root / bin / MGX_EdgeDetect.py @ 20
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| 1 | 20 | akiss | import os |
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| 2 | 20 | akiss | |
| 3 | 20 | akiss | '''
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| 4 | 20 | akiss | Input:
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| 5 | 20 | akiss | - directory with grey images of sepals
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| 6 | 20 | akiss |
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| 7 | 20 | akiss | Output:
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| 8 | 20 | akiss | - detected sepal contour stacks
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| 9 | 20 | akiss |
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| 10 | 20 | akiss | '''
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| 11 | 20 | akiss | |
| 12 | 20 | akiss | # directory of grey images
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| 13 | 20 | akiss | filedata="/home/biophysics/Desktop/Annamaria/Sepals"
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| 14 | 20 | akiss | |
| 15 | 20 | akiss | |
| 16 | 20 | akiss | ################### Parameters ###########
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| 17 | 20 | akiss | |
| 18 | 20 | akiss | # smoothing
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| 19 | 20 | akiss | #gaussianblurvalue=str(1)
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| 20 | 20 | akiss | gaussianblurvalue=str(2) |
| 21 | 20 | akiss | |
| 22 | 20 | akiss | # threshold value for the Edgedetect procedure
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| 23 | 20 | akiss | #edgedetectvalue=str(10000)
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| 24 | 20 | akiss | edgedetectvalue=str(2000) |
| 25 | 20 | akiss | |
| 26 | 20 | akiss | # xy dilation value
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| 27 | 20 | akiss | dilatevalue=str(0) |
| 28 | 20 | akiss | |
| 29 | 20 | akiss | #########################################
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| 30 | 20 | akiss | |
| 31 | 20 | akiss | path=filedata+'/'
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| 32 | 20 | akiss | outputdir=filedata+'-MGX-EdgeDetect_Blur'+gaussianblurvalue+'_ED'+edgedetectvalue+'_d'+dilatevalue+'/' |
| 33 | 20 | akiss | os.system("mkdir "+outputdir)
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| 34 | 20 | akiss | |
| 35 | 20 | akiss | listfiles=os.listdir(path) |
| 36 | 20 | akiss | listfiles=[ i for i in listfiles if '.tif' in i] |
| 37 | 20 | akiss | |
| 38 | 20 | akiss | Process.Stack__System__Clear_Work_Stack('0')
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| 39 | 20 | akiss | Process.Stack__System__Clear_Main_Stack('0')
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| 40 | 20 | akiss | Process.Stack__System__Clear_Main_Stack('1')
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| 41 | 20 | akiss | Process.Stack__System__Clear_Work_Stack('1')
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| 42 | 20 | akiss | for i in listfiles: |
| 43 | 20 | akiss | Process.Stack__System__Set_Current_Stack('Main', '0') |
| 44 | 20 | akiss | Process.Stack__System__Open(path+i, 'Main', '0','','Yes') |
| 45 | 20 | akiss | Process.Stack__System__Open(path+i, 'Main', '1','','Yes') |
| 46 | 20 | akiss | Process.Stack__Filters__Gaussian_Blur_Stack(gaussianblurvalue, gaussianblurvalue, gaussianblurvalue) |
| 47 | 20 | akiss | Process.Stack__MultiStack__Copy_Work_to_Main_Stack() |
| 48 | 20 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 -> 2') |
| 49 | 20 | akiss | Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000') |
| 50 | 20 | akiss | Process.Stack__MultiStack__Copy_Work_to_Main_Stack() |
| 51 | 20 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <-> 2') |
| 52 | 20 | akiss | Process.Stack__System__Set_Current_Stack('Main', '0') |
| 53 | 20 | akiss | Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes') |
| 54 | 20 | akiss | Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000') |
| 55 | 20 | akiss | Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes') |
| 56 | 20 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <- 2') |
| 57 | 20 | akiss | Process.Stack__System__Set_Current_Stack('Both', '0') |
| 58 | 20 | akiss | Process.Stack__MultiStack__Combine_Stacks('Product')
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| 59 | 20 | akiss | Process.Stack__System__Set_Current_Stack('Work', '0') |
| 60 | 20 | akiss | Process.Stack__Morphology__Dilate(dilatevalue, dilatevalue, "0", 'No', 'No') |
| 61 | 20 | akiss | Process.Stack__System__Save(outputdir+"MGX_"+i[:-4]+'_e'+edgedetectvalue+'_d'+dilatevalue+'.tif', 'Work', '0', '0','Yes') |
| 62 | 20 | akiss | Process.Stack__System__Clear_Work_Stack('0')
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| 63 | 20 | akiss | Process.Stack__System__Clear_Main_Stack('0')
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| 64 | 20 | akiss | Process.Stack__System__Clear_Main_Stack('1')
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| 65 | 20 | akiss | Process.Stack__System__Clear_Work_Stack('1')
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| 66 | 20 | akiss | Process.Stack__System__Clear_Main_Stack('2')
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| 67 | 20 | akiss | Process.Stack__System__Clear_Work_Stack('2') |