[Feature Request] let imviz load jwst data model objects directly

[eteq]

Jdaviz component

Imviz

Description

The documentation for Imviz.load_data implies that it should be possible to load asdf-in-fits files from jwst directly. However, when I try to do that (see "how to reproduce"), I get the error below.

---------------------------------------------------------------------------
NotImplementedError                       Traceback (most recent call last)
Cell In[59], line 1
----> 1 imviz.load_data(im)

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/helper.py:174, in Imviz.load_data(self, data, data_label, show_in_viewer, **kwargs)
    172     if data_label:
    173         kwargs['data_label'] = data_label
--> 174     self.app.load_data(data, parser_reference='imviz-data-parser', **kwargs)
    176 # find the current label(s) - TODO: replace this by calling default label functionality
    177 # above instead of having to refind it
    178 applied_labels = []

File ~/REDACTED/python3.12/site-packages/jdaviz/app.py:851, in Application.load_data(self, file_obj, parser_reference, **kwargs)
    848         parser = data_parser_registry.members.get(data_parser)
    850 if parser is not None:
--> 851     parser(self, file_obj, **kwargs)
    852 else:
    853     self._application_handler.load_data(file_obj)

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:149, in parse_data(app, file_obj, ext, data_label, parent, cache, local_path, timeout)
    147             _parse_image(app, pf, data_label, ext=ext, parent=parent)
    148 else:
--> 149     _parse_image(app, file_obj, data_label, ext=ext, parent=parent)

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:227, in _parse_image(app, file_obj, data_label, ext, parent)
    225 if data_label is None:
    226     data_label = app.return_data_label(file_obj, ext, alt_name="image_data")
--> 227 data_iter = get_image_data_iterator(app, file_obj, data_label, ext=ext)
    229 # Save the SCI extension to this list:
    230 sci_ext = None

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:217, in get_image_data_iterator(app, file_obj, data_label, ext)
    214     data_iter = _roman_asdf_2d_to_glue_data(file_obj, data_label, ext=ext)
    216 else:
--> 217     raise NotImplementedError(f'Imviz does not support {file_obj}')
    219 return data_iter

NotImplementedError: Imviz does not support <ImageModel(1994, 2404) from contents>

Note if I load using stdatamodels.asdf_in_fits instead of jwst.datamodels I get a different error but still an error:

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
Cell In[61], line 1
----> 1 imviz.load_data(im)

File ~/casA_light_echos/.pixi/envs/default/lib/python3.12/site-packages/jdaviz/configs/imviz/helper.py:174, in Imviz.load_data(self, data, data_label, show_in_viewer, **kwargs)
    172     if data_label:
    173         kwargs['data_label'] = data_label
--> 174     self.app.load_data(data, parser_reference='imviz-data-parser', **kwargs)
    176 # find the current label(s) - TODO: replace this by calling default label functionality
    177 # above instead of having to refind it
    178 applied_labels = []

File ~/REDACTED/python3.12/site-packages/jdaviz/app.py:851, in Application.load_data(self, file_obj, parser_reference, **kwargs)
    848         parser = data_parser_registry.members.get(data_parser)
    850 if parser is not None:
--> 851     parser(self, file_obj, **kwargs)
    852 else:
    853     self._application_handler.load_data(file_obj)

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:149, in parse_data(app, file_obj, ext, data_label, parent, cache, local_path, timeout)
    147             _parse_image(app, pf, data_label, ext=ext, parent=parent)
    148 else:
--> 149     _parse_image(app, file_obj, data_label, ext=ext, parent=parent)

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:232, in _parse_image(app, file_obj, data_label, ext, parent)
    229 # Save the SCI extension to this list:
    230 sci_ext = None
--> 232 for data, data_label in data_iter:
    233 
    234     # if the science extension hasn't been identified yet, do so here:
    235     if sci_ext is None and data.ndim == 2 and ('[DATA' in data_label or '[SCI' in data_label):
    236         sci_ext = data_label

File ~/REDACTED/python3.12/site-packages/jdaviz/configs/imviz/plugins/parsers.py:440, in _roman_asdf_2d_to_glue_data(file_obj, data_label, ext)
    437     ext_list = (ext, )
    439 roman = file_obj.tree.get('roman')
--> 440 meta = roman.get('meta', {})
    441 coords = meta.get('wcs', None)
    443 for cur_ext in ext_list:

