Add warnings mechanism for non-dealbreak problems

src/napari_imagej/java.py

@@ -11,7 +11,7 @@
  * jc
  - object whose fields are lazily-loaded Java Class instances.
 """
-from typing import Any, Callable, Dict
+from typing import Any, Callable, Dict, List
 
 import imagej
 from jpype import JClass
@@ -39,6 +39,7 @@
 # -- ImageJ API -- #
 
 _ij = None
+_init_warnings: List[str] = []
 
 
 def ij():
@@ -49,6 +50,14 @@ def ij():
  return _ij
 
 
+def init_warnings():
+ if _ij is None:
+ raise Exception(
+ "The ImageJ instance has not yet been initialized! Please run init_ij()"
+ )
+ return _init_warnings
+
+
 def init_ij() -> "jc.ImageJ":
  """
  Creates the ImageJ instance
@@ -174,6 +183,7 @@ def _validate_imagej():
  )
  violations.insert(0, failure_str)
  failure_str = "\n\t".join(violations)
+ _init_warnings.append(failure_str)
  warn(failure_str)
 
 

src/napari_imagej/settings.py

@@ -35,6 +35,11 @@
  Additional command line arguments to pass to the Java Virtual Machine (JVM).
  For example, "-Xmx4g" to allow Java to use up to 4 GB of memory.
  By default, no arguments are passed.
+
+display_imagej_initialization_warnings: bool = True
+ When napari-imagej encounters a warnable issue pertaining to Java components
+ it will display the warnings iff this flag is true.
+ Defaults to True.
 """
 
 import os
@@ -56,6 +61,7 @@
  "include_imagej_legacy": True,
  "enable_imagej_gui": True,
  "jvm_command_line_arguments": "",
+ "display_java_warnings": True,
 }
 
 # -- Configuration options --
@@ -65,6 +71,7 @@
 include_imagej_legacy: bool = defaults["include_imagej_legacy"]
 enable_imagej_gui: bool = defaults["enable_imagej_gui"]
 jvm_command_line_arguments: str = defaults["jvm_command_line_arguments"]
+display_java_warnings: bool = defaults["display_java_warnings"]
 
 _test_mode = bool(os.environ.get("NAPARI_IMAGEJ_TESTING", None))
 _is_macos = sys.platform == "darwin"

src/napari_imagej/widgets/napari_imagej.py

@@ -5,7 +5,7 @@
 This Widget is made accessible to napari through napari.yml
 """
 from traceback import format_exception
-from typing import Callable
+from typing import Callable, List
 
 from jpype import JArray, JImplements, JOverride
 from magicgui.widgets import FunctionGui, Widget
@@ -15,7 +15,8 @@
 from qtpy.QtWidgets import QTreeWidgetItem, QVBoxLayout, QWidget
 from scyjava import isjava, jstacktrace, when_jvm_stops
 
-from napari_imagej.java import ij, init_ij, jc
+from napari_imagej import settings
+from napari_imagej.java import ij, init_ij, init_warnings, jc
 from napari_imagej.utilities._module_utils import _non_layer_widget
 from napari_imagej.utilities.event_subscribers import (
  NapariEventSubscriber,
@@ -33,7 +34,10 @@
  SearchResultTreeItem,
 )
 from napari_imagej.widgets.searchbar import JVMEnabledSearchbar
-from napari_imagej.widgets.widget_utils import JavaErrorMessageBox
+from napari_imagej.widgets.widget_utils import (
+ JavaErrorMessageBox,
+ JavaWarningMessageBox,
+)
 
 
 class NapariImageJWidget(QWidget):
@@ -42,6 +46,7 @@ class NapariImageJWidget(QWidget):
  output_handler = Signal(object)
  progress_handler = Signal(object)
  ij_error_handler = Signal(object)
+ ij_warning_handler = Signal(object)
 
  def __init__(self, napari_viewer: Viewer):
  super().__init__()
@@ -118,6 +123,7 @@ def return_search_bar():
  self.output_handler.connect(self._handle_output)
  self.progress_handler.connect(self._update_progress)
  self.ij_error_handler.connect(self._handle_ij_init_error)
+ self.ij_warning_handler.connect(self._handle_ij_init_warning)
 
