# napari-stl-exporter
[](https://github.com/jo-mueller/napari-stl-exporter/raw/master/LICENSE)
[](https://pypi.org/project/napari-stl-exporter)
[](https://python.org)
[](https://github.com/jo-mueller/napari-stl-exporter/actions)
[](https://codecov.io/gh/jo-mueller/napari-stl-exporter)
This plugin allows to import and export surface data in Napari to common file formats. The generated file formats can be read by other common applications, and - in particular - allow *3D-printing*.
### Supported file formats:
Currently supported file formats for export include and rely on the [vedo io API](https://vedo.embl.es/autodocs/content/vedo/io.html#vedo.io).
* *.stl*: [Standard triangle language](https://en.wikipedia.org/wiki/STL_%28file_format%29)
* *.ply*: [Polygon file format](https://en.wikipedia.org/wiki/PLY_(file_format))
* *.obj*: [Wavefront object](https://en.wikipedia.org/wiki/Wavefront_.obj_file)
### Supported Napari layers:
Currently supported Napari layer types are:
* [Surface layers](https://napari.org/howtos/layers/surface.html)
* [Label layers](https://napari.org/howtos/layers/labels.html): The label data is converted to surface data under the hood using the [marching cubes algorithm](https://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.marching_cubes) implemented in [scikit-image](https://scikit-image.org/) and is then exported using [Vedo](https://vedo.embl.es/). Warning: This can be slow for large image data!
### Import/export
**Interactively:** To export the data, simply save the selected layer with `File > Save Selected Layer(s)` and specify the file ending to be `some_file.[file_ending]`, for supported file types, see above. Similarly, supported file types can be imported into Napari with `File > `
**From code**: A [Napari Label layer](https://napari.org/api/napari.layers.Labels.html) can be added to the viewer as described in the [napari reference](https://napari.org/gallery/add_labels.html?highlight=add_labels) with this code snippet:
```python
import napari
import numpy as np
# Load and binarize image
label_image = np.zeros((100, 100, 100), dtype=int)
label_image[25:75, 25:75, 25:75] = 1
# Add data to viewer
viewer = napari.Viewer()
label_layer = viewer.add_labels(data, name='3D object')
# save the layer as 3D printable file to disc
napari.save_layers(r'/some/path/test.stl', [label_layer])
```
### Sample data
You can create sample label/surface data for export using the built-in functions as shown here:
...or from code with
```Python
import napari_stl_exporter
pyramid = napari_stl_exporter.make_pyramid_surface()
```
### 3D-printing
To actually send your object to a 3D-printer, it has to be further converted to the *.gcode* format with a Slicer program. The latter convert the 3D object to machine-relevant parameters (printing detail, motor trajectories, etc). Popular slicers are:
* [Slic3r](https://slic3r.org/): Documentation [here](https://manual.slic3r.org/intro/overview)
* [Prusa Slicer](https://www.prusa3d.com/prusaslicer/): Tutorial [here](https://help.prusa3d.com/en/article/first-print-with-prusaslicer_1753)
*Note*: You can also upload the STL file to [github.com](https://github.com) and interact with it in the browser:
#### Digital elevation models
DIgital elevation models (DEMs) can be printed with the napari-stl-exporter following these steps:
1. Go to the [open topography repository](https://portal.opentopography.org/raster?opentopoID=OTSDEM.032021.4326.2) and select a region of your choice, then download it as a GeoTiff file (`.tif`, intensity encodes elevation)
2. Open the downloaded tif image use the image conversion plugin (´Plugins > napari-stl-exporter > 2D image to surface´) to convert the downloaded image to a surface. CHeck the `solidify` option to make it readily 3D-printable.
3. Export the created surface layer as `.stl` or `.ply` file. Open it in your Slicer of choice (you may have to scale it according to the size limitations of your printer) and off you go!
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/docs/plugins/index.html
-->
## Installation
You can install `napari-stl-exporter` via [pip]:
pip install napari-stl-exporter
## Contributing
Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.
