Working with Roman datamodels and ASDF files¶
Please refer to Roman Documentation
for more details about roman_datamodels.
This section assumes that you are familiar with the ASDF standard format. If that’s not the case, a good starting point would be to go over the ASDF Documentation.
If you have installed the roman calibration pipeline you should also have access to the standalone tool asdfinfo which allows access to ASDF (and roman) files from the terminal prompt,:
asdftool info r0000101001001001001_01101_0001_WFI16_cal.asdf
root (AsdfObject)
├─asdf_library (Software)
│ ├─author (str): The ASDF Developers
...
also useful is:
asdftool help
usage: asdftool [-h] [--verbose] {help,explode,implode,extract,defragment,diff,edit,remove-hdu,info,extensions,tags,to_yaml} ...
Commandline utilities for managing ASDF files.
optional arguments:
-h, --help show this help message and exit
--verbose, -v Increase verbosity
subcommands:
{help,explode,implode,extract,defragment,diff,edit,remove-hdu,info,extensions,tags,to_yaml}
help Display usage information
explode Explode a ASDF file.
implode Implode a ASDF file.
extract Extract ASDF extensions in ASDF-in-FITS files into pure ASDF files
defragment Defragment an ASDF file..
diff Report differences between two ASDF files
remove-hdu Remove ASDF extension from ASDF-in-FITS file
info Print a rendering of an ASDF tree.
extensions Show information about installed extensions
tags List currently available tags
to_yaml Convert as ASDF file to pure YAML.
which gives a list of possible actions one of the more useful can be:
asdftool edit file.asdf
Which will open the file in an editor you have set via the EDITOR environment variable. A more complete description of the options can be found in the asdftool documentation.
To access the files via a python session,
import roman_datamodels as rdm
import asdf
with rdm.open('r0000101001001001001_01101_0001_WFI16_cal.asdf') as model:
<Manipulate the files>
with asdf.open('r0000101001001001001_01101_0001_WFI16_cal.asdf', copy_arrays=True) as model:
<Manipulate the files>
Once the files are loaded you can access various attributes. Below is a table showing how to access various properties using the roman_datamodels and the asdf.open methods,
Roman Datamodels |
ASDF |
rdm_a.meta
rdm_a.meta.aperture
rdm_a.meta.aperture.position_angle
120
|
asdf_a.tree['roman']['meta']
asdf_a.tree['roman']['meta']['aperture']
asdf_a.tree['roman']['meta']['aperture']['position_angle']
120
|
You can also update or modify the metadata in Roman datamodels
rdm_a.meta.aperture.position_angle = 120.21
rdm_a.meta.aperture.position_angle
120.21
The ASDF equivalent is
asdf_a.tree['roman']['meta']['aperture']['position_angle'] = 120.05
asdf_a.tree['roman']['meta']['aperture']['position_angle']
120.05
Hint
If you trigger an error, “ValueError: assignment destination is read-only” make sure the asdf file was opened with copy_arrays=True, or with mode=’rw’
You can also access and modify the data arrays
rdm_a.data
<array (unloaded) shape: [4096, 4096] dtype: float32>
rdm_a.data[10,11]
0.0
rdm_a.data[10,11] = 122.1
rdm_a.data[10,11]
122.1
or by modifying the ASDF tree,
asdf_a.tree['roman']['data']
<array (unloaded) shape: [4096, 4096] dtype: float32>
asdf_a.tree['roman']['data'][10,11]
0.0
asdf_a.tree['roman']['data'][10,11] = 3.14159
asdf_a.tree['roman']['data'][10,11]
3.14159
Using the info method¶
You can examine a roman data model using the info and search methods provided from the asdf package. The info fuction will print a representation of the asdf tree.
>>> from roman_datamodels import datamodels as rdm
>>> d_uncal = rdm.open('r0000101001001001001_01101_0001_WFI01_uncal.asdf')
>>> d_uncal.info()
root (AsdfObject)
├─asdf_library (Software)
│ ├─author (str): The ASDF Developers
│ ├─homepage (str): http://github.com/asdf-format/asdf
│ ├─name (str): asdf
│ └─version (str): 2.8.1
├─history (dict)
│ └─extensions (list)
│ ├─[0] (ExtensionMetadata) ...
│ ├─[1] (ExtensionMetadata) ...
│ └─[2] (ExtensionMetadata) ...
└─roman (WfiScienceRaw)
├─meta (dict)
│ ├─aperture (Aperture) ...
