napari-mlarray 0.0.1__py3-none-any.whl

napari_mlarray/__init__.py

@@ -0,0 +1,13 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+
+
+from ._reader import napari_get_reader
+from ._writer import write_single_image
+
+__all__ = (
+    "napari_get_reader",
+    "write_single_image",
+)

napari_mlarray/_reader.py

@@ -0,0 +1,77 @@
+"""
+This module is an example of a barebones numpy reader plugin for napari.
+
+It implements the Reader specification, but your plugin may choose to
+implement multiple readers or even other plugin contributions. see:
+https://napari.org/stable/plugins/building_a_plugin/guides.html#readers
+"""
+from mlarray import MLArray
+
+
+def napari_get_reader(path):
+    """A basic implementation of a Reader contribution.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    function or None
+        If the path is a recognized format, return a function that accepts the
+        same path or list of paths, and returns a list of layer data tuples.
+    """
+    if isinstance(path, list):
+        # reader plugins may be handed single path, or a list of paths.
+        # if it is a list, it is assumed to be an image stack...
+        # so we are only going to look at the first file.
+        path = path[0]
+
+    # the get_reader function should make as many checks as possible
+    # (without loading the full file) to determine if it can read
+    # the path. Here, we check the dtype of the array by loading
+    # it with memmap, so that we don't actually load the full array into memory.
+    # We pretend that this reader can only read integer arrays.
+    try:
+        if not str(path).endswith(".mla"):
+            return None
+    # napari_get_reader should never raise an exception, because napari
+    # raises its own specific errors depending on what plugins are
+    # available for the given path, so we catch
+    # the OSError that np.load might raise if the file is malformed
+    except OSError:
+        return None
+
+    # otherwise we return the *function* that can read ``path``.
+    return reader_function
+
+
+def reader_function(path):
+    """Take a path or list of paths and return a list of LayerData tuples.
+
+    Readers are expected to return data as a list of tuples, where each tuple
+    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
+    both optional.
+
+    Parameters
+    ----------
+    path : str or list of str
+        Path to file, or list of paths.
+
+    Returns
+    -------
+    layer_data : list of tuples
+        A list of LayerData tuples where each tuple in the list contains
+        (data, metadata, layer_type), where data is a numpy array, metadata is
+        a dict of keyword arguments for the corresponding viewer.add_* method
+        in napari, and layer_type is a lower-case string naming the type of
+        layer. Both "meta", and "layer_type" are optional. napari will
+        default to layer_type=="image" if not provided
+    """
+    # handle both a string and a list of strings
+    paths = [path] if isinstance(path, str) else path
+    # load all files into array
+    mlarrays = [MLArray.open(_path) for _path in paths]
+    layer_data = [(mlarray, {"affine": mlarray.affine, "metadata": mlarray.meta.to_dict()}, "labels" if mlarray.meta.is_seg.is_seg == True else "image") for mlarray in mlarrays]
+    return layer_data

napari_mlarray/_version.py

@@ -0,0 +1,34 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
+else:
+    VERSION_TUPLE = object
+    COMMIT_ID = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '0.0.1'
+__version_tuple__ = version_tuple = (0, 0, 1)
+
+__commit_id__ = commit_id = None

