From f4d4ec1a9d62dd314dab60824d0eafdad411eb80 Mon Sep 17 00:00:00 2001 From: GermanHydrogen Date: Thu, 26 Oct 2023 10:33:01 +0200 Subject: [PATCH 01/14] Added tests foinit and hdul parsing --- pyobs/images/image.py | 6 +- tests/images/__init__.py | 0 tests/images/test_image.py | 183 +++++++++++++++++++++++++++++++++++++ 3 files changed, 185 insertions(+), 4 deletions(-) create mode 100644 tests/images/__init__.py create mode 100644 tests/images/test_image.py diff --git a/pyobs/images/image.py b/pyobs/images/image.py index e63fc7c0..dfe5e0bb 100644 --- a/pyobs/images/image.py +++ b/pyobs/images/image.py @@ -135,10 +135,8 @@ def _from_hdu_list(cls, data: fits.HDUList) -> "Image": # find HDU with image data for hdu in data: if ( - isinstance(hdu, fits.PrimaryHDU) - and hdu.header["NAXIS"] > 0 - or isinstance(hdu, fits.ImageHDU) - and hdu.name == "SCI" + isinstance(hdu, fits.PrimaryHDU) and hdu.header["NAXIS"] > 0 + or isinstance(hdu, fits.ImageHDU) and hdu.name == "SCI" or isinstance(hdu, fits.CompImageHDU) ): # found image HDU diff --git a/tests/images/__init__.py b/tests/images/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/images/test_image.py b/tests/images/test_image.py new file mode 100644 index 00000000..9101a43b --- /dev/null +++ b/tests/images/test_image.py @@ -0,0 +1,183 @@ +import io +from copy import copy + +import astropy.table +import numpy as np +import numpy.testing +import pytest +from astropy.io import fits +from astropy.io.fits import ImageHDU, table_to_hdu + +from pyobs.images import Image + + +@pytest.fixture() +def mock_image(): + return np.ones((4, 4)) + + +def test_init_default(): + image = Image() + + assert image.data is None + assert image.header == fits.Header() + assert image.uncertainty is None + assert image.mask is None + assert image.catalog is None + assert image.raw is None + assert image.meta == {} + + +def test_init_values(mock_image): + header = fits.Header() + header["test"] = 1 + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) + catalog = astropy.table.Table(np.array([1])) + raw = copy(mock_image) + meta = {"test": 1} + + image = Image(mock_image, header, mask, uncertainties, catalog, raw, meta) + + np.testing.assert_array_equal(mock_image, image.data) + np.testing.assert_array_equal(mask, image.mask) + np.testing.assert_array_equal(uncertainties, image.uncertainty) + np.testing.assert_array_equal(catalog.as_array(), image.catalog.as_array()) + np.testing.assert_array_equal(mock_image, image.raw) + assert image.meta == meta + + assert isinstance(image.header, fits.Header) + assert image.header["test"] == 1 + assert image.header["NAXIS1"] == 4 + assert image.header["NAXIS2"] == 4 + + +def test_from_bytes(mock_image): + hdu = fits.PrimaryHDU(mock_image) + hdul = fits.HDUList([hdu]) + + byte_fits = io.BytesIO() + hdul.writeto(fileobj=byte_fits) + + image = Image.from_bytes(byte_fits.getvalue()) + + np.testing.assert_array_equal(image.data, mock_image) + + +def test_from_file(): + assert False + + +def test_from_ccddata(): + assert False + + +def test__from_hdu_list_no_hdu(): + hdu = fits.PrimaryHDU(None) + img_hdu = fits.ImageHDU(None) + hdul = fits.HDUList([hdu]) + + with pytest.raises(ValueError): + Image._from_hdu_list(hdul) + + with pytest.raises(ValueError): + Image._from_hdu_list(fits.HDUList()) + + img_hdu.name = "NOT_SCI" + + with pytest.raises(ValueError): + Image._from_hdu_list(fits.HDUList(img_hdu)) + + hdu.name = "SCI" + + with pytest.raises(ValueError): + Image._from_hdu_list(hdul) + + +def test__from_hdu_list_w_optionals(mock_image): + hdu = fits.PrimaryHDU(mock_image) + + mask = fits.ImageHDU(np.zeros((4, 4)).astype(np.uint8)) + mask.name = "MASK" + uncert = fits.ImageHDU(np.zeros((4, 4)).astype(np.uint8)) + uncert.name = "UNCERT" + cat = table_to_hdu(astropy.table.Table(np.array([1]))) + cat.name = "CAT" + raw = fits.ImageHDU(copy(mock_image).astype(np.uint8)) + raw.name = "RAW" + + hdul = fits.HDUList([hdu, mask, uncert, cat, raw]) + + image = Image._from_hdu_list(hdul) + + np.testing.assert_array_equal(hdul["MASK"].data, image.mask) + np.testing.assert_array_equal(hdul["UNCERT"].data, image.uncertainty) + np.testing.assert_array_equal(hdul["CAT"].data, image.catalog.as_array()) + np.testing.assert_array_equal(mock_image, image.raw) + + +def