From 101c39d535fc88e0165c9ca0fe827751714aeeb1 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sat, 5 Nov 2022 23:16:22 +0900
Subject: [PATCH 01/10] updating reference...

---
 docs/reference.rst | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/docs/reference.rst b/docs/reference.rst
index 10dab73a..ab7a4e3a 100644
--- a/docs/reference.rst
+++ b/docs/reference.rst
@@ -34,3 +34,9 @@ score calculation utilities
 
 .. automodule:: laptrack.scores
    :members:
+
+metric utilities
+-------------------------------
+
+.. automodule:: laptrack.metric_utils
+   :members:

From 202b9ec0d24fab97406a073ac8c78d00a97a2e3f Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 13:21:30 +0900
Subject: [PATCH 02/10] updated reference...

---
 docs/examples/overlap_tracking.ipynb | 2 +-
 docs/reference.rst                   | 1 +
 src/laptrack/metric_utils.py         | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/docs/examples/overlap_tracking.ipynb b/docs/examples/overlap_tracking.ipynb
index 36aa5ecf..b7e17aed 100644
--- a/docs/examples/overlap_tracking.ipynb
+++ b/docs/examples/overlap_tracking.ipynb
@@ -415,7 +415,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Here is the core of this example: we can define arbitrary function as the metric to measure how points are close.\n",
+    "Here is the core of this example: we can define an arbitrary function as the metric to measure how points are close.\n",
     "\n",
     "In this example, `metric` function retrive the pre-computed overlap between the segmented regions, and use\n",
     "$$\n",
diff --git a/docs/reference.rst b/docs/reference.rst
index ab7a4e3a..309f4bf6 100644
--- a/docs/reference.rst
+++ b/docs/reference.rst
@@ -40,3 +40,4 @@ metric utilities
 
 .. automodule:: laptrack.metric_utils
    :members:
+   :special-members: __init__
diff --git a/src/laptrack/metric_utils.py b/src/laptrack/metric_utils.py
index 041147c3..7c583618 100644
--- a/src/laptrack/metric_utils.py
+++ b/src/laptrack/metric_utils.py
@@ -38,7 +38,7 @@ def __init__(self, label_images: IntArray):
         Parameters
         ----------
         label_images : IntArray
-            The labeled images. The first dimension is interpreted as the time dimension.
+            The labeled images. The first dimension is interpreted as the frame dimension.
         """
         self.label_images = label_images
         self.ndim = label_images.ndim - 1

From 4153ccb1b968a43b330a335a83cd5c8093d7efa3 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 13:35:22 +0900
Subject: [PATCH 03/10] added version and bumped patch

---
 pyproject.toml               | 4 +++-
 src/laptrack/__init__.py     | 2 ++
 src/laptrack/metric_utils.py | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index f72ac64c..5baba9f9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "laptrack"
-version = "0.9.0"
+version = "0.9.1"
 description = "LapTrack"
 authors = ["Yohsuke Fukai <ysk@yfukai.net>"]
 license = "BSD-3-Clause"
@@ -83,3 +83,5 @@ show_error_context = true
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.poetry_bumpversion.file."src/laptrack/__init__.py"]
diff --git a/src/laptrack/__init__.py b/src/laptrack/__init__.py
index 3e955602..55db1f06 100644
--- a/src/laptrack/__init__.py
+++ b/src/laptrack/__init__.py
@@ -15,3 +15,5 @@
     "scores",
     "metric_utils",
 ]
+
+__version__ = "0.9.1"
diff --git a/src/laptrack/metric_utils.py b/src/laptrack/metric_utils.py
index 7c583618..57c3b38d 100644
--- a/src/laptrack/metric_utils.py
+++ b/src/laptrack/metric_utils.py
@@ -40,6 +40,9 @@ def __init__(self, label_images: IntArray):
         label_images : IntArray
             The labeled images. The first dimension is interpreted as the frame dimension.
         """
+        label_images = np.array(label_images)
+        if label_images.ndim < 3:
+            raise ValueError("label_images dimension must be >=3.")
         self.label_images = label_images
         self.ndim = label_images.ndim - 1
         dfs = []

