From 42e17d081ef5f325ea6d398e63edeb54c21dc08e Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Fri, 18 Jul 2025 15:29:11 -0400
Subject: [PATCH 1/9] Create _labeling folder

---
 blobid/_labeling/__init__.py                        | 8 ++++++++
 blobid/{utils => _labeling}/ccl.py                  | 2 +-
 blobid/{utils/labeling.py => _labeling/database.py} | 0
 blobid/solver.py                                    | 6 +++---
 tests/test_boundaries.py                            | 3 +--
 tests/{test_labeling.py => test_database.py}        | 2 +-
 6 files changed, 14 insertions(+), 7 deletions(-)
 create mode 100644 blobid/_labeling/__init__.py
 rename blobid/{utils => _labeling}/ccl.py (97%)
 rename blobid/{utils/labeling.py => _labeling/database.py} (100%)
 rename tests/{test_labeling.py => test_database.py} (98%)

diff --git a/blobid/_labeling/__init__.py b/blobid/_labeling/__init__.py
new file mode 100644
index 0000000..ed78ab0
--- /dev/null
+++ b/blobid/_labeling/__init__.py
@@ -0,0 +1,8 @@
+"""
+Provides methods for labeling given connectedness
+"""
+
+from .ccl import get_temporary_labels, stitch_boundaries
+from .database import LabelDatabase
+
+__all__ = ['get_temporary_labels', 'stitch_boundaries', 'LabelDatabase']
diff --git a/blobid/utils/ccl.py b/blobid/_labeling/ccl.py
similarity index 97%
rename from blobid/utils/ccl.py
rename to blobid/_labeling/ccl.py
index 14caff2..16f8b8a 100644
--- a/blobid/utils/ccl.py
+++ b/blobid/_labeling/ccl.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 from blobid.utils.numba_support import njit
-from blobid.utils.labeling import LabelDatabase, _DatabaseStorage, _merge
+from .database import LabelDatabase, _DatabaseStorage, _merge
 
 
 def get_temporary_labels(
diff --git a/blobid/utils/labeling.py b/blobid/_labeling/database.py
similarity index 100%
rename from blobid/utils/labeling.py
rename to blobid/_labeling/database.py
diff --git a/blobid/solver.py b/blobid/solver.py
index f9ed2a9..71d8e37 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -7,7 +7,7 @@
 
 from blobid.utils.domain import VOFDomain
 
-from blobid.utils.ccl import get_temporary_labels, stitch_boundaries
+from . import _labeling as labeling
 from blobid.utils.reconstruction import normals
 
 
@@ -163,10 +163,10 @@ def get_labels(
                                      norm=normals(domain.vof(padding=1), normals_method) if use_normals else None)
 
     # do initial labeling
-    (labels, label_database) = get_temporary_labels(is_object, is_connected, label_type)
+    (labels, label_database) = labeling.get_temporary_labels(is_object, is_connected, label_type)
 
     # stitch together periodic boundaries
-    label_database = stitch_boundaries(labels, label_database, domain.periodic)
+    label_database = labeling.stitch_boundaries(labels, label_database, domain.periodic)
 
     # do final labeling with sequential labels
     labels = label_database.get_sequential_lookup_table()[labels]
diff --git a/tests/test_boundaries.py b/tests/test_boundaries.py
index 2e1b099..8522461 100644
--- a/tests/test_boundaries.py
+++ b/tests/test_boundaries.py
@@ -1,9 +1,8 @@
 import pytest
 import numpy as np
 
-from blobid.utils.ccl import stitch_boundaries
 from blobid.utils.domain import _pad_array
-from blobid.utils.labeling import LabelDatabase
+from blobid._labeling import LabelDatabase, stitch_boundaries
 from blobid.utils.reconstruction import normals
 
 
diff --git a/tests/test_labeling.py b/tests/test_database.py
similarity index 98%
rename from tests/test_labeling.py
rename to tests/test_database.py
index 7a1c2c5..8a31e47 100644
--- a/tests/test_labeling.py
+++ b/tests/test_database.py
@@ -1,7 +1,7 @@
 import pytest as pt
 import numpy as np
 
-from blobid.utils.labeling import LabelDatabase
+from blobid._labeling import LabelDatabase
 
 
 def test_label_sets():

