Laboratoire RDP » Biophysics Team » FLORIVAR

filedata="/home/biophysics/Desktop/Annamaria/Sepals"

#gaussianblurvalue=str(1)

gaussianblurvalue=str(2)

# threshold value for the Edgedetect procedure

#edgedetectvalue=str(10000)

edgedetectvalue=str(2000)

	Process.Stack__System__Open(path+i, 'Main', '0','','Yes')

	Process.Stack__System__Open(path+i, 'Main', '1','','Yes')

	Process.Stack__System__Save(outputdir+"MGX_"+i[:-4]+'_e'+edgedetectvalue+'_d'+dilatevalue+'.tif', 'Work', '0', '0','Yes')

import os

'''

Input:

 - directory with detected sepal contour stacks .tif

Output:

 - segmented meshes (up and down surfaces treated as cells)

 - csv file / sepale containing : up and down surface areas

'''

# directory with detected sepal contours

filedata1="/home/akiss/RDP/Projects/Sepals/RNA-Seq_Final/06.ContourDetection/JL_22C/mgx-contours"

################### Parameters ###########

# cubesize for mesh creation

cubesize=str(15)

# size of neighbourhood for the segmented curvature map

curv_neighb=str(100)

# segmentation

signal_ratio=str(3) # minimal border / cell signal ratio (if less, cells are fused)

# - cell

cell_blur_radius=str(100)

seed_radius=str(150)

# - border

border_distance=str(100)

border_blur_radius=str(100)

#########################################

filedata=filedata1+'/'

meshresult=filedata1+'-MGX-mesh'+cubesize+'/'

curvaturecsvresult=filedata1+'-MGX-curvature-csv/'

arearesult=filedata1+'-MGX-area/'

segresult=filedata1+'-MGX-seg/'

os.system("mkdir "+meshresult)

os.system("mkdir "+curvaturecsvresult)

os.system("mkdir "+arearesult)

os.system("mkdir "+segresult)

listfiles=os.listdir(filedata)

listfiles=[ i for i in listfiles if '.tif' in i]

Process.Stack__System__Clear_Work_Stack('0')

Process.Stack__System__Clear_Main_Stack('0')

Process.Stack__System__Clear_Main_Stack('1')

Process.Stack__System__Clear_Work_Stack('1')

for i in listfiles:	

	Process.Stack__System__Set_Current_Stack('Main', '0')

	Process.Stack__System__Open(filedata+i, 'Main', '0')

	# --- creating surface mesh

	Process.Mesh__Creation__Marching_Cubes_Surface(cubesize, '5000')

	Process.Mesh__Structure__Smooth_Mesh('1', 'No')

	Process.Mesh__Structure__Smooth_Mesh('1', 'No')

	Process.Mesh__Structure__Smooth_Mesh('1', 'No')

	Process.Mesh__Structure__Smooth_Mesh('1', 'No')

	# --- computing maximal curvature

	csvname=i[:-4]+'-carte-courbure-Maximal'+curv_neighb+'.csv'

	Process.Mesh__Signal__Project_Mesh_Curvature(curvaturecsvresult+csvname, 'Maximal', curv_neighb, 'Yes', '-50.0', '50.0', '85')

	meshname=i[:-4]+'-mesh.mgxm'

	Process.Mesh__System__Save(meshresult+meshname, 'no', '0')

	Process.Stack__System__Clear_Work_Stack('0')

	Process.Stack__System__Clear_Main_Stack('0')

	Process.Stack__System__Clear_Main_Stack('1')

	Process.Stack__System__Clear_Work_Stack('1')

	# --- watershed segmentation of the maximal curvature map

	Process.Mesh__Segmentation__Auto_Segmentation('Yes', 'No', cell_blur_radius, seed_radius, border_blur_radius, '100.0', border_distance, signal_ratio)

	segname=i[:-4]+'-seg.mgxm'

	Process.Mesh__System__Save(segresult+segname, 'no', '0')

	# --- computing the area of the faces

	csvname=i[:-4]+'-area.csv'

