niwrap-afni 0.5.0__py3-none-any.whl

niwrap_afni/afni/dicom_hdr.py

@@ -0,0 +1,263 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DICOM_HDR_METADATA = Metadata(
+    id="f1dd7c5e97c664a21c6f4e09518ffc5513e4e54f.boutiques",
+    name="dicom_hdr",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+DicomHdrParameters = typing.TypedDict('DicomHdrParameters', {
+    "__STYX_TYPE__": typing.Literal["dicom_hdr"],
+    "files": list[InputPathType],
+    "hex": bool,
+    "noname": bool,
+    "sexinfo": bool,
+    "mulfram": bool,
+    "v_dump": typing.NotRequired[float | None],
+    "no_length": bool,
+    "slice_times": bool,
+    "slice_times_verb": bool,
+    "siemens_csa_data": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dicom_hdr": dicom_hdr_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class DicomHdrOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dicom_hdr(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dicom_hdr_params(
+    files: list[InputPathType],
+    hex_: bool = False,
+    noname: bool = False,
+    sexinfo: bool = False,
+    mulfram: bool = False,
+    v_dump: float | None = None,
+    no_length: bool = False,
+    slice_times: bool = False,
+    slice_times_verb: bool = False,
+    siemens_csa_data: bool = False,
+) -> DicomHdrParameters:
+    """
+    Build parameters.
+    
+    Args:
+        files: DICOM file(s) to read.
+        hex_: Include hexadecimal printout for integer values.
+        noname: Don't include element names in the printout.
+        sexinfo: Dump Siemens EXtra INFO text (0029 1020), if present (can be\
+            VERY lengthy).
+        mulfram: Dump multi-frame information, if present (1 line per frame,\
+            plus an XML-style header/footer). This option also implies -noname.
+        v_dump: Dump n words of binary data also.
+        no_length: Skip lengths and offsets (helps diffs).
+        slice_times: Show slice times from Siemens mosaic images.
+        slice_times_verb: Show slice times from Siemens mosaic images\
+            verbosely. (multiple uses increase verbosity, can dump CSA data).
+        siemens_csa_data: Same as 3 -slice_times_verb opts.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dicom_hdr",
+        "files": files,
+        "hex": hex_,
+        "noname": noname,
+        "sexinfo": sexinfo,
+        "mulfram": mulfram,
+        "no_length": no_length,
+        "slice_times": slice_times,
+        "slice_times_verb": slice_times_verb,
+        "siemens_csa_data": siemens_csa_data,
+    }
+    if v_dump is not None:
+        params["v_dump"] = v_dump
+    return params
+
+
+def dicom_hdr_cargs(
+    params: DicomHdrParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("dicom_hdr")
+    cargs.extend([execution.input_file(f) for f in params.get("files")])
+    if params.get("hex"):
+        cargs.append("-hex")
+    if params.get("noname"):
+        cargs.append("-noname")
+    if params.get("sexinfo"):
+        cargs.append("-sexinfo")
+    if params.get("mulfram"):
+        cargs.append("-mulfram")
+    if params.get("v_dump") is not None:
+        cargs.extend([
+            "-v",
+            str(params.get("v_dump"))
+        ])
+    if params.get("no_length"):
+        cargs.append("-no_length")
+    if params.get("slice_times"):
+        cargs.append("-slice_times")
+    if params.get("slice_times_verb"):
+        cargs.append("-slice_times_verb")
+    if params.get("siemens_csa_data"):
+        cargs.append("-siemens_csa_data")
+    return cargs
+
+
+def dicom_hdr_outputs(
+    params: DicomHdrParameters,
+    execution: Execution,
+) -> DicomHdrOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = DicomHdrOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dicom_hdr_execute(
+    params: DicomHdrParameters,
+    execution: Execution,
+) -> DicomHdrOutputs:
+    """
+    A tool to print DICOM file information to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DicomHdrOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dicom_hdr_cargs(params, execution)
+    ret = dicom_hdr_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dicom_hdr(
+    files: list[InputPathType],
+    hex_: bool = False,
+    noname: bool = False,
+    sexinfo: bool = False,
+    mulfram: bool = False,
+    v_dump: float | None = None,
+    no_length: bool = False,
+    slice_times: bool = False,
+    slice_times_verb: bool = False,
+    siemens_csa_data: bool = False,
+    runner: Runner | None = None,
+) -> DicomHdrOutputs:
+    """
+    A tool to print DICOM file information to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        files: DICOM file(s) to read.
+        hex_: Include hexadecimal printout for integer values.
+        noname: Don't include element names in the printout.
+        sexinfo: Dump Siemens EXtra INFO text (0029 1020), if present (can be\
+            VERY lengthy).
+        mulfram: Dump multi-frame information, if present (1 line per frame,\
+            plus an XML-style header/footer). This option also implies -noname.
+        v_dump: Dump n words of binary data also.
+        no_length: Skip lengths and offsets (helps diffs).
+        slice_times: Show slice times from Siemens mosaic images.
+        slice_times_verb: Show slice times from Siemens mosaic images\
+            verbosely. (multiple uses increase verbosity, can dump CSA data).
+        siemens_csa_data: Same as 3 -slice_times_verb opts.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DicomHdrOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_HDR_METADATA)
+    params = dicom_hdr_params(
+        files=files,
+        hex_=hex_,
+        noname=noname,
+        sexinfo=sexinfo,
+        mulfram=mulfram,
+        v_dump=v_dump,
+        no_length=no_length,
+        slice_times=slice_times,
+        slice_times_verb=slice_times_verb,
+        siemens_csa_data=siemens_csa_data,
+    )
+    return dicom_hdr_execute(params, execution)
+
+
+__all__ = [
+    "DICOM_HDR_METADATA",
+    "DicomHdrOutputs",
+    "DicomHdrParameters",
+    "dicom_hdr",
+    "dicom_hdr_params",
+]

