def converter_sem(interface_spec):
names = interface_spec.all_trait_names()
fields_pdr_dict = {}
position_dict = {}
for nm in names:
try:
fld = interface_spec.traits()[nm]
except KeyError:
pass
else:
if nm in ['output_type', 'args', 'environ', 'environ_items', '__all__',
'trait_added', 'trait_modified', "printVersionInfo"]:
continue
fld_pdr, pos = pydra_input_spec(fld, nm)
fields_pdr_dict[nm] = fld_pdr
if pos is not None:
position_dict[nm] = pos
if position_dict:
fields_pdr_dict = fix_position(fields_pdr_dict, position_dict)
fields_pdr_l = list(fields_pdr_dict.items())
spec_pdr = specs.SpecInfo(name="Input", fields=fields_pdr_l, bases=(specs.ShellSpec,))
return spec_pdr
def pydra_specs(self, write=False, dirname=None):
""" creating pydra input/output spec from nipype specs
if write is True, a pydra Task class will be written to the file together with tests
"""
input_fields_pdr, inp_templates = self.convert_input_fields()
output_fields_pdr = self.convert_output_spec(
fields_from_template=inp_templates)
input_spec_pydra = specs.SpecInfo(name="Input",
fields=input_fields_pdr,
bases=(specs.ShellSpec, ))
output_spec_pydra = specs.SpecInfo(name="Output",
fields=output_fields_pdr,
bases=(specs.ShellOutSpec, ))
if write:
if dirname is None:
raise Exception("dirname has to be provided if write is True")
self.write_pydra_files(dirname=dirname,
pydra_input_spec=input_fields_pdr,
pydra_output_spec=output_fields_pdr)
return input_spec_pydra, output_spec_pydra
(
"outputVolume",
attr.ib(
type=File,
metadata={
"help_string": "Resulting deformed image",
"exists": True
}
),
),
(
"transform",
attr.ib(
type=File,
metadata={
"help_string": "Filename for the transform file",
"exists": True
}
),
),
]
input_spec_pdr = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
output_spec_pdr = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellSpec,))
BRAINSStripRotation_task = pydra.ShellCommandTask(
name="BRAINSStripRotation",
executable=" BRAINSStripRotation ",
input_spec=input_spec_pdr,
output_spec=output_spec_pdr
)
"argstr": "{z_size}",
"position": 7
}),
("t_min", int, {
"help_string": "",
"argstr": "{t_min}",
"position": 8
}),
("t_size", int, {
"help_string": "",
"argstr": "{t_size}",
"position": 9
}),
]
ExtractROI_input_spec = specs.SpecInfo(name="Input",
fields=input_fields,
bases=(specs.ShellSpec, ))
output_fields = []
ExtractROI_output_spec = specs.SpecInfo(name="Output",
fields=output_fields,
bases=(specs.ShellOutSpec, ))
class ExtractROI(ShellCommandTask):
"""
Example
-------
>>> task = ExtractROI()
>>> task.inputs.in_file = "test.nii.gz"
>>> task.inputs.t_min = 0
"position": 1,
"output_file_template": "{dest_file}",
},
),
(
"ignore_dims",
bool,
{
"help_string": "Do not copy image dimensions",
"argstr": "-d",
"position": "-1",
},
),
]
CopyGeom_input_spec = specs.SpecInfo(name="Input",
fields=input_fields,
bases=(specs.ShellSpec, ))
output_fields = [(
"out_file",
specs.File,
{
"help_string": "image with new geometry header",
"requires": ["in_file", "dest_file"],
"output_file_template": "{dest_file}",
},
)]
CopyGeom_output_spec = specs.SpecInfo(name="Output",
fields=output_fields,
bases=(specs.ShellOutSpec, ))
{
"help_string": "save rms displacement parameters",
"argstr": "-rmsabs -rmsrel",
},
),
(
"ref_file",
specs.File,
{
"help_string": "target image for motion correction",
"argstr": "-reffile {ref_file}",
},
),
]
MCFLIRT_input_spec = specs.SpecInfo(
name="Input", fields=input_fields, bases=(specs.ShellSpec,)
)
output_fields = [
(
"variance_img",
specs.File,
{
"help_string": "variance image",
"requires": ["in_file", ("stats_imgs", True)],
"output_file_template": "{out_file}_variance.ext",
},
),
(
"std_img",
specs.File,
