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Bump codecov/codecov-action from 3 to 4 #18

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Bump codecov/codecov-action from 3 to 4 #18

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6c17ef9
Bump codecov/codecov-action from 3 to 4
dependabot[bot] Mar 25, 2024
af4104b
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Mar 25, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci-cd.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -193,7 +193,7 @@ jobs:
--cov-report xml

- name: Upload to CodeCov
uses: codecov/codecov-action@v3
uses: codecov/codecov-action@v4
if: ${{ always() }}
with:
files: coverage.xml
Expand Down
10 changes: 8 additions & 2 deletions src/pydra/tasks/ants/__init__.py
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Expand Up @@ -7,8 +7,14 @@

from pydra.tasks.ants.apply_transforms import ApplyTransforms
from pydra.tasks.ants.bias_correction import N4BiasFieldCorrection
from pydra.tasks.ants.create_jacobian_determinant_image import CreateJacobianDeterminantImage
from pydra.tasks.ants.registration import Registration, registration_syn, registration_syn_quick
from pydra.tasks.ants.create_jacobian_determinant_image import (
CreateJacobianDeterminantImage,
)
from pydra.tasks.ants.registration import (
Registration,
registration_syn,
registration_syn_quick,
)

__all__ = [
"ApplyTransforms",
Expand Down
83 changes: 66 additions & 17 deletions src/pydra/tasks/ants/apply_transforms.py
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Expand Up @@ -25,7 +25,9 @@ def _format_output(
)


def _format_interpolation(interpolator: str, sigma: float, alpha: float, order: int) -> str:
def _format_interpolation(
interpolator: str, sigma: float, alpha: float, order: int
) -> str:
return "-n {}{}".format(
interpolator,
f"[{order}]"
Expand Down Expand Up @@ -70,7 +72,11 @@ class ApplyTransforms(ShellCommandTask):
@define(kw_only=True)
class InputSpec(ShellSpec):
dimensionality: int = field(
metadata={"help_string": "image dimensionality", "argstr": "-d", "allowed_values": {2, 3, 4}}
metadata={
"help_string": "image dimensionality",
"argstr": "-d",
"allowed_values": {2, 3, 4},
}
)

image_type: str = field(
Expand All @@ -85,19 +91,32 @@ class InputSpec(ShellSpec):
},
)

moving_image: PathLike = field(metadata={"help_string": "moving image", "mandatory": True, "argstr": "-i"})
moving_image: PathLike = field(
metadata={"help_string": "moving image", "mandatory": True, "argstr": "-i"}
)

fixed_image: PathLike = field(metadata={"help_string": "fixed image", "mandatory": True, "argstr": "-r"})
fixed_image: PathLike = field(
metadata={"help_string": "fixed image", "mandatory": True, "argstr": "-r"}
)

output_: str = field(
metadata={"help_string": "output parameter", "readonly": True, "formatter": _format_output}
metadata={
"help_string": "output parameter",
"readonly": True,
"formatter": _format_output,
}
)

output_image: str = field(
metadata={"help_string": "output image", "output_file_template": "{moving_image}_warped"}
metadata={
"help_string": "output image",
"output_file_template": "{moving_image}_warped",
}
)

save_warp_field: bool = field(metadata={"help_string": "save composite warp field"})
save_warp_field: bool = field(
metadata={"help_string": "save composite warp field"}
)

output_warp_field: str = field(
metadata={
Expand All @@ -107,7 +126,9 @@ class InputSpec(ShellSpec):
}
)

save_transform: bool = field(metadata={"help_string": "save composite transform"})
save_transform: bool = field(
metadata={"help_string": "save composite transform"}
)

output_transform: str = field(
metadata={
Expand All @@ -118,10 +139,16 @@ class InputSpec(ShellSpec):
}
)

invert_transform: bool = field(default=False, metadata={"help_string": "invert composite transform"})
invert_transform: bool = field(
default=False, metadata={"help_string": "invert composite transform"}
)

