def mincblob(op : str, grid : MincAtom, subdir : str = "tmp") -> Result[MincAtom]:
"""
Low-level mincblob wrapper with the one exception being the determinant option. By
default the inner clockwork of mincblob subtracts 1 from all determinant values that
are being calculated. As such, 1 needs to be added to the result of the mincblob call.
We will do that here, because it makes most sense here.
>>> stages = mincblob('determinant', MincAtom("/images/img_1.mnc", pipeline_sub_dir="/tmp")).stages
>>> [s.render() for s in stages]
['mincblob -clobber -determinant /images/img_1.mnc /tmp/img_1/img_1_determinant.mnc']
"""
if op not in ["determinant", "trace", "translation", "magnitude"]:
raise ValueError('mincblob: invalid operation %s' % op)
# if we are calculating the determinant, the first file produced is a temp file:
if op == "determinant":
out_file = grid.newname_with_suffix("_temp_det", subdir=subdir)
else:
out_file = grid.newname_with_suffix('_' + op, subdir=subdir)
stage = CmdStage(inputs=(grid,), outputs=(out_file,),
cmd=['mincblob', '-clobber', '-' + op, grid.path, out_file.path])
s = Stages([stage])
# now create the proper determinant if that's what was asked for
if op == "determinant":
result_file = s.defer(mincmath(op='add',
const=1,
vols=[out_file],
subdir=subdir,
new_name=grid.filename_wo_ext + "_det"))
else:
result_file = out_file
return Result(stages=s, output=result_file)
def reconstitute_laplacian_grid(cortex : MincAtom,
grid : MincAtom,
midline : MincAtom) -> Result[MincAtom]:
output_grid = grid.newname_with_suffix("_reconstituted")
stage = CmdStage(inputs=(cortex, grid, midline), outputs=(output_grid,),
cmd=["reconstitute_laplacian_grid", midline.path, cortex.path, grid.path, output_grid.path])
return Result(stages=Stages([stage]), output=output_grid)
def smooth_vector(source: MincAtom, fwhm: float) -> Result[MincAtom]:
outf = source.newname_with_suffix(
"_smooth_fwhm%s" % fwhm, subdir="tmp") # TODO smooth_displacement_?
cmd = [
'smooth_vector', '--clobber', '--filter',
'--fwhm=%s' % fwhm, source.path, outf.path
]
stage = CmdStage(inputs=(source, ), outputs=(outf, ), cmd=cmd)
return Result(stages=Stages([stage]), output=outf)
def reconstitute_laplacian_grid(cortex: MincAtom, grid: MincAtom,
midline: MincAtom) -> Result[MincAtom]:
output_grid = grid.newname_with_suffix("_reconstituted")
stage = CmdStage(inputs=(cortex, grid, midline),
outputs=(output_grid, ),
cmd=[
"reconstitute_laplacian_grid", midline.path,
cortex.path, grid.path, output_grid.path
])
return Result(stages=Stages([stage]), output=output_grid)
def minclaplace(input_grid : MincAtom,
extra_args : List[str] = [],
solution_vertices : Optional[FileAtom] = None,
create_surface : bool = True,) -> Result[FileAtom]:
# TODO the ambiguity of the return type is slightly annoying ...
# best to create separate minclaplace_at_vertices for the case when `--solve-at-vertices` is used?
solved = input_grid.newname_with_suffix("_solved", ext=".txt" if solution_vertices else ".mnc")
if create_surface:
out_surface = input_grid.newname_with_suffix("_surface", ext=".obj")
stage = CmdStage(inputs=(input_grid,), outputs=(solved,) + ((out_surface,) if create_surface else ()),
cmd=["minclaplace"]
+ (["--solve-at-vertices=%s" % solution_vertices.path]
if solution_vertices is not None else [])
+ (["--create-surface=%s" % out_surface.path] if create_surface else [])
+ extra_args
+ [input_grid.path, solved.path])
return Result(stages=Stages([stage]),
output=Namespace(solved=solved, surface=out_surface)
if create_surface else Namespace(solved=solved))
def mincblob(op: str, grid: MincAtom, subdir: str = "tmp") -> Result[MincAtom]:
"""
Low-level mincblob wrapper with the one exception being the determinant option. By
default the inner clockwork of mincblob subtracts 1 from all determinant values that
are being calculated. As such, 1 needs to be added to the result of the mincblob call.
We will do that here, because it makes most sense here.
>>> stages = mincblob('determinant', MincAtom("/images/img_1.mnc", pipeline_sub_dir="/tmp")).stages
>>> [s.render() for s in stages]
['mincblob -clobber -determinant /images/img_1.mnc /tmp/img_1/img_1_determinant.mnc']
"""
if op not in ["determinant", "trace", "translation", "magnitude"]:
raise ValueError('mincblob: invalid operation %s' % op)
# if we are calculating the determinant, the first file produced is a temp file:
if op == "determinant":
out_file = grid.newname_with_suffix("_temp_det", subdir=subdir)
else:
out_file = grid.newname_with_suffix('_' + op, subdir=subdir)
stage = CmdStage(
inputs=(grid, ),
outputs=(out_file, ),
cmd=['mincblob', '-clobber', '-' + op, grid.path, out_file.path])
s = Stages([stage])
# now create the proper determinant if that's what was asked for
if op == "determinant":
result_file = s.defer(
mincmath(op='add',
const=1,
vols=[out_file],
subdir=subdir,
new_name=grid.filename_wo_ext + "_det"))
else:
result_file = out_file
return Result(stages=s, output=result_file)
def minclaplace(
input_grid: MincAtom,
extra_args: List[str] = [],
solution_vertices: Optional[FileAtom] = None,
create_surface: bool = True,
) -> Result[FileAtom]:
# TODO the ambiguity of the return type is slightly annoying ...
# best to create separate minclaplace_at_vertices for the case when `--solve-at-vertices` is used?
solved = input_grid.newname_with_suffix(
"_solved", ext=".txt" if solution_vertices else ".mnc")
if create_surface:
out_surface = input_grid.newname_with_suffix("_surface", ext=".obj")
stage = CmdStage(
inputs=(input_grid, ),
outputs=(solved, ) + ((out_surface, ) if create_surface else ()),
cmd=["minclaplace"] +
(["--solve-at-vertices=%s" %
solution_vertices.path] if solution_vertices is not None else []) +
(["--create-surface=%s" % out_surface.path] if create_surface else [])
+ extra_args + [input_grid.path, solved.path])
return Result(stages=Stages([stage]),
output=Namespace(solved=solved, surface=out_surface)
if create_surface else Namespace(solved=solved))
def smooth_vector(source : MincAtom, fwhm : float) -> Result[MincAtom]:
outf = source.newname_with_suffix("_smooth_fwhm%s" % fwhm, subdir="tmp") # TODO smooth_displacement_?
cmd = ['smooth_vector', '--clobber', '--filter', '--fwhm=%s' % fwhm,
source.path, outf.path]
stage = CmdStage(inputs=(source,), outputs=(outf,), cmd=cmd)
return Result(stages=Stages([stage]), output=outf)