AttributeError: 'NoneType' object has no attribute 'get'

How to Reproduce

from jdaviz import Imviz
import jwst.datamodels

image = jwst.datamodels.open('https://archive.stsci.edu/hlsps/jwst-ero/hlsp_jwst-ero_jwst_miri_stephansquintet_f770w_v1_i2d.fits')

imviz = Imviz()
imviz.load_data(image)

can substitute stdatamodels.asdf_in_fits for jwst.datamodels and I still get an error

Expected behavior

The image should load without complaint.

Browser

Latest Stable Chrome

Jupyter

import sys; print("Python", sys.version)
Python 3.12.7 | packaged by conda-forge | (main, Oct 4 2024, 16:05:46) [GCC 13.3.0]
import numpy; print("Numpy", numpy.version)
Numpy 2.1.2
import astropy; print("astropy", astropy.version)
astropy 6.1.4
import matplotlib; print("matplotlib", matplotlib.version)
matplotlib 3.9.2
import scipy; print("scipy", scipy.version)
scipy 1.14.1
import skimage; print("scikit-image", skimage.version)
scikit-image 0.24.0
import asdf; print("asdf", asdf.version)
asdf 3.5.0
import stdatamodels; print("stdatamodels", stdatamodels.version)
stdatamodels 1.10.1
import gwcs; print("gwcs", gwcs.version)
gwcs 0.21.0
import regions; print("regions", regions.version)
regions 0.10
import specutils; print("specutils", specutils.version)
specutils 1.18.0
import specreduce; print("specreduce", specreduce.version)
specreduce 1.4.1
import photutils; print("photutils", photutils.version)
photutils 2.0.1
import astroquery; print("astroquery", astroquery.version)
astroquery 0.4.7
import yaml; print("pyyaml", yaml.version)
pyyaml 6.0.2
import asteval; print("asteval", asteval.version)
asteval 1.0.5
import idna; print("idna", idna.version)
idna 3.10
import traitlets; print("traitlets", traitlets.version)
traitlets 5.14.3
import bqplot; print("bqplot", bqplot.version)
bqplot 0.12.43
import bqplot_image_gl; print("bqplot-image-gl", bqplot_image_gl.version)
bqplot-image-gl 1.5.0
import glue; print("glue-core", glue.version)
glue-core 1.21.1
import glue_jupyter; print("glue-jupyter", glue_jupyter.version)
glue-jupyter 0.23.0
import glue_astronomy; print("glue-astronomy", glue_astronomy.version)
glue-astronomy 0.10.0
import echo; print("echo", echo.version)
echo 0.9.0
import ipyvue; print("ipyvue", ipyvue.version)
ipyvue 1.11.1
import ipyvuetify; print("ipyvuetify", ipyvuetify.version)
ipyvuetify 1.10.0
import ipysplitpanes; print("ipysplitpanes", ipysplitpanes.version)
ipysplitpanes 0.2.0
import ipygoldenlayout; print("ipygoldenlayout", ipygoldenlayout.version)
ipygoldenlayout 0.4.0
import ipypopout; print("ipypopout", ipypopout.version)
ipypopout 2.0.0
import jinja2; print("Jinja2", jinja2.version)
Jinja2 3.1.4
import solara; print("solara", solara.version)
solara 1.40.0
import vispy; print("vispy", vispy.version)
vispy 0.14.3
import sidecar; print("sidecar", sidecar.version)
sidecar 0.7.0
import jdaviz; print("Jdaviz", jdaviz.version)
Jdaviz 4.0.0

