NIflow: NIflow Class
In neuroconductor/wf4ni: Work-Flows for Neuroimage Processing

Description Usage Format Value Methods Examples

NIflow Class

NIflow

R6Class object.

Object of R6Class and NIflow.

Documentation: For full documentation of each method follow the corresponding link.
initialize(name, inputs = list()): Create a new flow with the given name and inputs. Documented in NIflow.initialize.
name(): Returns the name of the flow. Documented in NIflow.name.
get_private(): Returns the private environment inside the class object. Documented in NIflow.get_private.
set_name(new_name): Changes the name of the flow. Documented in NIflow.set_name.
get_inputs(): Returns the inputs of the flow. Documented in NIflow.get_inputs.
get_outputs(): Returns the outputs of the flow. Documented in NIflow.get_outputs.
get_required_inputs(outputs): Returns the inputs required to compute given outputs. Documented in NIflow.get_required_inputs.
get_process(output): Returns the function that computes the given output. Documented in NIflow.get_process.
get_dependencies(): Returns the list of package dependencies of the flow. Documented in NIflow.get_dependencies.
check_dependencies(): Checks if all flow dependencies are installed. Documented in NIflow.check_dependencies.
replace(output, with): Replace a function that computes an output with another function. Documented in NIflow.replace.
add(what = NULL, inputs = NULL, output = NULL, ...): Adds a function to the flow, that transforms the given inputs into the given output. Documented in NIflow.add.
execute(inputs = list(), desired_outputs = NULL, initialize_outputs = TRUE, ...): Execute the flow to obtain some outputs, given input files. Documented in NIflow.execute.
run(...): Just a wrapper for execute. Documented in NIflow.run.
log(level = c("DEBUG", "INFO", "WARNING", "ERROR"), message = '...'): Add a message to the flow log, including the level of the message and a timestamp. Documented in NIflow.log.
print_log(level = c("DEBUG", "WARNING", "INFO", "ERROR")): Prints the log of the flow. Documented in NIflow.print_log.
errors(): Just prints the errors in the flow log. Documented in NIflow.errors.
warnings(): Just prints the warnings in the flow log. Documented in NIflow.warnings.
save_log(filename, level = c("DEBUG", "WARNING", "INFO", "ERROR")): Saves a the flow log to file. Documented in NIflow.save_log.
graph(): Returns the graph of the flow. Documented in NIflow.graph.
plot(): Plots the graph of the flow. Documented in NIflow.plot.
memory_used(): Total memory used by the flow, including its internal variables. Documented in NIflow.memory_used.
save(path = tempdir(), file_prefix = self$name()): Save the flow to disk. Documented in NIflow.save.
load(filename): Load a flow from disk. Documented in NIflow.load.
deep_clone(): Clone a flow. Documented in NIflow.deep_clone.
subset(outputs): Take a subset of the flow, for given outputs. Documented in NIflow.subset.
to_package(path, package_name = self$name()): Creates a package with functions provided by the execution of the flow. Documented in NIflow.to_package.