Fix a few typos

README.md

@@ -5,18 +5,18 @@
 
 # Spectractor
 
-The goal of Spectractor is to measure the atmospheric transmission and intempt extracting spectra from slitless spectrophotometric images. It has been optimized on CTIO images but can be configured to analyse any kind of slitless data that contains the order 0 and the order 1 of a spectrum. In particular it can  be used to estimate the atmospheric transmission of the LSST site using the dedicated  Auxiliary Telescope. 
+The goal of Spectractor is to measure the atmospheric transmission and attempt to extract spectra from slitless spectrophotometric images. It has been optimized on CTIO images but can be configured to analyse any kind of slitless data that contains the order 0 and the order 1 of a spectrum. In particular it can be used to estimate the atmospheric transmission of the LSST site using the dedicated Auxiliary Telescope.
 
-Spectractor is structured in three subpackages: 
-- `spectractor.extractor`: extracts as most information as possible from a slitless data  image, as the amplitude of the spectrum, the PSF evolution with the wavelength, the pixel to wavelength calibration, an estimate of the background under the spectrum, the position of the order 0;
-- `spectractor.simulation`: contains all the tools to simulate a spectrogram, as the atmospheric transmission simulation, the inclusion of instrumental throughput, the simulation of mock  slitless  data images;
+Spectractor is structured in three subpackages:
+- `spectractor.extractor`: extracts as much information as possible from a slitless data  image, such as the amplitude of the spectrum, the PSF evolution with the wavelength, the pixel to wavelength calibration, an estimate of the background under the spectrum, and the position of the order 0;
+- `spectractor.simulation`: contains all the tools to simulate a spectrogram, such as atmospheric transmission simulation, the inclusion of instrumental throughput, the simulation of mock slitless data images;
 - `spectractor.fit`: compares the extracted data with simulations to estimate the atmospheric transmission and refine the spectral extraction.
 
-Some submodules complete the structures with generic functions:
-- `spectractor.parameters`: contains all the global parameters of Spectractor to set its general behaviour, the instrumental characteritics, etc;
+Some submodules complete the structure with generic functions:
+- `spectractor.parameters`: contains all the global parameters of Spectractor to set its general behaviour, the instrumental characteristics, etc;
 - `spectractor.config`: tools to read config `.ini` text files and set the global parameters;
 - `spectractor.logbook`: tools to read logbook `.csv` text files and get some metadata relative to the data images that are not contained in the header;
-- `spectractor.tools`: contains generic functions shared by all  the subpackages (fitting procedures, plotting functions, etc).
+- `spectractor.tools`: contains generic functions shared by all the subpackages (fitting procedures, plotting functions, etc).
 
 ## Installation
 
@@ -50,9 +50,9 @@ Spectractor is able to perform parameter fits using the MCMC library [emcee](htt
 ## Basic extraction
 
