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Merge pull request #219 from simontorres/add_test_code_2
Add test code for wavelength module
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,170 +1,160 @@ | ||
| from __future__ import absolute_import | ||
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| import numpy as np | ||
| import os | ||
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| from astropy.convolution import convolve, Gaussian1DKernel, Box1DKernel | ||
| from astropy.io import fits | ||
| from astropy.modeling import models, Model | ||
| from ccdproc import CCDData | ||
| from unittest import TestCase, skip | ||
| from ..wavelength import (WavelengthCalibration, | ||
| WavelengthSolution) | ||
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| # TODO (simon): Figure out what tests are required and/or if some major | ||
| # refactoring is required. | ||
| from ..redspec import get_args | ||
| from ...core import add_wcs_keys | ||
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| def test_process_spectroscopy_data(): | ||
| pass | ||
| class WavelengthCalibrationTests(TestCase): | ||
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| def setUp(self): | ||
| argument_list = ['--data-path', os.getcwd(), | ||
| '--proc-path', os.getcwd(), | ||
| '--search-pattern', 'cfzsto', | ||
| '--output-prefix', 'w', | ||
| '--extraction', 'fractional', | ||
| '--reference-files', 'data/ref_comp', | ||
| '--max-targets', '3', | ||
| ] | ||
| arguments = get_args(argument_list) | ||
| self.wc = WavelengthCalibration(args=arguments) | ||
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| def test_wavelength_calibration___init__(): | ||
| pass | ||
| self.ccd = CCDData(data=np.random.random_sample(200), | ||
| meta=fits.Header(), | ||
| unit='adu') | ||
| self.ccd = add_wcs_keys(ccd=self.ccd) | ||
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| def test_add_wavelength_solution(self): | ||
| self.wc.rms_error = 0.1 | ||
| self.wc.n_points = 100 | ||
| self.wc.n_rejections = 2 | ||
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| def test_wavelength_calibration___call__(): | ||
| pass | ||
| self.wc.calibration_lamp = 'non-existent.fits' | ||
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| crval1 = 3977.948 | ||
| npix = 4060 | ||
| cdelt = 0.9910068 | ||
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| def test_wavelength_calibration_get_wsolution(): | ||
| pass | ||
| x_axis = np.linspace(crval1, | ||
| crval1 + cdelt * npix, | ||
| npix) | ||
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| self.ccd = self.wc.add_wavelength_solution(ccd=self.ccd, | ||
| x_axis=x_axis) | ||
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| def test_wavelength_calibration_get_calibration_lamp(): | ||
| pass | ||
| self.assertEqual(self.ccd.header['CTYPE1'], 'LINEAR') | ||
| self.assertEqual(self.ccd.header['CRVAL1'], crval1) | ||
| self.assertEqual(self.ccd.header['CRPIX1'], 1) | ||
| self.assertAlmostEqual(self.ccd.header['CDELT1'], cdelt, places=3) | ||
| self.assertEqual(self.ccd.header['DCLOG1'], | ||
| 'REFSPEC1 = {:s}'.format(self.wc.calibration_lamp)) | ||
| self.assertEqual(self.ccd.header['GSP_WRMS'], self.wc.rms_error) | ||
| self.assertEqual(self.ccd.header['GSP_WPOI'], self.wc.n_points) | ||
| self.assertEqual(self.ccd.header['GSP_WREJ'], self.wc.n_rejections) | ||
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| @skip | ||
| def test_automatic_wavelength_solution(self): | ||
| pass | ||
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| def test_wavelength_calibration_get_lines_in_lamp(): | ||
| pass | ||
| def test__bin_reference_data(self): | ||
| wavelength = np.linspace(3000, 7000, 4000) | ||
| intensity = np.random.random_sample(4000) | ||
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| for i in range(1, 4): | ||
| self.wc.serial_binning = i | ||
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| def test_wavelength_calibration_get_best_filling_value(): | ||
| pass | ||
| new_wavelength, new_intensity = self.wc._bin_reference_data( | ||
| wavelength=wavelength, | ||
| intensity=intensity) | ||
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| self.assertEqual(len(wavelength), len(intensity)) | ||
| self.assertEqual(len(new_wavelength), len(new_intensity)) | ||
| self.assertEqual(len(new_wavelength), np.floor(len(wavelength) / i)) | ||
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| def test_wavelength_calibration_recenter_lines(): | ||
| pass | ||
| def test__cross_correlation(self): | ||
| self.wc.lamp = self.ccd.copy() | ||
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| x_axis = np.arange(0, 4060, 1) | ||
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| def test_wavelength_calibration_recenter_broad_lines(): | ||
| pass | ||
| reference = np.zeros(4060) | ||
| gaussian = models.Gaussian1D(stddev=2) | ||
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| for i in sorted(np.random.choice(x_axis, 30)): | ||
| gaussian.mean.value = i | ||
| reference += gaussian(x_axis) | ||
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| def test_wavelength_calibration_get_spectral_characteristics(): | ||
| pass | ||
| offset = np.random.choice(range(1, 15), 1)[0] | ||
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| for slit in [1, 2, 3, 4, 5]: | ||
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| new_array = np.append(reference[offset:], np.zeros(offset)) | ||
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| def test_wavelength_calibration_interpolate(): | ||
| pass | ||
| if slit > 3: | ||
| box_kernel = Box1DKernel(width=slit / 0.15) | ||
| new_array = convolve(new_array, box_kernel) | ||