From 59b3c7dfae10f757253707398731f2216a7cfdb0 Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Fri, 18 Jul 2025 17:15:27 -0400
Subject: [PATCH 2/9] Move labeling into one accessible call

---
 blobid/__init__.py                         |  3 +-
 blobid/_labeling/__init__.py               |  8 ---
 blobid/labeling/__init__.py                |  3 +
 blobid/{_labeling => labeling}/ccl.py      | 23 -------
 blobid/{_labeling => labeling}/database.py |  0
 blobid/labeling/labeling.py                | 79 ++++++++++++++++++++++
 blobid/solver.py                           | 17 +++--
 tests/test_boundaries.py                   |  5 +-
 tests/test_database.py                     |  2 +-
 9 files changed, 96 insertions(+), 44 deletions(-)
 delete mode 100644 blobid/_labeling/__init__.py
 create mode 100644 blobid/labeling/__init__.py
 rename blobid/{_labeling => labeling}/ccl.py (78%)
 rename blobid/{_labeling => labeling}/database.py (100%)
 create mode 100644 blobid/labeling/labeling.py

diff --git a/blobid/__init__.py b/blobid/__init__.py
index 80e88e8..f13abce 100644
--- a/blobid/__init__.py
+++ b/blobid/__init__.py
@@ -1,3 +1,4 @@
 from .solver import get_labels
+from . import labeling
 
-__all__ = ['get_labels',]
+__all__ = ['get_labels', 'labeling']
diff --git a/blobid/_labeling/__init__.py b/blobid/_labeling/__init__.py
deleted file mode 100644
index ed78ab0..0000000
--- a/blobid/_labeling/__init__.py
+++ /dev/null
@@ -1,8 +0,0 @@
-"""
-Provides methods for labeling given connectedness
-"""
-
-from .ccl import get_temporary_labels, stitch_boundaries
-from .database import LabelDatabase
-
-__all__ = ['get_temporary_labels', 'stitch_boundaries', 'LabelDatabase']
diff --git a/blobid/labeling/__init__.py b/blobid/labeling/__init__.py
new file mode 100644
index 0000000..e17d2eb
--- /dev/null
+++ b/blobid/labeling/__init__.py
@@ -0,0 +1,3 @@
+from .labeling import apply_ccl
+
+__all__ = ['apply_ccl']
diff --git a/blobid/_labeling/ccl.py b/blobid/labeling/ccl.py
similarity index 78%
rename from blobid/_labeling/ccl.py
rename to blobid/labeling/ccl.py
index 16f8b8a..f396372 100644
--- a/blobid/_labeling/ccl.py
+++ b/blobid/labeling/ccl.py
@@ -1,7 +1,6 @@
 """
 Tools for running connected component labeling
 """
-from typing import Tuple
 
 import numpy as np
 from blobid.utils.numba_support import njit
@@ -39,28 +38,6 @@ def get_temporary_labels(
     return (labels, label_database)
 
