to extract the features. This is achieved in a two-step
+process: ``run`` and ``collect``.
+
+The ``run`` command is used to extract the features from each element in the
+dataset. However, depending on the storage interface, this may create one file
+per subject. The ``collect`` command is then used to collect all of the
+individual results into a single file.
+
+Assuming that we have a configuration file named ``config.yaml``, the following
+commands will extract the features:
+
+.. code-block:: bash
+
+    junifer run config.yaml
+
+The ``run`` command accepts the following additional arguments:
+
+* ``--help``: Show a help message.
+* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
+  ``debug``.
+* ``--element``: The *element* to run. If not specified, all elements will be
+  run. This parameter can be specified multiple times to run multiple elements.
+  If the *element* requires several parameters, they can be specified by
+  separating them with ``,``. It also accepts a file (e.g., ``elements.txt``)
+  containing complete or partial element(s).
+
+Example of running two elements:
+--------------------------------
+
+.. code-block:: bash
+
+    junifer run config.yaml --element sub-01 --element sub-02
+
+You can also specify the elements via a text file like so:
+
+.. code-block:: bash
+
+    junifer run config.yaml --element elements.txt
+
+And the corresponding ``elements.txt`` would be like so:
+
+.. code-block:: text
+
+    sub-01
+    sub-02
+
+Example of elements with multiple parameters and verbose output:
+----------------------------------------------------------------
+
+.. code-block:: bash
+
+    junifer run --verbose info config.yaml --element sub-01,ses-01
+
+You can also specify the elements via a text file like so:
+
+.. code-block:: bash
+
+    junifer run --verbose info config.yaml --element elements.txt
+
+And the corresponding ``elements.txt`` would be like so:
+
+.. code-block:: text
+
+    sub-01,ses-01
+
+In case you wanted to run for all possible sessions (e.g., ``ses-01``,
+``ses-02``, ``ses-03``) but only for ``sub-01``, you could also do:
+
+.. code-block:: bash
+
+    junifer run --verbose info config.yaml --element sub-01
+
+or,
+
+.. code-block:: bash
+
+    junifer run --verbose info config.yaml --element elements.txt
+
+and then the ``elements.txt`` would be like so:
+
+.. code-block:: text
+
+    sub-01
+
+
+.. _collect:
+
+Collecting Results
+==================
+
+Once the ``run`` command has been executed, the results are stored in the output
+directory. However, depending on the storage interface, this may create one file
+per subject. The ``collect`` command is then used to collect all of the
+individual results into a single file.
+
+Assuming that we have a configuration file named ``config.yaml``, the following
+commands will collect the results:
+
+.. code-block:: bash
+
+    junifer collect config.yaml
+
+The ``collect`` command accepts the following additional arguments:
+
+* ``--help``: Show a help message.
+* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
+  ``debug``.
+
+
+.. _analysing_extracted_features:
+
+Analysing Results
+=================
+
+After ``collect``-ing the results into a single file, we can analyse them as we
+wish. We would need to do this programmatically so feel free to choose your
+Python interpreter of choice or use it via a Python script.
+
+First we load the storage like so:
+
+.. code-block:: python
+
+    from junifer.storage import HDF5FeatureStorage
+
+    # You need to import and use SQLiteFeatureStorage if you chose that
+    # for storage while extracting features
+    storage = HDF5FeatureStorage("<path/to/your/collected/file>")
+
+The best way to start analysing would be to list all the extracted features
+like so:
+
+.. code-block:: python
+
+    # This would output a dictionary with MD5 checksum of the features as keys
+    # and metadata of the features as values
+    storage.list_features()
+
+.. code-block::
+
+   {'eb85b61eefba61f13d712d425264697b': {'datagrabber': {'class': 'SPMAuditoryTestingDataGrabber',
+                                                         'types': ['BOLD', 'T1w']},
+                                          'dependencies': {'scikit-learn': '1.3.0', 'nilearn': '0.9.2'},
