Merge pull request #391 from BiAPoL/add-surface-sample-data

Add surface sample data

Author: jo-mueller

src/napari_clusters_plotter/__init__.py

@@ -5,11 +5,12 @@
     DimensionalityReductionWidget,
 )
 from ._new_plotter_widget import PlotterWidget
-from ._sample_data import bbbc_1_dataset
+from ._sample_data import bbbc_1_dataset, cells3d_curvatures
 
 __all__ = [
     "PlotterWidget",
     "DimensionalityReductionWidget",
     "ClusteringWidget",
     "bbbc_1_dataset",
+    "cells3d_curvatures",
 ]

src/napari_clusters_plotter/_sample_data.py

@@ -58,3 +58,38 @@ def bbbc_1_dataset() -> List["LayerData"]:  # noqa: F821
         labels_layers.append(ldtuple_labels)
 
     return image_layers + labels_layers
+
+
+def cells3d_curvatures() -> List["LayerData"]:  # noqa: F821
+    import numpy as np
+    import pandas as pd
+    from skimage import io
+
+    path = Path(__file__).parent / "sample_data" / "cells3d"
+
+    # load data
+    vertices = np.loadtxt(path / "vertices.txt")
+    faces = np.loadtxt(path / "faces.txt").astype(int)
+    hks = pd.read_csv(path / "signature.csv")
+    nuclei = io.imread(path / "nucleus.tif")
+
+    # create layer data tuples
+    layer_data_surface = [
+        (vertices, faces),
+        {
+            "name": "cells_3d_heat_kernel_signature",
+            "features": hks,
+        },
+        "surface",
+    ]
+
+    layer_data_nuclei = (
+        nuclei,
+        {
+            "name": "cells_3d_nucleus",
+            "colormap": "gray",
+        },
+        "image",
+    )
+
+    return [layer_data_nuclei, layer_data_surface]

src/napari_clusters_plotter/_tests/test_sample_data.py

@@ -1,11 +1,24 @@
-def test_sample_data(make_napari_viewer):
-    from napari.layers import Layer
+import pytest
+
+from napari_clusters_plotter._sample_data import (
+    bbbc_1_dataset,
+    cells3d_curvatures,
+)
 
-    import napari_clusters_plotter as ncp
+
+@pytest.mark.parametrize(
+    "sample_data_function",
+    [
+        bbbc_1_dataset,
+        cells3d_curvatures,
+    ],
+)
+def test_bbbc_1_sample_data(make_napari_viewer, sample_data_function):
+    from napari.layers import Layer
 
     viewer = make_napari_viewer()
 
-    sample_dataset = ncp.bbbc_1_dataset()
+    sample_dataset = sample_data_function()
     for sample in sample_dataset:
         layer = Layer.create(sample[0], sample[1], sample[2])
         viewer.add_layer(layer)

src/napari_clusters_plotter/napari.yaml

@@ -17,6 +17,9 @@ contributions:
   - id: napari-clusters-plotter.bbbc_sample_data
     python_name: napari_clusters_plotter:bbbc_1_dataset
     title: Load bbbc sample data
+  - id: napari-clusters-plotter.cells3d_curvatures
+    python_name: napari_clusters_plotter:cells3d_curvatures
+    title: Load cells3d mitotic nucleus surface curvatures
 
   menus:
     napari/layers/visualize:
@@ -44,3 +47,6 @@ contributions:
   - command: napari-clusters-plotter.bbbc_sample_data
     key: bbbc1
     display_name: BBBC 1 dataset & segmentations
+  - command: napari-clusters-plotter.cells3d_curvatures
+    key: cells3d_curvatures
+    display_name: Cells3D mitotic nucleus surface curvatures