napari-memmap-tiff 1.0.0__py3-none-any.whl

napari_memmap_tiff/__init__.py

@@ -0,0 +1,7 @@
+try:
+    from ._version import version as __version__
+except ImportError:
+    __version__ = "unknown"
+from ._widget import memmap_config_widget
+
+__all__ = ("memmap_config_widget",)

napari_memmap_tiff/_tests/test_widget.py

@@ -0,0 +1,12 @@
+from napari_memmap_tiff._widget import memmap_config_widget
+
+
+def test_memmap_config_widget():
+    from imageio.config.plugins import known_plugins
+
+    widget = memmap_config_widget()
+
+    widget(True)
+    assert "tifffile_memmap" in known_plugins
+    widget(False)
+    assert "tifffile_memmap" not in known_plugins

napari_memmap_tiff/_version.py

@@ -0,0 +1,21 @@
+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '1.0.0'
+__version_tuple__ = version_tuple = (1, 0, 0)

napari_memmap_tiff/_widget.py

@@ -0,0 +1,56 @@
+from typing import TYPE_CHECKING
+
+import numpy as np
+from imageio.config.extensions import extension_list
+from imageio.config.plugins import PluginConfig, known_plugins
+from imageio.plugins.tifffile_v3 import TifffilePlugin
+from magicgui import magic_factory
+
+if TYPE_CHECKING:
+    pass
+
+
+class MemmapTifffilePlugin(TifffilePlugin):
+
+    def read(self, *args, **kwargs) -> np.ndarray:
+        return super().read(*args, **kwargs, out="memmap")
+
+
+@magic_factory(auto_call=True, persist=False)
+def memmap_config_widget(
+    enable_memory_map: bool,
+) -> None:
+    """
+    Sets whether to use memory mapping.
+
+    :param enable_memory_map: If enabled, tiff or tif files will be loaded as
+        memory mapped data directly from disk, instead of loading it fully into
+        memory at once.
+    """
+    if enable_memory_map:
+        if "tifffile_memmap" in known_plugins:
+            return
+
+        known_plugins["tifffile_memmap"] = PluginConfig(
+            name="tifffile_memmap",
+            class_name="MemmapTifffilePlugin",
+            module_name="napari_memmap_tiff._widget",
+            is_legacy=False,
+        )
+        for ext in extension_list:
+            if (
+                ext.extension in (".tif", ".tiff")
+                and "tifffile_memmap" not in ext.priority
+            ):
+                ext.priority.insert(0, "tifffile_memmap")
+    else:
+        if "tifffile_memmap" not in known_plugins:
+            return
+
+        del known_plugins["tifffile_memmap"]
+        for ext in extension_list:
+            if (
+                ext.extension in (".tif", ".tiff")
+                and "tifffile_memmap" in ext.priority
+            ):
+                ext.priority.remove("tifffile_memmap")

napari_memmap_tiff/napari.yaml

@@ -0,0 +1,14 @@
+name: napari-memmap-tiff
+display_name: Loading tiffs using memory map
+# 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: ["Annotation", "Segmentation", "Acquisition"]
+contributions:
+  commands:
+    - id: napari-memmap-tiff.make_function_widget
+      python_name: napari_memmap_tiff:memmap_config_widget
+      title: Make memmap config widget
+  widgets:
+    - command: napari-memmap-tiff.make_function_widget
+      display_name: Enable / disable memory mapping tiffs