"xor": ["out_relwarp"],
},
),
(
"out_relwarp",
bool,
{
"help_string":
"If set it indicates that the warps in --out should be relative, i.e. the values in --out are displacements from the coordinates in --ref.",
"argstr": "--relout",
"xor": ["out_abswarp"],
},
),
]
ConvertWarp_input_spec = specs.SpecInfo(name="Input",
fields=input_fields,
bases=(specs.ShellSpec, ))
output_fields = []
ConvertWarp_output_spec = specs.SpecInfo(name="Output",
fields=output_fields,
bases=(specs.ShellOutSpec, ))
class ConvertWarp(ShellCommandTask):
"""
Example
-------
>>> task = ConvertWarp()
>>> task.inputs.warp1 = "warpfield.nii"
>>> task.inputs.reference = "test.nii.gz"
"label_file",
str,
{
"help_string": "saving the area labels output",
"argstr": "--labels={label_file}",
},
),
(
"removeramps",
bool,
{
"help_string": "remove phase ramps during unwrapping",
"argstr": "--removeramps",
},
),
]
PRELUDE_input_spec = specs.SpecInfo(
name="Input", fields=input_fields, bases=(specs.ShellSpec,)
)
output_fields = []
PRELUDE_output_spec = specs.SpecInfo(
name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
)
class PRELUDE(ShellCommandTask):
input_spec = PRELUDE_input_spec
output_spec = PRELUDE_output_spec
executable = "prelude"
{
"help_string": "3-tuple of new dimension order",
"argstr": "{new_dims} {new_dims} {new_dims}",
"mandatory": True,
},
),
(
"out_file",
str,
{
"help_string": "image to write",
"argstr": "{out_file}",
"output_file_template": "{in_file}_newdims",
},
),
]
SwapDimensions_input_spec = specs.SpecInfo(
name="Input", fields=input_fields, bases=(specs.ShellSpec,)
)
output_fields = []
SwapDimensions_output_spec = specs.SpecInfo(
name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
)
class SwapDimensions(ShellCommandTask):
input_spec = SwapDimensions_input_spec
output_spec = SwapDimensions_output_spec
executable = "fslswapdim"
"argstr": ""
},
),
(
"index_mask_file",
specs.File,
{
"help_string":
"generate seperate n submasks from indexMask, for indexvalues 1..n where n is the maximum index value in indexMask, and generate statistics for each submask",
"argstr": "-K {index_mask_file}",
"position": 2,
},
),
]
ImageStats_input_spec = specs.SpecInfo(name="Input",
fields=input_fields,
bases=(specs.ShellSpec, ))
output_fields = [(
"out_stat",
ty.Any,
{
"help_string": "stats output",
"requires": ["in_file", "op_string"]
},
)]
ImageStats_output_spec = specs.SpecInfo(name="Output",
fields=output_fields,
bases=(specs.ShellOutSpec, ))
{
"argstr": "--tglobal",
"help_string": "shift in fraction of TR, range 0:1 (default is 0.5 = no shift)",
},
),
(
"custom_order",
specs.File,
{
"argstr": "--ocustom={custom_order}",
"help_string": "filename of single-column custom interleave order file (first slice is referred to as 1 not 0)",
},
),
]
SliceTimer_input_spec = specs.SpecInfo(
name="Input", fields=input_fields, bases=(specs.ShellSpec,)
)
output_fields = [
(
"slice_time_corrected_file",
specs.File,
{
"help_string": "slice time corrected file",
"requires": ["out_file"],
"output_file_template": "{out_file}",
},
)
]
SliceTimer_output_spec = specs.SpecInfo(
name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
(
"userDefineMinimum",
attr.ib(
type=float,
metadata={
"help_string": "User define minimum value",
"argstr": "--userDefineMinimum %f",
},
),
),
(
"userDefineMinimum",
attr.ib(
type=float,
metadata={
"help_string": "User define maximum value",
"argstr": "--userDefineMaximum %f",
},
),
),
]
input_spec_pdr = specs.SpecInfo(name="Input",
fields=fields,
bases=(specs.ShellSpec, ))
task = pydra.ShellCommandTask(name="example",
executable=" BRAINSLabelStats ",
input_spec=input_spec_pdr)
#print("task command line generated by pydra", task.cmdline)
