Merge pull request #192 from kelle/spec-update2

Fix JWST spectra plotting

Author: dr-rodriguez

requirements.txt

@@ -10,7 +10,7 @@ numpy==1.26.4
 pandas==2.0.3
 pytest==8.3.4
 requests==2.32.4
-specutils==2.0.0
+specutils==2.2.0
 SQLAlchemy==2.0.38
 tqdm==4.67.1
 Werkzeug==3.1.4

simple_app/plots.py

@@ -152,7 +152,7 @@ def normalise() -> np.ndarray:
     db = SimpleDB(db_file)  # open database
     t_spectra: Table = db.query(db.Spectra).\
         filter(db.Spectra.c.source == query).\
-        table(spectra=['access_url'])
+        table()  # do not use spectra=['access_url'] here, it will try to read the spectra as Spectrum objects
 
     # initialise plot
     n_fail, fail_string_list = 0, []
@@ -173,7 +173,12 @@ def normalise() -> np.ndarray:
 
     # checking each spectra in table
     for spec in t_spectra:
-        spectrum: Spectrum1D = spec['access_url']
+        try:
+            # Manually convert the spectrum to a Spectrum object
+            spectrum = Spectrum.read(spec['access_url'], cache=True)
+        except Exception as e:
+            print(f"Unable to read {spec['access_url']} as Spectrum. Error: {e}")
+            continue
 
         # checking spectrum has good units and not only NaNs or 0s
         try:

simple_app/simports.py

@@ -1,47 +1,69 @@
 """
 Importing all packages
 """
-# external packages
+
+import argparse  # parsing the arguments given with file
+import os  # operating system
+import sys  # system arguments
+from copy import deepcopy  # memory control
+from difflib import get_close_matches  # for redirecting bad file paths
+from io import BufferedIOBase, BytesIO, StringIO  # writing files without saving to disk
+from shutil import copy  # copying files
+from sqlite3 import Warning as SqliteWarning  # errors from sqlite
+from time import localtime, strftime  # time stuff for naming files
+from typing import Dict, Generator, List, Optional, Tuple, Union  # type hinting (good in IDEs)
+from urllib.parse import quote  # handling strings into url friendly form
+from zipfile import ZipFile  # zipping files together
+
+import astropy.units as u  # units
+import multiprocess as mp  # multiprocessing for efficiency
+import numpy as np  # numerical python
+import pandas as pd  # running dataframes
+import pytest  # testing
+import requests  # accessing internet
 from astrodbkit.astrodb import Database  # used for pulling out database and querying
 from astropy.coordinates import SkyCoord  # coordinates
 from astropy.io import fits  # handling fits files
-import astropy.units as u  # units
 from astropy.table import Table  # tables in astropy
 from bokeh.embed import components  # converting python bokeh to javascript
-from bokeh.layouts import row, column  # bokeh displaying nicely
-from bokeh.models import ColumnDataSource, Range1d, CustomJS, \
-    Select, Toggle, TapTool, OpenURL, HoverTool, Span, RangeSlider, Label, ColorBar, FixedTicker  # bokeh models
+from bokeh.layouts import column, row  # bokeh displaying nicely
+from bokeh.models import (
+                   ColorBar,
+                   ColumnDataSource,
+                   CustomJS,
+                   FixedTicker,
+                   HoverTool,
+                   Label,
+                   OpenURL,
+                   Range1d,
+                   RangeSlider,
+                   Select,  # bokeh models
+                   Span,
+                   TapTool,
+                   Toggle,
+)
 from bokeh.palettes import Colorblind8, Turbo256  # plotting palettes
-from bokeh.plotting import figure, curdoc  # bokeh plotting
+from bokeh.plotting import curdoc, figure  # bokeh plotting
 from bokeh.resources import CDN  # resources for webpage
-from bokeh.themes import built_in_themes, Theme  # appearance of bokeh glyphs
+from bokeh.themes import Theme, built_in_themes  # appearance of bokeh glyphs
 from bokeh.transform import linear_cmap  # making colour maps
-from flask import (Flask, render_template, jsonify, send_from_directory, redirect, url_for,
-                   Response, abort, request, session)  # website
+from flask import (
+                   Flask,
+                   Response,  # website
+                   abort,
+                   jsonify,
+                   redirect,
+                   render_template,
+                   request,
+                   send_from_directory,
+                   session,
+                   url_for,
+)
 from flask_cors import CORS  # cross origin fix (aladin mostly)
 from flask_wtf import FlaskForm  # web forms
 from markdown2 import markdown  # using markdown formatting
-import numpy as np  # numerical python
-import pandas as pd  # running dataframes
-import pytest  # testing
-from specutils import Spectrum1D  # spectrum objects
-from sqlalchemy.exc import ResourceClosedError, OperationalError, ProgrammingError  # errors from sqlalchemy
-from sqlite3 import Warning as SqliteWarning  # errors from sqlite
+from specutils import Spectrum
+from sqlalchemy.exc import OperationalError, ProgrammingError, ResourceClosedError  # errors from sqlalchemy
 from tqdm import tqdm  # progress bars
 from werkzeug.exceptions import HTTPException  # underlying http
 from wtforms import StringField, SubmitField, TextAreaField, ValidationError  # web forms
-
-# internal packages
-import argparse  # parsing the arguments given with file
-from copy import deepcopy  # memory control
-from difflib import get_close_matches  # for redirecting bad file paths
-from io import StringIO, BytesIO, BufferedIOBase  # writing files without saving to disk
-import multiprocess as mp  # multiprocessing for efficiency
-import os  # operating system
-import requests  # accessing internet
-from shutil import copy  # copying files
-import sys  # system arguments
-from time import strftime, localtime  # time stuff for naming files
-from typing import Tuple, Optional, List, Union, Dict, Generator  # type hinting (good in IDEs)
-from urllib.parse import quote  # handling strings into url friendly form
-from zipfile import ZipFile  # zipping files together