Chimera Functions #15

imogenagle · 2024-05-22T10:31:57Z

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CHIMERA_V2.py

samaloney

Hey this looks really good.

I think the main thing need to transfer these over to a new file in the package and also add doc strings and test

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samaloney

Really good progress, some improvements to be made. Please don't get discouraged this is a process and getting much nearer the end now.

Map - should load the data into sunpy map and then use maps as much as possible
Function should take in arguments and reurn some thing e.g. thres_171 = threshold(171map, threshold) ideally not changing the inputs (if they do need to indicate this in the name/docstring)

I think it would be worth while to write out the major blocks/functions in an issue and what each function should take and return etc

rescale()
remove_neg()
threshold()  # maybe call clip
countour()  # better name - intensity ratio ?
create_mask() # better name - logarithmic_threshold ?

chimerapy/chimera.py

samaloney · 2024-07-09T15:41:59Z

pyproject.toml

This fixes the ruff/isort issue

chimerapy/chimera.py

samaloney · 2024-07-09T16:26:34Z

chimerapy/tests/test_chimera.py

+from chimerapy.chimera import (
+    Bounds,
+    Xeb,
+    Xnb,
+    Xsb,
+    Xwb,
+    Yeb,
+    Ynb,
+    Ysb,
+    Ywb,
+    ang,
+    arcar,
+    arccent,
+    area,
+    cent,
+    centlat,
+    centlon,
+    chpts,
+    cont,
+    coords,
+    csys,
+    data,
+    datb,
+    datc,
+    datm,
+    dist,
+    eastl,
+    extent,
+    filter,
+    hg,
+    ins_prop,
+    mB,
+    mBneg,
+    mBpos,
+    npix,
+    pos,
+    remove_neg,
+    rescale_aia,
+    rescale_hmi,
+    set_contour,
+    sort,
+    threshold,
+    truarcar,
+    trummar,
+    trupixar,
+    westl,
+    width,
+    xpos,
+    ypos,
+)


Suggested change

from chimerapy.chimera import (

Bounds,

Xeb,

Xnb,

Xsb,

Xwb,

Yeb,

Ynb,

Ysb,

Ywb,

ang,

arcar,

arccent,

area,

cent,

centlat,

centlon,

chpts,

cont,

coords,

csys,

data,

datb,

datc,

datm,

dist,

eastl,

extent,

filter,

hg,

ins_prop,

mB,

mBneg,

mBpos,

npix,

pos,

remove_neg,

rescale_aia,

rescale_hmi,

set_contour,

sort,

threshold,

truarcar,

trummar,

trupixar,

westl,

width,

xpos,

ypos,

)

from chimerapy.chimera import *

samaloney · 2024-07-09T16:27:15Z

chimerapy/tests/test_chimera.py

-INPUT_FILES = {
-    "aia171": "https://solarmonitor.org/data/2016/09/22/fits/saia/saia_00171_fd_20160922_103010.fts.gz",
-    "aia193": "https://solarmonitor.org/data/2016/09/22/fits/saia/saia_00193_fd_20160922_103041.fts.gz",
-    "aia211": "https://solarmonitor.org/data/2016/09/22/fits/saia/saia_00211_fd_20160922_103046.fts.gz",
-    "hmi_mag": "https://solarmonitor.org/data/2016/09/22/fits/shmi/shmi_maglc_fd_20160922_094640.fts.gz",
-}


you need to use this as the files won't be in the local directory

samaloney · 2024-07-09T16:29:15Z

chimerapy/tests/test_chimera.py

+for i in range(len(cont)):
+    x = np.append(x, len(cont[i]))


ideally dont want to test in loop like this

samaloney

Lots of good stuff in here still some improvements to be made

Map - should load the data into sunpy map and then use maps as much as possible
Function should take in arguments and reurn some thing e.g. thres_171 = threshold(171map, threshold) ideally not changing the inputs
Write out high level functions and there input and outputs (maybe in an new issue)

rescale()
remove_neg()
threshold()  # maybe call clip
countour()  # maybe call intensity_ratio
create_mask() #  maybe call threshold

samaloney

Nice some good improvements left some more detailed comments.

Few general things map isn't a great name as there is python builtin function called map so amap or inmap or similar is usually better.

Want to make use of the units so avoid dropping if you can and when you do have to get a number use to_value(u.arcsec) because maybe the value as set in kiloarcsec or milliarcsec and better to not assume.

samaloney · 2024-07-15T09:36:47Z

chimerapy/chimera_copy.py

+# --noverify
+
+plt.style.use(astropy_mpl_style)
+
+"""Defining the paths for example files used to run program locally"""
+
+file_path = "./"


samaloney · 2024-07-15T09:37:20Z

chimerapy/chimera_copy.py

+        new_x_scale = map1.scale[0].to(u.arcsec / u.pixel).value
+        new_y_scale = map1.scale[1].to(u.arcsec / u.pixel).value
+        map1.meta["cdelt1"] = new_x_scale
+        map1.meta["cdelt2"] = new_y_scale
+        map1.meta["cunit1"] = "arcsec"
+        map1.meta["cunit2"] = "arcsec"


You shouldn't have to do this?

when you do reproject, it changes the plate scale and this was the only way I could figure out how to change the plate scale back

I think this is related to the above comment, as after reprojecting to the same WCS the maps should have the WCS information including the pixel size? Before you were reprojecting the 171 image to 193, 211 wcs rather than the other way around.

samaloney · 2024-07-15T09:38:11Z

chimerapy/chimera_copy.py

+        return map1
+
+
+im171 = rescale(im171, im171)


Don't need to reproject the 171 map to itself

samaloney · 2024-07-15T09:39:35Z

chimerapy/chimera_copy.py

+
+    """
+    with propagate_with_solar_surface():
+        map1 = proj_to.reproject_to(input_map.wcs)


So this is going the opposite way around I think you want but see above comment too.

