pyAFQ 1.3.5__tar.gz → 2.0__tar.gz

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/docbuild.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/docker_pyafq.yml

@@ -1,6 +1,6 @@
 name: Build and Push pyAFQ Docker Image
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/docker_pyafq_cuda12.yml

@@ -1,6 +1,6 @@
 name: Build and Push pyAFQ CUDA12 Image
 
-on: [push]
+on: [push, pull_request]
 
 jobs:
   build:

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_anisotropic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_basic_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_custom_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_pft_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_reco80_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_reco_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/nightly_test.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.12"]
 
     steps:
     - name: Checkout repo

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/publish-to-test-pypi.yml

@@ -10,7 +10,7 @@ jobs:
     - name: Set up Python 3.11
       uses: actions/setup-python@v1
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install pep517
       run: >-
         python -m

{pyafq-1.3.5 → pyafq-2.0}/.github/workflows/test.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.10", "3.11", "3.12"]
         nibabel-pre: [true, false]
 
     steps:
@@ -33,7 +33,7 @@ jobs:
         pip install --pre nibabel
     - name: Check Dependencies
       run: |
-        pipconflictchecker
+        python -m pip check
     - name: Lint
       run: |
         flake8 --ignore N802,N806,W503 --select W504 `find . -name \*.py | grep -v setup.py | grep -v version.py | grep -v __init__.py | grep -v /docs/`

{pyafq-1.3.5 → pyafq-2.0}/AFQ/_fixes.py

@@ -2,6 +2,7 @@ import numpy as np
 import logging
 
 from scipy.special import lpmv, gammaln
+from scipy.linalg import pinvh
 
 from tqdm import tqdm
 
@@ -215,17 +216,20 @@ def gaussian_weights(bundle, n_points=100, return_mahalnobis=False,
     for i in range(n_nodes):
         # This should come back as a 3D covariance matrix with the spatial
         # variance covariance of this node across the different streamlines,
-        # reorganized as an upper diagonal matrix for expected Mahalanobis
+        # converted to a positive semi-definite matrix if necessary
         cov = np.cov(sls[:, i, :].T, ddof=0)
-        while np.any(np.linalg.eigvals(cov) < 0):
-            cov += np.eye(cov.shape[0]) * 1e-12
+        if np.any(np.linalg.eigvals(cov) < 0):
+            eigenvalues, eigenvectors = np.linalg.eigh((cov + cov.T) / 2)
+            eigenvalues[eigenvalues < 0] = 0
+            cov = eigenvectors @ np.diag(eigenvalues) @ eigenvectors.T
 
         # calculate Mahalanobis for node in every fiber
         if np.any(cov > 0):
-            ci = np.linalg.inv(cov)
-
-            dist = (diff[:, i, :] @ ci) * diff[:, i, :]
-            weights[:, i] = np.sqrt(np.sum(dist, axis=1))
+            weights[:, i] = np.sqrt(np.einsum(
+                'ij,jk,ik->i',
+                diff[:, i, :],
+                pinvh(cov),
+                diff[:, i, :]))
 
         # In the special case where all the streamlines have the exact same
         # coordinate in this node, the covariance matrix is all zeros, so

{pyafq-1.3.5 → pyafq-2.0}/AFQ/api/bundle_dict.py

@@ -5,6 +5,7 @@ import AFQ.data.fetch as afd
 import AFQ.utils.volume as auv
 from AFQ.tasks.utils import get_fname, str_to_desc
 from AFQ.definitions.utils import find_file
+from AFQ.utils.path import space_from_fname
 
