WIP: Centralize ImageJ2 gateway into nij object

This provides a place to keep track of not only the ImageJ2 gateway, but
also any affiliated data structures, such as our singleton ScriptREPL.

.github/workflows/build.yml

@@ -9,9 +9,6 @@ on:
  - main
  tags:
  - "*-[0-9]+.*"
- pull_request:
- branches:
- - main
 
 env:
  NAPARI_IMAGEJ_TEST_TIMEOUT: 60000

src/napari_imagej/__init__.py

@@ -20,5 +20,9 @@
 
 import scyjava as sj
 
+from napari_imagej.model import NapariImageJ
+
 __author__ = "ImageJ2 developers"
 __version__ = sj.get_version("napari-imagej")
+
+nij = NapariImageJ()

src/napari_imagej/java.py

@@ -4,8 +4,6 @@
 Notable functions included in the module:
  * init_ij()
  - used to create the ImageJ instance.
- * ij()
- - used to access the ImageJ instance.
 
 Notable fields included in the module:
  * jc
@@ -33,57 +31,40 @@
  "sc.fiji:TrackMate": "7.11.0",
 }
 
-# -- ImageJ API -- #
-
-_ij = None
-
-def ij():
- if _ij is None:
- raise Exception(
- "The ImageJ instance has not yet been initialized! Please run init_ij()"
- )
- return _ij
-
 # -- Public functions -- #
 
+
 def init_ij() -> "jc.ImageJ":
  """
  Create an ImageJ2 gateway.
  """
- global _ij
- if _ij:
- return _ij
  log_debug("Initializing ImageJ2")
 
- # determine whether imagej is already running
- imagej_already_initialized: bool = hasattr(imagej, "gateway") and imagej.gateway
-
  # -- CONFIGURATION -- #
 
- # Configure napari-imagej
  from napari_imagej.types.converters import install_converters
-
  install_converters()
-
  log_debug("Completed JVM Configuration")
 
  # -- INITIALIZATION -- #
 
  # Launch ImageJ
- if imagej_already_initialized:
- _ij = imagej.gateway
- else:
- _ij = imagej.init(**_configure_imagej())
+ ij = (
+ imagej.gateway
+ if hasattr(imagej, "gateway") and imagej.gateway
+ else imagej.init(**_configure_imagej())
+ )
 
  # Log initialization
- log_debug(f"Initialized at version {_ij.getVersion()}")
+ log_debug(f"Initialized at version {ij.getVersion()}")
 
  # -- VALIDATION -- #
 
  # Validate PyImageJ
- _validate_imagej()
+ _validate_imagej(ij)
+
+ return ij
 
- return _ij
 
 # -- Private functions -- #
 
@@ -112,7 +93,7 @@ def _configure_imagej() -> Dict[str, Any]:
  return init_settings
 
 
-def _validate_imagej():
+def _validate_imagej(ij: "jc.ImageJ"):
  """
  Ensure minimum requirements on java component versions are met.
  """
@@ -131,7 +112,7 @@ def _validate_imagej():
  "org.scijava:scijava-common": jc.Module,
  "org.scijava:scijava-search": jc.Searcher,
  }
- component_requirements.update(_optional_requirements())
+ component_requirements.update(_optional_requirements(ij))
  # Find version that violate the minimum
  violations = []
  for component, cls in component_requirements.items():
@@ -153,11 +134,11 @@ def _validate_imagej():
  raise RuntimeError(failure_str)
 
 
-def _optional_requirements():
+def _optional_requirements(ij: "jc.ImageJ"):
  optionals = {}
  # Add additional minimum versions for legacy components
- if _ij.legacy and _ij.legacy.isActive():
- optionals["net.imagej:imagej-legacy"] = _ij.legacy.getClass()
+ if ij.legacy and ij.legacy.isActive():
+ optionals["net.imagej:imagej-legacy"] = ij.legacy.getClass()
  # Add additional minimum versions for fiji components
  try:
  optionals["sc.fiji:TrackMate"] = jimport("fiji.plugin.trackmate.TrackMate")
@@ -267,10 +248,6 @@ def BigDecimal(self):
  def BigInteger(self):
  return "java.math.BigInteger"
 
