<reponame>jeffreypaul15/sunkit-image<filename>examples/tracing_loops.py
"""
=====================
Coronal Loops Tracing
=====================

This example traces out the coronal loops in a FITS image
using `~sunkit_image.trace.occult2`. In this example we will use the settings
and the data from <NAME>'s tutorial on his IDL implementation of
the ``OCCULT2`` algorithm, which can be found
`here <http://www.lmsal.com/~aschwand/software/tracing/tracing_tutorial1.html>`__.
The aim of this example is to demonstrate that `~sunkit_image.trace.occult2` provides similar
results compared to the IDL version.
"""
# sphinx_gallery_thumbnail_number = 2

import matplotlib.pyplot as plt
import numpy as np

import sunpy.map
from astropy import units as u
from astropy.io import fits

import sunkit_image.trace as trace

###########################################################################
# We will be using `astropy.io.fits.open` to read the FITS file from the tutorial website
# and read in the header and data information.
hdu = fits.open("http://data.sunpy.org/sunkit-image/trace_1998-05-19T22:21:43.000_171_1024.fits")[0]

# We can now make this into a `sunpy.map.GenericMap`. There is currently not an instrument specific
# class for the TRACE instrument.
trace_map = sunpy.map.Map(hdu.data, hdu.header)

# We can now plot the map, of which we can see coronal loops.
trace_map.plot()

###########################################################################
# Now the loop tracing will begin. We will use the same set of parameters
# as in the IDL tutorial.
# The lowpass filter boxcar filter size ``nsm1`` is taken to be 3.
# The minimum radius of curvature at any point in the loop ``rmin`` is 30 pixels.
# The length of the smallest loop to be detected ``lmin`` is 25 pixels.
# The maximum number of structures to be examined ``nstruc`` is 1000.
# The number of extra points in the loop below noise level to terminate a loop tracing ``ngap`` is 0.
# The base flux and median flux ratio ``qthresh1`` is 0.0.
# The noise threshold in the image with repect to median flux ``qthresh2`` is 3.0 .
# For the meaning of these parameters please consult the OCCULT2 article.
loops = trace.occult2(
    trace_map.data, nsm1=3, rmin=30, lmin=25, nstruc=1000, ngap=0, qthresh1=0.0, qthresh2=3.0
)

###############################################################################
# `~sunkit_image.trace.occult2` returns a list, each element of which is a detected loop.
# Each detected loop is stored as a list of ``x`` positions in image pixels, and a list of ``y``
# positions in image pixels, of the pixels traced out by OCCULT2.
# Now plot all the detected loops on the original image, we convert the image pixels to
# to world coordinates to be plotted on the map.

fig = plt.figure()

ax = plt.subplot(projection=trace_map)

trace_map.plot()

# We can now plot each loop in the list of loops. We plot these in world coordinates, converting them
# through the `pixel_to_world` functionality which converts the pixel coordinates to coordinates (in arcsec)
# on the `trace_map`.
for loop in loops:

    loop = np.array(loop)  # convert to array as easier to index `x` and `y` coordinates

    coord_loops = trace_map.pixel_to_world(loop[:, 0] * u.pixel, loop[:, 1] * u.pixel)

    ax.plot_coord(coord_loops, color="b")

plt.show()

"""
=====================
Coronal Loops Tracing
=====================

This example traces out the coronal loops in a FITS image
using `~sunkit_image.trace.occult2`. In this example we will use the settings
and the data from <NAME>'s tutorial on his IDL implementation of
the ``OCCULT2`` algorithm, which can be found
`here <http://www.lmsal.com/~aschwand/software/tracing/tracing_tutorial1.html>`__.
The aim of this example is to demonstrate that `~sunkit_image.trace.occult2` provides similar
results compared to the IDL version.
"""
# sphinx_gallery_thumbnail_number = 2

import matplotlib.pyplot as plt
import numpy as np

import sunpy.map
from astropy import units as u
from astropy.io import fits

import sunkit_image.trace as trace

###########################################################################
# We will be using `astropy.io.fits.open` to read the FITS file from the tutorial website
# and read in the header and data information.
hdu = fits.open("http://data.sunpy.org/sunkit-image/trace_1998-05-19T22:21:43.000_171_1024.fits")[0]

