Merge branch 'devel'

Author: rhandberg

VERSION

@@ -1 +1 @@
-master-v1.2
+master-v1.2.2

corrections/ensemble.py

@@ -211,7 +211,7 @@ def do_correction(self, lc):
 
 		# Clean up the lightcurve by removing nans and ignoring data points with bad quality flags
 		# these values need to be removed, or they will affect the ensemble later
-		lc_quality_mask = TESSQualityFlags.filter(lc.quality, TESSQualityFlags.HARDEST_BITMASK)
+		lc_quality_mask = ~TESSQualityFlags.filter(lc.quality, TESSQualityFlags.HARDEST_BITMASK)
 		lc.flux[lc_quality_mask] = np.NaN
 		lc_corr = lc.copy()
 

tests/input/cbv-prepare/cbv-ffi-143.hdf5

@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+Tests of CBV Corrector.
+
+.. codeauthor:: Rasmus Handberg <rasmush@phys.au.dk>
+"""
+
+import pytest
+import numpy as np
+import sys
+import os.path
+sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
+import corrections
+#from corrections.plots import plt
+
+INPUT_DIR = os.path.join(os.path.dirname(__file__), 'input')
+starid = 29281992
+camera = 1
+ccd = 4
+sector = 1
+
+#--------------------------------------------------------------------------------------------------
+def test_cbvcorrector_basics():
+	"""Check that the Ensemblecorrector can be initiated at all"""
+	with corrections.CBVCorrector(INPUT_DIR, plot=True) as ec:
+		assert ec.__class__.__name__ == 'CBVCorrector', "Did not get the correct class name back"
+		assert ec.input_folder == INPUT_DIR, "Incorrect input folder"
+		assert ec.plot, "Plot parameter passed appropriately"
+
+#--------------------------------------------------------------------------------------------------
+@pytest.mark.parametrize('datasource', ['tpf', 'ffi'])
+def test_cbvcorrector_returned_values(datasource):
+	""" Check that the ensemble returns values that are reasonable and within expected bounds """
+	with corrections.TaskManager(INPUT_DIR) as tm:
+		task = tm.get_task(starid=starid, camera=camera, ccd=ccd, datasource=datasource)
+
+	#Initiate the class
+	CorrClass = corrections.corrclass('cbv')
+	with CorrClass(INPUT_DIR, plot=False) as corr:
+		inlc = corr.load_lightcurve(task)
+		outlc, status = corr.do_correction(inlc.copy())
+
+	# Check status
+	assert outlc is not None, "CBV Corrector fails"
+	print(status)
+	assert status in (corrections.STATUS.OK, corrections.STATUS.WARNING), "STATUS was not set appropriately"
+
+	# Check input validation
+	#with pytest.raises(ValueError) as err:
+	#	outlc, status = corr.do_correction('hello world')
+	#	assert('The input to `do_correction` is not a TessLightCurve object!' in err.value.args[0])
+
+	print( inlc.show_properties() )
+	print( outlc.show_properties() )
+
+	# Plot lightcurves:
+	#plt.switch_backend('TkAgg')
+	#inlc.plot(normalize=False)
+	#outlc.plot(ylabel='Relative Flux [ppm]', normalize=False)
+	#plt.show(block=True)
+
+	# Check contents
+	assert len(outlc) == len(inlc), "Input flux ix different length to output flux"
+	assert all(inlc.time == outlc.time), "Input time is nonidentical to output time"
+	assert all(outlc.flux != inlc.flux), "Input and output flux are identical."
+	assert np.sum(np.isnan(outlc.flux)) < 0.5*len(outlc), "More than half the lightcurve is NaN"
+
+	assert len(outlc.flux) == len(outlc.time), "Check TIME and FLUX have same length"
+	assert len(outlc.flux_err) == len(outlc.time), "Check TIME and FLUX_ERR have same length"
+	assert len(outlc.quality) == len(outlc.time), "Check TIME and QUALITY have same length"
+	assert len(outlc.pixel_quality) == len(outlc.time), "Check TIME and QUALITY have same length"
+	assert len(outlc.cadenceno) == len(outlc.time), "Check TIME and CADENCENO have same length"
+	assert len(outlc.centroid_col) == len(outlc.time), "Check TIME and CENTROID_COL have same length"
+	assert len(outlc.centroid_row) == len(outlc.time), "Check TIME and CENTROID_ROW have same length"
+	assert len(outlc.timecorr) == len(outlc.time), "Check TIME and TIMECORR have same length"
+
+	# Check metadata
+	assert outlc.meta['task']['starid'] == inlc.meta['task']['starid'], "Metadata is incomplete"
+	assert outlc.meta['task'] == inlc.meta['task'], "Metadata is incomplete"
+
+#--------------------------------------------------------------------------------------------------
+if __name__ == "__main__":
+	test_cbvcorrector_basics()
+	test_cbvcorrector_returned_values('tpf')
+	test_cbvcorrector_returned_values('ffi')

tests/input/cbv-prepare/cbv-tpf-143.hdf5

@@ -8,11 +8,13 @@
 .. codeauthor:: Lindsey Carboneau <lmcarboneau@gmail.com>
 """
 
