yabplot 0.3.1__tar.gz → 0.5.0__tar.gz

{yabplot-0.3.1/yabplot.egg-info → yabplot-0.5.0}/PKG-INFO

@@ -1,12 +1,13 @@
 Metadata-Version: 2.4
 Name: yabplot
-Version: 0.3.1
+Version: 0.5.0
 Summary: yet another brain plot
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: cmocean>=4.0.3
 Requires-Dist: ipywidgets>=8.1.8
+Requires-Dist: matplotlib>=3.10.7
 Requires-Dist: nibabel>=5.3.2
 Requires-Dist: pandas>=2.3.3
 Requires-Dist: pooch>=1.8.2
@@ -31,17 +32,18 @@ Dynamic: license-file
 [![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18237144.svg)](https://doi.org/10.5281/zenodo.18237144)
 
-**yabplot** is a Python library for creating beautiful, publication-quality 3D brain visualizations. it supports plotting cortical regions (+ vertexwise), subcortical structures, and white matter bundles.
+**yabplot** is a Python library for creating publication-quality 3D brain visualizations. it provides a unified interface for cortical regions, subcortical structures, white matter bundles, connectomes, voxel-wise maps, and vertex-wise maps.
 
-the idea is simple. while there are already amazing visualization tools available, they often focus on specific domains—using one tool for white matter tracts and another for cortical surfaces inevitably leads to inconsistent styles. i wanted a unified, simple-to-use tool that enables me (and hopefully others) to perform most brain visualizations in a single place. recognizing that neuroscience evolves daily, i designed **yabplot** to be modular: it supports standard pre-packaged atlases out of the box, but easily accepts any custom parcellation or tractography dataset you might need.
+the idea is simple. while there are already amazing visualization tools available, they often focus on specific domains—using one tool for white matter tracts and another for cortical surfaces inevitably leads to inconsistent styles. i wanted a unified, simple-to-use tool that enables me (and hopefully others) to perform most brain visualizations in a single place. recognizing that neuroscience evolves daily, i designed **yabplot** to be modular: it supports standard pre-packaged atlases out of the box, but easily accepts any custom parcellation or tractography dataset you might need. moreover, it enables to plot volumetric data either voxel-wise or by projecting the data to cortical surface or white matter tracts.
 
 ## features
 
-* **pre-existing atlases:** access many commonly used atlases (schaefer2018, brainnetome, aparc, aseg, musus100, xtract, etc) on demand.
-* [new!] **vertexwise plotting:** project volume (.nii) to cortical surface and plot.
-* **simple to use:** plug-n-play functions for cortex, subcortex, and tracts with a unified API.
-* **custom atlases:** easily use your own parcellations, segmentations (.nii/.gii), or tractograms (.trk).
-* **flexible inputs:** accepts data as dictionaries (for partial mapping) or arrays (for strict mapping).
+* **unified plotting API:** plot cortical regions, vertex-wise maps, subcortical structures, voxel-wise maps, white-matter tracts, and connectomes with a consistent interface.
+* **pre-packaged resources:** access commonly used atlases and meshes on demand, including schaefer, brainnetome, aparc, aseg, musus100, and xtract atlases.
+* **flexible data mapping:** pass data as arrays for strict ordering or dictionaries for partial/name-based mapping.
+* **custom atlases:** build and use custom cortical parcellations, subcortical segmentations, and tractography datasets.
+* **volume projection:** project nifti images to cortical surfaces or tractograms for vertex-wise and tractometry visualizations, or plot the volumes voxel-wise.
+* **publication-oriented output:** generate static figures, saved images, and interactive 3D views.
 
