add sample data and reader plugin (#18)

* add sample data plugin

* add demo CLI

* add comments

* add obj file reader plugin

* add higher level import

* add higher level import

setup.cfg

@@ -35,6 +35,7 @@ install_requires =
     magicgui
     mrcfile
     numpy
+    pooch
     qtpy
     rich
     scikit-image

src/surforama/_cli.py

@@ -1,12 +1,8 @@
 from typing import Optional
 
-import mrcfile
-import napari
 import typer
 from typing_extensions import Annotated
 
-from surforama.app import QtSurforama, read_obj_file_and_compute_normals
-
 app = typer.Typer(
     help="Surforama: wiew tomogram densities on a surface.",
     no_args_is_help=True,
@@ -21,21 +17,64 @@ def launch_surforama(
     mesh_path: Annotated[
         Optional[str], typer.Option(help="Path to the mesh to load.")
     ] = None,
+    demo: Annotated[
+        bool, typer.Option("--demo", help="launch surforama with sample data")
+    ] = False,
 ):
+    if demo and (image_path is not None or mesh_path is not None):
+        raise ValueError(
+            "Please do not specify an image/mesh path when launching in demo mode."
+        )
+
+    # delay imports
+    import mrcfile
+    import napari
+
+    from surforama.app import QtSurforama
+    from surforama.io.mesh import read_obj_file
+
     viewer = napari.Viewer(ndisplay=3)
-    if image_path is not None:
-        # load the image if the path was passed
-        image = mrcfile.read(image_path)
-        volume_layer = viewer.add_image(image)
-    else:
-        volume_layer = None
 
-    if mesh_path is not None:
-        # load the mesh if a path was passed
-        mesh_data = read_obj_file_and_compute_normals(mesh_path)
+    if demo:
+        # set up the viewer in demo mode
+        from surforama.data._datasets import thylakoid_membrane
+
+        # fetch the data
+        tomogram, mesh_data = thylakoid_membrane()
+
+        # Add the data to the viewer
+        volume_layer = viewer.add_image(
+            tomogram, blending="translucent", depiction="plane"
+        )
         surface_layer = viewer.add_surface(mesh_data)
+
+        # set up the slicing plane position
+        volume_layer.plane = {"normal": [1, 0, 0], "position": [66, 187, 195]}
+
+        # set up the camera
+        viewer.camera.center = (64.0, 124.0, 127.5)
+        viewer.camera.zoom = 3.87
+        viewer.camera.angles = (
+            -5.401480002668876,
+            -0.16832643131442776,
+            160.28901483338126,
+        )
+
     else:
-        surface_layer = None
+        # set up the viewer with the user-requested images
+        if image_path is not None:
+            # load the image if the path was passed
+            image = mrcfile.read(image_path)
+            volume_layer = viewer.add_image(image)
+        else:
+            volume_layer = None
+
+        if mesh_path is not None:
+            # load the mesh if a path was passed
+            mesh_data = read_obj_file(mesh_path)
+            surface_layer = viewer.add_surface(mesh_data)
+        else:
+            surface_layer = None
 
     # Instantiate the widget and add it to Napari
     surforama_widget = QtSurforama(viewer, surface_layer, volume_layer)

src/surforama/app.py

@@ -19,28 +19,7 @@
     QWidget,
 )
 
-
-def read_obj_file_and_compute_normals(file_path, scale_factor=1):
-    mesh = trimesh.load(file_path, file_type="obj", process=True)
-
-    # Subdivide
-    # verts, faces = trimesh.remesh.subdivide_to_size(
-    # mesh.vertices, mesh.faces, 1
-    # )
-
-    # Subdivide can introduce holes
-    # mesh = trimesh.Trimesh(vertices=verts, faces=faces)
-    # trimesh.repair.fill_holes(mesh)
-
-    verts = mesh.vertices
-    faces = mesh.faces
-
-    verts = verts[:, [2, 1, 0]]
-
-    values = np.ones((len(verts),))
-
-    return verts, faces, values
-
+from surforama.io.mesh import read_obj_file
 
 # column names for the starfile
 STAR_X_COLUMN_NAME = "rlnCoordinateX"
@@ -401,7 +380,7 @@ def _write_star_file(self, output_path: Path):
     mrc = mrcfile.open(tomo_path, permissive=True)
     tomo_mrc = np.array(mrc.data)
 