 import numpy as np
 import nibabel as nib
@@ -229,28 +230,42 @@ def default18_bd():
                                    'exclude': [templates['SLF_roi1_L']],
                                    'space': 'template',
                                    'start': templates['pARC_L_start'],
-                                   'primary_axis': 2,
+                                   'primary_axis': 'I/S',
                                    'primary_axis_percentage': 40},
         'Right Posterior Arcuate': {'cross_midline': False,
                                     'include': [templates['SLFt_roi2_R']],
                                     'exclude': [templates['SLF_roi1_R']],
                                     'space': 'template',
                                     'start': templates['pARC_R_start'],
-                                    'primary_axis': 2,
+                                    'primary_axis': 'I/S',
                                     'primary_axis_percentage': 40},
         'Left Vertical Occipital': {'cross_midline': False,
                                     'space': 'template',
                                     'start': templates['VOF_L_start'],
                                     'end': templates['VOF_L_end'],
                                     'inc_addtol': [4, 0],
-                                    'primary_axis': 2,
+                                    'Left Arcuate': {
+                                        'node_thresh': 20},
+                                    'Left Posterior Arcuate': {
+                                        'node_thresh': 1,
+                                        'core': 'Anterior'},
+                                    'Left Inferior Longitudinal': {
+                                        'core': 'Right'},
+                                    'primary_axis': 'I/S',
                                     'primary_axis_percentage': 40},
         'Right Vertical Occipital': {'cross_midline': False,
                                      'space': 'template',
                                      'start': templates['VOF_R_start'],
                                      'end': templates['VOF_R_end'],
                                      'inc_addtol': [4, 0],
-                                     'primary_axis': 2,
+                                     'Right Arcuate': {
+                                         'node_thresh': 20},
+                                     'Right Posterior Arcuate': {
+                                         'node_thresh': 1,
+                                         'core': 'Anterior'},
+                                     'Right Inferior Longitudinal': {
+                                         'core': 'Left'},
+                                     'primary_axis': 'I/S',
                                      'primary_axis_percentage': 40}})
 
 
@@ -467,7 +482,7 @@ def baby_bd():
             "exclude": [templates["SLF_roi1_L"]],
             "start": templates["pARC_L_start"],
             "end": templates["VOF_box_small_L"],
-            "primary_axis": 2,
+            "primary_axis": 'I/S',
             "primary_axis_percentage": 40,
             "cross_midline": False,
             "mahal": {"distance_threshold": 4}},
@@ -476,21 +491,21 @@ def baby_bd():
             "exclude": [templates["SLF_roi1_R"]],
             "start": templates["pARC_R_start"],
             "end": templates["VOF_box_small_R"],
-            "primary_axis": 2,
+            "primary_axis": 'I/S',
             "primary_axis_percentage": 40,
             "cross_midline": False,
             "mahal": {"distance_threshold": 4}},
         'Left Vertical Occipital': {
             "start": templates["VOF_L_start"],
             "end": templates["VOF_box_small_L"],
-            "primary_axis": 2,
+            "primary_axis": 'I/S',
             "primary_axis_percentage": 40,
             "cross_midline": False,
             "mahal": {"distance_threshold": 4}},
         'Right Vertical Occipital': {
             "start": templates["VOF_R_start"],
             "end": templates["VOF_box_small_R"],
-            "primary_axis": 2,
+            "primary_axis": 'I/S',
             "primary_axis_percentage": 40,
             "cross_midline": False,
             "mahal": {"distance_threshold": 4}}},
@@ -750,6 +765,14 @@ class BundleDict(MutableMapping):
             "cross_midline": False
         }
     })
+
+    Note
+    ----
+    The order of include ROIs may affect your results. This is
+    because ROI order within the include list determines the orientation of the
+    streamlines (from the first to the last) and the clipping of streamlines
+    when `clip_edges` is used, because the streamlines are clipped to
+    between the first and last ROIs.
     """
 
     def __init__(self,
@@ -799,6 +822,9 @@ class BundleDict(MutableMapping):
                 " Only Callosum Anterior Frontal will be used."))
             self.bundle_names.remove("Forceps Minor")
 
+    def __print__(self):
+        print(self._dict)
+
     def update_max_includes(self, new_max):
         if new_max > self.max_includes:
             self.max_includes = new_max
@@ -921,62 +947,16 @@ class BundleDict(MutableMapping):
             resample_subject_to=self.resample_subject_to,
             keep_in_memory=self.keep_in_memory)
 
