From 6851933277c6cc6ce5dd536487efe8a23fba1652 Mon Sep 17 00:00:00 2001
From: Alessia Saccardo <s212246@dtu.dk>
Date: Tue, 18 Feb 2025 08:58:35 +0100
Subject: [PATCH] fix descriptions and examples
---
docs/doc/data_handling/io.md | 4 ++--
qim3d/mesh/_common_mesh_methods.py | 28 ++++++++++++++++++++++++++--
qim3d/viz/_k3d.py | 3 ++-
3 files changed, 30 insertions(+), 5 deletions(-)
diff --git a/docs/doc/data_handling/io.md b/docs/doc/data_handling/io.md
index 82c984bb..607d81ed 100644
--- a/docs/doc/data_handling/io.md
+++ b/docs/doc/data_handling/io.md
@@ -8,5 +8,5 @@
- Downloader
- export_ome_zarr
- import_ome_zarr
- - save_mesh
- - load_mesh
\ No newline at end of file
+ - load_mesh
+ - save_mesh
\ No newline at end of file
diff --git a/qim3d/mesh/_common_mesh_methods.py b/qim3d/mesh/_common_mesh_methods.py
index ace4749a..7ff2dbe8 100644
--- a/qim3d/mesh/_common_mesh_methods.py
+++ b/qim3d/mesh/_common_mesh_methods.py
@@ -7,11 +7,35 @@ from qim3d.utils._logger import log
def from_volume(
volume: np.ndarray,
- **Kwargs
+ **kwargs
) -> hmesh.Manifold:
+ """ Convert a 3D numpy array to a mesh object using the [volumetric_isocontour](https://www2.compute.dtu.dk/projects/GEL/PyGEL/pygel3d/hmesh.html#volumetric_isocontour) function from Pygel3D.
+
+ Args:
+ volume (np.ndarray): A 3D numpy array representing a volume.
+ **kwargs: Additional arguments to pass to the Pygel3D volumetric_isocontour function.
+
+ Raises:
+ ValueError: If the input volume is not a 3D numpy array.
+
+ Returns:
+ hmesh.Manifold: A Pygel3D mesh object representing the input volume.
+
+ Example:
+ Convert a 3D numpy array to a Pygel3D mesh object:
+ ```python
+ import qim3d
+
+ # Generate a 3D blob
+ synthetic_blob = qim3d.generate.noise_object(noise_scale = 0.015)
+
+ # Convert the 3D numpy array to a Pygel3D mesh object
+ mesh = qim3d.mesh.from_volume(synthetic_blob)
+ ```
+ """
if volume.ndim != 3:
raise ValueError("The input volume must be a 3D numpy array.")
- mesh = hmesh.volumetric_isocontour(volume)
+ mesh = hmesh.volumetric_isocontour(volume, **kwargs)
return mesh
\ No newline at end of file
diff --git a/qim3d/viz/_k3d.py b/qim3d/viz/_k3d.py
index aab60d40..2bfe1273 100644
--- a/qim3d/viz/_k3d.py
+++ b/qim3d/viz/_k3d.py
@@ -211,7 +211,8 @@ def mesh(
See full reference: https://www2.compute.dtu.dk/projects/GEL/PyGEL/pygel3d/jupyter_display.html#display
Returns:
- k3d.Plot or None:
+ k3d.Plot or None:
+
- If `backend="k3d"`, returns a `k3d.Plot` object.
- If `backend="pygel3d"`, the function displays the mesh but does not return a plot object.
Example:
--
GitLab