│ ├─cal_step (L2CalStep) ...
│ ├─calibration_software_version (str): 0.4.3.dev89+gca5771d
│ ├─coordinates (Coordinates) ...
│ ├─crds_context_used (str): roman_0020.pmap
│ ├─crds_software_version (str): 11.5.0
│ ├─ephemeris (Ephemeris) ...
│ ├─exposure (Exposure) ...
│ └─17 not shown
└─data (NDArrayType): shape=(8, 4096, 4096), dtype=uint16
Some nodes not shown.
The info command also gives you control over the number of lines displayed
by passing the argument max_rows. As an integer, max_rows
will be interpreted as an overall limit on the number of displayed lines.
If max_rows is a tuple, then each member limits lines per node at the
depth corresponding to its tuple index.
For example, to show all top-level nodes and 5 of each’s children:
>>> d_uncal.info(max_rows=(None,5))
root (AsdfObject)
├─asdf_library (Software)
│ ├─author (str): The ASDF Developers
│ ├─homepage (str): http://github.com/asdf-format/asdf
│ ├─name (str): asdf
│ └─version (str): 2.8.1
├─history (dict)
│ └─extensions (list) ...
└─roman (WfiScienceRaw)
├─meta (dict) ...
└─data (NDArrayType): shape=(8, 4096, 4096), dtype=uint16
Some nodes not shown.
Or you can use the asdf.info method to view the contents of the tree
>> asdf.info(d_uncal)
Will print the same information as the above d_uncal.info command but also
gives you enhanced capabilities. For instance you can display the first three
lines for each of the meta entries,
>>> asdf.info(d_uncal.meta, max_rows=(None, 3))
root (DNode)
├─aperture (Aperture)
│ ├─name (str): WFI_CEN
│ └─position_angle (int): 120
├─cal_step (L2CalStep)
│ ├─assign_wcs (str): INCOMPLETE
│ ├─flat_field (str): INCOMPLETE
│ └─6 not shown
├─calibration_software_version (str): 0.4.3.dev89+gca5771d
├─coordinates (Coordinates)
│ └─reference_frame (str): ICRS
├─crds_context_used (str): roman_0020.pmap
├─crds_software_version (str): 11.5.0
├─ephemeris (Ephemeris)
│ ├─earth_angle (float): 3.3161255787892263
│ ├─moon_angle (float): 3.3196162372932148
│ └─10 not shown
...
or you can concentrate on a given attribute. To list all the attributes
in cal_step without listing the values,
>>> asdf.info(d_uncal.meta.cal_step,max_rows=(None, 3),show_values=False)
root (L2CalStep)
├─assign_wcs (str)
├─flat_field (str)
├─dark (str)
├─dq_init (str)
├─jump (str)
├─linearity (str)
├─ramp_fit (str)
└─saturation (str)
More information on the info method can be found in the ASDF documentation at rendering the ASDF trees.
Using the search method¶
You can also use the search method to find attributes,
>>> d_uncal.search('cal_step')
root (AsdfObject)
└─roman (WfiScienceRaw)
└─meta (dict)
└─cal_step (L2CalStep)
or a a general search for all attributes with cal in the name
>>> d_uncal.search('cal')
root (AsdfObject)
└─roman (WfiScienceRaw)
└─meta (dict)
├─cal_step (L2CalStep)
├─calibration_software_version (str): 0.4.3.dev89+gca5771d
├─instrument (WfiMode)
│ └─optical_element (str): F158
└─velocity_aberration (VelocityAberration)
└─scale_factor (float): 0.9999723133902021
This will do a regular expression search for cal in the attribute name. More
information on using regular expressions in the search method can be found
in the ASDF documentation linked below.
To search only within the meta tree,
>>> d_uncal.search('cal_')['roman']['meta']
meta (dict)
├─cal_step (L2CalStep)
└─instrument (WfiMode)
└─optical_element (str): F158
You can also use the search method to find attributes by type in the asdf tree. For instance, you can find all integers, floats, or booleans by using the type keyword,
>>> d_uncal.search(type=bool)
root (AsdfObject)
└─roman (WfiScienceRaw)
└─meta (dict)
├─exposure (Exposure)
│ └─data_problem (bool): False
└─visit (Visit)
├─internal_target (bool): False
└─target_of_opportunity (bool): False
>>> d_uncal.search(type=bool, value=True)
No results found.
More information and options for the search method can be found in the ASDF documentation here.