-    def apply_to_rois(self, b_name, func, *args,
-                      dry_run=False, apply_to_recobundles=False,
-                      **kwargs):
+    def apply_to_rois(self, b_name, *args, **kwargs):
         """
-        Applies some transformation to all ROIs (include, exclude, end, start)
-        and the prob_map in a given bundle.
+        See: AFQ.api.bundle_dict.apply_to_roi_dict
 
         Parameters
         ----------
         b_name : name
             bundle name of bundle whose ROIs will be transformed.
-        func : function
-            function whose first argument must be a Nifti1Image and which
-            returns a Nifti1Image
-        dry_run : bool
-            Whether to actually apply changes returned by `func` to the ROIs.
-            If has_return is False, dry_run is not used.
-        apply_to_recobundles : bool, optional
-            Whether to apply the transformation to recobundles
-            TRKs as well.
-            Default: False
-
-        *args :
-            Additional arguments for func
-        **kwargs
-            Optional arguments for func
-
-        Returns
-        -------
-        A dictionary where keys are
-        the roi type and values are the transformed ROIs.
         """
-        return_vals = {}
-        for roi_type in [
-                "include", "exclude",
-                "start", "end", "prob_map"]:
-            if roi_type in self._dict[b_name]:
-                if roi_type in ["start", "end", "prob_map"]:
-                    return_vals[roi_type] = func(
-                        self._dict[b_name][roi_type], *args, **kwargs)
-                else:
-                    changed_rois = []
-                    for _roi in self._dict[b_name][roi_type]:
-                        changed_rois.append(func(
-                            _roi, *args, **kwargs))
-                    return_vals[roi_type] = changed_rois
-        if apply_to_recobundles and "recobundles" in self._dict[b_name]:
-            return_vals["recobundles"] = {}
-            for sl_type in ["sl", "centroid"]:
-                return_vals["recobundles"][sl_type] = func(
-                    self._dict[b_name]["recobundles"][sl_type],
-                    *args, **kwargs)
-        if not dry_run:
-            for roi_type, roi in return_vals.items():
-                self._dict[b_name][roi_type] = roi
-        return return_vals
+        return apply_to_roi_dict(self._dict[b_name], *args, **kwargs)
 
     def _cond_load_bundle(self, b_name, dry_run=False):
         """
@@ -1018,7 +998,8 @@ class BundleDict(MutableMapping):
             return roi_or_sl
 