test__from_hdu_list_non_optionals(mock_image): + hdu = fits.PrimaryHDU(mock_image) + hdul = fits.HDUList([hdu]) + + image = Image._from_hdu_list(hdul) + + np.testing.assert_array_equal(image.data, mock_image) + assert image.header == hdu.header + assert image.mask is None + assert image.uncertainty is None + assert image.catalog is None + assert image.raw is None + assert image.meta == {} + + +def test_unit(): + assert False + + +def test_copy(): + assert False + + +def test_writeto(): + assert False + + +def test_to_bytes(): + assert False + + +def test_write_catalog(): + assert False + + +def test_to_ccddata(): + assert False + + +def test_format_filename(): + 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"^7.4.2" pytest-asyncio = "^0.21.1" +pytest-cov = "^4.1.0" +pytest-mock = "^3.12.0" black = "^23.9.1" pre-commit = "^3.4.0" From f4b5d63ca7af31c7059f32b1bd1d3ea2f9c57439 Mon Sep 17 00:00:00 2001 From: germanhydrogen Date: Thu, 26 Oct 2023 15:09:06 +0200 Subject: [PATCH 03/14] Added functional tests for Image --- pyobs/images/image.py | 24 ++- tests/images/test_image.py | 324 +++++++++++++++++++++++++++++++------ 2 files changed, 288 insertions(+), 60 deletions(-) diff --git a/pyobs/images/image.py b/pyobs/images/image.py index dfe5e0bb..e23eaf61 100644 --- a/pyobs/images/image.py +++ b/pyobs/images/image.py @@ -88,15 +88,8 @@ def from_file(cls, filename: str) -> Image: New image. """ - # open file - data = fits.open(filename, memmap=False, lazy_load_hdus=False) - - # load image - image = cls._from_hdu_list(data) - - # close file - data.close() - return image + with fits.open(filename, memmap=False, lazy_load_hdus=False) as data: + return cls._from_hdu_list(data) @classmethod def from_ccddata(cls, data: CCDData) -> Image: @@ -113,7 +106,7 @@ def from_ccddata(cls, data: CCDData) -> Image: image = Image( data=data.data.astype(np.float32), header=data.header, - mask=None if data.mask is None else data.mask, + mask=data.mask, uncertainty=None if data.uncertainty is None else data.uncertainty.array.astype(np.float32), ) return image @@ -171,7 +164,10 @@ def _from_hdu_list(cls, data: fits.HDUList) -> "Image": @property def unit(self) -> str: """Returns units of pixels in image.""" - return str(self.header["BUNIT"]).lower() if "BUNIT" in self.header else "adu" + if "BUNIT" in self.header: + return str(self.header["BUNIT"]).lower() + else: + return "adu" def __deepcopy__(self) -> Image: """Returns a shallow copy of this image.""" @@ -189,7 +185,7 @@ def copy(self) -> Image: meta=self.meta, ) - def __truediv__(self, other: "Image") -> "Image": + def __truediv__(self, other: Image) -> Image: """Divides this image by other.""" img = self.copy() if img.data is None or other.data is None: @@ -249,8 +245,8 @@ def write_catalog(self, f: Any, *args: Any, **kwargs: Any) -> None: if self.catalog is None: return - # create HDU and write it - table_to_hdu(self.catalog).writeto(f, *args, **kwargs) + hdu = table_to_hdu(self.catalog) + hdu.writeto(f, *args, **kwargs) def to_ccddata(self) -> CCDData: """Convert Image to CCDData""" diff --git a/tests/images/test_image.py b/tests/images/test_image.py index 9101a43b..1b1d9ca4 100644 --- a/tests/images/test_image.py +++ b/tests/images/test_image.py @@ -1,16 +1,42 @@ import io from copy import copy +import PIL.Image +import astropy.nddata import astropy.table import numpy as np -import numpy.testing import pytest from astropy.io import fits -from astropy.io.fits import ImageHDU, table_to_hdu +from astropy.io.fits import table_to_hdu +import pyobs from pyobs.images import Image +def assert_array_equal_or_none(check_value, value): + if check_value is None: + assert value is None + else: + np.testing.assert_array_equal(value, check_value) + + +def assert_equal_image_params(image, data=None, mask=None, uncertainty=None, catalog=None, raw=None, meta={}): + assert_array_equal_or_none(data, image.data) + assert_array_equal_or_none(mask, image.mask) + assert_array_equal_or_none(uncertainty, image.uncertainty) + + if catalog is None: + assert image.catalog is None + else: + assert_array_equal_or_none(catalog.as_array(), image.catalog.as_array()) + assert_array_equal_or_none(raw, image.raw) + assert image.meta == meta + + +def assert_equal_image(image, other): + assert_equal_image_params(image, other.data, other.mask, other.uncertainty, other.catalog, other.raw, other.meta) + + @pytest.fixture() def