Sourcery refactored master branch

octotribble/Combine_nod_spectra.py

@@ -5,7 +5,7 @@
 
 Script that take one imput parameter which is the path to the normobs directory
 
-Needs functions/modules to get the filenames, export to a fits tablefile, change fits hdr
+Needs functions/modules to get the filenames, export them to a fits tablefile, change fits hdr
 """
 import argparse
 import fnmatch
@@ -48,10 +48,7 @@ def SumNods(Spectra, Headers, Pos="All", Norm="None"):
     If want to be more sure the correct nods are added the headers
     should be checked for its nod position.
     """
-    if Pos == "All":
-        NodNum = len(Spectra)
-    else:
-        NodNum = len(Spectra) / 2.0
+    NodNum = len(Spectra) if Pos == "All" else len(Spectra) / 2.0
     # print("number of nods ", NodNum)
     # if Headers[i]["HIERARCH ESO SEQ NODPOS"] == Pos:
     NodSum = np.zeros_like(Spectra[0])

octotribble/Compare_pipelines.py

@@ -61,7 +61,7 @@ def ccf_astro(spectrum1, spectrum2, rvmin=0, rvmax=200, drv=1):
     s = False
     w, f = spectrum1
     tw, tf = spectrum2
-    if not len(w) or not len(tw):
+    if not (len(w) and len(tw)):
         return 0, 0, 0, 0, 0
     c = 299792.458
     drvs = np.arange(rvmin, rvmax, drv)
@@ -441,7 +441,7 @@ def main(fname, fname2, lines=False, model=False, telluric=False, sun=False,
         else:
             print('Warning: Solar spectrum not available in wavelength range.')
             sun = False
-    elif sun and model:
+    elif sun:
         print('Warning: Both solar spectrum and a model spectrum are selected. Using model spectrum.')
         sun = False
 
@@ -495,7 +495,7 @@ def main(fname, fname2, lines=False, model=False, telluric=False, sun=False,
     if ccf != 'none':
         if ccf in ['sun', 'both'] and sun:
             # remove tellurics from the Solar spectrum
-            if telluric and sun:
+            if telluric:
                 print('Correcting solar spectrum for tellurics...')
                 i_sun = i_sun / i_tel
             print('Calculating CCF for the Sun...')
@@ -628,9 +628,9 @@ def main(fname, fname2, lines=False, model=False, telluric=False, sun=False,
     elif rv1 and rv2:
         ax1.set_title(
             '{0!s}\nSun/model: {1!s} km/s, telluric: {2!s} km/s'.format(fname, rv1, rv2))
-    elif rv1 and not rv2:
+    elif rv1:
         ax1.set_title('{0!s}\nSun/model: {1!s} km/s'.format(fname, rv1))
-    elif not rv1 and rv2:
+    elif rv2:
         ax1.set_title('{0!s}\nTelluric: {1!s} km/s'.format(fname, rv2))
     elif ccf == 'model':
         ax1.set_title('{0!s}\nModel(CCF): {1!s} km/s'.format(fname, rv1))

octotribble/Convolution/IP_Convolution.py

@@ -35,9 +35,7 @@ def unitary_Gauss(x, center, fwhm):
     sigma = np.abs(fwhm) / (2 * np.sqrt(2 * np.log(2)))
     Amp = 1.0 / (sigma * np.sqrt(2 * np.pi))
     tau = -((x - center)**2) / (2 * (sigma**2))
-    result = Amp * np.exp(tau)
-
-    return result
+    return Amp * np.exp(tau)
 
 
 def fast_convolve(wav_val, R, wav_extended, flux_extended, fwhm_lim):

octotribble/Convolution/IP_compare_single_vs_multiproc.py

@@ -42,9 +42,7 @@ def unitary_Gauss(x, center, fwhm):
     sigma = np.abs(fwhm) / (2 * np.sqrt(2 * np.log(2)))
     Amp = 1.0 / (sigma * np.sqrt(2 * np.pi))
     tau = -((x - center) ** 2) / (2 * (sigma ** 2))
-    result = Amp * np.exp(tau)
-
-    return result
+    return Amp * np.exp(tau)
 
 
 def fast_convolve(wav_val, R, wav_extended, flux_extended, fwhm_lim):

