niwrap-afni 0.5.1__py3-none-any.whl → 0.5.3__py3-none-any.whl

niwrap_afni/afni/v_3d_lrflip.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LRFLIP_METADATA = Metadata(
-    id="b3e8fe43a4546f9996744e159107df5ff817046b.boutiques",
+    id="cccfbbdb6c5cece891a86f81aefb3b59ea32fe70.boutiques",
     name="3dLRflip",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,11 @@ V_3D_LRFLIP_METADATA = Metadata(
 
 V3dLrflipParameters = typing.TypedDict('V3dLrflipParameters', {
     "__STYX_TYPE__": typing.Literal["3dLRflip"],
+    "flip_lr": bool,
+    "flip_ap": bool,
+    "flip_is": bool,
+    "flip_x": bool,
+    "flip_y": bool,
     "flip_z": bool,
     "output_prefix": typing.NotRequired[str | None],
     "datasets": list[InputPathType],
@@ -65,6 +70,11 @@ class V3dLrflipOutputs(typing.NamedTuple):
 
 def v_3d_lrflip_params(
     datasets: list[InputPathType],
+    flip_lr: bool = False,
+    flip_ap: bool = False,
+    flip_is: bool = False,
+    flip_x: bool = False,
+    flip_y: bool = False,
     flip_z: bool = False,
     output_prefix: str | None = None,
 ) -> V3dLrflipParameters:
@@ -73,6 +83,11 @@ def v_3d_lrflip_params(
     
     Args:
         datasets: Datasets to flip.
+        flip_lr: Flip about Left-Right axis.
+        flip_ap: Flip about Anterior-Posterior axis.
+        flip_is: Flip about Inferior-Superior axis.
+        flip_x: Flip about the 1st direction.
+        flip_y: Flip about the 2nd direction.
         flip_z: Flip about the 3rd direction.
         output_prefix: Prefix to use for output. If multiple datasets are\
             input, the program will choose a prefix for each output.
@@ -81,6 +96,11 @@ def v_3d_lrflip_params(
     """
     params = {
         "__STYXTYPE__": "3dLRflip",
+        "flip_lr": flip_lr,
+        "flip_ap": flip_ap,
+        "flip_is": flip_is,
+        "flip_x": flip_x,
+        "flip_y": flip_y,
         "flip_z": flip_z,
         "datasets": datasets,
     }
@@ -104,6 +124,16 @@ def v_3d_lrflip_cargs(
     """
     cargs = []
     cargs.append("3dLRflip")
+    if params.get("flip_lr"):
+        cargs.append("-LR")
+    if params.get("flip_ap"):
+        cargs.append("-AP")
+    if params.get("flip_is"):
+        cargs.append("-IS")
+    if params.get("flip_x"):
+        cargs.append("-X")
+    if params.get("flip_y"):
+        cargs.append("-Y")
     if params.get("flip_z"):
         cargs.append("-Z")
     if params.get("output_prefix") is not None:
@@ -162,6 +192,11 @@ def v_3d_lrflip_execute(
 
 def v_3d_lrflip(
     datasets: list[InputPathType],
+    flip_lr: bool = False,
+    flip_ap: bool = False,
+    flip_is: bool = False,
+    flip_x: bool = False,
+    flip_y: bool = False,
     flip_z: bool = False,
     output_prefix: str | None = None,
     runner: Runner | None = None,
@@ -176,6 +211,11 @@ def v_3d_lrflip(
     
     Args:
         datasets: Datasets to flip.
+        flip_lr: Flip about Left-Right axis.
+        flip_ap: Flip about Anterior-Posterior axis.
+        flip_is: Flip about Inferior-Superior axis.
+        flip_x: Flip about the 1st direction.
+        flip_y: Flip about the 2nd direction.
         flip_z: Flip about the 3rd direction.
         output_prefix: Prefix to use for output. If multiple datasets are\
             input, the program will choose a prefix for each output.
@@ -186,6 +226,11 @@ def v_3d_lrflip(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_LRFLIP_METADATA)
     params = v_3d_lrflip_params(
+        flip_lr=flip_lr,
+        flip_ap=flip_ap,
+        flip_is=flip_is,
+        flip_x=flip_x,
+        flip_y=flip_y,
         flip_z=flip_z,
         output_prefix=output_prefix,
         datasets=datasets,

niwrap_afni/afni/v_3d_lss.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_LSS_METADATA = Metadata(
-    id="d793e92300ed18c69c7d31223293711fdbbfaaf7.boutiques",
+    id="d4c111d4b5225efa7f8cd3f4642fd461a7ab156b.boutiques",
     name="3dLSS",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,14 @@ V_3D_LSS_METADATA = Metadata(
 