niwrap_afni/afni/dicom_hinfo.py

@@ -0,0 +1,220 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DICOM_HINFO_METADATA = Metadata(
+    id="0de7df6566656068c4dc0dc5d6d2bae576cab754.boutiques",
+    name="dicom_hinfo",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+DicomHinfoParameters = typing.TypedDict('DicomHinfoParameters', {
+    "__STYX_TYPE__": typing.Literal["dicom_hinfo"],
+    "tag": list[str],
+    "sepstr": typing.NotRequired[str | None],
+    "full_entry": bool,
+    "no_name": bool,
+    "namelast": bool,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dicom_hinfo": dicom_hinfo_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+    }.get(t)
+
+
+class DicomHinfoOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dicom_hinfo(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+
+
+def dicom_hinfo_params(
+    tag: list[str],
+    sepstr: str | None = None,
+    full_entry: bool = False,
+    no_name: bool = False,
+    namelast: bool = False,
+) -> DicomHinfoParameters:
+    """
+    Build parameters.
+    
+    Args:
+        tag: Specify one or more DICOM tags to print, in the format aaaa,bbbb\
+            where aaaa and bbbb are hexadecimal digits.
+        sepstr: Use the specified string to separate fields instead of space.
+        full_entry: Output the full entry if it is more than one word or\
+            contains white space.
+        no_name: Omit the filename from the output.
+        namelast: Place the filename last in the output instead of first.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dicom_hinfo",
+        "tag": tag,
+        "full_entry": full_entry,
+        "no_name": no_name,
+        "namelast": namelast,
+    }
+    if sepstr is not None:
+        params["sepstr"] = sepstr
+    return params
+
+
+def dicom_hinfo_cargs(
+    params: DicomHinfoParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("dicom_hinfo")
+    cargs.extend([
+        "-tag",
+        *params.get("tag")
+    ])
+    if params.get("sepstr") is not None:
+        cargs.extend([
+            "-sepstr",
+            params.get("sepstr")
+        ])
+    if params.get("full_entry"):
+        cargs.append("-full_entry")
+    if params.get("no_name"):
+        cargs.append("-no_name")
+    if params.get("namelast"):
+        cargs.append("-namelast")
+    cargs.append("[FILES...]")
+    return cargs
+
+
+def dicom_hinfo_outputs(
+    params: DicomHinfoParameters,
+    execution: Execution,
+) -> DicomHinfoOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = DicomHinfoOutputs(
+        root=execution.output_file("."),
+    )
+    return ret
+
+
+def dicom_hinfo_execute(
+    params: DicomHinfoParameters,
+    execution: Execution,
+) -> DicomHinfoOutputs:
+    """
+    Prints selected information from one or more DICOM files to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DicomHinfoOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dicom_hinfo_cargs(params, execution)
+    ret = dicom_hinfo_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dicom_hinfo(
+    tag: list[str],
+    sepstr: str | None = None,
+    full_entry: bool = False,
+    no_name: bool = False,
+    namelast: bool = False,
+    runner: Runner | None = None,
+) -> DicomHinfoOutputs:
+    """
+    Prints selected information from one or more DICOM files to stdout.
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        tag: Specify one or more DICOM tags to print, in the format aaaa,bbbb\
+            where aaaa and bbbb are hexadecimal digits.
+        sepstr: Use the specified string to separate fields instead of space.
+        full_entry: Output the full entry if it is more than one word or\
+            contains white space.
+        no_name: Omit the filename from the output.
+        namelast: Place the filename last in the output instead of first.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DicomHinfoOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_HINFO_METADATA)
+    params = dicom_hinfo_params(
+        tag=tag,
+        sepstr=sepstr,
+        full_entry=full_entry,
+        no_name=no_name,
+        namelast=namelast,
+    )
+    return dicom_hinfo_execute(params, execution)
+
+
+__all__ = [
+    "DICOM_HINFO_METADATA",
+    "DicomHinfoOutputs",
+    "DicomHinfoParameters",
+    "dicom_hinfo",
+    "dicom_hinfo_params",
+]