# We can now make this into a `sunpy.map.GenericMap`. There is currently not an instrument specific
# class for the TRACE instrument.
trace_map = sunpy.map.Map(hdu.data, hdu.header)

# We can now plot the map, of which we can see coronal loops.
trace_map.plot()

###########################################################################
# Now the loop tracing will begin. We will use the same set of parameters
# as in the IDL tutorial.
# The lowpass filter boxcar filter size ``nsm1`` is taken to be 3.
# The minimum radius of curvature at any point in the loop ``rmin`` is 30 pixels.
# The length of the smallest loop to be detected ``lmin`` is 25 pixels.
# The maximum number of structures to be examined ``nstruc`` is 1000.
# The number of extra points in the loop below noise level to terminate a loop tracing ``ngap`` is 0.
# The base flux and median flux ratio ``qthresh1`` is 0.0.
# The noise threshold in the image with repect to median flux ``qthresh2`` is 3.0 .
# For the meaning of these parameters please consult the OCCULT2 article.
loops = trace.occult2(
    trace_map.data, nsm1=3, rmin=30, lmin=25, nstruc=1000, ngap=0, qthresh1=0.0, qthresh2=3.0
)

###############################################################################
# `~sunkit_image.trace.occult2` returns a list, each element of which is a detected loop.
# Each detected loop is stored as a list of ``x`` positions in image pixels, and a list of ``y``
# positions in image pixels, of the pixels traced out by OCCULT2.
# Now plot all the detected loops on the original image, we convert the image pixels to
# to world coordinates to be plotted on the map.

fig = plt.figure()

ax = plt.subplot(projection=trace_map)

trace_map.plot()

# We can now plot each loop in the list of loops. We plot these in world coordinates, converting them
# through the `pixel_to_world` functionality which converts the pixel coordinates to coordinates (in arcsec)
# on the `trace_map`.
for loop in loops:

    loop = np.array(loop)  # convert to array as easier to index `x` and `y` coordinates

    coord_loops = trace_map.pixel_to_world(loop[:, 0] * u.pixel, loop[:, 1] * u.pixel)

    ax.plot_coord(coord_loops, color="b")

plt.show()
===================== Coronal Loops Tracing =====================  This example traces out the coronal loops in a FITS image using `~sunkit_image.trace.occult2`. In this example we will use the settings and the data from <NAME>'s tutorial on his IDL implementation of the ``OCCULT2`` algorithm, which can be found `here <http://www.lmsal.com/~aschwand/software/tracing/tracing_tutorial1.html>`__. The aim of this example is to demonstrate that `~sunkit_image.trace.occult2` provides similar results compared to the IDL version. # sphinx_gallery_thumbnail_number = 2 ########################################################################### # We will be using `astropy.io.fits.open` to read the FITS file from the tutorial website # and read in the header and data information. # We can now make this into a `sunpy.map.GenericMap`. There is currently not an instrument specific # class for the TRACE instrument. # We can now plot the map, of which we can see coronal loops. ########################################################################### # Now the loop tracing will begin. We will use the same set of parameters # as in the IDL tutorial. # The lowpass filter boxcar filter size ``nsm1`` is taken to be 3. # The minimum radius of curvature at any point in the loop ``rmin`` is 30 pixels. # The length of the smallest loop to be detected ``lmin`` is 25 pixels. # The maximum number of structures to be examined ``nstruc`` is 1000. # The number of extra points in the loop below noise level to terminate a loop tracing ``ngap`` is 0. # The base flux and median flux ratio ``qthresh1`` is 0.0. # The noise threshold in the image with repect to median flux ``qthresh2`` is 3.0 . # For the meaning of these parameters please consult the OCCULT2 article. ############################################################################### # `~sunkit_image.trace.occult2` returns a list, each element of which is a detected loop. # Each detected loop is stored as a list of ``x`` positions in image pixels, and a list of ``y`` # positions in image pixels, of the pixels traced out by OCCULT2. # Now plot all the detected loops on the original image, we convert the image pixels to # to world coordinates to be plotted on the map. # We can now plot each loop in the list of loops. We plot these in world coordinates, converting them # through the `pixel_to_world` functionality which converts the pixel coordinates to coordinates (in arcsec) # on the `trace_map`. # convert to array as easier to index `x` and `y` coordinates