pyLQT 1.0.dev4__tar.gz → 1.0.dev6__tar.gz

{pylqt-1.0.dev4/src/pyLQT.egg-info → pylqt-1.0.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLQT
-Version: 1.0.dev4
+Version: 1.0.dev6
 Summary: Python version of LQT from Griffis et al. 2021 (https://www.sciencedirect.com/science/article/pii/S2213158221000838)
 Author-email: Antonin HUDRY <hudryantoninm@gmail.com>
 License-Expression: GPL-3.0-only

{pylqt-1.0.dev4 → pylqt-1.0.dev6}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta"
 [project]
 name = "pyLQT"
 keywords = ["LQT", "lqt", "lesion", "brain", ""]
-version = "1.0.dev4"
+version = "1.0.dev6"
 authors = [
     {name="Antonin HUDRY", email="hudryantoninm@gmail.com"},
 ]

{pylqt-1.0.dev4 → pylqt-1.0.dev6}/src/pyLQT/cli.py

@@ -1,6 +1,6 @@
 import argparse
 
-from pipeline import run_pyLQT
+from pyLQT.pipeline import run_pyLQT
 
 
 def main():

{pylqt-1.0.dev4/src/pyLQT/lesion_metrics/gray_matter → pylqt-1.0.dev6/src/pyLQT/lesion_metrics/grey_matter}/metrics.py

@@ -12,6 +12,7 @@ def get_parcel_damage(
     parcel_column,
     out_path = None
     ):
+    
     """Compute lesion damage for each parcel of an atlas.
 
     The lesion is resampled to the atlas grid, and the proportion of
@@ -39,7 +40,7 @@ def get_parcel_damage(
     Returns
     -------
     pandas.DataFrame
-        Copy of ``atlas_labels`` with an additional ``PercentDamage``
+        Copy of ``atlas_labels`` with an additional ``Damage``
         column containing the proportion of each parcel affected by the
         lesion.
     """
@@ -56,10 +57,10 @@ def get_parcel_damage(
 
     for parcel in atlas_labels[parcel_column]:
         parcel_volume = atlas_volume == parcel
-        parcel_damage = compute_parcel_damage(parcel_volume, lesion_volume)
+        parcel_damage = np.round(compute_parcel_damage(parcel_volume, lesion_volume), 5)
 
         parcel_damages.append(parcel_damage)
-        parcel_damage_map[parcel_volume] = np.round(parcel_damage, 5)
+        parcel_damage_map[parcel_volume] = parcel_damage
 
     if out_path:
         out_path.mkdir(parents=True, exist_ok=True)
@@ -70,7 +71,7 @@ def get_parcel_damage(
         )
 
     damage_frame = atlas_labels.copy(deep=True)
-    damage_frame["PercentDamage"] = parcel_damages
+    damage_frame["Damage"] = parcel_damages
     if out_path:
         damage_frame.to_csv(out_path / 'parcel_damage_frame.csv', index=False)
     

{pylqt-1.0.dev4 → pylqt-1.0.dev6}/src/pyLQT/lesion_metrics/utils/downloads.py

@@ -189,7 +189,7 @@ def default_atlas_download(out_folder: Path):
     config = {
         "name": "glasser360",
         "atlas": "glasser360_MNI152NLin2009cAsym.nii.gz",
-        "atlas_labels": "glasser360_labels.csv",
+        "labels": "glasser360_labels.csv",
         "space": "MNI152NLin2009cAsym"
     }
             

{pylqt-1.0.dev4 → pylqt-1.0.dev6}/src/pyLQT/pipeline.py

@@ -1,7 +1,7 @@
 from pyLQT.lesion_metrics.white_matter.metrics import get_tracts_disconnections_severity, get_tracts_disconnections_map
 from pyLQT.lesion_metrics.white_matter.utils import get_streamlines_disconnection, get_aggregated_tracts, clip_tractogram_to_grid
 from pyLQT.lesion_metrics.network.metrics import get_sspl_increase, get_parcel_wise_disconnection_severity
-from pyLQT.lesion_metrics.gray_matter.metrics import get_parcel_damage
+from pyLQT.lesion_metrics.grey_matter.metrics import get_parcel_damage
 from pyLQT.lesion_metrics.utils.configs import atlas_cfg_read, tracts_cfg_read, lesion_cfg_read
 from pyLQT.lesion_metrics.utils.downloads import default_tracts_download, default_atlas_download, create_tract_list, uncompress_trk_gz, get_ref_space_tf
 from pyLQT.lesion_metrics.utils.registration import register_affine, register_syn
@@ -83,7 +83,28 @@ def run_pyLQT(
         tracts_ref_space = nib.load(tracts_space)
     else:
         tracts_ref_space = get_ref_space_tf(tracts_space)
+        
+    #### TEST ####
+    import numpy as np
+    from nibabel.orientations import aff2axcodes
+    for lesion_path in lesion_folder.glob("*.nii*"):
+        lesion = nib.load(lesion_path)
+
+        print("Lesion shape:", lesion.shape)
+        print("Moving reference shape:", lesion_ref_space.shape)
 
+        print("Lesion affine:\n", lesion.affine)
+        print("Moving reference affine:\n", lesion_ref_space.affine)
+
+        print(
+            "Same grid:",
+            lesion.shape == lesion_ref_space.shape
+            and np.allclose(lesion.affine, lesion_ref_space.affine),
+        )
+        print("Lesion:", aff2axcodes(lesion.affine))
+        print("Moving reference:", aff2axcodes(lesion_ref_space.affine))
+    #### TEST ####
+    
     registrator = (register_affine if registration_type == "affine" else register_syn)
 
     lesion_tracts_mapping = registrator(lesion_ref_space, tracts_ref_space)

{pylqt-1.0.dev4 → pylqt-1.0.dev6/src/pyLQT.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyLQT
-Version: 1.0.dev4
+Version: 1.0.dev6
 Summary: Python version of LQT from Griffis et al. 2021 (https://www.sciencedirect.com/science/article/pii/S2213158221000838)
 Author-email: Antonin HUDRY <hudryantoninm@gmail.com>
 License-Expression: GPL-3.0-only

{pylqt-1.0.dev4 → pylqt-1.0.dev6}/src/pyLQT.egg-info/SOURCES.txt

@@ -11,9 +11,9 @@ src/pyLQT.egg-info/entry_points.txt
 src/pyLQT.egg-info/requires.txt
 src/pyLQT.egg-info/top_level.txt
 src/pyLQT/lesion_metrics/__init__.py
-src/pyLQT/lesion_metrics/gray_matter/__init__.py
-src/pyLQT/lesion_metrics/gray_matter/metrics.py
-src/pyLQT/lesion_metrics/gray_matter/utils.py
+src/pyLQT/lesion_metrics/grey_matter/__init__.py
+src/pyLQT/lesion_metrics/grey_matter/metrics.py
+src/pyLQT/lesion_metrics/grey_matter/utils.py
 src/pyLQT/lesion_metrics/network/__init__.py
 src/pyLQT/lesion_metrics/network/metrics.py
 src/pyLQT/lesion_metrics/network/utils.py