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WIP: Fixing issues with RegionPropNodes #227

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2 changes: 2 additions & 0 deletions src/tracksdata/nodes/_regionprops.py
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Original file line number Diff line number Diff line change
Expand Up @@ -230,6 +230,8 @@ def add_nodes(

if "shape" not in graph.metadata:
graph.update_metadata(shape=labels.shape)
elif graph.metadata["shape"] != labels.shape:
raise ValueError("Stored shape is different from the provided labels shape.")

if t is None:
time_points = range(labels.shape[0])
Expand Down
136 changes: 66 additions & 70 deletions src/tracksdata/nodes/_test/test_regionprops.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
from skimage.measure._regionprops import RegionProperties

from tracksdata.constants import DEFAULT_ATTR_KEYS
from tracksdata.graph import RustWorkXGraph
from tracksdata.graph import BaseGraph
from tracksdata.nodes import Mask, RegionPropsNodes
from tracksdata.options import get_options, options_context

Expand Down Expand Up @@ -68,25 +68,23 @@ def custom_prop(region: RegionProperties) -> float:
]


def test_regionprops_add_nodes_2d() -> None:
def test_regionprops_add_nodes_2d(graph_backend: BaseGraph) -> None:
"""Test adding nodes from 2D labels."""
graph = RustWorkXGraph()

# Create simple 2D labels
labels = np.array([[[1, 1, 0], [1, 0, 2], [0, 2, 2]]], dtype=np.int32)

extra_properties = SUPPORTED_PROPERTIES + SUPPORTED_PROPERTIES_2D
operator = RegionPropsNodes(extra_properties=extra_properties)
operator.add_nodes(graph, labels=labels)
operator.add_nodes(graph_backend, labels=labels)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added
assert graph.num_nodes == 2 # Two regions (labels 1 and 2)
assert graph_backend.num_nodes == 2 # Two regions (labels 1 and 2)

# Check node attributes
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
assert len(nodes_df) == 2
assert DEFAULT_ATTR_KEYS.T in nodes_df.columns
assert "y" in nodes_df.columns
Expand All @@ -102,27 +100,25 @@ def test_regionprops_add_nodes_2d() -> None:
assert areas == [3, 3]


def test_regionprops_add_nodes_3d() -> None:
def test_regionprops_add_nodes_3d(graph_backend: BaseGraph) -> None:
"""Test adding nodes from 3D labels."""
graph = RustWorkXGraph()

# Create simple 3D labels
labels = np.array([[[[1, 1, 0], [1, 0, 0], [0, 0, 0]]], [[[0, 0, 0], [2, 2, 0], [0, 0, 0]]]], dtype=np.int32)

assert labels.shape == (2, 1, 3, 3)

extra_properties = SUPPORTED_PROPERTIES
operator = RegionPropsNodes(extra_properties=extra_properties)
operator.add_nodes(graph, labels=labels)
operator.add_nodes(graph_backend, labels=labels)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added
assert graph.num_nodes == 2 # Two regions
assert graph_backend.num_nodes == 2 # Two regions

# Check node attributes
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
assert len(nodes_df) == 2
assert DEFAULT_ATTR_KEYS.T in nodes_df.columns
assert "z" in nodes_df.columns
Expand All @@ -132,10 +128,8 @@ def test_regionprops_add_nodes_3d() -> None:
assert DEFAULT_ATTR_KEYS.MASK in nodes_df.columns


def test_regionprops_add_nodes_with_intensity() -> None:
def test_regionprops_add_nodes_with_intensity(graph_backend: BaseGraph) -> None:
"""Test adding nodes with intensity image."""
graph = RustWorkXGraph()

