Step I/O Design

Design

The Step architecture is designed such that a Step’s intended sole responsibility is to perform the calculation required. Any input/output operations are handled by the surrounding Step architecture. This is to help facilitate the use of Step’s from both a command-line environment, and from an interactive Python environment, such as Jupyter notebooks or IPython.

For command-line usage, all inputs and outputs are designed to come from and save to files.

For interactive Python use, inputs and outputs are expected to be Python objects, negating the need to save and reload data after every Step call. This allows users to write Python scripts without having to worry about doing I/O at every step, unless, of course, if the user wants to do so.

The high-level overview of the input/output design is given in Writing a step. The following discusses the I/O API and best practices.

To facilitate this design, a basic Step is suggested to have the following structure:

class MyStep(stpipe.Step):

    spec = ''  # Desired configuration parameters

    def process(self, input):
        return do_calculation(input)

When run from the command line:

strun MyStep input_data.asdf

the result will be saved in a file called:

input_data_mystep.asdf

Similarly, the same code can be used in a Python script or interactive environment as follows:

result = MyStep.call(input)
# result contains the resulting data
# which can then be used by further steps or
# other functions.
#
# when done, the data can be saved with the DataModel.save
# method
result.save('my_final_results.asdf')

Input Source

All input files, except for references files provided by CRDS, are expected to be co-resident in the same directory. That directory is determined by the directory in which the primary input file resides. For programmatic use, this directory is available in the Step.input_dir attribute.

Output

When Files are Created

Whether a Step produces an output file or not is ultimately determined by the built-in parameter option save_results. If True, output files will be created. save_results is set under a number of conditions:

Explicitly through a parameter file or as a command-line option.
Implicitly when a step is called by strun.

Output File Naming

File names are constructed based on three components: basename, suffix, and extension:

basename_suffix.extension

The extension will often be the same as the primary input file. This will not be the case if the data format of the output needs to be something different, such as a text table with .ecsv extension.

Similarly, the basename will usually be derived from the primary input file. However, there are some caveats discussed below.

Ultimately, the suffix is what Step use to identify their output.

A Step’s suffix is defined in a couple of different ways:

By the Step.name attribute. This is the default.
By the suffix parameter.
Explicitly in the code. Often this is done in Pipelines where a single pipeline creates numerous different output files.

Basename Determination

Most often, the output file basename is determined through any of the following, given from higher precedence to lower:

The --output_file command-line option.
The output_file parameter option.
Primary input file name.
If the output is a DataModel, from the DataModel.meta.filename.

In all cases, if the originating file name has a known suffix on it, that suffix is removed and replaced by the Step’s own suffix.

In very rare cases, when there is no other source for the basename, a basename of step_<step_name> is used. This can happen when a Step is being programmatically used and only the save_results parameter option is given.

Sub-Steps and Output

Normally, the value of a parameter option is completely local to the Step: A Step, called from another Step or Pipeline, can only access its own parameters. Hence, options such as save_results do not affect a called Step.

The exceptions to this are the parameters output_file and output_dir. If either of these parameters are queried by a Step, but are not defined for that Step, values will be retrieved up through the parent. The reason is to provide consistency in output from Step and Pipeline. All file names will have the same basename and will all appear in the same directory.

As expected, if either parameter is specified for the Step in question, the local value will override the parent value.

Also, for output_file, there is another option, search_output_file, that can also control this behavior. If set to False, a Step will never query its parent for its value.

Output API: When More Control Is Needed

In summary, the standard output API, as described so far, is basically “set a few parameters, and let the Step framework handle the rest”. However, there are always the exceptions that require finer control, such as saving intermediate files or multiple files of different formats. This section discusses the method API and conventions to use in these situations.

Save That Model: Step.save_model

If a Step needs to save a DataModel before the step completes, use of stpipe.Step.save_model() is the recommended over directly calling DataModel.save. Step.save_model uses the Step framework and hence will honor the following:

If Step.save_results is False, nothing will happen.
Will ensure that Step.output_dir is used.
Will use Step.suffix if not otherwise specified.
Will determine the output basename through the Step framework, if not otherwise specified.

The basic usage, in which nothing is overridden, is:

class MyStep(Step):

    def process(self, input):
        # ...
        result = some_DataModel
        self.save_model(result)

The most common use case, however, is for saving some intermediate results that would have a different suffix:

self.save_model(intermediate_result_datamodel, suffix='intermediate')

See stpipe.Step.save_model() for further information.

Make That Filename: Step.make_output_path

For the situations when a filename is needed to be constructed before saving, either to know what the filename will be or for data that is not a DataModel, use stpipe.Step.make_output_path. By default, calling make_output_path without any arguments will return what the default output file name will be:

output_path = self.make_output_path()

This method encapsulates the following Step framework functions:

Will ensure that Step.output_dir is used.
Will use Step.suffix if not otherwise specified.
Will determine the output basename through the Step framework, if not otherwise specified.

A typical use case is when a Step needs to save data that is not a DataModel. The current Step architecture does not know how to handle these, so saving needs to be done explicitly. The pattern of usage would be:

# A table need be saved and needs a different
# suffix than what the Step defines.
table = some_astropy_table_data
if self.save_results:
    table_path = self.make_output_path(suffix='cat', ext='ecsv')
    table.save(table_path, format='ascii.ecsv', overwrite=True)