Adjusted for stare mode of gianob (44e91aa3) · Commits · GUIBRUSHR / DataReductionGIANOB

DataReductionGIANOB/DataReductionGIANOB.py

+5 −5

Original line number	Diff line number	Diff line
		@@ -57,10 +57,10 @@ class DataReduction:
		self.global_start = 0
		# Window
		m = get_monitors()
		self.width = int(m[0].width * 0.95)
		self.height = int(m[0].height * 0.8)
		self.displace_x = int(m[0].width * 0.04)
		self.displace_y = int(m[0].height * 0.04)
		self.width = int(m[0].width * 0.9)
		self.height = int(m[0].height * 0.75)
		self.displace_x = 0 # int(m[0].width * 0.04)
		self.displace_y = 0 # int(m[0].height * 0.04)
		self.path_default = path_default
		self.dialog = None
		self.window = tk.Tk()
		@@ -77,7 +77,7 @@ class DataReduction:
		self.window.resizable(True, True)
		# self.window.option_add('*Dialog.msg.width', 50)
		# Input frame
		self.frame_gofio = Frame_Gofio(self.window, self, path_default, int(0.95self.width), int(0.95self.height))
		self.frame_gofio = Frame_Gofio(self.window, self, path_default, int(0.9self.width), int(0.9self.height))
		#
		self.window.rowconfigure(0, weight=1)
		self.window.columnconfigure(0, weight=1)

DataReductionGIANOB/Frame_Gofio.py

+47 −20

Original line number	Diff line number	Diff line
		@@ -31,6 +31,7 @@ matplotlib.use('TkAgg')
		import matplotlib.pyplot as plt


		# noinspection PyTypeChecker,SqlNoDataSourceInspection
		class Frame_Gofio:
		gui = None
		frame_gofio = None
		@@ -55,7 +56,7 @@ class Frame_Gofio:
		self.path_fromheader = ""
		self.global_exc = 0
		self.gofio_folder_program = ""
		username = os.environ.get('USER')
		# username = os.environ.get('USER')
		self.gui = gui
		self.frame_gofio = tk.Frame(window, highlightbackground="black", highlightthickness=1, padx=5, pady=2)
		#
		@@ -79,7 +80,7 @@ class Frame_Gofio:
		nights = DataInterface.get_target_nights(
		self.path_target, target_list[0], "Transmission", self.option_list_instrument[0], 0
		)
		except:
		except Exception as e:
		nights = ""
		self.target_name, self.target_radius, self.target_mass, self.target_gravity, self.target_t_eq, self.target_stellar_radius, self.target_stellar_mass, self.target_p0, self.target_hjd0, self.target_period, self.target_vsys, self.target_limph, self.target_kp, self.target_ecc, self.target_opi, self.target_stellar_teff, self.target_ra, self.target_dec, self.target_a_Rs_ratio, self.target_projected_obliquity, self.target_inclination, self.target_v_sini = DataInterface.get_target_info(
		self.path_target, target_list[0])
		@@ -526,6 +527,15 @@ class Frame_Gofio:
		self.chosen_flat_var_post.set(self.option_list_flat[0])
		self.opt_flat_mode_post = tk.OptionMenu(self.tab_post_gofio, self.chosen_flat_var_post, *self.option_list_flat)
		self.opt_flat_mode_post.grid(column=2, row=2, sticky=tk.W)
		# Observation Mode
		self.label = tk.Label(master=self.tab_post_gofio, text='Observation Mode (giano, crires): ',
		font=('Sans', '9', 'bold'))
		self.label.grid(column=3, row=2, sticky=tk.W, )
		self.option_list_obs_mode = ["Nodding", "Stare"]
		self.chosen_obs_mode_var_post = tk.StringVar(value="Nodding")
		self.chosen_obs_mode_var_post.set(self.option_list_obs_mode[0])
		self.opt_obs_mode_post = tk.OptionMenu(self.tab_post_gofio, self.chosen_obs_mode_var_post, *self.option_list_obs_mode)
		self.opt_obs_mode_post.grid(column=4, row=2, columnspan=2, sticky=tk.W)

