tkmatrix 0.8.2__tar.gz → 0.8.4__tar.gz

{tkmatrix-0.8.2/tkmatrix.egg-info → tkmatrix-0.8.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tkmatrix
-Version: 0.8.2
+Version: 0.8.4
 Summary: ToolKit for Multi-phAse Transits Recovery from Injected eXoplanets
 Home-page: https://github.com/PlanetHunters/tkmatrix
 Author: M. Dévora-Pajares & F.J. Pozuelos

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/setup.py

@@ -2,7 +2,7 @@ import setuptools
 
 with open("README.md", "r") as fh:
     long_description = fh.read()
-version = "0.8.2"
+version = "0.8.4"
 setuptools.setup(
     name="tkmatrix",
     version=version,
@@ -25,7 +25,7 @@ setuptools.setup(
                         'configparser==5.0.1',
                         "corner==2.1.0",
                         "ellc==1.8.5",
-                        "lcbuilder==0.16.1",
+                        "lcbuilder==0.16.2",
                         "mock==4.0.3",
                         'pyparsing==2.4.7', # Matplotlib dependency
                         "seaborn==0.11.1",

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix/custom_algorithms/BlsCustomSearchAlgorithm.py

@@ -42,7 +42,7 @@ class BlsCustomSearchAlgorithm(CustomSearchAlgorithm):
                                                                                   oversampling, star_info,
                                                                                   transits_min_count)
             lc = lightkurve.LightCurve(time=time, flux=flux)
-            results = lc.to_periodogram(method='bls', period=tls_period_grid)
+            results = lc.to_periodogram(method='bls', period=tls_period_grid, frequency_factor=oversampling)
             max_power_index = np.argmax(results.power)
             sde = results.power[max_power_index].value / np.nanmedian(results.power).value
             t0 = results.transit_time_at_max_power.value