 ## installation
 
@@ -55,7 +57,7 @@ pip install yabplot # to install
 pip install yabplot --upgrade # to update
 ```
 
-dependencies: python 3.11 with ipywidgets, nibabel, pandas, pooch, pyvista, scikit-image, trame, trame-vtk, trame-vuetify
+dependencies: python 3.11 with ipywidgets, nibabel, matplotlib, pandas, pooch, pyvista, scikit-image, trame, trame-vtk, trame-vuetify
 
 (Connectome Workbench (`wb_command`) is a requirement to create custom cortical atlases unless you plan to only use pre-loaded atlases; see more in docs)
 
@@ -77,36 +79,53 @@ print(yab.get_available_resources())
 # see the region names for a specific atlas
 print(yab.get_atlas_regions(atlas='aseg', category='subcortical'))
 
-# cortical surfaces
+# plotting cortical surface regions
 atlas = 'aparc'
-dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086, ...}
-dmap2 = {'L_fusiform': 0.218, 'L_supramarginal': 0.119, ...}
-yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[-0.1, 0.3], 
-                  bmesh_type='midthickness', views=['left_lateral', 'left_medial'],
-                  figsize=(600, 300), cmap='viridis', proc_vertices='sharp')
-yab.plot_cortical(data=dmap2, atlas=atlas, vminmax=[-0.1, 0.3], 
-                  bmesh_type='swm', views=['left_lateral', 'left_medial'],
-                  figsize=(1200, 600), cmap='viridis', proc_vertices='sharp')
-
-# subcortical structures
+dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086}
+ax = yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[0.0, 0.3], cmap='viridis',
+    bmesh='midthickness', views=['left_lateral', 'left_medial'])
+
+# plotting subcortical regions
 atlas = 'aseg'
 regs = yab.get_atlas_regions(atlas=atlas, category='subcortical')
 data = np.arange(1, len(regs)+1)
-yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
-                     views=['left_lateral', 'superior', 'right_lateral'], 
-                     bmesh_alpha=0.1, figsize=(600, 300), cmap='viridis')
+ax = yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
+    views=['left_lateral', 'superior', 'right_lateral'], 
+    bmesh_alpha=0.1, cmap='plasma')
 
-# white matter bundles
-atlas = 'xtract_tiny'
+# plotting white matter tracts
+atlas = 'xtract_medium'
 regs = yab.get_atlas_regions(atlas=atlas, category='tracts')
 data = {reg: np.sin(i) for i, reg in enumerate(regs)}
-yab.plot_tracts(data=data, atlas=atlas, style='matte',
-                views=['left_lateral', 'anterior', 'superior'], bmesh_type='pial',
-                bmesh_alpha=0.1, figsize=(1600, 800), cmap='viridis')
+ax = yab.plot_tracts(data=data, atlas=atlas, style='matte', cmap='coolwarm',
+    views=['left_lateral', 'anterior', 'superior'], bmesh='pial')
+
+# plotting connectome
+data = np.random.rand(400, 400)
+ax = yab.plot_connectome(matrix=data, atlas='schaefer400',
+    edge_cmap='dense', node_cmap='binary', edge_threshold='95%', 
+    views=['left_lateral', 'superior', 'posterior']
+)
+
+# volume projection to cortical surface and vertexwise plotting
+threshold = 4
+b_lh_path, b_rh_path = yab.data.get_surface_paths('midthickness', 'bmesh')
+lh_data, rh_data = yab.project_vol2surf('path/to/yourdata.nii.gz', bmesh='midthickness')
+lh_data = np.where(lh_data > threshold, lh_data, np.nan)
+rh_data = np.where(rh_data > threshold, rh_data, np.nan)
+lh_mesh, rh_mesh = yab.load_vertexwise_mesh(b_lh_path, b_rh_path, lh_data, rh_data)
+ax = yab.plot_vertexwise(lh_mesh, rh_mesh, cmap='viridis', vminmax=[-10, 10], 
+                    views=['left_lateral', 'left_medial'])
+
+# plotting volume voxel-wise 
+threshold = '99.5%'
+nii_path = 'path/to/yourdata.nii.gz'
+ax = yab.plot_voxelwise(nii_path, threshold='99%', cmap='Reds',
+    views=['left_lateral', 'superior', 'anterior'])
 
 ```
 
-![examples](docs/assets/examples.png)
+![examples](docs/assets/overview.png)
 
