Lighter output

spectractor/astrometry.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import warnings
 from copy import deepcopy
 import subprocess
 import shutil
@@ -153,7 +154,9 @@ def get_gaia_coords_after_proper_motion(gaia_catalog, date_obs):
                               np.array(gaia_catalog['dec']) * np.pi / 180),
                           pm_dec=gaia_catalog['pmdec'].filled(0),
                           distance=Distance(parallax=parallax * u.mas, allow_negative=True))
-    gaia_coords_after_proper_motion = gaia_stars.apply_space_motion(new_obstime=Time(date_obs))
+    with warnings.catch_warnings():
+        warnings.filterwarnings("ignore", message=".*distance overridden.*", category=Warning)
+        gaia_coords_after_proper_motion = gaia_stars.apply_space_motion(new_obstime=Time(date_obs))
     return gaia_coords_after_proper_motion
 
 

spectractor/config.py

@@ -110,16 +110,19 @@ def load_config(config_filename, rebin=True):
     """
     my_logger = set_logger(__name__)
     mypath = os.path.dirname(__file__)
-    if not os.path.isfile(os.path.join(mypath, parameters.CONFIG_DIR, "default.ini")):
+    # Use the bundled config/ directory relative to this file, not parameters.CONFIG_DIR
+    # (parameters.CONFIG_DIR can be overwritten at runtime, e.g. by loading a spectrum FITS file)
+    config_dir = os.path.join(mypath, "config")
+    if not os.path.isfile(os.path.join(config_dir, "default.ini")):
         raise FileNotFoundError('Config file default.ini does not exist.')
     # Load the configuration file
-    from_config_to_parameters(os.path.join(mypath, parameters.CONFIG_DIR, "default.ini"))
+    from_config_to_parameters(os.path.join(config_dir, "default.ini"))
 
     if not os.path.isfile(config_filename):
-        if not os.path.isfile(os.path.join(mypath, parameters.CONFIG_DIR, config_filename)):
+        if not os.path.isfile(os.path.join(config_dir, config_filename)):
             raise FileNotFoundError(f'Config file {config_filename} does not exist.')
         else:
-            config_filename = os.path.join(mypath, parameters.CONFIG_DIR, config_filename)
+            config_filename = os.path.join(config_dir, config_filename)
     # Load the configuration file
     my_logger.info(f"\n\tLoading {config_filename} with {parameters.VERBOSE=}...")
     from_config_to_parameters(config_filename)
@@ -160,7 +163,7 @@ def load_config(config_filename, rebin=True):
         txt = ""
         # default.ini should be the config file with the most parameters
         config = configparser.ConfigParser()
-        config.read(os.path.join(mypath, parameters.CONFIG_DIR, "default.ini"))
+        config.read(os.path.join(config_dir, "default.ini"))
         for section in config.sections():
             txt += f"Section: {section}\n"
             for options in config.options(section):

spectractor/extractor/dispersers/HoloAmAg_7.5/NOTES

@@ -0,0 +1,6 @@
+- ratio_order_2over1.txt: fit of a model to Sylvie's data from CTIO spectra observed with a blue filter
+- transmission.txt: fit on CTIO data 2017/30/05 normalized with multispectra_Thor300_HD111980_CTIO_throughput_prod7.5.txt
+../CTIODataJune2017_reduced_RG715_v2_prod7.5/data_30may17_A2=0.1/multispectra_HoloAmAg_HD111980_HoloAmAg_throughput.txt
+(see jupyter notebook Multispectra.ipynb)
+- N.txt: interpolation of Neff estimated with CTIO scan of the hologram
+- hologram_*.txt: same

spectractor/extractor/dispersers/Thor300_7.5/NOTES

@@ -0,0 +1,5 @@
+- ratio_order_2over1.txt: fit of a model to Sylvie's data from CTIO spectra observed with a blue filter
+- transmission.txt: model best fit on a mix of measurements coming from the Thorlabs data sheet (300-450nm), Laurent's measurement
+at DCCD=200mm (450-920nm), Arthur's measurement at DCCD=58mm (1000>920nm) and Thorlabs data sheet again (>1000nm)
+(see jupyter notebook Disperser_efficiencies.ipynb)
+- N.txt: estimation with CTIO data

spectractor/extractor/dispersers/blue300lpmm_qn1_old/NOTES

@@ -0,0 +1 @@
+Blue quad notch filter

spectractor/extractor/spectrum.py

@@ -633,7 +633,7 @@ def save_spectrum(self, output_file_name, overwrite=False):
             Path of the output fits file.
         overwrite: bool
             If True overwrite the output file if needed (default: False).
-
+            
         Examples
         --------
         >>> import os
@@ -677,7 +677,8 @@ def save_spectrum(self, output_file_name, overwrite=False):
             hdu1.header[header_key] = value
             # print(f"Set header key {header_key} to {value} from attr {attribute}")
 