- @JavaClasses.java_import
- def ByteArrayOutputStream(self):
- "java.io.ByteArrayOutputStream"
-
  @JavaClasses.java_import
  def Date(self):
  return "java.util.Date"

src/napari_imagej/model.py

@@ -0,0 +1,40 @@
+from jpype import JImplements, JOverride
+
+from napari_imagej.java import init_ij, jc
+
+
+class NapariImageJ:
+ """
+ An object offering a central access point to napari-imagej's core business logic.
+ """
+ def __init__(self):
+ self._ij = None
+ self._repl = None
+ self._repl_callbacks = []
+
+ @property
+ def ij(self):
+ if self._ij is None:
+ self._ij = init_ij()
+ return self._ij
+
+ @property
+ def repl(self) -> "jc.ScriptREPL":
+ if self._repl is None:
+ ctx = self.ij.context()
+ model = self
+
+ @JImplements("java.util.consumer.Consumer")
+ class REPLOutput:
+ @JOverride
+ def accept(self, t):
+ s = str(t)
+ for callback in model._repl_callbacks:
+ callback(s)
+
+ self._repl = jc.ScriptREPL(ctx, "jython", REPLOutput())
+ self._repl.lang("jython")
+ return self._repl
+
+ def add_repl_callback(self, repl_callback) -> None:
+ self._repl_callbacks.append(repl_callback)

src/napari_imagej/readers/trackMate_reader.py

@@ -6,7 +6,8 @@
 from napari.utils import progress
 from scyjava import jimport
 
-from napari_imagej.java import ij, init_ij, jc
+from napari_imagej import nij
+from napari_imagej.java import jc
 from napari_imagej.types.converters.trackmate import (
  model_and_image_to_tracks,
  trackmate_present,
@@ -39,7 +40,7 @@ def napari_get_reader(path):
 
 def reader_function(path):
  pbr = progress(total=4, desc="Importing TrackMate XML: Starting JVM")
- init_ij()
+ ij = nij.ij
  TmXMLReader = jimport("fiji.plugin.trackmate.io.TmXmlReader")
  pbr.update()
 
@@ -50,7 +51,7 @@ def reader_function(path):
  pbr.update()
 
  pbr.set_description("Importing TrackMate XML: Converting Image")
- py_imp = ij().py.from_java(imp)
+ py_imp = ij.py.from_java(imp)
  pbr.update()
 
  pbr.set_description("Importing TrackMate XML: Converting Tracks and ROIs")

src/napari_imagej/types/converters/images.py

@@ -13,13 +13,14 @@
 from scyjava import Priority
 from xarray import DataArray
 
-from napari_imagej.java import ij, jc
+from napari_imagej import nij
+from napari_imagej.java import jc
 from napari_imagej.types.converters import java_to_py_converter, py_to_java_converter
 from napari_imagej.utilities.logging import log_debug
 
 
 @java_to_py_converter(
- predicate=lambda obj: ij().convert().supports(obj, jc.DatasetView),
+ predicate=lambda obj: nij.ij.convert().supports(obj, jc.DatasetView),
  priority=Priority.VERY_HIGH + 1,
 )
 def _java_image_to_image_layer(image: Any) -> Image:
@@ -33,9 +34,9 @@ def _java_image_to_image_layer(image: Any) -> Image:
  :return: a napari Image layer
  """
  # Construct a DatasetView from the Java image
- view = ij().convert().convert(image, jc.DatasetView)
+ view = nij.ij.convert().convert(image, jc.DatasetView)
  # Construct an xarray from the DatasetView
- xarr: DataArray = java_to_xarray(ij(), view.getData())
+ xarr: DataArray = java_to_xarray(nij.ij, view.getData())
  # Construct a map of Image layer parameters
  kwargs = dict(
  data=xarr,
@@ -59,7 +60,7 @@ def _image_layer_to_dataset(image: Image, **kwargs) -> "jc.Dataset":
  :return: a Dataset
  """
  # Construct a dataset from the data
- dataset: "jc.Dataset" = ij().py.to_dataset(image.data, **kwargs)
+ dataset: "jc.Dataset" = nij.ij.py.to_dataset(image.data, **kwargs)
 
