package is working; renaming scripts

javijv4 · javijv4 · commit a71e0179b03f · 2026-02-11T18:52:25.000-08:00
diff --git a/utilities/fiber_generation/README.md b/utilities/fiber_generation/README.md
@@ -1,12 +1,12 @@
-# SV-fibergen
+# svMultiPhysics fiber generation codes
 Python + svMultiPhysics codes for fiber generation. Two methods are implemented:
 * Bayer et al. (2012). [link](https://doi.org/10.1007/s10439-012-0593-5)
 * Doste et al. (2018). [link](https://doi.org/10.1002/cnm.3185)
 
 ## Installation
 
 ### Installing as a Python Package
-You can install `sv-fibergen` as a package using pip:
+You can install the `fiber_generation` codes as a package using pip:
 
 ```bash
 pip install -e .
diff --git a/utilities/fiber_generation/example/biv_truncated/bayer_angle_correlations.png b/utilities/fiber_generation/example/biv_truncated/bayer_angle_correlations.png
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diff --git a/utilities/fiber_generation/fiber_generation/__init__.py b/utilities/fiber_generation/fiber_generation/__init__.py
@@ -0,0 +1,27 @@
+"""Fiber generation package for biventricular heart models.
+
+This package provides classes and utilities to generate myocardial fiber
+orientations for biventricular heart models using Laplace-Dirichlet
+rule-based methods.
+
+Modules:
+    fiber_generator: Core fiber generation classes (FibGen, FibGenBayer, FibGenDoste)
+    laplace_solver: Laplace-Dirichlet equation solver
+    surface_names: Surface name definitions for heart geometry
+    surface_utils: Utility functions for surface operations
+    quat_utils: Quaternion utilities for rotation operations
+"""
+
+from fiber_generation.fiber_generator import FibGen, FibGenBayer, FibGenDoste
+from fiber_generation.laplace_solver import LaplaceSolver
+from fiber_generation.surface_names import SurfaceName
+
+__all__ = [
+    'FibGen',
+    'FibGenBayer',
+    'FibGenDoste',
+    'LaplaceSolver',
+    'SurfaceName',
+]
+
+__version__ = '0.1.0'
diff --git a/utilities/fiber_generation/fiber_generation/fiber_generator.py b/utilities/fiber_generation/fiber_generation/fiber_generator.py
@@ -18,7 +18,7 @@
 import numpy as np
 import pyvista as pv
 
-import src.quat_utils as qu
+import fiber_generation.quat_utils as qu
 
 
 class FibGen:
diff --git a/utilities/fiber_generation/fiber_generation/laplace_solver.py b/utilities/fiber_generation/fiber_generation/laplace_solver.py
@@ -14,7 +14,7 @@
 import os
 from xml.etree import ElementTree as ET
 from xml.dom import minidom
-from .SurfaceNames import SurfaceName
+from .surface_names import SurfaceName
 
 
 class LaplaceSolver:
@@ -252,7 +252,7 @@ def _get_doste_equations(self):
             list: List of (alias, boundary_conditions) tuples.
         """
         return [
-            # Trans_BiV: Ventricular transmural (LV=1, RV=0)
+            # Trans_BiV: Ventricular transmural (LV=-2, RV=1)
             ("Trans_BiV", [
                 ("lv_endocardium", -2.0),
                 ("rv_endocardium", 1.0),
diff --git a/utilities/fiber_generation/fiber_generation/quat_utils.py b/utilities/fiber_generation/fiber_generation/quat_utils.py
diff --git a/utilities/fiber_generation/fiber_generation/surface_names.py b/utilities/fiber_generation/fiber_generation/surface_names.py
diff --git a/utilities/fiber_generation/fiber_generation/surface_utils.py b/utilities/fiber_generation/fiber_generation/surface_utils.py
@@ -9,7 +9,7 @@
 import os
 import numpy as np
 import pyvista as pv
-from .SurfaceNames import SurfaceName
+from .surface_names import SurfaceName
 
 
 def get_normal_plane_svd(points):
diff --git a/utilities/fiber_generation/main_bayer.py b/utilities/fiber_generation/main_bayer.py
@@ -15,10 +15,10 @@
 import argparse
 import os
 import pyvista as pv
-from src.LaplaceSolver import LaplaceSolver
-from src.FibGen import FibGenBayer
-from src.SurfaceNames import SurfaceName
-from src.surface_utils import generate_epi_apex
+from fiber_generation.laplace_solver import LaplaceSolver
+from fiber_generation.fiber_generator import FibGenBayer
+from fiber_generation.surface_names import SurfaceName
+from fiber_generation.surface_utils import generate_epi_apex
 from time import time
 
 
diff --git a/utilities/fiber_generation/main_doste.py b/utilities/fiber_generation/main_doste.py
@@ -15,10 +15,10 @@
 import os
 import argparse
 import pyvista as pv
-from src.LaplaceSolver import LaplaceSolver
-from src.FibGen import FibGenDoste
-from src.SurfaceNames import SurfaceName
-from src.surface_utils import generate_epi_apex
+from fiber_generation.laplace_solver import LaplaceSolver
+from fiber_generation.fiber_generator import FibGenDoste
+from fiber_generation.surface_names import SurfaceName
+from fiber_generation.surface_utils import generate_epi_apex
 from time import time
 
 
diff --git a/utilities/fiber_generation/pyproject.toml b/utilities/fiber_generation/pyproject.toml
@@ -7,8 +7,7 @@ name = "sv-fibergen"
 version = "0.1.0"
 description = "Python + svMultiPhysics codes for biventricular fiber generation"
 readme = "README.md"
-
-license = {text = "MIT"}
+license = "MIT"
 requires-python = ">=3.8"
 
 dependencies = [
@@ -17,3 +16,7 @@ dependencies = [
     "scipy>=1.7.0",
     "matplotlib>=3.4.0",
 ]
+
+[tool.setuptools]
+packages = ["fiber_generation"]
+
diff --git a/utilities/fiber_generation/test_fibgen_functions.py b/utilities/fiber_generation/test_fibgen_functions.py
@@ -8,11 +8,7 @@
 import numpy as np
 import sys
 import os
-
-# Add src to path
-sys.path.insert(0, os.path.join(os.path.dirname(__file__), 'src'))
-
-from src.FibGen import FibGen
+from fiber_generation.fiber_generator import FibGen
 
 
 class TestFibGen(unittest.TestCase):
diff --git a/utilities/fiber_generation/validation_bayer.py b/utilities/fiber_generation/validation_bayer.py
@@ -5,7 +5,7 @@
 import numpy as np
 import pyvista as pv
 
-from src.FibGen import FibGenBayer
+from fiber_generation.fiber_generator import FibGenBayer
 from scipy import stats
 import matplotlib.pyplot as plt
 
diff --git a/utilities/fiber_generation/validation_doste.py b/utilities/fiber_generation/validation_doste.py
@@ -5,7 +5,7 @@
 import numpy as np
 import pyvista as pv
 
-from src.FibGen import FibGenDoste
+from fiber_generation.fiber_generator import FibGenDoste
 from scipy import stats
 import matplotlib.pyplot as plt
 
