Re-spiking level 1 images

This example demonstrates how to “re-spike” AIA level 1 images

import matplotlib.pyplot as plt

import astropy.units as u
import sunpy.map
from astropy.coordinates import SkyCoord

import aiapy.data.sample as sample_data
from aiapy.calibrate import fetch_spikes, respike

AIA level 1 images have been corrected for hot-pixels (commonly referred to as “spikes”) using an automated correction algorithm which detects them, removes them, and replaces the “holes” left in the image via interpolation. However, for certain research topics, this automated hot-pixel removal process may result in unwanted removal of bright points which may be physically meaningful. In this example, we will demonstrate how to revert this removal by putting back all the removed pixel values with the aiapy.calibrate.respike in function. This corresponds to the aia_respike.pro IDL procedure as described in the SDO Analysis Guide.

The header keywords LVL_NUM and NSPIKES describe the level number of the AIA data (e.g. level 1) and how many hot pixels were removed from the image (i.e. the “spikes”). The data containing the information of the pixel position and the intensities of the removed hot pixels are available from the Joint Science Operations Center (JSOC) as a separate segment of the aia.lev1_euv_12s and aia.lev1_uv_24s data series

First, let’s read a level 1 193 Å AIA image from the aiapy sample data into a Map object.

The spike data are stored as separate data segments in JSOC as a \(3\times N\) arrays, where \(N\) is the number of spikes removed and the three dimensions correspond to the the 1-D pixel index of the spike, intensity value of the removed spikes, and the intensity value used in replacing the removed spike (via interpolation). The spike pixel positions are given with respect to the level 1 full-disk image.

We can use the aiapy.calibrate.fetch_spikes function to query the JSOC for the spike positions and intensity values and convert the positions of the spikes to the 2D pixel full-disk pixel coordinate system given a Map representing a level 1 AIA image.

positions, values = fetch_spikes(m)

Now we are ready to respike the level 1 AIA image. The aiapy.calibrate.respike function performs the respike operation on the given input image and returns a Map with the respiked image. This operation also alters the metadata by updating the LVL_NUM, NSPIKES, and COMMENTS keywords.

Note that explicitly specifying the spike positions and values is optional. If they are not given, they are automatically queried from the JSOC.

m_respiked = respike(m, spikes=(positions, values))

Now let’s create a cutouts of the original level 1 and “re-spiked” (i.e. level 0.5) images for a region with hot pixels.

Note that we can also retrieve the positions of the spikes as SkyCoord objects in the projected coordinate system of the image using the as_coords=True keyword argument. This gives us only those spikes in the field of view of the cutout.

spike_coords, _ = fetch_spikes(m_cutout, as_coords=True)

Finally, let’s plot the two cutouts for comparison and plot the positions of the spikes in both images, denoted by white circles.

fig = plt.figure()
ax = fig.add_subplot(121, projection=m_cutout)
ax.plot_coord(spike_coords, "o", color="white", fillstyle="none", markersize=15)
m_cutout.plot(axes=ax, title='Level 1 "de-spiked" data')
lon, lat = ax.coords
lon.set_axislabel("HPC Longitude")
lat.set_axislabel("HPC Latitude")
ax = fig.add_subplot(122, projection=m_respiked_cutout)
ax.plot_coord(spike_coords, "o", color="white", fillstyle="none", markersize=15)
m_respiked_cutout.plot(axes=ax, annotate=False)
ax.set_title('Level 0.5 "re-spiked" data')
lon, lat = ax.coords
lon.set_axislabel("HPC Longitude")
lat.set_axislabel(" ")
lat.set_ticklabel_visible(False)
plt.show()
Level 1

Lastly, let’s check the metadata in both the level 1 and resulting 0.5 images to double check that the appropriate keywords have been updated.

for k in ["lvl_num", "nspikes", "comments"]:
    print(f"Level 1: {k}: {m_cutout.meta.get(k)}")
    print(f"Level 0.5: {k}: {m_respiked_cutout.meta.get(k)}")
Level 1: lvl_num: 1.0
Level 0.5: lvl_num: 0.5
Level 1: nspikes: 167
Level 0.5: nspikes: 0
Level 1: comments: None
Level 0.5: comments: Respike applied; 167 hot pixels reinserted.

Total running time of the script: ( 0 minutes 2.096 seconds)

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