PyNOT-redux 2.1.2__tar.gz → 2.2__tar.gz

{pynot_redux-2.1.2 → pynot_redux-2.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.1.2
+Version: 2.2
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager
@@ -28,6 +28,18 @@ Requires-Dist: sep
 Requires-Dist: astroalign
 Requires-Dist: astroquery
 Requires-Dist: beautifulsoup4
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # PyNOT-redux
  A Data Processing Pipeline for ALFOSC at the Nordic Optical Telescope

{pynot_redux-2.1.2 → pynot_redux-2.2}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.1.2
+Version: 2.2
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager
@@ -28,6 +28,18 @@ Requires-Dist: sep
 Requires-Dist: astroalign
 Requires-Dist: astroquery
 Requires-Dist: beautifulsoup4
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 # PyNOT-redux
  A Data Processing Pipeline for ALFOSC at the Nordic Optical Telescope

{pynot_redux-2.1.2 → pynot_redux-2.2}/PyNOT_redux.egg-info/SOURCES.txt

@@ -91,4 +91,24 @@ pynot/data/obs.py
 pynot/data/organizer.py
 pynot/data/help/welcome_msg_extract.html
 pynot/data/help/welcome_msg_identify.html
-pynot/data/help/welcome_msg_response.html
+pynot/data/help/welcome_msg_response.html
+pynot/viewer/__init__.py
+pynot/viewer/containers.py
+pynot/viewer/default_linelists.json
+pynot/viewer/dust.py
+pynot/viewer/linelists.py
+pynot/viewer/messages.py
+pynot/viewer/models.py
+pynot/viewer/notes.py
+pynot/viewer/spectrum.py
+pynot/viewer/tablemodels.py
+pynot/viewer/targets.py
+pynot/viewer/viewer.py
+pynot/viewer/templates/Assef_2010.dat
+pynot/viewer/templates/FeII.Vestergaard.dat
+pynot/viewer/templates/FeIII.Vestergaard.dat
+pynot/viewer/templates/Hernan_Caballero_quasar_NIR_template.txt
+pynot/viewer/templates/QSO_selsing.dat
+pynot/viewer/templates/QSO_template.Krawczyk_all.dat
+pynot/viewer/templates/QSO_template.Krawczyk_high.dat
+pynot/viewer/templates/QSO_template.Krawczyk_low.dat

pynot_redux-2.2/pynot/VERSION

@@ -0,0 +1 @@
+2.2

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/data/io.py

@@ -23,6 +23,7 @@ def get_header_info(fname):
         slit = hdr['SLIT']
         filter = '...'
         shape = "..."
+        binning = "NxM_NA"
     else:
         hdr = instrument.get_header(fname)
         object = instrument.get_object(hdr)
@@ -31,7 +32,8 @@ def get_header_info(fname):
         slit = instrument.get_slit(hdr)
         filter = instrument.get_filter(hdr)
         shape = "%ix%i" % (hdr['NAXIS1'], hdr['NAXIS2'])
-    return object, exptime, grism, slit, filter, shape
+        binning = instrument.get_binning_from_hdr(hdr)
+    return object, exptime, grism, slit, filter, shape, binning
 
 
 def save_database(database, output_fname):
@@ -46,20 +48,20 @@ def save_database(database, output_fname):
             for fname in sorted_files:
                 try:
                     if fname[0] == '#':
-                        object, exptime, grism, slit, filter, shape = get_header_info(fname[1:])
+                        object, exptime, grism, slit, filter, shape, binning = get_header_info(fname[1:])
                     else:
-                        object, exptime, grism, slit, filter, shape = get_header_info(fname)
+                        object, exptime, grism, slit, filter, shape, binning = get_header_info(fname)
                 except FileNotFoundError:
                     print("[WARNING] - File not found: %s" % fname)
                     continue
                 except Exception:
                     print("[WARNING] - Problem reading header information: %s" % fname)
-                    object, exptime, grism, slit, filter, shape = '-', '-', '-', '-', '-', '-'
-                file_list.append((fname, filetype, object, exptime, grism, slit, filter, shape))
+                    object, exptime, grism, slit, filter, shape, binning = '-', '-', '-', '-', '-', '-', '-'
+                file_list.append((fname, filetype, object, exptime, grism, slit, filter, shape, binning))
             file_list = np.array(file_list, dtype=str)
             if len(file_list) == 0:
                 continue
-            header_names = ('FILENAME', 'TYPE', 'OBJECT', 'EXPTIME', 'GRISM', 'SLIT', 'FILTER', 'SHAPE')
+            header_names = ('FILENAME', 'TYPE', 'OBJECT', 'EXPTIME', 'GRISM', 'SLIT', 'FILTER', 'SHAPE', 'BINNING')
             max_len = np.max(veclen(file_list), 0)
             max_len = np.max([max_len, [len(n) for n in header_names]], 0)
             line_fmt = "  ".join(["%-{}s".format(n) for n in max_len])