 V3dLssParameters = typing.TypedDict('V3dLssParameters', {
     "__STYX_TYPE__": typing.Literal["3dLSS"],
+    "matrix": InputPathType,
+    "input": typing.NotRequired[InputPathType | None],
+    "nodata": bool,
+    "mask": typing.NotRequired[InputPathType | None],
+    "automask": bool,
+    "prefix": typing.NotRequired[str | None],
+    "save1D": typing.NotRequired[str | None],
+    "verbose": bool,
 })
 
 
@@ -59,22 +67,57 @@ class V3dLssOutputs(typing.NamedTuple):
     output_dataset: OutputPathType
     """Output dataset containing the LSS estimates of the beta weights for the
     '-stim_times_IM' stimuli."""
-    save1_d_output: OutputPathType
+    save1_d_output: OutputPathType | None
     """Estimator vectors saved in a 1D formatted file."""
 
 
 def v_3d_lss_params(
+    matrix: InputPathType,
+    input_: InputPathType | None = None,
+    nodata: bool = False,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    prefix: str | None = None,
+    save1_d: str | None = None,
+    verbose: bool = False,
 ) -> V3dLssParameters:
     """
     Build parameters.
     
     Args:
+        matrix: Read the matrix 'mmm', which should have been output from\
+            3dDeconvolve via the '-x1D' option. It should have included exactly one\
+            '-stim_times_IM' option.
+        input_: Read time series dataset 'ddd'.
+        nodata: Just compute the estimator matrix -- to be saved with\
+            '-save1D'.
+        mask: Dataset 'MMM' will be used as a mask for the input; voxels\
+            outside the mask will not be fit by the regression model.
+        automask: If you don't know what this does by now, please don't use\
+            this program.
+        prefix: Prefix name for the output dataset; this dataset will contain\
+            ONLY the LSS estimates of the beta weights for the '-stim_times_IM'\
+            stimuli.
+        save1_d: Save the estimator vectors to a 1D formatted file named 'qqq'.
+        verbose: Write out progress reports.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "3dLSS",
+        "matrix": matrix,
+        "nodata": nodata,
+        "automask": automask,
+        "verbose": verbose,
     }
+    if input_ is not None:
+        params["input"] = input_
+    if mask is not None:
+        params["mask"] = mask
+    if prefix is not None:
+        params["prefix"] = prefix
+    if save1_d is not None:
+        params["save1D"] = save1_d
     return params
 
 
@@ -93,7 +136,36 @@ def v_3d_lss_cargs(
     """
     cargs = []
     cargs.append("3dLSS")
-    cargs.append("[OPTIONS]")
+    cargs.extend([
+        "-matrix",
+        execution.input_file(params.get("matrix"))
+    ])
+    if params.get("input") is not None:
+        cargs.extend([
+            "-input",
+            execution.input_file(params.get("input"))
+        ])
+    if params.get("nodata"):
+        cargs.append("-nodata")
+    if params.get("mask") is not None:
+        cargs.extend([
+            "-mask",
+            execution.input_file(params.get("mask"))
+        ])
+    if params.get("automask"):
+        cargs.append("-automask")
+    if params.get("prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("prefix")
+        ])
+    if params.get("save1D") is not None:
+        cargs.extend([
+            "-save1D",
+            params.get("save1D")
+        ])
+    if params.get("verbose"):
+        cargs.append("-verb")
     return cargs
 
 
@@ -113,7 +185,7 @@ def v_3d_lss_outputs(
     ret = V3dLssOutputs(
         root=execution.output_file("."),
         output_dataset=execution.output_file("LSSout+orig.HEAD"),
-        save1_d_output=execution.output_file("[SAVE1D]"),
+        save1_d_output=execution.output_file(params.get("save1D")) if (params.get("save1D") is not None) else None,
     )
     return ret
 
