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

niwrap_afni/afni/v__grayplot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__GRAYPLOT_METADATA = Metadata(
-    id="3d444976676cbb4979c872f1285979b9e0bd687d.boutiques",
+    id="530147880dced9ec34da9598833b42371288db6a.boutiques",
     name="@grayplot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,9 @@ V__GRAYPLOT_METADATA = Metadata(
 VGrayplotParameters = typing.TypedDict('VGrayplotParameters', {
     "__STYX_TYPE__": typing.Literal["@grayplot"],
     "dirname": str,
+    "pvorder": bool,
+    "peelorder": bool,
+    "ijkorder": bool,
     "allorder": bool,
 })
 
@@ -64,6 +67,9 @@ class VGrayplotOutputs(typing.NamedTuple):
 
 def v__grayplot_params(
     dirname: str,
+    pvorder: bool = False,
+    peelorder: bool = False,
+    ijkorder: bool = False,
     allorder: bool = False,
 ) -> VGrayplotParameters:
     """
@@ -71,6 +77,12 @@ def v__grayplot_params(
     
     Args:
         dirname: Directory containing afni_proc.py results.
+        pvorder: Within each partition, voxels are ordered by a simple\
+            similarity measure.
+        peelorder: Within each partition, voxels are ordered by how many 'peel'\
+            operations are needed to reach a given voxel.
+        ijkorder: Within each partition, voxels are ordered by the 3D index in\
+            which they appear in the dataset.
         allorder: Create grayplots for all ordering methods.
     Returns:
         Parameter dictionary
@@ -78,6 +90,9 @@ def v__grayplot_params(
     params = {
         "__STYXTYPE__": "@grayplot",
         "dirname": dirname,
+        "pvorder": pvorder,
+        "peelorder": peelorder,
+        "ijkorder": ijkorder,
         "allorder": allorder,
     }
     return params
@@ -99,6 +114,12 @@ def v__grayplot_cargs(
     cargs = []
     cargs.append("@grayplot")
     cargs.append(params.get("dirname"))
+    if params.get("pvorder"):
+        cargs.append("-pvorder")
+    if params.get("peelorder"):
+        cargs.append("-peelorder")
+    if params.get("ijkorder"):
+        cargs.append("-ijkorder")
     if params.get("allorder"):
         cargs.append("-ALLorder")
     return cargs
@@ -152,6 +173,9 @@ def v__grayplot_execute(
 
 def v__grayplot(
     dirname: str,
+    pvorder: bool = False,
+    peelorder: bool = False,
+    ijkorder: bool = False,
     allorder: bool = False,
     runner: Runner | None = None,
 ) -> VGrayplotOutputs:
@@ -166,6 +190,12 @@ def v__grayplot(
     
     Args:
         dirname: Directory containing afni_proc.py results.
+        pvorder: Within each partition, voxels are ordered by a simple\
+            similarity measure.
+        peelorder: Within each partition, voxels are ordered by how many 'peel'\
+            operations are needed to reach a given voxel.
+        ijkorder: Within each partition, voxels are ordered by the 3D index in\
+            which they appear in the dataset.
         allorder: Create grayplots for all ordering methods.
         runner: Command runner.
     Returns:
@@ -175,6 +205,9 @@ def v__grayplot(
     execution = runner.start_execution(V__GRAYPLOT_METADATA)
     params = v__grayplot_params(
         dirname=dirname,
+        pvorder=pvorder,
+        peelorder=peelorder,
+        ijkorder=ijkorder,
         allorder=allorder,
     )
     return v__grayplot_execute(params, execution)

niwrap_afni/afni/v__help_afni.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__HELP_AFNI_METADATA = Metadata(
-    id="87ebd1e4083856099825a6ef50fde5abb2dad615.boutiques",
+    id="feadd2af7149741e9f9192b504b7c09e3ad50dc5.boutiques",
     name="@help.AFNI",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,12 @@ V__HELP_AFNI_METADATA = Metadata(
 
 VHelpAfniParameters = typing.TypedDict('VHelpAfniParameters', {
     "__STYX_TYPE__": typing.Literal["@help.AFNI"],
+    "match": typing.NotRequired[str | None],
+    "lynx": bool,
+    "vi": bool,
+    "less": bool,
+    "nedit": bool,
+    "noview": bool,
 })
 
 
@@ -58,17 +64,38 @@ class VHelpAfniOutputs(typing.NamedTuple):
 
 
 def v__help_afni_params(
+    match: str | None = None,
+    lynx: bool = False,
+    vi: bool = False,
+    less: bool = False,
+    nedit: bool = False,
+    noview: bool = False,
 ) -> VHelpAfniParameters:
     """
     Build parameters.
     