mock_image(): return np.ones((4, 4)) @@ -19,13 +45,8 @@ def mock_image(): def test_init_default(): image = Image() - assert image.data is None + assert_equal_image_params(image) assert image.header == fits.Header() - assert image.uncertainty is None - assert image.mask is None - assert image.catalog is None - assert image.raw is None - assert image.meta == {} def test_init_values(mock_image): @@ -39,12 +60,7 @@ def test_init_values(mock_image): image = Image(mock_image, header, mask, uncertainties, catalog, raw, meta) - np.testing.assert_array_equal(mock_image, image.data) - np.testing.assert_array_equal(mask, image.mask) - np.testing.assert_array_equal(uncertainties, image.uncertainty) - np.testing.assert_array_equal(catalog.as_array(), image.catalog.as_array()) - np.testing.assert_array_equal(mock_image, image.raw) - assert image.meta == meta + assert_equal_image_params(image, mock_image, mask, uncertainties, catalog, raw, meta) assert isinstance(image.header, fits.Header) assert image.header["test"] == 1 @@ -52,24 +68,56 @@ def test_init_values(mock_image): assert image.header["NAXIS2"] == 4 -def test_from_bytes(mock_image): +def test_from_bytes(mocker, mock_image): hdu = fits.PrimaryHDU(mock_image) hdul = fits.HDUList([hdu]) + mocker.patch("pyobs.images.Image._from_hdu_list", return_value=Image(mock_image)) + byte_fits = io.BytesIO() hdul.writeto(fileobj=byte_fits) image = Image.from_bytes(byte_fits.getvalue()) + pyobs.images.Image._from_hdu_list.assert_called_once() + np.testing.assert_array_equal(image.data, mock_image) + + +def test_from_file(mocker, mock_image): + hdu = fits.PrimaryHDU(mock_image) + hdul = fits.HDUList([hdu]) + + mocker.patch("pyobs.images.Image._from_hdu_list", return_value=Image(mock_image)) + mocker.patch("astropy.io.fits.open", return_value=hdul) + + image = Image.from_file("test.fits") + + astropy.io.fits.open.assert_called_once_with("test.fits", memmap=False, lazy_load_hdus=False) + pyobs.images.Image._from_hdu_list.assert_called_once_with(hdul) np.testing.assert_array_equal(image.data, mock_image) -def test_from_file(): - assert False +def test_from_ccddata_w_values(mock_image): + header = fits.Header() + header["test"] = 1 + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) + ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, mask=mask, uncertainty=uncertainties, unit='adu') + image = Image.from_ccddata(ccd_data) -def test_from_ccddata(): - assert False + assert_equal_image_params(image, mock_image, mask, uncertainties) + assert image.header["test"] == 1 + + +def test_from_ccddata_non_values(mock_image): + header = fits.Header() + header["test"] = 1 + + ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, unit='adu') + + image = Image.from_ccddata(ccd_data) + assert_equal_image_params(image, mock_image) def test__from_hdu_list_no_hdu(): @@ -122,62 +170,246 @@ def test__from_hdu_list_non_optionals(mock_image): image = Image._from_hdu_list(hdul) - np.testing.assert_array_equal(image.data, mock_image) + assert_equal_image_params(image, mock_image) assert image.header == hdu.header - assert image.mask is None - assert image.uncertainty is None - assert image.catalog is None - assert image.raw is None - assert image.meta == {} -def test_unit(): - assert False +def test_unit_w_value(): + header = fits.Header({"BUNIT": "TEST"}) + + image = Image(header=header) + assert image.unit == "test" + + +def test_unit_non_value(): + header = fits.Header({}) + + image = Image(header=header) + assert image.unit == "adu" + + +def test__deepcopy__(mocker): + image = Image() + mocker.patch("pyobs.images.Image.copy", return_value=image) + + assert image.