Convert segmentation HDF to .mod file appropriate for imod.

tomoseg_to_imod.py

"""
Script to convert eman2 segmentation hdf maps to imod model files at a user defined contour level.
Requires python>=3.5 as well as having Eman2 and IMOD in the path.

Usage: `python3 tomoseg_to_imod.py -i EXAMPLE.hdf -o EXAMPLE.mod -t 0.8`

Author: Benjamin Barad <benjamin.barad@gmail.com>
"""

import argparse
import shutil
import subprocess


# Confirm utilities are in path before proceeding
try:
        assert shutil.which("e2proc3d.py") is not None
except AssertionError as e:
        print("Eman2 is not in the path")
        raise
try:
        assert shutil.which("imodauto") is not None
except AssertionError as e:
        print("IMOD is not in the path")
        raise

# Parse Arguments
parser = argparse.ArgumentParser(description='Convert eman2 segmentations to imod model files')
parser.add_argument('-i', "--input", dest="input", type=str, required=True,
                    help='Input HDF tomoseg file.')
parser.add_argument('-o', '--output', dest="output", type=str, nargs="?", default=None, help="Output imod .mod files - default same as input file")
parser.add_argument('-t', '--threshold', dest='threshold', type=float, nargs="?", default=0.8, help='Threshold for contouring')
parser.add_argument('-k', dest='sigma', type=float, nargs="?", default=10, help='Sigma for gaussian filtering')
parser.add_argument('-R', '--reduction', dest='reduction_tolerance', type=float, nargs="?", default=0.5, help="Tolerance for point reduction in contour creation.")
parser.add_argument('-S', '--smoothing', dest='smoothing', type=bool, action='store_true', help="Smooth contours using smoothsurf before meshing?")
parser.add_argument('-z', '--zpasses', dest='z_pass', type=int, default=3, help="Distance used to join meshes in z (in voxels)")



args = parser.parse_args()
inputfile = args.input
print(inputfile)

if not inputfile[-4:] == ".hdf":
        print("Input file not hdf file, please adjust.")
        print("Input file: {}".format(inputfile))
        exit(1)
outputfile = args.output
if outputfile == None:
        outputfile = inputfile[:-4] + ".mod"

threshold = args.threshold

# Make MRC file
mrcfile = inputfile[:-4] + ".mrc"
subprocess.run(["e2proc3d.py","--origin=0,0,0",inputfile, mrcfile])

# Make IMOD mod file:
subprocess.run(["imodauto","-u","-R", str(args.reduction_tolerance) ,"-k", str(args.sigma),"-h", str(threshold),"-c 0.392, 0.584, 0.929","-o", mrcfile, outputfile])
if args.smoothing:
	subprocess.run(["smoothsurf", "-nz", "1", "-dist", "3" ,"-cont", "3", outputfile, outputfile])
subprocess.run(["imodmesh", "-CTs", "-P", args.z_pass, outputfile, outputfile])