lime-stable 1.3.0__tar.gz → 2.0.dev2__tar.gz

lime_stable-2.0.dev2/MANIFEST.in

@@ -0,0 +1,7 @@
+include src/reader/*.toml
+include src/lime/lime.toml
+include src/lime/changelog.txt
+include src/lime/resources/parent_mask.txt
+include src/lime/resources/types_params.txt
+include src/lime/resources/lines_database_v2.0.0.txt
+include src/lime/plotting/theme_lime.toml

{lime-stable-1.3.0/src/lime_stable.egg-info → lime_stable-2.0.dev2}/PKG-INFO

@@ -1,33 +1,38 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: lime-stable
-Version: 1.3.0
+Version: 2.0.dev2
 Summary: Line measuring algorithm for astronomical spectra
-Home-page: https://github.com/Vital-Fernandez/lime
-Author: Vital Fernandez
 Author-email: Vital Fernández <vgf@umich.edu>
-Classifier: License :: OSI Approved :: MIT License
+License-Expression: GPL-3.0-or-later
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.7
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
-Requires-Dist: asdf~=3.0
-Requires-Dist: astropy~=6.0
-Requires-Dist: joblib~=1.3
-Requires-Dist: lmfit~=1.2
-Requires-Dist: matplotlib~=3.7
-Requires-Dist: mplcursors~=0.5
-Requires-Dist: nbsphinx~=0.9
-Requires-Dist: numpy~=1.24
-Requires-Dist: openpyxl~=3.1
-Requires-Dist: pandas~=2.0
-Requires-Dist: PyLaTeX~=1.4
-Requires-Dist: pytest~=7.4
-Requires-Dist: pytest-cov~=4.1
-Requires-Dist: pytest-mpl~=0.16
-Requires-Dist: scipy~=1.10
-Requires-Dist: toml~=0.10
+Requires-Dist: astropy~=7.0
+Requires-Dist: lmfit~=1.3
+Requires-Dist: matplotlib~=3.10
+Requires-Dist: numpy~=2.2
+Requires-Dist: pandas~=2.2
+Requires-Dist: scipy~=1.15
 Requires-Dist: tomli>=2.0.0; python_version < "3.11"
+Provides-Extra: full
+Requires-Dist: asdf~=4.1; extra == "full"
+Requires-Dist: aspect-stable~=0.3.0; extra == "full"
+Requires-Dist: bokeh~=3.6; 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"
+Provides-Extra: tests
+Requires-Dist: pytest~=8.3; extra == "tests"
+Requires-Dist: pytest-cov~=6.0; extra == "tests"
+Requires-Dist: pytest-mpl~=0.17; extra == "tests"
+Dynamic: license-file
 
 
 .. image:: https://github.com/Vital-Fernandez/lime/blob/0afedb150b0169deec6c7f159def99750a3a30da/docs/source/_static/logo_transparent.png?raw=true

lime_stable-2.0.dev2/pyproject.toml

@@ -0,0 +1,47 @@
+[build-system]
+requires = ["setuptools>=61.0.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "lime-stable"
+version = "2.0.dev2"
+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",
+                "lmfit~=1.3",
+                "matplotlib~=3.10",
+                "numpy~=2.2",
+                "pandas~=2.2",
+                "scipy~=1.15",
+                "tomli >= 2.0.0 ; python_version < '3.11'"]
+
+classifiers = ["Programming Language :: Python :: 3",
+               "Programming Language :: Python :: 3.11"]
+
+[project.optional-dependencies]
+full = ["asdf~=4.1",
+        "aspect-stable~=0.3.0",
+        "bokeh~=3.6",
+        "mplcursors~=0.6",
+        "openpyxl~=3.1",
+        "PyLaTeX~=1.4",
+        "toml~=0.10",]
+
+docs = ["nbsphinx~=0.9",
+        "ipympl~=0.9",
+        "sphinx-rtd-theme~=3.0"]
+
+tests = ["pytest~=8.3",
+         "pytest-cov~=6.0",
+         "pytest-mpl~=0.17"]
+
+[tool.pytest.ini_options]
+pythonpath = ["src"]
+mpl-baseline-path = 'tests/baseline'
+mpl-results-path = 'tests/outputs'
+mpl-results-always = false
+addopts = "-p no:asdf_schema_tester"

lime_stable-2.0.dev2/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

{lime-stable-1.3.0 → lime_stable-2.0.dev2}/src/lime/__init__.py

@@ -26,25 +26,23 @@ __python_version__ = sys.version_info
 
 # Read lime configuration .toml
 _inst_dir = Path(__file__).parent
-_conf_path = _inst_dir/'config.toml'
+_conf_path = _inst_dir/'lime.toml'
 with open(_conf_path, mode="rb") as fp:
     _setup_cfg = tomllib.load(fp)
 