 ## acknowledgements
 

yabplot-0.5.0/README.md

@@ -0,0 +1,107 @@
+# yabplot: yet another brain plot
+
+![logo](docs/assets/yabplot_logo.png)
+
+[![PyPI version](https://img.shields.io/pypi/v/yabplot.svg)](https://pypi.org/project/yabplot/)
+[![Docs](https://github.com/teanijarv/yabplot/actions/workflows/docs.yml/badge.svg)](https://teanijarv.github.io/yabplot/)
+[![Tests](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml/badge.svg)](https://github.com/teanijarv/yabplot/actions/workflows/tests.yml)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.18237144.svg)](https://doi.org/10.5281/zenodo.18237144)
+
+**yabplot** is a Python library for creating publication-quality 3D brain visualizations. it provides a unified interface for cortical regions, subcortical structures, white matter bundles, connectomes, voxel-wise maps, and vertex-wise maps.
+
+the idea is simple. while there are already amazing visualization tools available, they often focus on specific domains—using one tool for white matter tracts and another for cortical surfaces inevitably leads to inconsistent styles. i wanted a unified, simple-to-use tool that enables me (and hopefully others) to perform most brain visualizations in a single place. recognizing that neuroscience evolves daily, i designed **yabplot** to be modular: it supports standard pre-packaged atlases out of the box, but easily accepts any custom parcellation or tractography dataset you might need. moreover, it enables to plot volumetric data either voxel-wise or by projecting the data to cortical surface or white matter tracts.
+
+## features
+
+* **unified plotting API:** plot cortical regions, vertex-wise maps, subcortical structures, voxel-wise maps, white-matter tracts, and connectomes with a consistent interface.
+* **pre-packaged resources:** access commonly used atlases and meshes on demand, including schaefer, brainnetome, aparc, aseg, musus100, and xtract atlases.
+* **flexible data mapping:** pass data as arrays for strict ordering or dictionaries for partial/name-based mapping.
+* **custom atlases:** build and use custom cortical parcellations, subcortical segmentations, and tractography datasets.
+* **volume projection:** project nifti images to cortical surfaces or tractograms for vertex-wise and tractometry visualizations, or plot the volumes voxel-wise.
+* **publication-oriented output:** generate static figures, saved images, and interactive 3D views.
+
+## installation
+
+```bash
+uv add yabplot # to install
+uv sync --upgrade-package yabplot # to update
+```
+or
+```bash
+pip install yabplot # to install
+pip install yabplot --upgrade # to update
+```
+
+dependencies: python 3.11 with ipywidgets, nibabel, matplotlib, pandas, pooch, pyvista, scikit-image, trame, trame-vtk, trame-vuetify
+
+(Connectome Workbench (`wb_command`) is a requirement to create custom cortical atlases unless you plan to only use pre-loaded atlases; see more in docs)
+
+
+## quick start
+
+please refer to the [documentation](https://teanijarv.github.io/yabplot/) for more comprehensive guides.
+
+```python
+import yabplot as yab
+import numpy as np
+
+# check that you have the latest version
+print(yab.__version__)
+
+# see available atlases and brain meshes
+print(yab.get_available_resources())
+
+# see the region names for a specific atlas
+print(yab.get_atlas_regions(atlas='aseg', category='subcortical'))
+
+# plotting cortical surface regions
+atlas = 'aparc'
+dmap1 = {'L_lateraloccipital': 0.265, 'L_postcentral': 0.086}
+ax = yab.plot_cortical(data=dmap1, atlas=atlas, vminmax=[0.0, 0.3], cmap='viridis',
+    bmesh='midthickness', views=['left_lateral', 'left_medial'])
+
+# plotting subcortical regions
+atlas = 'aseg'
+regs = yab.get_atlas_regions(atlas=atlas, category='subcortical')
+data = np.arange(1, len(regs)+1)
+ax = yab.plot_subcortical(data=data, atlas=atlas, vminmax=[2, 14], 
+    views=['left_lateral', 'superior', 'right_lateral'], 
+    bmesh_alpha=0.1, cmap='plasma')
+
+# plotting white matter tracts
+atlas = 'xtract_medium'
+regs = yab.get_atlas_regions(atlas=atlas, category='tracts')
+data = {reg: np.sin(i) for i, reg in enumerate(regs)}
+ax = yab.plot_tracts(data=data, atlas=atlas, style='matte', cmap='coolwarm',
+    views=['left_lateral', 'anterior', 'superior'], bmesh='pial')
+
+# plotting connectome
+data = np.random.rand(400, 400)
+ax = yab.plot_connectome(matrix=data, atlas='schaefer400',
+    edge_cmap='dense', node_cmap='binary', edge_threshold='95%', 
+    views=['left_lateral', 'superior', 'posterior']
+)
+
+# volume projection to cortical surface and vertexwise plotting
+threshold = 4
+b_lh_path, b_rh_path = yab.data.get_surface_paths('midthickness', 'bmesh')
+lh_data, rh_data = yab.project_vol2surf('path/to/yourdata.nii.gz', bmesh='midthickness')
+lh_data = np.where(lh_data > threshold, lh_data, np.nan)
+rh_data = np.where(rh_data > threshold, rh_data, np.nan)
+lh_mesh, rh_mesh = yab.load_vertexwise_mesh(b_lh_path, b_rh_path, lh_data, rh_data)
+ax = yab.plot_vertexwise(lh_mesh, rh_mesh, cmap='viridis', vminmax=[-10, 10], 
+                    views=['left_lateral', 'left_medial'])
+
+# plotting volume voxel-wise 
+threshold = '99.5%'
+nii_path = 'path/to/yourdata.nii.gz'
+ax = yab.plot_voxelwise(nii_path, threshold='99%', cmap='Reds',
+    views=['left_lateral', 'superior', 'anterior'])
+
+```
+
+![examples](docs/assets/overview.png)
+
+## acknowledgements
+
+yabplot relies on the extensive work of the neuroimaging community. if you use these atlases in your work, please cite the original authors. if you use this package for any scientific work, please cite the DOI (see more info on [Zenodo](https://doi.org/10.5281/zenodo.18237144)).

