Chimerapy function + test #45

FionnStack · 2025-02-11T14:09:39Z

Changed the Chimerapy function to include sphinx NumPy style Python docstrings and created a file to test the function

samaloney

Nearly there just a few small things

samaloney · 2025-02-11T15:28:36Z

chimerapy/chimera_func_test.py

+# Assuming process_solar_images and plot_mask have been imported from your module
+from chimerapy.chimera_func import process_solar_images
+
+class TestSolarImageProcessing(unittest.TestCase):


Sorry I should have said we use pytest and generally don't use class based tests.

samaloney · 2025-02-11T15:29:16Z

chimerapy/chimera_func_test.py

+        self.assertEqual(final_mask.shape, self.m171.data.shape)
+
+        unique_values = np.unique(final_mask)
+        self.assertTrue(np.all(np.isin(unique_values, [0, 1])))


We really want to test the mask matches the expected mask given the data

samaloney · 2025-02-11T15:29:28Z

chimerapy/chimera_func_test.py

+if __name__ == "__main__":
+    unittest.main()


Remove

Suggested change

if __name__ == "__main__":

unittest.main()

samaloney · 2025-02-11T15:30:11Z

examples/paper-figures.py

Were these changes on purpose?

samaloney · 2025-02-11T15:31:53Z

chimerapy/chimera_func.py

Maybe rename this to just chimera.py

samaloney · 2025-02-11T15:32:39Z

chimerapy/chimera_func.py

+from sunpy.map import all_coordinates_from_map, coordinate_is_on_solar_disk
+
+
+def process_solar_images(m171, m193, m211):


Suggested change

def process_solar_images(m171, m193, m211):

def generate_candiate_mask(m171, m193, m211):

FionnStack · 2025-02-14T12:38:20Z

`C:\Users\aoife\CHIMERApy\chimerapy\tests>pytest test_chimera.py
================================================= test session starts =================================================
platform win32 -- Python 3.13.1, pytest-8.3.4, pluggy-1.5.0
rootdir: C:\Users\aoife\CHIMERApy
configfile: pyproject.toml
plugins: asdf-4.0.0, doctestplus-1.4.0
collected 1 item

test_chimera.py F [100%]

====================================================== FAILURES =======================================================
____________________________________________ test_generate_candidate_mask _____________________________________________

def test_generate_candidate_mask():

    result_mask = generate_candidate_mask(aia171, aia193, aia211)

    expected_shape = aia171.data.shape
    assert result_mask.shape == expected_shape, "Mask shape does not match expected shape."

    expected_mask = mask_map

  np.testing.assert_allclose(result_mask, expected_mask, atol=0.1)

test_chimera.py:22:

......\AppData\Local\Programs\Python\Python313\Lib\site-packages\numpy\testing_private\utils.py:1674: in compare
return np._core.numeric.isclose(x, y, rtol=rtol, atol=atol,
......\AppData\Local\Programs\Python\Python313\Lib\site-packages\numpy_core\numeric.py:2447: in isclose
result = (less_equal(abs(x-y), atol + rtol * abs(y))
......\AppData\Local\Programs\Python\Python313\Lib\site-packages\sunpy\map\mapbase.py:561: in rsub
return self.neg().add(value)
......\AppData\Local\Programs\Python\Python313\Lib\site-packages\sunpy\util\decorators.py:216: in inner
return func(instance, value)
......\AppData\Local\Programs\Python\Python313\Lib\site-packages\sunpy\map\mapbase.py:551: in add
new_data = self.quantity + value

self = <Quantity [[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0... [0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]>
function = <ufunc 'add'>, method = 'call'
inputs = (<Quantity [[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., ... 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]]>, False)
kwargs = {}, converters = [None, None], unit = Unit(dimensionless), out = None
arrays = [array([[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.],
[0., 0., 0., ..., 0., 0., 0.]], shape=(1024, 1024)), False]
input_ = False, converter = None

def __array_ufunc__(self, function, method, *inputs, **kwargs):
    """Wrap numpy ufuncs, taking care of units.

    Parameters
    ----------
    function : callable
        ufunc to wrap.
    method : str
        Ufunc method: ``__call__``, ``at``, ``reduce``, etc.
    inputs : tuple
        Input arrays.
    kwargs : keyword arguments
        As passed on, with ``out`` containing possible quantity output.

