added support for vtp read and write

.github/workflows/test_and_deploy.yml

@@ -36,18 +36,6 @@ jobs:
       # these libraries enable testing on Qt on linux
       - uses: tlambert03/setup-qt-libs@v1
 
-      - name: Set up conda ${{ matrix.python-version }}
-        uses: conda-incubator/setup-miniconda@v2.0.0
-        with:
-          auto-update-conda: true
-          activate-environment: test
-          python-version: ${{ matrix.python-version }}
-          channels: conda-forge
-
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-
       # note: if you need dependencies from conda, considering using
       # setup-miniconda: https://github.com/conda-incubator/setup-miniconda
       # and

src/napari_stl_exporter/_reader.py

@@ -5,18 +5,23 @@
 import numpy as np
 from typing import Optional, List
 
-supported_formats = ['.stl', '.ply', '.obj']
+supported_surface_formats = ['.stl', '.ply', '.obj']
+suported_points_formats = ['.vtp']
+
 
 def get_reader(path: str) -> Optional[callable]:
     # Taken from https://napari.org/plugins/guides.html
 
     file_ext = os.path.splitext(path)[1]
-    if isinstance(path, str) and file_ext in supported_formats:
+    if isinstance(path, str) and file_ext in supported_surface_formats:
         return napari_import_surface
+    elif isinstance(path, str) and file_ext in suported_points_formats:
+        return napari_import_points
 
     # otherwise we return None.
     return None
 
+
 def napari_import_surface(path: str) -> List[LayerDataTuple]:
     """
     Read supported surface files using the vedo io functionality.
@@ -33,3 +38,23 @@ def napari_import_surface(path: str) -> List[LayerDataTuple]:
     mesh = vedo.load(path, unpack=True, force=False)
     _mesh = [mesh.points(), np.asarray(mesh.faces())]
     return [tuple([_mesh, {}, 'surface'])]
+
+
+def napari_import_points(path: str) -> List[LayerDataTuple]:
+    """
+    Read supported point cloud files using the vedo io functionality.
+
+    Parameters
+    ----------
+    path : str
+
+    Returns
+    -------
+    PointsData
+
+    """
+    import pandas as pd
+    points = vedo.load(path, unpack=True, force=False)
+    features = pd.DataFrame(dict(points.pointdata))
+    return [(points.points(), {'features': features,
+                               'face_color': features.columns[0]}, 'points')]

src/napari_stl_exporter/_tests/test_writer_and_readers.py

@@ -2,7 +2,9 @@
 import os
 import vedo
 
-supported_formats = ['.stl', '.ply', '.obj']
+supported_surface_formats = ['.stl', '.ply', '.obj']
+supported_points_formats = ['.vtp']
+
 
 def test_label_conversion():
     import vedo
@@ -14,40 +16,70 @@ def test_label_conversion():
 
     assert isinstance(mesh, vedo.mesh.Mesh)
 
+
 def test_writer(tmpdir):
     from skimage import measure
-    from napari_stl_exporter._writer import napari_write_labels, napari_write_surfaces
+    import pandas as pd
+    from napari_stl_exporter._writer import (
+        napari_write_labels,
+        napari_write_surfaces,
+        napari_write_points)
+
     label_image = np.zeros((100, 100, 100))
     label_image[25:75, 25:75, 25:75] = 1
 
-    for ext in supported_formats:
+    points_data_3d = np.random.rand(100, 3)
+    points_data_3d_features = pd.DataFrame(
+        np.random.rand(100, 3),
+        columns=['feat1', 'feat2', 'feat3'])
+
+    for ext in supported_surface_formats:
         pth = os.path.join(str(tmpdir), "test_export" + ext)
         stl_file = napari_write_labels(pth, label_image, None)
         assert os.path.exists(pth)
         assert stl_file is not None
 
     surf = measure.marching_cubes(label_image)
 
-    for ext in supported_formats:
+    for ext in supported_surface_formats:
         pth = os.path.join(str(tmpdir), "test_export" + ext)
         stl_file = napari_write_surfaces(pth, surf, None)
         assert os.path.exists(pth)
         assert stl_file is not None
 
+    for ext in supported_points_formats:
+        pth = os.path.join(str(tmpdir), "test_export" + ext)
+        vtp_file3d = napari_write_points(
+            pth,
+            points_data_3d,
+            {'features': points_data_3d_features})
+        assert os.path.exists(pth)
+        assert vtp_file3d is not None
+
+
 def test_writer_viewer(make_napari_viewer, tmpdir):
     import napari
+    import pandas as pd
     # Load and binarize image
     label_image = np.zeros((100, 100, 100), dtype=int)
+    points_data_3d = np.random.rand(100, 3)
+    points_data_3d_features = pd.DataFrame(
+        np.random.rand(100, 3),
+        columns=['feat1', 'feat2', 'feat3'])
     label_image[25:75, 25:75, 25:75] = 1
 
     # Add data to viewer
     viewer = make_napari_viewer()
     label_layer = viewer.add_labels(label_image, name='3D object')
+    points_layer = viewer.add_points(points_data_3d, name='3D points',
+                                     features=points_data_3d_features)
 
     # save the layer as 3D printable file to disc
     napari.save_layers(os.path.join(tmpdir, 'test.stl'), [label_layer])
+    napari.save_layers(os.path.join(tmpdir, 'test.vtp'), [points_layer])
     assert os.path.exists(os.path.join(tmpdir, 'test.stl'))
 