tkmatrix-0.8.4/tkmatrix/programmatic.py

@@ -0,0 +1,109 @@
+import os
+
+from lcbuilder.star.starinfo import StarInfo
+
+from tkmatrix.tkmatrix_class import MATRIX
+
+matrix_user_properties = {}
+matrix_user_properties['TARGET'] = "KIC 11615498"
+star_properties = {}
+star_properties['MASS'] = 1.977
+star_properties['MASS_LOWER_ERROR'] = 0.062
+star_properties['MASS_UPPER_ERROR'] = 0.062
+star_properties['RADIUS'] = 9.863
+star_properties['RADIUS_LOWER_ERROR'] = 0.015
+star_properties['RADIUS_UPPER_ERROR'] = 0.015
+star_properties['TEFF'] = 4978.6
+star_properties['LD_COEFFICIENTS'] = [0.4356, 0.2367]
+star_info = StarInfo(matrix_user_properties['TARGET'],
+         tuple(star_properties["LD_COEFFICIENTS"]) if "LD_COEFFICIENTS" in star_properties else None,
+         star_properties["TEFF"] if "TEFF" in star_properties else None,
+         star_properties["LUM"] if "LUM" in star_properties else None,
+         star_properties["LOGG"] if "LOGG" in star_properties else None,
+         star_properties["LOGG_ERR"] if "LOGG_ERR" in star_properties else None,
+         star_properties["RADIUS"] if "RADIUS" in star_properties else None,
+         star_properties["RADIUS_LOWER_ERROR"] if "RADIUS_LOWER_ERROR" in star_properties else None,
+         star_properties["RADIUS_UPPER_ERROR"] if "RADIUS_UPPER_ERROR" in star_properties else None,
+         star_properties["MASS"] if "MASS" in star_properties else None,
+         star_properties["MASS_LOWER_ERROR"] if "MASS_LOWER_ERROR" in star_properties else None,
+         star_properties["MASS_UPPER_ERROR"] if "MASS_UPPER_ERROR" in star_properties else None,
+         star_properties["RA"] if "RA" in star_properties else None,
+         star_properties["DEC"] if "DEC" in star_properties else None)
+matrix_user_properties['SECTORS'] = 'all'
+matrix_user_properties['PERIOD_GRID'] = None
+matrix_user_properties['RADIUS_GRID'] = None
+matrix_user_properties['PERIOD_GRID_GEOM'] = 'lin'
+matrix_user_properties['RADIUS_GRID_GEOM'] = 'lin'
+matrix_user_properties['PHASES'] = 2
+matrix_user_properties["CPUS"] = os.cpu_count() - 1
+matrix_user_properties['MIN_PERIOD'] = 4
+matrix_user_properties['MAX_PERIOD'] = 20
+matrix_user_properties['MIN_PERIOD_SEARCH'] = 0.5
+matrix_user_properties['MAX_PERIOD_SEARCH'] = 40
+matrix_user_properties['STEPS_PERIOD'] = 2
+matrix_user_properties['MIN_RADIUS'] = 4
+matrix_user_properties['MAX_RADIUS'] = 22
+matrix_user_properties['STEPS_RADIUS'] = 2
+matrix_user_properties['PHASES'] = 2
+matrix_user_properties['DETREND_WS'] = 3.5
+matrix_user_properties['OVERSAMPLING'] = 1
+matrix_user_properties['SIGNAL_SELECTION_MODE'] = 'period'
+matrix_user_properties['FIT_METHOD'] = 'bls-periodogram'
+matrix_user_properties['SNR_THRESHOLD'] = 5
+matrix_user_properties['USE_SEARCH_CACHE'] = True
+matrix_user_properties['DETREND_METHOD'] = 'biweight'
+matrix_user_properties['RUN_LIMIT'] = 2
+target = matrix_user_properties["TARGET"]
+file = None
+author = None
+custom_search = None
+prepare_algorithm = None
+initial_mask = None
+initial_smooth_enabled = False
+initial_transit_mask = None
+auto_detrend_period = None
+auto_detrend_ratio = 1
+auto_detrend_method = 'biweight'
+auto_detrend_enabled = False
+oscillation_reduction = False
+oscillation_min_snr = 3
+oscillation_amplitude_threshold = 0.1
+oscillation_ws_percent = 60
+oscillation_min_period = 0.0006875
+oscillation_max_period = 0.25
+high_rms_bin_hours = 4
+high_rms_threshold = 3
+high_rms_enabled = False
+outliers_sigma = 3
+exptime = 1800
+eleanor_corr_flux = "pca_flux"
+cache_dir = None
+if cache_dir is None:
+    cache_dir = os.path.expanduser('~') + "/"
+search_engine = 'cpu'
+run_dir = './'
+ir = MATRIX(target, matrix_user_properties["SECTORS"], author, run_dir, False, star_info, file, exptime,
+                initial_mask, initial_transit_mask, eleanor_corr_flux, outliers_sigma, high_rms_enabled,
+                high_rms_threshold, high_rms_bin_hours, initial_smooth_enabled, auto_detrend_enabled,
+                auto_detrend_method, auto_detrend_ratio, auto_detrend_period, prepare_algorithm, cache_dir,
+                oscillation_reduction, oscillation_min_snr, oscillation_amplitude_threshold, oscillation_ws_percent,
+                oscillation_min_period, oscillation_max_period, matrix_user_properties["CPUS"],
+                search_engine=search_engine)
+inject_dir = None
+inject_dir, period_grid, radius_grid = ir.inject(matrix_user_properties["PHASES"],
+                           matrix_user_properties["MIN_PERIOD"], matrix_user_properties["MAX_PERIOD"],
+                           matrix_user_properties["STEPS_PERIOD"],
+                           matrix_user_properties["MIN_RADIUS"], matrix_user_properties["MAX_RADIUS"],
+                           matrix_user_properties["STEPS_RADIUS"],
+                           period_grid=matrix_user_properties['PERIOD_GRID'],
+                           radius_grid=matrix_user_properties['RADIUS_GRID'],
+                           period_grid_geom=matrix_user_properties["PERIOD_GRID_GEOM"],
+                           radius_grid_geom=matrix_user_properties["RADIUS_GRID_GEOM"],
+                           inject_dir=inject_dir)
+ir.recovery(inject_dir, matrix_user_properties["SNR_THRESHOLD"],
+            matrix_user_properties["DETREND_METHOD"],
+            matrix_user_properties["DETREND_WS"], matrix_user_properties["FIT_METHOD"],
+            matrix_user_properties["RUN_LIMIT"],
+            None, matrix_user_properties["MAX_PERIOD_SEARCH"], matrix_user_properties["OVERSAMPLING"],
+            matrix_user_properties["SIGNAL_SELECTION_MODE"],
+            use_search_cache=matrix_user_properties["USE_SEARCH_CACHE"])

