rename spectrogram in spectrogram_data

spectractor/extractor/extractor.py

@@ -120,7 +120,7 @@ def __init__(self, spectrum, amplitude_priors_method="noprior", verbose=False, p
         # crop data to fit faster
         self.lambdas = self.spectrum.lambdas
         self.bgd_width = parameters.PIXWIDTH_BACKGROUND + parameters.PIXDIST_BACKGROUND - parameters.PIXWIDTH_SIGNAL
-        self.data = spectrum.spectrogram[self.bgd_width:-self.bgd_width, :]
+        self.data = spectrum.spectrogram_data[self.bgd_width:-self.bgd_width, :]
         self.err = spectrum.spectrogram_err[self.bgd_width:-self.bgd_width, :]
         self.bgd = spectrum.spectrogram_bgd[self.bgd_width:-self.bgd_width, :]
         self.bgd_flat = self.bgd.flatten()
@@ -643,7 +643,7 @@ def plot_spectrogram_comparison_simple(self, ax, title='', extent=None, dispersi
 
         lambdas = self.spectrum.lambdas
         sub = np.where((lambdas > parameters.LAMBDA_MIN) & (lambdas < parameters.LAMBDA_MAX))[0]
-        sub = np.where(sub < self.spectrum.spectrogram.shape[1])[0]
+        sub = np.where(sub < self.spectrum.spectrogram_data.shape[1])[0]
         data = (data + self.bgd_flat).reshape((self.Ny, self.Nx))
         err = self.err.reshape((self.Ny, self.Nx))
         model = (self.model + self.params["B"] * self.bgd_flat).reshape((self.Ny, self.Nx))
@@ -1411,7 +1411,7 @@ def bgd_model_func(x, y):
                    f'\n\tNew target position in spectrogram frame: {target_pixcoords_spectrogram}')
 
     # Save results
-    spectrum.spectrogram = data
+    spectrum.spectrogram_data = data
     spectrum.spectrogram_err = err
     spectrum.spectrogram_x0 = target_pixcoords_spectrogram[0]
     spectrum.spectrogram_y0 = target_pixcoords_spectrogram[1]
@@ -1491,7 +1491,7 @@ def run_spectrogram_deconvolution_psf2d(spectrum, bgd_model_func):
     """
     my_logger = set_logger(__name__)
     s = spectrum.chromatic_psf
-    Ny, Nx = spectrum.spectrogram.shape
+    Ny, Nx = spectrum.spectrogram_data.shape
 
     # build 1D priors
     Dx_rot = np.copy(s.table['Dx'])
@@ -1525,7 +1525,7 @@ def run_spectrogram_deconvolution_psf2d(spectrum, bgd_model_func):
                     f"\n{s.table[['amplitude', 'x_c', 'y_c', 'Dx', 'Dy', 'Dy_disp_axis']]}")
     my_logger.info(f'\n\tStart ChromaticPSF polynomial fit with '
                    f'mode={mode} and amplitude_priors_method={method}...')
-    data = spectrum.spectrogram
+    data = spectrum.spectrogram_data
     err = spectrum.spectrogram_err
 
     my_logger.info('\n\t  ======================= ChromaticPSF2D polynomial fit  =============================')

spectractor/extractor/spectrum.py

@@ -133,7 +133,7 @@ class Spectrum:
         Outside relative humidity in fraction of one.
     throughput: callable
         Instrumental throughput of the telescope.
-    spectrogram: array
+    spectrogram_data: array
         Spectrogram 2D image in image units.
     spectrogram_bgd: array
         Estimated 2D background fitted below the spectrogram in image units.
@@ -237,7 +237,7 @@ def __init__(self, file_name="", image=None, order=1, target=None, config="", fa
         self.rotation_angle = 0
         self.parallactic_angle = None
         self.camera_angle = 0
-        self.spectrogram = None
+        self.spectrogram_data = None
         self.spectrogram_bgd = None
         self.spectrogram_bgd_rms = None
         self.spectrogram_err = None
@@ -504,7 +504,7 @@ def plot_spectrogram(self, ax=None, scale="lin", title="", units="Image units",
         if ax is None:
             plt.figure(figsize=figsize)
             ax = plt.gca()
-        data = np.copy(self.spectrogram)
+        data = np.copy(self.spectrogram_data)
         if plot_stats:
             data = np.copy(self.spectrogram_err)
         plot_image_simple(ax, data=data, scale=scale, title=title, units=units, cax=cax,
@@ -587,7 +587,7 @@ def generate_axes(fig):
         widthPlot.set_xlabel(r'$\lambda$ [nm]')
         widthPlot.grid()
 