     Args:
+        match: Looks for occurrence of each word in the list in the help file.\
+            For a match with multiple words, all the words must be on the same line\
+            of text in the help file.
+        lynx: Set viewer to lynx.
+        vi: Set viewer to vi.
+        less: Set viewer to less (default).
+        nedit: Set viewer to nedit.
+        noview: Set viewer to no view.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "@help.AFNI",
+        "lynx": lynx,
+        "vi": vi,
+        "less": less,
+        "nedit": nedit,
+        "noview": noview,
     }
+    if match is not None:
+        params["match"] = match
     return params
 
 
@@ -87,7 +114,21 @@ def v__help_afni_cargs(
     """
     cargs = []
     cargs.append("@help.AFNI")
-    cargs.append("[OPTIONS]")
+    if params.get("match") is not None:
+        cargs.extend([
+            "-match",
+            params.get("match")
+        ])
+    if params.get("lynx"):
+        cargs.append("-lynx")
+    if params.get("vi"):
+        cargs.append("-vi")
+    if params.get("less"):
+        cargs.append("-less")
+    if params.get("nedit"):
+        cargs.append("-nedit")
+    if params.get("noview"):
+        cargs.append("-noview")
     return cargs
 
 
@@ -135,6 +176,12 @@ def v__help_afni_execute(
 
 
 def v__help_afni(
+    match: str | None = None,
+    lynx: bool = False,
+    vi: bool = False,
+    less: bool = False,
+    nedit: bool = False,
+    noview: bool = False,
     runner: Runner | None = None,
 ) -> VHelpAfniOutputs:
     """
@@ -145,6 +192,14 @@ def v__help_afni(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        match: Looks for occurrence of each word in the list in the help file.\
+            For a match with multiple words, all the words must be on the same line\
+            of text in the help file.
+        lynx: Set viewer to lynx.
+        vi: Set viewer to vi.
+        less: Set viewer to less (default).
+        nedit: Set viewer to nedit.
+        noview: Set viewer to no view.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VHelpAfniOutputs`).
@@ -152,6 +207,12 @@ def v__help_afni(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V__HELP_AFNI_METADATA)
     params = v__help_afni_params(
+        match=match,
+        lynx=lynx,
+        vi=vi,
+        less=less,
+        nedit=nedit,
+        noview=noview,
     )
     return v__help_afni_execute(params, execution)
 

niwrap_afni/afni/v__make_label_table.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__MAKE_LABEL_TABLE_METADATA = Metadata(
-    id="20feae505751ac89a0b8a088a83f7ee7d488f8c6.boutiques",
+    id="287075a9705f1e3aa4609a67bab5671fa4e1d6b9.boutiques",
     name="@MakeLabelTable",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -19,6 +19,7 @@ VMakeLabelTableParameters = typing.TypedDict('VMakeLabelTableParameters', {
     "atlas_pointlist": typing.NotRequired[str | None],
     "lab_r": typing.NotRequired[list[str] | None],
     "lab_v": typing.NotRequired[list[str] | None],
+    "lab_file_delim": typing.NotRequired[str | None],
     "lab_file": typing.NotRequired[list[str] | None],
     "dset": typing.NotRequired[InputPathType | None],
     "longnames": typing.NotRequired[float | None],
@@ -105,6 +106,7 @@ def v__make_label_table_params(
     atlas_pointlist: str | None = None,
     lab_r: list[str] | None = None,
     lab_v: list[str] | None = None,
+    lab_file_delim: str | None = None,
     lab_file: list[str] | None = None,
     dset: InputPathType | None = None,
     longnames: float | None = None,
@@ -144,6 +146,7 @@ def v__make_label_table_params(
         atlas_pointlist: Instead of a label table, produce an atlas point list.
         lab_r: Define a label with its minimum and maximum key values.
         lab_v: Define a label and its value.
+        lab_file_delim: Set column delimiter for -lab_file option.
         lab_file: Specify labels and keys from a text file.
         dset: Attach the label table (or atlas point list) to dataset.
         longnames: Allow for another column of long names for regions.
@@ -202,6 +205,8 @@ def v__make_label_table_params(
         params["lab_r"] = lab_r
     if lab_v is not None:
         params["lab_v"] = lab_v
+    if lab_file_delim is not None:
+        params["lab_file_delim"] = lab_file_delim
     if lab_file is not None:
         params["lab_file"] = lab_file
     if dset is not None:
@@ -279,6 +284,11 @@ def v__make_label_table_cargs(
             "-lab_v",
             *params.get("lab_v")
         ])
+    if params.get("lab_file_delim") is not None:
+        cargs.extend([
+            "-lab_file_delim",
+            params.get("lab_file_delim")
+        ])
     if params.get("lab_file") is not None:
         cargs.extend([
             "-lab_file",
@@ -454,6 +464,7 @@ def v__make_label_table(
     atlas_pointlist: str | None = None,
     lab_r: list[str] | None = None,
     lab_v: list[str] | None = None,
+    lab_file_delim: str | None = None,
     lab_file: list[str] | None = None,
     dset: InputPathType | None = None,
     longnames: float | None = None,
@@ -498,6 +509,7 @@ def v__make_label_table(
         atlas_pointlist: Instead of a label table, produce an atlas point list.
         lab_r: Define a label with its minimum and maximum key values.
         lab_v: Define a label and its value.
+        lab_file_delim: Set column delimiter for -lab_file option.
         lab_file: Specify labels and keys from a text file.
         dset: Attach the label table (or atlas point list) to dataset.
         longnames: Allow for another column of long names for regions.
@@ -544,6 +556,7 @@ def v__make_label_table(
         atlas_pointlist=atlas_pointlist,
         lab_r=lab_r,
         lab_v=lab_v,
+        lab_file_delim=lab_file_delim,
         lab_file=lab_file,
         dset=dset,
         longnames=longnames,

