feature/convert-to-npe2 (#49)

* feat: convert to npe2

* add nbytes threshold

* add test

* lint

Author: tlambert03

napari_aicsimageio/__init__.py

@@ -2,8 +2,8 @@
 
 """Top-level package for napari-aicsimageio."""
 
-__author__ = "Jackson Maxfield Brown"
-__email__ = "jacksonb@alleninstitute.org"
+__author__ = "Eva Maxfield Brown"
+__email__ = "evamaxfieldbrown@gmail.com"
 # Do not edit this string manually, always use bumpversion
 # Details in CONTRIBUTING.md
 __version__ = "0.6.1"

napari_aicsimageio/core.py

@@ -1,12 +1,12 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
+from __future__ import annotations
 
 from functools import partial
+from logging import getLogger
 from pathlib import Path
 from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
-import napari
-import xarray as xr
 from aicsimageio import AICSImage, exceptions
 from aicsimageio.dimensions import DimensionNames
 from qtpy.QtWidgets import (
@@ -18,8 +18,11 @@
 )
 
 if TYPE_CHECKING:
+    import xarray as xr
     from napari.types import LayerData, PathLike, ReaderFunction
 
+logger = getLogger(__name__)
+
 ###############################################################################
 
 AICSIMAGEIO_CHOICES = "AICSImageIO Scene Management"
@@ -28,6 +31,9 @@
 
 SCENE_LABEL_DELIMITER = " :: "
 
+# Threshold above which to use out-of-memory loading
+IN_MEM_THRESHOLD_PERCENT = 0.3
+IN_MEM_THRESHOLD_SIZE_BYTES = 4e9  # 4GB
 ###############################################################################
 
 
@@ -44,7 +50,7 @@ def _get_full_image_data(
 
         # Catch reader does not support tile stitching
         except NotImplementedError:
-            print(
+            logger.warning(
                 "AICSImageIO: Mosaic tile stitching "
                 "not yet supported for this file format reader."
             )
@@ -104,6 +110,8 @@ def _get_meta(data: xr.DataArray, img: AICSImage) -> Dict[str, Any]:
 
 
 def _widget_is_checked(widget_name: str) -> bool:
+    import napari
+
     # Get napari viewer from current process
     viewer = napari.current_viewer()
 
@@ -119,6 +127,8 @@ def _widget_is_checked(widget_name: str) -> bool:
 
 # Function to handle multi-scene files.
 def _get_scenes(path: "PathLike", img: AICSImage, in_memory: bool) -> None:
+    import napari
+
     # Get napari viewer from current process
     viewer = napari.current_viewer()
 
@@ -186,47 +196,64 @@ def open_scene(item: QListWidgetItem) -> None:
     list_widget.currentItemChanged.connect(open_scene)  # type: ignore
 
 
-def reader_function(path: "PathLike", in_memory: bool) -> Optional[List["LayerData"]]:
+def reader_function(
+    path: "PathLike", in_memory: Optional[bool] = None
+) -> Optional[List["LayerData"]]:
     """
     Given a single path return a list of LayerData tuples.
     """
-    # Alert console of how we are loading the image
-    print(f"AICSImageIO: Reader will load image in-memory: {in_memory}")
-
     # Only support single path
     if isinstance(path, list):
-        print("AICSImageIO: Multi-file reading not yet supported.")
+        logger.info("AICSImageIO: Multi-file reading not yet supported.")
         return None
 
+    if in_memory is None:
+        from psutil import virtual_memory
+
+        imsize = Path(path).stat().st_size
+        available_mem = virtual_memory().available
+        _in_memory = (
+            imsize <= IN_MEM_THRESHOLD_SIZE_BYTES
+            and imsize / available_mem <= IN_MEM_THRESHOLD_PERCENT
+        )
+    else:
+        _in_memory = in_memory
+
+    # Alert console of how we are loading the image
+    logger.info(f"AICSImageIO: Reader will load image in-memory: {_in_memory}")
+
     # Open file and get data
     img = AICSImage(path)
 
