30 lines
1.2 KiB
Python
30 lines
1.2 KiB
Python
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"""This script is supposed to be launched from fiji's jython interpreter
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"""
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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 raw_images_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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sys.path.append('/Users/graffy/ownCloud/ipr/lipase/lipase.git') # necessary if run from fiji as script otherwise jython fails to find lipase's modules such as catalog
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from ij import IJ
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from lipase import Lipase, ImageLogger
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from catalog import ImageCatalog
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def run_script():
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catalog = ImageCatalog(raw_images_root_path) # eg '/Users/graffy/ownCloud/ipr/lipase/raw-images'
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lipase = Lipase(catalog, debugger=ImageLogger())
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sequence = catalog.sequences['res_soleil2018/GGH/GGH_2018_cin2_phiG_I_327_vis_-40_1/Pos2']
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white_estimate = lipase.estimate_white(sequence, 'DM300_327-353_fluo')
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print(white_estimate)
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IJ.saveAsTiff(white_estimate, './white_estimate.tiff')
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print('end')
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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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