 
-def stitch_boundaries(
-        labels: np.ndarray,
-        sets: LabelDatabase,
-        periodic: Tuple[bool, bool, bool]
-        ) -> LabelDatabase:
-    """Stitch together periodic boundaries and remove padding"""
-
-    if periodic[0]:
-        for a, b in zip(labels[0, :, :].flat, labels[-2, :, :].flat):
-            sets.merge(a, b)
-
-    if periodic[1]:
-        for a, b in zip(labels[:, 0, :].flat, labels[:, -2, :].flat):
-            sets.merge(a, b)
-
-    if periodic[2]:
-        for a, b in zip(labels[:, :, 0].flat, labels[:, :, -2].flat):
-            sets.merge(a, b)
-
-    return sets
-
-
 @njit
 def _tail_pass(
         labels: np.ndarray,
diff --git a/blobid/_labeling/database.py b/blobid/labeling/database.py
similarity index 100%
rename from blobid/_labeling/database.py
rename to blobid/labeling/database.py
diff --git a/blobid/labeling/labeling.py b/blobid/labeling/labeling.py
new file mode 100644
index 0000000..fe07f24
--- /dev/null
+++ b/blobid/labeling/labeling.py
@@ -0,0 +1,79 @@
+from typing import Tuple
+
+import numpy as np
+
+from .database import LabelDatabase
+from .ccl import get_temporary_labels
+
+
+def apply_ccl(
+        is_object: np.ndarray,
+        is_connected: np.ndarray,
+        periodic: Tuple[bool, bool, bool],
+        label_type
+) -> np.ndarray:
+    r"""
+    Given connectedness, calculate unique labels for each connected region of object cells.
+
+    Parameters
+    ----------
+    is_object : ndarray[ni, nj, nk]
+        `is_object[i, j, k]` is true if cell `[i,j,k]` is an object cell
+    is_connected : ndarray[ni, nj, nk, 3]
+        `is_connected[i, j, k, d]` is true if cell `[i,j,k]` us connected to the neighbor in the negative d direction.
+        For example, `is_connected[i, j, k, 0]` is true if cell `[i,j,k]` is connected to cell `[i-1,j,k]`
+    periodic: (bool, bool, bool)
+        If `periodic[d]`, then cells on each edge in direction `d` are considered the same cell.
+        For example, cell `[0,j,k]` is the same as cell `[-1,j,k]` if `periodic[0]` is true.
+    label_type : dtype
+        Determines the integer data-type of `labels`
+
+    Returns
+    -------
+        labels : ndarray[ni, nj, nk]
+            An array of type `label_type` with the same shape as `is_object`.
+
+    """
+    # checks
+    assert is_object.ndim == 3
+    assert is_connected.ndim == 4
+    print(is_object.shape)
+    print(is_connected.shape)
+    assert np.all(is_object.shape == is_connected.shape[:-1])
+
+    assert not np.any(is_connected[0, :, :, 0])
+    assert not np.any(is_connected[:, 0, :, 1])
+    assert not np.any(is_connected[:, :, 0, 2])
+
+    # do initial labeling
+    (labels, label_database) = get_temporary_labels(is_object, is_connected, label_type)
+
+    # stitch together periodic boundaries
+    label_database = _stitch_boundaries(labels, label_database, periodic)
+
+    # do final labeling with sequential labels
+    labels = label_database.get_sequential_lookup_table()[labels]
+
+    return labels
+
+
+def _stitch_boundaries(
+        labels: np.ndarray,
+        sets: LabelDatabase,
+        periodic: Tuple[bool, bool, bool]
+        ) -> LabelDatabase:
+    """Stitch together periodic boundaries and remove padding"""
+
+    if periodic[0]:
+        for a, b in zip(labels[0, :, :].flat, labels[-2, :, :].flat):
+            sets.merge(a, b)
+
+    if periodic[1]:
+        for a, b in zip(labels[:, 0, :].flat, labels[:, -2, :].flat):
+            sets.merge(a, b)
+
+    if periodic[2]:
+        for a, b in zip(labels[:, :, 0].flat, labels[:, :, -2].flat):
+            sets.merge(a, b)
+
+    return sets
diff --git a/blobid/solver.py b/blobid/solver.py
index 71d8e37..11eb3b2 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -7,7 +7,7 @@
 
 from blobid.utils.domain import VOFDomain
 
-from . import _labeling as labeling
+from . import labeling
 from blobid.utils.reconstruction import normals
 
 
@@ -162,14 +162,13 @@ def get_labels(
     is_connected = _calc_connections(is_object,
                                      norm=normals(domain.vof(padding=1), normals_method) if use_normals else None)
 
-    # do initial labeling
-    (labels, label_database) = labeling.get_temporary_labels(is_object, is_connected, label_type)
-
-    # stitch together periodic boundaries
-    label_database = labeling.stitch_boundaries(labels, label_database, domain.periodic)
-
-    # do final labeling with sequential labels
-    labels = label_database.get_sequential_lookup_table()[labels]
+    # do the labeling
+    labels = labeling.apply_ccl(
+        is_object=is_object,
+        is_connected=is_connected,
+        periodic=domain.periodic,
+        label_type=label_type
+        )
 
     # reshape to original dimensions (removes padding in periodic directions)
     return domain.convert_to_original_shape(labels)
diff --git a/tests/test_boundaries.py b/tests/test_boundaries.py
index 8522461..c58bdd8 100644
--- a/tests/test_boundaries.py
+++ b/tests/test_boundaries.py
@@ -2,7 +2,8 @@
 import numpy as np
 
 from blobid.utils.domain import _pad_array
-from blobid._labeling import LabelDatabase, stitch_boundaries
+from blobid.labeling.database import LabelDatabase
+from blobid.labeling.labeling import _stitch_boundaries
 from blobid.utils.reconstruction import normals
 