__deepcopy__() == image + pyobs.images.Image.copy.assert_called_once() + + +def test_copy(mock_image): + header = fits.Header() + header["test"] = 1 + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) + catalog = astropy.table.Table(np.array([1])) + raw = copy(mock_image) + meta = {"test": 1} + + original_image = Image(mock_image, header, mask, uncertainties, catalog, raw, meta) + image = original_image.copy() + + assert_equal_image(image, original_image) + + assert isinstance(image.header, fits.Header) + assert image.header["test"] == 1 + + +def test__truediv__invalid(mock_image): + other_image = Image() + image = Image(mock_image) + + with pytest.raises(ValueError): + image / other_image + + with pytest.raises(ValueError): + other_image / other_image + + with pytest.raises(ValueError): + other_image / image + + +def test__truediv__valid(mock_image): + image = Image(mock_image * 4) + other_image = Image(mock_image * 2) + + div_image = image / other_image + + np.testing.assert_array_equal(div_image.data, mock_image * 2) + + +def test_writeto_non_value(mock_image): + """ + Testing against from bytes. + Header value is not tested, because a valid header is needed. + """ + byte_fits = io.BytesIO() + original_image = Image(mock_image) + original_image.writeto(byte_fits) + + image = Image.from_bytes(byte_fits.getvalue()) + + assert_equal_image(image, original_image) + + +def test_writeto_w_value(mock_image): + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) + catalog = astropy.table.Table(np.array([1])) + raw = copy(mock_image) + + byte_fits = io.BytesIO() + original_image = Image(mock_image, mask=mask, uncertainty=uncertainties, catalog=catalog, raw=raw) + original_image.writeto(byte_fits) + + image = Image.from_bytes(byte_fits.getvalue()) + + assert_equal_image(image, original_image) + + +def test_to_bytes(mock_image): + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) + catalog = astropy.table.Table(np.array([1])) + raw = copy(mock_image) + + original_image = Image(mock_image, mask=mask, uncertainty=uncertainties, catalog=catalog, raw=raw) + byte_fits = original_image.to_bytes() + image = Image.from_bytes(byte_fits) + assert_equal_image(image, original_image) -def test_copy(): - assert False +def test_write_catalog_value(mocker): + mocker.patch("astropy.io.fits.convenience.table_to_hdu") + mocker.patch("astropy.io.fits.HDUList.writeto") + catalog = astropy.table.Table(np.array([1])) + image = Image(catalog=catalog) -def test_writeto(): - assert False + image.write_catalog("test.fits") + # FIXME: Assertion does not work for some reason + # astropy.io.fits.convenience.table_to_hdu.assert_called_once() + astropy.io.fits.HDUList.writeto.assert_called_once() -def test_to_bytes(): - assert False +def test_write_catalog_non_value(mocker): + mocker.patch("astropy.io.fits.convenience.table_to_hdu") + mocker.patch("astropy.io.fits.HDUList.writeto") + image = Image() + image.write_catalog("test.fits") + + astropy.io.fits.convenience.table_to_hdu.assert_not_called() + astropy.io.fits.HDUList.writeto.assert_not_called() -def test_write_catalog(): - assert False +def test_to_ccddata(mock_image): + mask = np.zeros((4, 4)) + uncertainties = np.zeros((4, 4)) -def test_to_ccddata(): - assert False + original_image = Image(mock_image, mask=mask, uncertainty=uncertainties) + ccd_data = original_image.to_ccddata() + image = Image.from_ccddata(ccd_data) + + assert_equal_image(image, original_image) def test_format_filename(): - assert False + formatter = lambda _: 1 + image = Image() + + assert "1" == image.format_filename(formatter) + assert image.header["FNAME"] == 1 def test_pixel_scale(): - assert False + header = fits.Header() + + image = Image(header=header) + assert image.pixel_scale is None + + image.header["CD1_1"] = 1.0 + assert image.pixel_scale == 3600.0 + + image.header["CDELT1"] = 1.0 + assert image.pixel_scale == 3600.0 + +def test_to_jpeg_no_data(): + image = Image() + + with pytest.raises(ValueError): + image.to_jpeg() + + +def test_to_jpeg_w_data(mocker, mock_image): + image = Image(mock_image) + + spy = mocker.spy(PIL.Image, "fromarray") + + jpeg_image = image.to_jpeg() + assert isinstance(jpeg_image, bytes) + + data = (0 * mock_image).astype(np.uint8) + + np.testing.assert_array_equal(spy.spy_return, data) -def test_to_jpeg(): - assert False + +def test_to_jpeg_w_vmin(mocker, mock_image): + image = Image(mock_image) + + spy = mocker.spy(PIL.Image, "fromarray") + + jpeg_image = image.to_jpeg(0.5, 1.5) + assert isinstance(jpeg_image, bytes) + + data = (255/2 * mock_image).astype(np.uint8) + + np.testing.assert_array_equal(spy.spy_return, data) def test_set_meta(): - assert False + image = Image() + data: int = 1 + + image.set_meta(data) + assert image.meta[int] == 1 def test_has_meta(): - assert False + image = Image() + assert image.has_meta(int) is False -def test_get_meta(): - assert False + image.meta[int] = 