{yabplot-0.3.1 → yabplot-0.5.0}/pyproject.toml

@@ -1,12 +1,13 @@
 [project]
 name = "yabplot"
-version = "0.3.1"
+version = "0.5.0"
 description = "yet another brain plot"
 readme = "README.md"
 requires-python = ">=3.10"
 dependencies = [
     "cmocean>=4.0.3",
     "ipywidgets>=8.1.8",
+    "matplotlib>=3.10.7",
     "nibabel>=5.3.2",
     "pandas>=2.3.3",
     "pooch>=1.8.2",

{yabplot-0.3.1 → yabplot-0.5.0}/tests/test_smoke.py

@@ -10,6 +10,37 @@ def test_version():
     """Check that the package has a version string."""
     assert yab.__version__ is not None
 
+def test_none_returns_empty_dict():
+    """
+    Unit test: Verify that passing None disables the background mesh 
+    by correctly returning an empty dictionary.
+    """
+    result = yab.mesh.load_bmesh(None)
+    assert result == {}
+
+def test_dict_passthrough():
+    """
+    Unit test: Verify that custom dictionary keys for hemispheres 
+    are properly sanitized to strict 'L' and 'R' keys.
+    """
+    mesh_l = pv.Sphere()
+    mesh_r = pv.Cube()
+    mesh_other = pv.Cone()
+    d = {'left': mesh_l, 'RIGHT': mesh_r, 'other': mesh_other}
+    result = yab.mesh.load_bmesh(d)
+    expected = {'L': mesh_l, 'R': mesh_r, 'other': mesh_other}
+    assert result == expected
+
+def test_polydata_wrapped_in_both():
+    """
+    Unit test: Verify that passing a single PyVista mesh (whole brain) 
+    safely wraps it in a dictionary with the 'both' key.
+    """
+    mesh = pv.Sphere()
+    result = yab.mesh.load_bmesh(mesh)
+    assert 'both' in result
+    assert result['both'] is mesh
+
 def test_plotter_instantiation():
     """
     Smoke test: Can we create a Plotter without crashing?
@@ -46,4 +77,4 @@ def test_plot_vertexwise():
     rh = pv.Sphere()
     lh['Data'] = np.random.rand(lh.n_points)
     rh['Data'] = np.random.rand(rh.n_points)
-    yab.plot_vertexwise(lh, rh, display_type=None)
+    yab.plot_vertexwise(lh, rh, display_type=None)

{yabplot-0.3.1 → yabplot-0.5.0}/yabplot/__init__.py

@@ -2,7 +2,8 @@ from importlib.metadata import version, PackageNotFoundError
 
 from .plotting import (
     plot_cortical, plot_subcortical, plot_tracts, 
-    clear_tract_cache, plot_vertexwise
+    clear_cache, plot_vertexwise, plot_connectome,
+    plot_voxelwise
 )
 from .data import (
     get_available_resources, get_atlas_regions
@@ -11,7 +12,10 @@ from .atlas_builder import (
     build_cortical_atlas, build_subcortical_atlas
 )
 from .mesh import (
-    load_vertexwise_mesh, project_vol2surf
+    load_vertexwise_mesh, make_cortical_mesh, load_nii_as_mesh
+)
+from .projection import (
+    project_vol2surf, project_vol2tract, project_vol2tract_atlas
 )
 
 try:

