Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Convert output types from File to String #197

Merged
merged 1 commit into from
Dec 19, 2024
Merged

Convert output types from File to String #197

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
57 changes: 43 additions & 14 deletions descriptors/fsl/fugue.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@
{
"id": "fmap_out_file",
"name": "Fmap out file",
"type": "File",
"type": "String",
"value-key": "[FMAP_OUT_FILE]",
"command-line-flag": "--savefmap",
"command-line-flag-separator": "=",
Expand Down Expand Up @@ -103,7 +103,9 @@
"command-line-flag": "--icorr",
"description": "Apply intensity correction to unwarping (pixel shift method only).",
"optional": true,
"requires-inputs": ["shift_in_file"]
"requires-inputs": [
"shift_in_file"
]
},
{
"id": "icorr_only",
Expand All @@ -113,7 +115,9 @@
"command-line-flag": "--icorronly",
"description": "Apply intensity correction only.",
"optional": true,
"requires-inputs": ["unwarped_file"]
"requires-inputs": [
"unwarped_file"
]
},
{
"id": "in_file",
Expand Down Expand Up @@ -178,7 +182,12 @@
"value-key": "[OUTPUT_TYPE]",
"description": "'nifti' or 'nifti_pair' or 'nifti_gz' or 'nifti_pair_gz'. Fsl output type.",
"optional": true,
"value-choices": ["NIFTI", "NIFTI_PAIR", "NIFTI_GZ", "NIFTI_PAIR_GZ"]
"value-choices": [
"NIFTI",
"NIFTI_PAIR",
"NIFTI_GZ",
"NIFTI_PAIR_GZ"
]
},
{
"id": "pava",
Expand Down Expand Up @@ -268,7 +277,7 @@
{
"id": "shift_out_file",
"name": "Shift out file",
"type": "File",
"type": "String",
"value-key": "[SHIFT_OUT_FILE]",
"command-line-flag": "--saveshift",
"command-line-flag-separator": "=",
Expand Down Expand Up @@ -304,29 +313,40 @@
"command-line-flag-separator": "=",
"description": "'x' or 'y' or 'z' or 'x-' or 'y-' or 'z-'. Specifies direction of warping (default y).",
"optional": true,
"value-choices": ["x", "y", "z", "x-", "y-", "z-"]
"value-choices": [
"x",
"y",
"z",
"x-",
"y-",
"z-"
]
},
{
"id": "unwarped_file",
"name": "Unwarped file",
"type": "File",
"type": "String",
"value-key": "[UNWARPED_FILE]",
"command-line-flag": "--unwarp",
"command-line-flag-separator": "=",
"description": "Apply unwarping and save as filename.",
"optional": true,
"requires-inputs": ["in_file"]
"requires-inputs": [
"in_file"
]
},
{
"id": "warped_file",
"name": "Warped file",
"type": "File",
"type": "String",
"value-key": "[WARPED_FILE]",
"command-line-flag": "--warp",
"command-line-flag-separator": "=",
"description": "Apply forward warping and save as filename.",
"optional": true,
"requires-inputs": ["in_file"]
"requires-inputs": [
"in_file"
]
}
],
"output-files": [
Expand Down Expand Up @@ -363,19 +383,28 @@
{
"id": "mutex_group",
"name": "Mutex group",
"members": ["warped_file", "unwarped_file"],
"members": [
"warped_file",
"unwarped_file"
],
"mutually-exclusive": true
},
{
"id": "mutex_group_2",
"name": "Mutex group 2",
"members": ["save_unmasked_shift", "save_shift"],
"members": [
"save_unmasked_shift",
"save_shift"
],
"mutually-exclusive": true
},
{
"id": "mutex_group_3",
"name": "Mutex group 3",
"members": ["save_fmap", "save_unmasked_fmap"],
"members": [
"save_fmap",
"save_unmasked_fmap"
],
"mutually-exclusive": true
}
],
Expand All @@ -385,4 +414,4 @@
"type": "docker",
"image": "brainlife/fsl:6.0.4-patched2"
}
}
}
26 changes: 13 additions & 13 deletions python/src/niwrap/fsl/fugue.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
import dataclasses

