Area, Centroid and Extent values added to ChimeraPy #49

FionnStack · 2025-04-09T11:01:04Z

Updates to ChimeraPy

codecov · 2025-04-09T11:03:45Z

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❌ Patch coverage is 63.80952% with 38 lines in your changes missing coverage. Please review.
✅ Project coverage is 88.14%. Comparing base (78e4102) to head (b7f5b38).
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Files with missing lines	Patch %	Lines
chimerapy/chimera.py	58.53%	34 Missing ⚠️
chimerapy/chimera_original.py	69.23%	4 Missing ⚠️

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@@             Coverage Diff             @@
##             main      #49       +/-   ##
===========================================
- Coverage   98.55%   88.14%   -10.42%     
===========================================
  Files           2        3        +1     
  Lines         277      371       +94     
===========================================
+ Hits          273      327       +54     
- Misses          4       44       +40

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samaloney

Great work definitely on the right track!

samaloney · 2025-04-09T11:27:33Z

chimerapy/chimera.py

    final_mask = mask_171_211 * mask_211_193 * mask_171_193
    return final_mask
+
+def filter_by_area(mask, min_area=100):


So the area here is in pixels I assume it would be better and more flexible to specify as an area also good to use quantity decorator.

samaloney · 2025-04-09T11:30:42Z

chimerapy/chimera.py

+        A list of dictionaries containing properties of each coronal hole.
+    """
+    coronal_holes = []
+    labeled_mask = measure.label(ch_mask)


So you are calling measure.label twice one in filter_by_area and again here could you return the filtered regions and mask from filter_by_area and call it in this function or before?

samaloney · 2025-04-09T12:01:24Z

chimerapy/chimera.py

+        min_row, min_col, max_row, max_col = region.bbox
+        width_pixels = {
+            "E-W": max_col - min_col,
+            "N-S": max_row - min_row
+        }


What about transforming all the pixels of the contour to world coordinates first, then transform to heliographic?

I also think want to keep a few of the intermediate values you calculate below e.g min/max of lat and lon as well as the difference or extent

samaloney · 2025-04-09T12:02:23Z

chimerapy/chimera.py

+            bottom_left = map_obj.pixel_to_world(min_col * u.pix, min_row * u.pix).transform_to("heliographic_stonyhurst")
+            top_right = map_obj.pixel_to_world(max_col * u.pix, max_row * u.pix).transform_to("heliographic_stonyhurst")


So I have a pixel off the solar disk what would the corresponding lat and lon be in Heliogprohic?

samaloney · 2025-04-09T12:03:54Z

chimerapy/chimera.py

+
+        centroid = region.centroid
+        centroid_world = map_obj.pixel_to_world(centroid[1] * u.pix, centroid[0] * u.pix)
+        area_percentage = (region.area / solar_disk_area_pixels) * 100


This should be an area e.g m**2 can convert to other units later

samaloney · 2025-04-09T12:05:26Z

chimerapy/chimera.py

+    solar_radius_arcsec = map_obj.rsun_obs
+    pixel_scale_arcsec = map_obj.scale[0]
+    solar_radius_pixels = (solar_radius_arcsec / pixel_scale_arcsec).value
+    solar_disk_area_pixels = np.pi * (solar_radius_pixels ** 2)


Do this account for the difference between pixel near the middle of the disk compare to the edge - remember we're projecting as sphere, the sun, onto a plane?

samaloney

Nearly there just some small issues on the area calculations.

samaloney · 2025-04-22T10:55:45Z

chimerapy/chimera.py

+    im_map : `~sunpy.map.Map`
+        Processed magnetogram map.
+    """
+    im_map.data[~coordinate_is_on_solar_disk(all_coordinates_from_map(im_map))] = np.nan


So this is actually changing the data array is that what you want?