 __version__ = _setup_cfg['metadata']['version']
-_lines_database_path = (os.path.join(_inst_dir, 'resources/parent_bands.txt'))
 
 # Logging configuration
 _logger.debug(f'Launching LiMe {__version__} in Python {__python_version__}')
 
 
-class Error(Exception):
-    """LiMe exception function"""
+# class Error(Exception):
+#     """LiMe exception function"""
 
-from .observations import Spectrum, Sample, Cube
-from .io import *
-from .tools import *
-from .transitions import Line, label_decomposition, bands_from_frame
-from .read_fits import OpenFits, show_instrument_cfg
-from .recognition import detection_function
-from .plots import theme
-from .workflow import line_bands
+from lime.observations import Spectrum, Sample, Cube
+from lime.io import *
+from lime.tools import *
+from lime.transitions import Line, label_decomposition, bands_from_frame
+from lime.archives.read_fits import OpenFits, show_instrument_cfg
+from lime.plotting.plots import theme
+from lime.workflow import line_bands

{lime-stable-1.3.0/src/lime → lime_stable-2.0.dev2/src/lime/archives}/read_fits.py

@@ -5,7 +5,7 @@ from astropy.io import fits
 from astropy.wcs import WCS
 import logging
 
-from .io import LiMe_Error
+from lime.io import LiMe_Error
 from urllib.parse import urlparse
 
 try:
@@ -32,7 +32,10 @@ SPECTRUM_FITS_PARAMS = {'nirspec': {'redshift': None, 'norm_flux': None, 'res_po
                                  'units_flux': '1e-17*FLAM', 'pixel_mask': 'nan', 'id_label': None},
 
                         'desi': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
-                                 'units_flux': '1e-17*FLAM', 'pixel_mask': "nan", 'id_label': None}}
+                                 'units_flux': '1e-17*FLAM', 'pixel_mask': "nan", 'id_label': None},
+
+                        'text': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
+                                 'units_flux': 'FLAM', 'pixel_mask': None, 'id_label': None}}
 
 CUBE_FITS_PARAMS = {'manga': {'redshift': None, 'norm_flux': None, 'res_power': None, 'units_wave': 'Angstrom',
                               'units_flux': '1e-17*FLAM', 'pixel_mask': "nan", 'id_label': None},
@@ -51,13 +54,13 @@ CUBE_FITS_PARAMS = {'manga': {'redshift': None, 'norm_flux': None, 'res_power':
 
 def show_instrument_cfg():
 
-    print(f'\nSingle ".fits" spectra files configuration:')
+    print(f'\nLong-slit ".fits" observation instrument configuration:')
     for i, items in enumerate(SPECTRUM_FITS_PARAMS.items()):
         key, value = items
         print(f'{i} {key}) \t units_wave: {value["units_wave"]}, units_flux: {value["units_flux"]}, '
               f'pixel_mask: {value["pixel_mask"]}, res_power: {value["res_power"]}')
 
-    print(f'\nCube ".fits" spectra files configuration:')
+    print(f'\nCube ".fits" observation instrument configuration:')
     for i, items in enumerate(CUBE_FITS_PARAMS.items()):
         key, value = items
         print(f'{i} {key}) \t units_wave: {value["units_wave"]}, units_flux: {value["units_flux"]},'
@@ -264,6 +267,26 @@ def check_fits_instructions(fits_source, online_provider=False):
 
     return fits_reader
 
+def load_txt(text_address):
+
+    # Columns
+    out_array = np.loadtxt(text_address)
+
+    # 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):
 
@@ -347,9 +370,9 @@ class OpenFits:
         # Mask requested entries
         if pixel_mask is not None:
             pixel_mask = np.atleast_1d(pixel_mask)
-            mask_array = np.zeros(flux_array.shape).astype(bool)
+            mask_bool_array = np.zeros(flux_array.shape).astype(bool)
 
