Configuring a Step¶
This section describes how to instantiate a Step and set configuration parameters on it.
Steps can be configured by either:
Writing a configuration file
Instantiating the Step directly from Python
Running a Step from a configuration file¶
A Step configuration file contains one or more of a
Step’s parameters. Any
parameter not specified in the file will take its value from the CRDS-retrieved
configuration or the defaults coded directly into the
Step. Note that any
parameter specified on the command line overrides all other values.
The preferred format of configuration files is the ASDF Configuration Files format. Refer to the minimal example for a complete description of the contents. The rest of this documented will focus on the step parameters themselves.
All step parameters appear under the
parameters: section, and they must be
indented. The amount of indentation does not matter, as long as all parameters
are indented equally.
Every step configuration file must contain the parameter
class, followed by
name followed by any parameters that are specific to the step
class specifies the Python class to run. It should be a
fully-qualified Python path to the class. Step classes can ship with
stpipe itself, they may be part of other Python packages, or they
exist in freestanding modules alongside the configuration file. For
example, to use the
SystemCall step included with
stpipe.subprocess.SystemCall. To use a class called
Custom defined in a file
mysteps.py in the same directory as
the configuration file, set
name defines the name of the step. This is distinct from the
class of the step, since the same class of Step may be configured in
different ways, and it is useful to be able to have a way of
distinguishing between them. For example, when Steps are combined
into Pipelines, a Pipeline may use the same Step class
multiple times, each with different configuration parameters.
class in the configuration file are parameters
specific to the Step. The set of accepted parameters is defined in
the Step’s spec member. You can print out a Step’s configspec using
stspec commandline utility. For example, to print the
configspec for an imaginary step called
$ stspec stpipe.cleanup # The threshold below which to apply cleanup threshold = float() # A scale factor scale = float() # The output file to save to output_file = output_file(default = None)
Configspec information can also be displayed from Python, just
print_configspec on any Step class.
>>> from jwst.stpipe import cleanup >>> cleanup.print_configspec() >>> # The threshold below which to apply cleanup >>> threshold = float() >>> # A scale factor >>> scale = float()
Using this information, one can write a configuration file to use this
step. For example, here is a configuration file (
that runs the
stpipe.cleanup step to clean up an image.
#ASDF 1.0.0 #ASDF_STANDARD 1.3.0 %YAML 1.1 %TAG ! tag:stsci.edu:asdf/ --- !core/asdf-1.1.0 parameters: class = "stpipe.cleanup" name = "MyCleanup" threshold = 42.0 scale = 0.01 ...
Running a Step from the commandline¶
strun command can be used to run Steps from the commandline.
The first argument may be either:
The path to a configuration file
A Python class
Additional configuration parameters may be passed on the commandline. These parameters override any that are present in the configuration file. Any extra positional parameters on the commandline are passed to the step’s process method. This will often be input filenames.
For example, to use an existing configuration file from above, but override it so the threshold parameter is different:
$ strun do_cleanup.asdf input.fits --threshold=86
To display a list of the parameters that are accepted for a given Step
class, pass the
-h parameter, and the name of a Step class or
$ strun -h do_cleanup.asdf usage: strun [--logcfg LOGCFG] cfg_file_or_class [-h] [--pre_hooks] [--post_hooks] [--skip] [--scale] [--extname] optional arguments: -h, --help show this help message and exit --logcfg LOGCFG The logging configuration file to load --verbose, -v Turn on all logging messages --debug When an exception occurs, invoke the Python debugger, pdb --pre_hooks --post_hooks --skip Skip this step --scale A scale factor --threshold The threshold below which to apply cleanup --output_file File to save the output to
Every step has an
--output_file parameter. If one is not provided,
the output filename is determined based on the input file by appending
the name of the step. For example, in this case,
foo.fits is output
Finally, the parameters a
Step actually ran with can be saved to a new
configuration file using the
--save-parameters option. This file will have all
the parameters, specific to the step, and the final values used.
There are a number of places where the value of a parameter can be specified. The order of precedence, from most to least significant, for parameter value assignment is as follows:
Value specified on the command-line:
strun step.asdf --par=value_that_will_be_used
Value found in the user-specified configuration file
Step-coded default, determined by the parameter definition
For pipelines, if a pipeline parameter file specifies a value for a step in the pipeline, that takes precedence over any step-specific value found, either from a step-specific parameter file or CRDS-retrieved step-specific parameter file. The full order of precedence for a pipeline and its sub steps is as follows:
Value specified on the command-line:
strun pipeline.asdf --steps.step.par=value_that_will_be_used
Value found in the user-specified pipeline configuration file:
Value found in the step configuration file specified in a pipeline configuration file
CRDS-retrieved configuration for the pipeline
CRDS-retrieved configuration for each sub-step
Pipeline-coded default for itself and all sub-steps
Step-coded default for each sub-step
To output all logging output from the step, add the
to the commandline. (If more fine-grained control over logging is
required, see Logging).
To start the Python debugger if the step itself raises an exception,
--debug option to the commandline.
CRDS Retrieval of Step Parameters¶
In general, CRDS uses the input to a
Step to determine which reference files
to use. Nearly all JWST-related steps take only a single input file. However,
often times that input file is an association. Since step parameters are
configured only once per execution of a step or pipeline, only the first
qualifying member, usually of type
science is used.
Step parameters from CRDS can be completely disabled by
--disable-crds-steppars command-line switch, or setting the
Running a Step in Python¶
Running a step can also be done inside the Python interpreter and is as simple
as calling its
run() classmethod will run a previously instantiated step class. This is
very useful if one wants to setup the step’s attributes first, then run it:
from jwst.flatfield import FlatFieldStep mystep = FlatFieldStep() mystep.override_sflat = ‘sflat.fits’ output = mystep.run(input)
Unlike in the use of
call, a configuration file supplied while instantiating
run() will be ignored.
.run() method is the same as calling the instance or class directly.
They are equivalent:
output = mystep(input)
If one has all the configuration in a configuration file or can pass the
arguments directly to the step, one can use the
call() method, which creates a new
instance of the class every time you call it. So:
from jwst.jump import JumpStep output = JumpStep.call(input)
makes a new instance of
FlatFieldStep and then runs. Because it is a new
instance, it ignores any attributes of
mystep that one may have set earlier,
such overriding the sflat.
The nice thing about call() is that it can take a configuration file, so:
output = mystep.call(input, config_file=’my_flatfield.asdf’)
and it will take all the configuration from the config file.
Configuration parameters may be passed to the step by setting the
call (which takes a path to a configuration file) or as keyword
arguments. Any remaining positional arguments are passed along to the step’s
from jwst.stpipe import cleanup cleanup.call('image.fits', config_file='do_cleanup.cfg', threshold=42.0)
So use call() if you’re passing a config file or passing along args or kwargs. Otherwise use run().