+
 def test_sample_data():
     from napari_stl_exporter._sample_data import make_pyramid_label, make_pyramid_surface
     label_image = make_pyramid_label()
@@ -56,16 +88,23 @@ def test_sample_data():
     surface_image = make_pyramid_surface()
     assert surface_image is not None
 
+
 def test_reader(make_napari_viewer, tmpdir):
     import napari_stl_exporter
+    import pandas as pd
     from napari_stl_exporter._sample_data import make_pyramid_surface
-    from napari_stl_exporter._writer import napari_write_surfaces
-    from napari_stl_exporter._reader import napari_import_surface
+    from napari_stl_exporter._writer import napari_write_surfaces, napari_write_points
+    from napari_stl_exporter._reader import napari_import_surface, napari_import_points
+
+    points_data_3d = np.random.rand(100, 3)
+    points_data_3d_features = pd.DataFrame(
+        np.random.rand(100, 3),
+        columns=['feat1', 'feat2', 'feat3'])
 
     pyramid = napari_stl_exporter.make_pyramid_surface()[0][0]
     viewer = make_napari_viewer()
 
-    for ext in supported_formats:
+    for ext in supported_surface_formats:
         path = os.path.join(tmpdir, 'test' + ext)
         napari_write_surfaces(path, pyramid, None)
         _pyramid = napari_import_surface(path)[0]
@@ -76,13 +115,23 @@ def test_reader(make_napari_viewer, tmpdir):
         data = reader(path)
         assert data is not None
 
+    for ext in supported_points_formats:
+        path = os.path.join(tmpdir, 'test' + ext)
+        napari_write_points(path, points_data_3d, {'features': points_data_3d_features})
+        _points = napari_import_points(path)[0]
+
+        layer = viewer.add_points(_points[0], **_points[1])
+        assert hasattr(layer, 'features')
+
+
 def test_image_surface_conversion():
     from skimage import data
     from napari_stl_exporter._image_to_surface import image_to_surface
 
     image = data.cell()
     surface = image_to_surface(image)
 
+
 def test_widgets(make_napari_viewer):
     from napari_stl_exporter._image_to_surface import image_to_surface_widget, extrude_widget
 
@@ -93,7 +142,3 @@ def test_widgets(make_napari_viewer):
 
     viewer.window.add_dock_widget(widget_surface)
     viewer.window.add_dock_widget(widget_extrude)
-
-if  __name__ == '__main__':
-    import napari
-    test_widgets(napari.Viewer)

src/napari_stl_exporter/_writer.py

@@ -2,28 +2,54 @@
 from skimage import measure
 import vedo
 
-from napari.types import LabelsData, SurfaceData
+from napari.types import LabelsData, SurfaceData, PointsData
 from typing import Optional
 
 
 supported_layers = ['labels']
-supported_formats = ['.stl', '.ply', '.obj']
+supported_surface_formats = ['.stl', '.ply', '.obj']
+supported_points_formats = ['.vtp']
+
 
 def napari_write_surfaces(path: str, data: SurfaceData, meta: dict
                          ) -> Optional[str]:
     file_ext = os.path.splitext(path)[1]
-    if file_ext in supported_formats:
+    if file_ext in supported_surface_formats:
         mesh = vedo.mesh.Mesh((data[0], data[1]))
         vedo.write(mesh, path)
 
         return path
 
 
+def napari_write_points(
+        path: str, data: PointsData, meta: dict
+        ) -> Optional[str]:
+    file_ext = os.path.splitext(path)[1]
+    if file_ext in supported_points_formats:
+        points = vedo.Points(data)
+
+        # if metadata doesn't exist
+        if meta is None:
+            vedo.write(points, path)
+            return path
+
+        # add features to pointcloud
+        if 'properties' in meta:
+            features = meta['properties']
+        elif 'features' in meta:
+            features = meta['features']
+        for key in features:
+            points.pointdata[key] = features[key]
+        vedo.write(points, path)
+
+        return path
+
+
 def napari_write_labels(path: str, data: LabelsData, meta: dict
                         ) -> Optional[str]:
 
     file_ext = os.path.splitext(path)[1]
-    if file_ext in supported_formats:
+    if file_ext in supported_surface_formats:
 
         mesh = _labels_to_mesh(data)
         vedo.write(mesh, path)

src/napari_stl_exporter/napari.yaml

@@ -10,6 +10,13 @@ contributions:
       title: Write Surface
       python_name: napari_stl_exporter._writer:napari_write_surfaces
 
+    - id: napari-stl-exporter.write_points
+      title: Write Points
+      python_name: napari_stl_exporter._writer:napari_write_points
+    - id: napari_stl_exporter.read_points
+      title: Read Points
+      python_name: napari_stl_exporter._reader:napari_import_points
+
     - id: napari-stl-exporter.make_pyramid_label
       title: Create a label image of a pyramid
       python_name: napari_stl_exporter._sample_data:make_pyramid_label
@@ -61,10 +68,20 @@ contributions:
       filename_extensions: [".stl", ".ply", ".obj"]
       display_name: surface
 
+    - command: napari-stl-exporter.write_points
+      layer_types:
+      - points
+      filename_extensions: [".vtp"]
+      display_name: points
+
     readers:
     - command: napari-stl-exporter.import_surface
       accepts_directories: false
       filename_patterns:
       - "*.stl"
       - "*.ply"
       - "*.obj"
+    - command: napari-stl-exporter.read_points
+      accepts_directories: false
+      filename_patterns:
+      - "*.vtp"