niwrap-afni 0.5.0__py3-none-any.whl → 0.5.2__py3-none-any.whl

niwrap_afni/afni/tedana_wrapper_py.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 TEDANA_WRAPPER_PY_METADATA = Metadata(
-    id="2a5d2d42a60628be534dad0f8a18d103f5db8377.boutiques",
+    id="2c08ca0025238427f67e66b767bc36524812cd16.boutiques",
     name="tedana_wrapper.py",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -26,6 +26,8 @@ TedanaWrapperPyParameters = typing.TypedDict('TedanaWrapperPyParameters', {
     "tedana_is_exec": bool,
     "ted_label": typing.NotRequired[str | None],
     "tedana_opts": typing.NotRequired[str | None],
+    "help": bool,
+    "detailed_help": bool,
 })
 
 
@@ -85,6 +87,8 @@ def tedana_wrapper_py_params(
     tedana_is_exec: bool = False,
     ted_label: str | None = None,
     tedana_opts: str | None = None,
+    help_: bool = False,
+    detailed_help: bool = False,
 ) -> TedanaWrapperPyParameters:
     """
     Build parameters.
@@ -106,6 +110,8 @@ def tedana_wrapper_py_params(
             PATH).
         tedana_opts: Additional options to pass to tedana.py. (In quotes)\
             Example: '--initcost=tanh --conv=2.5e-5'.
+        help_: Show help message and exit.
+        detailed_help: Show detailed help and exit.
     Returns:
         Parameter dictionary
     """
@@ -117,6 +123,8 @@ def tedana_wrapper_py_params(
         "save_all": save_all,
         "prep_only": prep_only,
         "tedana_is_exec": tedana_is_exec,
+        "help": help_,
+        "detailed_help": detailed_help,
     }
     if results_dir is not None:
         params["results_dir"] = results_dir
@@ -189,6 +197,10 @@ def tedana_wrapper_py_cargs(
             "-tedana_opts",
             params.get("tedana_opts")
         ])
+    if params.get("help"):
+        cargs.append("-h")
+    if params.get("detailed_help"):
+        cargs.append("-help")
     return cargs
 
 
@@ -249,6 +261,8 @@ def tedana_wrapper_py(
     tedana_is_exec: bool = False,
     ted_label: str | None = None,
     tedana_opts: str | None = None,
+    help_: bool = False,
+    detailed_help: bool = False,
     runner: Runner | None = None,
 ) -> TedanaWrapperPyOutputs:
     """
@@ -275,6 +289,8 @@ def tedana_wrapper_py(
             PATH).
         tedana_opts: Additional options to pass to tedana.py. (In quotes)\
             Example: '--initcost=tanh --conv=2.5e-5'.
+        help_: Show help message and exit.
+        detailed_help: Show detailed help and exit.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `TedanaWrapperPyOutputs`).
@@ -293,6 +309,8 @@ def tedana_wrapper_py(
         tedana_is_exec=tedana_is_exec,
         ted_label=ted_label,
         tedana_opts=tedana_opts,
+        help_=help_,
+        detailed_help=detailed_help,
     )
     return tedana_wrapper_py_execute(params, execution)
 