  # Clean up the axes
  axes = [
@@ -94,7 +95,7 @@ def _image_layer_to_dataset(image: Image, **kwargs) -> "jc.Dataset":
  properties = dataset.getProperties()
  for k, v in image.metadata.items():
  try:
- properties.put(ij().py.to_java(k), ij().py.to_java(v))
+ properties.put(nij.ij.py.to_java(k), nij.ij.py.to_java(v))
  except Exception:
  log_debug(f"Could not add property ({k}, {v}) to dataset {dataset}:")
  return dataset

src/napari_imagej/types/converters/labels.py

@@ -7,7 +7,8 @@
 from napari.layers import Labels
 from scyjava import Priority
 
-from napari_imagej.java import ij, jc
+from napari_imagej import nij
+from napari_imagej.java import jc
 from napari_imagej.types.converters import java_to_py_converter, py_to_java_converter
 
 
@@ -41,7 +42,7 @@ def _imglabeling_to_layer(imgLabeling: "jc.ImgLabeling") -> Labels:
  :param imgLabeling: the Java ImgLabeling
  :return: a Labels layer
  """
- labeling: Labeling = imglabeling_to_labeling(ij(), imgLabeling)
+ labeling: Labeling = imglabeling_to_labeling(nij.ij, imgLabeling)
  return _labeling_to_layer(labeling)
 
 
@@ -55,4 +56,4 @@ def _layer_to_imglabeling(layer: Labels) -> "jc.ImgLabeling":
  :return: the Java ImgLabeling
  """
  labeling: Labeling = _layer_to_labeling(layer)
- return ij().py.to_java(labeling)
+ return nij.ij.py.to_java(labeling)

src/napari_imagej/types/converters/trackmate.py

@@ -6,8 +6,7 @@
 from napari.layers import Labels, Tracks
 from scyjava import JavaClasses, Priority
 
-from napari_imagej import settings
-from napari_imagej.java import ij
+from napari_imagej import nij, settings
 from napari_imagej.types.converters import java_to_py_converter
 
 
@@ -36,7 +35,7 @@ def track_overlay_predicate(obj):
  if not trackmate_present():
  return False
  # TrackMate data is wrapped in ImageJ Rois - we need ImageJ Legacy
- if not (ij().legacy and ij().legacy.isActive()):
+ if not (nij.ij.legacy and nij.ij.legacy.isActive()):
  return False
  # TrackMate data will be wrapped within a ROITree
  if not isinstance(obj, jc.ROITree):
@@ -106,7 +105,7 @@ def model_and_image_to_tracks(model: "jc.Model", imp: "jc.ImagePlus"):
  java_label_img = jc.LabelImgExporter.createLabelImagePlus(
  model, imp, False, False, False
  )
- py_label_img = ij().py.from_java(java_label_img)
+ py_label_img = nij.ij.py.from_java(java_label_img)
  labels = Labels(data=py_label_img.data, name=rois_name)
 
  return (tracks, labels)
@@ -119,7 +118,7 @@ def _trackMate_model_to_tracks(obj: "jc.ROITree"):
  """
  Converts a TrackMate overlay into a napari Tracks layer
  """
- trackmate_plugins = ij().object().getObjects(jc.TrackMate)
+ trackmate_plugins = nij.ij.object().getObjects(jc.TrackMate)
  if len(trackmate_plugins) == 0:
  raise IndexError("Expected a TrackMate instance, but there was none!")
  model: jc.Model = trackmate_plugins[-1].getModel()

src/napari_imagej/types/type_conversions.py

@@ -21,7 +21,8 @@
 from jpype import JObject
 from scyjava import Priority
 
-from napari_imagej.java import ij, jc
+from napari_imagej import nij
+from napari_imagej.java import jc
 from napari_imagej.types.enum_likes import enum_like
 from napari_imagej.types.enums import py_enum_for
 from napari_imagej.types.type_hints import type_hints
@@ -201,6 +202,6 @@ def canConvertChecker(item: "jc.ModuleItem") -> Optional[Type]:
  """
 
  def isAssignable(from_type, to_type) -> bool:
- return ij().convert().supports(from_type, to_type)
+ return nij.ij.convert().supports(from_type, to_type)
 
  return _checkerUsingFunc(item, isAssignable)