Added the ability of the user to choose the channel for which he wants to compute the white estimate.

As a result the Estimate White plugin is now usable.

src/ij-plugins/Ipr/Lipase/Estimate_White.py

@@ -28,13 +28,79 @@ from lipase.imagej.ijimageengine import IJImageEngine
 from lipase.preprocessing import WhiteEstimator
 from lipase.catalog import ImageCatalog
 
+from ij import IJ
+from ij.gui import GenericDialog, DialogListener
+from java.awt.event import ItemListener
+
+# class MyListener(DialogListener):
+#     def dialogItemChanged(self, gd, event):
+#         IJ.log("Something was changed (event = %s)" % event)
+#         IJ.log("event's attributes : %s" % str(dir(event)))
+        
+#         # 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)
+
+#         # 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']
+
+
+class SequenceChoiceListener(ItemListener):
+
+    def __init__(self, channel_choice, catalog):
+        ItemListener.__init__(self)
+        self.channel_choice = channel_choice
+        self.catalog = catalog
+
+    def itemStateChanged(self, event):
+        IJ.log("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)))
+        # 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)))
+        selected_sequence_id = event.item
+        selected_sequence = self.catalog.sequences[selected_sequence_id]
+        channel_ids = selected_sequence.get_channel_names()
+
+        self.channel_choice.removeAll()
+        for channel_id in channel_ids:
+            self.channel_choice.add(channel_id)
+
+
+def ask_for_sequence(catalog):
+    title = 'select the sequence to process'
+    gd = GenericDialog(title)
+    # gd.addDialogListener(MyListener())
+    sequence_ids = catalog.sequences.keys()
+    assert len(sequence_ids) > 0
+    default_sequence_id = sequence_ids[0]
+    gd.addChoice('sequence', sequence_ids, default_sequence_id)
+    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)
+    sequence_choice = choices[0]
+    channel_choice = choices[1]
+    sequence_choice.addItemListener(SequenceChoiceListener(channel_choice, catalog))
+    gd.showDialog()
+    if gd.wasCanceled():
+        return {}
+    selected_sequence_id = sequence_ids[gd.getNextChoiceIndex()]  # eg 'res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2'
+    selected_channel_id = catalog.sequences[selected_sequence_id].get_channel_names()[gd.getNextChoiceIndex()]  # eg 'DM300_327-353_fluo'
+    print("chosen sequence : %s" % selected_sequence_id)
+    print("chosen channel : %s" % selected_channel_id)
+    return {'sequence': catalog.sequences[selected_sequence_id], 'channel_id':selected_channel_id}
+
+
 def run_script():
     user_settings = UserSettings()
     IImageEngine.set_instance(IJImageEngine())
     catalog = ImageCatalog(user_settings.raw_images_root_path)
-    sequence = catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
+    user_selection = ask_for_sequence(catalog)
+    if len(user_selection) == 0:
+        return
+    sequence = user_selection['sequence']
+    channel_id = user_selection['channel_id']
     white_estimator = WhiteEstimator(open_size=75, close_size=75, average_size=75)
-    white_estimate = white_estimator.estimate_white([sequence], ['DM300_327-353_fluo'])
+    white_estimate = white_estimator.estimate_white([sequence], [channel_id])
     print(type(white_estimate))
     global WHITE_ESTIMATE
     WHITE_ESTIMATE = white_estimate.ij_image

src/lipase/catalog.py

@@ -98,6 +98,10 @@ class Sequence(object):
         summary = self.mmm['Summary']
         return summary['ChNames'][channel_index]
 
+    def get_channel_names(self):
+        summary = self.mmm['Summary']
+        return summary['ChNames']
+
     def get_black(self):
         ''' returns the black sequence related to the the sequence self