		# Help Button for Second Phase Reduction
		help_text_post_gofio = {
		@@ -1275,6 +1285,7 @@ class Frame_Gofio:
		def fromgofio(self):
		night = self.night.get("1.0", tk.END).strip()
		separate_A_B = self.chosen_separation_var.get()
		obs_mode = self.chosen_obs_mode_var_post.get()
		night_results = night + "AB" if separate_A_B else night
		target = self.chosen_target_var.get()
		instrument = self.chosen_instrument_var_post.get()
		@@ -1309,32 +1320,30 @@ class Frame_Gofio:
		listB = list()
		if instrument == "criresp":
		folder = Path(dirr)
		if self.chosen_single_var_criresp.get() == "Nodding":
		if obs_mode == "Nodding":
		# Trova file A e B
		dictA = {int(f.stem.split("_")[-1]): f
		for f in folder.glob("cr2res_obs_nodding_extractedA_*.fits")}
		dictB = {int(f.stem.split("_")[-1]): f
		for f in folder.glob("cr2res_obs_nodding_extractedB_*.fits")}
		if not separate_A_B:
		# Tutti gli indici trovati
		if separate_A_B:
		all_indices = sorted(set(dictA.keys()) \| set(dictB.keys()))
		listAB = []
		for i in all_indices:
		if i in dictA:
		listAB.append(dictA[i])
		listA.append(dictA[i])
		if i in dictB:
		listAB.append(dictB[i])
		listB.append(dictB[i])
		else:
		# Tutti gli indici trovati
		all_indices = sorted(set(dictA.keys()) \| set(dictB.keys()))
		listAB = []
		for i in all_indices:
		if i in dictA:
		listA.append(dictA[i])
		listAB.append(dictA[i])
		if i in dictB:
		listB.append(dictB[i])
		listAB.append(dictB[i])
		else:
		listAB = list(folder.glob("cr2res_obs_staring_extracted_*.fits"))

		else:
		#
		for file in os.listdir(dirr):
		@@ -1345,18 +1354,17 @@ class Frame_Gofio:
		listA.append(os.path.join(dirr, file))
		elif "_B_" in file:
		listB.append(os.path.join(dirr, file))
		# elif "_A_" in file or "_B_" in file:
		else:
		listAB.append(os.path.join(dirr, file))
		#
		self.run_from_gofio.configure(state="disabled")
		if separate_A_B and instrument in ["gianob", "criresp"]:
		if separate_A_B and instrument in ["gianob", "criresp"] and obs_mode == "Nodding":
		if len(listA) == len(listB):
		self.procedure_fromgofio(listA, "A_", night, dirn, threshold_SNR_f, target, yaml_file, instrument)
		self.procedure_fromgofio(listB, "B_", night, dirn, threshold_SNR_f, target, yaml_file, instrument)
		else:
		print("The amount of files A is not equal to the amount of file B")
		else:
		else: # for nodding/stare mode of gianob/criresp and for espresso or harpsn
		self.procedure_fromgofio(listAB, "", night, dirn, threshold_SNR_f, target, yaml_file, instrument)
		self.run_from_gofio.configure(state="normal")

		@@ -1636,8 +1644,12 @@ class Frame_Gofio:

