Skip to content

Commit

Permalink
fixed pathing issues in test
Browse files Browse the repository at this point in the history
  • Loading branch information
@cylammarco
cylammarco committed Mar 23, 2023
1 parent 66efb97 commit d2fe67a
Showing 1 changed file with 24 additions and 63 deletions.
87 changes: 24 additions & 63 deletions test/test_onedspec.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -957,7 +957,6 @@ def test_add_fit_coeff_standard_not_fail_spec_id():
# Note that this is testing the "relay" to the WavelengthCalibrator, but
# not testing the calibrator itself.
def test_calibrator_science():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand Down Expand Up @@ -987,9 +986,7 @@ def test_calibrator_science():

onedspec.set_hough_properties(num_slopes=1000, stype="science")
onedspec.set_hough_properties(spec_id=0, num_slopes=1000, stype="science")
onedspec.set_hough_properties(
spec_id=[1], num_slopes=1000, stype="science"
)
onedspec.set_hough_properties(spec_id=[1], num_slopes=1000, stype="science")
onedspec.set_hough_properties(
spec_id=[11, 75], num_slopes=1000, stype="science"
)
Expand Down Expand Up @@ -1092,7 +1089,6 @@ def test_calibrator_science():
# Fail at the RASCAL initilisation
@pytest.mark.xfail(raises=TypeError)
def test_calibrator_science2():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1110,7 +1106,6 @@ def test_calibrator_science2():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_calibrator_properties_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1128,7 +1123,6 @@ def test_calibrator_science_fail_calibrator_properties_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_hough_properties_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1147,7 +1141,6 @@ def test_calibrator_science_fail_hough_properties_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_ransac_properties_science():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1167,7 +1160,6 @@ def test_calibrator_ransac_properties_science():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_known_pairs_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1188,7 +1180,6 @@ def test_calibrator_science_fail_known_pairs_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_add_user_atlas_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1211,7 +1202,6 @@ def test_calibrator_science_fail_add_user_atlas_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_add_atlas_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1232,7 +1222,6 @@ def test_calibrator_science_fail_add_atlas_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_remove_atlas_lines_range_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1256,7 +1245,6 @@ def test_calibrator_science_fail_remove_atlas_lines_range_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_clear_atlas_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1282,7 +1270,6 @@ def test_calibrator_science_fail_clear_atlas_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_list_atlas_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1302,7 +1289,6 @@ def test_calibrator_science_fail_list_atlas_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_hough_transform_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1326,7 +1312,6 @@ def test_calibrator_science_fail_hough_transform_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_fit_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1349,7 +1334,6 @@ def test_calibrator_science_fail_fit_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_refine_fit_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1373,7 +1357,6 @@ def test_calibrator_science_fail_refine_fit_spec_id():

@pytest.mark.xfail(raises=ValueError)
def test_calibrator_science_fail_ap_extract_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1382,56 +1365,54 @@ def test_calibrator_science_fail_ap_extract_spec_id():


img = image_reduction.ImageReduction(log_file_name=None)
img.add_filelist(
filelist=os.path.join(HERE, "test_data", "sprat_LHS6328.list")
)
img.add_filelist(filelist=os.path.join(HERE, "test_data", "sprat_LHS6328.list"))
img.load_data()
img.reduce()
twodspec = spectral_reduction.TwoDSpec(log_file_name=None)
twodspec.add_data(img)
twodspec.ap_trace()
twodspec.ap_extract(model="lowess")
twodspec.save_fits(
filename="test/test_output/twodspec_output.fits", overwrite=True
filename=os.path.join(HERE, "test_output", "twodspec_output.fits"),
overwrite=True,
)


def test_from_twodspec():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
onedspec.from_twodspec(twodspec, spec_id=0)


def test_from_fits_path():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
onedspec.from_fits("test/test_output/twodspec_output_0.fits", spec_id=0)
onedspec.from_fits(
os.path.join(HERE, "test_output", "twodspec_output_0.fits"), spec_id=0
)


def test_from_fits():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
twodspec_fits = fits.open("test/test_output/twodspec_output_0.fits")
twodspec_fits = fits.open(
os.path.join(HERE, "test_output", "twodspec_output_0.fits")
)
onedspec.from_fits(twodspec_fits, spec_id=0)


@pytest.mark.xfail()
def test_from_twodspec_fail_spec_id():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
onedspec.from_twodspec(twodspec, spec_id=10)


def test_extinction_function():

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1444,7 +1425,6 @@ def test_extinction_function():

@patch("plotly.graph_objects.Figure.show")
def test_standard_library_lookup(mock_show):

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1460,7 +1440,6 @@ def test_standard_library_lookup(mock_show):

@patch("plotly.graph_objects.Figure.show")
def test_sensitivity(mock_show):

onedspec = spectral_reduction.OneDSpec(
log_file_name=None, log_level="ERROR"
)
Expand All @@ -1469,9 +1448,7 @@ def test_sensitivity(mock_show):
np.ones(70) * 37, np.ones(70), spec_id=0, stype="science+standard"
)
onedspec.add_spec(np.arange(1, 71), spec_id=0, stype="science+standard")
onedspec.add_arc_spec(
np.arange(1, 71), spec_id=0, stype="science+standard"
)
onedspec.add_arc_spec(np.arange(1, 71), spec_id=0, stype="science+standard")
onedspec.add_fit_coeff(
np.array((4000.0, 1, 0.2, 0.0071)), spec_id=0, stype="science+standard"
)
Expand Down Expand Up @@ -1553,7 +1530,6 @@ def test_sensitivity(mock_show):


def test_adding_telluric_function():

global_onedspec.add_telluric_function(
lambda x: np.polynomial.polynomial.polyval(x, coeff)
)
Expand All @@ -1575,7 +1551,6 @@ def test_adding_telluric_function():