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/data/organizer.py

@@ -200,7 +200,8 @@ def sort_bias(file_list, date=False):
     for fname in file_list:
         hdr = instrument.get_header(fname)
         size = "%ix%i" % (hdr['NAXIS1'], hdr['NAXIS2'])
-        file_id = size
+        binning = instrument.get_binning_from_hdr(hdr)
+        file_id = f"{size}_{binning}"
         if date:
             date_str = instrument.get_date(hdr)
             if 'T' in date_str:
@@ -677,6 +678,10 @@ class RawImage(object):
                 criteria.append(this_filter == self.filter)
                 criteria_name.append('filter')
 
+            if debug:
+                print(criteria_name)
+                print(criteria)
+
             if np.all(criteria):
                 matches.append(fname)
                 all_times.append(this_mjd)

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/extract_gui.py

@@ -51,27 +51,6 @@ def run_gui(input_fname, output_fname, app=None, **ext_kwargs):
     del gui
 
 
-# def save_ascii_spectrum(fname, wl, flux, err, hdr, bg=None):
-#     """Write spectrum to an ascii text file with header saved to separate text file."""
-#     if bg is not None:
-#         data_table = np.column_stack([wl, flux, err, bg])
-#         fmt = "%12.4f  % .3e  %.3e  %.3e"
-#         col_names = "# Wavelength       Flux        Error      Sky"
-#     else:
-#         data_table = np.column_stack([wl, flux, err])
-#         fmt = "%12.4f  % .3e  %.3e"
-#         col_names = "# Wavelength       Flux        Error"
-#
-#     basename, ext = os.path.splitext(fname)
-#     header_fname = basename + '_hdr.txt'
-#
-#     with open(fname, 'w') as output:
-#         output.write(col_names + "\n")
-#         np.savetxt(output, data_table, fmt=fmt)
-#     hdr.tofile(header_fname, sep='\n', endcard=False, padding=False, overwrite=True)
-#     return True, "File saved successfully"
-
-
 def get_FWHM(y, x=None):
     """
     Measure the FWHM of the profile given as `y`.
@@ -285,8 +264,8 @@ class BackgroundModel(object):
         self.patches[index].remove()
         self.patches.pop(index)
         self.ranges[index] = [i_low, i_high]
-        self.vlines[index][0].set_xdata(i_low)
-        self.vlines[index][1].set_xdata(i_high)
+        self.vlines[index][0].set_xdata([i_low])
+        self.vlines[index][1].set_xdata([i_high])
         patch = self.axis.axvspan(i_low, i_high, color='#29b6f6', alpha=0.3, picker=True)
         self.patches.insert(index, patch)
 
@@ -407,13 +386,13 @@ class TraceModel(object):
 
     def set_centroid(self, cen):
         self.cen = cen
-        self.vlines[1].set_xdata(cen)
+        self.vlines[1].set_xdata([cen])
 
     def set_range(self, lower, upper):
         self.lower = lower
         self.upper = upper
-        self.vlines[0].set_xdata(lower)
-        self.vlines[2].set_xdata(upper)
+        self.vlines[0].set_xdata([lower])
+        self.vlines[2].set_xdata([upper])
 
     def get_range(self):
         return (self.lower, self.upper)
@@ -1380,11 +1359,11 @@ class ExtractGUI(QtWidgets.QMainWindow):
 
         elif artist.get_label() == 'lower':
             trace_model.lower = new_position
-            artist.set_xdata(new_position)
+            artist.set_xdata([new_position])
 
         elif artist.get_label() == 'upper':
             trace_model.upper = new_position
-            artist.set_xdata(new_position)
+            artist.set_xdata([new_position])
         self.canvas_spsf.draw()
 