 The main file is `spectractor/extractor/extractor.py` with the function `Spectractor`. It extracts the spectrum from a science data image (deflatted, debiased), given:
-- the path to the FITS image from which to extract the image, 
+- the path to the FITS image from which to extract the image,
 - the path of the output directory to save the extracted spectrum (created automatically if it does not exist yet),
-- the rough pr exact position of the object in the image (in pixels),
+- the rough or exact position of the object in the image (in pixels),
 - the name of the disperser (as it is named in the `spectractor/extractor/dispersers/` folder),
 - the name of the config .ini file,
 - optionally the name of the target (to search for the extra-atmospheric spectrum if available).
@@ -66,7 +66,7 @@ config = "./config/ctio.ini"
 target = "HD111980"
 ```
 
-Then the spectrum is simply extracted from the image and saved in a new fits file using the `Spectractor` function:
+Then the spectrum is simply extracted from the image and saved in a new FITS file using the `Spectractor` function:
 ```
 spectrum = Spectractor(filename, output_directory, guess=guess, target_label=target, disperser_label=disperser_label, config=config)
 ```

spectractor/astrometry.py

@@ -371,7 +371,7 @@ def load_gaia_catalog_around_target(self):
     def load_sources_from_file(self):
         """Load the sources from the class associated self.sources_file_name file.
 
-        By default, the creation of an Astrometry class instance try to load the default
+        By default, the creation of an Astrometry class instance tries to load the default
         source file if it exists.
 
         Returns
@@ -397,7 +397,7 @@ def load_sources_from_file(self):
         return sources
 
     def get_target_pixel_position(self):
-        """Gives the principal targetted object position in pixels in the image given the WCS.
+        """Gives the principal targeted object position in pixels in the image given the WCS.
         The object proper motion is taken into account.
 
         Returns
@@ -495,7 +495,7 @@ def get_quad_stars_pixel_positions(self):
             if np.sum(coord) > 0:
                 coords.append(coord)
         if len(coords) < 4:
-            self.my_logger.warning(f"\n\tOnly {len(coords)} calibration stars has been extracted from "
+            self.my_logger.warning(f"\n\tOnly {len(coords)} calibration stars have been extracted from "
                                    f"{self.match_file_name}, with positions {coords}. "
                                    f"A quad of at least 4 stars is expected. "
                                    f"Please check {self.match_file_name}.")
@@ -754,7 +754,7 @@ def plot_astrometry_shifts(self, vmax=3, margin=parameters.CCD_IMSIZE):
 
     def set_constraints(self, min_stars=100, flux_log10_threshold=0.1, min_range=3 * u.arcsec, max_range=5 * u.arcmin,
                         max_sep=1 * u.arcsec):
-        """Gives a boolean array for sources that respect certain criterai (see below).
+        """Gives a boolean array for sources that respect certain criteria (see below).
 
         Parameters
         ----------

spectractor/config.py

@@ -20,7 +20,7 @@
 
 
 def from_config_to_dict(path):
-    """Convert config file keywords into dictionnary.
+    """Convert config file keywords into dictionary.
 
     Parameters
     ----------
@@ -243,7 +243,6 @@ def set_logger(logger):
     >>> parameters.DEBUG = True
     >>> test = Test()
     >>> test.log()
-    
     """
     my_logger = logging.getLogger(logger)
     my_format = "%(asctime)-20s %(name)-10s %(funcName)-20s %(levelname)-6s %(message)s"

spectractor/config/auxtel.ini

@@ -38,7 +38,7 @@ OBS_EPOCH = J2000.0
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
+OBS_FULL_INSTRUMENT_TRANSMISSION = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
 # systematics on the instrument transmission
 OBS_TRANSMISSION_SYSTEMATICS = 0.005
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system
@@ -121,7 +121,7 @@ PSF_PIXEL_STEP_TRANSVERSE_FIT = 50
 PSF_FWHM_CLIP = 2
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 7

spectractor/config/auxtel_quicklook.ini

@@ -28,7 +28,7 @@ OBS_EPOCH = J2000.0
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
+OBS_FULL_INSTRUMENT_TRANSMISSION = multispectra_holo4_003_HD142331_AuxTel_throughput.txt
 # systematics on the instrument transmission
 OBS_TRANSMISSION_SYSTEMATICS = 0.005
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system
@@ -109,7 +109,7 @@ PSF_FIT_REG_PARAM = 1
 PSF_PIXEL_STEP_TRANSVERSE_FIT = 50
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 7

spectractor/config/ctio.ini

@@ -34,7 +34,7 @@ OBS_EPOCH = J2000.0
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = multispectra_Thor300_HD111980_CTIO_throughput_prod7.5.4.txt
+OBS_FULL_INSTRUMENT_TRANSMISSION = multispectra_Thor300_HD111980_CTIO_throughput_prod7.5.4.txt
 # systematics on the instrument transmission
 OBS_TRANSMISSION_SYSTEMATICS = 0.0
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system
@@ -113,7 +113,7 @@ PSF_PIXEL_STEP_TRANSVERSE_FIT = 10
 PSF_FWHM_CLIP = 2
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 7

spectractor/config/default.ini