  # -- Final setup -- #
 
@@ -216,6 +222,24 @@ def _handle_ij_init_error(self, exc: Exception):
  msg: JavaErrorMessageBox = JavaErrorMessageBox(title, exception_str)
  msg.exec()
 
+ @Slot(object)
+ def _handle_ij_init_warning(self, warnings: List[Exception]):
+ """
+ Handles warnings associated initializing ImageJ.
+ Initializing ImageJ can fail for all sorts of reasons,
+ so we give it special attention here.
+
+ NB: This MUST be done within this slot, as slot functions
+ are run on the GUI thread. napari-imagej runs ImageJ initialization
+ on a separate Qt thread, which isn't the GUI thread.
+ """
+ # Print thet error
+ if not settings.display_java_warnings or len(warnings) == 0:
+ return
+ title = "During the initialization of ImageJ, warnings were raised:"
+ msg: JavaWarningMessageBox = JavaWarningMessageBox(title, "\n\n".join(warnings))
+ msg.exec()
+
 
 class ImageJInitializer(QThread):
  """
@@ -236,6 +260,8 @@ def run(self):
  try:
  # Initialize ImageJ
  init_ij()
+ # Log any warnings
+ self.widget.ij_warning_handler.emit(init_warnings())
  # Finalize the menu
  self.widget.menu.finalize()
  # Finalize the search bar
@@ -249,6 +275,7 @@ def run(self):
  except Exception as e:
  # Handle the exception on the GUI thread
  self.widget.ij_error_handler.emit(e)
+ return
 
  def _finalize_results_tree(self):
  """

src/napari_imagej/widgets/widget_utils.py

@@ -7,6 +7,7 @@
 from qtpy.QtGui import QFontMetrics
 from qtpy.QtWidgets import (
  QApplication,
+ QCheckBox,
  QComboBox,
  QDialog,
  QDialogButtonBox,
@@ -20,6 +21,7 @@
  QWidget,
 )
 
+from napari_imagej import settings
 from napari_imagej.java import ij, jc
 from napari_imagej.utilities._module_utils import (
  execute_function_modally,
@@ -140,6 +142,48 @@ def __init__(self, title: str, error_message: str, *args, **kwargs):
  self.layout().addWidget(btn_box, 2, 0, 1, self.layout().columnCount())
 
 
+class JavaWarningMessageBox(QDialog):
+ def __init__(self, title: str, error_message: str, *args, **kwargs):
+ QDialog.__init__(self, *args, **kwargs)
+ self.setLayout(QGridLayout())
+ # Write the title to a Label
+ self.layout().addWidget(
+ QLabel(title, self), 0, 0, 1, self.layout().columnCount()
+ )
+
+ # Write the error message to a TextEdit
+ msg_edit = QTextEdit(self)
+ msg_edit.setReadOnly(True)
+ msg_edit.setText(error_message)
+ self.layout().addWidget(msg_edit, 1, 0, 1, self.layout().columnCount())
+ msg_edit.setLineWrapMode(0)
+
+ # Default size - size of the error message
+ font = msg_edit.document().defaultFont()
+ fontMetrics = QFontMetrics(font)
+ textSize = fontMetrics.size(0, error_message)
+ textWidth = textSize.width() + 100
+ textHeight = textSize.height() + 100
+ self.resize(textWidth, textHeight)
+ # Maximum size - ~80% of the user's screen
+ screen_size = QApplication.desktop().screenGeometry()
+ self.setMaximumSize(
+ int(screen_size.width() * 0.8), int(screen_size.height() * 0.8)
+ )
+ self.checkbox: QCheckBox = QCheckBox("Don't warn me again")
+ self.layout().addWidget(self.checkbox, 2, 0, 1, self.layout().columnCount())
+
+ btn_box = QDialogButtonBox(QDialogButtonBox.Ok)
+ btn_box.accepted.connect(self.accept)
+ self.layout().addWidget(btn_box, 3, 0, 1, self.layout().columnCount())
+
+ def accept(self):
+ super().accept()
+ if self.checkbox.isChecked():
+ settings.display_java_warnings = False
+ settings.save()
+
+
 _IMAGE_LAYER_TYPES = (Image, Labels)
 _ROI_LAYER_TYPES = (Points, Shapes)
 