 
@@ -121,7 +122,7 @@ def check_periodicity(labels, sets, periodicity):
             for a, b in zip(labels[:, :, -1].flat, labels[:, :, -2].flat):
                 sets.merge(a, b)
 
-        sets = stitch_boundaries(labels, sets, per)
+        sets = _stitch_boundaries(labels, sets, per)
 
         # make sure the size is right
         assert labels.shape[0] == 5 + 2 * per[0]
diff --git a/tests/test_database.py b/tests/test_database.py
index 8a31e47..31f4dcb 100644
--- a/tests/test_database.py
+++ b/tests/test_database.py
@@ -1,7 +1,7 @@
 import pytest as pt
 import numpy as np
 
-from blobid._labeling import LabelDatabase
+from blobid.labeling.database import LabelDatabase
 
 
 def test_label_sets():

From 76ab9ed1dce8ce8b702a2f78defb07c6f0dc3b05 Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Fri, 18 Jul 2025 17:32:49 -0400
Subject: [PATCH 3/9] Move numba_support

---
 blobid/{utils/numba_support.py => _numba_support.py} | 4 ++--
 blobid/labeling/ccl.py                               | 2 +-
 blobid/labeling/database.py                          | 2 +-
 blobid/utils/reconstruction.py                       | 4 ++--
 tests/test_reconstruction.py                         | 4 ++--
 5 files changed, 8 insertions(+), 8 deletions(-)
 rename blobid/{utils/numba_support.py => _numba_support.py} (74%)

diff --git a/blobid/utils/numba_support.py b/blobid/_numba_support.py
similarity index 74%
rename from blobid/utils/numba_support.py
rename to blobid/_numba_support.py
index 764e471..e3d32d3 100644
--- a/blobid/utils/numba_support.py
+++ b/blobid/_numba_support.py
@@ -1,10 +1,10 @@
 """Setup Numba if available"""
 
-_numba_availible = True
+numba_availible = True
 try:
     from numba import njit
 except ImportError:
-    _numba_availible = False
+    numba_availible = False
 
     # create a dummy njit decorator
     def njit(func): return func
diff --git a/blobid/labeling/ccl.py b/blobid/labeling/ccl.py
index f396372..c094ba8 100644
--- a/blobid/labeling/ccl.py
+++ b/blobid/labeling/ccl.py
@@ -3,7 +3,7 @@
 """
 
 import numpy as np
-from blobid.utils.numba_support import njit
+from .._numba_support import njit
 from .database import LabelDatabase, _DatabaseStorage, _merge
 
 
diff --git a/blobid/labeling/database.py b/blobid/labeling/database.py
index 03de62c..27b7a52 100644
--- a/blobid/labeling/database.py
+++ b/blobid/labeling/database.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from blobid.utils.numba_support import njit
+from .._numba_support import njit
 
 _DatabaseStorage = namedtuple('_DatabaseStorage', 'r, n, t')
 _END_OF_SET = 0
diff --git a/blobid/utils/reconstruction.py b/blobid/utils/reconstruction.py
index fb99302..46269a8 100644
--- a/blobid/utils/reconstruction.py
+++ b/blobid/utils/reconstruction.py
@@ -4,7 +4,7 @@
 import warnings
 import numpy as np
 
-from blobid.utils.numba_support import njit, _numba_availible
+from .._numba_support import njit, numba_availible
 
 NORMALS_TYPE = np.int8
 
@@ -38,7 +38,7 @@ def normals_CD(f: np.ndarray) -> np.ndarray:
 
 def normals_WY(f: np.ndarray) -> np.ndarray:
     # Numba only supports float32 and float64
-    if _numba_availible and (f.dtype not in (np.float32, np.float64)):
+    if numba_availible and (f.dtype not in (np.float32, np.float64)):
         warnings.warn(f"void_fraction type {f.dtype.name} not supported, using float32")
         f = f.astype(np.float32)
 
diff --git a/tests/test_reconstruction.py b/tests/test_reconstruction.py
index abddef1..bf7a652 100644
--- a/tests/test_reconstruction.py
+++ b/tests/test_reconstruction.py
@@ -3,7 +3,7 @@
 import pytest
 import numpy as np
 