		def fromheader(self):
		separate_A_B = self.chosen_separation_var.get()
		obs_mode = self.chosen_obs_mode_var_post.get()
		night = self.night.get("1.0", tk.END).strip()
		if separate_A_B:
		if obs_mode == "Stare":
		messagebox.showinfo("Incompatibility", "Stare mode is not compatible with separation of A and B")
		return
		night += "AB"
		target = self.chosen_target_var.get()
		instrument = self.chosen_instrument_var_post.get()
		@@ -1649,7 +1661,7 @@ class Frame_Gofio:
		[
		"python3", str(Path(self.path_default, "DataReductionGIANOB", "fromheader.py")),
		self.path_fromheader, night, str(self.target_hjd0), str(self.target_period),
		str(self.target_limph), str(separate_A_B), self.path_default
		str(self.target_limph), str(separate_A_B), str(obs_mode), str(instrument), self.path_default
		], stderr=subprocess.STDOUT, universal_newlines=True
		)
		self.gui.window.after(500, self.check_proc_from_header)
		@@ -1688,8 +1700,12 @@ class Frame_Gofio:
		instrument)
		# Get the night identifier from the text widget, stripping any extra whitespace.
		separate_A_B = self.chosen_separation_var.get()
		night_str = self.night.get("1.0", tk.END).strip() # Determines if A and B channels are treated separately.
		obs_mode = self.chosen_obs_mode_var_post.get()
		night_str = self.night.get("1.0", tk.END).strip()
		if separate_A_B:
		if obs_mode == "Stare":
		messagebox.showinfo("Incompatibility", "Stare mode is not compatible with separation of A and B")
		return
		night_str += "AB"
		# Retrieve additional parameters from the GUI.
		niter = int(self.niter.get())
		@@ -1716,6 +1732,8 @@ class Frame_Gofio:
		pickle.dump(use_gauss, fo)
		pickle.dump(numpy_pearson, fo)
		pickle.dump(self.chosen_no_alignment_wcal_var.get(), fo)
		pickle.dump(instrument, fo)
		pickle.dump(obs_mode, fo)
		# Determine the names of the output PDF files.
		# For a specific instrument "gianob" with separate channels, use distinct filenames for A and B.
		if separate_A_B and instrument in ["gianob", "criresp"]:
		@@ -1752,13 +1770,18 @@ class Frame_Gofio:
		yaml_file = yaml.safe_load(f)
		pixel_dv = yaml_file["pixel_dv"]
		path_instrument = str(
		Path(self.path_target, target, "HR_Instruments", self.chosen_rad_mode_var_post.get(), instrument))
		Path(self.path_target, target, "HR_Instruments", self.chosen_rad_mode_var_post.get(), instrument)
		)
		separate_A_B = self.chosen_separation_var.get()
		night_str = self.night.get("1.0", tk.END).strip() # Determines if A and B channels are treated separately.
		minimum_lines = int(self.minimum_lines.get())
		maximum_elements = int(self.maximum_elements.get())
		threshold_km_s = float(self.threshold_km_s.get())
		obs_mode = self.chosen_obs_mode_var_post.get()
		night_str = self.night.get("1.0", tk.END).strip()
		if separate_A_B:
		if obs_mode == "Stare":
		messagebox.showinfo("Incompatibility", "Stare mode is not compatible with separation of A and B")
		return
		night_str += "AB"
		# showf = self.chosen_show_wcal_var.get()
		starf = self.chosen_star_wcal_var.get()
		@@ -1791,7 +1814,7 @@ class Frame_Gofio:
		return
		pathf = str(Path(path_instrument,
		night_str)) # + os.sep + self.chosen_flat_var_post.get() + os.sep + yaml_file["files_type"] + os.sep
		if separate_A_B and instrument in ["gianob", "criresp"]:
		if separate_A_B and instrument in ["gianob", "criresp"] and obs_mode == "Nodding":
		specf = fits.open(str(Path(pathf, "A_aligned.fits")))
		wlenf = fits.open(str(Path(pathf, "A_wlen.fits")))
		with open(str(Path(pathf, "A_coefficient_pol.pkl")), "rb") as fo:
		@@ -1832,8 +1855,12 @@ class Frame_Gofio:
		path_instrument = str(
		Path(self.path_target, target, "HR_Instruments", self.chosen_rad_mode_var_post.get(), instrument))
		separate_A_B = self.chosen_separation_var.get()
		night_str = self.night.get("1.0", tk.END).strip() # Determines if A and B channels are treated separately.
		obs_mode = self.chosen_obs_mode_var_post.get()
		night_str = self.night.get("1.0", tk.END).strip()
		if separate_A_B:
		if obs_mode == "Stare":
		messagebox.showinfo("Incompatibility", "Stare mode is not compatible with separation of A and B")
		return
		night_str += "AB"
		starf = self.chosen_star_test_var.get()
		use_plank = self.chosen_planck_test_var.get()

DataReductionGIANOB/fromheader.py

+4 −2

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ from astropy.time import Time
		import scipy.io as sio
		from pathlib import Path

		path_default = sys.argv[7]
		path_default = sys.argv[9]
		sys.path.append(path_default)
		os.chdir(path_default)
		from barycorrpy_fold import utc_tdb
		@@ -21,8 +21,10 @@ target_hjd0 = float(sys.argv[3])
		target_period = float(sys.argv[4])
		target_limph = float(sys.argv[5])
		separate_A_B = int(sys.argv[6])
		obs_mode = sys.argv[7]
		instrument = sys.argv[8]
		print("STARTING fromheader")
		if separate_A_B:
		if separate_A_B and obs_mode == "Nodding":
		prefix = ["A_", "B_"]
		else:
		prefix = [""]