niwrap_afni/afni/v__no_ext.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__NO_EXT_METADATA = Metadata(
-    id="e146bd1bed02e711ff41cccbd0a20832085fd087.boutiques",
+    id="b30bcb77c107d7bb2ff272f07e711f98bc966c50.boutiques",
     name="@NoExt",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -15,6 +15,7 @@ V__NO_EXT_METADATA = Metadata(
 
 VNoExtParameters = typing.TypedDict('VNoExtParameters', {
     "__STYX_TYPE__": typing.Literal["@NoExt"],
+    "inputfile": str,
     "extensions": typing.NotRequired[list[str] | None],
 })
 
@@ -62,18 +63,21 @@ class VNoExtOutputs(typing.NamedTuple):
 
 
 def v__no_ext_params(
+    inputfile: str,
     extensions: list[str] | None = None,
 ) -> VNoExtParameters:
     """
     Build parameters.
     
     Args:
+        inputfile: Input file name with extension.
         extensions: Extensions to be removed.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "@NoExt",
+        "inputfile": inputfile,
     }
     if extensions is not None:
         params["extensions"] = extensions
@@ -95,7 +99,7 @@ def v__no_ext_cargs(
     """
     cargs = []
     cargs.append("@NoExt")
-    cargs.append("<inputfile>")
+    cargs.append(params.get("inputfile"))
     if params.get("extensions") is not None:
         cargs.extend(params.get("extensions"))
     return cargs
@@ -146,6 +150,7 @@ def v__no_ext_execute(
 
 
 def v__no_ext(
+    inputfile: str,
     extensions: list[str] | None = None,
     runner: Runner | None = None,
 ) -> VNoExtOutputs:
@@ -157,6 +162,7 @@ def v__no_ext(
     URL: https://afni.nimh.nih.gov/
     
     Args:
+        inputfile: Input file name with extension.
         extensions: Extensions to be removed.
         runner: Command runner.
     Returns:
@@ -165,6 +171,7 @@ def v__no_ext(
     runner = runner or get_global_runner()
     execution = runner.start_execution(V__NO_EXT_METADATA)
     params = v__no_ext_params(
+        inputfile=inputfile,
         extensions=extensions,
     )
     return v__no_ext_execute(params, execution)

niwrap_afni/afni/v__reorder.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__REORDER_METADATA = Metadata(
-    id="93af53020ee1088a33b0e58234dc8960b688e23e.boutiques",
+    id="a1aaf6dbb807ea79af1609bee99a7c13181932fa.boutiques",
     name="@Reorder",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -21,6 +21,7 @@ VReorderParameters = typing.TypedDict('VReorderParameters', {
     "offset": typing.NotRequired[float | None],
     "save_work": bool,
     "test": bool,
+    "help": bool,
 })
 