Suggested change

map1 = proj_to.reproject_to(input_map.wcs)

map1 = input_map.reproject_to(proj_to.wcs)

samaloney · 2024-07-15T09:41:37Z

chimerapy/chimera_copy.py

+imhmi = Map(INPUT_FILES["hmi_mag"])
+
+
+def rescale(proj_to: sunpy.map.Map, input_map: sunpy.map.Map):


To make this more explicit

Suggested change

def rescale(proj_to: sunpy.map.Map, input_map: sunpy.map.Map):

def reproject_diff_rot(target_wcs: astropy.wcs.wcs.WCS, input_map: sunpy.map.Map):

samaloney · 2024-07-15T09:54:51Z

CHIMERA_V3.py

samaloney · 2024-07-15T09:59:24Z

chimerapy/chimera_copy.py

+"""defines the shape of the arrays as "s" and "rs" as the solar radius"""
+s = np.shape(im171.data)
+# do we want the solar radius in arcsec or pixels?
+rs = im171.rsun_obs
+rs_pixels = im171.rsun_obs / im171.scale[0]


anything like this needs to be in a function e.g.

def chimera(maps, ...): ... im171, im193, im211 = filter(im171, im193, im211) # defines the shape of the arrays as "s" and "rs" as the solar radius s = np.shape(im171.data) # do we want the solar radius in arcsec or pixels? rs = im171.rsun_obs rs_pixels = im171.rsun_obs / im171.scale[0] dattoarc, conver, convermul = pix_arc(im171)

samaloney · 2024-07-15T10:02:35Z

chimerapy/chimera_copy.py

+
+    """
+    dattoarc = map.scale[0].value
+    conver = ((s[0]) / 2) * dattoarc / map.meta["cdelt1"] - (s[1] / 2)


map.meta["cdelt1"] is map.scale[0] so this dattoarc / map.meta["cdelt1"] should be 1 then this entire line should be 0, but the units don't make sense either

m171nrt = Map('http://jsoc.stanford.edu/data/aia/synoptic/2016/09/22/H1000/AIA20160922_1030_0171.fits') s = m171nrt.dimensions (s.x/2) * m171nrt.scale[0] / m171nrt.meta["cdelt1"], (s.y / 2) (<Quantity 512. arcsec>, <Quantity 512. pix>)

samaloney · 2024-07-15T10:08:24Z

chimerapy/chimera_copy.py

+pix_size = (2000 * u.arcsec).value
+garr = Gaussian2D(
+    1,
+    im171.reference_pixel.x.value,
+    im171.reference_pixel.y.value,
+    pix_size / im171.scale[0].value,
+    pix_size / im171.scale[0].value,
+)(x, y)


Suggested change

pix_size = (2000 * u.arcsec).value

garr = Gaussian2D(

1,

im171.reference_pixel.x.value,

im171.reference_pixel.y.value,

pix_size / im171.scale[0].value,

pix_size / im171.scale[0].value,

)(x, y)

width = (2000 * u.arcsec)

garr = Gaussian2D(

1,

im171.reference_pixel.x.to_value(u.pix),

im171.reference_pixel.y.to_value(u.pix),

width / im171.scale[0],

width / im171.scale[1],

)(x, y)

samaloney · 2024-07-15T10:30:17Z

chimerapy/chimera_copy.py

+    centlat = hg.lat[int(ypos), int(xpos)]
+    centlon = hg.lon[int(ypos), int(xpos)]


Where do ypos, xpos come from there they should be function arguments if they are used?

They were inputs in my last version - not sure why I deleted them but I'm including them again now

Just looked a little more closely, they are the x and y positions of the center point which are used later in the for loop. I assumed we'd change that so they weren't calculated manually which I think is why I got rid of them.

… document attached at the end in a link that describes all of the important processes, functions, and variables

imogenagle added 2 commits May 22, 2024 12:20

initial commit

2462804

Working CHIMERA 11/4

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imogenagle added 2 commits June 14, 2024 09:52

work in progress

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adding new chimera file

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imogenagle force-pushed the functions branch from 4c6404e to 9aeafef Compare July 9, 2024 13:19

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The updated chimera code is in chimera_copy

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Here is the updated pull request with some changes I made and a large…

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… document attached at the end in a link that describes all of the important processes, functions, and variables

imogenagle force-pushed the functions branch from ec3dc56 to a67d8a8 Compare July 18, 2024 19:41

Updated pull request with a few changes

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imogenagle force-pushed the functions branch from 1f09863 to 1c12edb Compare July 25, 2024 16:59

new clip/scale function

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Chimera Functions #15

Chimera Functions #15

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	map1 = proj_to.reproject_to(input_map.wcs)
	map1 = input_map.reproject_to(proj_to.wcs)

		imhmi = Map(INPUT_FILES["hmi_mag"])


		def rescale(proj_to: sunpy.map.Map, input_map: sunpy.map.Map):

	def rescale(proj_to: sunpy.map.Map, input_map: sunpy.map.Map):
	def reproject_diff_rot(target_wcs: astropy.wcs.wcs.WCS, input_map: sunpy.map.Map):

		centlat = hg.lat[int(ypos), int(xpos)]
		centlon = hg.lon[int(ypos), int(xpos)]

Chimera Functions #15

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