tests/test_java.py

@@ -3,8 +3,7 @@
 from scyjava import get_version, is_version_at_least, jimport
 
 from napari_imagej import __version__, settings
-from napari_imagej.java import _validate_imagej, minimum_versions
-from napari_imagej.utilities.logging import logger
+from napari_imagej.java import _validate_imagej, init_warnings, minimum_versions
 
 version_checks = {
  "io.scif:scifio": "io.scif.SCIFIO",
@@ -67,23 +66,16 @@ def test_recommended_version(ij):
  existing = napari_imagej.java.recommended_versions
  napari_imagej.java.recommended_versions = {"org.scijava:scijava-common": "999.0.0"}
 
- # Setup log handler to capture warning
- import io
- import logging
-
- log_capture_string = io.StringIO()
- ch = logging.StreamHandler(log_capture_string)
- ch.setLevel(logging.WARN)
- logger().addHandler(ch)
  # Validate ImageJ - capture lower-than-recommended version
  _validate_imagej()
- log_contents = log_capture_string.getvalue()
- log_capture_string.close()
+ warnings = init_warnings()
+ assert len(warnings) == 1
+
  # Assert warning given
- assert log_contents == (
- f"napari-imagej: napari-imagej v{__version__} recommends using the "
+ assert warnings[0] == (
+ f"napari-imagej v{__version__} recommends using the "
  "following component versions:\n\torg.scijava:scijava-common : "
- "999.0.0 (Installed: 2.94.1)\n"
+ "999.0.0 (Installed: 2.94.1)"
  )
 
  # restore recommended versions

tests/widgets/test_napari_imagej.py

@@ -19,7 +19,10 @@
 from napari_imagej.widgets.napari_imagej import NapariImageJWidget, ResultRunner
 from napari_imagej.widgets.result_tree import SearchResultTree
 from napari_imagej.widgets.searchbar import JVMEnabledSearchbar
-from napari_imagej.widgets.widget_utils import JavaErrorMessageBox
+from napari_imagej.widgets.widget_utils import (
+ JavaErrorMessageBox,
+ JavaWarningMessageBox,
+)
 from tests.utils import jc
 from tests.widgets.widget_utils import _searcher_tree_named
 
@@ -307,3 +310,30 @@ def new_exec(self):
 
  # Finally, restore JavaErrorMessageBox.exec
  JavaErrorMessageBox.exec = old_exec
+
+
+def test_handle_ij_init_warning(imagej_widget: NapariImageJWidget):
+ """
+ Ensure that napari-imagej's ij init warnings are displayed correctly
+ """
+ title = ""
+ contents = ""
+
+ # first, mock JavaErrorMessageBox.exec
+ old_exec = JavaWarningMessageBox.exec
+
+ def new_exec(self):
+ nonlocal title, contents
+ title = self.findChild(QLabel).text()
+ contents = self.findChild(QTextEdit).toPlainText()
+
+ JavaWarningMessageBox.exec = new_exec
+
+ # Then, test a Java exception is correctly configured
+ warnings = ["This is a warning"]
+ imagej_widget._handle_ij_init_warning(warnings)
+ assert title == "During the initialization of ImageJ, warnings were raised:"
+ assert contents == "This is a warning"
+
+ # Finally, restore JavaErrorMessageBox.exec
+ JavaWarningMessageBox.exec = old_exec