{yabplot-0.3.1 → yabplot-0.5.0}/yabplot/atlas_builder.py

@@ -224,10 +224,10 @@ def qc_custom_cortical_atlas(atlas_dir, atlasname='atlas'):
             plot_file = os.path.join(qc_dir, f"{rid:03d}_{name}.png")
             
             try:
-                plot_cortical(
+                ax = plot_cortical(
                     data={name: 1},
                     custom_atlas_path=atlas_dir,
-                    cmap='binary',vminmax=[0, 1],
+                    cmap='binary', vminmax=[0, 1],
                     export_path=plot_file
                 )
             except Exception as e:
@@ -328,6 +328,12 @@ def build_subcortical_atlas(nii_path, labels_dict, out_dir, include_list=None, e
         # save as a vtk file
         out_file = os.path.join(out_dir, f"{name}.vtk")
         mesh.save(out_file)
+    
+    # file for ordering the labels
+    lut_path = os.path.join(out_dir, "atlas_LUT.txt")
+    with open(lut_path, 'w') as f:
+        for rid, name in targets.items():
+            f.write(f"{rid} {name}\n")
 
     print(f"\nsubcortical atlas successfully saved to: {out_dir}")
 
@@ -391,7 +397,7 @@ def qc_custom_subcortical_atlas(atlas_dir):
             plot_file = os.path.join(qc_dir, f"{region_name}.png")
             
             try:
-                plot_subcortical(
+                ax = plot_subcortical(
                     data={region_name: 1},
                     custom_atlas_path=atlas_dir,
                     cmap='binary', vminmax=[0, 1],

{yabplot-0.3.1 → yabplot-0.5.0}/yabplot/data/__init__.py

@@ -6,6 +6,7 @@ import os
 import glob
 from pathlib import Path
 import pooch
+import shutil
 
 from ..utils import parse_lut
 
@@ -165,8 +166,7 @@ def get_atlas_regions(atlas, category, custom_atlas_path=None):
     elif category == 'subcortical':
         try:
             file_map = _find_subcortical_files(atlas_dir)
-            # the plotting function sorts keys alphabetically
-            return sorted(list(file_map.keys()))
+            return _get_ordered_names(atlas_dir, file_map)
         except Exception as e:
             print(f"Error listing subcortical regions: {e}")
             return []
@@ -175,8 +175,7 @@ def get_atlas_regions(atlas, category, custom_atlas_path=None):
     elif category == 'tracts':
         try:
             file_map = _find_tract_files(atlas_dir)
-            # the plotting function sorts keys alphabetically
-            return sorted(list(file_map.keys()))
+            return _get_ordered_names(atlas_dir, file_map)
         except Exception as e:
             print(f"Error listing tracts: {e}")
             return []
@@ -188,26 +187,44 @@ def get_atlas_regions(atlas, category, custom_atlas_path=None):
 def _fetch_and_unpack(resource_key):
     """
     Downloads zip, unpacks it, deletes the zip to save space, 
-    and returns the extraction path.
+    and returns the extraction path. Forces a redownload if the 
+    registry hash changes (indicating an update).
     """
     extract_dir_name = resource_key.replace(".zip", "")
     extract_path = os.path.join(GOODBOY.path, extract_dir_name)
+    hash_file = os.path.join(extract_path, ".registry_hash")
 
-    # optimization: check if unpacked folder already exists
-    # if yes, skip pooch check entirely to avoid re-downloading
-    if os.path.isdir(extract_path) and os.listdir(extract_path):
-        return extract_path
+    # get the expected hash from the registry
+    expected_hash = GOODBOY.registry.get(resource_key)
+    if not expected_hash:
+        raise ValueError(f"Resource '{resource_key}' not found in registry.")
 