# Create labels and intensity image
labels = np.array([[[1, 1, 0], [1, 0, 2], [0, 2, 2]]], dtype=np.int32)

Expand All @@ -148,13 +142,13 @@ def test_regionprops_add_nodes_with_intensity() -> None:
extra_properties = SUPPORTED_PROPERTIES + SUPPORTED_PROPERTIES_INTENSITY
operator = RegionPropsNodes(extra_properties=extra_properties)

operator.add_nodes(graph, labels=labels, intensity_image=intensity)
operator.add_nodes(graph_backend, labels=labels, intensity_image=intensity)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added with intensity attributes
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
assert "intensity_mean" in nodes_df.columns

# Check that mean intensities are calculated
Expand All @@ -166,10 +160,8 @@ def test_regionprops_add_nodes_with_intensity() -> None:


@pytest.mark.parametrize("n_workers", [1, 2])
def test_regionprops_add_nodes_timelapse(n_workers: int) -> None:
def test_regionprops_add_nodes_timelapse(graph_backend: BaseGraph, n_workers: int) -> None:
"""Test adding nodes from timelapse (t=None) with different worker counts."""
graph = RustWorkXGraph()

# Create timelapse labels (time x height x width)
labels = np.array([[[1, 1], [0, 0]], [[0, 2], [2, 2]]], dtype=np.int32) # t=0 # t=1

Expand All @@ -179,13 +171,13 @@ def test_regionprops_add_nodes_timelapse(n_workers: int) -> None:
operator = RegionPropsNodes(extra_properties=extra_properties)

with options_context(n_workers=n_workers):
operator.add_nodes(graph, labels=labels)
operator.add_nodes(graph_backend, labels=labels)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added for both time points
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
time_points = sorted(nodes_df[DEFAULT_ATTR_KEYS.T].unique())
assert time_points == [0, 1]

Expand All @@ -195,10 +187,8 @@ def test_regionprops_add_nodes_timelapse(n_workers: int) -> None:
assert len(nodes_at_t) == 1


def test_regionprops_add_nodes_timelapse_with_intensity() -> None:
def test_regionprops_add_nodes_timelapse_with_intensity(graph_backend: BaseGraph) -> None:
"""Test adding nodes from timelapse with intensity images."""
graph = RustWorkXGraph()

# Create timelapse labels and intensity
labels = np.array([[[1, 1], [0, 0]], [[0, 2], [2, 2]]], dtype=np.int32) # t=0 # t=1

Expand All @@ -207,13 +197,13 @@ def test_regionprops_add_nodes_timelapse_with_intensity() -> None:
extra_properties = SUPPORTED_PROPERTIES + SUPPORTED_PROPERTIES_2D + SUPPORTED_PROPERTIES_INTENSITY
operator = RegionPropsNodes(extra_properties=extra_properties)

operator.add_nodes(graph, labels=labels, intensity_image=intensity)
operator.add_nodes(graph_backend, labels=labels, intensity_image=intensity)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added with intensity attributes
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
assert "intensity_mean" in nodes_df.columns

# Check mean intensities for each time point
Expand All @@ -222,10 +212,24 @@ def test_regionprops_add_nodes_timelapse_with_intensity() -> None:
assert len(nodes_at_t) == 1


def test_regionprops_custom_properties() -> None:
"""Test with custom property functions."""
graph = RustWorkXGraph()
def test_regionprops_multichannel_intensity(graph_backend: BaseGraph) -> None:
"""Test that multichannel intensity images populate per-channel stats."""
labels = np.array([[[1, 0], [0, 2]]], dtype=np.int32)
# two channels, each with a different max for each label
intensity = np.array([[[[10, 100], [0, 0]], [[0, 0], [20, 200]]]], dtype=np.float32)

operator = RegionPropsNodes(extra_properties=["intensity_max"])
operator.add_nodes(graph_backend, labels=labels, intensity_image=intensity)

nodes_df = graph_backend.node_attrs()
max_values = sorted(nodes_df["intensity_max"].to_list(), key=lambda arr: arr[0])

assert np.allclose(max_values[0], [10, 100])
assert np.allclose(max_values[1], [20, 200])


def test_regionprops_custom_properties(graph_backend: BaseGraph) -> None:
"""Test with custom property functions."""
# Create simple labels
labels = np.array([[[1, 1, 0], [1, 0, 0], [0, 0, 0]]], dtype=np.int32)

