lime-stable 2.0.dev7__tar.gz → 2.0.dev13__tar.gz

{lime_stable-2.0.dev7/src/lime_stable.egg-info → lime_stable-2.0.dev13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lime-stable
-Version: 2.0.dev7
+Version: 2.0.dev13
 Summary: Line measuring algorithm for astronomical spectra
 Author-email: Vital Fernández <vgf@umich.edu>
 License-Expression: GPL-3.0-or-later
@@ -9,28 +9,28 @@ Classifier: Programming Language :: Python :: 3.11
 Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
-Requires-Dist: astropy~=7.0
+Requires-Dist: astropy~=7.1
 Requires-Dist: lmfit~=1.3
 Requires-Dist: matplotlib~=3.10
-Requires-Dist: numpy~=2.2
+Requires-Dist: numpy~=2.3
 Requires-Dist: pandas~=2.2
-Requires-Dist: scipy~=1.15
-Requires-Dist: aspect-stable~=0.3.1
+Requires-Dist: scipy~=1.16
+Requires-Dist: aspect-stable~=0.4.1
 Requires-Dist: tomli>=2.0.0; python_version < "3.11"
 Provides-Extra: full
 Requires-Dist: asdf~=4.1; extra == "full"
-Requires-Dist: bokeh~=3.7; extra == "full"
+Requires-Dist: bokeh~=3.8; extra == "full"
 Requires-Dist: mplcursors~=0.6; extra == "full"
 Requires-Dist: openpyxl~=3.1; extra == "full"
 Requires-Dist: PyLaTeX~=1.4; extra == "full"
 Requires-Dist: toml~=0.10; extra == "full"
 Provides-Extra: docs
-Requires-Dist: nbsphinx~=0.9; extra == "docs"
-Requires-Dist: ipympl~=0.9; extra == "docs"
 Requires-Dist: sphinx-rtd-theme~=3.0; extra == "docs"
+Requires-Dist: ipympl~=0.9; extra == "docs"
+Requires-Dist: myst-nb~=1.3; extra == "docs"
 Provides-Extra: tests
-Requires-Dist: pytest~=8.3; extra == "tests"
-Requires-Dist: pytest-cov~=6.0; extra == "tests"
+Requires-Dist: pytest~=8.4; extra == "tests"
+Requires-Dist: pytest-cov~=7.0; extra == "tests"
 Requires-Dist: pytest-mpl~=0.17; extra == "tests"
 Dynamic: license-file
 

{lime_stable-2.0.dev7 → lime_stable-2.0.dev13}/pyproject.toml

@@ -4,20 +4,20 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "lime-stable"
-version = "2.0.dev7"
+version = "2.0.dev13"
 readme = "README.rst"
 requires-python = ">=3.11"
 license = "GPL-3.0-or-later"
 authors = [{name = "Vital Fernández", email = "vgf@umich.edu"}]
 description = "Line measuring algorithm for astronomical spectra"
 
-dependencies = ["astropy~=7.0",
+dependencies = ["astropy~=7.1",
                 "lmfit~=1.3",
                 "matplotlib~=3.10",
-                "numpy~=2.2",
+                "numpy~=2.3",
                 "pandas~=2.2",
-                "scipy~=1.15",
-                "aspect-stable~=0.3.1",
+                "scipy~=1.16",
+                "aspect-stable~=0.4.1",
                 "tomli >= 2.0.0 ; python_version < '3.11'"]
 
 classifiers = ["Programming Language :: Python :: 3",
@@ -25,18 +25,18 @@ classifiers = ["Programming Language :: Python :: 3",
 
 [project.optional-dependencies]
 full = ["asdf~=4.1",
-        "bokeh~=3.7",
+        "bokeh~=3.8",
         "mplcursors~=0.6",
         "openpyxl~=3.1",
         "PyLaTeX~=1.4",
         "toml~=0.10",]
 
-docs = ["nbsphinx~=0.9",
+docs = ["sphinx-rtd-theme~=3.0",
         "ipympl~=0.9",
-        "sphinx-rtd-theme~=3.0"]
+        "myst-nb~=1.3"]
 
-tests = ["pytest~=8.3",
-         "pytest-cov~=6.0",
+tests = ["pytest~=8.4",
+         "pytest-cov~=7.0",
          "pytest-mpl~=0.17"]
 