     def on_release(self, event):
@@ -1394,12 +1373,12 @@ class ExtractGUI(QtWidgets.QMainWindow):
         if artist.get_label() == 'lower':
             if trace_model.lower > trace_model.cen - 1:
                 trace_model.lower = trace_model.cen - 1
-                artist.set_xdata(trace_model.cen - 1)
+                artist.set_xdata([trace_model.cen - 1])
                 self.canvas_spsf.draw()
         elif artist.get_label() == 'upper':
             if trace_model.upper < trace_model.cen + 1:
                 trace_model.upper = trace_model.cen + 1
-                artist.set_xdata(trace_model.cen + 1)
+                artist.set_xdata([trace_model.cen + 1])
                 self.canvas_spsf.draw()
         centroid_shift = trace_model.cen - old_centroid
         if np.abs(centroid_shift) > 0:
@@ -1669,7 +1648,10 @@ class ExtractGUI(QtWidgets.QMainWindow):
     def update_xmask_in_points(self):
         # Clear old shapes:
         for item in self.xmask:
-            item.remove()
+            try:
+                item.remove()
+            except NotImplementedError:
+                pass
         self.xmask = list()
         xmin, xmax, ymin, ymax = self.get_limits()
         if xmin > 0 or xmax < self.image2d.data.shape[1]+1:

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/fitsio.py

@@ -3,6 +3,8 @@ __author__ = "Jens-Kristian Krogager"
 
 import warnings
 from astropy.io import fits
+from astropy import units as u
+from astropy.table import QTable
 import numpy as np
 import os
 
@@ -129,17 +131,17 @@ def get_wavelength_from_header(hdr):
 
 # -- These names are used to define proper column names for Wavelength, Flux and Error:
 wavelength_column_names = ['wl', 'lam', 'lambda', 'loglam', 'wave', 'wavelength', 'awav']
-flux_column_names = ['data', 'spec', 'flux', 'flam', 'fnu', 'flux_density']
-error_column_names = ['err', 'sig', 'error', 'ivar', 'sigma', 'var']
+flux_column_names = ['data', 'spec', 'flux', 'flam', 'fnu', 'flux_density', 'reduced_flux']
+error_column_names = ['err', 'sig', 'error', 'ivar', 'sigma', 'var', 'err_flux', 'flux_ivar', 'flux_var', 'flux_err']
 mask_column_names = ['mask', 'qual', 'dq', 'qc']
 
 # -- These names are used to define proper ImageHDU names for Flux and Error:
 flux_HDU_names = ['FLUX', 'SCI', 'FLAM', 'FNU']
-error_HDU_names = ['ERR', 'ERRS', 'SIG', 'SIGMA', 'ERROR', 'ERRORS', 'IVAR', 'VAR']
+error_HDU_names = ['ERR', 'ERRS', 'SIG', 'SIGMA', 'ERROR', 'ERRORS', 'IVAR', 'VAR', 'ERR_FLUX']
 mask_HDU_names = ['MASK', 'QUAL', 'QC', 'DQ']
 
 
-def get_spectrum_fits_table(tbdata):
+def get_spectrum_fits_table(table_hdu):
     """
     Scan the TableData for columns containing wavelength, flux, error and mask.
     All arrays of {wavelength, flux and error} must be present.
@@ -163,7 +165,12 @@ def get_spectrum_fits_table(tbdata):
         Numpy boolean array of pixel mask. `True` if the pixel is 'good',
         `False` if the pixel is bad and should not be used.
     """
-    table_names = [name.lower() for name in tbdata.names]
+    tbdata = QTable.read(table_hdu)
+    # table_names = [name.lower() for name in tbdata.names]
+    for colname in tbdata.colnames:
+        tbdata.rename_column(colname, colname.lower())
+    table_names = tbdata.colnames
+
     wl_in_table = False
     for colname in wavelength_column_names:
         if colname in table_names:
@@ -185,9 +192,10 @@ def get_spectrum_fits_table(tbdata):
     for colname in error_column_names:
         if colname in table_names:
             error_in_table = True
-            if colname == 'ivar':
-                error = 1./np.sqrt(tbdata[colname])
-            elif colname == 'var':
+            if 'ivar' in colname.lower():
+                with np.errstate(divide='ignore', invalid='ignore'):
+                    error = 1 / np.sqrt(tbdata[colname])
+            elif 'var' in colname.lower():
                 error = np.sqrt(tbdata[colname])
             else:
                 error = tbdata[colname]
@@ -208,6 +216,7 @@ def get_spectrum_fits_table(tbdata):
 
     return wavelength.flatten(), data.flatten(), error.flatten(), mask.flatten()
 
