xcp_d.interfaces.plotting.SlicesDir
- class xcp_d.interfaces.plotting.SlicesDir(**inputs)[source]
Wrapped executable:
slicesdir
.Run slicesdir.
Notes
Usage: slicesdir [-o] [-p <image>] [-e <thr>] [-S] <filelist> -o : filelist is pairs ( <underlying> <red-outline> ) of images -p <image> : use <image> as red-outline image on top of all images in <filelist> -e <thr> : use the specified threshold for edges (if >0 use this proportion of max-min,
if <0, use the absolute value)
- -S
: output every second axial slice rather than just 9 ortho slices
- Mandatory Inputs:
in_files (a list of items which are a pathlike object or string representing an existing file) – List of files to process. Maps to a command-line argument:
%s
(position: -1).- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.edge_threshold (a float) – Use the specified threshold for edges (if >0 use this proportion of max-min, if <0, use the absolute value). Maps to a command-line argument:
-e %.03f
(position: 2).environ (a dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’) – Environment variables. (Nipype default value:
{}
)is_pairs (a boolean) – Filelist is pairs ( <underlying> <red-outline> ) of images. Maps to a command-line argument:
-o
(position: 0).out_extension (‘.gif’ or ‘.png’ or ‘.svg’) – Convenience parameter to let xcp_d select the extension. (Nipype default value:
.gif
)outline_image (a pathlike object or string representing an existing file) – Use <image> as red-outline image on top of all images in <filelist>. Maps to a command-line argument:
-p %s
(position: 1).output_odd_axials (a boolean) – Output every second axial slice rather than just 9 ortho slices. Maps to a command-line argument:
-S
(position: 3).output_type (‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’) – FSL output type.
- Outputs:
out_dir (a pathlike object or string representing an existing directory) – Output directory.
out_files (a list of items which are a pathlike object or string representing an existing file) – List of generated PNG files.
Methods
__init__
(**inputs)Subclasses must implement __init__
aggregate_outputs
([runtime, needed_outputs])Collate expected outputs and apply output traits validation.
help
([returnhelp])Prints class help
load_inputs_from_json
(json_file[, overwrite])A convenient way to load pre-set inputs from a JSON file.
raise_exception
(runtime)run
([cwd, ignore_exception])Execute this interface.
save_inputs_to_json
(json_file)A convenient way to save current inputs to a JSON file.
set_default_output_type
(output_type)Set the default output type for FSL classes.
set_default_terminal_output
(output_type)Set the default terminal output for CommandLine Interfaces.
version_from_command
([flag, cmd])Attributes
always_run
Should the interface be always run even if the inputs were not changed? Only applies to interfaces being run within a workflow context.
can_resume
Defines if the interface can reuse partial results after interruption.
cmd
sets base command, immutable
cmdline
command plus any arguments (args) validates arguments and generates command line
resource_monitor
terminal_output
version
interfaces should implement a version property
write_cmdline