xfmjoin

#!/usr/bin/env python3
#
# Joins together several xfm files, leaving the original displacement volumes
# where they are.
#
# Note: this operation means that resulting xfm file uses absolute paths, and
# so will become invalid if any of the displacement volumes are moved.
#
# Assuming the following structure for and XFM file:
#
#    MNI Transform File
#    %Thu Jan 10 17:15:06 2013>>> minctracc ....
#
#    Transform_Type = Grid_Transform;
#    Displacement_Volume = 0021_0295_0413_grid_0.mnc;
#    Transform_Type = Linear;
#    Linear_Transform =
#     0.9772509301 -0.09474506176 -0.03084412052 -19.081777
#     0.07106130268 0.9716283851 -0.18306245 -24.92575407
#     0.04604540017 0.2288221291 0.9933863879 -4.204577453;
#    Transform_Type = Grid_Transform;
#    Displacement_Volume = 0021_0295_0413_grid_1.mnc;
#    Transform_Type = Linear;
#    Linear_Transform =
#     0.9938300533 0.007599120733 -0.03030895914 12.17102408
#     -0.006040286116 0.9816438948 0.1181265793 2.516647066
#     0.02683032485 -0.118368505 0.9499845023 4.303799096;
#
#
# Jon Pipitone, jon.pipitone@utoronto.ca, 2013
#

from __future__ import print_function
from builtins import str
from builtins import map
from builtins import object
import sys
import copy
import datetime
from os import getcwd
from os.path import dirname, normpath, join


def _pop(l):
    while l and l[0].strip() == "":
        l.pop(0)
    return l and l.pop(0).strip() or None


class Transform(object):

    def __repr__(self):
        return "\n".join([self.type] + self.transform)


class GridTransform(Transform):

    def update_volume_path(self, relative_to='source'):
        if relative_to == 'source':
            relative_to_path = dirname(self.fromfile)
        else:
            relative_to_path = relative_to

        key, grid = [x.strip().strip(';') for x in self.transform[0].split("=")]
        grid = normpath(join(relative_to_path, grid))
        self.transform = ["%s = %s;" % (key, grid)]


class XFM(object):

    def __init__(self, xfmfile_path=None):
        self.header = None
        self.history = []
        self.transforms = []
        self.xfmfile_path = xfmfile_path

        if xfmfile_path:
            self.populate(xfmfile_path)

    def populate(self, xfmfile_path=None):

        lines = open(xfmfile_path).readlines()
        while lines:
            line = _pop(lines)
            if line.startswith('%'):
                self.history.append(line)
                continue
            if line.startswith("MNI"):
                self.header = line
                continue

            if line.startswith("Transform_Type = Grid_Transform;"):
                transform = GridTransform()
                transform.fromfile = xfmfile_path
                transform.type = line
                transform.transform = [_pop(lines)]
                self.transforms.append(transform)
                continue
            if line.startswith("Transform_Type = Linear;"):
                transform = Transform()
                transform.fromfile = xfmfile_path
                transform.type = line
                transform.transform = [
                    _pop(lines),
                    _pop(lines),
                    _pop(lines),
                    _pop(lines)]
                self.transforms.append(transform)
                continue

            print(("Ignoring line:", line))

    def __repr__(self):
        return "\n".join([self.header] + self.history +
                         list(map(str, self.transforms)))

    def merge(self, xfms, paths_relative_to='source'):
        self.history.append(
            "%% %s >> Merging %s" %
            (datetime.datetime.now().isoformat(),
             ", ".join([x.xfmfile_path for x in xfms])))
        for xfm in xfms:
            self.header = xfm.header
            self.history.extend(xfm.history)
            for transform in map(copy.deepcopy, xfm.transforms):
                if isinstance(transform, GridTransform):
                    transform.update_volume_path(relative_to=paths_relative_to)
                self.transforms.append(transform)


if __name__ == '__main__':

    if len(sys.argv) <= 1:
        print("Joins together several xfm files, leaving the original displacement volumes")
        print("in place.")
        print("")
        print("Usage: %s xfm [xfm ...] merged.xfm" % sys.argv[0])
        print("")
        sys.exit(-1)

    merged_xfm = XFM()
    merged_xfm.merge(list(map(XFM, sys.argv[1:-1])))
    open(sys.argv[-1], 'w').write(str(merged_xfm))