niwrap_afni/afni/dicom_to_raw.py

@@ -0,0 +1,176 @@
+# This file was auto generated by Styx.
+# Do not edit this file directly.
+
+import typing
+import pathlib
+from styxdefs import *
+
+DICOM_TO_RAW_METADATA = Metadata(
+    id="7eb027b7c5690d1e6ebc29a721254ed558470f1d.boutiques",
+    name="dicom_to_raw",
+    package="afni",
+    container_image_tag="afni/afni_make_build:AFNI_24.2.06",
+)
+
+
+DicomToRawParameters = typing.TypedDict('DicomToRawParameters', {
+    "__STYX_TYPE__": typing.Literal["dicom_to_raw"],
+    "input_dicom": InputPathType,
+})
+
+
+def dyn_cargs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build cargs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build cargs function.
+    """
+    return {
+        "dicom_to_raw": dicom_to_raw_cargs,
+    }.get(t)
+
+
+def dyn_outputs(
+    t: str,
+) -> typing.Any:
+    """
+    Get build outputs function by command type.
+    
+    Args:
+        t: Command type.
+    Returns:
+        Build outputs function.
+    """
+    return {
+        "dicom_to_raw": dicom_to_raw_outputs,
+    }.get(t)
+
+
+class DicomToRawOutputs(typing.NamedTuple):
+    """
+    Output object returned when calling `dicom_to_raw(...)`.
+    """
+    root: OutputPathType
+    """Output root folder. This is the root folder for all outputs."""
+    output_raw_file: OutputPathType
+    """Output raw file(s)"""
+
+
+def dicom_to_raw_params(
+    input_dicom: InputPathType,
+) -> DicomToRawParameters:
+    """
+    Build parameters.
+    
+    Args:
+        input_dicom: Input DICOM file.
+    Returns:
+        Parameter dictionary
+    """
+    params = {
+        "__STYXTYPE__": "dicom_to_raw",
+        "input_dicom": input_dicom,
+    }
+    return params
+
+
+def dicom_to_raw_cargs(
+    params: DicomToRawParameters,
+    execution: Execution,
+) -> list[str]:
+    """
+    Build command-line arguments from parameters.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Command-line arguments.
+    """
+    cargs = []
+    cargs.append("dicom_to_raw")
+    cargs.append(execution.input_file(params.get("input_dicom")))
+    return cargs
+
+
+def dicom_to_raw_outputs(
+    params: DicomToRawParameters,
+    execution: Execution,
+) -> DicomToRawOutputs:
+    """
+    Build outputs object containing output file paths and possibly stdout/stderr.
+    
+    Args:
+        params: The parameters.
+        execution: The execution object for resolving input paths.
+    Returns:
+        Outputs object.
+    """
+    ret = DicomToRawOutputs(
+        root=execution.output_file("."),
+        output_raw_file=execution.output_file(pathlib.Path(params.get("input_dicom")).name + ".raw.0001"),
+    )
+    return ret
+
+
+def dicom_to_raw_execute(
+    params: DicomToRawParameters,
+    execution: Execution,
+) -> DicomToRawOutputs:
+    """
+    Reads images from DICOM file and writes them to raw file(s).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        params: The parameters.
+        execution: The execution object.
+    Returns:
+        NamedTuple of outputs (described in `DicomToRawOutputs`).
+    """
+    params = execution.params(params)
+    cargs = dicom_to_raw_cargs(params, execution)
+    ret = dicom_to_raw_outputs(params, execution)
+    execution.run(cargs)
+    return ret
+
+
+def dicom_to_raw(
+    input_dicom: InputPathType,
+    runner: Runner | None = None,
+) -> DicomToRawOutputs:
+    """
+    Reads images from DICOM file and writes them to raw file(s).
+    
+    Author: AFNI Developers
+    
+    URL: https://afni.nimh.nih.gov/
+    
+    Args:
+        input_dicom: Input DICOM file.
+        runner: Command runner.
+    Returns:
+        NamedTuple of outputs (described in `DicomToRawOutputs`).
+    """
+    runner = runner or get_global_runner()
+    execution = runner.start_execution(DICOM_TO_RAW_METADATA)
+    params = dicom_to_raw_params(
+        input_dicom=input_dicom,
+    )
+    return dicom_to_raw_execute(params, execution)
+
+
+__all__ = [
+    "DICOM_TO_RAW_METADATA",
+    "DicomToRawOutputs",
+    "DicomToRawParameters",
+    "dicom_to_raw",
+    "dicom_to_raw_params",
+]