How To Create Reference files in ASDF format

All WCS reference files are in ASDF format. ASDF is a human-readable, hierarchical metadata structure, made up of basic dynamic data types such as strings, numbers, lists and mappings. Data is saved as binary arrays. It is primarily intended as an interchange format for delivering products from instruments to scientists or between scientists. It’s based on YAML and JSON schema and as such provides automatic structure and metadata validation.

While it is possible to write or edit an ASDF file in a text editor, or to use the ASDF interface, the best way to create reference files is using the datamodels in the jwst pipeline jwst.datamodels and astropy.modeling .

There are two steps in this process:

  • create a transform using the simple models and the rules to combine them

  • save the transform to an ASDF file (this automatically validates it)

The rest of this document provides a brief description and examples of models in astropy.modeling which are most relevant to WCS and examples of creating WCS reference files.

Create a transform

astropy.modeling is a framework for representing, evaluating and fitting models. All available models can be imported from the models module.

>>> from astropy.modeling import models as astmodels

If necessary all fitters can be imported through the fitting module.

>>> from astropy.modeling import fitting

Many analytical models are already implemented and it is easy to implement new ones. Models are initialized with their parameter values. They are evaluated by passing the inputs directly, similar to the way functions are called. For example,

>>> poly_x = astmodels.Polynomial2D(degree=2, c0_0=.2, c1_0=.11, c2_0=2.3, c0_1=.43, c0_2=.1, c1_1=.5)
>>> poly_x(1, 1)   

Models have their analytical inverse defined if it exists and accessible through the inverse property. An inverse model can also be (re)defined by assigning to the inverse property.

>>> rotation = astmodels.Rotation2D(angle=23.4)
>>> rotation.inverse
>>> poly_x.inverse = astmodels.Polynomial2D(degree=3, **coeffs) 

astropy.modeling also provides the means to combine models in various ways.

Model concatenation uses the & operator. Models are evaluated on independent inputs and results are concatenated. The total number of inputs must be equal to the sum of the number of inputs of all models.

>>> shift_x = astmodels.Shift(-34.2)
>>> shift_y = astmodels.Shift(-120)
>>> model = shift_x & shift_y
>>> model(1, 1)
    (-33.2, -119.0)

Model composition uses the | operator. The output of one model is passed as input to the next one, so the number of outputs of one model must be equal to the number of inputs to the next one.

>>> model = poly_x | shift_x | astmodels.Scale(-2.3)
>>> model = shift_x & shift_y | poly_x

Two models, Mapping and Identity, are useful for axes manipulation - dropping or creating axes, or switching the order of the inputs.

Mapping takes a tuple of integers and an optional number of inputs. The tuple represents indices into the inputs. For example, to represent a 2D Polynomial distortion in x and y, preceded by a shift in both axes:

>>> poly_y = astmodels.Polynomial2D(degree=2, c0_0=.2, c1_0=1.1, c2_0=.023, c0_1=3, c0_2=.01, c1_1=2.2)
>>> model = shift_x & shift_y | astmodels.Mapping((0, 1, 0, 1)) | poly_x & poly_y
>>> model(1, 1) 
    (5872.03, 8465.401)

Identity takes an integer which represents the number of inputs to be passed unchanged. This can be useful when one of the inputs does not need more processing. As an example, two spatial (V2V3) and one spectral (wavelength) inputs are passed to a composite model which transforms the spatial coordinates to celestial coordinates and needs to pass the wavelength unchanged.

>>> tan = astmodels.Pix2Sky_TAN()
>>> model = tan & astmodels.Identity(1)
>>> model(0.2, 0.3, 10**-6)
   (146.30993247402023, 89.63944963170002, 1e-06)

Arithmetic Operators can be used to combine models. In this case each model is evaluated with all inputs and the operator is applied to the results, e.g. model = m1 + m2 * m3 m4/m5**m6

>>> model = shift_x + shift_y
>>> model(1)

Create the reference file

The DistortionModel in jwst.datamodels is used as an example of how to create a reference file. Similarly data models should be used to create other types of reference files as this process provides validation of the file structure.

>>> from stdatamodels.jwst.datamodels import DistortionModel
>>> dist = DistortionModel(model=model, strict_validation=True)
>>> dist.meta.description = "New distortion model"
>>> = "INS team"
>>> dist.meta.useafter = "2012/01/21"
>>> = "MIRI"
>>> dist .meta.instrument.detector = "MIRIMAGE"
>>> dist.meta.pedigree = "GROUND"
>>> dist.meta.reftype = "distortion"
>>> dist.meta.input_units = "pixel"
>>> dist.meta.output_units = "arcsec"
>>> dist.validate()

Save a transform to an ASDF file

asdf is used to read and write reference files in ASDF format. Once the model has been created using the rules in the above section, it needs to be assigned to the ASDF tree.

>>> import asdf
>>> from asdf import AsdfFile
>>> f = AsdfFile()
>>> f.tree['model'] = model
>>> f.write_to('reffile.asdf')

The write_to command validates the file and writes it to disk. It will catch any errors due to inconsistent inputs/outputs or invalid parameters.

To test the file, it can be read in again using the function:

>>> with'reffile.asdf') as ff:
...     model = ff.tree['model']
...     model(1)