napari_memmap_tiff-1.0.0.dist-info/METADATA

@@ -0,0 +1,138 @@
+Metadata-Version: 2.4
+Name: napari-memmap-tiff
+Version: 1.0.0
+Summary: When installed and enabled in the options, it adds an option that when enabled will make napari load tiffs via memory mapping instead of fully into RAM.
+Author: Matthew Einhorn
+Author-email: matt@einhorn.dev
+License: 
+        The MIT License (MIT)
+        
+        Copyright (c) 2025 Matthew Einhorn
+        
+        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.
+        
+Project-URL: Bug Tracker, https://github.com/matham/napari-memmap-tiff/issues
+Project-URL: Documentation, https://github.com/matham/napari-memmap-tiff#README.md
+Project-URL: Source Code, https://github.com/matham/napari-memmap-tiff
+Project-URL: User Support, https://github.com/matham/napari-memmap-tiff/issues
+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: numpy
+Requires-Dist: magicgui
+Requires-Dist: qtpy
+Requires-Dist: scikit-image
+Requires-Dist: tifffile
+Provides-Extra: testing
+Requires-Dist: tox; extra == "testing"
+Requires-Dist: pytest; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+Requires-Dist: pytest-qt; extra == "testing"
+Requires-Dist: napari; extra == "testing"
+Requires-Dist: pyqt5; extra == "testing"
+Dynamic: license-file
+
+# napari-memmap-tiff
+
+[![License MIT](https://img.shields.io/pypi/l/napari-memmap-tiff.svg?color=green)](https://github.com/matham/napari-memmap-tiff/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/napari-memmap-tiff.svg?color=green)](https://pypi.org/project/napari-memmap-tiff)
+[![Python Version](https://img.shields.io/pypi/pyversions/napari-memmap-tiff.svg?color=green)](https://python.org)
+[![tests](https://github.com/matham/napari-memmap-tiff/workflows/tests/badge.svg)](https://github.com/matham/napari-memmap-tiff/actions)
+[![codecov](https://codecov.io/gh/matham/napari-memmap-tiff/branch/main/graph/badge.svg)](https://codecov.io/gh/matham/napari-memmap-tiff)
+[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-memmap-tiff)](https://napari-hub.org/plugins/napari-memmap-tiff)
+[![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)
+
+When installed and enabled in the options, it adds an option that when enabled
+will make napari load tiffs via memory mapping instead of fully into RAM.
+
+That is, `.tif` and `.tiff` files will be loaded into memory using memory
+mapping, which loads the data directly from disk instead of loading the file
+at once into RAM. This is beneficial for large files that may not fit into
+available RAM.
+
+----------------------------------
+
+This [napari] plugin was generated with [copier] using the [napari-plugin-template].
+
+<!--
+Don't miss the full getting started guide to set up your new package:
+https://github.com/napari/napari-plugin-template#getting-started
+
+and review the napari docs for plugin developers:
+https://napari.org/stable/plugins/index.html
+-->
+
+## Installation
+
+You can install `napari-memmap-tiff` via [pip]:
+
+    pip install napari-memmap-tiff
+
+
+
+To install latest development version :
+
+    pip install git+https://github.com/matham/napari-memmap-tiff.git
+
+
+## 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-memmap-tiff" 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
+
+[file an issue]: https://github.com/matham/napari-memmap-tiff/issues
+
+[napari]: https://github.com/napari/napari
+[tox]: https://tox.readthedocs.io/en/latest/
+[pip]: https://pypi.org/project/pip/
+[PyPI]: https://pypi.org/

napari_memmap_tiff-1.0.0.dist-info/RECORD

@@ -0,0 +1,12 @@
+napari_memmap_tiff/__init__.py,sha256=QjsJIUwEYceKGbOvURi2pHFOa2XFhBXiHyzzPsgnM4I,181
+napari_memmap_tiff/_version.py,sha256=fo5PXsZuloQZu3LdpIFTUAXvJmY2L9N5sNGe2tvdU98,511
+napari_memmap_tiff/_widget.py,sha256=hEotDzhU3CmwV-gdB9SpZ1824b7v2rtyW4rgWWUORDA,1710
+napari_memmap_tiff/napari.yaml,sha256=WW43IHcG3Hi_8LEgUVopoUrsQsXd-ZteKOcWj3fKYn8,612
+napari_memmap_tiff/_tests/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+napari_memmap_tiff/_tests/test_widget.py,sha256=rltLZlP8bLvyRK4WVpX4I8fAjSRTQzBpgcXxTviz8A0,317
+napari_memmap_tiff-1.0.0.dist-info/licenses/LICENSE,sha256=AKMeoFqPgD4lKUkLDHO1Hj5-Noqm2LFV8_qK6VlposU,1083
+napari_memmap_tiff-1.0.0.dist-info/METADATA,sha256=WEeWqtbFQKaRFOI-qSwtSSNoW7HSGEfpieGmRcjer-E,6339
+napari_memmap_tiff-1.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+napari_memmap_tiff-1.0.0.dist-info/entry_points.txt,sha256=F2ggm_mIQqjB0RzmAKAAWYA6Ut2NKT25xlUz0i5nvLo,70
+napari_memmap_tiff-1.0.0.dist-info/top_level.txt,sha256=xgp7Jn5_5Cyj_qhu67lx2Wz176Gp4aecnmVF95jB_K4,19
+napari_memmap_tiff-1.0.0.dist-info/RECORD,,

napari_memmap_tiff-1.0.0.dist-info/WHEEL

@@ -0,0 +1,5 @@
+Wheel-Version: 1.0
+Generator: setuptools (80.9.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

napari_memmap_tiff-1.0.0.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[napari.manifest]
+napari-memmap-tiff = napari_memmap_tiff:napari.yaml

napari_memmap_tiff-1.0.0.dist-info/licenses/LICENSE

@@ -0,0 +1,22 @@
+
+The MIT License (MIT)
+
+Copyright (c) 2025 Matthew Einhorn
+
+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_memmap_tiff-1.0.0.dist-info/top_level.txt

@@ -0,0 +1 @@
+napari_memmap_tiff