 
@@ -73,6 +74,7 @@ def v__reorder_params(
     offset: float | None = None,
     save_work: bool = False,
     test: bool = False,
+    help_: bool = False,
 ) -> VReorderParameters:
     """
     Build parameters.
@@ -84,6 +86,7 @@ def v__reorder_params(
         offset: Offset mapfile TR indices by OFFSET (in TRs).
         save_work: Do not delete work directory (reorder.work.dir) at the end.
         test: Just report sub-bricks, do not create datasets.
+        help_: Show help message.
     Returns:
         Parameter dictionary
     """
@@ -94,6 +97,7 @@ def v__reorder_params(
         "prefix": prefix,
         "save_work": save_work,
         "test": test,
+        "help": help_,
     }
     if offset is not None:
         params["offset"] = offset
@@ -127,6 +131,8 @@ def v__reorder_cargs(
         cargs.append("-save_work")
     if params.get("test"):
         cargs.append("-test")
+    if params.get("help"):
+        cargs.append("-help")
     return cargs
 
 
@@ -182,6 +188,7 @@ def v__reorder(
     offset: float | None = None,
     save_work: bool = False,
     test: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> VReorderOutputs:
     """
@@ -199,6 +206,7 @@ def v__reorder(
         offset: Offset mapfile TR indices by OFFSET (in TRs).
         save_work: Do not delete work directory (reorder.work.dir) at the end.
         test: Just report sub-bricks, do not create datasets.
+        help_: Show help message.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VReorderOutputs`).
@@ -212,6 +220,7 @@ def v__reorder(
         offset=offset,
         save_work=save_work,
         test=test,
+        help_=help_,
     )
     return v__reorder_execute(params, execution)
 

niwrap_afni/afni/v__skull_strip_touch_up.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SKULL_STRIP_TOUCH_UP_METADATA = Metadata(
-    id="b6fb601a41c80b9729bd9c95da0d4f3540060f61.boutiques",
+    id="460010f2b657da6818c5cc52af6697286e7b7fd3.boutiques",
     name="@SkullStrip_TouchUp",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -20,6 +20,7 @@ VSkullStripTouchUpParameters = typing.TypedDict('VSkullStripTouchUpParameters',
     "head_dataset": InputPathType,
     "mask_out": bool,
     "orig_dim": bool,
+    "help": bool,
 })
 
 
@@ -73,6 +74,7 @@ def v__skull_strip_touch_up_params(
     head_dataset: InputPathType,
     mask_out: bool = False,
     orig_dim: bool = False,
+    help_: bool = False,
 ) -> VSkullStripTouchUpParameters:
     """
     Build parameters.
@@ -83,6 +85,7 @@ def v__skull_strip_touch_up_params(
         head_dataset: Whole head anatomical data set.
         mask_out: Output a binary mask in addition to actual data.
         orig_dim: Edit in the original image dimensions.
+        help_: Show this help message.
     Returns:
         Parameter dictionary
     """
@@ -93,6 +96,7 @@ def v__skull_strip_touch_up_params(
         "head_dataset": head_dataset,
         "mask_out": mask_out,
         "orig_dim": orig_dim,
+        "help": help_,
     }
     return params
 
@@ -128,6 +132,8 @@ def v__skull_strip_touch_up_cargs(
         cargs.append("-mask_out")
     if params.get("orig_dim"):
         cargs.append("-orig_dim")
+    if params.get("help"):
+        cargs.append("-help")
     return cargs
 
 
@@ -183,6 +189,7 @@ def v__skull_strip_touch_up(
     head_dataset: InputPathType,
     mask_out: bool = False,
     orig_dim: bool = False,
+    help_: bool = False,
     runner: Runner | None = None,
 ) -> VSkullStripTouchUpOutputs:
     """
@@ -199,6 +206,7 @@ def v__skull_strip_touch_up(
         head_dataset: Whole head anatomical data set.
         mask_out: Output a binary mask in addition to actual data.
         orig_dim: Edit in the original image dimensions.
+        help_: Show this help message.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSkullStripTouchUpOutputs`).
@@ -211,6 +219,7 @@ def v__skull_strip_touch_up(
         head_dataset=head_dataset,
         mask_out=mask_out,
         orig_dim=orig_dim,
+        help_=help_,
     )
     return v__skull_strip_touch_up_execute(params, execution)
 