@@ -38,7 +38,7 @@ OBS_EPOCH = J2000.0
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = ctio_throughput_300517_v2.txt
+OBS_FULL_INSTRUMENT_TRANSMISSION = ctio_throughput_300517_v2.txt
 # systematics on the instrument transmission
 OBS_TRANSMISSION_SYSTEMATICS = 0
 
@@ -125,7 +125,7 @@ PSF_FIT_REG_PARAM = 0.01
 PSF_POLY_TYPE = polynomial
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 7

spectractor/config/lpnhe.ini

@@ -89,7 +89,7 @@ PSF_FIT_REG_PARAM = 0.01
 PSF_PIXEL_STEP_TRANSVERSE_FIT = 10
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 3

spectractor/config/stardice.ini

@@ -34,7 +34,7 @@ OBS_EPOCH = J2000.0
 # observed object to choose between STAR, HG-AR, MONOCHROMATOR
 OBS_OBJECT_TYPE = STAR
 # full instrument transmission file
-OBS_FULL_INSTRUMENT_TRANSMISSON = StarDice_EMPTY_response_75um_pinhole.txt
+OBS_FULL_INSTRUMENT_TRANSMISSION = StarDice_EMPTY_response_75um_pinhole.txt
 # systematics on the instrument transmission
 OBS_TRANSMISSION_SYSTEMATICS = 0.005
 # Camera (x,y) rotation angle with respect to (north-up, east-left) system
@@ -117,7 +117,7 @@ PSF_PIXEL_STEP_TRANSVERSE_FIT = 10
 PSF_FWHM_CLIP = 2
 
 [detection line algorithm parameters]
-# order of the background polynome to fit
+# order of the background polynomial to fit
 CALIB_BGD_ORDER = 3
 # half range to look for local extrema in pixels around tabulated line values
 CALIB_PEAK_WIDTH = 7

spectractor/extractor/chromaticpsf.py

@@ -113,7 +113,7 @@ def init_from_table(self, table, saturation=None):
         self.saturation = saturation
         if saturation is None:
             self.saturation = 1e20
-            self.my_logger.warning(f"\n\tSaturation level should be given to instanciate the ChromaticPSF "
+            self.my_logger.warning(f"\n\tSaturation level should be given to instantiate the ChromaticPSF "
                                    f"object. self.saturation is set arbitrarily to 1e20. Good luck.")
         for name in self.psf.params.labels:
             if "amplitude" in name:
@@ -619,8 +619,8 @@ def convolve_psf_cube_masked(psf_cube_masked):
 
     @staticmethod
     def set_rectangular_boundaries(psf_cube_masked):
-        """Compute the ChromaticPSF computation boundaries, as a dictionnary of integers giving
-        the `"xmin"`, `"xmax"`, `"ymin"` and `"ymax"` edges where to compute the PSF for each wavelength.
+        """Compute the ChromaticPSF computation boundaries, as a dictionary of integers giving
+        the `"xmin"`, `"xmax"`, `"ymin"` and `"ymax"` edges where the PSF is computed for each wavelength.
         True regions are rectangular after this operation. The `psf_cube_masked` cube is updated accordingly and returned.
 
         Parameters
@@ -631,7 +631,7 @@ def set_rectangular_boundaries(psf_cube_masked):
         Returns
         -------
         boundaries: dict
-            The dictionnary of PSF edges per wavelength.
+            The dictionary of PSF edges per wavelength.
         psf_cube_masked: np.ndarray
             Updated cube of boolean values where `psf_cube` cube is positive, eventually convolved.
 
@@ -684,12 +684,12 @@ def set_rectangular_boundaries(psf_cube_masked):
         return boundaries, psf_cube_masked
 
     def get_sparse_indices(self, boundaries):
-        """Methods that returns the indices to build sparse matrices from rectangular `boundaries`.
+        """Method that returns the indices to build sparse matrices from rectangular `boundaries`.
 
         Parameters
         ----------
         boundaries: dict
-            The dictionnary of PSF edges per wavelength.
+            The dictionary of PSF edges per wavelength.
 
         Returns
         -------
@@ -1813,7 +1813,7 @@ def fit_chromatic_psf(self, data, mask=None, bgd_model_func=None, data_errors=No
             # first fit order 0 terms
             w.my_logger.info("\n\tFit order 0 parameters...")
             fixed_default = np.copy(w.params.fixed)
-            # fix higher order coefficients of polynomes
+            # fix higher-order coefficients of polynomials
             for k in range(w.params.ndim):
                 if "_0" not in w.params.labels[k] and not w.params.fixed[k]:
                     w.params.fixed[k] = True  # _k parameters that are yet fixed

spectractor/extractor/extractor.py

@@ -122,7 +122,7 @@ def __init__(self, spectrum, amplitude_priors_method="noprior", verbose=False, p
             params.fixed[params.get_index("A2")] = (not spectrum.disperser.flat_ratio_order_2over1) and (not ("A2_T" in spectrum.header))
         if spectrum.spectrogram_starfield is None:
             params.fixed[params.get_index("A_star")] = True  # Astar
-        params.fixed[params.get_index("D_CCD [mm]")] = True  # D2CCD: spectrogram can not tell something on this parameter: rely on calibrate_spectrum
+        params.fixed[params.get_index("D_CCD [mm]")] = True  # D2CCD: spectrogram cannot constrain this parameter: rely on calibrate_spectrum
         params.fixed[params.get_index("shift_x [pix]")] = True  # delta x: if False, extracted spectrum is biased compared with truth
         params.fixed[params.get_index("shift_y [pix]")] = False  # delta y
         params.fixed[params.get_index("angle [deg]")] = False  # angle