octotribble/Convolution/IP_multi_Convolution.py

@@ -51,9 +51,7 @@ def unitary_Gauss(x, center, fwhm):
     sigma = np.abs(fwhm) / (2 * np.sqrt(2 * np.log(2)))
     Amp = 1.0 / (sigma * np.sqrt(2 * np.pi))
     tau = -((x - center) ** 2) / (2 * (sigma ** 2))
-    result = Amp * np.exp(tau)
-
-    return result
+    return Amp * np.exp(tau)
 
 
 def fast_convolve(wav_val, R, wav_extended, flux_extended, fwhm_lim):

octotribble/Doppler_factor_test.py

@@ -21,15 +21,13 @@ def doppler_factor_shift(wave, velocity):
     beta = velocity / constants.c
     doppler_factor = ((1 + beta) / (1 - beta)) ** 0.5
 
-    y = wave * doppler_factor
-    return y
+    return wave * doppler_factor
 
 
 def doppler_shift(wave, velocity):
     """Doppler shift using non-realtivistically."""
     beta = velocity / constants.c
-    y = wave * (1 + beta)
-    return y
+    return wave * (1 + beta)
 
 
 shift_factor = doppler_factor_shift(wavelength, rv)

octotribble/Misc/tick_label_modification.py

@@ -7,8 +7,7 @@
 def convert_labels_to_rv(x, labels):
     x_mid = np.mean(x)
     c = 299792.458   # km/s
-    transform = ["{0:2.1f}".format((label / x_mid) * c) for label in labels]
-    return transform
+    return ["{0:2.1f}".format((label / x_mid) * c) for label in labels]
 
 
 x = np.arange(10) + 2110

octotribble/RVCalculations.py

@@ -14,8 +14,7 @@
 
 def Calculate_RV(Lambda, deltalambda):
     c = 299792458.  # m/s
-    V = [c * deltalambda / lmda for lmda in Lambda]
-    return V
+    return [c * deltalambda / lmda for lmda in Lambda]
 
 
 def Calculate_WLshift(wav, v):
@@ -27,22 +26,19 @@ def Calculate_WLshift(wav, v):
     if isinstance(v, (int, float)):
         return (v / c) * wav
     else:
-        deltalambda = [(v / c) * lmda for lmda in wav]
-        return deltalambda
+        return [(v / c) * lmda for lmda in wav]
 
 
 def Calc_RV(Lambda, deltalambda):
     # Fixed wavelength
     c = 299792458.  # m/s
-    V = [c * (delta / Lambda) for delta in deltalambda]
-    return V
+    return [c * (delta / Lambda) for delta in deltalambda]
 
 
 def Calc_WLshift(Lambda, vels):
     # Fixed wavelength
     c = 299792458.  # m/s
-    V = [(vel / c) * Lambda for vel in vels]
-    return V
+    return [(vel / c) * Lambda for vel in vels]
 # NIR range we have
 # 2110 nm to 2170 nm
 

octotribble/SpectralTools.py

@@ -120,15 +120,15 @@ def wl_interpolation(wl, spec, ref_wl, method="scipy", kind="linear", verbose=Fa
     v_print = print if verbose else lambda *a, **k: None
 
     starttime = time.time()
-    if method == "scipy":
-        v_print(kind + " scipy interpolation")
-        linear_interp = interp1d(wl, spec, kind=kind)
-        new_spec = linear_interp(ref_wl)
-    elif method == "numpy":
+    if method == "numpy":
         if kind.lower() is not "linear":
             v_print("Warning: Cannot do " + kind + " interpolation with numpy, switching to linear")
         v_print("Linear numpy interpolation")
         new_spec = np.interp(ref_wl, wl, spec)  # 1-d peicewise linear interpolat
+    elif method == "scipy":
+        v_print(kind + " scipy interpolation")
+        linear_interp = interp1d(wl, spec, kind=kind)
+        new_spec = linear_interp(ref_wl)
     else:
         v_print("Method was given as " + method)
         raise("Interpolation method not correct")
@@ -150,9 +150,7 @@ def unitary_Gauss(x, center, FWHM):
     sigma = np.abs(FWHM) / (2 * np.sqrt(2 * np.log(2)))
     amp = 1.0 / (sigma * np.sqrt(2 * np.pi))
     tau = -((x - center)**2) / (2 * (sigma**2))
-    result = amp * np.exp(tau)
-
-    return result
+    return amp * np.exp(tau)
 
 
 def fast_convolve(wav_val, R, wav_extended, flux_extended, fwhm_lim):

octotribble/Tapas/tapas_spectra_namer.py

@@ -26,8 +26,7 @@ def _parser():
     parser.add_argument("-k", "--keep_original", help="Keep the original file", action="store_true")
     parser.add_argument("-s", "--species", help="Specify constituents if known e.g. h20, noh20", type=str)
 