+                                          'datareader': {'class': 'DefaultDataReader'},
+                                          'type': 'BOLD',
+                                          'marker': {'class': 'FunctionalConnectivityParcels',
+                                                     'parcellation': 'Schaefer100x7',
+                                                     'agg_method': 'mean',
+                                                     'agg_method_params': None,
+                                                     'cor_method': 'covariance',
+                                                     'cor_method_params': {'empirical': False},
+                                                     'masks': None,
+                                                     'name': 'schaefer_100x7_fc_parcels'},
+                                          '_element_keys': ['subject'],
+                                          'name': 'BOLD_schaefer_100x7_fc_parcels'}}
+
+Once we have this, we can retrieve a single feature like so:
+
+.. code-block:: python
+
+    feature_dict = storage.read("<name-key-from-feature-metadata>")
+
+to get the stored dictionary or,
+
+.. code-block:: python
+
+    feature_df = storage.read_df("<name-key-from-feature-metadata>")
+
+to get it as a :class:`pandas.DataFrame`.
+
+If there are features with duplicate ``name`` s, then we would need to use
+the MD5 checksum and pass it like so:
+
+.. code-block:: python
+
+    feature_df = storage.read_df(feature_md5="<md5-hash-of-feature>")
+
+We can now manipulate the dictionary or the :class:`pandas.DataFrame` as we
+wish or use the DataFrame directly with `julearn`_ if desired.
+
+
+On-the-fly transforms
+---------------------
+
+``junifer`` supports performing some computationally cheap operations
+(like computing brain connectivity or BrainPrint post-analysis) directly
+on the storage objects. To make sure everything works, install ``junifer``
+like so:
+
+.. code-block:: bash
+
+    pip install junifer[onthefly]
+
+or if installed via ``conda``, everything should be there and no further action
+is required.
+
+Computing brain connectivity via `bctpy <https://github.com/aestrivex/bctpy>`_
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can compute for example, the degree of each node considering an undirected
+graph via `bctpy`_ like so:
+
+.. code-block:: python
+
+    from junifer.onthefly import read_transform
+
+    transformed_df = read_transform(
+        storage,
+        # md5 hash can also be passed via `feature_md5`
+        feature_name="<name-key-from-feature-metadata>",
+        # format is `package_function`
+        transform="bctpy_degrees_und",
+    )
+
+Post-analysis of BrainPrint results
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To perform post-analysis on BrainPrint results, start by importing:
+
+.. code-block:: python
+
+    from junifer.onthefly import brainprint
+
+
+Normalising:
+~~~~~~~~~~~~
+
+Surface normalisation can be done by:
+
+.. code-block:: python
+
+    surface_normalised_df = brainprint.normalize(
+        storage,
+        {
+            "areas": {
+                "feature_name": "<name-key-from-areas-feature>",
+                # if md5 hash is passed, the above should be None
+                "feature_md5": None,
+            },
+            "eigenvalues": {
+                "feature_name": "<name-key-from-eigenvalues-feature>",
+                "feature_md5": None,
+            },
+        },
+        kind="surface",
+    )
+
+and volume normalisation can be done by:
+
+.. code-block:: python
+
+    volume_normalised_df = brainprint.normalize(
+        storage,
+        {
+            "volumes": {
+                "feature_name": "<name-key-from-volumes-feature>",
+                "feature_md5": None,
+            },
+            "eigenvalues": {
+                "feature_name": "<name-key-from-eigenvalues-feature>",
+                "feature_md5": None,
+            },
+        },
+        kind="volume",
+    )
+
+Re-weighting:
+~~~~~~~~~~~~~
+
+To perform re-weighting, run like so:
+
+.. code-block:: python
+
+    reweighted_df = brainprint.reweight(
+        storage,
+        # md5 hash can also be passed via `feature_md5`
+        feature_name="<name-key-from-eigenvalues-feature>",
+    )