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| self.assertEqual(len(reference), len(new_array)) | ||
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| def test_wavelength_calibration_recenter_line_by_data(): | ||
| pass | ||
| self.wc.lamp.header['SLIT'] = '{:d}.0" long slit'.format(slit) | ||
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| correlation_value = self.wc._cross_correlation(reference=reference, | ||
| new_array=new_array) | ||
| self.assertEqual(correlation_value, offset) | ||
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| def test_wavelength_calibration_predicted_wavelength(): | ||
| pass | ||
| def test__evaluate_solution(self): | ||
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| differences = np.array([0.5] * 10) | ||
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| clipped_differences = np.ma.masked_array(differences, | ||
| mask=[0, | ||
| 0, | ||
| 1, | ||
| 0, | ||
| 0, | ||
| 1, | ||
| 0, | ||
| 0, | ||
| 1, | ||
| 0]) | ||
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| def test_wavelength_calibration_automatic_wavelength_solution(): | ||
| pass | ||
| rms_error, n_points, n_rej = self.wc._evaluate_solution( | ||
| clipped_differences=clipped_differences) | ||
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| self.assertEqual(rms_error, 0.5) | ||
| self.assertEqual(n_points, 10) | ||
| self.assertEqual(n_rej, 3) | ||
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| def test_wavelength_calibration_interactive_wavelength_solution(): | ||
| pass | ||
| @skip | ||
| def test__get_lines_in_lamp(self): | ||
| pass | ||
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| def test__get_spectral_characteristics(self): | ||
| self.ccd.header.set('GRATING', 'SYZY_400') | ||
| self.ccd.header.set('GRT_ANG', 7.5) | ||
| self.ccd.header.set('CAM_ANG', 16.1) | ||
| self.ccd.header.set('CCDSUM', '1 1') | ||
| self.wc.lamp = self.ccd.copy() | ||
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| def test_wavelength_calibration_cross_correlation(): | ||
| pass | ||
| spec_charact = self.wc._get_spectral_characteristics() | ||
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| self.assertIsInstance(spec_charact, dict) | ||
| self.assertEqual(len(spec_charact), 7) | ||
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| def test_wavelength_calibration_on_click(): | ||
| pass | ||
| def test_get_wsolution(self): | ||
| self.assertIsNone(self.wc.get_wsolution()) | ||
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| def test_wavelength_calibration_key_pressed(): | ||
| pass | ||
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| def test_wavelength_calibration_register_mark(): | ||
| pass | ||
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| def test_wavelength_calibration_find_more_lines(): | ||
| pass | ||
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| def test_wavelength_calibration_update_marks_plot(): | ||
| pass | ||
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| def test_wavelength_calibration_plot_raw_over_reference(): | ||
| pass | ||
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| def test_wavelength_calibration_evaluate_solution(): | ||
| pass | ||
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| def test_wavelength_calibration_fit_pixel_to_wavelength(): | ||
| pass | ||
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| def test_wavelength_calibration_linearize_spectrum(): | ||
| pass | ||
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| def test_wavelength_calibration_add_wavelength_solution(): | ||
| pass | ||
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| def test_wavelength_calibration_display_onscreen_message(): | ||
| pass | ||
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| def test_wavelength_calibration_display_help_text(): | ||
| pass | ||
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| def test_wavelength_solution___init__(): | ||
| pass | ||
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| def test_wavelength_solution_set_spectral_features(): | ||
| pass | ||
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| def test_wavelength_solution_check_compatibility(): | ||
| pass | ||
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| def test_wavelength_solution_set_solution_name(): | ||
| pass | ||
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| # old tests | ||
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| def test_wavelength_calibration_instantiate(): | ||
| from ..wavelength import WavelengthCalibration | ||
| from .test_redspec import test_get_args | ||
| import os | ||
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| test_args = test_get_args() | ||
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| wavelength_calibration = WavelengthCalibration(args=test_args) | ||
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| assert isinstance(wavelength_calibration, WavelengthCalibration) | ||
| assert os.path.exists(test_args.reference_dir) | ||
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| def test_get_wsolution_none(): | ||
| pass | ||
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| def test_lambda_pipeline_to_iraf(): | ||
| pass | ||
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| def test_lamp_correlation(): | ||
| """Cross correlate lamp | ||
| :return: | ||
| """ | ||
| pass | ||
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| def test_rms_pipeline_to_iraf(): | ||
| pass | ||
| self.wc.wsolution = models.Chebyshev1D(degree=2) | ||
| self.wc.wsolution.c0.value = 3977.9485 | ||
| self.wc.wsolution.c1.value = 1.00153387 | ||
| self.wc.wsolution.c2.value = -1.2891437 | ||
| self.assertIsInstance(self.wc.get_wsolution(), Model) |