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix/properties.yaml

@@ -44,7 +44,7 @@ DETREND_METHOD: "biweight"
 DETREND_WS: 0
 # Number of CPU processes to be used
 CPUS:
-# Fit method to be used. [tls|bls|grazing]
+# Fit method to be used. [tls|bls|grazing|bls-periodogram]
 FIT_METHOD: 'tls'
 # The number of TLS search trials to be run for each period & radius & epoch before considering as not recovered.
 RUN_LIMIT: 2
@@ -53,7 +53,8 @@ SIGNAL_SELECTION_MODE: 'period-epoch'
 # The SNR limit for a TLS found signal to be considered as not recovered.
 SNR_THRESHOLD: 5
 # The density of the period grid for the TLS search. Increasing this will enhance the TLS accuracy sometimes but it
-# adds a high increase of computational cost.
+# adds a high increase of computational cost. When FIT_METHOD: bls-periodogram, OVERSAMPLING represents the
+# frequency_factor and hence, increasing it will reduce the period grid size (as opposite to the standard search).
 OVERSAMPLING: 1
 # An array of time tuples to be masked in your curve. E.g: [[1401.25, 1401.60], [1415.2, 1416.0]]
 INITIAL_MASK:

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix/tests/test_tkmatrix.py

@@ -16,26 +16,26 @@ class TestsMatrix(unittest.TestCase):
         inject_dir = None
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5, 1, 3, 3, 1)
-            self.assertEquals(10, len(os.listdir(inject_dir)))
-            self.assertEquals([1], matrix.sectors)
+            self.assertEqual(10, len(os.listdir(inject_dir)))
+            self.assertEqual([1], matrix.sectors)
             self.assertAlmostEqual(0.47, matrix.mass, 2)
             self.assertAlmostEqual(0.44, matrix.massmin, 2)
             self.assertAlmostEqual(0.5, matrix.massmax, 2)
             self.assertAlmostEqual(0.18, matrix.radius, 2)
             self.assertAlmostEqual(0.076, matrix.radiusmin, 3)
             self.assertAlmostEqual(0.284, matrix.radiusmax, 3)
-            self.assertEquals("TIC 220513363", matrix.object_info.mission_id())
-            self.assertEquals("TIC 220513363", matrix.id)
+            self.assertEqual("TIC 220513363", matrix.object_info.mission_id())
+            self.assertEqual("TIC 220513363", matrix.id)
             self.assertAlmostEqual(0.47, matrix.mstar.value, 2)
             self.assertAlmostEqual(0.44, matrix.mstar_min.value, 2)
             self.assertAlmostEqual(0.5, matrix.mstar_max.value, 2)
             self.assertAlmostEqual(0.18, matrix.rstar.value, 2)
             self.assertAlmostEqual(0.076, matrix.rstar_min.value, 3)
             self.assertAlmostEqual(0.284, matrix.rstar_max.value, 3)
-            self.assertEquals(".", matrix.dir)
+            self.assertEqual(".", matrix.dir)
             matrix.recovery(inject_dir, 5, detrend_ws=0, oversampling=0.1)
             matrix.plot_results(target, inject_dir)
-            self.assertEquals(9, len(os.listdir(inject_dir)))
+            self.assertEqual(9, len(os.listdir(inject_dir)))
         finally:
             if inject_dir is not None:
                 shutil.rmtree(inject_dir, ignore_errors=True)
@@ -48,7 +48,7 @@ class TestsMatrix(unittest.TestCase):
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5, 1, 3, 3, 1)
             matrix.recovery(inject_dir, 5, detrend_ws=0, oversampling=0.1)
             matrix.plot_results(target, inject_dir)
-            self.assertEquals(10, len(os.listdir(inject_dir)))
+            self.assertEqual(10, len(os.listdir(inject_dir)))
         finally:
             if inject_dir is not None:
                 shutil.rmtree(inject_dir, ignore_errors=True)
@@ -59,7 +59,7 @@ class TestsMatrix(unittest.TestCase):
         inject_dir = None
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5.1, 2, 3, 3.1, 2)
-            self.assertEquals(13, len(os.listdir(inject_dir)))
+            self.assertEqual(13, len(os.listdir(inject_dir)))
         finally:
             if inject_dir is not None:
                 shutil.rmtree(inject_dir, ignore_errors=True)
@@ -70,7 +70,7 @@ class TestsMatrix(unittest.TestCase):
         inject_dir = None
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(2, 5, 5, 1, 3, 3, 1)
-            self.assertEquals(11, len(os.listdir(inject_dir)))
+            self.assertEqual(11, len(os.listdir(inject_dir)))
         finally:
             if inject_dir is not None:
                 shutil.rmtree(inject_dir, ignore_errors=True)
@@ -135,9 +135,9 @@ class TestsMatrix(unittest.TestCase):
         inject_dir = None
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5, 1, 3, 3, 1)
-            self.assertEquals(10, len(os.listdir(inject_dir)))
-            self.assertEquals((0.2, 0.5), matrix.star_info.ld_coefficients)
-            self.assertEquals(2000, matrix.star_info.teff)
+            self.assertEqual(10, len(os.listdir(inject_dir)))
+            self.assertEqual((0.2, 0.5), matrix.star_info.ld_coefficients)
+            self.assertEqual(2000, matrix.star_info.teff)
             self.assertAlmostEqual(0.7, matrix.star_info.mass)
             self.assertAlmostEqual(0.55, matrix.star_info.mass_min)
             self.assertAlmostEqual(0.75, matrix.star_info.mass_max)
@@ -151,9 +151,9 @@ class TestsMatrix(unittest.TestCase):
         inject_dir = None
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5, 1, 3, 3, 1)
-            self.assertEquals(10, len(os.listdir(inject_dir)))
-            self.assertEquals((0.1258, 0.235), matrix.star_info.ld_coefficients)
-            self.assertEquals(31000.0, matrix.star_info.teff)
+            self.assertEqual(10, len(os.listdir(inject_dir)))
+            self.assertEqual((0.1258, 0.235), matrix.star_info.ld_coefficients)
+            self.assertEqual(31000.0, matrix.star_info.teff)
             self.assertAlmostEqual(0.47, matrix.star_info.mass)
             self.assertAlmostEqual(0.44, matrix.star_info.mass_min)
             self.assertAlmostEqual(0.5, matrix.star_info.mass_max)
@@ -173,9 +173,9 @@ class TestsMatrix(unittest.TestCase):
         try:
             inject_dir, period_grid, radius_grid = matrix.inject(1, 5, 5.1, 2, 3, 3.1, 2, period_grid=period_grid_expected,
                                                                  radius_grid=radius_grid_expected)
-            self.assertEquals(29, len(os.listdir(inject_dir)))
-            self.assertEquals(period_grid_expected, period_grid)
-            self.assertEquals(radius_grid_expected, radius_grid)
+            self.assertEqual(29, len(os.listdir(inject_dir)))
+            self.assertEqual(period_grid_expected, period_grid)
+            self.assertEqual(radius_grid_expected, radius_grid)
         finally:
             if inject_dir is not None:
                 shutil.rmtree(inject_dir, ignore_errors=True)