niwrap_afni/afni/v_1d_bport.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_BPORT_METADATA = Metadata(
-    id="4be892d519b77ae339eb9adf3a74b7d897d73650.boutiques",
+    id="3e21c923df63dc56e984c041d63c42544214ee22.boutiques",
     name="1dBport",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -17,6 +17,7 @@ V1dBportParameters = typing.TypedDict('V1dBportParameters', {
     "__STYX_TYPE__": typing.Literal["1dBport"],
     "band": list[float],
     "invert": bool,
+    "nozero": bool,
     "noconst": bool,
     "quad": bool,
     "input_dataset": typing.NotRequired[InputPathType | None],
@@ -72,6 +73,7 @@ class V1dBportOutputs(typing.NamedTuple):
 def v_1d_bport_params(
     band: list[float],
     invert: bool = False,
+    nozero: bool = False,
     noconst: bool = False,
     quad: bool = False,
     input_dataset: InputPathType | None = None,
@@ -87,6 +89,8 @@ def v_1d_bport_params(
         band: Specify lowest and highest frequencies in the passband.
         invert: Invert the selection after computing which frequency indexes\
             correspond to the input band(s).
+        nozero: Do NOT generate the 0 frequency (constant) component when fbot\
+            = 0.
         noconst: Same as -nozero. Do NOT generate the 0 frequency (constant)\
             component when fbot = 0.
         quad: Add regressors for linear and quadratic trends.
@@ -103,6 +107,7 @@ def v_1d_bport_params(
         "__STYXTYPE__": "1dBport",
         "band": band,
         "invert": invert,
+        "nozero": nozero,
         "noconst": noconst,
         "quad": quad,
     }
@@ -140,6 +145,8 @@ def v_1d_bport_cargs(
     ])
     if params.get("invert"):
         cargs.append("-invert")
+    if params.get("nozero"):
+        cargs.append("-nozero")
     if params.get("noconst"):
         cargs.append("-noconst")
     if params.get("quad"):
@@ -219,6 +226,7 @@ def v_1d_bport_execute(
 def v_1d_bport(
     band: list[float],
     invert: bool = False,
+    nozero: bool = False,
     noconst: bool = False,
     quad: bool = False,
     input_dataset: InputPathType | None = None,
@@ -239,6 +247,8 @@ def v_1d_bport(
         band: Specify lowest and highest frequencies in the passband.
         invert: Invert the selection after computing which frequency indexes\
             correspond to the input band(s).
+        nozero: Do NOT generate the 0 frequency (constant) component when fbot\
+            = 0.
         noconst: Same as -nozero. Do NOT generate the 0 frequency (constant)\
             component when fbot = 0.
         quad: Add regressors for linear and quadratic trends.
@@ -257,6 +267,7 @@ def v_1d_bport(
     params = v_1d_bport_params(
         band=band,
         invert=invert,
+        nozero=nozero,
         noconst=noconst,
         quad=quad,
         input_dataset=input_dataset,

niwrap_afni/afni/v_1d_correlate.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_CORRELATE_METADATA = Metadata(
-    id="be0ac3e4b1a192ead53f328b4b3ecf125d8d36fe.boutiques",
+    id="f3dbbb641ceed6bf13990065b1b59dc542a7a7fa.boutiques",
     name="1dCorrelate",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -18,7 +18,11 @@ V1dCorrelateParameters = typing.TypedDict('V1dCorrelateParameters', {
     "ktaub": bool,
     "nboot": typing.NotRequired[float | None],
     "alpha": typing.NotRequired[float | None],
+    "block": bool,
     "blk": bool,
+    "pearson": bool,
+    "spearman": bool,
+    "quadrant": bool,
     "input_files": list[InputPathType],
 })
 
@@ -67,7 +71,11 @@ def v_1d_correlate_params(
     ktaub: bool = False,
     nboot: float | None = None,
     alpha: float | None = None,
+    block: bool = False,
     blk: bool = False,
+    pearson: bool = False,
+    spearman: bool = False,
+    quadrant: bool = False,
 ) -> V1dCorrelateParameters:
     """
     Build parameters.
@@ -77,14 +85,23 @@ def v_1d_correlate_params(
         ktaub: Kendall's tau_b correlation (popular somewhere, maybe).
         nboot: Set the number of bootstrap replicates.
         alpha: Set the 2-sided confidence interval width to '100-A' percent.
+        block: Use variable-length block resampling to account for serial\
+            correlation.
         blk: Alternate flag for variable-length block resampling.
+        pearson: Pearson correlation (the default method).
+        spearman: Spearman (rank) correlation (more robust versus outliers).
+        quadrant: Quadrant (binarized) correlation (most robust, but weaker).
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "1dCorrelate",
         "ktaub": ktaub,
+        "block": block,
         "blk": blk,
+        "pearson": pearson,
+        "spearman": spearman,
+        "quadrant": quadrant,
         "input_files": input_files,
     }
     if nboot is not None:
@@ -121,8 +138,16 @@ def v_1d_correlate_cargs(
             "-alpha",
             str(params.get("alpha"))
         ])
+    if params.get("block"):
+        cargs.append("-block")
     if params.get("blk"):
         cargs.append("-blk")
+    if params.get("pearson"):
+        cargs.append("-Pearson")
+    if params.get("spearman"):
+        cargs.append("-Spearman")
+    if params.get("quadrant"):
+        cargs.append("-Quadrant")
     cargs.extend([execution.input_file(f) for f in params.get("input_files")])
     return cargs
 