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main(fname, extract=False, prefix="", keep_original=False, species=False):

octotribble/Tapas/tapas_xml_request_generator.py

@@ -48,8 +48,7 @@ def _parser():
     parser.add_argument("-n", "--request_number", help="Tapas request number. Iterate on previous request number.",
                         type=int)
     parser.add_argument("-v", "--verbose", action="store_true", help="Turn on verbosity.")
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main(fname=("/home/jneal/Phd/data/Crires/BDs-DRACS/HD30501-1/Combined_Nods/"

octotribble/combine_nod_errors.py

@@ -8,6 +8,8 @@
 
 def combine_errors(chips=range(1, 5), save_path=None):
     """Assumes the current directory contains the files for the nod cycle."""
+    # Update header
+    from datetime import datetime
     for chip in chips:
         # print("Chip", chip)
         ms_files = sorted(glob("C*_{0}.*ms.fits.*".format(chip)))
@@ -19,8 +21,8 @@ def combine_errors(chips=range(1, 5), save_path=None):
         assert len(norm_sum_file) == 1
         norm_sum_file = norm_sum_file[0]
         # Check ms_file and norm_file match the start of norm_sum_file
-        assert any([os.path.basename(norm_sum_file)[0:29] in name for name in ms_files])
-        assert any([os.path.basename(norm_sum_file)[0:29] in name for name in norm_files])
+        assert any(os.path.basename(norm_sum_file)[0:29] in name for name in ms_files)
+        assert any(os.path.basename(norm_sum_file)[0:29] in name for name in norm_files)
 
         # Combine Spectrum errors quadratically
         square_error = np.zeros(1024)
@@ -48,8 +50,6 @@ def combine_errors(chips=range(1, 5), save_path=None):
 
         assert error_spectrum.shape == sum_spectrum.shape
 
-        # Update header
-        from datetime import datetime
         header["history"] = "Errors combined on {}".format(datetime.now())
         header["comment"] = "Errors normalized, added in quadrature, then divide by number of nods"
 

octotribble/extraction/dracs_quicklooks2017.py

@@ -42,8 +42,7 @@ def _parser():
         choices=["1", "2", "3"],
         default=None,
     )
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main(chip=None, band=None, showplots=False):

octotribble/extraction/plot_mixed_combination.py

@@ -30,16 +30,11 @@ def _parser():
         choices=["1", "2", "3", "4"],
         default=None,
     )
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main(chip=None, showplots=False):
-    if chip is None:
-        chips = range(1, 5)
-    else:
-        chips = [int(chip)]
-
+    chips = range(1, 5) if chip is None else [int(chip)]
     dir_path = os.getcwd()
 
     intermediate_path = os.path.join(dir_path, "Intermediate_steps", "")

octotribble/file_renamer.py

@@ -19,8 +19,7 @@ def _parser():
     parser.add_argument('filenames', nargs='+', type=str, help='List of Filenames')
     parser.add_argument("-x", "--cut", type=str, default=":", help="Character to Remove (cut)")
     parser.add_argument("-v", "--paste", type=str, default="", help="Character to replace with (paste)")
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def char_replace(fname, remove_char, replace_char=""):
@@ -48,8 +47,7 @@ def char_replace(fname, remove_char, replace_char=""):
 
     """
     name_parts = fname.split(remove_char)
-    new_name = replace_char.join(name_parts)
-    return new_name
+    return replace_char.join(name_parts)
 
 
 def main(filenames, cut=":", paste=""):

octotribble/grid_chisquare.py

@@ -31,28 +31,38 @@ def chi_squared(observed, expected, error=None):
 
 
 def parallel_chisqr_1D(iter_1, obs, model, model_params, n_jobs=4):
-    grid = Parallel(n_jobs=n_jobs)(delayed(chi_squared)(obs, model(a, *model_params)) for a in iter_1)
-    return grid
+    return Parallel(n_jobs=n_jobs)(
+        delayed(chi_squared)(obs, model(a, *model_params)) for a in iter_1
+    )
 
