{ "cells": [ { "cell_type": "markdown", "id": "ff11395c-5b0c-4df8-8b20-a5ab712d31ff", "metadata": {}, "source": [ "# Saving and loading surfaces\n", "In this notebook we will save a surface to disk and reload it from there using [vedo](https://vedo.embl.es/).\n", "\n", "See also\n", "* https://vedo.embl.es/docs/vedo/io.html#write\n", "* https://vedo.embl.es/docs/vedo/io.html#load" ] }, { "cell_type": "code", "execution_count": 1, "id": "a43114eb-755f-485d-b602-4d0b6f5330da", "metadata": {}, "outputs": [], "source": [ "import napari_process_points_and_surfaces as nppas\n", "import vedo\n", "\n", "from branchoid import branchoid" ] }, { "cell_type": "markdown", "id": "526101a6-9bec-461c-9f27-140252b1ee0b", "metadata": {}, "source": [ "Starting point is again the surface of the simulated branchoid." ] }, { "cell_type": "code", "execution_count": 2, "id": "0bec9a3c-4553-40e9-b51e-3a4d666cb855", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "nppas.SurfaceTuple
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
origin (z/y/x)[0. 0. 0.]
center of mass(z/y/x)50.000,46.575,42.589
scale(z/y/x)1.000,1.000,1.000
bounds (z/y/x)25.500...74.500
2.500...88.500
2.500...83.500
average size31.277
number of vertices19040
number of faces38076
\n", "\n", "
" ], "text/plain": [ "(array([[25.5, 44. , 47. ],\n", " [26. , 43.5, 47. ],\n", " [26. , 44. , 46.5],\n", " ...,\n", " [74.5, 56. , 51. ],\n", " [74.5, 56. , 52. ],\n", " [74.5, 56. , 53. ]], dtype=float32),\n", " array([[ 2, 1, 0],\n", " [ 4, 3, 0],\n", " [ 4, 0, 1],\n", " ...,\n", " [19038, 18870, 18872],\n", " [19038, 18872, 19039],\n", " [19039, 18872, 18852]], dtype=int64))" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "binary_image = branchoid()\n", "surface = nppas.all_labels_to_surface(binary_image)\n", "surface" ] }, { "cell_type": "markdown", "id": "9a7a1d1c-3e06-4015-bf11-fcd26cd09586", "metadata": {}, "source": [ "## Saving surfaces to disk\n", "The [vedo](https://vedo.embl.es/) library functions for saving and loading surfaces meshes. To convert them from/to napari-compatible surface-tuples, we use [napari-process-points-and-surfaces (nppas)](https://github.com/haesleinhuepf/napari-process-points-and-surfaces)." ] }, { "cell_type": "code", "execution_count": 3, "id": "2c40840a-d892-4071-9286-752924170582", "metadata": {}, "outputs": [], "source": [ "mesh = nppas.to_vedo_mesh(surface)\n", "\n", "filename = \"../../data/branchoid.ply\"\n", "\n", "_ = vedo.write(mesh, filename)" ] }, { "cell_type": "markdown", "id": "8563f75b-3320-4151-b29f-b54caf5418aa", "metadata": {}, "source": [ "## Loading meshes from disk" ] }, { "cell_type": "code", "execution_count": 4, "id": "827dffde-feb0-4b74-8666-b8dee735e379", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "
\n", "\n", "
\n", "vedo.mesh.Mesh
(../../data/branchoid.ply)\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
bounds
(x/y/z) 		25.50 ... 74.50
2.500 ... 88.50
2.500 ... 83.50
center of mass (50.0, 46.6, 42.6)
average size 31.277
nr. points / faces 19040 / 38076
\n", "
" ], "text/plain": [ "" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "new_mesh = vedo.load(filename)\n", "new_mesh" ] }, { "cell_type": "code", "execution_count": 5, "id": "a35e74e4-113d-41f5-9bde-25a7875d4a0a", "metadata": {}, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "
\n", "\n", "\n", "nppas.SurfaceTuple
\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
origin (z/y/x)[0. 0. 0.]
center of mass(z/y/x)50.000,46.575,42.589
scale(z/y/x)1.000,1.000,1.000
bounds (z/y/x)25.500...74.500
2.500...88.500
2.500...83.500
average size31.277
number of vertices19040
number of faces38076
\n", "\n", "
" ], "text/plain": [ "(array([[25.5, 44. , 47. ],\n", " [26. , 43.5, 47. ],\n", " [26. , 44. , 46.5],\n", " ...,\n", " [74.5, 56. , 51. ],\n", " [74.5, 56. , 52. ],\n", " [74.5, 56. , 53. ]], dtype=float32),\n", " array([[ 2, 1, 0],\n", " [ 4, 3, 0],\n", " [ 4, 0, 1],\n", " ...,\n", " [19038, 18870, 18872],\n", " [19038, 18872, 19039],\n", " [19039, 18872, 18852]], dtype=int64))" ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "new_surface = nppas.to_napari_surface_data(new_mesh)\n", "new_surface" ] }, { "cell_type": "code", "execution_count": null, "id": "5cebe5c5-06b8-423e-8632-ac2a3297967a", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.15" } }, "nbformat": 4, "nbformat_minor": 5 }