interpolation_: str = field(
metadata={"help_string": "interpolation parameter", "readonly": True, "formatter": _format_interpolation}
metadata={
"help_string": "interpolation parameter",
"readonly": True,
"formatter": _format_interpolation,
}
)

interpolator: str = field(
Expand All @@ -141,17 +168,31 @@ class InputSpec(ShellSpec):
},
)

sigma: float = field(default=1.0, metadata={"help_string": "sigma parameter interpolation"})
sigma: float = field(
default=1.0, metadata={"help_string": "sigma parameter interpolation"}
)

alpha: float = field(default=1.0, metadata={"help_string": "alpha parameter for interpolation"})
alpha: float = field(
default=1.0, metadata={"help_string": "alpha parameter for interpolation"}
)

order: int = field(default=3, metadata={"help_string": "order parameter for interpolation"})
order: int = field(
default=3, metadata={"help_string": "order parameter for interpolation"}
)

output_datatype: str = field(
metadata={
"help_string": "force output image datatype",
"argstr": "-u",
"allowed_values": {"char", "uchar", "short", "int", "float", "double", "default"},
"allowed_values": {
"char",
"uchar",
"short",
"int",
"float",
"double",
"default",
},
}
)

Expand All @@ -163,16 +204,24 @@ class InputSpec(ShellSpec):
if not input_transforms
else " ".join(f"-t {f}" for f in input_transforms)
if not invert_transforms
else " ".join(f"-t [{f},{int(i)}]" for f, i in zip(input_transforms, invert_transforms))
else " ".join(
f"-t [{f},{int(i)}]"
for f, i in zip(input_transforms, invert_transforms)
)
),
}
)

invert_transforms: Sequence[bool] = field(
metadata={"help_string": "which transforms to invert", "requires": {"input_transforms"}}
metadata={
"help_string": "which transforms to invert",
"requires": {"input_transforms"},
}
)

default_value: float = field(metadata={"help_string": "default voxel value", "argstr": "-f"})
default_value: float = field(
metadata={"help_string": "default voxel value", "argstr": "-f"}
)

use_float_precision: bool = field(
default=False,
Expand Down
64 changes: 49 additions & 15 deletions src/pydra/tasks/ants/bias_correction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,12 +22,20 @@ class N4BiasFieldCorrection(ShellCommandTask):
@define(kw_only=True)
class InputSpec(ShellSpec):
dimensionality: int = field(
metadata={"help_string": "image dimensionality", "argstr": "-d", "allowed_values": {2, 3, 4}}
metadata={
"help_string": "image dimensionality",
"argstr": "-d",
"allowed_values": {2, 3, 4},
}
)

input_image: PathLike = field(metadata={"help_string": "input image", "mandatory": True, "argstr": "-i"})
input_image: PathLike = field(
metadata={"help_string": "input image", "mandatory": True, "argstr": "-i"}
)

mask_image: PathLike = field(metadata={"help_string": "mask image", "argstr": "-x"})
mask_image: PathLike = field(
metadata={"help_string": "mask image", "argstr": "-x"}
)

rescale_intensities: bool = field(
default=True,
Expand All @@ -37,9 +45,13 @@ class InputSpec(ShellSpec):
},
)

weight_image: PathLike = field(metadata={"help_string": "weight image", "argstr": "-w"})
weight_image: PathLike = field(
metadata={"help_string": "weight image", "argstr": "-w"}
)

shrink_factor: int = field(default=4, metadata={"help_string": "shrink factor", "argstr": "-s"})
shrink_factor: int = field(
default=4, metadata={"help_string": "shrink factor", "argstr": "-s"}
)

bspline_fitting_: str = field(
metadata={
Expand All @@ -49,7 +61,9 @@ class InputSpec(ShellSpec):
}
)

spline_distance: float = field(default=200, metadata={"help_string": "spline distance"})
spline_distance: float = field(
default=200, metadata={"help_string": "spline distance"}
)

spline_order: int = field(default=3, metadata={"help_string": "spline order"})

Expand All @@ -58,7 +72,9 @@ class InputSpec(ShellSpec):
"help_string": "convergence parameters",
"readonly": True,
"formatter": lambda num_iterations, threshold: (
"-c [{},{}]".format("x".join(str(i) for i in num_iterations), threshold)
"-c [{},{}]".format(
"x".join(str(i) for i in num_iterations), threshold
)
),
}
)
Expand All @@ -67,7 +83,9 @@ class InputSpec(ShellSpec):
default=(50, 50, 50, 50), metadata={"help_string": "number of iterations"}
)

threshold: float = field(default=0.0, metadata={"help_string": "convergence threshold"})
threshold: float = field(
default=0.0, metadata={"help_string": "convergence threshold"}
)

histogram_sharpening_: str = field(
metadata={
Expand All @@ -77,30 +95,46 @@ class InputSpec(ShellSpec):
}
)

bias_field_fwhm: float = field(default=0.15, metadata={"help_string": "Bias field FWHM"})
bias_field_fwhm: float = field(
default=0.15, metadata={"help_string": "Bias field FWHM"}
)

wiener_filter_noise: float = field(default=0.01, metadata={"help_string": "Wiener filter noise"})
wiener_filter_noise: float = field(
default=0.01, metadata={"help_string": "Wiener filter noise"}
)

num_histogram_bins: int = field(default=200, metadata={"help_string": "number of histogram bins"})
num_histogram_bins: int = field(
default=200, metadata={"help_string": "number of histogram bins"}
)

output_ = field(
metadata={
"help_string": "output parameters",
"readonly": True,
"formatter": lambda output_image, save_bias_field, output_bias_field: (
f"-o [{output_image},{output_bias_field}]" if save_bias_field else f"-o {output_image}"
f"-o [{output_image},{output_bias_field}]"
if save_bias_field
else f"-o {output_image}"
),
}
)

output_image: str = field(
metadata={"help_string": "output image", "output_file_template": "{input_image}_corrected"}
metadata={
"help_string": "output image",
"output_file_template": "{input_image}_corrected",
}
)

save_bias_field: bool = field(default=False, metadata={"help_string": "save bias field"})
save_bias_field: bool = field(
default=False, metadata={"help_string": "save bias field"}
)

output_bias_field: str = field(
metadata={"help_string": "output bias field", "output_file_template": "{input_image}_biasfield"}
metadata={
"help_string": "output bias field",
"output_file_template": "{input_image}_biasfield",
}
)

input_spec = SpecInfo(name="Input", bases=(InputSpec,))
Expand Down
21 changes: 18 additions & 3 deletions src/pydra/tasks/ants/create_jacobian_determinant_image.py
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Expand Up @@ -22,13 +22,28 @@ class CreateJacobianDeterminantImage(ShellCommandTask):
@define(kw_only=True)
class InputSpec(ShellSpec):
dimensionality: int = field(
metadata={"help_string": "image dimensionality", "mandatory": True, "argstr": "", "allowed_values": {2, 3}}
metadata={
"help_string": "image dimensionality",
"mandatory": True,
"argstr": "",
"allowed_values": {2, 3},
}
)

warp_field: PathLike = field(metadata={"help_string": "displacement field", "mandatory": True, "argstr": ""})
warp_field: PathLike = field(
metadata={
"help_string": "displacement field",
"mandatory": True,
"argstr": "",
}
)

output_image: str = field(
metadata={"help_string": "output image", "argstr": "", "output_file_template": "{warp_field}_jac"}
metadata={
"help_string": "output image",
"argstr": "",
"output_file_template": "{warp_field}_jac",
}
)

calculate_log_jacobian: bool = field(
Expand Down
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