     # Check for multiple scenes
     if len(img.scenes) > 1:
-        print(
+        logger.info(
             f"AICSImageIO: Image contains {len(img.scenes)} scenes. "
             f"Supporting more than the first scene is experimental. "
             f"Select a scene from the list widget. There may be dragons!"
         )
         # Launch the list widget
-        _get_scenes(path=path, img=img, in_memory=in_memory)
+        _get_scenes(path=path, img=img, in_memory=_in_memory)
 
         # Return an empty LayerData list; ImgLayers will be handled via the widget.
         # HT Jonas Windhager
         return [(None,)]
     else:
-        data = _get_full_image_data(img, in_memory=in_memory)
+        data = _get_full_image_data(img, in_memory=_in_memory)
         meta = _get_meta(data, img)
         return [(data.data, meta, "image")]
 
 
-def get_reader(path: "PathLike", in_memory: bool) -> Optional["ReaderFunction"]:
+def get_reader(
+    path: "PathLike", in_memory: Optional[bool] = None
+) -> Optional["ReaderFunction"]:
     """
     Given a single path or list of paths, return the appropriate aicsimageio reader.
     """
     # Only support single path
     if isinstance(path, list):
-        print("AICSImageIO: Multi-file reading not yet supported.")
+        logger.info("AICSImageIO: Multi-file reading not yet supported.")
+        return None
 
     # See if there is a supported reader for the file(s) provided
     try:
@@ -241,13 +268,13 @@ def get_reader(path: "PathLike", in_memory: bool) -> Optional["ReaderFunction"]:
 
     # No supported reader, return None
     except exceptions.UnsupportedFileFormatError:
-        print("AICSImageIO: Unsupported file format.")
+        logger.warning("AICSImageIO: Unsupported file format.")
         return None
 
     except Exception as e:
-        print("AICSImageIO: exception occurred during reading...")
-        print(e)
-        print(
+        logger.warning("AICSImageIO: exception occurred during reading...")
+        logger.warning(e)
+        logger.warning(
             "If this issue looks like a problem with AICSImageIO, "
             "please file a bug report: "
             "https://github.com/AllenCellModeling/napari-aicsimageio"