-            # String array:
+            # String array: TODO Lime2.0 make this a method and add it to the spectrum and flux entries and add inf
             if pixel_mask.dtype.kind in ['U', 'S']:
                 for entry in pixel_mask:
                     if entry == 'negative':
@@ -361,24 +384,24 @@ class OpenFits:
                     else:
                         raise LiMe_Error(f'Pixel entry "{entry}" is not recognized. Only boolean masks for the masked '
                                          f'data or these strings are supported: "nan", "negative", "zero"')
-                    mask_array[idcs] = True
+                    mask_bool_array[idcs] = True
 
             # Boolean mask
             else:
                 assert flux_array.shape == pixel_mask.shape, LiMe_Error(f'- Input pixel mask shape {pixel_mask.shape}'
                                                                         f'is different from data array shape {flux_array.shape}')
-                mask_array = pixel_mask
+                mask_bool_array = pixel_mask
 
         else:
-            mask_array = None
+            mask_bool_array = None
 
         # Construct attributes for LiMe object
-        fits_args = {'input_wave': wave_array, 'input_flux': flux_array, 'input_err': err_array}#'pixel_mask': mask_array}
+        fits_args = {'input_wave': wave_array, 'input_flux': flux_array, 'input_err': err_array}
         fits_args.update(fits_params)
 
         # Add mask entry
-        if mask_array is not None:
-            fits_args['pixel_mask'] = mask_array
+        if mask_bool_array is not None:
+            fits_args['pixel_mask'] = mask_bool_array
 
         return fits_args
 
@@ -416,6 +439,30 @@ class OpenFits:
 
         return fits_args
 
+    @staticmethod
+    def text(file_address):
+
+        # Read text file dividing the columns into the spectrum axis and the comments as its parameters
+        data_arr, params_dict = load_txt(file_address)
+
+        # Unpack the columns into the spectrum axes
+        wave_array, flux_array = data_arr[:, 0], data_arr[:, 1]
+
+        # Check if pixel error and masks are included
+        err_array = data_arr[:, 2] if data_arr.shape[1] > 2 else None
+        mask_array = data_arr[:, 3] if data_arr.shape[1] > 3 else None
+
+        # 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['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):
 
@@ -776,7 +823,6 @@ class OpenFits:
 
         return wave_array, flux_cube, err_cube, header_list, fits_params
 
-
     @staticmethod
     def desi(target_id, root_url='https://data.desi.lbl.gov/public/edr/spectro/redux', **kwargs):
 

{lime-stable-1.3.0/src/lime → lime_stable-2.0.dev2/src/lime/archives}/tables.py

@@ -111,7 +111,7 @@ def table_fluxes(lines_df, table_address, header_format_latex, table_type='pdf',
         pdf.addTableRow(row_raw, last_row=lastRow_check)
 
     for key, value in kwargs.items():
-        text_line = r'{}:{}'.format(key.replace('_', '\_'), value)
+        text_line = r'{}:{}'.format(key.replace('_', r'\_'), value)
         pdf.table.add_row([pylatex.NoEscape(r'\footnotesize{{{}}}'.format(text_line))],
                           escape=False, strict=False)
 
@@ -139,7 +139,7 @@ class PdfMaker:
         self.table = None
         self.theme_table = None
 
-        # TODO add dictionary with numeric formats for tables depending on the variable
+        # TODO add dictionary with numeric formats for archives depending on the variable
 
     def create_pdfDoc(self, pdf_type=None, geometry_options=None, document_class=u'article', theme='white'):
         """
@@ -176,8 +176,8 @@ class PdfMaker:
             self.pdfDoc = pylatex.Document(documentclass=document_class, geometry_options=self.pdf_geometry_options)
 
             if theme == 'dark':
-                self.pdfDoc.append(pylatex.NoEscape('\definecolor{background}{rgb}{0.169, 0.169, 0.169}'))
-                self.pdfDoc.append(pylatex.NoEscape('\definecolor{foreground}{rgb}{0.702, 0.780, 0.847}'))
+                self.pdfDoc.append(pylatex.NoEscape(r'\definecolor{background}{rgb}{0.169, 0.169, 0.169}'))
+                self.pdfDoc.append(pylatex.NoEscape(r'\definecolor{foreground}{rgb}{0.702, 0.780, 0.847}'))
                 self.pdfDoc.append(pylatex.NoEscape(r'\arrayrulecolor{foreground}'))
 
