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ADD all utils interfaces the current converter can handle
Remaining issues: * implement parser for argstr: a series of float ("%f %f") and %g * parser for plain text output (possibly a pydra general function; see AvScale) * expand test data type (ConvertXFM)
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‎pydra/tasks/fsl/utils/complex.py

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from pydra.engine import specs
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from pydra import ShellCommandTask
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import typing as ty
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def complex_output(inputs, in_file):
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import attr
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if inputs.complex_cartesian:
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in_file = inputs.real_in_file
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elif inputs.complex_polar:
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in_file = inputs.magnitude_in_file
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elif inputs.complex_split or inputs.complex_merge:
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in_file = inputs.complex_in_file
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else:
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return None
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return f"{in_file}_cplx"
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input_fields = [
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(
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"complex_in_file",
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specs.File,
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{"help_string": "", "argstr": "{complex_in_file}", "position": 2},
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),
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(
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"complex_in_file2",
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specs.File,
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{"help_string": "", "argstr": "{complex_in_file2}", "position": 3},
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),
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(
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"real_in_file",
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specs.File,
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{"help_string": "", "argstr": "{real_in_file}", "position": 2},
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),
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(
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"imaginary_in_file",
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specs.File,
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{"help_string": "", "argstr": "{imaginary_in_file}", "position": 3},
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),
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(
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"magnitude_in_file",
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specs.File,
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{"help_string": "", "argstr": "{magnitude_in_file}", "position": 2},
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),
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(
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"phase_in_file",
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specs.File,
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{"help_string": "", "argstr": "{phase_in_file}", "position": 3},
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),
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(
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"complex_out_file",
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str,
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{
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"help_string": "",
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"argstr": "{complex_out_file}",
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"position": -3,
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"xor": [
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"complex_out_file",
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"magnitude_out_file",
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"phase_out_file",
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"real_out_file",
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"imaginary_out_file",
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"real_polar",
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"real_cartesian",
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],
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},
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),
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(
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"magnitude_out_file",
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str,
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{
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"help_string": "",
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"argstr": "{magnitude_out_file}",
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"position": -4,
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"xor": [
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"complex_out_file",
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"real_out_file",
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"imaginary_out_file",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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"output_file_template": "{in_file}_mag",
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},
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),
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(
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"phase_out_file",
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str,
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{
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"help_string": "",
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"argstr": "{phase_out_file}",
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"position": -3,
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"xor": [
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"complex_out_file",
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"real_out_file",
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"imaginary_out_file",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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"output_file_template": "{in_file}_phase",
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},
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),
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(
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"real_out_file",
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str,
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{
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"help_string": "",
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"argstr": "{real_out_file}",
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"position": -4,
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"xor": [
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"complex_out_file",
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"magnitude_out_file",
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"phase_out_file",
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"real_polar",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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"output_file_template": "{in_file}_real",
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},
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),
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(
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"imaginary_out_file",
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str,
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{
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"help_string": "",
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"argstr": "{imaginary_out_file}",
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"position": -3,
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"xor": [
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"complex_out_file",
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"magnitude_out_file",
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"phase_out_file",
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"real_polar",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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"output_file_template": "{in_file}_imag",
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},
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),
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("start_vol", int, {"help_string": "", "argstr": "{start_vol}", "position": -2}),
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("end_vol", int, {"help_string": "", "argstr": "{end_vol}", "position": -1}),
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(
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"real_polar",
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bool,
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{
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"help_string": "",
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"argstr": "-realpolar",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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},
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),
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(
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"real_cartesian",
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bool,
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{
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"help_string": "",
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"argstr": "-realcartesian",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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},
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),
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(
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"complex_cartesian",
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bool,
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{
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"help_string": "",
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"argstr": "-complex",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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},
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),
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(
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"complex_polar",
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bool,
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{
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"help_string": "",
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"argstr": "-complexpolar",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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},
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),
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(
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"complex_split",
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bool,
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{
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"help_string": "",
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"argstr": "-complexsplit",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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],
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},
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),
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(
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"complex_merge",
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bool,
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{
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"help_string": "",
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"argstr": "-complexmerge",
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"position": 1,
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"xor": [
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"real_polar",
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"real_cartesian",
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"complex_cartesian",
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"complex_polar",
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"complex_split",
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"complex_merge",
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"start_vol",
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"end_vol",
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],
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},
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),
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]
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Complex_input_spec = specs.SpecInfo(
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name="Input", fields=input_fields, bases=(specs.ShellSpec,)
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)
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output_fields = []
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Complex_output_spec = specs.SpecInfo(
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name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
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)
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class Complex(ShellCommandTask):
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input_spec = Complex_input_spec
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output_spec = Complex_output_spec
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executable = "fslcomplex"

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