    Returns
    -------
    result : `~astropy.units.Quantity` or `NotImplemented`
        Results of the ufunc, with the unit set properly.
    """
    # Determine required conversion functions -- to bring the unit of the
    # input to that expected (e.g., radian for np.sin), or to get
    # consistent units between two inputs (e.g., in np.add) --
    # and the unit of the result (or tuple of units for nout > 1).
    try:
        converters, unit = converters_and_unit(function, method, *inputs)

        out = kwargs.get("out")
        # Avoid loop back by turning any Quantity output into array views.
        if out is not None:
            # If pre-allocated output is used, check it is suitable.
            # This also returns array view, to ensure we don't loop back.
            if function.nout == 1:
                out = out[0]
            out_array = check_output(out, unit, inputs, function=function)
            # Ensure output argument remains a tuple.
            kwargs["out"] = (out_array,) if function.nout == 1 else out_array

        if method == "reduce" and "initial" in kwargs and unit is not None:
            # Special-case for initial argument for reductions like
            # np.add.reduce.  This should be converted to the output unit as
            # well, which is typically the same as the input unit (but can
            # in principle be different: unitless for np.equal, radian
            # for np.arctan2, though those are not necessarily useful!)
            kwargs["initial"] = self._to_own_unit(
                kwargs["initial"], check_precision=False, unit=unit
            )

        # Same for inputs, but here also convert if necessary.
        arrays = []
        for input_, converter in zip(inputs, converters):
            input_ = getattr(input_, "value", input_)
            arrays.append(converter(input_) if converter else input_)

        # Call our superclass's __array_ufunc__

      result = super().__array_ufunc__(function, method, *arrays, **kwargs)

E numpy._core._exceptions._ArrayMemoryError: Unable to allocate 8.00 MiB for an array with shape (1024, 1024) and data type float64

......\AppData\Local\Programs\Python\Python313\Lib\site-packages\astropy\units\quantity.py:658: MemoryError
================================================== warnings summary ===================================================
....\examples\paper_figures.py:227
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:227: RuntimeWarning: divide by zero encountered in power
fit193v211 = 2600 * xx**-threshold_193v211

....\examples\paper_figures.py:349
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:349: RuntimeWarning: divide by zero encountered in log10
d171_clipped = np.clip(np.log10(m171.data), d171_min, d171_max)

....\examples\paper_figures.py:349
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:349: RuntimeWarning: invalid value encountered in log10
d171_clipped = np.clip(np.log10(m171.data), d171_min, d171_max)

....\examples\paper_figures.py:352
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:352: RuntimeWarning: divide by zero encountered in log10
d193_clipped = np.clip(np.log10(m193.data), d193_min, d193_max)

....\examples\paper_figures.py:352
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:352: RuntimeWarning: invalid value encountered in log10
d193_clipped = np.clip(np.log10(m193.data), d193_min, d193_max)

....\examples\paper_figures.py:355
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:355: RuntimeWarning: divide by zero encountered in log10
d211_clipped = np.clip(np.log10(m211.data), d211_min, d211_max)

....\examples\paper_figures.py:355
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:355: RuntimeWarning: invalid value encountered in log10
d211_clipped = np.clip(np.log10(m211.data), d211_min, d211_max)

......\AppData\Local\Programs\Python\Python313\Lib\site-packages\astropy\visualization\lupton_rgb.py:305
C:\Users\aoife\AppData\Local\Programs\Python\Python313\Lib\site-packages\astropy\visualization\lupton_rgb.py:305: RuntimeWarning: invalid value encountered in divide
fInorm = np.where(Int <= 0, 0, np.true_divide(fI, Int))

......\AppData\Local\Programs\Python\Python313\Lib\site-packages\astropy\visualization\basic_rgb.py:153
C:\Users\aoife\AppData\Local\Programs\Python\Python313\Lib\site-packages\astropy\visualization\basic_rgb.py:153: RuntimeWarning: invalid value encountered in cast
return image_rgb.astype(output_dtype)