@patch("plotly.graph_objects.Figure.show")
def test_getting_telluric_profile(mock_show):

global_onedspec.add_telluric_function([np.arange(10000), np.arange(10000)])

global_onedspec.inspect_telluric_profile(
Expand All @@ -1598,7 +1573,6 @@ def test_getting_telluric_profile(mock_show):

@pytest.mark.xfail(raises=ValueError)
def test_adding_telluric_function_wrong_spec_id():

global_onedspec.add_telluric_function(
lambda x: np.polynomial.polynomial.polyval(x, coeff), spec_id=1000
)
Expand All @@ -1607,32 +1581,26 @@ def test_adding_telluric_function_wrong_spec_id():
# spec_id is irrelevant, there is only ONE standard spectrum
@pytest.mark.xfail(raises=ValueError)
def test_getting_telluric_profile_wrong_spec_id():

global_onedspec.get_telluric_profile(spec_id=1000)


@pytest.mark.xfail(raises=ValueError)
def test_inspecting_telluric_correction_wrong_spec_id():

global_onedspec.inspect_telluric_correction(spec_id=1000)


@pytest.mark.xfail(raises=ValueError)
def test_applying_atmospheric_extinction_correction_wrong_spec_id():

global_onedspec.apply_atmospheric_extinction_correction(spec_id=1000)


@patch("plotly.graph_objects.Figure.show")
def test_miscellaneous(mock_show):

global_onedspec.apply_flux_calibration()
global_onedspec.apply_flux_calibration(spec_id=0)
global_onedspec.apply_flux_calibration(spec_id=[0])

global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2
)
global_onedspec.apply_atmospheric_extinction_correction(science_airmass=1.2)
global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2, standard_airmass=1.5
)
Expand All @@ -1649,9 +1617,7 @@ def test_miscellaneous(mock_show):
extinction_func=np.poly1d([1, 2, 3])
)

global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2
)
global_onedspec.apply_atmospheric_extinction_correction(science_airmass=1.2)
global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2, standard_airmass=1.5
)
Expand All @@ -1665,9 +1631,7 @@ def test_miscellaneous(mock_show):
global_onedspec.apply_flux_calibration()
global_onedspec.set_atmospheric_extinction()

global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2
)
global_onedspec.apply_atmospheric_extinction_correction(science_airmass=1.2)
global_onedspec.apply_atmospheric_extinction_correction(
science_airmass=1.2, standard_airmass=1.5
)
Expand Down Expand Up @@ -1707,15 +1671,19 @@ def test_miscellaneous(mock_show):
)

global_onedspec.create_fits(
output="trace+count+weight_map+arc_spec+wavecal_coefficients+"
"wavelength+count_resampled+sensitivity+flux+flux_atm_ext_corrected+"
"sensitivity_resampled+flux_resampled+flux_resampled_atm_ext_corrected",
output=(
"trace+count+weight_map+arc_spec+wavecal_coefficients+"
"wavelength+count_resampled+sensitivity+flux+flux_atm_ext_corrected+"
"sensitivity_resampled+flux_resampled+flux_resampled_atm_ext_corrected"
),
empty_primary_hdu=False,
)
global_onedspec.create_fits(
output="trace+count+weight_map+arc_spec+wavecal_coefficients+"
"wavelength+count_resampled+sensitivity+flux+flux_atm_ext_corrected+"
"sensitivity_resampled+flux_resampled+flux_resampled_atm_ext_corrected",
output=(
"trace+count+weight_map+arc_spec+wavecal_coefficients+"
"wavelength+count_resampled+sensitivity+flux+flux_atm_ext_corrected+"
"sensitivity_resampled+flux_resampled+flux_resampled_atm_ext_corrected"
),
recreate=True,
)
global_onedspec.create_fits(
Expand Down Expand Up @@ -1922,7 +1890,6 @@ def test_save_csv_fail_spec_id():


def test_linear_fit():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -1987,7 +1954,6 @@ def test_linear_fit():


def test_manual_refit():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -2061,7 +2027,6 @@ def test_manual_refit():


def test_manual_refit_add_points():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -2138,7 +2103,6 @@ def test_manual_refit_add_points():


def test_manual_refit_remove_points():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -2214,7 +2178,6 @@ def test_manual_refit_remove_points():


def test_quadratic_fit():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -2281,7 +2244,6 @@ def test_quadratic_fit():


def test_quadratic_fit_legendre():

peaks = np.sort(np.random.random(31) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=5.0)
Expand Down Expand Up @@ -2355,7 +2317,6 @@ def test_quadratic_fit_legendre():

@pytest.mark.skip()
def test_quadratic_fit_chebyshev():

peaks = np.sort(np.random.random(51) * 1000.0)
# Removed the closely spaced peaks
distance_mask = np.isclose(peaks[:-1], peaks[1:], atol=10.0)
Expand Down

0 comments on commit d2fe67a

Please sign in to comment.