@@ -176,7 +201,11 @@ def v_1d_correlate(
     ktaub: bool = False,
     nboot: float | None = None,
     alpha: float | None = None,
+    block: bool = False,
     blk: bool = False,
+    pearson: bool = False,
+    spearman: bool = False,
+    quadrant: bool = False,
     runner: Runner | None = None,
 ) -> V1dCorrelateOutputs:
     """
@@ -192,7 +221,12 @@ def v_1d_correlate(
         ktaub: Kendall's tau_b correlation (popular somewhere, maybe).
         nboot: Set the number of bootstrap replicates.
         alpha: Set the 2-sided confidence interval width to '100-A' percent.
+        block: Use variable-length block resampling to account for serial\
+            correlation.
         blk: Alternate flag for variable-length block resampling.
+        pearson: Pearson correlation (the default method).
+        spearman: Spearman (rank) correlation (more robust versus outliers).
+        quadrant: Quadrant (binarized) correlation (most robust, but weaker).
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dCorrelateOutputs`).
@@ -203,7 +237,11 @@ def v_1d_correlate(
         ktaub=ktaub,
         nboot=nboot,
         alpha=alpha,
+        block=block,
         blk=blk,
+        pearson=pearson,
+        spearman=spearman,
+        quadrant=quadrant,
         input_files=input_files,
     )
     return v_1d_correlate_execute(params, execution)

niwrap_afni/afni/v_1d_marry.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_MARRY_METADATA = Metadata(
-    id="bf4086d827742de99647b8c529893b01461d76ef.boutiques",
+    id="7a4e380e9b92893751b846cf2eca95ba7f37ec68.boutiques",
     name="1dMarry",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -118,7 +118,6 @@ def v_1d_marry_cargs(
     if params.get("divorce"):
         cargs.append("-divorce")
     cargs.extend([execution.input_file(f) for f in params.get("files")])
-    cargs.append("[FILE2]")
     return cargs
 
 

niwrap_afni/afni/v_1d_rplot.py

@@ -6,7 +6,7 @@ import pathlib
 from styxdefs import *
 
 V_1D_RPLOT_METADATA = Metadata(
-    id="97370e286ceee3c0b1e0eb62c1b51f85396f905d.boutiques",
+    id="a023c13860bb79baca3021cecec486f2e6d4bf18.boutiques",
     name="1dRplot",
     package="afni",
     container_image_tag="afni/afni_make_build:AFNI_24.2.06",
@@ -16,6 +16,24 @@ V_1D_RPLOT_METADATA = Metadata(
 V1dRplotParameters = typing.TypedDict('V1dRplotParameters', {
     "__STYX_TYPE__": typing.Literal["1dRplot"],
     "input_file": InputPathType,
+    "output_prefix": typing.NotRequired[str | None],
+    "save_size": typing.NotRequired[list[float] | None],
+    "TR": typing.NotRequired[float | None],
+    "title": typing.NotRequired[str | None],
+    "input_type": typing.NotRequired[typing.Literal["VOLREG", "XMAT"] | None],
+    "legend_font_size": typing.NotRequired[float | None],
+    "left_y_margin_text": typing.NotRequired[str | None],
+    "right_y_margin_text": typing.NotRequired[str | None],
+    "x_axis_label": typing.NotRequired[str | None],
+    "y_axis_label": typing.NotRequired[str | None],
+    "x_axis_range": typing.NotRequired[list[float] | None],
+    "y_axis_range": typing.NotRequired[list[float] | None],
+    "plot_char": typing.NotRequired[list[str] | None],
+    "group_labels": typing.NotRequired[list[str] | None],
+    "legend_show": bool,
+    "legend_position": typing.NotRequired[typing.Literal["bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"] | None],
+    "save_plot": bool,
+    "column_name_show": bool,
 })
 
 
@@ -57,25 +75,98 @@ class V1dRplotOutputs(typing.NamedTuple):
     """
     root: OutputPathType
     """Output root folder. This is the root folder for all outputs."""
-    output_plot: OutputPathType
+    output_plot: OutputPathType | None
     """Output plot file"""
 
 
 def v_1d_rplot_params(
     input_file: InputPathType,
+    output_prefix: str | None = None,
+    save_size: list[float] | None = None,
+    tr: float | None = None,
+    title: str | None = None,
+    input_type: typing.Literal["VOLREG", "XMAT"] | None = None,
+    legend_font_size: float | None = None,
+    left_y_margin_text: str | None = None,
+    right_y_margin_text: str | None = None,
+    x_axis_label: str | None = None,
+    y_axis_label: str | None = None,
+    x_axis_range: list[float] | None = None,
+    y_axis_range: list[float] | None = None,
+    plot_char: list[str] | None = None,
+    group_labels: list[str] | None = None,
+    legend_show: bool = False,
+    legend_position: typing.Literal["bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"] | None = None,
+    save_plot: bool = False,
+    column_name_show: bool = False,
 ) -> V1dRplotParameters:
     """
     Build parameters.
     