Not important now but coordinate_is_on_solar_disk(all_coordinates_from_map(im_map) is an expensive operation maybe could calculate once and store?

samaloney · 2025-04-22T10:56:24Z

chimerapy/chimera.py

+m171_corrected = m171.data * cos_correction_171
+m193_corrected = m193.data * cos_correction_193
+m211_corrected = m211.data * cos_correction_211


What data is being corrected here?

samaloney · 2025-04-22T12:14:56Z

chimerapy/chimera.py

+    cos_correction = np.ones_like(im_map.data)
+
+    radial_angle = np.arccos(np.cos(coordinates.Tx[on_disk]) * np.cos(coordinates.Ty[on_disk]))
+    cos_cor_ratio = (radial_angle / im_map.rsun_obs).value


What are units of radial_angle and im_map.rsun_obs, do the values of cos_cor_ratio make sense?

samaloney · 2025-04-22T12:17:54Z

chimerapy/chimera.py

+
+    cos_correction = np.ones_like(im_map.data)
+
+    radial_angle = np.arccos(np.cos(coordinates.Tx[on_disk]) * np.cos(coordinates.Ty[on_disk]))


What do you want the output at the end to be a list or a 2d array?

samaloney · 2025-04-22T12:19:02Z

chimerapy/chimera.py

+@u.quantity_input(min_area=u.m**2)
+def filter_by_area(mask, map_obj, solar_radius_pixels, min_area=1e10 * u.m**2):
+    solar_radius_meters = map_obj.rsun_meters
+    pixel_scale_arcsec = map_obj.scale[0].value


Careful with value if you really need a raw number use to_value, but is that what you really want here?

samaloney · 2025-04-22T12:33:27Z

chimerapy/chimera.py

+    pixel_scale_arcsec = map_obj.scale[0].value
+    pixel_scale_meters = (pixel_scale_arcsec * u.arcsec).to(u.rad).value * solar_radius_meters
+    pixel_area_meters2 = pixel_scale_meters**2
+    min_area_pixels = (min_area / pixel_area_meters2).decompose().value


Does this account for the cosine correction?

samaloney · 2025-04-22T13:18:22Z

chimerapy/chimera.py

+m193 = map_threshold(m193)
+m211 = map_threshold(m211)
+
+cos_correction_171 = calculate_cosine_correction(m171)


Are the values in the maps that go into the cosine correction very different, could be calculate only once?

samaloney · 2025-04-22T13:19:06Z

chimerapy/chimera.py

+        coords = region.coords
+        world_coords = map_obj.pixel_to_world(coords[:, 1] * u.pix, coords[:, 0] * u.pix)


Maybe?

Suggested change

coords = region.coords

world_coords = map_obj.pixel_to_world(coords[:, 1] * u.pix, coords[:, 0] * u.pix)

coords = region.coords * u.pix

world_coords = map_obj.pixel_to_world(coords[:, 1], coords[:, 0])

Refactor area calculation and add tests.

FionnStack · 2025-06-04T14:27:12Z

auto fix

samaloney · 2025-06-04T14:34:44Z

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pyproject.toml

Area,Centroid and Extent values added to ChimeraPy

881c361

samaloney requested changes Apr 9, 2025

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Added reccommended changes from Shane

98e0b76

samaloney requested changes Apr 22, 2025

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samaloney and others added 9 commits April 23, 2025 14:39

WIP changes from PR

2c2b58b

WIP: get_area_map

81b955d

Updated to pass test for expected area map

d0dc6f5

Updated contours and extents code + plots

a7237d5

Refactor area calculation and add tests.

5f39249

Add tests for old chimera code

d227cb1

Add wrapper function and more tests

0168b1e

Merge pull request #1 from samaloney/feat-area-calculation

eea7f9d

Refactor area calculation and add tests.

Fix tests and typo

d964250

[pre-commit.ci] auto fixes from pre-commit.com hooks

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samaloney reviewed Jun 4, 2025

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samaloney approved these changes Jun 4, 2025

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samaloney merged commit d6a5f8b into TCDSolar:main Jun 4, 2025
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		bottom_left = map_obj.pixel_to_world(min_col * u.pix, min_row * u.pix).transform_to("heliographic_stonyhurst")
		top_right = map_obj.pixel_to_world(max_col * u.pix, max_row * u.pix).transform_to("heliographic_stonyhurst")


		cos_correction = np.ones_like(im_map.data)

		radial_angle = np.arccos(np.cos(coordinates.Tx[on_disk]) * np.cos(coordinates.Ty[on_disk]))

		coords = region.coords
		world_coords = map_obj.pixel_to_world(coords[:, 1] * u.pix, coords[:, 0] * u.pix)

Area, Centroid and Extent values added to ChimeraPy #49

Area, Centroid and Extent values added to ChimeraPy #49

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FionnStack commented Apr 9, 2025

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FionnStack commented Jun 4, 2025

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