     def transform_rois(self, bundle_name, mapping, new_affine,
-                       base_fname=None, apply_to_recobundles=False):
+                       base_fname=None, to_space="subject",
+                       apply_to_recobundles=False):
         """
         Get the bundle definition with transformed ROIs
         for a given bundle into a
@@ -1039,6 +1020,10 @@ class BundleDict(MutableMapping):
             Base file path to save ROIs too. Additional BIDS
             descriptors will be added to this file path. If None,
             do not save the ROIs.
+        to_space : str, optional
+            Name for space for exported ROIs. Only used if base_fname
+            is not None.
+            Default: "subject"
         apply_to_recobundles : bool, optional
             Whether to apply the transformation to recobundles
             TRKs as well.
@@ -1071,14 +1056,29 @@ class BundleDict(MutableMapping):
         if base_fname is not None:
             fnames = []
             for roi_type, rois in transformed_rois.items():
+                if roi_type == "prob_map":
+                    suffix = "probseg"
+                    roi_type_name = ""
+                else:
+                    suffix = "mask"
+                    roi_type_name = roi_type.lower().replace(
+                        " ", "").replace(
+                            "_", "").replace(
+                                "-", "")
+                    roi_type_name = roi_type_name[0].upper() \
+                        + roi_type_name[1:]
                 if not isinstance(rois, list):
                     rois = [rois]
                 for ii, roi in enumerate(rois):
+                    desc = f"{str_to_desc(bundle_name)}{roi_type_name}"
+                    if roi_type in ["include", "exclude"]:
+                        desc = f"{desc}{ii}"
                     fname = get_fname(
                         base_fname,
-                        "_space-subject_desc-"
-                        f"{str_to_desc(bundle_name)}{roi_type}{ii}"
-                        "_mask.nii.gz")
+                        f"_space-{to_space}_desc-"
+                        f"{desc}"
+                        f"_{suffix}.nii.gz",
+                        "ROIs")
                     nib.save(
                         nib.Nifti1Image(
                             roi.get_fdata().astype(np.float32),
@@ -1121,3 +1121,67 @@ class BundleDict(MutableMapping):
             self.resample_to,
             self.resample_subject_to,
             self.keep_in_memory)
+
+
+def apply_to_roi_dict(dict_, func, *args,
+                      dry_run=False, apply_to_recobundles=False,
+                      apply_to_prob_map=True,
+                      **kwargs):
+    """
+    Applies some transformation to all ROIs (include, exclude, end, start)
+    and the prob_map in a given bundle.
+
+    Parameters
+    ----------
+    dict_: dict
+        dict describing the bundle using pyAFQ's format. An entry
+        in a BundleDict.
+    func : function
+        function whose first argument must be a Nifti1Image and which
+        returns a Nifti1Image
+    dry_run : bool
+        Whether to actually apply changes returned by `func` to the ROIs.
+        If has_return is False, dry_run is not used.
+    apply_to_recobundles : bool, optional
+        Whether to apply the transformation to recobundles
+        TRKs as well.
+        Default: False
+    apply_to_prob_map : bool, optional
+        Whether to apply the transformation to the prob_map.
+        Default: True
+
+    *args :
+        Additional arguments for func
+    **kwargs
+        Optional arguments for func
+
+    Returns
+    -------
+    A dictionary where keys are
+    the roi type and values are the transformed ROIs.
+    """
+    return_vals = {}
+    roi_types = ["include", "exclude", "start", "end"]
+    if apply_to_prob_map:
+        roi_types.append("prob_map")
+    for roi_type in roi_types:
+        if roi_type in dict_:
+            if roi_type in ["start", "end", "prob_map"]:
+                return_vals[roi_type] = func(
+                    dict_[roi_type], *args, **kwargs)
+            else:
+                changed_rois = []
+                for _roi in dict_[roi_type]:
+                    changed_rois.append(func(
+                        _roi, *args, **kwargs))
+                return_vals[roi_type] = changed_rois
+    if apply_to_recobundles and "recobundles" in dict_:
+        return_vals["recobundles"] = {}
+        for sl_type in ["sl", "centroid"]:
+            return_vals["recobundles"][sl_type] = func(
+                dict_["recobundles"][sl_type],
+                *args, **kwargs)
+    if not dry_run:
+        for roi_type, roi in return_vals.items():
+            dict_[roi_type] = roi
+    return return_vals

{pyafq-1.3.5 → pyafq-2.0}/AFQ/api/group.py

@@ -14,6 +14,7 @@ from AFQ.api.utils import (
     export_all_helper, valid_exports_string)
 import AFQ.utils.streamlines as aus
 from AFQ.viz.utils import get_eye
+from AFQ.data.utils import aws_import_msg_error
 
 from dipy.utils.parallel import paramap
 from dipy.io.stateful_tractogram import StatefulTractogram, Space
@@ -30,11 +31,9 @@ import os
 import os.path as op
 from tqdm import tqdm
 import json
-import s3fs
 from time import time
 import nibabel as nib
 from PIL import Image
-from s3bids.utils import S3BIDSStudy
 import glob
 
 from bids.layout import BIDSLayout, BIDSLayoutIndexer
@@ -45,7 +44,7 @@ except ImportError:
     using_afqb = False
 
 
-__all__ = ["GroupAFQ", "get_afq_bids_entities_fname"]
+__all__ = ["GroupAFQ"]
 
 
 logger = logging.getLogger('AFQ')
@@ -59,11 +58,6 @@ def clean_pandas_df(df):
     return df
 