     Args:
         input_file: Input 1D file to plot.
+        output_prefix: Output prefix. See also -save.
+        save_size: Save figure size in pixels. Default is 2000 2000.
+        tr: Sampling period, in seconds.
+        title: Graph title. File name is used by default. Use NONE to be sure\
+            no title is used.
+        input_type: Type of data in 1D file. Choose from 'VOLREG' or 'XMAT'.
+        legend_font_size: Font size for legend text.
+        left_y_margin_text: Text to be placed at left Y margin. You need one\
+            string per column.
+        right_y_margin_text: Text to be placed at right Y margin. You need one\
+            string per column.
+        x_axis_label: Labels for the X axis.
+        y_axis_label: Labels for the Y axis.
+        x_axis_range: Range of X axis. STEP is optional.
+        y_axis_range: Range of Y axis. STEP is optional.
+        plot_char: Symbols for each column in input.
+        group_labels: Legends assigned to each group. Default is no labeling.
+        legend_show: Show legend.
+        legend_position: Legend position. Choose from: bottomright, bottom,\
+            bottomleft, left, topleft, top, topright, right, center.
+        save_plot: Save plot and quit. No need for -prefix with this option.
+        column_name_show: Show names of column in input.
     Returns:
         Parameter dictionary
     """
     params = {
         "__STYXTYPE__": "1dRplot",
         "input_file": input_file,
+        "legend_show": legend_show,
+        "save_plot": save_plot,
+        "column_name_show": column_name_show,
     }
+    if output_prefix is not None:
+        params["output_prefix"] = output_prefix
+    if save_size is not None:
+        params["save_size"] = save_size
+    if tr is not None:
+        params["TR"] = tr
+    if title is not None:
+        params["title"] = title
+    if input_type is not None:
+        params["input_type"] = input_type
+    if legend_font_size is not None:
+        params["legend_font_size"] = legend_font_size
+    if left_y_margin_text is not None:
+        params["left_y_margin_text"] = left_y_margin_text
+    if right_y_margin_text is not None:
+        params["right_y_margin_text"] = right_y_margin_text
+    if x_axis_label is not None:
+        params["x_axis_label"] = x_axis_label
+    if y_axis_label is not None:
+        params["y_axis_label"] = y_axis_label
+    if x_axis_range is not None:
+        params["x_axis_range"] = x_axis_range
+    if y_axis_range is not None:
+        params["y_axis_range"] = y_axis_range
+    if plot_char is not None:
+        params["plot_char"] = plot_char
+    if group_labels is not None:
+        params["group_labels"] = group_labels
+    if legend_position is not None:
+        params["legend_position"] = legend_position
     return params
 
 
@@ -98,7 +189,87 @@ def v_1d_rplot_cargs(
         "-input",
         execution.input_file(params.get("input_file"))
     ])
-    cargs.append("[OPTIONS]")
+    if params.get("output_prefix") is not None:
+        cargs.extend([
+            "-prefix",
+            params.get("output_prefix")
+        ])
+    if params.get("save_size") is not None:
+        cargs.extend([
+            "-save.size",
+            *map(str, params.get("save_size"))
+        ])
+    if params.get("TR") is not None:
+        cargs.extend([
+            "-TR",
+            str(params.get("TR"))
+        ])
+    if params.get("title") is not None:
+        cargs.extend([
+            "-title",
+            params.get("title")
+        ])
+    if params.get("input_type") is not None:
+        cargs.extend([
+            "-input_type",
+            params.get("input_type")
+        ])
+    if params.get("legend_font_size") is not None:
+        cargs.extend([
+            "-leg.fontsize",
+            str(params.get("legend_font_size"))
+        ])
+    if params.get("left_y_margin_text") is not None:
+        cargs.extend([
+            "-col.text.lym",
+            params.get("left_y_margin_text")
+        ])
+    if params.get("right_y_margin_text") is not None:
+        cargs.extend([
+            "-col.text.rym",
+            params.get("right_y_margin_text")
+        ])
+    if params.get("x_axis_label") is not None:
+        cargs.extend([
+            "-xax.label",
+            params.get("x_axis_label")
+        ])
+    if params.get("y_axis_label") is not None:
+        cargs.extend([
+            "-yax.label",
+            params.get("y_axis_label")
+        ])
+    if params.get("x_axis_range") is not None:
+        cargs.extend([
+            "-xax.lim",
+            *map(str, params.get("x_axis_range"))
+        ])
+    if params.get("y_axis_range") is not None:
+        cargs.extend([
+            "-yax.lim",
+            *map(str, params.get("y_axis_range"))
+        ])
+    if params.get("plot_char") is not None:
+        cargs.extend([
+            "-col.plot.char",
+            *params.get("plot_char")
+        ])
+    if params.get("group_labels") is not None:
+        cargs.extend([
+            "-grp.label",
+            *params.get("group_labels")
+        ])
+    if params.get("legend_show"):
+        cargs.append("-leg.show")
+    if params.get("legend_position") is not None:
+        cargs.extend([
+            "-leg.position",
+            params.get("legend_position")
+        ])
+    if params.get("save_plot"):
+        cargs.append("-save")
+    if params.get("column_name_show"):
+        cargs.append("-col.name.show")
     return cargs
 