 [tool.pytest.ini_options]

{lime_stable-2.0.dev7 → lime_stable-2.0.dev13}/src/lime/__init__.py

@@ -35,14 +35,10 @@ __version__ = _setup_cfg['metadata']['version']
 # Logging configuration
 _logger.debug(f'Launching LiMe {__version__} in Python {__python_version__}')
 
-
-# class Error(Exception):
-#     """LiMe exception function"""
-
 from lime.observations import Spectrum, Sample, Cube
 from lime.io import *
 from lime.tools import *
-from lime.transitions import Line, label_decomposition, bands_from_measurements
+from lime.transitions import label_decomposition, lines_frame, bands_from_measurements, Line
 from lime.archives.read_fits import OpenFits, show_instrument_cfg
 from lime.plotting.plots import theme
-from lime.workflow import line_bands
+from lime.rsrc_manager import lineDB

{lime_stable-2.0.dev7 → lime_stable-2.0.dev13}/src/lime/archives/read_fits.py

@@ -23,12 +23,18 @@ DESI_SPECTRA_BANDS = ('B', 'R', 'Z')
 SPECTRUM_FITS_PARAMS = {'nirspec': {'redshift': None, 'norm_flux': None, 'res_power': None,
                                     'units_wave': 'um', 'units_flux': 'MJy', 'pixel_mask': "nan", 'id_label': None},
 
+                        'nirspec_grizli': {'redshift': None, 'norm_flux': None, 'res_power': None,
+                                           'units_wave': 'um', 'units_flux': 'uJy', 'pixel_mask': "nan", 'id_label': None},
+
                         'isis': {'redshift': None, 'norm_flux': None, 'res_power': None,
                                  'units_wave': 'Angstrom', 'units_flux': 'FLAM', 'pixel_mask': "nan", 'id_label': None},
 
                         'osiris': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
                                    'units_flux': 'FLAM', 'pixel_mask': "nan", 'id_label': None},
 
+                        'cos': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
+                                   'units_flux': 'FLAM', 'pixel_mask': "nan", 'id_label': None},
+
                         'sdss': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
                                  'units_flux': '1e-17*FLAM', 'pixel_mask': 'nan', 'id_label': None},
 
@@ -257,38 +263,49 @@ def check_fits_instructions(fits_source, online_provider=False):
     else:
         fits_reader = None
 
-    # # Check for url location for surveys function
-    # if online_provider:
-    #     if hasattr(UrlFitsSurvey, fits_source):
-    #         url_locator = getattr(UrlFitsSurvey, fits_source)
-    #     else:
-    #         raise LiMe_Error(f'Input {fits_source} does not have a url manager for LiMe could not be created.')
-    # else:
-    #     url_locator = None
-
     return fits_reader
 
-def load_txt(text_address):
+
+def load_txt(text_address, **kwargs):
 
     # Columns
-    out_array = np.loadtxt(text_address)
+    out_array = np.loadtxt(text_address, **kwargs)
 
-    # Transform foot comments as dictionary data
-    params_dict = {}
-    with open(text_address, "r") as f:
+    # File address
+    if not type(text_address).__name__ == "UploadedFile":
+        with open(text_address, "r") as f:
+            lines = f.readlines()
 
-        # Reverse loop while the lines start by a "#"
-        for line in reversed(f.readlines()):
-            line = line.strip()
-            if not line.startswith("#") or (line.startswith("# LiMe")):
-                break
+    # Uploaded file
+    else:
+        lines = text_address.getvalue().decode("utf-8").splitlines()
 
-            # Extract key-value pairs
-            key, value = line[1:].split(":", 1)  # Split at the first ':'
-            params_dict[key.strip()] = value.strip()
+    # Reverse loop over the lines
+    params_dict = {}
+    for line in reversed(lines):
+        line = line.strip()
+        if not line.startswith("#") or line.startswith("# LiMe"):
+            break
+        key, value = line[1:].split(":", 1)
+        params_dict[key.strip()] = value.strip()
+
+    # # Transform foot comments as dictionary data
+    # params_dict = {}
+    # with open(text_address, "r") as f:
+    #
+    #     # Reverse loop while the lines start by a "#"
+    #     for line in reversed(f.readlines()):
+    #         line = line.strip()
+    #         if not line.startswith("#") or (line.startswith("# LiMe")):
+    #             break
+    #
+    #         # Extract key-value pairs
+    #         key, value = line[1:].split(":", 1)  # Split at the first ':'
+    #         params_dict[key.strip()] = value.strip()
 
     return out_array, params_dict
 
+
 def load_fits(fits_address, data_ext_list=None, hdr_ext_list=None, url_check=False):
 