-        extnames = ["SPECTRUM", "SPEC_COV", "ORDER2", "ORDER0"]  # spectrum data
+        extnames = ["SPECTRUM", "SPEC_COV", "ORDER2"]  # spectrum data
+        extnames += ["ORDER0"]  # spectrum order0 timestamps
         extnames += ["S_DATA", "S_ERR", "S_BGD", "S_BGD_ER", "S_FIT", "S_RES", "S_FLAT", "S_STAR", "S_MASK"]
         extnames += ["PSF_TAB"]  # PSF parameter table
         extnames += ["LINES"]  # spectroscopic line table
@@ -1095,9 +1096,9 @@ def load_spectrum_latest(self, input_file_name):
 
         if not self.fast_load:
             with (fits.open(input_file_name) as hdu_list):
-                # load other spectrum info
                 self.cov_matrix = hdu_list["SPEC_COV"].data
                 _, self.data_next_order, self.err_next_order = hdu_list["ORDER2"].data
+                # load other spectrum info
                 self.target.image = hdu_list["ORDER0"].data
                 self.target.image_x0 = float(hdu_list["ORDER0"].header["IM_X0"])
                 self.target.image_y0 = float(hdu_list["ORDER0"].header["IM_Y0"])
@@ -1117,7 +1118,7 @@ def load_spectrum_latest(self, input_file_name):
                     if self.spectrogram_mask is not None:
                         self.spectrogram_mask = self.spectrogram_mask.astype(bool)
                 self.chromatic_psf.init_from_table(Table.read(hdu_list["PSF_TAB"]),
-                                                   saturation=self.spectrogram_saturation)
+                                                saturation=self.spectrogram_saturation)
                 self.lines.table = Table.read(hdu_list["LINES"], unit_parse_strict="silent")
 
     def load_spectrogram(self, input_file_name):  # pragma: no cover

spectractor/tools.py

@@ -52,25 +52,6 @@ def _safe_tight_layout(self, *args, **kwargs):
 plt.Figure.tight_layout = _safe_tight_layout
 
 
-# Monkey-patch matplotlib tight_layout to handle LaTeX parsing errors
-# This is needed for matplotlib versions in LSST environment that don't fully support LaTeX
-_original_tight_layout = plt.Figure.tight_layout
-
-
-def _safe_tight_layout(self, *args, **kwargs):
-    """Wrapper for Figure.tight_layout that catches ValueError from LaTeX parsing errors."""
-    try:
-        return _original_tight_layout(self, *args, **kwargs)
-    except ValueError:
-        # Silently ignore LaTeX parsing errors in tight_layout
-        # This typically happens with Greek letters and complex math expressions
-        # in axis labels or titles when matplotlib's mathtext parser has issues
-        pass
-
-
-plt.Figure.tight_layout = _safe_tight_layout
-
-
 # do not increase speed:
 # @njit(fastmath=True, cache=True)
 def gauss(x, A, x0, sigma):
@@ -1896,11 +1877,11 @@ def plot_image_simple(ax, data, scale="lin", title="", units="Image units", cmap
         >>> if parameters.DISPLAY: plt.show()
     """
     if cmap is not None and isinstance(cmap, str):
-        colormap = copy.copy(cm.get_cmap(cmap))
+        colormap = copy.copy(matplotlib.colormaps[cmap])
     elif isinstance(cmap, matplotlib.colors.Colormap):
         colormap = cmap
     else:
-        colormap = copy.copy(cm.get_cmap('viridis'))
+        colormap = copy.copy(matplotlib.colormaps['viridis'])
     cmap_nan = copy.copy(colormap)
     cmap_nan.set_bad(color='lightgrey')