 
@@ -117,7 +288,7 @@ def v_1d_rplot_outputs(
     """
     ret = V1dRplotOutputs(
         root=execution.output_file("."),
-        output_plot=execution.output_file("[OUTPUT_PREFIX]*.jpg"),
+        output_plot=execution.output_file(params.get("output_prefix") + "*.jpg") if (params.get("output_prefix") is not None) else None,
     )
     return ret
 
@@ -148,6 +319,24 @@ def v_1d_rplot_execute(
 
 def v_1d_rplot(
     input_file: InputPathType,
+    output_prefix: str | None = None,
+    save_size: list[float] | None = None,
+    tr: float | None = None,
+    title: str | None = None,
+    input_type: typing.Literal["VOLREG", "XMAT"] | None = None,
+    legend_font_size: float | None = None,
+    left_y_margin_text: str | None = None,
+    right_y_margin_text: str | None = None,
+    x_axis_label: str | None = None,
+    y_axis_label: str | None = None,
+    x_axis_range: list[float] | None = None,
+    y_axis_range: list[float] | None = None,
+    plot_char: list[str] | None = None,
+    group_labels: list[str] | None = None,
+    legend_show: bool = False,
+    legend_position: typing.Literal["bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right", "center"] | None = None,
+    save_plot: bool = False,
+    column_name_show: bool = False,
     runner: Runner | None = None,
 ) -> V1dRplotOutputs:
     """
@@ -159,6 +348,28 @@ def v_1d_rplot(
     
     Args:
         input_file: Input 1D file to plot.
+        output_prefix: Output prefix. See also -save.
+        save_size: Save figure size in pixels. Default is 2000 2000.
+        tr: Sampling period, in seconds.
+        title: Graph title. File name is used by default. Use NONE to be sure\
+            no title is used.
+        input_type: Type of data in 1D file. Choose from 'VOLREG' or 'XMAT'.
+        legend_font_size: Font size for legend text.
+        left_y_margin_text: Text to be placed at left Y margin. You need one\
+            string per column.
+        right_y_margin_text: Text to be placed at right Y margin. You need one\
+            string per column.
+        x_axis_label: Labels for the X axis.
+        y_axis_label: Labels for the Y axis.
+        x_axis_range: Range of X axis. STEP is optional.
+        y_axis_range: Range of Y axis. STEP is optional.
+        plot_char: Symbols for each column in input.
+        group_labels: Legends assigned to each group. Default is no labeling.
+        legend_show: Show legend.
+        legend_position: Legend position. Choose from: bottomright, bottom,\
+            bottomleft, left, topleft, top, topright, right, center.
+        save_plot: Save plot and quit. No need for -prefix with this option.
+        column_name_show: Show names of column in input.
         runner: Command runner.
     Returns:
         NamedTuple of outputs (described in `V1dRplotOutputs`).
@@ -167,6 +378,24 @@ def v_1d_rplot(
     execution = runner.start_execution(V_1D_RPLOT_METADATA)
     params = v_1d_rplot_params(
         input_file=input_file,
+        output_prefix=output_prefix,
+        save_size=save_size,
+        tr=tr,
+        title=title,
+        input_type=input_type,
+        legend_font_size=legend_font_size,
+        left_y_margin_text=left_y_margin_text,
+        right_y_margin_text=right_y_margin_text,
+        x_axis_label=x_axis_label,
+        y_axis_label=y_axis_label,
+        x_axis_range=x_axis_range,
+        y_axis_range=y_axis_range,
+        plot_char=plot_char,
+        group_labels=group_labels,
+        legend_show=legend_show,
+        legend_position=legend_position,
+        save_plot=save_plot,
+        column_name_show=column_name_show,
     )
     return v_1d_rplot_execute(params, execution)