napari_mlarray/_widget.py

@@ -0,0 +1,128 @@
+"""
+This module contains four napari widgets declared in
+different ways:
+
+- a pure Python function flagged with `autogenerate: true`
+    in the plugin manifest. Type annotations are used by
+    magicgui to generate widgets for each parameter. Best
+    suited for simple processing tasks - usually taking
+    in and/or returning a layer.
+- a `magic_factory` decorated function. The `magic_factory`
+    decorator allows us to customize aspects of the resulting
+    GUI, including the widgets associated with each parameter.
+    Best used when you have a very simple processing task,
+    but want some control over the autogenerated widgets. If you
+    find yourself needing to define lots of nested functions to achieve
+    your functionality, maybe look at the `Container` widget!
+- a `magicgui.widgets.Container` subclass. This provides lots
+    of flexibility and customization options while still supporting
+    `magicgui` widgets and convenience methods for creating widgets
+    from type annotations. If you want to customize your widgets and
+    connect callbacks, this is the best widget option for you.
+- a `QWidget` subclass. This provides maximal flexibility but requires
+    full specification of widget layouts, callbacks, events, etc.
+
+References:
+- Widget specification: https://napari.org/stable/plugins/building_a_plugin/guides.html#widgets
+- magicgui docs: https://pyapp-kit.github.io/magicgui/
+
+Replace code below according to your needs.
+"""
+from typing import TYPE_CHECKING
+
+from magicgui import magic_factory
+from magicgui.widgets import CheckBox, Container, create_widget
+from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget
+from skimage.util import img_as_float
+
+if TYPE_CHECKING:
+    import napari
+
+
+# Uses the `autogenerate: true` flag in the plugin manifest
+# to indicate it should be wrapped as a magicgui to autogenerate
+# a widget.
+def threshold_autogenerate_widget(
+    img: "napari.types.ImageData",
+    threshold: "float",
+) -> "napari.types.LabelsData":
+    return img_as_float(img) > threshold
+
+
+# the magic_factory decorator lets us customize aspects of our widget
+# we specify a widget type for the threshold parameter
+# and use auto_call=True so the function is called whenever
+# the value of a parameter changes
+@magic_factory(
+    threshold={"widget_type": "FloatSlider", "max": 1}, auto_call=True
+)
+def threshold_magic_widget(
+    img_layer: "napari.layers.Image", threshold: "float"
+) -> "napari.types.LabelsData":
+    return img_as_float(img_layer.data) > threshold
+
+
+# if we want even more control over our widget, we can use
+# magicgui `Container`
+class ImageThreshold(Container):
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        super().__init__()
+        self._viewer = viewer
+        # use create_widget to generate widgets from type annotations
+        self._image_layer_combo = create_widget(
+            label="Image", annotation="napari.layers.Image"
+        )
+        self._threshold_slider = create_widget(
+            label="Threshold", annotation=float, widget_type="FloatSlider"
+        )
+        self._threshold_slider.min = 0
+        self._threshold_slider.max = 1
+        # use magicgui widgets directly
+        self._invert_checkbox = CheckBox(text="Keep pixels below threshold")
+
+        # connect your own callbacks
+        self._threshold_slider.changed.connect(self._threshold_im)
+        self._invert_checkbox.changed.connect(self._threshold_im)
+
+        # append into/extend the container with your widgets
+        self.extend(
+            [
+                self._image_layer_combo,
+                self._threshold_slider,
+                self._invert_checkbox,
+            ]
+        )
+
+    def _threshold_im(self):
+        image_layer = self._image_layer_combo.value
+        if image_layer is None:
+            return
+
+        image = img_as_float(image_layer.data)
+        name = image_layer.name + "_thresholded"
+        threshold = self._threshold_slider.value
+        if self._invert_checkbox.value:
+            thresholded = image < threshold
+        else:
+            thresholded = image > threshold
+        if name in self._viewer.layers:
+            self._viewer.layers[name].data = thresholded
+        else:
+            self._viewer.add_labels(thresholded, name=name)
+
+
+class ExampleQWidget(QWidget):
+    # your QWidget.__init__ can optionally request the napari viewer instance
+    # use a type annotation of 'napari.viewer.Viewer' for any parameter
+    def __init__(self, viewer: "napari.viewer.Viewer"):
+        super().__init__()
+        self.viewer = viewer
+
+        btn = QPushButton("Click me!")
+        btn.clicked.connect(self._on_click)
+
+        self.setLayout(QHBoxLayout())
+        self.layout().addWidget(btn)
+
+    def _on_click(self):
+        print("napari has", len(self.viewer.layers), "layers")

napari_mlarray/_writer.py

@@ -0,0 +1,41 @@
+"""
+This module is an example of a barebones writer plugin for napari.
+
+It implements the Writer specification.
+see: https://napari.org/stable/plugins/building_a_plugin/guides.html#writers
+
+Replace code below according to your needs.
+"""
+from __future__ import annotations
+
+from collections.abc import Sequence
+from typing import TYPE_CHECKING, Any, Union
+from mlarray import MLArray, Meta
+
+if TYPE_CHECKING:
+    DataType = Union[Any, Sequence[Any]]
+    FullLayerData = tuple[DataType, dict, str]
+
+
+def write_single_image(path: str, data: Any, meta: dict) -> list[str]:
+    """Writes a single image layer.
+
+    Parameters
+    ----------
+    path : str
+        A string path indicating where to save the image file.
+    data : The layer data
+        The `.data` attribute from the napari layer.
+    meta : dict
+        A dictionary containing all other attributes from the napari layer
+        (excluding the `.data` layer attribute).
+
+    Returns
+    -------
+    [path] : A list containing the string path to the saved file.
+    """
+    mlarray = MLArray(data, meta=Meta.from_dict(meta["metadata"]))
+    mlarray.save(path)
+
+    # return path to any file(s) that were successfully written
+    return [path]

napari_mlarray/napari.yaml

@@ -0,0 +1,22 @@
+name: napari-mlarray
+display_name: Mlarray
+# use 'hidden' to remove plugin from napari hub search results
+visibility: public
+# see https://napari.org/stable/plugins/technical_references/manifest.html#fields for valid categories
+# categories: []
+contributions:
+  commands:
+    - id: napari-mlarray.get_reader
+      python_name: napari_mlarray._reader:napari_get_reader
+      title: Open data with Mlarray
+    - id: napari-mlarray.write_single_image
+      python_name: napari_mlarray._writer:write_single_image
+      title: Save image data with Mlarray
+  readers:
+    - command: napari-mlarray.get_reader
+      accepts_directories: false
+      filename_patterns: ['*.mla']
+  writers:
+    - command: napari-mlarray.write_single_image
+      layer_types: ['image']
+      filename_extensions: ['.mla']