     """
@@ -362,10 +379,10 @@ class OpenFits:
 
         return
 
-    def parse_data_from_file(self, file_address, pixel_mask=None):
+    def parse_data_from_file(self, file_address, pixel_mask, **kwargs):
 
         # Read the fits data
-        wave_array, flux_array, err_array, header_list, fits_params = self.fits_reader(file_address)
+        wave_array, flux_array, err_array, header_list, fits_params = self.fits_reader(file_address, **kwargs)
         pixel_mask = pixel_mask if pixel_mask is not None else fits_params['pixel_mask']
 
         # Mask requested entries
@@ -441,10 +458,10 @@ class OpenFits:
         return fits_args
 
     @staticmethod
-    def text(file_address):
+    def text(file_address, **kwargs):
 
         # Read text file dividing the columns into the spectrum axis and the comments as its parameters
-        data_arr, params_dict = load_txt(file_address)
+        data_arr, params_dict = load_txt(file_address, **kwargs)
 
         # Unpack the columns into the spectrum axes
         wave_array, flux_array = data_arr[:, 0], data_arr[:, 1]
@@ -456,16 +473,13 @@ class OpenFits:
         # Convert strings to expected format
         params_dict['redshift'] = float(params_dict['redshift']) if 'redshift' in params_dict else None
         params_dict['norm_flux'] = float(params_dict['norm_flux']) if 'norm_flux' in params_dict else None
-        params_dict['id_label'] = params_dict['id_label'] if 'norm_flux' in params_dict else None
+        params_dict['id_label'] = params_dict['id_label'] if 'id_label' in params_dict else None
         params_dict['pixel_mask'] = mask_array
 
-        # metadata['units_wave'] = au.Unit(metadata['units_wave']) if 'units_wave' in metadata else au.Unit('AA')
-        # metadata['units_flux'] = au.Unit(metadata['units_flux']) if 'units_flux' in metadata else au.Unit('FLAM')
-
         return wave_array, flux_array, err_array, None, params_dict
 
     @staticmethod
-    def nirspec(fits_address, data_ext_list=1, hdr_ext_list=(0, 1), pixel_mask=None):
+    def nirspec(fits_address, data_ext_list=1, hdr_ext_list=(0, 1), **kwargs):
 
         """
 
@@ -503,7 +517,47 @@ class OpenFits:
         return wave_array, flux_array, err_array, header_list, params_dict
 
     @staticmethod
-    def isis(fits_address, data_ext_list=0, hdr_ext_list=0, pixel_mask=None):
+    def nirspec_grizli(fits_address, data_ext_list=1, hdr_ext_list=(0, 1), **kwargs):
+
+        """
+
+        This method returns the spectrum array data and headers from a GRIZLI (Brammer (2023a) and Valentino et al.
+        (2023)) reduction of a NIRSPEC observation.
+
+        The function returns numpy arrays with the wavelength, flux and uncertainty flux (if available this is the
+        standard deviation available), a list with the requested headers and a dictionary with the parameters to
+        construct a LiMe Spectrum or Cube. These parameters include the observation wavelength/flux units, normalization
+        and wcs from the input fits file.
+
+        :param fits_address: File location address for the observation .fits file.
+        :type fits_address: str, Path
+
+        :param data_ext_list: Data extension number or name to extract from the .fits file.
+        :type fits_address: int, str or list of either, optional
+
+        :param hdr_ext_list: header extension number or name to extract from the .fits file.
+        :type hdr_ext_list: int, str or list of either, optional
+
+        :return: wavelength array, flux array, uncertainty array, header list, observation parameter dict
+
+        """
+
+        # Get data table and header dict lists
+        data_list, header_list = load_fits(fits_address, data_ext_list, hdr_ext_list, url_check=False)
+
+        # Re-construct spectrum arrays
+        wave_array, flux_array, err_array = data_list[0]['wave'], data_list[0]['flux'], data_list[0]['err']
+        pixel_mask = np.isnan(flux_array) | np.isnan(err_array)
+
+        # Spectrum properties
+        params_dict = SPECTRUM_FITS_PARAMS['nirspec_grizli']
+        params_dict['pixel_mask'] = pixel_mask
+
+        return wave_array, flux_array, err_array, header_list, params_dict
+
+
+    @staticmethod
+    def isis(fits_address, data_ext_list=0, hdr_ext_list=0, **kwargs):
 