-    vertices, faces, values = read_obj_file_and_compute_normals(obj_path)
+    vertices, faces, values = read_obj_file(obj_path)
     surface = (vertices, faces, values)
 
     viewer = napari.Viewer(ndisplay=3)

src/surforama/data/__init__.py

@@ -0,0 +1,3 @@
+from surforama.data._datasets import thylakoid_membrane
+
+__all__ = ("thylakoid_membrane",)

src/surforama/data/_datasets.py

@@ -0,0 +1,56 @@
+from typing import List, Tuple
+
+import mrcfile
+import numpy as np
+import pooch
+from napari.types import LayerDataTuple
+
+from surforama.io.mesh import read_obj_file
+
+_data_registry = pooch.create(
+    path=pooch.os_cache("mypackage"),
+    base_url="doi:10.5281/zenodo.10814409",
+    registry={
+        "S1_M3b_StII_grow2_1_mesh_data.mrc": "md5:a6e34bbf4edc767aa6c2c854c81c9c97",
+        "S1_M3b_StII_grow2_1_mesh_data.obj": "md5:63b7d681204d7d3a3937154a0f4d7fc1",
+        "S1_M3b_StII_grow2_1_mesh_data_seg.mrc": "md5:d88460eb3bdf3164be6053d281fc45be",
+        "S1_M3c_StOI_grow2_1_mesh_data.mrc": "md5:296fbc48917c2baab7784a5ede6aae70",
+        "S1_M3c_StOI_grow2_1_mesh_data.obj": "md5:076e6e8a825f67a24e28beba09edcf70",
+        "S1_M3c_StOI_grow2_1_mesh_data_seg.mrc": "md5:878d4b3fc076dfc01e788cc08f9c9201",
+    },
+)
+
+
+def thylakoid_membrane() -> (
+    Tuple[np.ndarray, Tuple[np.ndarray, np.ndarray, np.ndarray]]
+):
+    """Fetch the thylakoid membrane sample data.
+
+    Data originally from Wietrzynski and Schaffer et al., eLife, 2020.
+    https://doi.org/10.7554/eLife.53740
+    """
+    # get the tomogram
+    tomogram_path = _data_registry.fetch(
+        "S1_M3b_StII_grow2_1_mesh_data.mrc", progressbar=True
+    )
+    tomogram = mrcfile.read(tomogram_path)
+
+    # get the mesh
+    mesh_path = _data_registry.fetch(
+        "S1_M3b_StII_grow2_1_mesh_data.obj", progressbar=True
+    )
+    mesh_data = read_obj_file(mesh_path)
+
+    return tomogram, mesh_data
+
+
+def _thylakoid_membrane_sample_data_plugin() -> List[LayerDataTuple]:
+    """napari sample data plugin for thylakoid membrane dataset."""
+
+    # get the data
+    tomogram, mesh_data = thylakoid_membrane()
+
+    return [
+        (tomogram, {"name": "tomogram"}, "image"),
+        (mesh_data, {"name": "mesh"}, "surface"),
+    ]

src/surforama/io/__init__.py

@@ -0,0 +1,3 @@
+from surforama.io.mesh import read_obj_file
+
+__all__ = ("read_obj_file",)

src/surforama/io/_reader_plugin.py

@@ -0,0 +1,18 @@
+from typing import Callable, List
+
+from napari.types import LayerDataTuple
+
+from surforama.io import read_obj_file
+
+
+def mesh_reader_plugin(path: str) -> Callable[[str], LayerDataTuple]:
+    if isinstance(path, str) and path.endswith(".obj"):
+        return obj_reader
+
+    # format not recognized
+    return None
+
+
+def obj_reader(path: str) -> List[LayerDataTuple]:
+    mesh_data = read_obj_file(path)
+    return [(mesh_data, {}, "surface")]

src/surforama/io/mesh.py

@@ -0,0 +1,24 @@
+import numpy as np
+import trimesh
+
+
+def read_obj_file(file_path):
+    mesh = trimesh.load(file_path, file_type="obj", process=True)
+
+    # Subdivide
+    # verts, faces = trimesh.remesh.subdivide_to_size(
+    # mesh.vertices, mesh.faces, 1
+    # )
+
+    # Subdivide can introduce holes
+    # mesh = trimesh.Trimesh(vertices=verts, faces=faces)
+    # trimesh.repair.fill_holes(mesh)
+
+    verts = mesh.vertices
+    faces = mesh.faces
+
+    verts = verts[:, [2, 1, 0]]
+
+    values = np.ones((len(verts),))
+
+    return verts, faces, values

src/surforama/napari.yaml

@@ -9,6 +9,21 @@ contributions:
     - id: surforama.make_widget
       python_name: surforama:QtSurforama
       title: Make Surforama
+    - id: surforama.thylakoid
+      python_name: surforama.data._datasets:_thylakoid_membrane_sample_data_plugin
+      title: Thylakoid membrane
+    - id: surforama.mesh_reader
+      python_name: surforama.io._reader_plugin:mesh_reader_plugin
+      title: Mesh reader
+  sample_data:
+    - command: surforama.thylakoid
+      key: thylakoid
+      display_name: thylakoid membrane
+  readers:
+    - command: surforama.mesh_reader
+      filename_patterns:
+        - '*.obj'
+      accepts_directories: false
   widgets:
     - command: surforama.make_widget
       display_name: Surforama