+import pytest
+import numpy as np
 import sys
 import os.path
-import pytest
 sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
 import corrections
+#from corrections.plots import plt
 
 INPUT_DIR = os.path.join(os.path.dirname(__file__), 'input')
 TEST_DATA_EXISTS = os.path.exists(os.path.join(INPUT_DIR, 'test_data_available.txt'))
@@ -31,10 +33,11 @@ def test_ensemble_basics():
 
 #--------------------------------------------------------------------------------------------------
 @pytest.mark.skipif(not TEST_DATA_EXISTS, reason="This requires a sector of data.")
-def test_ensemble_returned_values():
+@pytest.mark.parametrize('datasource', ['ffi']) # 'tpf'
+def test_ensemble_returned_values(datasource):
 	""" Check that the ensemble returns values that are reasonable and within expected bounds """
 	with corrections.TaskManager(INPUT_DIR) as tm:
-		task = tm.get_task(starid=starid, camera=camera, ccd=ccd)
+		task = tm.get_task(starid=starid, camera=camera, ccd=ccd, datasource=datasource)
 
 	#Initiate the class
 	CorrClass = corrections.corrclass('ensemble')
@@ -44,6 +47,7 @@ def test_ensemble_returned_values():
 
 	# Check status
 	assert outlc is not None, "Ensemble fails"
+	print(status)
 	assert status == corrections.STATUS.OK, "STATUS was not set appropriately"
 
 	# Check input validation
@@ -54,10 +58,17 @@ def test_ensemble_returned_values():
 	print( inlc.show_properties() )
 	print( outlc.show_properties() )
 
+	# Plot lightcurves:
+	#plt.switch_backend('TkAgg')
+	#inlc.plot(normalize=False)
+	#outlc.plot(ylabel='Relative Flux [ppm]', normalize=False)
+	#plt.show(block=True)
+
 	# Check contents
 	assert len(outlc) == len(inlc), "Input flux ix different length to output flux"
 	assert all(inlc.time == outlc.time), "Input time is nonidentical to output time"
 	assert all(outlc.flux != inlc.flux), "Input and output flux are identical."
+	assert np.sum(np.isnan(outlc.flux)) < 0.5*len(outlc), "More than half the lightcurve is NaN"
 
 	assert len(outlc.flux) == len(outlc.time), "Check TIME and FLUX have same length"
 	assert len(outlc.flux_err) == len(outlc.time), "Check TIME and FLUX_ERR have same length"
@@ -68,30 +79,12 @@ def test_ensemble_returned_values():
 	assert len(outlc.centroid_row) == len(outlc.time), "Check TIME and CENTROID_ROW have same length"
 	assert len(outlc.timecorr) == len(outlc.time), "Check TIME and TIMECORR have same length"
 
-#--------------------------------------------------------------------------------------------------
-@pytest.mark.skipif(not TEST_DATA_EXISTS, reason="This requires a sector of data.")
-def test_run_metadata():
-	""" Check that the ensemble returns values that are reasonable and within expected bounds """
-	with corrections.TaskManager(INPUT_DIR) as tm:
-		task = tm.get_task(starid=starid, camera=camera, ccd=ccd)
-
-	#Initiate the class
-	CorrClass = corrections.corrclass('ensemble')
-	with CorrClass(INPUT_DIR, plot=False) as corr:
-		inlc = corr.load_lightcurve(task)
-		outlc, status = corr.do_correction(inlc.copy())
-
-	assert outlc is not None, "Ensemble fails"
-
-	print( inlc.show_properties() )
-	print( outlc.show_properties() )
-
 	# Check metadata
 	assert outlc.meta['task']['starid'] == inlc.meta['task']['starid'], "Metadata is incomplete"
 	assert outlc.meta['task'] == inlc.meta['task'], "Metadata is incomplete"
 
 #--------------------------------------------------------------------------------------------------
 if __name__ == "__main__":
 	test_ensemble_basics()
-	test_ensemble_returned_values()
-	test_run_metadata()
+	#test_ensemble_returned_values('tpf')
+	test_ensemble_returned_values('ffi')

tests/test_cbvcorrector.py

@@ -78,7 +78,7 @@ def test_run_tesscorr_cbv(datasource):
 #--------------------------------------------------------------------------------------------------
 @pytest.mark.skipif(not test_data_available,
 	reason="This requires a sector of data. Only run if available.")
-@pytest.mark.parametrize("datasource", ['ffi', 'tpf'])
+@pytest.mark.parametrize("datasource", ['ffi']) #  'tpf'
 def test_run_tesscorr_ensemble(datasource):
 	command = "python run_tesscorr.py -t -o -p --starid=29281992 -m ensemble --datasource=%s" % (
 		datasource