From 1851cf6c88bcbc26b4d76e2e604cd41152fd4c55 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 13:45:34 +0900
Subject: [PATCH 04/10] fixing doc typo

---
 docs/examples/api_example.ipynb | 8 +++++---
 src/laptrack/metric_utils.py    | 3 ++-
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/docs/examples/api_example.ipynb b/docs/examples/api_example.ipynb
index 5a577e54..85a3c85e 100644
--- a/docs/examples/api_example.ipynb
+++ b/docs/examples/api_example.ipynb
@@ -64,8 +64,10 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "Load the example point coordinates from a CSV file.\n",
+    "\n",
     "`spots_df` has columns `[\"frame\", \"position_x\", \"position_y\"]` \n",
-    "(can be arbitrary, and the column names for trackign will be specified later)"
+    "(can be arbitrary, and the column names for tracking will be specified later)."
    ]
   },
   {
@@ -111,8 +113,8 @@
     "    track_dist_metric=\"sqeuclidean\",  # The similarity metric for particles. See `scipy.spatial.distance.cdist` for allowed values.\n",
     "    splitting_dist_metric=\"sqeuclidean\",\n",
     "    merging_dist_metric=\"sqeuclidean\",\n",
-    "    track_cost_cutoff=max_distance\n",
-    "    ** 2,  # the square of the cutoff distance for the \"sqeuclidean\" metric\n",
+    "    # the square of the cutoff distance for the \"sqeuclidean\" metric\n",
+    "    track_cost_cutoff=max_distance**2,\n",
     "    splitting_cost_cutoff=max_distance**2,  # or False for non-splitting case\n",
     "    merging_cost_cutoff=max_distance**2,  # or False for non-merging case\n",
     ")"
diff --git a/src/laptrack/metric_utils.py b/src/laptrack/metric_utils.py
index 57c3b38d..e0222375 100644
--- a/src/laptrack/metric_utils.py
+++ b/src/laptrack/metric_utils.py
@@ -40,7 +40,8 @@ def __init__(self, label_images: IntArray):
         label_images : IntArray
             The labeled images. The first dimension is interpreted as the frame dimension.
         """
-        label_images = np.array(label_images)
+        if not isinstance(label_images, np.ndarray):
+            label_images = np.array(label_images)
         if label_images.ndim < 3:
             raise ValueError("label_images dimension must be >=3.")
         self.label_images = label_images

From 3043dd558d4ff57e627708209636b9f1e9ed94d4 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 13:56:15 +0900
Subject: [PATCH 05/10] mentioned poetry-bumpversion

---
 CONTRIBUTING.rst | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 681ff836..5404728f 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -48,6 +48,7 @@ You need Python 3.8+ and the following tools:
 - Poetry_
 - Nox_
 - nox-poetry_
+- poetry-bumpversion_
 
 Install the package with development requirements:
 
@@ -61,11 +62,11 @@ or the command-line interface:
 .. code:: console
 
    $ poetry run python
-   $ poetry run laptrack
 
 .. _Poetry: https://python-poetry.org/
 .. _Nox: https://nox.thea.codes/
 .. _nox-poetry: https://nox-poetry.readthedocs.io/
+.. _poetry-bumpversion: https://github.com/monim67/poetry-bumpversion
 
 
 How to test the project

From f252aeb627e282ed9b509b3e801c1ac48cbcb594 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 14:02:13 +0900
Subject: [PATCH 06/10] updating contributing explanations

---
 CONTRIBUTING.rst | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
index 5404728f..0c1125f9 100644
--- a/CONTRIBUTING.rst
+++ b/CONTRIBUTING.rst
@@ -56,12 +56,11 @@ Install the package with development requirements:
 
    $ poetry install
 
-You can now run an interactive Python session,
-or the command-line interface:
+You can now run an interactive shell session:
 