-        spectrogram = np.copy(self.spectrogram)
+        spectrogram = np.copy(self.spectrogram_data)
         res = self.spectrogram_residuals.reshape((-1, self.spectrogram_Nx))
         std = np.std(res)
         if spectrogram.shape[0] != res.shape[0]:
@@ -688,7 +688,7 @@ def save_spectrum(self, output_file_name, overwrite=False):
                 hdus[extname].header["IM_X0"] = self.target.image_x0
                 hdus[extname].header["IM_Y0"] = self.target.image_y0
             elif extname == "S_DATA":
-                hdus[extname].data = self.spectrogram
+                hdus[extname].data = self.spectrogram_data
                 hdus[extname].header['UNIT1'] = self.units
             elif extname == "S_ERR":
                 hdus[extname].data = self.spectrogram_err
@@ -784,7 +784,7 @@ def save_spectrogram(self, output_file_name, overwrite=False):  # pragma: no cov
         hdu6 = fits.ImageHDU()
         hdu6.header["EXTNAME"] = "S_RES"
         hdu1.header = self.header
-        hdu1.data = self.spectrogram
+        hdu1.data = self.spectrogram_data
         hdu2.data = self.spectrogram_err
         hdu3.data = self.spectrogram_bgd
         hdu4.data = self.spectrogram_bgd_rms
@@ -961,7 +961,7 @@ def load_spectrum_older_24(self, input_file_name, spectrogram_file_name_override
                             self.target.image_y0 = float(hdu_list["ORDER0"].header["IM_Y0"])
                 # load spectrogram info
                 if len(hdu_list) > 4:
-                    self.spectrogram = hdu_list["S_DATA"].data
+                    self.spectrogram_data = hdu_list["S_DATA"].data
                     self.spectrogram_err = hdu_list["S_ERR"].data
                     self.spectrogram_bgd = hdu_list["S_BGD"].data
                     if len(hdu_list) > 7:
@@ -1074,7 +1074,7 @@ def load_spectrum_latest(self, input_file_name):
                 self.target.image_x0 = float(hdu_list["ORDER0"].header["IM_X0"])
                 self.target.image_y0 = float(hdu_list["ORDER0"].header["IM_Y0"])
                 # load spectrogram info
-                self.spectrogram = hdu_list["S_DATA"].data
+                self.spectrogram_data = hdu_list["S_DATA"].data
                 self.spectrogram_err = hdu_list["S_ERR"].data
                 self.spectrogram_bgd = hdu_list["S_BGD"].data
                 self.spectrogram_bgd_rms = hdu_list["S_BGD_ER"].data
@@ -1100,7 +1100,7 @@ def load_spectrogram(self, input_file_name):  # pragma: no cover
         if os.path.isfile(input_file_name):
             with fits.open(input_file_name) as hdu_list:
                 header = hdu_list[0].header
-                self.spectrogram = hdu_list[0].data
+                self.spectrogram_data = hdu_list[0].data
                 self.spectrogram_err = hdu_list[1].data
                 self.spectrogram_bgd = hdu_list[2].data
                 if len(hdu_list) > 3:

spectractor/fit/fit_spectrogram.py

@@ -125,8 +125,8 @@ def __init__(self, spectrum, atmgrid_file_name="", fit_angstrom_exponent=False,
         if self.spectrum.spectrogram_Ny > 2 * parameters.PIXDIST_BACKGROUND:
             self.crop_spectrogram()
         self.lambdas = self.spectrum.lambdas
-        self.Ny, self.Nx = self.spectrum.spectrogram.shape
-        self.data = self.spectrum.spectrogram.flatten()
+        self.Ny, self.Nx = self.spectrum.spectrogram_data.shape
+        self.data = self.spectrum.spectrogram_data.flatten()
         self.err = self.spectrum.spectrogram_err.flatten()
         self.fit_angstrom_exponent = fit_angstrom_exponent
 
@@ -164,11 +164,11 @@ def crop_spectrogram(self):
         self.spectrum.spectrogram_ymax = self.spectrum.spectrogram_ymax - bgd_width
         self.spectrum.spectrogram_ymin += bgd_width
         self.spectrum.spectrogram_bgd = self.spectrum.spectrogram_bgd[bgd_width:-bgd_width, :]
-        self.spectrum.spectrogram = self.spectrum.spectrogram[bgd_width:-bgd_width, :]
+        self.spectrum.spectrogram_data = self.spectrum.spectrogram_data[bgd_width:-bgd_width, :]
         self.spectrum.spectrogram_err = self.spectrum.spectrogram_err[bgd_width:-bgd_width, :]
         self.spectrum.spectrogram_y0 -= bgd_width
         self.spectrum.chromatic_psf.y0 -= bgd_width
-        self.spectrum.spectrogram_Ny, self.spectrum.spectrogram_Nx = self.spectrum.spectrogram.shape
+        self.spectrum.spectrogram_Ny, self.spectrum.spectrogram_Nx = self.spectrum.spectrogram_data.shape
         self.spectrum.chromatic_psf.table["y_c"] -= bgd_width
         self.my_logger.debug(f'\n\tSize of the spectrogram region after cropping: '
                              f'({self.spectrum.spectrogram_Nx},{self.spectrum.spectrogram_Ny})')

spectractor/simulation/image_simulation.py

@@ -325,10 +325,10 @@ def compute(self, star, background, spectrogram, starfield=None):
         yy, xx = np.mgrid[0:parameters.CCD_IMSIZE:1, 0:parameters.CCD_IMSIZE:1]
         self.data = star.psf.evaluate(np.array([xx, yy])) + background.model()
         if spectrogram.full_image:
-            self.data[spectrogram.spectrogram_ymin:spectrogram.spectrogram_ymax, :] += spectrogram.spectrogram
+            self.data[spectrogram.spectrogram_ymin:spectrogram.spectrogram_ymax, :] += spectrogram.spectrogram_data
         else:
             self.data[spectrogram.spectrogram_ymin:spectrogram.spectrogram_ymax,
-                      spectrogram.spectrogram_xmin:spectrogram.spectrogram_xmax] += spectrogram.spectrogram
+                      spectrogram.spectrogram_xmin:spectrogram.spectrogram_xmax] += spectrogram.spectrogram_data
         # - spectrogram.spectrogram_bgd)
         if starfield is not None:
             self.data += starfield.model(xx, yy)