napari_aicsimageio/in_memory.py

@@ -0,0 +1,44 @@
+name: napari-aicsimageio
+schema_version: 0.1.0
+contributions:
+  commands:
+  - id: napari-aicsimageio.get_reader
+    title: Get AICSImageIO Reader
+    python_name: napari_aicsimageio.core:get_reader
+  readers:
+  - command: napari-aicsimageio.get_reader
+    filename_patterns: [
+      '*.1sc', '*.2fl', '*.3fr', '*.acff', '*.acqp', '*.afi', '*.afm', '*.aim', '*.al3d',
+      '*.ali', '*.am', '*.amiramesh', '*.ano', '*.apl', '*.arf', '*.array-like', '*.arw',
+      '*.avi', '*.bay', '*.bif', '*.bin', '*.bip', '*.bmp', '*.bmq', '*.bsdf', '*.bufr',
+      '*.bw', '*.c01', '*.cap', '*.cat', '*.cfg', '*.ch5', '*.cif', '*.cine', '*.cr2',
+      '*.crw', '*.cs1', '*.csv', '*.ct', '*.ct.img', '*.cur', '*.cut', '*.cxd', '*.czi',
+      '*.dat', '*.db', '*.dc2', '*.dcm', '*.dcr', '*.dcx', '*.dds', '*.df3', '*.dicom',
+      '*.dm2', '*.dm3', '*.dng', '*.drf', '*.dsc', '*.dti', '*.dv', '*.ecw', '*.emf',
+      '*.eps', '*.epsi', '*.erf', '*.exp', '*.exr', '*.fake', '*.fdf', '*.fff', '*.ffr',
+      '*.fid', '*.fit', '*.fits', '*.flc', '*.flex', '*.fli', '*.fpx', '*.frm', '*.ftc',
+      '*.fts', '*.ftu', '*.fz', '*.g3', '*.gbr', '*.gdcm', '*.gel', '*.gif', '*.gipl',
+      '*.grey', '*.grib', '*.h5', '*.hdf', '*.hdf5', '*.hdp', '*.hdr', '*.hed', '*.his',
+      '*.htd', '*.htm', '*.html', '*.hx', '*.i2i', '*.ia', '*.icns', '*.ico', '*.ics',
+      '*.ids', '*.iff', '*.iim', '*.iiq', '*.im', '*.im3', '*.img', '*.imggz', '*.ims',
+      '*.inf', '*.inr', '*.ipl', '*.ipm', '*.ipw', '*.j2c', '*.j2k', '*.jfif', '*.jif',
+      '*.jng', '*.jp2', '*.jpc', '*.jpe', '*.jpeg', '*.jpf', '*.jpg', '*.jpk', '*.jpx',
+      '*.jxr', '*.k25', '*.kc2', '*.kdc', '*.klb', '*.koa', '*.l2d', '*.labels', '*.lbm',
+      '*.lei', '*.lfp', '*.lfr', '*.lif', '*.liff', '*.lim', '*.lms', '*.lsm', '*.mdb',
+      '*.mdc', '*.mef', '*.mgh', '*.mha', '*.mhd', '*.mic', '*.mkv', '*.mnc', '*.mnc2',
+      '*.mng', '*.mod', '*.mos', '*.mov', '*.mp4', '*.mpeg', '*.mpg', '*.mpo', '*.mrc',
+      '*.mri', '*.mrw', '*.msp', '*.msr', '*.mtb', '*.mvd2', '*.naf', '*.nd', '*.nd2',
+      '*.ndpi', '*.ndpis', '*.nef', '*.nhdr', '*.nia', '*.nii', '*.nii.gz', '*.niigz',
+      '*.npz', '*.nrrd', '*.nrw', '*.obf', '*.oib', '*.oif', '*.oir', '*.ome', '*.ome.tif',
+      '*.ome.tiff', '*.orf', '*.par', '*.pbm', '*.pcd', '*.pcoraw', '*.pct', '*.pcx',
+      '*.pef', '*.pfm', '*.pgm', '*.pic', '*.pict', '*.png', '*.pnl', '*.ppm', '*.pr3',
+      '*.ps', '*.psd', '*.ptx', '*.pxn', '*.pxr', '*.qptiff', '*.qtk', '*.r3d', '*.raf',
+      '*.ras', '*.raw', '*.rcpnl', '*.rdc', '*.rec', '*.rgb', '*.rgba', '*.rw2', '*.rwl',
+      '*.rwz', '*.scan', '*.scn', '*.sdt', '*.seq', '*.sif', '*.sld', '*.sm2', '*.sm3',
+      '*.spc', '*.spe', '*.spi', '*.sr2', '*.srf', '*.srw', '*.st', '*.sti', '*.stk',
+      '*.stp', '*.svs', '*.swf', '*.sxm', '*.targa', '*.tfr', '*.tga', '*.thm', '*.tif',
+      '*.tiff', '*.tim', '*.tnb', '*.top', '*.txt', '*.v', '*.vff', '*.vms', '*.vsi',
+      '*.vtk', '*.vws', '*.wap', '*.wat', '*.wav', '*.wbm', '*.wbmp', '*.wdp', '*.webp',
+      '*.wlz', '*.wmf', '*.wmv', '*.wpi', '*.xbm', '*.xdce', '*.xml', '*.xpm', '*.xqd',
+      '*.xqf', '*.xv', '*.xys', '*.zfp', '*.zfr', '*.zip', '*.zpo', '*.zvi'
+    ]

napari_aicsimageio/napari.yaml

@@ -2,16 +2,20 @@
 # -*- coding: utf-8 -*-
 
 from pathlib import Path
-from typing import Any, Callable, Dict, Tuple, Type
+from typing import TYPE_CHECKING, Any, Callable, Dict, Tuple, Type
 
 import dask.array as da
-import napari
+import npe2
 import numpy as np
 import pytest
-from napari.types import ArrayLike
 
 from napari_aicsimageio import core
 
+if TYPE_CHECKING:
+    from napari import Viewer
+    from napari.types import ArrayLike
+    from npe2._pytest_plugin import TestPluginManager
+
 ###############################################################################
 