             if pdf_type == 'table':

lime_stable-2.0.dev2/src/lime/changelog.txt

@@ -0,0 +1,108 @@
+LiMe release - 1.0.0 - 04/29/2024
+   - First stable release
+
+LiMe minor update - 1.0.1 - 05/04/2024
+   - Created lime.io.parce_lime_cfg function to convert the .toml sections with lime suffix to the expected format to be its own operation
+   - Created lime.plots.spectrum_labels to generate spectrum figure axis labels
+   - Delete "log" attribute from lime.Cube class
+   - Fix error normalize_fluxes was not cropping the lines frame for an input line list. Need to fix normalize flux error
+   - log now returns the dataframe
+
+LiMe minor update - 1.0.2 - 05/09/2024
+   - SDSS lime.Spectrum.from_file no reads redshift from fits header
+
+LiMe minor update - 1.0.3 - 05/09/2024
+   - Restored deleted config.toml
+
+LiMe minor update - 1.0.4 - 05/17/2024
+   - Corrected MANGA flux error measurement
+   - New tests for comparison between standard and lime loading of SDSS and MANGA observations
+   - Change cm.get_cmap to plt.get_cmap due to matplotlib depreciation
+   - Bug fix for multi-index flux extraction function due to pandas depreciation
+
+LiMe minor update - 1.0.5 - 05/25/2024
+   - Change "continuum_fit" keyword for toml keyword in continuum fitting configuration to "continuum" to match function name
+
+LiMe minor update - 1.0.6 - 06/20/2024
+   - Fix error in unit conversion of Cubes
+   - Clearer messages for bands not matching the spectrum wavelength range
+   - Added test for line fitting with line detection using implicit and explicit configuration and bands declaration
+   - Plots using the automatic scale now show the scale as in figure text.
+   - Added own stringBool from distiutils because it is being discontinued in python 3.12
+
+LiMe minor update - 1.0.7 - 07/19/2024
+   - define_masks function has been replaces by line.index_bands()
+   - The line.index_bands() now warns if line does not have bands at the point of indexing an input spectrum wavelength.
+   - Corrections on the measurements documentation page
+
+LiMe minor update - 1.0.8 - 09/15/2024
+   - The check_fit_cfg function now reviews if the continuum and line_detection functions parameters are present and gives a warning if not.
+   - show_masks attribute in Spectrum.plot.spectrum to hide the pixels masks on the output plot.
+
+LiMe medium update - 1.1.0 - 09/30/2024
+   - By default LiMe will now mask the input spectrum if "nan" and "inf" entries are present in the flux and err_flux arrays but the user does not provide a pixel mask. If the user provides a mask but "nan" or "inf" entries are detected only a warning will be provided.
+   - The website now includes the changelog with the LiMe updates.
+   - Fixed bug where nan entries would cause an error in the line band detection.
+   - New logic operator to store bands which only cover one pixel in band detection.
+   - Documentation corrections by E.C. Herenz
+
+LiMe minor update - 1.1.1 - 10/29/2024
+    - Adding bands from frame function
+    - Bug fix for re-normalization in the units_conversion function
+    - Bug fix to normalize by 1 if nanmedian flux is <= 0
+    - Added security fix for re-normalization in the units_conversion function
+    - The review_bands function now checks if all the line_band pixels flux and all the continuum_band pixels flux sum is zero. This is done to avoid all zero line or continuum entries.
+
+LiMe medium update - 1.2.0 - 11/05/2024
+    - The unit_conversion functions have been updated to avoid bugs on betwen certain units
+    - The unit_conversion functions now review the normalization and masking the same way as in the spectrum creation
+    - The line detection function has been updated to account for masked data within the input line bands
+    - The automatic normalization function now using the mean instead of median as the scale_flux
+    - If the scale flux is negative the normalization will remove the lowest pixel value from the mean flux for the automatic normalization.
+    - Initial introduction for aspect functions for thea automatic detection of spectral features.
+    - New checks to avoid the measurements of bands where all the entries are masked.
+
+LiMe minor update - 1.2.1 - 10/29/2024
+    - Rename the "line_bands" argument in the lime.Spectrum.plot.spectrum function to "bands" to match library style
+    - The lime.Spectrum.plot.spectrum function will now only display "bands" w3 and w4 values are within the rest wavelength range (no need to crop the bands in advance now).
+    - Added support for reading MIRI IFU observations with MJy/str and um units