DataReductionGIANOB/procedure_align_pixel.py

+28 −29

Original line number	Diff line number	Diff line
		@@ -235,36 +235,33 @@ def procedure_align_pixel_opt(dataoff, niterf, path, prefix, interpol=None, gaus
		title_plot = ""
		# Compute shift statistics based on the alignment method.
		if interpol is not None:
		if separate_A_B:
		meanf = np.mean(shift[order_i, :])
		rmsf = np.std(shift[order_i, :])
		else:
		meanA = np.mean(shift[order_i, odd])
		rmsA = np.std(shift[order_i, odd])
		meanB = np.mean(shift[order_i, even])
		rmsB = np.std(shift[order_i, even])
		used_shift = shift
		title_plot = f"Ord {order_i} Drift (Interpol)"
		elif gauss is not None:
		if separate_A_B:
		meanf = np.mean(shift_fit[order_i, :])
		rmsf = np.std(shift_fit[order_i, :])
		else:
		meanA = np.mean(shift_fit[order_i, odd])
		rmsA = np.std(shift_fit[order_i, odd])
		meanB = np.mean(shift_fit[order_i, even])
		rmsB = np.std(shift_fit[order_i, even])
		used_shift = shift_fit
		title_plot = f"Ord {order_i} - Drift (Gaussian Fit)"
		# Plot the results.
		if separate_A_B:
		col_tr = "r" if prefix == "A_" else "b"
		trend = "A" if prefix == "A_" else "B"
		if separate_A_B or obs_mode == "Stare":
		if obs_mode == "Stare":
		trend = "Stare"
		col_tr = "r"
		else:
		if prefix == "A_":
		trend = "A"
		col_tr = "r"
		else:
		trend = "B"
		col_tr = "b"
		meanf = np.mean(used_shift[order_i, :])
		rmsf = np.std(used_shift[order_i, :])
		suptitle = f"Mean{trend} = {meanf:.2f} RMS = {rmsf:.3f}"
		plt.plot(full, shift[order_i, full], col_tr + "*", label=f"Shift {trend}")
		plt.axhline(meanf, color=col_tr, label=f"Mean {trend}")
		plt.xlabel("Image [#]")
		plt.ylabel("Shift [pixel]")
		plt.title(title_plot)
		plt.suptitle(f"Mean{trend} = {meanf:.2f} RMS = {rmsf:.3f}")
		else:
		meanA = np.mean(used_shift[order_i, odd])
		rmsA = np.std(used_shift[order_i, odd])
		meanB = np.mean(used_shift[order_i, even])
		rmsB = np.std(used_shift[order_i, even])
		suptitle = f"MeanA = {meanA:.2f} RMS = {rmsA:.3f} ; MeanB = {meanB:.2f} RMS = {rmsB:.3f}"
		plt.plot(odd, shift[order_i, odd], "b*", label="Odd images")
		plt.plot(even, shift[order_i, even], "r*", label="Even images")
		plt.axhline(meanA, color="b", label="MeanA")
		@@ -272,7 +269,7 @@ def procedure_align_pixel_opt(dataoff, niterf, path, prefix, interpol=None, gaus
		plt.xlabel("Image [#]")
		plt.ylabel("Shift [pixel]")
		plt.title(title_plot)
		plt.suptitle(f"MeanA = {meanA:.2f} RMS = {rmsA:.3f} ; MeanB = {meanB:.2f} RMS = {rmsB:.3f}")
		plt.suptitle(suptitle)
		plt.legend(bbox_to_anchor=(1.05, 1), loc='upper left', borderaxespad=0.)
		# Adjust right margin to make room for the legend.
		plt.subplots_adjust(right=0.75)
		@@ -314,8 +311,10 @@ with open(file_pkl, "rb") as fo:
		gaussf = pickle.load(fo)
		numpy_pearson_pkl = pickle.load(fo)
		no_alignment = pickle.load(fo)
		instrument = pickle.load(fo)
		obs_mode = pickle.load(fo)
		#
		if separate_A_B:
		if separate_A_B and obs_mode == "Nodding":
		if no_alignment:
		os.system("cp " + pathf + "/A_noaligned.fits " + pathf + "/A_aligned.fits")
		os.system("cp " + pathf + "/B_noaligned.fits " + pathf + "/B_aligned.fits")