1 + assert image.has_meta(int) is True + + +def test_get_meta_valid(): + image = Image() + image.meta[int] = 1 + + assert image.get_meta(int) == 1 + + +def test_get_meta_invalid(): + image = Image() + + with pytest.raises(ValueError): + image.get_meta(int) + + +def test_get_meta_wrong_type(): + image = Image() + image.meta[int] = 1.0 + + with pytest.raises(ValueError): + image.get_meta(int) def test_get_meta_safe(): - assert False + image = Image() + + assert image.get_meta_safe(int, 0) == 0 + + image.meta[int] = 1 + assert image.get_meta_safe(int, 0) == 1 From 1a449ec0cc4cc90a0e11e93ff9bcc60ac49f0467 Mon Sep 17 00:00:00 2001 From: GermanHydrogen Date: Tue, 31 Oct 2023 14:03:00 +0100 Subject: [PATCH 04/14] Added tests to meta classes --- tests/images/meta/__init__.py | 0 tests/images/meta/test_altazoffsets.py | 11 ++++ tests/images/meta/test_exptime.py | 8 +++ tests/images/meta/test_onskydistance.py | 10 +++ tests/images/meta/test_pixeloffsets.py | 11 ++++ tests/images/meta/test_radecoffsets.py | 12 ++++ tests/images/meta/test_skyoffsets.py | 86 +++++++++++++++++++++++++ 7 files changed, 138 insertions(+) create mode 100644 tests/images/meta/__init__.py create mode 100644 tests/images/meta/test_altazoffsets.py create mode 100644 tests/images/meta/test_exptime.py create mode 100644 tests/images/meta/test_onskydistance.py create mode 100644 tests/images/meta/test_pixeloffsets.py create mode 100644 tests/images/meta/test_radecoffsets.py create mode 100644 tests/images/meta/test_skyoffsets.py diff --git a/tests/images/meta/__init__.py b/tests/images/meta/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/images/meta/test_altazoffsets.py b/tests/images/meta/test_altazoffsets.py new file mode 100644 index 00000000..cfb523e1 --- /dev/null +++ b/tests/images/meta/test_altazoffsets.py @@ -0,0 +1,11 @@ +from pyobs.images.meta import AltAzOffsets + + +def test_alt_az_offsets(): + dalt = 1.0 + daz = 2.0 + + meta = AltAzOffsets(dalt, daz) + + assert meta.dalt == dalt + assert meta.daz == daz diff --git a/tests/images/meta/test_exptime.py b/tests/images/meta/test_exptime.py new file mode 100644 index 00000000..16c2d0f9 --- /dev/null +++ b/tests/images/meta/test_exptime.py @@ -0,0 +1,8 @@ +from pyobs.images.meta import ExpTime + + +def test_exp_time(): + exp_time = 1.0 + meta = ExpTime(exp_time) + + assert meta.exptime == exp_time diff --git a/tests/images/meta/test_onskydistance.py b/tests/images/meta/test_onskydistance.py new file mode 100644 index 00000000..be8605ec --- /dev/null +++ b/tests/images/meta/test_onskydistance.py @@ -0,0 +1,10 @@ +from astropy.coordinates import Angle +from pyobs.images.meta import OnSkyDistance + + +def test_onskydistance(): + distance = Angle(1.0, unit="deg") + meta = OnSkyDistance(distance) + + assert meta.distance.unit == distance.unit + assert meta.distance.value == distance.value diff --git a/tests/images/meta/test_pixeloffsets.py b/tests/images/meta/test_pixeloffsets.py new file mode 100644 index 00000000..5d56fbfb --- /dev/null +++ b/tests/images/meta/test_pixeloffsets.py @@ -0,0 +1,11 @@ +from pyobs.images.meta import PixelOffsets + + +def test_pixeloffsets(): + dx = 1.0 + dy = 2.0 + + meta = PixelOffsets(dx, dy) + + assert meta.dx == dx + assert meta.dy == dy diff --git a/tests/images/meta/test_radecoffsets.py b/tests/images/meta/test_radecoffsets.py new file mode 100644 index 00000000..a4c36ce1 --- /dev/null +++ b/tests/images/meta/test_radecoffsets.py @@ -0,0 +1,12 @@ +from pyobs.images.meta import RaDecOffsets + + +def test_radecoffsets(): + dra = 1.0 + ddec = 2.0 + + meta = RaDecOffsets(dra, ddec) + + assert meta.dra == dra + assert meta.ddec == ddec + diff --git a/tests/images/meta/test_skyoffsets.py b/tests/images/meta/test_skyoffsets.py new file mode 100644 index 00000000..fb1b5d81 --- /dev/null +++ b/tests/images/meta/test_skyoffsets.py @@ -0,0 +1,86 @@ +import astropy + +from pyobs.images.meta import SkyOffsets +from astropy.coordinates import SkyCoord, BaseCoordinateFrame + + +def test_init(): + coord0 = SkyCoord(ra=0.0, dec=0.0, unit="deg") + coord1 = SkyCoord(ra=1.0, dec=1.0, unit="deg") + + meta = SkyOffsets(coord0, coord1) + + assert meta.coord0.ra.deg == coord0.ra.deg + assert meta.coord0.dec.deg == coord0.dec.deg + + assert meta.coord1.ra.deg == coord1.ra.deg + assert