root / bin / image2geometry / MGX_EdgeDetect.py @ 16
Historique | Voir | Annoter | Télécharger (2,36 ko)
| 1 | 7 | akiss | import os |
|---|---|---|---|
| 2 | 9 | akiss | |
| 3 | 9 | akiss | '''
|
| 4 | 9 | akiss | Input:
|
| 5 | 9 | akiss | - directory with grey images of sepals
|
| 6 | 9 | akiss |
|
| 7 | 9 | akiss | Output:
|
| 8 | 9 | akiss | - detected sepal contour stacks
|
| 9 | 9 | akiss |
|
| 10 | 9 | akiss | '''
|
| 11 | 9 | akiss | |
| 12 | 9 | akiss | # directory of grey images
|
| 13 | 9 | akiss | filedata="/home/biophysics/Desktop/Fanfan/Col-0_A-tif"
|
| 14 | 9 | akiss | |
| 15 | 9 | akiss | |
| 16 | 9 | akiss | ################### Parameters ###########
|
| 17 | 9 | akiss | |
| 18 | 9 | akiss | # smoothing
|
| 19 | 9 | akiss | gaussianblurvalue=str(1) |
| 20 | 9 | akiss | |
| 21 | 9 | akiss | # threshold value for the Edgedetect procedure
|
| 22 | 7 | akiss | edgedetectvalue=str(8000) |
| 23 | 9 | akiss | |
| 24 | 9 | akiss | # xy dilation value
|
| 25 | 9 | akiss | dilatevalue=str(0) |
| 26 | 9 | akiss | |
| 27 | 9 | akiss | #########################################
|
| 28 | 9 | akiss | |
| 29 | 9 | akiss | path=filedata+'/'
|
| 30 | 9 | akiss | outputdir=filedata+'-MGX-EdgeDetect_Blur'+gaussianblurvalue+'_ED'+edgedetectvalue+'_d'+dilatevalue+'/' |
| 31 | 9 | akiss | os.system("mkdir "+outputdir)
|
| 32 | 9 | akiss | |
| 33 | 7 | akiss | listfiles=os.listdir(path) |
| 34 | 8 | akiss | listfiles=[ i for i in listfiles if '.tif' in i] |
| 35 | 8 | akiss | |
| 36 | 7 | akiss | Process.Stack__System__Clear_Work_Stack('0')
|
| 37 | 7 | akiss | Process.Stack__System__Clear_Main_Stack('0')
|
| 38 | 7 | akiss | Process.Stack__System__Clear_Main_Stack('1')
|
| 39 | 7 | akiss | Process.Stack__System__Clear_Work_Stack('1')
|
| 40 | 7 | akiss | for i in listfiles: |
| 41 | 7 | akiss | Process.Stack__System__Set_Current_Stack('Main', '0') |
| 42 | 7 | akiss | Process.Stack__System__Open(path+i, 'Main', '0') |
| 43 | 7 | akiss | Process.Stack__System__Open(path+i, 'Main', '1') |
| 44 | 7 | akiss | Process.Stack__Filters__Gaussian_Blur_Stack(gaussianblurvalue, gaussianblurvalue, gaussianblurvalue) |
| 45 | 7 | akiss | Process.Stack__MultiStack__Copy_Work_to_Main_Stack() |
| 46 | 7 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 -> 2') |
| 47 | 7 | akiss | Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000') |
| 48 | 7 | akiss | Process.Stack__MultiStack__Copy_Work_to_Main_Stack() |
| 49 | 7 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <-> 2') |
| 50 | 7 | akiss | Process.Stack__System__Set_Current_Stack('Main', '0') |
| 51 | 7 | akiss | Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes') |
| 52 | 7 | akiss | Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000') |
| 53 | 7 | akiss | Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes') |
| 54 | 7 | akiss | Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <- 2') |
| 55 | 7 | akiss | Process.Stack__System__Set_Current_Stack('Both', '0') |
| 56 | 7 | akiss | Process.Stack__MultiStack__Combine_Stacks('Product')
|
| 57 | 7 | akiss | Process.Stack__System__Set_Current_Stack('Work', '0') |
| 58 | 7 | akiss | Process.Stack__Morphology__Dilate(dilatevalue, dilatevalue, "0", 'No', 'No') |
| 59 | 9 | akiss | Process.Stack__System__Save(outputdir+"MGX_"+i[:-4]+'_e'+edgedetectvalue+'_d'+dilatevalue+'.tif', 'Work', '0', '0') |
| 60 | 7 | akiss | Process.Stack__System__Clear_Work_Stack('0')
|
| 61 | 7 | akiss | Process.Stack__System__Clear_Main_Stack('0')
|
| 62 | 7 | akiss | Process.Stack__System__Clear_Main_Stack('1')
|
| 63 | 7 | akiss | Process.Stack__System__Clear_Work_Stack('1')
|
| 64 | 7 | akiss | Process.Stack__System__Clear_Main_Stack('2')
|
| 65 | 7 | akiss | Process.Stack__System__Clear_Work_Stack('2') |