| Name | acquifer-napari JSON |
| Version |
0.0.2
JSON |
| download |
| home_page | |
| Summary | Loader plugin for napari, to load Acquifer Imaging Machine datasets in napari, using dask for efficient lazy data-loading. |
| upload_time | 2024-02-27 11:18:26 |
| maintainer | |
| docs_url | None |
| author | Laurent Thomas |
| requires_python | >=3.7 |
| license | GPL-3.0-only |
| keywords |
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# acquifer-napari
The acquifer-napari plugin allows loading IM04 dataset directory, as multi-dimensional images in napari.
Sliders for well, channel, time and Z are automatically rendered when there are more than 1 coordinates along the dimension.
The plugin uses Dask-Image for efficient data-loading "on request" similar to the VirtualStack in ImageJ.
## Installation
Via the napari plugin manager : acquifer-napari.
Or with pip : `pip install acquifer-napari`.
Use `pip install -e .` to install in developement mode, so any change in the source code is directly reflected.
Use `npe2 list` to check that the plugin is correctly installed and visible by napari.
For instance here, the package defines 1 command, which is a reader.
One could have more commands, which would be implement other types.
This should output something like following
┌──────────────────────────────┬─────────┬──────┬───────────────────────────────────────────────────────────┐
│ Name │ Version │ Npe2 │ Contributions │
├──────────────────────────────┼─────────┼──────┼───────────────────────────────────────────────────────────┤
│ acquifer-napari │ 0.0.1 │ ✅ │ commands (1), readers (1)
The plugin should be installed in an environment with napari installed.
Napari can be started with the `napari`command in a command prompt with a system wide python installation.
Once installed, napari can be opened in a IPython interactive session with
```python
>> import napari
>> napari.Viewer()
```
## Configurations
The file `napari.yaml` in `acquifer_napari_plugin` defines what functions of the python package are visible to napari.
The top level `name` field must be the same than the python package name defined in `setup.cfg`.
It first define a set of commands, which have a custom `id`, and a `python_name`, which is the actual location of the function in the python package (or module).
Then the napari.yaml has optional subsections `readers`, `writers`, `widget`, to reference some of the commands previously defined, to notify napari that they implemente those standard functions.
For instance I first define a command myReader pointing to myPackage.myReader, and I reference that command using the id it in the section readers
See https://napari.org/stable/plugins/first_plugin.html#add-a-napari-yaml-manifest
## Issues
If you encounter any problems, please [file an issue](https://github.com/Luxendo/acquifer-napari/issues) along with a detailed description.
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"description": "# acquifer-napari\r\n\r\nThe acquifer-napari plugin allows loading IM04 dataset directory, as multi-dimensional images in napari. \r\nSliders for well, channel, time and Z are automatically rendered when there are more than 1 coordinates along the dimension. \r\nThe plugin uses Dask-Image for efficient data-loading \"on request\" similar to the VirtualStack in ImageJ. \r\n\r\n## Installation\r\nVia the napari plugin manager : acquifer-napari.\r\nOr with pip : `pip install acquifer-napari`.\r\n\r\nUse `pip install -e .` to install in developement mode, so any change in the source code is directly reflected. \r\nUse `npe2 list` to check that the plugin is correctly installed and visible by napari. \r\nFor instance here, the package defines 1 command, which is a reader. \r\nOne could have more commands, which would be implement other types. \r\nThis should output something like following \r\n\u250c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u252c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u252c\u2500\u2500\u2500\u2500\u2500\u2500\u252c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2510\r\n\u2502 Name \u2502 Version \u2502 Npe2 \u2502 Contributions \u2502\r\n\u251c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u253c\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2500\u2524\r\n\u2502 acquifer-napari \u2502 0.0.1 \u2502 \u2705 \u2502 commands (1), readers (1)\r\n\r\nThe plugin should be installed in an environment with napari installed. \r\nNapari can be started with the `napari`command in a command prompt with a system wide python installation. \r\nOnce installed, napari can be opened in a IPython interactive session with\r\n\r\n```python\r\n>> import napari\r\n>> napari.Viewer()\r\n```\r\n\r\n## Configurations\r\nThe file `napari.yaml` in `acquifer_napari_plugin` defines what functions of the python package are visible to napari. \r\nThe top level `name` field must be the same than the python package name defined in `setup.cfg`.\r\nIt first define a set of commands, which have a custom `id`, and a `python_name`, which is the actual location of the function in the python package (or module). \r\nThen the napari.yaml has optional subsections `readers`, `writers`, `widget`, to reference some of the commands previously defined, to notify napari that they implemente those standard functions. \r\nFor instance I first define a command myReader pointing to myPackage.myReader, and I reference that command using the id it in the section readers \r\nSee https://napari.org/stable/plugins/first_plugin.html#add-a-napari-yaml-manifest \r\n\r\n\r\n## Issues\r\nIf you encounter any problems, please [file an issue](https://github.com/Luxendo/acquifer-napari/issues) along with a detailed description.\r\n",
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