 .. code:: console
 
-   $ poetry run python
+   $ poetry shell
 
 .. _Poetry: https://python-poetry.org/
 .. _Nox: https://nox.thea.codes/

From 52b0a8ddf2df62ed1c9a983e3b8af363b88b9834 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 14:10:04 +0900
Subject: [PATCH 07/10] updated colab example

---
 docs/examples/api_example.ipynb | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/docs/examples/api_example.ipynb b/docs/examples/api_example.ipynb
index 85a3c85e..cb4017b1 100644
--- a/docs/examples/api_example.ipynb
+++ b/docs/examples/api_example.ipynb
@@ -29,6 +29,13 @@
     "    %pip install -q --upgrade laptrack matplotlib pandas"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "**Important note** please restart the runtime when you're executing this notebook in Google Colaboratory."
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

From 3ac3723a5bffb93f1ba9607c8c14d1eb27852eb6 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 14:11:28 +0900
Subject: [PATCH 08/10] update test

---
 tests/test_metric_utils.py | 39 ++++++++++++++++++++------------------
 1 file changed, 21 insertions(+), 18 deletions(-)

diff --git a/tests/test_metric_utils.py b/tests/test_metric_utils.py
index 5db713db..df157ca8 100644
--- a/tests/test_metric_utils.py
+++ b/tests/test_metric_utils.py
@@ -13,22 +13,25 @@ def test_label_overlap() -> None:
             [[[0, 1, 1, 1, 0], [5, 5, 5, 5, 5]], [[0, 1, 1, 1, 0], [0, 1, 1, 1, 0]]],
         ]
     )
-    lo = LabelOverlap(labels)
-    frame_labels = [np.unique(label) for label in labels]
-    frame_labels = [x[x > 0] for x in frame_labels]
-    for f1, f2 in [(0, 0), (0, 1), (1, 2)]:
-        for l1, l2 in product(frame_labels[f1], frame_labels[f2]):
-            b1 = labels[f1] == l1
-            b2 = labels[f2] == l2
+    labelss = [labels, list(labels)]
 
-            intersect = np.sum(b1 & b2)
-            union = np.sum(b1 | b2)
-            r1 = np.sum(b1)
-            r2 = np.sum(b2)
-            res = lo.calc_overlap(f1, l1, f2, l2)
-            assert (
-                intersect,
-                (intersect / union),
-                (intersect / r1),
-                (intersect / r2),
-            ) == res
+    for labels in labelss:
+        lo = LabelOverlap(labels)
+        frame_labels = [np.unique(label) for label in labels]
+        frame_labels = [x[x > 0] for x in frame_labels]
+        for f1, f2 in [(0, 0), (0, 1), (1, 2)]:
+            for l1, l2 in product(frame_labels[f1], frame_labels[f2]):
+                b1 = labels[f1] == l1
+                b2 = labels[f2] == l2
+
+                intersect = np.sum(b1 & b2)
+                union = np.sum(b1 | b2)
+                r1 = np.sum(b1)
+                r2 = np.sum(b2)
+                res = lo.calc_overlap(f1, l1, f2, l2)
+                assert (
+                    intersect,
+                    (intersect / union),
+                    (intersect / r1),
+                    (intersect / r2),
+                ) == res

From 720815bbf9f209d3e7bd6142ee9b5b43ec4ee0b3 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 15:22:43 +0900
Subject: [PATCH 09/10] solved mypy issue

---
 src/laptrack/metric_utils.py |  6 ++++--
 tests/test_metric_utils.py   | 30 +++++++++++++++++-------------
 2 files changed, 21 insertions(+), 15 deletions(-)

diff --git a/src/laptrack/metric_utils.py b/src/laptrack/metric_utils.py
index e0222375..946b3674 100644
--- a/src/laptrack/metric_utils.py
+++ b/src/laptrack/metric_utils.py
@@ -1,5 +1,7 @@
 """Utilities for metric calculation."""
+from typing import List
 from typing import Tuple
+from typing import Union
 
 import numpy as np
 import pandas as pd
@@ -32,12 +34,12 @@ def _union_bbox(self, r1, r2):
             bbox.append((y0, y1))
         return bbox
 
-    def __init__(self, label_images: IntArray):
+    def __init__(self, label_images: Union[IntArray, List[IntArray]]):
         """Summarise the segmentation properties and initialize the object.
 