....\examples\paper_figures.py:362
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:362: RuntimeWarning: divide by zero encountered in divide
mask_171_211 = (d171_clipped_scaled / d211_clipped_scaled) >= (

....\examples\paper_figures.py:362
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:362: RuntimeWarning: invalid value encountered in divide
mask_171_211 = (d171_clipped_scaled / d211_clipped_scaled) >= (

....\examples\paper_figures.py:370
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:370: RuntimeWarning: divide by zero encountered in divide
mask_171_193 = (d171_clipped_scaled / d193_clipped_scaled) >= (

....\examples\paper_figures.py:370
C:\Users\aoife\CHIMERApy\examples\paper_figures.py:370: RuntimeWarning: invalid value encountered in divide
mask_171_193 = (d171_clipped_scaled / d193_clipped_scaled) >= (

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:40: RuntimeWarning: divide by zero encountered in log10
d171_clipped = np.clip(np.log10(m171.data), d171_min, d171_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:40: RuntimeWarning: invalid value encountered in log10
d171_clipped = np.clip(np.log10(m171.data), d171_min, d171_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:43: RuntimeWarning: divide by zero encountered in log10
d193_clipped = np.clip(np.log10(m193.data), d193_min, d193_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:43: RuntimeWarning: invalid value encountered in log10
d193_clipped = np.clip(np.log10(m193.data), d193_min, d193_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:46: RuntimeWarning: divide by zero encountered in log10
d211_clipped = np.clip(np.log10(m211.data), d211_min, d211_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:46: RuntimeWarning: invalid value encountered in log10
d211_clipped = np.clip(np.log10(m211.data), d211_min, d211_max)

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:49: RuntimeWarning: divide by zero encountered in divide
mask_171_211 = (d171_clipped_scaled / d211_clipped_scaled) >= (

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:49: RuntimeWarning: invalid value encountered in divide
mask_171_211 = (d171_clipped_scaled / d211_clipped_scaled) >= (

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:57: RuntimeWarning: divide by zero encountered in divide
mask_171_193 = (d171_clipped_scaled / d193_clipped_scaled) >= (

chimerapy/tests/test_chimera.py::test_generate_candidate_mask
C:\Users\aoife\CHIMERApy\chimerapy\chimera.py:57: RuntimeWarning: invalid value encountered in divide
mask_171_193 = (d171_clipped_scaled / d193_clipped_scaled) >= (

chimerapy/tests/test_chimera.py: 6294 warnings
C:\Users\aoife\AppData\Local\Programs\Python\Python313\Lib\site-packages\sunpy\map\mapbase.py:767: SunpyMetadataWarning: Could not parse unit string "1 / s" as a valid FITS unit.
See https://docs.sunpy.org/en/stable/how_to/fix_map_metadata.html for how to fix metadata before loading it with sunpy.map.Map.
See https://fits.gsfc.nasa.gov/fits_standard.html for the FITS unit standards.
warn_metadata(f'Could not parse unit string "{unit_str}" as a valid FITS unit.\n'

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=============================================== short test summary info ===============================================
FAILED test_chimera.py::test_generate_candidate_mask - numpy._core._exceptions._ArrayMemoryError: Unable to allocate 8.00 MiB for an array with shape (1024, 1024) and dat...
==================================== 1 failed, 6317 warnings in 189.58s (0:03:09) =====================================`

FionnStack added 3 commits January 31, 2025 14:16

Removing everything but the final mask and turning it into a function

ce48988

Updated Chimera function

fe28316

Updated Chimera py function and added test

f2e243e

FionnStack requested a review from samaloney February 11, 2025 14:17

samaloney requested changes Feb 11, 2025

View reviewed changes

FionnStack added 2 commits February 11, 2025 16:10

Fix example

f990de5

Added test and renamed new chimera file

9a5735e

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Chimerapy function + test #45

Chimerapy function + test #45

FionnStack commented Feb 11, 2025

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FionnStack commented Feb 14, 2025

		from sunpy.map import all_coordinates_from_map, coordinate_is_on_solar_disk


		def process_solar_images(m171, m193, m211):

	def process_solar_images(m171, m193, m211):
	def generate_candiate_mask(m171, m193, m211):

Chimerapy function + test #45

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Chimerapy function + test #45

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