added a plugin that allows the user to display his chosen sequence in imagej
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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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#from ij import IJ # pylint: disable=import-error
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#WHITE_ESTIMATE = IJ.openImage('/Users/graffy/ownCloud/ipr/lipase/lipase.git/white_estimate.tiff')
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# # note: fiji's jython doesn't support encoding keyword
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# https://imagej.net/Scripting_Headless
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# String lipase_src_root_path
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# String(label="Please enter your name",description="Name field") name
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# OUTPUT String greeting
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import sys
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print('python version %s' % sys.version) # prints python version
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from lipase.settings import UserSettings
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# it is necassary to add lipase's root path to the path if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
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# sys.path.append(lipase_src_root_path) # pylint: disable=undefined-variable
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# from lipase import Lipase, ImageLogger
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from lipase.preprocessing import test_preprocessing # noqa: E402 pylint: disable=import-error,wrong-import-position
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from lipase.imageengine import IImageEngine
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from lipase.imagej.ijimageengine import IJImageEngine
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from lipase.preprocessing import WhiteEstimator
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from lipase.catalog import ImageCatalog
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from lipase.imagej import open_sequence_in_imagej
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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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def ask_for_sequence(catalog):
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title = 'select the sequence to process'
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gd = GenericDialog(title)
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# gd.addDialogListener(MyListener())
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sequence_ids = catalog.sequences.keys()
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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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choices = gd.getChoices()
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IJ.log("choices = %s" % choices)
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sequence_choice = choices[0]
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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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print("chosen sequence : %s" % selected_sequence_id)
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return catalog.sequences[selected_sequence_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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return
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sequence_as_stack = open_sequence_in_imagej(sequence)
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print(type(sequence_as_stack))
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global SEQUENCE
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SEQUENCE = sequence_as_stack
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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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@ -127,44 +127,6 @@ class Sequence(object):
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white_sequence = seqid_to_white[self.sequence_id]
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return self.catalog.sequences[white_sequence]
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def as_hyperstack(self):
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, self.num_channels, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for channel_index in range(self.num_channels):
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def as_stack(self, channel_id):
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'''
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:param str channel_id: eg 'DM300_327-353_fluo'
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'''
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channel_index = self.get_channel_index(channel_id)
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hyperstack = IJ.createHyperStack(self.sequence_id, self.width, self.height, 1, self.num_slices, self.num_frames, self.num_bits_per_pixels)
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for frame_index in range(self.num_frames):
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slice_index = 0
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src_image_file_path = self.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def open_in_imagej(self):
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# ip = IJ.createHyperStack(title=self.sequence_id, width=self.width, height= self.height, channels=1, slices=1, frames=self.get_num_frames(), bitdepth=16)
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hyperstack = self.as_hyperstack()
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hyperstack.show()
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for channel_index in range(self.num_channels):
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hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
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IJ.run("Enhance Contrast", "saturated=0.35")
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return hyperstack
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class ImageCatalog(object):
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def __init__(self, raw_images_root):
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@ -0,0 +1,40 @@
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from ij import IJ # pylint: disable=import-error
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def open_sequence_as_hyperstack(sequence):
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hyperstack = IJ.createHyperStack(sequence.sequence_id, sequence.width, sequence.height, sequence.num_channels, sequence.num_slices, sequence.num_frames, sequence.num_bits_per_pixels)
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for channel_index in range(sequence.num_channels):
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for frame_index in range(sequence.num_frames):
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slice_index = 0
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src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def open_sequence_as_stack(sequence, channel_id):
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'''
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:param str channel_id: eg 'DM300_327-353_fluo'
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'''
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channel_index = sequence.get_channel_index(channel_id)
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hyperstack = IJ.createHyperStack(sequence.sequence_id, sequence.width, sequence.height, 1, sequence.num_slices, sequence.num_frames, sequence.num_bits_per_pixels)
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for frame_index in range(sequence.num_frames):
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slice_index = 0
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src_image_file_path = sequence.get_image_file_path(channel_index=channel_index, frame_index=frame_index)
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# print(src_image_file_path)
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src_image = IJ.openImage(src_image_file_path)
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# print(src_image.getProperties())
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hyperstack.setPositionWithoutUpdate(channel_index + 1, slice_index + 1, frame_index + 1)
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hyperstack.setProcessor(src_image.getProcessor())
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return hyperstack
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def open_sequence_in_imagej(sequence):
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# ip = IJ.createHyperStack(title=sequence.sequence_id, width=sequence.width, height= sequence.height, channels=1, slices=1, frames=sequence.get_num_frames(), bitdepth=16)
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hyperstack = open_sequence_as_hyperstack(sequence)
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hyperstack.show()
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for channel_index in range(sequence.num_channels):
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hyperstack.setPositionWithoutUpdate(channel_index + 1, 1, 1)
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IJ.run("Enhance Contrast", "saturated=0.35")
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return hyperstack
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