Expand All @@ -235,13 +239,13 @@ def double_area(region: RegionProperties) -> float:

operator = RegionPropsNodes(extra_properties=[double_area, "area"])

operator.add_nodes(graph, labels=labels, t=0)
operator.add_nodes(graph_backend, labels=labels, t=0)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that custom property was calculated
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
assert "double_area" in nodes_df.columns
assert "area" in nodes_df.columns

Expand All @@ -251,35 +255,31 @@ def double_area(region: RegionProperties) -> float:
assert double_area_val == area * 2


def test_regionprops_invalid_dimensions() -> None:
def test_regionprops_invalid_dimensions(graph_backend: BaseGraph) -> None:
"""Test error handling for invalid label dimensions."""
graph = RustWorkXGraph()

# Create 2D labels (invalid)
labels = np.array([[1, 2, 3], [4, 5, 6]], dtype=np.int32)

operator = RegionPropsNodes()

with pytest.raises(ValueError, match=r"`labels` must be 't \+ 2D' or 't \+ 3D'"):
operator.add_nodes(graph, labels=labels)
operator.add_nodes(graph_backend, labels=labels)


def test_regionprops_mask_creation() -> None:
def test_regionprops_mask_creation(graph_backend: BaseGraph) -> None:
"""Test that masks are properly created for regions."""
graph = RustWorkXGraph()

# Create simple labels
labels = np.array([[[1, 1, 0], [1, 0, 0], [0, 0, 2]]], dtype=np.int32)

operator = RegionPropsNodes()

operator.add_nodes(graph, labels=labels, t=0)
operator.add_nodes(graph_backend, labels=labels, t=0)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that masks were created
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()
masks = nodes_df[DEFAULT_ATTR_KEYS.MASK]

# All masks should be Mask objects
Expand All @@ -289,45 +289,41 @@ def test_regionprops_mask_creation() -> None:
assert mask._bbox is not None


def test_regionprops_spacing() -> None:
def test_regionprops_spacing(graph_backend: BaseGraph) -> None:
"""Test regionprops with custom spacing."""
graph = RustWorkXGraph()

# Create simple labels
labels = np.array([[[1, 1], [1, 1]]], dtype=np.int32)

operator = RegionPropsNodes(extra_properties=["area"], spacing=(2.0, 3.0)) # Custom spacing

operator.add_nodes(graph, labels=labels, t=0)
operator.add_nodes(graph_backend, labels=labels, t=0)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# Check that nodes were added (spacing affects internal calculations)
nodes_df = graph.node_attrs()
nodes_df = graph_backend.node_attrs()

assert len(nodes_df) == 1
assert "area" in nodes_df.columns
assert DEFAULT_ATTR_KEYS.MASK in nodes_df.columns
assert nodes_df[DEFAULT_ATTR_KEYS.BBOX].to_numpy().ndim == 2


def test_regionprops_empty_labels() -> None:
def test_regionprops_empty_labels(graph_backend: BaseGraph) -> None:
"""Test behavior with empty labels (no regions)."""
graph = RustWorkXGraph()

# Create labels with no regions
labels = np.zeros((1, 3, 3), dtype=np.int32)

operator = RegionPropsNodes()

operator.add_nodes(graph, labels=labels, t=0)
operator.add_nodes(graph_backend, labels=labels, t=0)

assert "shape" in graph.metadata
assert graph.metadata["shape"] == labels.shape
assert "shape" in graph_backend.metadata
assert graph_backend.metadata["shape"] == labels.shape

# No nodes should be added
assert graph.num_nodes == 0
assert graph_backend.num_nodes == 0


def test_regionprops_multiprocessing_isolation() -> None:
Expand Down
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