The user can now display just a specific channel of a sequence
This will be useful to allow the user to perform some processings on the currently opened stack instead of choosing the stack from a list each time an image processing is launched : this will ease adjustment of image processing parameters.
This commit is contained in:
Guillaume Raffy
parent
738a3a8c25
commit
44dacc1a97
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@ -1,3 +1,4 @@
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#@output ImagePlus SEQUENCE
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"""This script is supposed to be launched from fiji's jython interpreter
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"""
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@ -32,11 +33,39 @@ from ij import IJ
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from ij.gui import GenericDialog, DialogListener
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from java.awt.event import ItemListener
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# def SequenceSelectorDialog(GenericDialog):
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#
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# def __init__(self):
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# title = 'select the sequence to process'
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# GenericDialog.__init__(self)
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# class MyListener(DialogListener):
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# def dialogItemChanged(self, gd, event):
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# IJ.log("Something was changed (event = %s)" % event)
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# IJ.log("event's attributes : %s" % str(dir(event)))
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# # 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 choice0)
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# # 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']
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class SequenceChoiceListener(ItemListener):
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def __init__(self, channel_choice, catalog):
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ItemListener.__init__(self)
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self.channel_choice = channel_choice
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self.catalog = catalog
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def itemStateChanged(self, event):
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IJ.log("SequenceChoiceListener : Something was changed (event = %s)" % event)
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# 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)
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IJ.log("SequenceChoiceListener : event's attributes : %s" % str(dir(event)))
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# 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']
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IJ.log("SequenceChoiceListener : event.item : %s" % str(event.item))
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IJ.log("SequenceChoiceListener : type(event.item) : %s" % str(type(event.item)))
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selected_sequence_id = event.item
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selected_sequence = self.catalog.sequences[selected_sequence_id]
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channel_ids = selected_sequence.get_channel_names()
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self.channel_choice.removeAll()
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self.channel_choice.add('all')
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for channel_id in channel_ids:
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self.channel_choice.add(channel_id)
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def ask_for_sequence(catalog):
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title = 'select the sequence to process'
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@ -46,25 +75,45 @@ def ask_for_sequence(catalog):
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assert len(sequence_ids) > 0
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default_sequence_id = sequence_ids[0]
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gd.addChoice('sequence', sequence_ids, default_sequence_id)
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channel_ids = catalog.sequences[default_sequence_id].get_channel_names()
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gd.addChoice('channel', channel_ids, channel_ids[0])
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choices = gd.getChoices()
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IJ.log("choices = %s" % choices)
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sequence_choice = choices[0]
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channel_choice = choices[1]
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sequence_choice.addItemListener(SequenceChoiceListener(channel_choice, catalog))
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gd.showDialog()
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if gd.wasCanceled():
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return {}
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selected_sequence_id = sequence_ids[gd.getNextChoiceIndex()] # eg 'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'
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selected_sequence = catalog.sequences[selected_sequence_id]
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selected_channel_index = gd.getNextChoiceIndex()
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if selected_channel_index == 0:
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selected_channel_id = 'all'
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else:
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selected_channel_id = selected_sequence.get_channel_names()[selected_channel_index - 1] # eg 'DM300_327-353_fluo'
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print("chosen sequence : %s" % selected_sequence_id)
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return catalog.sequences[selected_sequence_id]
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print("chosen channel : %s" % selected_channel_id)
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return {'sequence': selected_sequence, 'channel_id':selected_channel_id}
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def run_script():
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user_settings = UserSettings()
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IImageEngine.set_instance(IJImageEngine())
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catalog = ImageCatalog(user_settings.raw_images_root_path)
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sequence = ask_for_sequence(catalog)
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if sequence is None:
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user_selection = ask_for_sequence(catalog)
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if len(user_selection) == 0:
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return
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sequence_as_stack = open_sequence_in_imagej(sequence)
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sequence = user_selection['sequence']
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channel_id = str(user_selection['channel_id'])
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#white_estimator = WhiteEstimator(open_size=OPEN_SIZE, close_size=CLOSE_SIZE, average_size=AVERAGE_SIZE)
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#white_estimate = white_estimator.estimate_white([sequence], [channel_id])
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IJ.log("channel_id = %s (type = %s)" % (channel_id, str(type(channel_id))))
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if channel_id == 'all':
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sequence_as_stack = open_sequence_in_imagej(sequence)
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else:
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hyperstack = sequence.as_hyperstack(selected_channel_ids=[channel_id], selected_frames=None, selected_slices=None)
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sequence_as_stack = hyperstack.hyperstack
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print(type(sequence_as_stack))
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global SEQUENCE
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@ -72,3 +121,4 @@ def run_script():
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# note : when launched from fiji, __name__ doesn't have the value "__main__", as when launched from python
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run_script()
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