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix/tkmatrix_class.py

@@ -450,12 +450,12 @@ class MATRIX:
                                               oversampling, signal_selection_mode)
                         else:
                             founds = [True]
-                            snrs = [float(found_entries.iloc[0]['snr'])]
-                            sdes = [float(found_entries.iloc[0]['sde'])]
-                            runs = [int(found_entries.iloc[0]['run'])]
-                            durations_found = [float(found_entries.iloc[0]['duration_found'])]
-                            periods_found = [float(found_entries.iloc[0]['period_found'])]
-                            epochs_found = [float(found_entries.iloc[0]['epoch_found'])]
+                            snrs = [float(str(found_entries.iloc[0]['snr']).split(',')[-1])]
+                            sdes = [float(str(found_entries.iloc[0]['sde']).split(',')[-1])]
+                            runs = [int(str(found_entries.iloc[0]['run']).split(',')[-1])]
+                            durations_found = [float(str(found_entries.iloc[0]['duration_found']).split(',')[-1])]
+                            periods_found = [float(str(found_entries.iloc[0]['period_found']).split(',')[-1])]
+                            epochs_found = [float(str(found_entries.iloc[0]['epoch_found']).split(',')[-1])]
                     new_report = {"period": period, "radius": r_planet, "epoch": epoch,
                                   "found": founds[-1], "snr": ','.join([str(i) for i in snrs]),
                                   "sde": ','.join([str(i) for i in sdes]), "run": ','.join([str(i) for i in runs]),
@@ -554,10 +554,12 @@ class MATRIX:
         fig, ax = plt.subplots(figsize=(2.7 * 5, 5))
         im = plt.imshow(normed_hist.T, origin='lower', extent=(x[0], x[-1], y[0], y[-1]), interpolation='none',
                         aspect='auto', cmap='viridis', vmin=0, vmax=100, rasterized=True)
-        plt.colorbar(im, label='Recovery rate (%)')
-        plt.xlabel('Injected period (days)')
-        plt.ylabel(r'Injected ' + 'radius' if not is_rv else 'mass' + ' (' + column_units + '$_\oplus$)')
-        ax.set_title(object_id + " - I&R (" + str(phases) + " " + phases_str + ")")
+        cbar = plt.colorbar(im)
+        cbar.set_label(label='Recovery rate (%)', size=16)
+        cbar.ax.tick_params(labelsize=14)
+        plt.xlabel('Injected period (days)', fontsize=18)
+        plt.ylabel(r'Injected ' + ('radius' if not is_rv else 'mass') + ' (' + column_units + '$_\oplus$)', fontsize=18)
+        ax.set_title(object_id + " - I&R (" + str(phases) + " " + phases_str + ")", fontsize=24)
         if xticks is not None:
             plt.xticks(xticks)
         else:
@@ -567,6 +569,7 @@ class MATRIX:
             ax.xaxis.set_major_formatter(FormatStrFormatter('%.' + str(period_ticks_decimals) + 'f'))
         if yticks is not None:
             plt.xticks(yticks)
+        ax.tick_params(axis='both', which='major', labelsize=14)
         plt.savefig(inject_dir + '/inj-rec' + ('-rv' if is_rv else '') + '.png', bbox_inches='tight', dpi=200)
         plt.close()
 