-from blobid.utils.numba_support import _numba_availible
+from blobid._numba_support import numba_availible
 from blobid.utils.reconstruction import normals, NORMALS_TYPE, _get_dominant_direction
 
 
@@ -71,7 +71,7 @@ def test_vof_type():
     f = np.random.rand(3, 3, 3)
 
     # float16 should give a warning
-    if _numba_availible:
+    if numba_availible:
         with pytest.warns():
             normals(f.astype(np.float16), 'WY')
 

From 6975de22732919c5d0f8765d161bbe62e86778ec Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Fri, 18 Jul 2025 17:38:04 -0400
Subject: [PATCH 4/9] Cleanup comment

---
 blobid/solver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/blobid/solver.py b/blobid/solver.py
index 11eb3b2..50360ce 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -155,7 +155,7 @@ def get_labels(
                        periodic_padding=1,
                        extra_padding=1 if (use_normals or (cutoff_method == 'neighbors')) else 0)
 
-    # calculate object cells, removing the extra padding
+    # calculate object cells
     is_object = _calc_object_cells(domain, cutoff, cutoff_method)
 
     # calculate connectivity

From debaf08822f08acc9dd69f5c62ff8eadee99ff7d Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Fri, 18 Jul 2025 17:40:27 -0400
Subject: [PATCH 5/9] Remove print statements left from debug

---
 blobid/labeling/labeling.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/blobid/labeling/labeling.py b/blobid/labeling/labeling.py
index fe07f24..18f462f 100644
--- a/blobid/labeling/labeling.py
+++ b/blobid/labeling/labeling.py
@@ -37,10 +37,7 @@ def apply_ccl(
     # checks
     assert is_object.ndim == 3
     assert is_connected.ndim == 4
-    print(is_object.shape)
-    print(is_connected.shape)
     assert np.all(is_object.shape == is_connected.shape[:-1])
-
     assert not np.any(is_connected[0, :, :, 0])
     assert not np.any(is_connected[:, 0, :, 1])
     assert not np.any(is_connected[:, :, 0, 2])

From 219c8fc84f5ce00aeefceedfd34a7a0e66ee681f Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Thu, 24 Jul 2025 17:43:42 -0400
Subject: [PATCH 6/9] Move utils/domain.py to _domain.py

---
 blobid/{utils/domain.py => _domain.py} | 0
 blobid/solver.py                       | 2 +-
 tests/test_boundaries.py               | 2 +-
 3 files changed, 2 insertions(+), 2 deletions(-)
 rename blobid/{utils/domain.py => _domain.py} (100%)

diff --git a/blobid/utils/domain.py b/blobid/_domain.py
similarity index 100%
rename from blobid/utils/domain.py
rename to blobid/_domain.py
diff --git a/blobid/solver.py b/blobid/solver.py
index 50360ce..9e90b54 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -5,7 +5,7 @@
 
 import numpy as np
 
-from blobid.utils.domain import VOFDomain
+from ._domain import VOFDomain
 
 from . import labeling
 from blobid.utils.reconstruction import normals
diff --git a/tests/test_boundaries.py b/tests/test_boundaries.py
index c58bdd8..56ad3fe 100644
--- a/tests/test_boundaries.py
+++ b/tests/test_boundaries.py
@@ -1,7 +1,7 @@
 import pytest
 import numpy as np
 
-from blobid.utils.domain import _pad_array
+from blobid._domain import _pad_array
 from blobid.labeling.database import LabelDatabase
 from blobid.labeling.labeling import _stitch_boundaries
 from blobid.utils.reconstruction import normals

From 6a3b66b503ef88d453f13f8222273c7a39e034e4 Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Thu, 24 Jul 2025 17:51:44 -0400
Subject: [PATCH 7/9] Move reconstruction to its own submodule

