Move core modules into autoflow package

.gitignore

@@ -1,7 +1,10 @@
 __pycache__/
 *.pyc
 *.pyo
+/*.py
 .ipynb_checkpoints/
+*.ipynb
+!library_demo.ipynb
 
 # Local data and generated outputs
 /111/
@@ -19,6 +22,4 @@ TODO.md
 app.png
 autoflow_mri.egg-info/
 build/
-test.ipynb
-utils_bgc.py
-/scripts/
+/scripts/

algorithms.py → autoflow/algorithms.py

@@ -9,7 +9,7 @@
 from scipy.signal import savgol_filter
 from skimage.morphology import skeletonize
 
-from models import PlaneData, GraphData, SkeletonParams
+from .models import PlaneData, GraphData, SkeletonParams
 
 
 def _axis_pair(a):

autoflow/api.py

@@ -6,8 +6,8 @@
 
 import numpy as np
 
-from models import Workspace
-from utils import collect_h5_files, process_single, resolve_reuse_plane_file
+from .models import Workspace
+from .utils import collect_h5_files, process_single, resolve_reuse_plane_file
 
 DEFAULT_WSS_BAR_CFG = {
     "position_x": 0.75,

app.py → autoflow/app.py

@@ -11,12 +11,12 @@
 from pyvistaqt import QtInteractor
 from pyvista import _vtk
 
-from models import Workspace, StepId, ObjectKind
-from pipeline import PipelineEngine
-from viewer import SceneController
-from editors import SkeletonEditor, PlaneEditor
-from ortho_viewer import OrthoViewer
-from algorithms import compute_plane_metrics, apply_internal_consistency_to_metrics, compute_plane_metrics_multithread
+from .models import Workspace, StepId, ObjectKind
+from .pipeline import PipelineEngine
+from .viewer import SceneController
+from .editors import SkeletonEditor, PlaneEditor
+from .ortho_viewer import OrthoViewer
+from .algorithms import compute_plane_metrics, apply_internal_consistency_to_metrics, compute_plane_metrics_multithread
 
 
 def _parse_plane_index(data_key):

editors.py → autoflow/editors.py

@@ -1,5 +1,5 @@
 import numpy as np
-from models import PlaneData, GraphData
+from .models import PlaneData, GraphData
 
 
 class SkeletonEditor:

autoflow/gui.py

@@ -6,7 +6,7 @@
 
 def launch_gui() -> None:
     try:
-        from app import main as app_main
+        from .app import main as app_main
     except ModuleNotFoundError as exc:
         module_name = exc.name or ""
         base_name = module_name.split(".", 1)[0]

io_utils.py → autoflow/io_utils.py

@@ -1,5 +1,5 @@
 import json
-from models import Workspace
+from .models import Workspace
 
 
 def save_workspace_file(path, workspace):
@@ -12,4 +12,4 @@ def load_workspace_file(path):
         d = json.load(f)
     ws = Workspace()
     ws.restore_dict(d)
-    return ws
+    return ws

pipeline.py → autoflow/pipeline.py

@@ -2,8 +2,8 @@
 import os
 import numpy as np
 
-from models import StepId, ObjectKind
-from algorithms import (
+from .models import StepId, ObjectKind
+from .algorithms import (
     load_h5_data,
     filter_segmask_labels, merge_segmask_to_3d,
     preprocess_mask_for_skeleton,
@@ -124,7 +124,7 @@ def run_step(self, ws, step, log):
     def _step_generate_skeleton(self, ws):
         self.preprocess(ws)
         if ws.skeleton_params.remove_small_cc:
-            from algorithms import remove_small_cc_from_binary_mask
+            from .algorithms import remove_small_cc_from_binary_mask
             ws.segmask_binary = remove_small_cc_from_binary_mask(
                 ws.segmask_binary, ws.resolution, ws.skeleton_params.min_cc_volume_mm3)
             ws.segmask_3d = merge_segmask_to_3d(ws.segmask_binary)

utils.py → autoflow/utils.py

@@ -10,9 +10,9 @@
 import imageio.v2 as imageio
 from PIL import Image
 
-from models import Workspace, StepId, PlaneData
-from pipeline import PipelineEngine
-from algorithms import (
+from .models import Workspace, StepId, PlaneData
+from .pipeline import PipelineEngine
+from .algorithms import (
     load_metrics_as_table,
     compute_derived_metrics,
     create_uniform_grid,

viewer.py → autoflow/viewer.py

@@ -1,8 +1,8 @@
 import numpy as np
 import pyvista as pv
 
-from models import ObjectKind
-from algorithms import (
+from .models import ObjectKind
+from .algorithms import (
     build_multilabel_surface_t,
     build_surface_from_mask3d,
     graph_to_polydata,

pyproject.toml

@@ -34,20 +34,6 @@ test = [
 autoflow-run = "autoflow.cli:main"
 autoflow-gui = "autoflow.gui:main"
 
-[tool.setuptools]
-include-package-data = false
-py-modules = [
-  "algorithms",
-  "app",
-  "editors",
-  "io_utils",
-  "models",
-  "ortho_viewer",
-  "pipeline",
-  "utils",
-  "viewer",
-]
-
 [tool.setuptools.packages.find]
 include = ["autoflow"]