FUGUE_METADATA = Metadata(
id="d264261226a39feda65ebd1686c5c1c1076e293f.boutiques",
id="e92886e40bebff1fca6ad036e63b3a6f487c4e4c.boutiques",
name="fugue",
package="fsl",
container_image_tag="brainlife/fsl:6.0.4-patched2",
Expand Down Expand Up @@ -37,7 +37,7 @@ def fugue(
dwell_time: float | None = None,
dwell_to_asym_ratio: float | None = None,
fmap_in_file: InputPathType | None = None,
fmap_out_file: InputPathType | None = None,
fmap_out_file: str | None = None,
forward_warping: bool = False,
fourier_order: int | None = None,
icorr: bool = False,
Expand All @@ -58,12 +58,12 @@ def fugue(
save_unmasked_fmap: bool = False,
save_unmasked_shift: bool = False,
shift_in_file: InputPathType | None = None,
shift_out_file: InputPathType | None = None,
shift_out_file: str | None = None,
smooth2d: float | None = None,
smooth3d: float | None = None,
unwarp_direction: typing.Literal["x", "y", "z", "x-", "y-", "z-"] | None = None,
unwarped_file: InputPathType | None = None,
warped_file: InputPathType | None = None,
unwarped_file: str | None = None,
warped_file: str | None = None,
runner: Runner | None = None,
) -> FugueOutputs:
"""
Expand Down Expand Up @@ -133,7 +133,7 @@ def fugue(
if fmap_in_file is not None:
cargs.append("--loadfmap=" + execution.input_file(fmap_in_file))
if fmap_out_file is not None:
cargs.append("--savefmap=" + execution.input_file(fmap_out_file))
cargs.append("--savefmap=" + fmap_out_file)
if forward_warping:
cargs.append("--forward_warping")
if fourier_order is not None:
Expand Down Expand Up @@ -175,23 +175,23 @@ def fugue(
if shift_in_file is not None:
cargs.append("--loadshift=" + execution.input_file(shift_in_file))
if shift_out_file is not None:
cargs.append("--saveshift=" + execution.input_file(shift_out_file))
cargs.append("--saveshift=" + shift_out_file)
if smooth2d is not None:
cargs.append("--smooth2=" + str(smooth2d))
if smooth3d is not None:
cargs.append("--smooth3=" + str(smooth3d))
if unwarp_direction is not None:
cargs.append("--unwarpdir=" + unwarp_direction)
if unwarped_file is not None:
cargs.append("--unwarp=" + execution.input_file(unwarped_file))
cargs.append("--unwarp=" + unwarped_file)
if warped_file is not None:
cargs.append("--warp=" + execution.input_file(warped_file))
cargs.append("--warp=" + warped_file)
ret = FugueOutputs(
root=execution.output_file("."),
fmap_out_file_outfile=execution.output_file(pathlib.Path(fmap_out_file).name) if (fmap_out_file is not None) else None,
shift_out_file_outfile=execution.output_file(pathlib.Path(shift_out_file).name) if (shift_out_file is not None) else None,
unwarped_file_outfile=execution.output_file(pathlib.Path(unwarped_file).name) if (unwarped_file is not None) else None,
warped_file_outfile=execution.output_file(pathlib.Path(warped_file).name) if (warped_file is not None) else None,
fmap_out_file_outfile=execution.output_file(fmap_out_file) if (fmap_out_file is not None) else None,
shift_out_file_outfile=execution.output_file(shift_out_file) if (shift_out_file is not None) else None,
unwarped_file_outfile=execution.output_file(unwarped_file) if (unwarped_file is not None) else None,
warped_file_outfile=execution.output_file(warped_file) if (warped_file is not None) else None,
)
execution.run(cargs)
return ret
Expand Down
Loading