         Parameters
         ----------
-        label_images : IntArray
+        label_images : Union[IntArray,List[IntArray]]
             The labeled images. The first dimension is interpreted as the frame dimension.
         """
         if not isinstance(label_images, np.ndarray):
diff --git a/tests/test_metric_utils.py b/tests/test_metric_utils.py
index df157ca8..5fece351 100644
--- a/tests/test_metric_utils.py
+++ b/tests/test_metric_utils.py
@@ -1,28 +1,32 @@
 from itertools import product
+from typing import List
+from typing import Union
 
 import numpy as np
 
+from laptrack._typing_utils import IntArray
 from laptrack.metric_utils import LabelOverlap
 
 
 def test_label_overlap() -> None:
-    labels = np.array(
-        [
-            [[[0, 1, 1, 1, 0], [0, 1, 2, 2, 2]], [[0, 1, 2, 2, 2], [3, 3, 3, 1, 0]]],
-            [[[0, 1, 1, 1, 2], [0, 4, 1, 2, 2]], [[0, 4, 4, 4, 4], [0, 4, 4, 4, 4]]],
-            [[[0, 1, 1, 1, 0], [5, 5, 5, 5, 5]], [[0, 1, 1, 1, 0], [0, 1, 1, 1, 0]]],
-        ]
-    )
-    labelss = [labels, list(labels)]
+    labels = [
+        [[[0, 1, 1, 1, 0], [0, 1, 2, 2, 2]], [[0, 1, 2, 2, 2], [3, 3, 3, 1, 0]]],
+        [[[0, 1, 1, 1, 2], [0, 4, 1, 2, 2]], [[0, 4, 4, 4, 4], [0, 4, 4, 4, 4]]],
+        [[[0, 1, 1, 1, 0], [5, 5, 5, 5, 5]], [[0, 1, 1, 1, 0], [0, 1, 1, 1, 0]]],
+    ]
+    labelss: List[Union[IntArray, List[IntArray]]] = [
+        np.array(labels),
+        [np.array(label).astype(np.int64) for label in labels],
+    ]
 
-    for labels in labelss:
-        lo = LabelOverlap(labels)
-        frame_labels = [np.unique(label) for label in labels]
+    for _labels in labelss:
+        lo = LabelOverlap(_labels)
+        frame_labels = [np.unique(label) for label in _labels]
         frame_labels = [x[x > 0] for x in frame_labels]
         for f1, f2 in [(0, 0), (0, 1), (1, 2)]:
             for l1, l2 in product(frame_labels[f1], frame_labels[f2]):
-                b1 = labels[f1] == l1
-                b2 = labels[f2] == l2
+                b1 = _labels[f1] == l1
+                b2 = _labels[f2] == l2
 
                 intersect = np.sum(b1 & b2)
                 union = np.sum(b1 | b2)

From 784ef53f85b0dfd7619080930cfdc46a6b8de428 Mon Sep 17 00:00:00 2001
From: Yohsuke Fukai <ysk@yfukai.net>
Date: Sun, 6 Nov 2022 21:52:33 +0900
Subject: [PATCH 10/10] added test to check value error

---
 tests/test_metric_utils.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/test_metric_utils.py b/tests/test_metric_utils.py
index 5fece351..15766376 100644
--- a/tests/test_metric_utils.py
+++ b/tests/test_metric_utils.py
@@ -3,6 +3,7 @@
 from typing import Union
 
 import numpy as np
+import pytest
 
 from laptrack._typing_utils import IntArray
 from laptrack.metric_utils import LabelOverlap
@@ -39,3 +40,5 @@ def test_label_overlap() -> None:
                     (intersect / r1),
                     (intersect / r2),
                 ) == res
+    with pytest.raises(ValueError):
+        LabelOverlap(np.array([[1, 2], [0, 1]]))