## License
Distributed under the terms of the [BSD-3] license,
"napari-stl-exporter" is free and open source software
## Issues
If you encounter any problems, please [file an issue](https://github.com/jo-mueller/napari-stl-exporter/issues) along with a detailed description or post to image.sc and tag ```El_Pollo_Diablo```
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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"description": "# napari-stl-exporter\n\n[](https://github.com/jo-mueller/napari-stl-exporter/raw/master/LICENSE)\n[](https://pypi.org/project/napari-stl-exporter)\n[](https://python.org)\n[](https://github.com/jo-mueller/napari-stl-exporter/actions)\n[](https://codecov.io/gh/jo-mueller/napari-stl-exporter)\n\nThis plugin allows to import and export surface data in Napari to common file formats. The generated file formats can be read by other common applications, and - in particular - allow *3D-printing*.\n\n\n\n\n### Supported file formats:\nCurrently supported file formats for export include and rely on the [vedo io API](https://vedo.embl.es/autodocs/content/vedo/io.html#vedo.io).\n* *.stl*: [Standard triangle language](https://en.wikipedia.org/wiki/STL_%28file_format%29)\n* *.ply*: [Polygon file format](https://en.wikipedia.org/wiki/PLY_(file_format))\n* *.obj*: [Wavefront object](https://en.wikipedia.org/wiki/Wavefront_.obj_file)\n\n### Supported Napari layers:\n\nCurrently supported Napari layer types are:\n* [Surface layers](https://napari.org/howtos/layers/surface.html)\n* [Label layers](https://napari.org/howtos/layers/labels.html): The label data is converted to surface data under the hood using the [marching cubes algorithm](https://scikit-image.org/docs/dev/api/skimage.measure.html#skimage.measure.marching_cubes) implemented in [scikit-image](https://scikit-image.org/) and is then exported using [Vedo](https://vedo.embl.es/). Warning: This can be slow for large image data!\n\n### Import/export\n\n**Interactively:** To export the data, simply save the selected layer with `File > Save Selected Layer(s)` and specify the file ending to be `some_file.[file_ending]`, for supported file types, see above. Similarly, supported file types can be imported into Napari with `File > `\n\n**From code**: A [Napari Label layer](https://napari.org/api/napari.layers.Labels.html) can be added to the viewer as described in the [napari reference](https://napari.org/gallery/add_labels.html?highlight=add_labels) with this code snippet:\n\n```python\nimport napari\nimport numpy as np\n\n# Load and binarize image\nlabel_image = np.zeros((100, 100, 100), dtype=int)\nlabel_image[25:75, 25:75, 25:75] = 1\n\n# Add data to viewer\nviewer = napari.Viewer()\nlabel_layer = viewer.add_labels(data, name='3D object')\n\n# save the layer as 3D printable file to disc\nnapari.save_layers(r'/some/path/test.stl', [label_layer])\n```\n\n### Sample data\nYou can create sample label/surface data for export using the built-in functions as shown here:\n\n\n\n...or from code with\n\n```Python\nimport napari_stl_exporter\n\npyramid = napari_stl_exporter.make_pyramid_surface()\n\n```\n\n### 3D-printing\nTo actually send your object to a 3D-printer, it has to be further converted to the *.gcode* format with a Slicer program. The latter convert the 3D object to machine-relevant parameters (printing detail, motor trajectories, etc). Popular slicers are:\n\n* [Slic3r](https://slic3r.org/): Documentation [here](https://manual.slic3r.org/intro/overview)\n* [Prusa Slicer](https://www.prusa3d.com/prusaslicer/): Tutorial [here](https://help.prusa3d.com/en/article/first-print-with-prusaslicer_1753)\n\n*Note*: You can also upload the STL file to [github.com](https://github.com) and interact with it in the browser:\n\n\n\n#### Digital elevation models\n\nDIgital elevation models (DEMs) can be printed with the napari-stl-exporter following these steps:\n\n1. Go to the [open topography repository](https://portal.opentopography.org/raster?opentopoID=OTSDEM.032021.4326.2) and select a region of your choice, then download it as a GeoTiff file (`.tif`, intensity encodes elevation)\n2. Open the downloaded tif image use the image conversion plugin (\u00b4Plugins > napari-stl-exporter > 2D image to surface\u00b4) to convert the downloaded image to a surface. CHeck the `solidify` option to make it readily 3D-printable.\n\n\n\n3. Export the created surface layer as `.stl` or `.ply` file. Open it in your Slicer of choice (you may have to scale it according to the size limitations of your printer) and off you go!\n\n----------------------------------\n\nThis [napari] plugin was generated with [Cookiecutter] using with [@napari]'s [cookiecutter-napari-plugin] template.\n\n<!--\nDon't miss the full getting started guide to set up your new package:\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\n\nand review the napari docs for plugin developers:\nhttps://napari.org/docs/plugins/index.html\n-->\n\n## Installation\n\nYou can install `napari-stl-exporter` via [pip]:\n\n pip install napari-stl-exporter\n\n## Contributing\n\nContributions are very welcome. Tests can be run with [tox], please ensure\nthe coverage at least stays the same before you submit a pull request.\n\n## License\n\nDistributed under the terms of the [BSD-3] license,\n\"napari-stl-exporter\" is free and open source software\n\n## Issues\n\nIf you encounter any problems, please [file an issue](https://github.com/jo-mueller/napari-stl-exporter/issues) along with a detailed description or post to image.sc and tag ```El_Pollo_Diablo```\n\n[napari]: https://github.com/napari/napari\n[Cookiecutter]: https://github.com/audreyr/cookiecutter\n[@napari]: https://github.com/napari\n[MIT]: http://opensource.org/licenses/MIT\n[BSD-3]: http://opensource.org/licenses/BSD-3-Clause\n[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt\n[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt\n[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0\n[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt\n[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin\n\n[napari]: https://github.com/napari/napari\n[tox]: https://tox.readthedocs.io/en/latest/\n[pip]: https://pypi.org/project/pip/\n[PyPI]: https://pypi.org/\n",
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