From 442645d7108c7f9b741d2fcbd55183ef7506a89f Mon Sep 17 00:00:00 2001 From: Guillaume Raffy Date: Tue, 25 Jan 2022 14:53:37 +0100 Subject: [PATCH] prevented the console window to appear and diaply messages that are irrelevant to users. To do this, I turned log messages into debug messages. While doing so, I also added an IJLogger that is able to log messages on imagej console, in case we need it in the future --- src/ij-plugins/Ipr/Lipase/Display_Sequence.py | 13 +++--- src/lipase/__init__.py | 42 +++++++++++++++---- 2 files changed, 41 insertions(+), 14 deletions(-) diff --git a/src/ij-plugins/Ipr/Lipase/Display_Sequence.py b/src/ij-plugins/Ipr/Lipase/Display_Sequence.py index 2bb23b3..742e073 100644 --- a/src/ij-plugins/Ipr/Lipase/Display_Sequence.py +++ b/src/ij-plugins/Ipr/Lipase/Display_Sequence.py @@ -29,6 +29,7 @@ from lipase.imagej.ijimageengine import IJImageEngine from lipase.telemos import WhiteEstimator from lipase.catalog import ImageCatalog from lipase.imagej import open_sequence_in_imagej +from lipase import logger from ij import IJ from ij.gui import GenericDialog, DialogListener @@ -52,12 +53,12 @@ class SequenceChoiceListener(ItemListener): self.catalog = catalog def itemStateChanged(self, event): - IJ.log("SequenceChoiceListener : Something was changed (event = %s)" % event) + logger.debug("SequenceChoiceListener : Something was changed (event = %s)" % event) # SequenceChoiceListener : Something was changed (event = java.awt.event.ItemEvent[ITEM_STATE_CHANGED,item=res_soleil2018/DARK/DARK_40X_60min_1 im pae min_1/Pos0,stateChange=SELECTED] on choice3) - IJ.log("SequenceChoiceListener : event's attributes : %s" % str(dir(event))) + logger.debug("SequenceChoiceListener : event's attributes : %s" % str(dir(event))) # SequenceChoiceListener : event's attributes : ['ACTION_EVENT_MASK', 'ADJUSTMENT_EVENT_MASK', 'COMPONENT_EVENT_MASK', 'CONTAINER_EVENT_MASK', 'DESELECTED', 'FOCUS_EVENT_MASK', 'HIERARCHY_BOUNDS_EVENT_MASK', 'HIERARCHY_EVENT_MASK', 'ID', 'INPUT_METHOD_EVENT_MASK', 'INVOCATION_EVENT_MASK', 'ITEM_EVENT_MASK', 'ITEM_FIRST', 'ITEM_LAST', 'ITEM_STATE_CHANGED', 'KEY_EVENT_MASK', 'MOUSE_EVENT_MASK', 'MOUSE_MOTION_EVENT_MASK', 'MOUSE_WHEEL_EVENT_MASK', 'PAINT_EVENT_MASK', 'RESERVED_ID_MAX', 'SELECTED', 'TEXT_EVENT_MASK', 'WINDOW_EVENT_MASK', 'WINDOW_FOCUS_EVENT_MASK', 'WINDOW_STATE_EVENT_MASK', '__class__', '__copy__', '__deepcopy__', '__delattr__', '__doc__', '__ensure_finalizer__', '__eq__', '__format__', '__getattribute__', '__hash__', '__init__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__setattr__', '__str__', '__subclasshook__', '__unicode__', 'class', 'equals', 'getClass', 'getID', 'getItem', 'getItemSelectable', 'getSource', 'getStateChange', 'hashCode', 'item', 'itemSelectable', 'notify', 'notifyAll', 'paramString', 'setSource', 'source', 'stateChange', 'toString', 'wait'] - IJ.log("SequenceChoiceListener : event.item : %s" % str(event.item)) - IJ.log("SequenceChoiceListener : type(event.item) : %s" % str(type(event.item))) + logger.debug("SequenceChoiceListener : event.item : %s" % str(event.item)) + logger.debug("SequenceChoiceListener : type(event.item) : %s" % str(type(event.item))) selected_sequence_id = event.item selected_sequence = self.catalog.sequences[selected_sequence_id] channel_ids = selected_sequence.get_channel_names() @@ -79,7 +80,7 @@ def ask_for_sequence(catalog): channel_ids = catalog.sequences[default_sequence_id].get_channel_names() gd.addChoice('channel', channel_ids, channel_ids[0]) choices = gd.getChoices() - IJ.log("choices = %s" % choices) + logger.debug("choices = %s" % choices) sequence_choice = choices[0] channel_choice = choices[1] sequence_choice.addItemListener(SequenceChoiceListener(channel_choice, catalog)) @@ -107,7 +108,7 @@ def run_script(): return sequence = user_selection['sequence'] channel_id = str(user_selection['channel_id']) - IJ.log("channel_id = %s (type = %s)" % (channel_id, str(type(channel_id)))) + logger.debug("channel_id = %s (type = %s)" % (channel_id, str(type(channel_id)))) if channel_id == 'all': sequence_as_stack = open_sequence_in_imagej(sequence) else: diff --git a/src/lipase/__init__.py b/src/lipase/__init__.py index 114750a..306c7b7 100644 --- a/src/lipase/__init__.py +++ b/src/lipase/__init__.py @@ -3,16 +3,42 @@ import logging import logging.handlers import logging import os +from ij import IJ + + +class IJLogger(): + '''a logger with the same interface as logging.getLogger() but which uses imagej's log() mechanism + + todo: apparently, IJ.log() logs an INFO message by default. I don't know how to log messages with other severities (WARNING, ERRORS). So, instead, I prepend the severity as a string to the message, which is not great... + ''' + def debug(self, message): + IJ.log('DEBUG : %s' % message) + + def info(self, message): + IJ.log('INFO : %s' % message) + + def warn(self, message): + IJ.log('WARN : %s' % message) + + def error(self, message): + IJ.log('ERROR : %s' % message) + + def create_logger(): - global logger - # logging.basicConfig( stream=sys.stderr ) - handler = logging.FileHandler(os.environ.get("LOGFILE", "/tmp/lipase.log")) - formatter = logging.Formatter(logging.BASIC_FORMAT) - handler.setFormatter(formatter) - logger = logging.getLogger(__name__) - logger.setLevel( logging.DEBUG ) - logger.addHandler(handler) + logger_type = 'std_python_logger' # 'std_python_logger' or 'ij_logger' + if logger_type == 'std_python_logger': + # logging.basicConfig( stream=sys.stderr ) + handler = logging.FileHandler(os.environ.get("LOGFILE", "/tmp/lipase.log")) + formatter = logging.Formatter(logging.BASIC_FORMAT) + handler.setFormatter(formatter) + logger = logging.getLogger(__name__) + logger.setLevel( logging.DEBUG ) + logger.addHandler(handler) + elif logger_type == 'std_python_logger': + logger = IJLogger() + else: + assert False return logger logger = create_logger()