 PNG_FILE = "example.png"
@@ -85,6 +89,7 @@ def test_reader(
     expected_dtype: type,
     expected_shape: Tuple[int, ...],
     expected_meta: Dict[str, Any],
+    npe2pm: "TestPluginManager",
 ) -> None:
     # Resolve filename to filepath
     if isinstance(filename, str):
@@ -111,6 +116,11 @@ def test_reader(
         meta.pop("metadata", None)
         assert meta == expected_meta  # type: ignore
 
+        # confirm that this also works via npe2
+        with npe2pm.tmp_plugin(package="napari-aicsimageio") as plugin:
+            [via_npe2] = npe2.read([path], stack=False, plugin_name=plugin.name)
+            assert via_npe2[0].shape == data.shape  # type: ignore
+
 
 SINGLESCENE_FILE = "s_1_t_1_c_1_z_1.czi"
 MULTISCENE_FILE = "s_3_t_1_c_3_z_5.czi"
@@ -131,11 +141,11 @@ def test_reader(
     ],
 )
 def test_for_multiscene_widget(
-    make_napari_viewer: Callable[..., napari.Viewer],
+    make_napari_viewer: Callable[..., "Viewer"],
     resources_dir: Path,
     filename: str,
     in_memory: bool,
-    expected_dtype: Type[ArrayLike],
+    expected_dtype: Type["ArrayLike"],
     expected_shape: Tuple[int, ...],
 ) -> None:
     # Make a viewer

napari_aicsimageio/out_of_memory.py

@@ -25,6 +25,7 @@ xfail_strict = true
 filterwarnings = 
 	ignore::UserWarning
 	ignore::FutureWarning
+	ignore:distutils Version classes are deprecated:
 
 [flake8]
 exclude = 

napari_aicsimageio/tests/test_core.py

@@ -46,7 +46,7 @@
     "aicsimageio[all]>=4.6.3",
     "fsspec[http]",  # no version pin, we pull from aicsimageio
     "napari>=0.4.11",
-    "napari_plugin_engine>=0.1.4",
+    "psutil>=5.7.0",
     # Formats not included by default with aicsimageio
     "aicspylibczi>=3.0.5",
     "bioformats_jar",
@@ -60,8 +60,8 @@
 }
 
 setup(
-    author="Jackson Maxfield Brown",
-    author_email="jmaxfieldbrown@gmail.com",
+    author="Eva Maxfield Brown",
+    author_email="evamaxfieldbrown@gmail.com",
     classifiers=[
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Science/Research",
@@ -81,19 +81,19 @@
         "Multiple file format reading directly into napari using pure Python."
     ),
     entry_points={
-        "napari.plugin": [
-            "aicsimageio-out-of-memory = napari_aicsimageio.out_of_memory",
-            "aicsimageio-in-memory = napari_aicsimageio.in_memory",
+        "napari.manifest": [
+            "napari-aicsimageio = napari_aicsimageio:napari.yaml",
         ],
     },
     install_requires=requirements,
-    license="BSD-3-Clause",
+    license="GPLv3",
     long_description=readme,
     long_description_content_type="text/markdown",
     include_package_data=True,
     keywords="napari, aicsimageio, TIFF, CZI, LIF, imageio, image reading, metadata",
     name="napari-aicsimageio",
     packages=find_packages(exclude=["tests", "*.tests", "*.tests.*"]),
+    package_data={"napari_aicsimageio": ["napari.yaml"]},
     python_requires=">=3.8",
     setup_requires=setup_requirements,
     test_suite="napari_aicsimageio/tests",