meta.coord1.dec.deg == coord1.dec.deg + + +def test_to_frame_non_value(): + coord0 = SkyCoord(ra=0.0, dec=0.0, unit="deg") + coord1 = SkyCoord(ra=1.0, dec=1.0, unit="deg") + + meta = SkyOffsets(coord0, coord1) + + framed_coord0, framed_coord1 = meta._to_frame() + + assert framed_coord0.ra.deg == coord0.ra.deg + assert framed_coord0.dec.deg == coord0.dec.deg + + assert framed_coord1.ra.deg == coord1.ra.deg + assert framed_coord1.dec.deg == coord1.dec.deg + + +def test_to_frame_w_value(mocker): + """ + Tests that SkyCoord.transform_to is correctly used + """ + frame = BaseCoordinateFrame() + + coord0 = SkyCoord(ra=0.0, dec=0.0, unit="deg") + coord1 = SkyCoord(ra=1.0, dec=1.0, unit="deg") + meta = SkyOffsets(coord0, coord1) + + mocker.patch("astropy.coordinates.SkyCoord.transform_to", return_value=0) + + x, y = meta._to_frame(frame) + + astropy.coordinates.SkyCoord.transform_to.assert_called_with(frame) + + assert x == 0 + assert y == 0 + + +def test_separation(mocker): + """ + Tests that _to_frame and separation is correctly used + """ + coord0 = SkyCoord(ra=0.0, dec=0.0, unit="deg") + coord1 = SkyCoord(ra=1.0, dec=1.0, unit="deg") + meta = SkyOffsets(coord0, coord1) + + mocker.patch.object(meta, "_to_frame", return_value=(coord0, coord1)) + mocker.patch("astropy.coordinates.SkyCoord.separation", return_value=0) + + assert meta.separation() == 0 + + meta._to_frame.assert_called_once_with(None) + astropy.coordinates.SkyCoord.separation.assert_called_once_with(coord1) + + +def test_spherical_offsets(mocker): + """ + Tests that _to_frame and spherical_offsets_to is correctly used + """ + coord0 = SkyCoord(ra=0.0, dec=0.0, unit="deg") + coord1 = SkyCoord(ra=1.0, dec=1.0, unit="deg") + meta = SkyOffsets(coord0, coord1) + + mocker.patch.object(meta, "_to_frame", return_value=(coord0, coord1)) + mocker.patch("astropy.coordinates.SkyCoord.spherical_offsets_to", return_value=(0, 1)) + + assert meta.spherical_offsets() == (0, 1) + + meta._to_frame.assert_called_once_with(None) + astropy.coordinates.SkyCoord.spherical_offsets_to.assert_called_once_with(coord1.frame) From 36fef537ecdc9f3b1be299ac4a1d7e7a47c34311 Mon Sep 17 00:00:00 2001 From: GermanHydrogen Date: Tue, 31 Oct 2023 14:03:19 +0100 Subject: [PATCH 05/14] Added ExpTime to meta init --- pyobs/images/meta/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/pyobs/images/meta/__init__.py b/pyobs/images/meta/__init__.py index 02544aca..a66eed9c 100644 --- a/pyobs/images/meta/__init__.py +++ b/pyobs/images/meta/__init__.py @@ -3,3 +3,4 @@ from .radecoffsets import RaDecOffsets from .skyoffsets import SkyOffsets from .onskydistance import OnSkyDistance +from .exptime import ExpTime \ No newline at end of file From 1d505ced1543f17b560ffe93df549bfecbbc3dca Mon Sep 17 00:00:00 2001 From: GermanHydrogen Date: Wed, 8 Nov 2023 08:56:19 +0100 Subject: [PATCH 06/14] Fixed poetry.lock --- poetry.lock | 114 +++++++++++++++++++++++++--------------------------- 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"error" in self._response_data async def send(self, url: str, timeout: int): diff --git a/pyobs/images/processors/astrometry/_dotnet_request_builder.py b/pyobs/images/processors/astrometry/_dotnet_request_builder.py index a36c8321..2b1c1c9f 100644 --- a/pyobs/images/processors/astrometry/_dotnet_request_builder.py +++ b/pyobs/images/processors/astrometry/_dotnet_request_builder.py @@ -1,4 +1,4 @@ -from typing import Dict, Any +from typing import Optional import pandas as pd from astropy.io.fits import Header @@ -14,17 +14,8 @@ def __init__(self, source_count: int, radius: float): self._radius = radius self._request_data = {} - self._catalog: pd.DataFrame = None - self._header: Header = None - - def add_catalog_from_image(self, image: Image): - if image.catalog is None: - raise exc.ImageError("No catalog found in image.") - - self._catalog = image.catalog[["x", "y", "flux", "peak"]].to_pandas() - - def add_header_from_image(self, image: Image): - self._header = image.header + self._catalog = pd.DataFrame() + self._header: Optional[Header] = None def _filter_catalog(self): self._catalog = self._catalog.dropna(how="any") @@ -57,13 +48,19 @@ def _build_request_data(self): "flux": self._catalog["flux"].tolist(), } - def __call__(self) -> _DotNetRequest: + def __call__(self, image: Image) -> _DotNetRequest: + # set catalog and header + if image.catalog is None: + raise exc.ImageError("No catalog found in image.") + self._catalog = image.catalog[["x", "y", "flux", "peak"]].to_pandas() + self._header = image.header + + # select stars self._filter_catalog() self._validate_catalog() self._select_brightest_stars() + # validate header and build request self._validate_header() - self._build_request_data() - return _DotNetRequest(self._request_data) diff --git a/pyobs/images/processors/astrometry/dotnet.py b/pyobs/images/processors/astrometry/dotnet.py index 0d7df503..76c4d31c 100644 --- a/pyobs/images/processors/astrometry/dotnet.py +++ b/pyobs/images/processors/astrometry/dotnet.py @@ -44,9 +44,8 @@ def __init__( self._request_builder = _DotNetRequestBuilder(source_count, radius) async def _process(self, image: Image) -> Image: - self._request_builder.add_catalog_from_image(image) - self._request_builder.add_header_from_image(image) - request = self._request_builder() + # build the request + request = self._request_builder(image) logger = _RequestLogger(log, image, request.request_data) logger.log_request_data() From dab6680edf7fe2bf6cd0cc6c2f1434c5c80c5de9 Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Sat, 11 Nov 2023 17:02:38 +0100 Subject: [PATCH 08/14] fixed bug in exception testing, closes #292 --- tests/utils/test_exceptions.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/utils/test_exceptions.py b/tests/utils/test_exceptions.py index 8ab3a65a..84290297 100644 --- a/tests/utils/test_exceptions.py +++ b/tests/utils/test_exceptions.py @@ -13,8 +13,8 @@ def setup_function() -> None: def test_log() -> None: exc.MotionError() - # should contain MotionError and PyObsError - assert len(exc._local_exceptions) == 2 + # should still be empty, since exception was not registered + assert len(exc._local_exceptions) == 0 def test_register() -> None: From cb0db7517ee293883db97f9feb35739064e8c8e0 Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Sat, 11 Nov 2023 17:19:02 +0100 Subject: [PATCH 09/14] fixed some tests --- tests/utils/test_exceptions.py | 21 +++++++++++++++------ 1 file changed, 15 insertions(+), 6 deletions(-) diff --git a/tests/utils/test_exceptions.py b/tests/utils/test_exceptions.py index 84290297..0610493b 100644 --- a/tests/utils/test_exceptions.py +++ b/tests/utils/test_exceptions.py @@ -1,12 +1,12 @@ import asyncio -from typing import Optional - import pytest - from pyobs.utils import exceptions as exc from pyobs.utils.exceptions import PyObsError +pytest_plugins = ("pytest_asyncio",) + + def setup_function() -> None: exc.clear() @@ -30,7 +30,8 @@ def test_empty() -> None: assert len(exc._handlers) == 0 -def test_callback() -> None: +@pytest.mark.asyncio +async def test_callback() -> None: event = asyncio.Event() async def cb(exception: PyObsError) -> None: @@ -42,18 +43,22 @@ async def cb(exception: PyObsError) -> None: # 1st is fine exc.MotionError() + await asyncio.sleep(0.01) assert event.is_set() is False # 2nd is fine exc.MotionError() + await asyncio.sleep(0.01) assert event.is_set() is False # 3rd triggers callback exc.MotionError() + await asyncio.sleep(0.01) assert event.is_set() is True -def test_raise() -> None: +@pytest.mark.asyncio +async def test_raise() -> None: event = asyncio.Event() async def cb(exception: PyObsError) -> None: @@ -75,6 +80,7 @@ async def cb(exception: PyObsError) -> None: assert isinstance(exc_info.value.exception, exc.MotionError) +@pytest.mark.asyncio async def test_timespan() -> None: event = asyncio.Event() @@ -94,18 +100,21 @@ async def cb(exception: PyObsError) -> None: # raise two more exc.MotionError() exc.MotionError() + await asyncio.sleep(0.01) with pytest.raises(exc.SevereError): raise exc.MotionError() assert event.is_set() -def test_remote() -> None: +@pytest.mark.asyncio +async def test_remote() -> None: # get triggered after 3 MotionErrors exc.register_exception(exc.MotionError, 3, throw=True) # raise two, shouldn't do anything exc.MotionError() exc.MotionError() + await asyncio.sleep(0.01) # one InvocationError should trigger MotionError with pytest.raises(exc.SevereError) as exc_info: From 51fe941467a496c1a1846930a21c9e1a10bc0670 Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Sat, 11 Nov 2023 17:21:10 +0100 Subject: [PATCH 10/14] fixed some tests --- tests/modules/camera/test_basecamera.py | 8 +++++++- tests/utils/skyflats/test_scheduler.py | 4 ++++ 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/tests/modules/camera/test_basecamera.py b/tests/modules/camera/test_basecamera.py index b1425c2f..7ab38129 100644 --- a/tests/modules/camera/test_basecamera.py +++ b/tests/modules/camera/test_basecamera.py @@ -1,8 +1,12 @@ from astropy.io import fits - +import pytest from pyobs.modules.camera import DummyCamera +pytest_plugins = ("pytest_asyncio",) + + +@pytest.mark.asyncio async def test_open_close(): """Test basic open/close of BaseCamera.""" @@ -12,6 +16,7 @@ async def test_open_close(): await camera.close() +@pytest.mark.asyncio async def test_remaining(): """Test the methods for remaining exposure time and progress.""" @@ -94,6 +99,7 @@ async def test_add_fits_headers(): ''' +@pytest.mark.asyncio async def test_trimsec(): # create camera, no need for opening it camera = DummyCamera() diff --git a/tests/utils/skyflats/test_scheduler.py b/tests/utils/skyflats/test_scheduler.py index d8852041..13bf6b7c 100644 --- a/tests/utils/skyflats/test_scheduler.py +++ b/tests/utils/skyflats/test_scheduler.py @@ -6,6 +6,10 @@ from pyobs.utils.time import Time +pytest_plugins = ("pytest_asyncio",) + + +@pytest.mark.asyncio async def test_scheduler(): # init observer and time observer = Observer.at_site("SAAO") From c2ab75a1e43b0cc82f8cf609d3c548b01526bd18 Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Sun, 12 Nov 2023 18:18:07 +0100 Subject: [PATCH 11/14] add pytest plugin pytest_mock --- tests/images/test_image.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/tests/images/test_image.py b/tests/images/test_image.py index 1b1d9ca4..904f51bf 100644 --- a/tests/images/test_image.py +++ b/tests/images/test_image.py @@ -13,6 +13,9 @@ from pyobs.images import Image +pytest_plugins = ("pytest_mock",) + + def assert_array_equal_or_none(check_value, value): if check_value is None: assert value is None @@ -102,7 +105,7 @@ def test_from_ccddata_w_values(mock_image): header["test"] = 1 mask = np.zeros((4, 4)) uncertainties = np.zeros((4, 4)) - ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, mask=mask, uncertainty=uncertainties, unit='adu') + ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, mask=mask, uncertainty=uncertainties, unit="adu") image = Image.from_ccddata(ccd_data) @@ -114,7 +117,7 @@ def test_from_ccddata_non_values(mock_image): header = fits.Header() header["test"] = 1 - ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, unit='adu') + ccd_data = astropy.nddata.CCDData(data=mock_image, header=header, unit="adu") image = Image.from_ccddata(ccd_data) assert_equal_image_params(image, mock_image) @@ -362,7 +365,7 @@ def test_to_jpeg_w_vmin(mocker, mock_image): jpeg_image = image.to_jpeg(0.5, 1.5) assert isinstance(jpeg_image, bytes) - data = (255/2 * mock_image).astype(np.uint8) + data = (255 / 2 * mock_image).astype(np.uint8) np.testing.assert_array_equal(spy.spy_return, data) From ec89aa2f6ef9a1b3cf01b76a05cc11700c136e7d Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Mon, 13 Nov 2023 13:23:46 +0100 Subject: [PATCH 12/14] check nested exception as well for triggered 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changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/pointing/test_guiding_statistic_uptime.py b/tests/modules/pointing/test_guiding_statistic_uptime.py index 425926d1..50a418cc 100644 --- a/tests/modules/pointing/test_guiding_statistic_uptime.py +++ b/tests/modules/pointing/test_guiding_statistic_uptime.py @@ -14,7 +14,7 @@ def test_end_to_end(): header = statistic.add_to_header(client, {}) - assert header["GUIDING UPTIME"] == (100.0, "Percentage of exposure time the guiding was closed.") + assert header["GUIDING UPTIME"][0] == 100.0 def test_calc_uptime_percentage(): From 22400b7bae9fd9e1c0e1d137a4e2d02cadb2c0de Mon Sep 17 00:00:00 2001 From: Tim-Oliver Husser Date: Mon, 13 Nov 2023 13:27:32 +0100 Subject: [PATCH 14/14] v1.6.4 --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 851e3fc2..403ee8e0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] name = "pyobs-core" packages = [{ include = "pyobs" }] -version = "1.6.3" +version = "1.6.4" description = "robotic telescope software" authors = ["Tim-Oliver Husser "] license = "MIT"