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Data Analysis Plugins

The Imviz data analysis plugins are meant to aid quick-look analysis of 2D image data. All plugins are accessed via the :guilabel:`plugin` icon in the upper right corner of the Imviz application.

Imviz Plugins

Metadata Viewer

This plugin allows viewing of any metadata associated with the selected data.

If the data is loaded from multi-extension FITS that contains a primary header, you will also see a :guilabel:`Show primary header` toggle, when enabled, would display just the primary header metadata.

Plot Options

This plugin gives access to per-viewer and per-layer plotting options.

.. seealso::

    :ref:`Display Settings <display-settings>`
        Documentation on various display settings in the Jdaviz viewers.

Subset Tools

Note that the subset plugin only displays information for regions defined via the region selector tools in the UI, and does not show static regions loaded via the API unless an interactive region is drawn after.

.. seealso::

    :ref:`Subset Tools <specviz-subset-plugin>`
        Specviz documentation on the Subset Tools plugin.

Link Control

This plugin is used to re-link images by pixels or WCS using :func:`~jdaviz.configs.imviz.helper.link_image_data`. All images are automatically linked by pixels on load but you can use it to re-link by pixels or WCS as needed. Once you have set your options, click :guilabel:`LINK` to perform the linking.

For WCS linking, the "fast approximation" option uses an affine transform to represent the offset between images, if possible. It is much more performant at the cost of accuracy but should be accurate to within a pixel for most cases. If approximation fails, WCS linking still automatically falls back to full transformation.

For more details on linking, see :ref:`dev_glue_linking`.

From the API (if linking by WCS):

imviz.link_data(link_type='wcs')

Compass

For an image with a valid WCS, the compass would show directions to North (N) and East (E) for ICRS sky coordinates. It also shows the currently displayed data label, the X and Y directions, and the zoom box.

When you have multiple viewers created in Imviz, use the Viewer dropdown menu to change the active viewer that it tracks.

Line Profiles

This plugin plots line profiles across X and Y for the pixel under cursor when l key is pressed on the image viewer. You can also manually type in the values of X and Y, and then press the :guilabel:`PLOT` button. The top visible image, the same one displayed under :ref:`imviz-compass`, will be used for these plots.

This plugin only considers pixel locations, not sky coordinates.

Simple Aperture Photometry

Warning

Results for dithered data linked by WCS might be inaccurate unless the selected data is the reference data. See glue-viz/glue-astronomy#52 for more details.

This plugin performs simple aperture photometry and plots a radial profile for one object within an interactively selected region. A typical workflow is as follows:

  1. Load image(s) in Imviz (see :ref:`imviz-import-data`).
  2. Draw a region over the object of interest (see :ref:`imviz_defining_spatial_regions`).
  3. Select the desired image using the :guilabel:`Data` drop-down menu.
  4. Select the desired region using the :guilabel:`Subset` drop-down menu.
  5. If you want to subtract background before performing photometry, you have the following 3 options. Otherwise if your image is already background subtracted, choose "Manual" and leave the background set at 0:
  • Manual: Enter the background value in the :guilabel:`Background value` field. This value must be in the same unit as display data, if applicable.
  • Annulus: Enter its inner radius and width in the :guilabel:`Annulus inner radius` and :guilabel:`Annulus width`, respectively. Median of the pixels within the annulus region will be used but the annulus shape will not be shown on display.
  • Subset: Define a region for background calculation (median) using Subset draw tool and select that region using the :guilabel:`Background` drop-down menu.
  1. For some JWST and HST images, pixel area in arcsec squared is automatically populated in the :guilabel:`Pixel area` field from image metadata. If it does not auto-populate for you, you can manually enter a value but it must be in the unit of arcsec squared. This field is only used if per steradian is detected in display data unit. Otherwise, it is only informational. If this field is not applicable for you, leave it at 0. This field resets every time Data selection changes if auto-population not possible.
  2. If you also want photometry result in the unit of counts, you can enter a conversion factor in the :guilabel:`Counts conversion factor` field. The value must be in the unit of display data unit per counts. This is used to convert linear flux unit (e.g., MJy/sr) to counts. This field is only used if data has a valid unit. If this field is not applicable for you, leave it at 0. This field resets every time Data selection changes.
  3. If you also want photometry result in magnitude unit, you can enter a flux scaling factor in the :guilabel:`Flux scaling` field. The value must be in the same unit as display data unit. A magnitude is then calculated using -2.5 * log(flux / flux_scaling). This calculation only makes sense if your display data unit is already in linear flux unit. Setting this to 1 is equivalent to not applying any scaling. This field is only used if data has a valid unit. If this field is not applicable for you, leave it at 0. This field resets every time Data selection changes.
  4. Select the desired radial profile plot type using the :guilabel:`Plot Type` drop-down menu:
  • Curve of Growth: :attr:`~photutils.aperture.ApertureStats.sum` (sum of flux in the aperture) across radii from center out to the edge of the aperture. This is calculated in the same way as the final aperture sum in the output table, which is explained farther down on this page.
  • Radial Profile: Binned average as a function of radius from the center of the region.
  • Radial Profile (Raw): Raw image data points as a function of radius from the center of the region. Caution: having too many data points may cause performance issues with this feature. The exact limitations depend on your hardware.
  1. Toggle :guilabel:`Fit Gaussian` on to fit a ~astropy.modeling.functional_models.Gaussian1D model to the radial profile data. This is disabled for curve-of-growth.
  2. Once all inputs are populated correctly, click on the :guilabel:`CALCULATE` button to perform simple aperture photometry.

Note

Masking and weights by uncertainty are currently not supported. However, if NaN exists in data, it will be treated as 0.

When calculation is complete, a plot would show the radial profile of the background subtracted data and the photometry and model fitting (if requested) results are displayed under the :guilabel:`CALCULATE` button.

Imviz radial profile plot.

Radial profile.

Imviz radial profile plot (raw).

Radial profile (raw).

If you opted to fit a ~astropy.modeling.functional_models.Gaussian1D to the radial profile, the last fitted model parameters will be displayed under the radial profile plot. The model itself can be obtained by as follows. See :ref:`astropy:astropy-modeling` on how to manipulate the model:

my_gaussian1d = imviz.app.fitted_models['phot_radial_profile']

You can also retrieve the photometry results as ~astropy.table.QTable as follows, assuming imviz is the instance of your Imviz application:

results = imviz.get_aperture_photometry_results()

When multiple calculations are done in the same session (e.g., calculating aperture photometry for the same region across different images or for different regions on the same image), imviz.get_aperture_photometry_results() will return all the calculations in the same table, if possible. However, if the newest result is incompatible with the existing ones (e.g., two images have very different units), only the newest is kept in the table. When you are unsure, save the results after each calculation as different variables in your Python session.

The output table contains the results you see in the plugin and then some. The columns are as follow:

Once you have the results in a table, you can further manipulated them as documented in :ref:`astropy:astropy-table`.

Export Plot

This plugin allows exporting the plot in a given viewer to a PNG or SVG file.