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import os
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path="/home/cmollier/Documents/WORK/Confocal_whole_sepal/CSI1-WT/20200723/Col-1/2_TIF/"
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outpath="/home/cmollier/Documents/WORK/Confocal_whole_sepal/CSI1-WT/20200723/Col-1/3_MGX/"
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edgedetectvalue=str(7000)
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'''
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Input:
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- directory with grey images of sepals
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Output:
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- detected sepal contour stacks
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'''
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# directory of grey images
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filedata="/home/biophysics/Desktop/Fanfan/Col-0_A-tif"
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################### Parameters ###########
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# smoothing
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gaussianblurvalue=str(1)
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# threshold value for the Edgedetect procedure
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edgedetectvalue=str(8000)
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# xy dilation value
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dilatevalue=str(0)
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#########################################
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path=filedata+'/'
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outputdir=filedata+'-MGX-EdgeDetect_Blur'+gaussianblurvalue+'_ED'+edgedetectvalue+'_d'+dilatevalue+'/'
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os.system("mkdir "+outputdir)
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listfiles=os.listdir(path)
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listfiles=[ i for i in listfiles if '.tif' in i]
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| ... | ... | |
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Process.Stack__System__Clear_Main_Stack('0')
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Process.Stack__System__Clear_Main_Stack('1')
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Process.Stack__System__Clear_Work_Stack('1')
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for i in listfiles:
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if i.split(".")[1]=="tif":
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Process.Stack__System__Set_Current_Stack('Main', '0')
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Process.Stack__System__Open(path+i, 'Main', '0')
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Process.Stack__System__Open(path+i, 'Main', '1')
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Process.Stack__Filters__Gaussian_Blur_Stack('10', '10', '10')
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Process.Stack__MultiStack__Copy_Work_to_Main_Stack()
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 -> 2')
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Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')
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Process.Stack__MultiStack__Copy_Work_to_Main_Stack()
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <-> 2')
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Process.Stack__System__Set_Current_Stack('Main', '0')
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Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')
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Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')
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Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <- 2')
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Process.Stack__System__Set_Current_Stack('Both', '0')
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Process.Stack__MultiStack__Combine_Stacks('Product')
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Process.Stack__System__Set_Current_Stack('Work', '0')
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Process.Stack__System__Save(outpath+i[:-4]+'_'+str(edgedetectvalue)+'.tif', 'Work', '0', '0')
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Process.Stack__System__Clear_Work_Stack('0')
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Process.Stack__System__Clear_Main_Stack('0')
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Process.Stack__System__Clear_Main_Stack('1')
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Process.Stack__System__Clear_Work_Stack('1')
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Process.Stack__System__Clear_Main_Stack('2')
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Process.Stack__System__Clear_Work_Stack('2')
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Process.Stack__System__Set_Current_Stack('Main', '0')
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Process.Stack__System__Open(path+i, 'Main', '0')
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Process.Stack__System__Open(path+i, 'Main', '1')
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Process.Stack__Filters__Gaussian_Blur_Stack(gaussianblurvalue, gaussianblurvalue, gaussianblurvalue)
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Process.Stack__MultiStack__Copy_Work_to_Main_Stack()
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 -> 2')
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Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')
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Process.Stack__MultiStack__Copy_Work_to_Main_Stack()
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <-> 2')
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Process.Stack__System__Set_Current_Stack('Main', '0')
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Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')
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Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')
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Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')
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Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <- 2')
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Process.Stack__System__Set_Current_Stack('Both', '0')
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Process.Stack__MultiStack__Combine_Stacks('Product')
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Process.Stack__System__Set_Current_Stack('Work', '0')
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Process.Stack__Morphology__Dilate(dilatevalue, dilatevalue, "0", 'No', 'No')
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Process.Stack__System__Save(outputdir+"MGX_"+i[:-4]+'_e'+edgedetectvalue+'_d'+dilatevalue+'.tif', 'Work', '0', '0')
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Process.Stack__System__Clear_Work_Stack('0')
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Process.Stack__System__Clear_Main_Stack('0')
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Process.Stack__System__Clear_Main_Stack('1')
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Process.Stack__System__Clear_Work_Stack('1')
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Process.Stack__System__Clear_Main_Stack('2')
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Process.Stack__System__Clear_Work_Stack('2')
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