napari_mlarray-0.0.1.dist-info/METADATA

@@ -0,0 +1,119 @@
+Metadata-Version: 2.4
+Name: napari-mlarray
+Version: 0.0.1
+Summary: A reader/writer Napari plugin for MLArray images.
+Author: Karol-G
+Author-email: karol.gotkowski@dkfz.de
+License: 
+        The MIT License (MIT)
+        
+        Copyright (c) 2026 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in
+        all copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+        THE SOFTWARE.
+        
+Classifier: Development Status :: 2 - Pre-Alpha
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: mlarray
+Provides-Extra: all
+Requires-Dist: napari[all]; extra == "all"
+Dynamic: license-file
+
+# napari-mlarray
+
+[![License MIT](https://img.shields.io/pypi/l/napari-mlarray.svg?color=green)](https://github.com/MIC-DKFZ/napari-mlarray/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-mlarray.svg?color=green)](https://pypi.org/project/napari-mlarray)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-mlarray.svg?color=green)](https://python.org)
+[![tests](https://github.com/MIC-DKFZ/napari-mlarray/workflows/tests/badge.svg)](https://github.com/MIC-DKFZ/napari-mlarray/actions)
+[![codecov](https://codecov.io/gh/MIC-DKFZ/napari-mlarray/branch/main/graph/badge.svg)](https://codecov.io/gh/MIC-DKFZ/napari-mlarray)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-mlarray)](https://napari-hub.org/plugins/napari-mlarray)
+[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
+[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)
+
+A reader/writer Napari plugin for [MLArray](https://github.com/MIC-DKFZ/mlarray) images. MLArray is an array format specialized for Machine Learning with Blosc2 backend and standardized metadata. 
+
+## Installation
+
+You can install `napari-mlarray` via [pip]:
+
+```
+pip install napari-mlarray
+```
+
+If napari is not already installed, you can install `napari-mlarray` with napari and Qt via:
+
+```
+pip install "napari-mlarray[all]"
+```
+
+
+
+## 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 [MIT] license,
+"napari-mlarray" is free and open source software
+
+## Issues
+
+If you encounter any problems, please [file an issue] along with a detailed description.
+
+[napari]: https://github.com/napari/napari
+[copier]: https://copier.readthedocs.io/en/stable/
+[@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
+[napari-plugin-template]: https://github.com/napari/napari-plugin-template
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/
+
+## Acknowledgments
+
+<p align="left">
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/HI_Logo.png" width="150"> &nbsp;&nbsp;&nbsp;&nbsp;
+  <img src="https://github.com/MIC-DKFZ/vidata/raw/main/imgs/Logos/DKFZ_Logo.png" width="500">
+</p>
+
+This repository is developed and maintained by the Applied Computer Vision Lab (ACVL)
+of [Helmholtz Imaging](https://www.helmholtz-imaging.de/) and the
+[Division of Medical Image Computing](https://www.dkfz.de/en/medical-image-computing) at DKFZ.

napari_mlarray-0.0.1.dist-info/RECORD

@@ -0,0 +1,12 @@
+napari_mlarray/__init__.py,sha256=c2b0_m5sORovlHyyozJS1l00lXjFM7ULIkrHqojq5N4,249
+napari_mlarray/_reader.py,sha256=TT6-L8t7wlYRA5laoVH-frf-ogBxXlEQWE7y70IUHHs,3045
+napari_mlarray/_version.py,sha256=qf6R-J7-UyuABBo8c0HgaquJ8bejVbf07HodXgwAwgQ,704
+napari_mlarray/_widget.py,sha256=K6MYwgFiQg7-dORp-kC_VivrfppiUwMmevbPMhwMT9c,4810
+napari_mlarray/_writer.py,sha256=tAFCX1-LnmDqeDFpO2H22Xrju58-3D-d0ZrEvdAXMbE,1206
+napari_mlarray/napari.yaml,sha256=HILzIxDmFpRPgCmM7uVzzZ86Ayp2ecWiSXHTCC1qjx4,796
+napari_mlarray-0.0.1.dist-info/licenses/LICENSE,sha256=LKlNG6Bx5z0YnzAp9GjCxCR0aypSPO_JcUHmuVGtwds,1162
+napari_mlarray-0.0.1.dist-info/METADATA,sha256=tHD_AJuOHEEWg3OU6FepCJSMQDbVPHtCGoVa1y6ZBHg,5541
+napari_mlarray-0.0.1.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+napari_mlarray-0.0.1.dist-info/entry_points.txt,sha256=ibu_ymiLzJPNpL0x0Fdendi5fQiq_baxx224E5pAW0c,62
+napari_mlarray-0.0.1.dist-info/top_level.txt,sha256=ZfJPiLTSmZ9eakEU1J6znzWi6dS_OTGAXQSI08HOgQg,15
+napari_mlarray-0.0.1.dist-info/RECORD,,

napari_mlarray-0.0.1.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.10.2)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

napari_mlarray-0.0.1.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[napari.manifest]
+napari-mlarray = napari_mlarray:napari.yaml

napari_mlarray-0.0.1.dist-info/licenses/LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2026 Division of Medical Image Computing, German Cancer Research Center (DKFZ), Heidelberg, Germany
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

napari_mlarray-0.0.1.dist-info/top_level.txt

@@ -0,0 +1 @@
+napari_mlarray