Software versions

import platform; print(platform.platform())
import sys; print("Python", sys.version)
import numpy; print("Numpy", numpy.version)
import astropy; print("astropy", astropy.version)
import matplotlib; print("matplotlib", matplotlib.version)
import scipy; print("scipy", scipy.version)
import skimage; print("scikit-image", skimage.version)
import asdf; print("asdf", asdf.version)
import stdatamodels; print("stdatamodels", stdatamodels.version)
import gwcs; print("gwcs", gwcs.version)
import regions; print("regions", regions.version)
import specutils; print("specutils", specutils.version)
import specreduce; print("specreduce", specreduce.version)
import photutils; print("photutils", photutils.version)
import astroquery; print("astroquery", astroquery.version)
import yaml; print("pyyaml", yaml.version)
import asteval; print("asteval", asteval.version)
import idna; print("idna", idna.version)
import traitlets; print("traitlets", traitlets.version)
import bqplot; print("bqplot", bqplot.version)
import bqplot_image_gl; print("bqplot-image-gl", bqplot_image_gl.version)
import glue; print("glue-core", glue.version)
import glue_jupyter; print("glue-jupyter", glue_jupyter.version)
import glue_astronomy; print("glue-astronomy", glue_astronomy.version)
import echo; print("echo", echo.version)
import ipyvue; print("ipyvue", ipyvue.version)
import ipyvuetify; print("ipyvuetify", ipyvuetify.version)
import ipysplitpanes; print("ipysplitpanes", ipysplitpanes.version)
import ipygoldenlayout; print("ipygoldenlayout", ipygoldenlayout.version)
import ipypopout; print("ipypopout", ipypopout.version)
import jinja2; print("Jinja2", jinja2.version)
import solara; print("solara", solara.version)
import vispy; print("vispy", vispy.version)
import sidecar; print("sidecar", sidecar.version)
import jdaviz; print("Jdaviz", jdaviz.version)

🐱

[pllim]

@eteq , is still a problem on your end? I cannot reproduce the error. The image loads fine with jdaviz 4.1.dev (current main).

[rosteen]

@eteq you can load this file just fine, by passing the filename to imviz.load_data() rather than passing the opened datamodels object. Our documentation says that you need extra steps to load the actual datamodels object, as described here: https://jdaviz.readthedocs.io/en/stable/imviz/import_data.html#jwst-datamodels/. I just checked and that method does still work in this case.

[eteq]

First I just want to confirm: @pllim , when you say you got it to work, do you mean you did it the https://jdaviz.readthedocs.io/en/stable/imviz/import_data.html#jwst-datamodels way, or the way my snippet shows above?

@rosteen - thanks for the pointer, I didn't notice that snippet! That said, it has two major problem that makes it not work for my use case:

1. It copies the data into a new nddata, which is both a problem from a "what if I want to modify it" perspective and a "run out of memory" perspective. The fix is probably just one or two copy=False's, though, right?
2. The metadata isn't present, which in practice is a huge limitation when you load multiple files and want to figure out which is which in the UI

And one minor problem:

1. It's a lot of code for what should be one of the most basic user cases!

Is there a reason why a more complete version of that snippet (e.g. with the copy=False's in place and the metadata copied over) can't be implemented? I forget now if imviz uses unified-I/O or similar, but that would seem to be the way to do it...

[pllim]

Yes sorry, I was only trying the ways we officially support, not the exact snippet using objects.

[pllim]

I wouldn't call loading model objects into Imviz a basic use case. Most users would pass in the filename and be done with it.

[eteq]

I disagree! There are many science use cases where the objects are the only available object. It is very not safe to assume a file is even present, and the regularity of which that's assumed is probably my single top "minor-to-moderate" annoyance when interacting with code as a scientist (not jdaviz specifically, which is much better than most, to be fair! I'm talking about the whole Python ecosystem).

At any rate, to be clear, I'm willing to spin up a PR myself to do this since I think I know the API-level interface of relevance. What I don't know is where the best place is to put more specific code like this - i.e., is there a unified I/O hook somewhere, or would I need to add a case to load_data? (and if the latter, is that an argument for trying to implement some sort of unified I/O or plugin approach?)

[pllim]

There are many science use cases where the objects are the only available object. It is very not safe to assume a file is even present

Can you please clarify? Did someone send you a pickled object instead of the JWST data product?

[pllim]

Checking for object at the load_data level is problematic because you need to import the object class at app level, which makes the package that holds the class a required dependency (in this case, it might be the entire pipeline). Unless you are willing to settle for static cls.__name__ checks only, which is pretty rigid because it does not account for subclasses or mixins.

And this is sounds like a feature request, not a bug.

[eteq]

Ah, point taken this is a feature request. Will re-label!