---
 blobid/reconstruction/__init__.py                  | 3 +++
 blobid/{utils => reconstruction}/reconstruction.py | 0
 blobid/solver.py                                   | 4 ++--
 tests/test_boundaries.py                           | 2 +-
 tests/test_reconstruction.py                       | 2 +-
 5 files changed, 7 insertions(+), 4 deletions(-)
 create mode 100644 blobid/reconstruction/__init__.py
 rename blobid/{utils => reconstruction}/reconstruction.py (100%)

diff --git a/blobid/reconstruction/__init__.py b/blobid/reconstruction/__init__.py
new file mode 100644
index 0000000..bd984a5
--- /dev/null
+++ b/blobid/reconstruction/__init__.py
@@ -0,0 +1,3 @@
+from .reconstruction import normals
+
+__all__ = ['normals']
diff --git a/blobid/utils/reconstruction.py b/blobid/reconstruction/reconstruction.py
similarity index 100%
rename from blobid/utils/reconstruction.py
rename to blobid/reconstruction/reconstruction.py
diff --git a/blobid/solver.py b/blobid/solver.py
index 9e90b54..e6be140 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -8,7 +8,7 @@
 from ._domain import VOFDomain
 
 from . import labeling
-from blobid.utils.reconstruction import normals
+from . import reconstruction
 
 
 def get_labels(
@@ -160,7 +160,7 @@ def get_labels(
 
     # calculate connectivity
     is_connected = _calc_connections(is_object,
-                                     norm=normals(domain.vof(padding=1), normals_method) if use_normals else None)
+                                     norm=reconstruction.normals(domain.vof(padding=1), normals_method) if use_normals else None)
 
     # do the labeling
     labels = labeling.apply_ccl(
diff --git a/tests/test_boundaries.py b/tests/test_boundaries.py
index 56ad3fe..3f4c47a 100644
--- a/tests/test_boundaries.py
+++ b/tests/test_boundaries.py
@@ -4,7 +4,7 @@
 from blobid._domain import _pad_array
 from blobid.labeling.database import LabelDatabase
 from blobid.labeling.labeling import _stitch_boundaries
-from blobid.utils.reconstruction import normals
+from blobid.reconstruction import normals
 
 
 @pytest.fixture
diff --git a/tests/test_reconstruction.py b/tests/test_reconstruction.py
index bf7a652..d1f03fc 100644
--- a/tests/test_reconstruction.py
+++ b/tests/test_reconstruction.py
@@ -4,7 +4,7 @@
 import numpy as np
 
 from blobid._numba_support import numba_availible
-from blobid.utils.reconstruction import normals, NORMALS_TYPE, _get_dominant_direction
+from blobid.reconstruction.reconstruction import normals, NORMALS_TYPE, _get_dominant_direction
 
 
 def test_reconstruction_CD():

From 01d1404a6fd4a093848294acd3b70b029a18404e Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Thu, 24 Jul 2025 18:22:22 -0400
Subject: [PATCH 8/9] Group tests

---
 tests/{ => labeling}/test_database.py             | 0
 tests/{ => reconstruction}/test_reconstruction.py | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/{ => labeling}/test_database.py (100%)
 rename tests/{ => reconstruction}/test_reconstruction.py (100%)

diff --git a/tests/test_database.py b/tests/labeling/test_database.py
similarity index 100%
rename from tests/test_database.py
rename to tests/labeling/test_database.py
diff --git a/tests/test_reconstruction.py b/tests/reconstruction/test_reconstruction.py
similarity index 100%
rename from tests/test_reconstruction.py
rename to tests/reconstruction/test_reconstruction.py

From ceaa31cf8f95254fce874c93788f931004a18ca4 Mon Sep 17 00:00:00 2001
From: Declan Gaylo <dgaylo@mit.edu>
Date: Thu, 24 Jul 2025 18:22:37 -0400
Subject: [PATCH 9/9] Fix long line

---
 blobid/solver.py | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/blobid/solver.py b/blobid/solver.py
index e6be140..662e436 100644
--- a/blobid/solver.py
+++ b/blobid/solver.py
@@ -159,8 +159,12 @@ def get_labels(
     is_object = _calc_object_cells(domain, cutoff, cutoff_method)
 
     # calculate connectivity
-    is_connected = _calc_connections(is_object,
-                                     norm=reconstruction.normals(domain.vof(padding=1), normals_method) if use_normals else None)
+    if use_normals:
+        normals = reconstruction.normals(domain.vof(padding=1), normals_method)
+    else:
+        normals = None
+
+    is_connected = _calc_connections(is_object, norm=normals)
 
     # do the labeling
     labels = labeling.apply_ccl(