+
 # Hack the doc-string of the function to input the variable names:
 output_column_names = {'WL_COL_NAMES': wavelength_column_names,
                        'FLUX_COL_NAMES': flux_column_names,
@@ -270,6 +279,7 @@ def get_spectrum_hdulist(HDUlist):
 
     return data, error, mask, data_hdr
 
+
 # Hack the doc-string of the function to input the variable names:
 output_hdu_names = {'FLUX_HDU_NAMES': flux_HDU_names,
                     'ERR_HDU_NAMES': error_HDU_names}
@@ -363,17 +373,19 @@ def load_fits_spectrum(fname, ext=None, iraf_obj=None):
         else:
             is_fits_table = isinstance(HDUlist[1], fits.BinTableHDU) or isinstance(HDUlist[1], fits.TableHDU)
             if is_fits_table:
-                if ext:
-                    tbdata = HDUlist[ext].data
-                    data_hdr = HDUlist[ext].header
-                else:
-                    tbdata = HDUlist[1].data
-                    data_hdr = HDUlist[1].header
+                if not ext:
+                    ext = 1
+
+                table_hdu = HDUlist[ext]
+                tbdata = table_hdu.data
+                data_hdr = table_hdu.header
 
                 has_multi_extensions = len(HDUlist) > 2
                 if has_multi_extensions and (ext is None):
                     msg = "[WARNING] - More than one data extension detected in the file"
-                wavelength, data, error, mask = get_spectrum_fits_table(tbdata)
+                wavelength, data, error, mask = get_spectrum_fits_table(table_hdu)
+                if 'CUNIT1' in data_hdr:
+                    wavelength *= u.Unit(data_hdr['CUNIT1'])
                 return wavelength, data, error, mask, data_hdr, msg
 
             elif len(HDUlist) == 2:
@@ -536,3 +548,11 @@ def create_error_image(base_fname, overwrite=False):
             hdu.append(ext)
     output_msg = "          - Successfully created an error image"
     return output_msg
+
+
+def detect_4most_MEC(fname):
+    prim = fits.getheader(fname)
+    is_qmost = prim.get('INSTRUME', 'NONE').strip() == 'QMOST'
+    hdr = fits.getheader(fname, 1)
+    has_mec_extname = hdr.get('EXTNAME') in ['OBMETATAB', 'SPECTAB', 'FIBMETATAB']
+    return is_qmost & has_mec_extname

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/identify_gui.py

@@ -21,6 +21,7 @@ from PyQt5 import QtWidgets
 from scipy.optimize import curve_fit
 from numpy.polynomial import Chebyshev
 from astropy.io import fits
+from astropy.table import Table
 
 from pynot import instrument
 from pynot.data import organizer
@@ -226,7 +227,7 @@ def load_linelist(fname):
 
 class GraphicInterface(QtWidgets.QMainWindow):
     def __init__(self, arc_fname='', grism_name='', pixtable='', linelist_fname='', output='',
-                 dispaxis=2, order_wl=3, air=False, loc=-1, parent=None, locked=False, vac=True):
+                 dispaxis=2, order_wl=3, air=False, loc=-1, parent=None, locked=False):
         QtWidgets.QMainWindow.__init__(self, parent)
         self.setWindowTitle('PyNOT: Identify Arc Lines')
         self._main = QtWidgets.QWidget()
@@ -572,9 +573,9 @@ class GraphicInterface(QtWidgets.QMainWindow):
             self.reftable.setItem(rowPosition, 1, item2)
 
     def load_spectrum(self, arc_fname=None):
-        if arc_fname is False:
+        if not arc_fname:
             current_dir = './'
-            filters = "FITS files (*.fits | *.fit)"
+            filters = "FITS or txt files (*.fits | *.fit | *.txt | *.csv)"
             arc_fname = QtWidgets.QFileDialog.getOpenFileName(self, 'Open Pixeltable', current_dir, filters)
             arc_fname = str(arc_fname[0])
             if self.first_time_open:
@@ -583,6 +584,31 @@ class GraphicInterface(QtWidgets.QMainWindow):
                 self.first_time_open = False
 