         """
 
@@ -548,7 +602,7 @@ class OpenFits:
         return wave_array, flux_array, err_array, header_list, params_dict
 
     @staticmethod
-    def osiris(fits_address, data_ext_list=0, hdr_ext_list=0, pixel_mask=None):
+    def osiris(fits_address, data_ext_list=0, hdr_ext_list=0, **kwargs):
 
         """
 
@@ -593,7 +647,45 @@ class OpenFits:
         return wave_array, flux_array, err_array, header_list, params_dict
 
     @staticmethod
-    def sdss(fits_address, data_ext_list=(1, 2), hdr_ext_list=(0), pixel_mask=None):
+    def cos(fits_address, data_ext_list=(1), hdr_ext_list=(0), **kwargs):
+
+        """
+
+        This method returns the spectrum array data and headers from the COS instrument at Hubble.
+
+        The function returns numpy arrays with the wavelength, flux and uncertainty flux (if available this is the
+        standard deviation available), a list with the requested headers and a dictionary with the parameters to
+        construct a LiMe Spectrum. These parameters include the observation wavelength/flux units, normalization and wcs
+        from the input fits file.
+
+        :param fits_address: File location address for the observation .fits file.
+        :type fits_address: str, Path
+
+        :param data_ext_list: Data extension number or name to extract from the .fits file.
+        :type fits_address: int, str or list of either, optional
+
+        :param hdr_ext_list: header extension number or name to extract from the .fits file.
+        :type hdr_ext_list: int, str or list of either, optional
+
+        :return: wavelength array, flux array, uncertainty array, header list, observation parameter dict
+
+        """
+
+        # Get data table and header dict lists
+        data_list, header_list = load_fits(fits_address, data_ext_list, hdr_ext_list, url_check=False)
+
+        wave_array = data_list[0]['WAVELENGTH'][0] # TODO check for additional extension to join the spectra
+        flux_array = data_list[0]['FLUX'][0]
+        err_array = data_list[0]['ERROR'][0]
+
+        # Spectrum properties
+        params_dict = SPECTRUM_FITS_PARAMS['cos']
+
+        return wave_array, flux_array, err_array, header_list, params_dict
+
+
+    @staticmethod
+    def sdss(fits_address, data_ext_list=(1, 2), hdr_ext_list=(0), **kwargs):
 
         """
 
@@ -645,7 +737,7 @@ class OpenFits:
         return wave_array, flux_array, err_array, header_list, params_dict
 
     @staticmethod
-    def manga(fits_address, data_ext_list=('WAVE', 'FLUX', 'IVAR'), hdr_ext_list=('FLUX'), pixel_mask=None):
+    def manga(fits_address, data_ext_list=('WAVE', 'FLUX', 'IVAR'), hdr_ext_list=('FLUX'), **kwargs):
 
         """
 
@@ -692,7 +784,7 @@ class OpenFits:
         return wave_array, flux_cube, err_cube, header_list, fits_params
 
     @staticmethod
-    def muse(fits_address, data_ext_list=(1, 2), hdr_ext_list=1, pixel_mask=None):
+    def muse(fits_address, data_ext_list=(1, 2), hdr_ext_list=1, **kwargs):
 
         """
 
@@ -737,7 +829,7 @@ class OpenFits:
         return wave_array, flux_cube, err_cube, header_list, fits_params
 
     @staticmethod
-    def megara(fits_address, data_ext_list=0, hdr_ext_list=(0, 1), pixel_mask=None):
+    def megara(fits_address, data_ext_list=0, hdr_ext_list=(0, 1), **kwargs):
 
         """
 
@@ -781,7 +873,7 @@ class OpenFits:
         return wave_array, flux_cube, err_cube, header_list, fits_params
 
     @staticmethod
-    def miri(fits_address, data_ext_list=(1,2), hdr_ext_list=(1), pixel_mask=None):
+    def miri(fits_address, data_ext_list=(1,2), hdr_ext_list=(1), **kwargs):
 
         """