niwrap_afni/afni/v__suma_make_spec_caret.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V__SUMA_MAKE_SPEC_CARET_METADATA = Metadata(
-    id="950a20d0f240b4840873e5b78497c9b7e5e19277.boutiques",
+    id="ef058c5698e2c248a0e9c472b24e31f1b02dc1ae.boutiques",
     name="@SUMA_Make_Spec_Caret",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,11 @@ V__SUMA_MAKE_SPEC_CARET_METADATA = Metadata(
 VSumaMakeSpecCaretParameters = typing.TypedDict('VSumaMakeSpecCaretParameters', {
     "__STYX_TYPE__": typing.Literal["@SUMA_Make_Spec_Caret"],
     "subject_id": str,
+    "help": bool,
+    "debug": typing.NotRequired[int | None],
+    "echo": bool,
+    "surface_path": typing.NotRequired[str | None],
+    "side_labels_style": typing.NotRequired[int | None],
 })
 
 
@@ -65,19 +70,39 @@ class VSumaMakeSpecCaretOutputs(typing.NamedTuple):
 
 def v__suma_make_spec_caret_params(
     subject_id: str,
+    help_: bool = False,
+    debug: int | None = None,
+    echo: bool = False,
+    surface_path: str | None = None,
+    side_labels_style: int | None = None,
 ) -> VSumaMakeSpecCaretParameters:
     """
     Build parameters.
     
     Args:
         subject_id: Subject ID for file naming.
+        help_: Show help information.
+        debug: Print debug information along the way.
+        echo: Turn shell echo on.
+        surface_path: Path to directory containing 'SURFACES' and AFNI volume\
+            used in creating the surfaces.
+        side_labels_style: Naming style for Left, Right sides. Allowed values:\
+            1 for L R LR style (default), 2 for LEFT RIGHT LR style, 3 for A B AB.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "@SUMA_Make_Spec_Caret",
         "subject_id": subject_id,
+        "help": help_,
+        "echo": echo,
     }
+    if debug is not None:
+        params["debug"] = debug
+    if surface_path is not None:
+        params["surface_path"] = surface_path
+    if side_labels_style is not None:
+        params["side_labels_style"] = side_labels_style
     return params
 
 
@@ -96,11 +121,29 @@ def v__suma_make_spec_caret_cargs(
     """
     cargs = []
     cargs.append("@SUMA_Make_Spec_Caret")
-    cargs.append("[OPTIONS]")
     cargs.extend([
         "-sid",
         params.get("subject_id")
     ])
+    if params.get("help"):
+        cargs.append("-help")
+    if params.get("debug") is not None:
+        cargs.extend([
+            "-debug",
+            str(params.get("debug"))
+        ])
+    if params.get("echo"):
+        cargs.append("-echo")
+    if params.get("surface_path") is not None:
+        cargs.extend([
+            "-sfpath",
+            params.get("surface_path")
+        ])
+    if params.get("side_labels_style") is not None:
+        cargs.extend([
+            "-side_labels_style",
+            str(params.get("side_labels_style"))
+        ])
     return cargs
 
 
@@ -151,6 +194,11 @@ def v__suma_make_spec_caret_execute(
 
 def v__suma_make_spec_caret(
     subject_id: str,
+    help_: bool = False,
+    debug: int | None = None,
+    echo: bool = False,
+    surface_path: str | None = None,
+    side_labels_style: int | None = None,
     runner: Runner | None = None,
 ) -> VSumaMakeSpecCaretOutputs:
     """
@@ -162,6 +210,13 @@ def v__suma_make_spec_caret(
     
     Args:
         subject_id: Subject ID for file naming.
+        help_: Show help information.
+        debug: Print debug information along the way.
+        echo: Turn shell echo on.
+        surface_path: Path to directory containing 'SURFACES' and AFNI volume\
+            used in creating the surfaces.
+        side_labels_style: Naming style for Left, Right sides. Allowed values:\
+            1 for L R LR style (default), 2 for LEFT RIGHT LR style, 3 for A B AB.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `VSumaMakeSpecCaretOutputs`).
@@ -170,6 +225,11 @@ def v__suma_make_spec_caret(
     execution = runner.start_execution(V__SUMA_MAKE_SPEC_CARET_METADATA)
     params = v__suma_make_spec_caret_params(
         subject_id=subject_id,
+        help_=help_,
+        debug=debug,
+        echo=echo,
+        surface_path=surface_path,
+        side_labels_style=side_labels_style,
     )
     return v__suma_make_spec_caret_execute(params, execution)