{junifer-0.0.6.dev16 → junifer-0.0.6.dev23}/junifer/_version.py

@@ -12,5 +12,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.0.6.dev16'
-__version_tuple__ = version_tuple = (0, 0, 6, 'dev16')
+__version__ = version = '0.0.6.dev23'
+__version_tuple__ = version_tuple = (0, 0, 6, 'dev23')

{junifer-0.0.6.dev16 → junifer-0.0.6.dev23}/junifer/preprocess/confounds/fmriprep_confound_remover.py

@@ -93,6 +93,9 @@ FMRIPREP_VALID_NAMES = [
     for t_list in x.values()
     for elem in t_list
 ]
+# NOTE: Check with @fraimondo about the spike mapping intent
+# Add spike_name to FMRIPREP_VALID_NAMES
+FMRIPREP_VALID_NAMES.append("framewise_displacement")
 
 
 @register_preprocessor

{junifer-0.0.6.dev16 → junifer-0.0.6.dev23}/junifer.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: junifer
-Version: 0.0.6.dev16
+Version: 0.0.6.dev23
 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-0.0.6.dev16 → junifer-0.0.6.dev23}/junifer.egg-info/SOURCES.txt

@@ -61,6 +61,8 @@ docs/changes/newsfragments/335.enh
 docs/changes/newsfragments/354.feature
 docs/changes/newsfragments/356.bugfix
 docs/changes/newsfragments/357.enh
+docs/changes/newsfragments/359.doc
+docs/changes/newsfragments/360.bugfix
 docs/extending/coordinates.rst
 docs/extending/datagrabber.rst
 docs/extending/dependencies.rst

junifer-0.0.6.dev16/docs/using/running.rst

@@ -1,115 +0,0 @@
-.. include:: ../links.inc
-
-.. _running:
-
-Running Jobs
-============
-
-Once we have the :ref:`code-less configuration file <codeless>`, we can use the
-command line interface to extract the features. This is achieved in a two-step
-process: ``run`` and ``collect``.
-
-The ``run`` command is used to extract the features from each element in the
-dataset. However, depending on the storage interface, this may create one file
-per subject. The ``collect`` command is then used to collect all of the
-individual results into a single file.
-
-Assuming that we have a configuration file named ``config.yaml``, the following
-commands will extract the features:
-
-.. code-block:: bash
-
-    junifer run config.yaml
-
-The ``run`` command accepts the following additional arguments:
-
-* ``--help``: Show a help message.
-* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
-  ``debug``.
-* ``--element``: The *element* to run. If not specified, all elements will be
-  run. This parameter can be specified multiple times to run multiple elements.
-  If the *element* requires several parameters, they can be specified by
-  separating them with ``,``. It also accepts a file (e.g., ``elements.txt``)
-  containing complete or partial element(s).
-
-Example of running two elements:
---------------------------------
-
-.. code-block:: bash
-
-    junifer run config.yaml --element sub-01 --element sub-02
-
-You can also specify the elements via a text file like so:
-
-.. code-block:: bash
-
-    junifer run config.yaml --element elements.txt
-
-And the corresponding ``elements.txt`` would be like so:
-
-.. code-block:: text
-
-    sub-01
-    sub-02
-
-Example of elements with multiple parameters and verbose output:
-----------------------------------------------------------------
-
-.. code-block:: bash
-
-    junifer run --verbose info config.yaml --element sub-01,ses-01
-
-You can also specify the elements via a text file like so:
-
-.. code-block:: bash
-
-    junifer run --verbose info config.yaml --element elements.txt
-
-And the corresponding ``elements.txt`` would be like so:
-
-.. code-block:: text
-
-    sub-01,ses-01
-
-In case you wanted to run for all possible sessions (e.g., ``ses-01``,
-``ses-02``, ``ses-03``) but only for ``sub-01``, you could also do:
-
-.. code-block:: bash
-
-    junifer run --verbose info config.yaml --element sub-01
-
-or,
-
-.. code-block:: bash
-
-    junifer run --verbose info config.yaml --element elements.txt
-
-and then the ``elements.txt`` would be like so:
-
-.. code-block:: text
-
-    sub-01
-
-
-.. _collect:
-
-Collecting Results
-==================
-
-Once the ``run`` command has been executed, the results are stored in the output
-directory. However, depending on the storage interface, this may create one file
-per subject. The ``collect`` command is then used to collect all of the
-individual results into a single file.
-
-Assuming that we have a configuration file named ``config.yaml``, the following
-commands will collect the results:
-
-.. code-block:: bash
-
-    junifer collect config.yaml
-
-The ``collect`` command accepts the following additional arguments:
-
-* ``--help``: Show a help message.
-* ``--verbose``: Set the verbosity level. Options are ``warning``, ``info``,
-  ``debug``.