         if arc_fname:
+
+            try:
+                tab1d = Table.read(arc_fname, hdu=1, format='fits')
+                self.pix = tab1d['pixel']
+                self.arc1d = tab1d['flux']
+                self.update_arc1d()
+                return
+
+            except (OSError, ValueError):
+                try:
+                    tab1d = Table.read(arc_fname, format='ascii')
+                    tab1d.rename_column(tab1d.colnames[0], 'pixel')
+                    tab1d.rename_column(tab1d.colnames[1], 'flux')
+                    self.pix = tab1d['pixel']
+                    self.arc1d = tab1d['flux']
+                    self.update_arc1d()
+                    return
+                except Exception:
+                    if 'fits' in arc_fname.lower():
+                        pass
+                    else:
+                        error_msg = "Could not read the spectrum. Must be a FITS or ASCII table, or a FITS 2D image"
+                        QtWidgets.QMessageBox.critical(None, 'Invalid Format!', error_msg)
+                        return
+
             self.arc_fname = arc_fname
             with fits.open(arc_fname) as hdu:
                 primhdr = hdu[0].header
@@ -647,7 +673,9 @@ class GraphicInterface(QtWidgets.QMainWindow):
 
         self.arc1d = np.nanmean(self.arc_image_data[:, ilow:ihigh], axis=1)
         self.pix = instrument.create_pixel_array(self.primhdr, self.dispaxis)
+        self.update_arc1d()
 
+    def update_arc1d(self):
         self.ax.lines[0].set_data(self.pix, self.arc1d)
         self.ax.relim()
         self.ax.autoscale()

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/main.py

@@ -372,6 +372,10 @@ def main(inspect=False):
                               help="Set this option for 2D spectra of extended sources to turn off automatic localization")
     parser_scomb.add_argument("--mef", action="store_false",
                               help="Set this option to save output as a multiextension FITS file instead of a FITS table.")
+    parser_scomb.add_argument("--imin", type=int, default=0,
+                              help="Slice each input spectrum along dispersion axis [imin:imax], only for 1D spectra")
+    parser_scomb.add_argument("--imax", type=int, default=None,
+                              help="Slice each input spectrum along dispersion axis [imin:imax], only for 1D spectra")
 
 
     # -- extract :: Extraction of 1D spectrum from 2D
@@ -389,6 +393,31 @@ def main(inspect=False):
     set_default_pars(parser_ext, section='extract', default_type=int,
                      ignore_pars=['interactive'])
 
+    # -- view :: View 1D spectra in an interactive window
+    parser_view = tasks.add_parser('view', formatter_class=set_help_width(31),
+                                   help="Display and interact with 1D spectra")
+    parser_view.add_argument("files", type=str, nargs='*',
+                             help="Filenames of spectral data to load. Each file is loaded as one target")
+    parser_view.add_argument("-t", "--table", type=str,
+                             help="Filename of association table. Each line in the file gives a comma-separated list of filenames. "
+                                  "All files in one line are loaded as a single target.")
+    parser_view.add_argument("-c", "--container", action="store_true",
+                             help="Load the file(s) as a FITS container "
+                                  "(such as 4MOST MEC, SDSS bricks, or a large collection of files)")
+    parser_view.add_argument("-l", "--list", type=str, default='',
+                             help="File list. Name of a text file where each line is the path of one spectrum."
+                                  "(Useful for loading many files in `container` mode with `-c`)")
+    # redshift_table=None, z_col=None, name_col=None, cls_col=None
+    parser_view.add_argument("-z", type=str, default='',
+                             help="Filename of redshift catalog with a name, redshift and spectral type column. "
+                                  "Set column names using `--ncol`, `--zcol`, `--tcol`")
+    parser_view.add_argument("--ncol", type=str, default='',
+                             help="Name of the target name column in `-z REDSHIFT_TABLE`")
+    parser_view.add_argument("--zcol", type=str, default='',
+                             help="Name of the redshift column in `-z REDSHIFT_TABLE`")
+    parser_view.add_argument("--tcol", type=str, default='',
+                             help="Name of the spectral type column in `-z REDSHIFT_TABLE`")
+
 