@@ -630,10 +633,12 @@ class MATRIX:
         fig, ax = plt.subplots(figsize=(2.7 * 5, 5))
         im = plt.imshow(normed_hist.T, origin='lower', extent=(x1[0], x1[-1], y1[0], y1[-1]), interpolation='none',
                         aspect='auto', cmap='viridis', vmin=-phases, vmax=phases, rasterized=True)
-        plt.colorbar(im, label='# Found samples diff.')
-        plt.xlabel('Injected period (days)')
-        plt.ylabel(r'Injected radius (R$_\oplus$)')
-        ax.set_title(object_id + " - P/R recovery diff(" + str(phases) + " " + phases_str + ")")
+        cbar = plt.colorbar(im)
+        cbar.set_label(label='# Found samples diff.', size=16)
+        cbar.ax.tick_params(labelsize=14)
+        plt.xlabel('Injected period (days)', fontsize=18)
+        plt.ylabel(r'Injected radius (R$_\oplus$)', fontsize=18)
+        ax.set_title(object_id + " - P/R recovery diff(" + str(phases) + " " + phases_str + ")", fontsize=24)
         if xticks is not None:
             plt.xticks(xticks)
         else:
@@ -643,6 +648,7 @@ class MATRIX:
             ax.xaxis.set_major_formatter(FormatStrFormatter('%.' + str(period_ticks_decimals) + 'f'))
         if yticks is not None:
             plt.xticks(yticks)
+        ax.tick_params(axis='both', which='major', labelsize=14)
         plt.savefig(output_dir + '/inj-rec-diff.png', bbox_inches='tight', dpi=200)
         plt.close()
 

{tkmatrix-0.8.2 → tkmatrix-0.8.4/tkmatrix.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: tkmatrix
-Version: 0.8.2
+Version: 0.8.4
 Summary: ToolKit for Multi-phAse Transits Recovery from Injected eXoplanets
 Home-page: https://github.com/PlanetHunters/tkmatrix
 Author: M. Dévora-Pajares & F.J. Pozuelos

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix.egg-info/SOURCES.txt

@@ -6,6 +6,7 @@ tkmatrix/__init__.py
 tkmatrix/__main__.py
 tkmatrix/inject_model.py
 tkmatrix/inject_rv_model.py
+tkmatrix/programmatic.py
 tkmatrix/properties.yaml
 tkmatrix/rv.py
 tkmatrix/tkmatrix_class.py

{tkmatrix-0.8.2 → tkmatrix-0.8.4}/tkmatrix.egg-info/requires.txt

@@ -3,7 +3,7 @@ beautifulsoup4==4.9.3
 configparser==5.0.1
 corner==2.1.0
 ellc==1.8.5
-lcbuilder==0.16.1
+lcbuilder==0.16.2
 mock==4.0.3
 pyparsing==2.4.7
 seaborn==0.11.1