@@ -144,6 +216,14 @@ def v_3d_lss_execute(
 
 
 def v_3d_lss(
+    matrix: InputPathType,
+    input_: InputPathType | None = None,
+    nodata: bool = False,
+    mask: InputPathType | None = None,
+    automask: bool = False,
+    prefix: str | None = None,
+    save1_d: str | None = None,
+    verbose: bool = False,
     runner: Runner | None = None,
 ) -> V3dLssOutputs:
     """
@@ -155,6 +235,21 @@ def v_3d_lss(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        matrix: Read the matrix 'mmm', which should have been output from\
+            3dDeconvolve via the '-x1D' option. It should have included exactly one\
+            '-stim_times_IM' option.
+        input_: Read time series dataset 'ddd'.
+        nodata: Just compute the estimator matrix -- to be saved with\
+            '-save1D'.
+        mask: Dataset 'MMM' will be used as a mask for the input; voxels\
+            outside the mask will not be fit by the regression model.
+        automask: If you don't know what this does by now, please don't use\
+            this program.
+        prefix: Prefix name for the output dataset; this dataset will contain\
+            ONLY the LSS estimates of the beta weights for the '-stim_times_IM'\
+            stimuli.
+        save1_d: Save the estimator vectors to a 1D formatted file named 'qqq'.
+        verbose: Write out progress reports.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V3dLssOutputs`).
@@ -162,6 +257,14 @@ def v_3d_lss(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V_3D_LSS_METADATA)
     params = v_3d_lss_params(
+        matrix=matrix,
+        input_=input_,
+        nodata=nodata,
+        mask=mask,
+        automask=automask,
+        prefix=prefix,
+        save1_d=save1_d,
+        verbose=verbose,
     )
     return v_3d_lss_execute(params, execution)
 

niwrap_afni/afni/v_3d_mask_to_ascii.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_3D_MASK_TO_ASCII_METADATA = Metadata(
-    id="00c7066c6c38f027299750536983f490b1c220de.boutiques",
+    id="20970426ca6ec9c84b1d7625189cb189cffb0a2f.boutiques",
     name="3dMaskToASCII",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,7 @@ V3dMaskToAsciiParameters = typing.TypedDict('V3dMaskToAsciiParameters', {
     "__STYX_TYPE__": typing.Literal["3dMaskToASCII"],
     "tobin_flag": bool,
     "dataset": InputPathType,
+    "outputfile": str,
 })
 
 
@@ -64,6 +65,7 @@ class V3dMaskToAsciiOutputs(typing.NamedTuple):
 
 def v_3d_mask_to_ascii_params(
     dataset: InputPathType,
+    outputfile: str,
     tobin_flag: bool = False,
 ) -> V3dMaskToAsciiParameters:
     """
@@ -71,6 +73,8 @@ def v_3d_mask_to_ascii_params(
     
     Args:
         dataset: Input dataset (e.g. mask.nii.gz).
+        outputfile: Output file where ASCII string mask or binary mask will be\
+            written.
         tobin_flag: Read ASCII mask, expand it to byte-valued dataset, and\
             write to stdout.
     Returns:
@@ -80,6 +84,7 @@ def v_3d_mask_to_ascii_params(
         "__STYXTYPE__": "3dMaskToASCII",
         "tobin_flag": tobin_flag,
         "dataset": dataset,
+        "outputfile": outputfile,
     }
     return params
 
@@ -102,8 +107,7 @@ def v_3d_mask_to_ascii_cargs(
     if params.get("tobin_flag"):
         cargs.append("-tobin")
     cargs.append(execution.input_file(params.get("dataset")))
-    cargs.append(">")
-    cargs.append("[OUTPUTFILE]")
+    cargs.append("> " + params.get("outputfile"))
     return cargs
 
 
@@ -122,7 +126,7 @@ def v_3d_mask_to_ascii_outputs(
     """
     ret = V3dMaskToAsciiOutputs(
         root=execution.output_file("."),
-        outputfile=execution.output_file("[OUTPUTFILE]"),
+        outputfile=execution.output_file(params.get("outputfile")),
     )
     return ret
 
@@ -153,6 +157,7 @@ def v_3d_mask_to_ascii_execute(
 
 def v_3d_mask_to_ascii(
     dataset: InputPathType,
+    outputfile: str,
     tobin_flag: bool = False,
     runner: Runner | None = None,
 ) -> V3dMaskToAsciiOutputs:
@@ -165,6 +170,8 @@ def v_3d_mask_to_ascii(
     
     Args:
         dataset: Input dataset (e.g. mask.nii.gz).
+        outputfile: Output file where ASCII string mask or binary mask will be\
+            written.
         tobin_flag: Read ASCII mask, expand it to byte-valued dataset, and\
             write to stdout.
         runner: Command runner.
@@ -176,6 +183,7 @@ def v_3d_mask_to_ascii(
     params = v_3d_mask_to_ascii_params(
         tobin_flag=tobin_flag,
         dataset=dataset,
+        outputfile=outputfile,
     )
     return v_3d_mask_to_ascii_execute(params, execution)