	Process.Mesh__Heat_Map__Heat_Map_Classic('Area', 'Geometry', arearesult+csvname, 'Geometry', 'No', '0', '65535', 'Yes', 'No', 'None', 'No', 'Decreasing', 'Ratio', '0.001', '1')

	# --- computing teh perimeter

	#csvname=i[:-4]+'-perimeter.csv'

	#Process.Mesh__Heat_Map__Heat_Map('/Geometry/Perimeter', 'No', 'No', '', 'No', '', '', 'Yes', 'Yes')

	# --- computing gaussian curvature

	#Process.Mesh__Signal__Project_Mesh_Curvature('', 'Gaussian', '100', 'Yes', '-50.0', '50.0', '85')

	"""print("Please put two seeds on the two sides of the sepal :-) ... ")

	a=input("")

	Process.Mesh__Segmentation__Watershed_Segmentation('50000')

	csvname=i[:-4]+'-area.csv'

	Process.Mesh__Heat_Map__Heat_Map_Classic('Area', 'Geometry', csvresult+csvname, 'Geometry', 'No', '0', '65535', 'Yes', 'No', 'None', 'No', 'Decreasing', 'Ratio', '0.001', '1')

	"""

import os

'''

Input:

 - directory with grey images of sepals

Output:

 - detected sepal contour stacks

'''

# directory of grey images

filedata="/home/biophysics/Desktop/Fanfan/Col-0_A-tif"

################### Parameters ###########

# smoothing

gaussianblurvalue=str(1)

# threshold value for the Edgedetect procedure 

edgedetectvalue=str(8000)

# xy dilation value

dilatevalue=str(0)

#########################################

path=filedata+'/'

outputdir=filedata+'-MGX-EdgeDetect_Blur'+gaussianblurvalue+'_ED'+edgedetectvalue+'_d'+dilatevalue+'/'

os.system("mkdir "+outputdir)

listfiles=os.listdir(path)

listfiles=[ i for i in listfiles if '.tif' in i]

Process.Stack__System__Clear_Work_Stack('0')

Process.Stack__System__Clear_Main_Stack('0')

Process.Stack__System__Clear_Main_Stack('1')

Process.Stack__System__Clear_Work_Stack('1')

for i in listfiles:	

	Process.Stack__System__Set_Current_Stack('Main', '0')

	Process.Stack__System__Open(path+i, 'Main', '0')

	Process.Stack__System__Open(path+i, 'Main', '1')

	Process.Stack__Filters__Gaussian_Blur_Stack(gaussianblurvalue, gaussianblurvalue, gaussianblurvalue)

	Process.Stack__MultiStack__Copy_Work_to_Main_Stack()

	Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 -> 2')

	Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')

	Process.Stack__MultiStack__Copy_Work_to_Main_Stack()

	Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <-> 2')

	Process.Stack__System__Set_Current_Stack('Main', '0')

	Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')

	Process.Stack__Morphology__Edge_Detect(edgedetectvalue, '2.0', '0.3', '30000')

	Process.Stack__Canvas__Reverse_Axes('No', 'No', 'Yes')

	Process.Stack__MultiStack__Swap_or_Copy_Stack_1_and_2('Main', '1 <- 2')

	Process.Stack__System__Set_Current_Stack('Both', '0')

	Process.Stack__MultiStack__Combine_Stacks('Product')

	Process.Stack__System__Set_Current_Stack('Work', '0')

	Process.Stack__Morphology__Dilate(dilatevalue, dilatevalue, "0", 'No', 'No')

	Process.Stack__System__Save(outputdir+"MGX_"+i[:-4]+'_e'+edgedetectvalue+'_d'+dilatevalue+'.tif', 'Work', '0', '0')

	Process.Stack__System__Clear_Work_Stack('0')

	Process.Stack__System__Clear_Main_Stack('0')

	Process.Stack__System__Clear_Main_Stack('1')

	Process.Stack__System__Clear_Work_Stack('1')

	Process.Stack__System__Clear_Main_Stack('2')

	Process.Stack__System__Clear_Work_Stack('2')

filedata1="/home/biophysics/Desktop/Annamaria/SepalContours"

#cubesize=str(15)

cubesize=str(5)

	Process.Stack__System__Open(filedata+i, 'Main', '0', '', "Yes")