 
-def get_afq_bids_entities_fname():
-    return op.dirname(op.dirname(op.abspath(
-        aus.__file__))) + "/afq_bids_entities.json"
-
-
 class _ParticipantAFQInputs:
     def __init__(
             self, dwi_data_file, bval_file, bvec_file, results_dir,
@@ -120,7 +114,7 @@ class GroupAFQ(object):
             Set "n_jobs" to -1 to automatically parallelize as
             the number of cpus. Here is an example for how to do
             multiprocessing with 4 cpus:
-            {"n_jobs": 4, "engine": "joblib", "backend": "loky"}
+            {"n_jobs": 4, "engine": "ray"}
             Default: {"engine": "serial"}
         bids_layout_kwargs: dict, optional
             Additional arguments to give to BIDSLayout from pybids.
@@ -278,6 +272,8 @@ class GroupAFQ(object):
                 if session is not None:
                     results_dir = op.join(results_dir, 'ses-' + session)
 
+                results_dir = op.join(results_dir, "dwi")
+
                 dwi_bids_filters = {
                     "subject": subject,
                     "session": session,
@@ -328,16 +324,19 @@ class GroupAFQ(object):
                                     this_kwargs["scalars"].remove(scalar)
                     elif key == "import_tract":
                         if isinstance(this_kwargs["import_tract"], dict):
+                            extension = this_kwargs["import_tract"].pop(
+                                "extension",
+                                ['.trk',
+                                 '.tck',
+                                 '.trx',
+                                 '.vtk',
+                                 '.fib',
+                                 '.dpy'])
                             it_res = \
                                 bids_layout.get(
                                     subject=subject,
                                     session=session,
-                                    extension=[
-                                        '.trk',
-                                        '.tck',
-                                        '.vtk',
-                                        '.fib',
-                                        '.dpy'],
+                                    extension=extension,
                                     return_type='filename',
                                     **this_kwargs["import_tract"])
                             if len(it_res) < 1:
@@ -875,6 +874,10 @@ class GroupAFQ(object):
 
     def upload_to_s3(self, s3fs, remote_path):
         """ Upload entire AFQ derivatives folder to S3"""
+        try:
+            import s3fs
+        except (ImportError, ModuleNotFoundError):
+            aws_import_msg_error("s3fs")
         s3fs.put(self.afq_path, remote_path, recursive=True)
         if op.exists(self.afqb_path):
             s3fs.put(self.afqb_path, remote_path, recursive=True)
@@ -897,6 +900,9 @@ class GroupAFQ(object):
         ex_density_init = nib.load(densities[
             self.valid_sub_list[0]][
                 self.valid_ses_list[0]])  # for shape and header
+        tmpl_name = self.export("tmpl_name", collapse=False)[
+            self.valid_sub_list[0]][
+                self.valid_ses_list[0]]
 
         group_density = np.zeros_like(ex_density_init.get_fdata())
         self.logger.info("Generating Group Density...")
@@ -917,7 +923,7 @@ class GroupAFQ(object):
 
         out_fname = op.abspath(op.join(
             self.afq_path,
-            f"desc-density_subjects-all_space-MNI_dwi.nii.gz"))
+            f"desc-density_subjects-all_space-{tmpl_name}_dwimap.nii.gz"))
         nib.save(group_density, out_fname)
         return out_fname
 
@@ -1165,6 +1171,12 @@ def download_and_combine_afq_profiles(bucket,
     -------
     Ouput CSV's pandas dataframe.
     """
+    try:
+        from s3bids.utils import S3BIDSStudy
+        import s3fs
+    except (ImportError, ModuleNotFoundError):
+        aws_import_msg_error("s3bids and s3fs")
+
     if "subjects" not in kwargs:
         kwargs["subjects"] = "all"
     if "anon" not in kwargs:

{pyafq-1.3.5 → pyafq-2.0}/AFQ/api/utils.py

@@ -126,6 +126,8 @@ def export_all_helper(api_afq_object, xforms, indiv, viz):
     api_afq_object.export("sl_counts")
     api_afq_object.export("median_bundle_lengths")
     api_afq_object.export("profiles")
+    api_afq_object.export("seed_thresh")
+    api_afq_object.export("stop_thresh")
 
     if viz:
         try: