From 3d05939b4cbc499a9b76df5a716768387cee11b1 Mon Sep 17 00:00:00 2001
From: NicolasGensollen <nicolas.gensollen@gmail.com>
Date: Fri, 3 Feb 2023 13:01:21 +0100
Subject: [PATCH 1/2] add eddy interface

---
 pydra/tasks/fsl/epi/__init__.py |   0
 pydra/tasks/fsl/epi/eddy.py     | 481 ++++++++++++++++++++++++++++++++
 2 files changed, 481 insertions(+)
 create mode 100644 pydra/tasks/fsl/epi/__init__.py
 create mode 100644 pydra/tasks/fsl/epi/eddy.py

diff --git a/pydra/tasks/fsl/epi/__init__.py b/pydra/tasks/fsl/epi/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/pydra/tasks/fsl/epi/eddy.py b/pydra/tasks/fsl/epi/eddy.py
new file mode 100644
index 0000000..b2ca99e
--- /dev/null
+++ b/pydra/tasks/fsl/epi/eddy.py
@@ -0,0 +1,481 @@
+from pydra.engine import specs
+from pydra import ShellCommandTask
+
+input_fields = [
+    (
+        "in_acqp",
+        str,
+        {
+            "help_string": "File containing acquisition parameters.",
+            "argstr": "--acqp={in_acqp}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "in_bval",
+        str,
+        {
+            "help_string": "File containing the b-values for all volumes in –imain.",
+            "argstr": "--bvals={in_bval}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "in_bvec",
+        str,
+        {
+            "help_string": "File containing the b-vectors for all volumes in –imain.",
+            "argstr": "--bvecs={in_bvec}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "in_file",
+        str,
+        {
+            "help_string": "File containing all the images to estimate distortions for.",
+            "argstr": "--imain={in_file}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "in_index",
+        str,
+        {
+            "help_string": "File containing indices for all volumes in –imain into –acqp and –topup.",
+            "argstr": "--index={in_index}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "in_mask",
+        str,
+        {
+            "help_string": "Mask to indicate brain.",
+            "argstr": "--mask={in_mask}",
+            "mandatory": True,
+        },
+    ),
+    (
+        "cnr_maps",
+        bool,
+        {
+            "help_string": "Output CNR-Maps.",
+            "argstr": "--cnr_maps",
+        },
+    ),
+    (
+        "dont_peas",
+        bool,
+        {
+            "help_string": "Do NOT perform a post-eddy alignment of shells.",
+            "argstr": "--dont_peas",
+        },
+    ),
+    (
+        "dont_sep_offs_move",
+        bool,
+        {
+            "help_string": "Do NOT attempt to separate field offset from subject movement.",
+            "argstr": "--dont_sep_offs_move",
+        },
+    ),
+    (
+        "estimate_move_by_susceptibility",
+        bool,
+        {
+            "help_string": "Estimate how susceptibility field changes with subject movement.",
+            "argstr": "--estimate_move_by_susceptibility",
+        },
+    ),
+    (
+        "fep",
+        bool,
+        {
+            "help_string": "Fill empty planes in x- or y-directions.",
+            "argstr": "--fep",
+        },
+    ),
+    (
+        "field",
+        specs.File,
+        {
+            "help_string": "Non-topup derived fieldmap scaled in Hz.",
+            "argstr": "--field={field}",
+        },
+    ),
+    (
+        "field_mat",
+        specs.File,
+        {
+            "help_string": (
+                "Matrix specifying the relative positions of the fieldmap, –field, "
+                "and the first volume of the input file, –imain."
+            ),
+            "argstr": "--field_mat={field_mat}",
+        },
+    ),
+    (
+        "flm",  # (‘quadratic’ or ‘linear’ or ‘cubic’)
+        str,
+        {
+            "help_string": "First level EC model.",
+            "argstr": "--flm={flm}",
+        },
+    ),
+    (
+        "fudge_factor",
+        float,
+        {
+            "help_string": "Fudge factor for hyperparameter error variance.",
+            "argstr": "--ff={fudge_factor}",
+        },
+    ),
+    (
+        "fwhm",
+        float,
+        {
+            "help_string": "FWHM for conditioning filter when estimating the parameters.",
+            "argstr": "--fwhm={fwhm}",
+        },
+    ),
+    (
+        "in_topup_fieldcoef",
+        specs.File,
+        {
+            "help_string": "Topup results file containing the field coefficients.",
+            "argstr": "--topup={in_topup_fieldcoef}",
+            "requires": [
+                "in_topup_movpar",
+            ],
+        },
+    ),
+    (
+        "in_topup_movpar",
+        specs.File,
+        {
+            "help_string": "Topup results file containing the movement parameters (movpar.txt).",
+            "requires": [
+                "in_topup_fieldcoef",
+            ],
+        },
+    ),
+    (
+        "initrand",
+        bool,
+        {
+            "help_string": "Resets rand for when selecting voxels.",
+            "argstr": "--initrand",
+        },
+    ),
+    (
+        "interp",  # (‘spline’ or ‘trilinear’)
+        str,
+        {
+            "help_string": "Interpolation model for estimation step.",
+            "argstr": "--interp=%s",
+        },
+    ),
+    (
+        "is_shelled",
+        bool,
+        {
+            "help_string": (
+                "Override internal check to ensure that date are "
+                "acquired on a set of b-value shells."
+            ),
+            "argstr": "--data_is_shelled",
+        },
+    ),
+    (
+        "json",
+        specs.File,
+        {
+            "help_string": "Name of .json text file with information about slice timing.",
+            "argstr": "--json={json}",
+            "xor": (
+                "slice_order",
+            ),
+            "requires": [
+                "mporder",
+            ],
+        },
+    ),
+    (
+        "mbs_ksp",
+        int,
+        {
+            "help_string": "Knot-spacing for MBS field estimation.",
+            "argstr": "--mbs_ksp={mbs_ksp}mm",
+            "requires": [
+                "estimate_move_by_susceptibility",
+            ],
+        },
+    ),
+    (
+        "mbs_lambda",
+        int,
+        {
+            "help_string": "Weighting of regularisation for MBS estimation.",
+            "argstr": "--mbs_lambda={mbs_lambda}",
+            "requires": [
+                "estimate_move_by_susceptibility",
+            ],
+        },
+    ),
+    (
+        "mbs_niter",
+        int,
+        {
+            "help_string": "Number of iterations for MBS estimation.",
+            "argstr": "--mbs_niter={mbs_niter}",
+            "requires": [
+                "estimate_move_by_susceptibility",
+            ],
+        },
+    ),
+    (
+        "method",  # (‘jac’ or ‘lsr’)
+        str,
+        {
+            "help_string": "Final resampling method (jacobian/least squares).",
+            "argstr": "--resamp={method}",
+        },
+    ),
+    (
+        "mporder",
+        int,
+        {
+            "help_string": "Order of slice-to-vol movement model.",
+            "argstr": "--mporder={mporder}",
+            "requires": [
+                "use_cuda",
+            ],
+        },
+    ),
+    (
+        "multiband_factor",
+        int,
+        {
+            "help_string": "Multi-band factor.",
+            "argstr": "--mb={multiband_factor}",
+        },
+    ),
+    (
+        "multiband_offset",  # (0 or 1 or -1)
+        int,
+        {
+            "help_string": "Multi-band offset (-1 if bottom slice removed, 1 if top slice removed.",
+            "argstr": "--mb_offs={multiband_offset}",
+            "requires": [
+                "multiband_factor",
+            ],
+        },
+    ),
+    (
+        "niter",
+        int,
+        {
+            "help_string": "Number of iterations.",
+            "argstr": "--niter={niter}",
+        },
+    ),
+    (
+        "num_threads",
+        int,
+        {
+            "help_string": "Number of openmp threads to use.",
+        },
+    ),
+    (
+        "nvoxhp",
+        int,
+        {
+            "help_string": "Number of voxels used to estimate the hyperparameters.",
+            "argstr": "--nvoxhp={nvoxhp}",
+        },
+    ),
+    (
+        "out_base",
+        str,
+        {
+            "help_string": "Basename for output image.",
+            "argstr": "--out={out_base}",
+        },
+    ),
+    (
+        "outlier_nstd",
+        int,
+        {
+            "help_string": "Number of std off to qualify as outlier.",
+            "argstr": "--ol_nstd",
+            "requires": [
+                "repol",
+            ],
+        },
+    ),
+    (
+        "outlier_nvox",
+        int,
+        {
+            "help_string": "Min number of voxels in a slice for inclusion in outlier detection.",
+            "argstr": "--ol_nvox",
+            "requires": [
+                "repol",
+            ],
+        },
+    ),
+    (
+        "outlier_pos",
+        bool,
+        {
+            "help_string": "Consider both positive and negative outliers if set.",
+            "argstr": "--ol_pos",
+            "requires": [
+                "repol",
+            ],
+        },
+    ),
+    (
+        "outlier_sqr",
+        bool,
+        {
+            "help_string": "Consider outliers among sums-of-squared differences if set.",
+            "argstr": "--ol_sqr",
+            "requires": [
+                "repol",
+            ],
+        },
+    ),
+    (
+        "outlier_type",  # (‘sw’ or ‘gw’ or ‘both’)
+        str,
+        {
+            "help_string": "Type of outliers, slicewise (sw), groupwise (gw) or both (both).",
+            "argstr": "--ol_type",
+            "requires": [
+                "repol",
+            ],
+        },
+    ),
+    (
+        "output_type",  # (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’)
+        str,
+        {
+            "help_string": "FSL output type.",
+        },
+    ),
+    (
+        "repol",
+        bool,
+        {
+            "help_string": "Detect and replace outlier slices.",
+            "argstr": "--repol",
+        },
+    ),
+    (
+        "residuals",
+        bool,
+        {
+            "help_string": "Output Residuals.",
+            "argstr": "--residuals",
+        },
+    ),
+    (
+        "session",
+        specs.File,
+        {
+            "help_string": "File containing session indices for all volumes in –imain.",
+            "argstr": "--session={session}",
+        },
+    ),
+    (
+        "slice2vol_interp",  # (‘trilinear’ or ‘spline’)
+        str,
+        {
+            "help_string": "Slice-to-vol interpolation model for estimation step.",
+            "argstr": "--s2v_interp={slice2vol_interp",
+            "requires": [
+                "mporder",
+            ],
+        },
+    ),
+    (
+        "slice2vol_lambda",
+        int,
+        {
+            "help_string": "Regularisation weight for slice-to-vol movement (reasonable range 1-10).",
+            "argstr": "--s2v_lambda={slice2vol_lambda}",
+            "requires": [
+                "mporder",
+            ],
+        },
+    ),
+    (
+        "slice2vol_niter",
+        int,
+        {
+            "help_string": "Number of iterations for slice-to-vol.",
+            "argstr": "--s2v_niter={slice2vol_niter}",
+            "requires": [
+                "mporder",
+            ],
+        },
+    ),
+    (
+        "slice_order",
+        specs.File,
+        {
+            "help_string": "Name of text file completely specifying slice/group acquisition.",
+            "argstr": "--slspec={slice_order}",
+            "xor": (
+                "json",
+            ),
+            "requires": [
+                "mporder",
+            ],
+        },
+    ),
+    (
+        "slm",  # (‘none’ or ‘linear’ or ‘quadratic’)
+        str,
+        {
+            "help_string": "Second level EC model.",
+            "argstr": "--slm={slm}",
+        },
+    ),
+    (
+        "use_cuda",
+        bool,
+        {
+            "help_string": "Run eddy using cuda gpu.",
+        },
+    ),
+]
+
+eddy_input_spec = specs.SpecInfo(name="Input", fields=input_fields, bases=(specs.ShellSpec,))
+
+output_fields = []
+
+eddy_output_spec = specs.SpecInfo(
+    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
+)
+
+
+class Eddy(ShellCommandTask):
+    """
+    Example
+    -------
+>>> eddy = Eddy()
+>>> eddy.inputs.in_file = "epi.nii"
+>>> eddy.inputs.in_mask = "epi_mask.nii"
+>>> eddy.inputs.in_index = "epi_index.txt"
+>>> eddy.inputs.in_acqp = "epi_acqp.txt"
+>>> eddy.inputs.in_bvec = "bvecs.scheme"
+>>> eddy.inputs.in_bval = "bvals.scheme"
+>>> eddy.cmdline
+    ‘eddy_openmp –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –slm=none’
+    """
+    input_spec = eddy_input_spec
+    output_spec = eddy_output_spec
+    executable = "eddy_openmp"

From 881747494605de6420b68bfb1647b38a194f1580 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 3 Feb 2023 12:04:47 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 pydra/tasks/fsl/epi/eddy.py | 35 +++++++++++++++--------------------
 1 file changed, 15 insertions(+), 20 deletions(-)

diff --git a/pydra/tasks/fsl/epi/eddy.py b/pydra/tasks/fsl/epi/eddy.py
index b2ca99e..769476d 100644
--- a/pydra/tasks/fsl/epi/eddy.py
+++ b/pydra/tasks/fsl/epi/eddy.py
@@ -193,9 +193,7 @@
         {
             "help_string": "Name of .json text file with information about slice timing.",
             "argstr": "--json={json}",
-            "xor": (
-                "slice_order",
-            ),
+            "xor": ("slice_order",),
             "requires": [
                 "mporder",
             ],
@@ -428,9 +426,7 @@
         {
             "help_string": "Name of text file completely specifying slice/group acquisition.",
             "argstr": "--slspec={slice_order}",
-            "xor": (
-                "json",
-            ),
+            "xor": ("json",),
             "requires": [
                 "mporder",
             ],
@@ -457,25 +453,24 @@
 
 output_fields = []
 
-eddy_output_spec = specs.SpecInfo(
-    name="Output", fields=output_fields, bases=(specs.ShellOutSpec,)
-)
+eddy_output_spec = specs.SpecInfo(name="Output", fields=output_fields, bases=(specs.ShellOutSpec,))
 
 
 class Eddy(ShellCommandTask):
     """
-    Example
-    -------
->>> eddy = Eddy()
->>> eddy.inputs.in_file = "epi.nii"
->>> eddy.inputs.in_mask = "epi_mask.nii"
->>> eddy.inputs.in_index = "epi_index.txt"
->>> eddy.inputs.in_acqp = "epi_acqp.txt"
->>> eddy.inputs.in_bvec = "bvecs.scheme"
->>> eddy.inputs.in_bval = "bvals.scheme"
->>> eddy.cmdline
-    ‘eddy_openmp –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –slm=none’
+        Example
+        -------
+    >>> eddy = Eddy()
+    >>> eddy.inputs.in_file = "epi.nii"
+    >>> eddy.inputs.in_mask = "epi_mask.nii"
+    >>> eddy.inputs.in_index = "epi_index.txt"
+    >>> eddy.inputs.in_acqp = "epi_acqp.txt"
+    >>> eddy.inputs.in_bvec = "bvecs.scheme"
+    >>> eddy.inputs.in_bval = "bvals.scheme"
+    >>> eddy.cmdline
+        ‘eddy_openmp –flm=quadratic –ff=10.0 –acqp=epi_acqp.txt –bvals=bvals.scheme –bvecs=bvecs.scheme –imain=epi.nii –index=epi_index.txt –mask=epi_mask.nii –interp=spline –resamp=jac –niter=5 –nvoxhp=1000 –out=…/eddy_corrected –slm=none’
     """
+
     input_spec = eddy_input_spec
     output_spec = eddy_output_spec
     executable = "eddy_openmp"