 
 # @memory.cache
 def parallel_chisqr_2D(iter_1, iter_2, obs, model, model_params, n_jobs=4):
-    grid = Parallel(n_jobs=n_jobs)(delayed(chi_squared)(obs, model(a, b, *model_params))
-                                   for a in iter_1 for b in iter_2)
-    return grid
+    return Parallel(n_jobs=n_jobs)(
+        delayed(chi_squared)(obs, model(a, b, *model_params))
+        for a in iter_1
+        for b in iter_2
+    )
 
 
 # @memory.cache
 def parallel_chisqr_3D(iter_1, iter_2, iter_3, obs, model, model_params, n_jobs=4):
-    grid = Parallel(n_jobs=n_jobs)(delayed(chi_squared)(obs, model(a, b, c, *model_params))
-                                   for a in iter_1 for b in iter_2 for c in iter_3)
-    return grid
+    return Parallel(n_jobs=n_jobs)(
+        delayed(chi_squared)(obs, model(a, b, c, *model_params))
+        for a in iter_1
+        for b in iter_2
+        for c in iter_3
+    )
 
 
 def parallel_chisqr_4D(iter_1, iter_2, iter_3, iter_4, obs, model, model_params, n_jobs=4):
-    grid = Parallel(n_jobs=n_jobs)(delayed(chi_squared)(obs, model(a, b, c, d, *model_params))
-                                   for a in iter_1 for b in iter_2 for c in iter_3 for d in iter_4)
-    return grid
+    return Parallel(n_jobs=n_jobs)(
+        delayed(chi_squared)(obs, model(a, b, c, d, *model_params))
+        for a in iter_1
+        for b in iter_2
+        for c in iter_3
+        for d in iter_4
+    )
 
 
 # @memory.cache

octotribble/normalize/cont_norm.py

@@ -28,8 +28,7 @@ def _parser():
                         help="Calculate normalization fucntion errors on the flux.")
     parser.add_argument("-p", "--plot", default=False, action="store_true",
                         help="Plot normalized result.")
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main():
@@ -69,10 +68,7 @@ def main():
 
 
     fitssave = args.fitsname.replace(".fits", ".{!s}.fits".format(args.suffix))
-    if len(data) == 2:
-        fits.writeto(fitssave, norm_flux, header=hdr)
-    else:
-        fits.writeto(fitssave, norm_flux, header=hdr)
+    fits.writeto(fitssave, norm_flux, header=hdr)
 
 
 def flux_error(wave, flux, c):

octotribble/normalize/fitsnorm.py

@@ -96,8 +96,7 @@ def _parser():
     parser.add_argument("filename", type=str,
                         help="Specturm to continuum normalize.")
 
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 if __name__ == "__main__":

octotribble/obs_info.py

@@ -29,8 +29,7 @@ def _parser():
     parser.add_argument("-o", "--output", help="Specify output filename", default=False)
     parser.add_argument("-s", "--separator", help="Separator for time section of fits", default=":")
 
-    args = parser.parse_args()
-    return args
+    return parser.parse_args()
 
 
 def main(fname, output=False, separator=":", verbose=True):

octotribble/phoenix_utils.py

@@ -42,17 +42,8 @@ def find_closest_phoenix(data_dir, teff, logg, feh, alpha=None):
     closest_logg = loggs[np.abs(loggs - logg).argmin()]
     closest_feh = fehs[np.abs(fehs - feh).argmin()]
 
-    if alpha is not None:
-        if abs(alpha) > 0.2:
-            print("Warning! Alpha is outside acceptable range -0.2->0.2")
-        closest_alpha = alphas[np.abs(alphas - alpha).argmin()]
-        phoenix_glob = ("/Z{2:+4.1f}.Alpha={3:+5.2f}/*{0:05d}{1:4.2f}"
-                        "{2:+4.1f}.Alpha={3:+5.2f}.PHOENIX*.fits"
-                        "").format(closest_teff, closest_logg, closest_feh,
-                                   closest_alpha)
-    else:
-        phoenix_glob = ("/Z{2:+4.1f}/*{0:05d}{1:4.2f}{2:+4.1f}.PHOENIX*.fits"
-                        "").format(closest_teff, closest_logg, closest_feh)
+    phoenix_glob = ("/Z{2:+4.1f}/*{0:05d}{1:4.2f}{2:+4.1f}.PHOENIX*.fits"
+                    "").format(closest_teff, closest_logg, closest_feh)
     files = glob.glob(data_dir + phoenix_glob)
     if len(files) > 1:
         print("More than one file returned")