-    # fetch and unzip
+    # check if unpacked folder already exists and is up-to-date
+    is_up_to_date = False
+    if os.path.isdir(extract_path) and os.path.exists(hash_file):
+        with open(hash_file, 'r') as f:
+            local_hash = f.read().strip()
+        if local_hash == expected_hash:
+            is_up_to_date = True
+    if is_up_to_date:
+        return extract_path
+    # if folder exists but hash is wrong (outdated), wipe it clean
+    elif os.path.exists(extract_path):
+        print(f"Update found for '{extract_dir_name}'. Removing legacy data...")
+        shutil.rmtree(extract_path)
+        
+    # fetch and unzip new data
     try:
         GOODBOY.fetch(
             resource_key, 
             processor=pooch.Unzip(extract_dir=extract_dir_name)
         )
-    except ValueError:
-        # if key not in registry
-        available = list(GOODBOY.registry.keys())
-        raise ValueError(f"Resource '{resource_key}' not found in registry.")
+    except Exception as e:
+        raise RuntimeError(f"Failed to fetch '{resource_key}': {e}")
+    
+    # stamp the new folder with the updated hash
+    with open(hash_file, 'w') as f:
+        f.write(expected_hash)
 
     # cleanup: delete the source zip to save space
     zip_path = os.path.join(GOODBOY.path, resource_key)
@@ -225,7 +242,9 @@ def _resolve_resource_path(name, category, custom_path=None):
     if custom_path:
         if os.path.isdir(custom_path):
             return custom_path
-        raise FileNotFoundError(f"Custom atlas directory not found: {custom_path}")
+        if os.path.isfile(custom_path):
+            return custom_path
+        raise FileNotFoundError(f"Custom atlas directory/file not found: {custom_path}")
 
     # 2. standard download logic
     resource_key = f"{category}-{name}.zip"
@@ -326,6 +345,46 @@ def _find_cortical_files(atlas_dir, strict_name=None):
         
     return csv_path, lut_path
 
+def _get_ordered_names(atlas_dir, file_map):
+    """
+    Attempts to read the strict region order from a LUT or order text file.
+    Falls back to alphabetical sorting if no file exists.
+    """
+    txt_files = []
+
+    # look for a LUT or order file, ignoring qc reports
+    for root, dirs, files in os.walk(atlas_dir):
+        dirs[:] = [d for d in dirs if not d.startswith(('.', '__')) and 'qc_report' not in d]
+        for file in files:
+            if file.endswith('.txt') and 'registry' not in file:
+                txt_files.append(os.path.join(root, file))
+    def file_priority(filepath):
+        name = filepath.lower()
+        if 'lut' in name: return 0
+        if 'order' in name: return 1
+        return 2
+    txt_files.sort(key=file_priority)
+
+    if txt_files:
+        ordered_names = []
+        with open(txt_files[0], 'r') as f:
+            for line in f:
+                parts = line.strip().split()
+                # assuming standard LUT format (ID Name ...) or simple list (ID Name)
+                if len(parts) >= 2:
+                    name = parts[1]
+                    if name in file_map and name not in ordered_names:
+                        ordered_names.append(name)
+        
+        # append any stray files that exist in the directory but weren't in the text file
+        for name in sorted(file_map.keys()):
+            if name not in ordered_names:
+                ordered_names.append(name)
+        
+        return ordered_names
+
+    # legacy fallback: alphabetical
+    return sorted(list(file_map.keys()))
 
 def _find_subcortical_files(atlas_dir):
     """
@@ -403,8 +462,15 @@ def _find_tract_files(atlas_dir):
             
         return candidates
 
-    # scan for both .trk and .tck
-    found_files = _scan_for_ext(atlas_dir, ".trk") + _scan_for_ext(atlas_dir, ".tck")
+    if  os.path.isdir(atlas_dir):
+        # scan for both .trk and .tck
+        found_files = _scan_for_ext(atlas_dir, ".trk") + _scan_for_ext(atlas_dir, ".tck")
+    elif os.path.isfile(atlas_dir):
+        if atlas_dir.endswith((".trk", ".tck")):
+            found_files = [atlas_dir]
+    else:
+        raise ValueError(f"Invalid atlas directory/file path: {atlas_dir}, no valid tck or trk file found.")
+
     
     if not found_files:
         raise FileNotFoundError(f"No .trk or .tck files found in {atlas_dir}")

yabplot-0.5.0/yabplot/data/registry.txt

@@ -0,0 +1,30 @@
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