+    - Corrected bug on the latex label generation in the lime.line_bands command not reproducing the expected format
+    - The unit_conversion function for Cube observations now uses the format from the previous update.
+
+LiMe medium update - 1.3.0 - 10/29/2024
+    - This update includes ASPECT as an optional dependency and has adapted several functions to include the possibility to use its predictions
+    - Added the Spectrum.retrieve attribute to group tasks which return data for the user related to the spectrum
+    - Added the Spectrum.retrieve.line_bands to return the line bands which match the observation redshift, wave interval and components detection.
+    - The lime.line_bands and Spectrum.retrieve.line_bands now use the argument "redshift" to adjust the output bands which are within a "wave_intvl" for that redshift (for the Spectrum.retrieve.line_bands this is always the case)
+    - The lime.line_bands has been moved to the workflow.py file
+    - The ".line_bands" have now use the new unit conversion function and includes more functionality via new update_labels=True, update_latex=True.
+    - The inst_FWHM at the creation of observations has been replaced by res_power (resolving power) and now can be a float or an array (same length as the observation wavelength). This provides a more robust computation of the sigma_instr
+    - The sigma_instr and sigma_thermal corrections are not computed within the sigma_corrections function
+    - During the lime.Sample.get_spectrum the user can now specify kwargs arguments to update the creation kwargs for that object.
+    - Several bugs were corrected on the lime.redshift_calculation to avoid very large errors when weak lines were present.
+    - Bug correction on the previous update lime.Spectrum.plot.spectrum to plot bands within the observation wavelength range.
+    - The lime.Sample.check.redshift function now has a new "initial_z" argument for the initial guess of the redshift measurement.
+    - The lime.Sample.check.redshift "title_label" argument has been renamed -> "title" for consistency
+    - The air_to_vacuum_function now only applies the theoretical relation, its inputs and outputs are wavelength arrays.
+    - The new lime.Line.update_label function can be used to update the line label by reviewing the line properties.
+
+LiMe Mayor update - 2.0.0 - XX/XX/XXXX
+    - Change installer convention from "setup.py + requirements.txt" to pyproject.toml
+    - Updated dependencies to current version of packages and for python 3.12
+    - Renamed cfg.toml to lime.toml
+    - Arrange library .py files into folder structure reproducing the .fit, .infer, .retrieve, .plot functions. The functions related to file types are are located in archives folder.
+    - Added new mechanic to compute the lines continuum from the line band edges or the continua bands.
+    - Added new mechanic to compute the pixel uncertainty from the provided uncertainty flux or the adjacent continua bands.
+    - Fix error where the error from the line profile center and sigma parameters was uncertainty was 0 if the line kinematics were imported from a previously measured line.
+    - Added support for bokeh plots.
+    - The theme configuration parameters are stored now in the src/plotting/theme_lime.toml.
+    - The .fit.report function now formats the output report to include the component label name and has the argument return_text=False to give the option to return the report message as a variable instead of printing on the terminal.
+    - Fix a bug where the kinematics export function was not applying the correct rest frame wavelength length on the radial velocity calculation.
+    - New ".infer" to host high level functions to predict spectroscopic features
+    - The "Spectrum.line_detection()" has been moved to "Spectrum.infer.peaks_troughs()". The old function now raises and error moving to the new function.
+    - Now the observations wave, flux, err_flux and wave_rest arrays are always masked arrays
+    - The lines database name has been changed from parent_bands.txt to "lines_database_v2.0.0.txt". The wavelength are based on van Hoof, P.A.M., 2018, Galaxies, 6, 63 and Roueff+ (2019).
+    - The central wavelenght bands are now calculated assuming a bands_vsigma=70 and n_sigma=4
+    - The function lime.Spectrum.retrieve.spectrum() returns the spectrum axes as a recarray or saves it into a text file if the user provides a file address.
+    - lime.Spectrum.from_file("fname", instrument='text') can now read the file from a text file following the format from the lime.Spectrum.retrieve.spectrum() function.
+    - Bug the .plot.spectrum(include_fittings) does not show the combined profile