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, perimeter

'''

# cubesize for mesh creation

cubesize=str(30)

# size of neighbourhood for the segmented curvature map

curv_neighb=str(50)

# directory with detected sepal contours

filedata1='/directory/of/sepal/contour/stacks'

filedata=filedata1+'/'

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

csvresult=filedata1+'-MGX-csv/'

segresult=filedata1+'-MGX-seg/'

os.system("mkdir "+meshresult)

os.system("mkdir "+csvresult)

os.system("mkdir "+segresult)

listfiles=os.listdir(filedata)

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')

	Process.Mesh__Creation__Marching_Cubes_Surface('30', '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')

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

	Process.Mesh__Signal__Project_Mesh_Curvature(csvresult+csvname, 'Maximal', '50', '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')

	#testing autosegmentation with updated parameters

	Process.Mesh__Segmentation__Auto_Segmentation('Yes', 'No', '170.0', '170.0', '65', '200.0', '100.0', '1.8')

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

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

	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')

	"""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')

"""

#Process.Mesh__Segmentation__Watershed_Segmentation('50000')

#Process.Mesh__Heat_Map__Heat_Map_Classic('Area', 'Geometry', '/home/biophysics/Desktop/Alexis/10_3Dshape/oriented-sepals-tif-test-MGX-csv/spreadsheet.csv', 'Geometry', 'No', '0', '65535', 'Yes', 'No', 'None', 'No', 'Decreasing', 'Ratio', '0.001', '1')

from titk_tools.rw.registration import apply_transfo_on_seg1

//////////////////////////////////////////////////////////////////////////////////

//The script will process all your .inr.gz files in the chosen folder.

//The stacks will be saved in subfolders named as the treated lif files.

print ("===========================");

print ("==== Macro flip-vertically-mgx.ijm ====");

//Choose the directory containing your .inr.gz files//

dir = getDirectory("Choose a directory")

setBatchMode(true);

list = getFileList(dir);

print(dir);

ShortNameDir=substring(dir,0,lastIndexOf(dir,"/"));

print (ShortNameDir);

dirout=ShortNameDir+"-flipped/";

print("Creating output directory ",dirout);

File.makeDirectory(dirout);

for (FileInd=0; FileInd<list.length; FileInd++){

	FileName = list[FileInd];

	if(endsWith (FileName, ".tif")){

		print ("### Processing ",FileName," ###");

		path = dir+FileName;

		pathout = dirout+FileName;

		print("avant open", FileName,"!");

		//run("Bio-Formats Importer", "open=["+path+"] color_mode=Default view=Hyperstack stack_order=XYCZT use_virtual_stack open_all_series ");

		open(path);

		print("apres open", FileName,"!");

		run("Flip Vertically", "stack");

		saveAs("Tiff", pathout);

		print("avant close", FileName,"!");

		run("Close All");

		print("Done with", FileName,"!");

	} else {

	print("### ",FileName," Not a .tif file ###");

	};

};	

print("Done with this folder!!!");