Laboratoire RDP » Biophysics Team » FLORIVAR

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')

        """