     # Spectral Redux:
     parser_redux = tasks.add_parser('spex', formatter_class=set_help_width(30),
@@ -770,7 +799,7 @@ def main(inspect=False):
 
         if data_is_1d:
             out_args = combine_1d(filelist, output=args.output, method=args.method,
-                                  scale=args.scale, table_output=args.mef)
+                                  scale=args.scale, table_output=args.mef, imin=args.imin, imax=args.imax)
         else:
             out_args = combine_2d(filelist, output=args.output, method=args.method, trim=args.trim,
                                   scale=args.scale, extended=args.extended, dispaxis=args.axis)
@@ -796,6 +825,28 @@ def main(inspect=False):
             gui.show()
             app.exit(app.exec_())
 
+    elif task == 'view':
+        from PyQt5 import QtWidgets
+        from pynot.viewer.viewer import MainWindow
+
+        app = QtWidgets.QApplication(sys.argv)
+        screenSize = app.primaryScreen().size()
+        ratio = 0.85
+        if args.list:
+            with open(args.list) as l:
+                input_files = [line.strip() for line in l.readlines()]
+        else:
+            input_files = args.files
+        main = MainWindow(input_files,
+                          assn_table=args.table,
+                          container_mode=args.container,
+                          width=ratio*screenSize.width(),
+                          height=ratio*screenSize.height(),
+                          redshift_table=args.z,
+                          z_col=args.zcol, name_col=args.ncol, cls_col=args.tcol,
+                          )
+        main.show()
+        app.exit(app.exec_())
 
     # -- Imaging tasks:
     elif task == 'phot':

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/redux.py

@@ -193,13 +193,13 @@ def run_pipeline(options_fname, object_id=None, verbose=True, interactive=False,
     identify_all = options['identify']['all']
     local_pixtables = glob.glob(os.path.join(output_base, "arcs", "pixtab_*.dat"))
     for fname in local_pixtables:
-        pixtab_id = os.path.splitext(fname)[0].split('_')[1]
+        pixtab_id = os.path.splitext(os.path.basename(fname))[0].split('_')[1]
         status[pixtab_id] = fname
     cached_pixtables = glob.glob(os.path.join(calib_dir, "*_pixeltable.dat"))
     for fname in cached_pixtables:
         # TODO: Potentially use `basename(fname)` to split
         # This avoids bugs if the filename contains more than one `_`
-        pixtab_id = fname.split('_')[0]
+        pixtab_id = os.path.basename(fname).split('_')[0]
         status[pixtab_id] = fname
 
 

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/scombine.py

@@ -5,7 +5,7 @@ from functools import reduce
 import warnings
 
 from pynot.functions import get_version_number
-from pynot.fitsio import load_fits_spectrum, save_fitstable_spectrum, save_fits_spectrum
+from pynot.fitsio import load_fits_spectrum, save_fitstable_spectrum, save_fits_spectrum, error_HDU_names
 from pynot.txtio import load_ascii_spectrum
 
 
@@ -55,18 +55,26 @@ def combine_2d(files, output=None, method='mean', scale=False, extended=False, d
         hdr = fits.getheader(fname)
         data2D = fits.getdata(fname)
 
-        try:
-            err2D = fits.getdata(fname, 'ERR')
-            err2D[err2D <= 0.] = np.nanmedian(err2D)*100
-            msg.append("          - Loaded error image")
-        except KeyError:
+        for err_name in error_HDU_names:
+            try:
+                err2D = fits.getdata(fname, err_name)
+                err2D[err2D <= 0.] = np.nanmedian(err2D)*100
+                msg.append(f"          - Loaded error image extension: {err_name}")
+                break
+            except KeyError:
+                pass
+        else:
             msg.append("[WARNING] - No ERR extension could be found in the FITS file!")
             err2D = np.ones_like(data2D)
 
-        try:
-            mask2D = fits.getdata(fname, 'MASK')
-            msg.append("          - Loaded mask image")
-        except KeyError:
+        for mask_name in ['MASK', 'QUAL']:
+            try:
+                mask2D = fits.getdata(fname, mask_name)
+                msg.append(f"          - Loaded mask image extension: {mask_name}")
+                break
+            except KeyError:
+                pass
+        else:
             msg.append("[WARNING] - No MASK extension could be found in the FITS file!")
             mask2D = np.zeros_like(data2D)
 
@@ -345,7 +353,7 @@ def combine_2d(files, output=None, method='mean', scale=False, extended=False, d
 
 
 
-def combine_1d(files, output=None, method='mean', scale=False, table_output=True):
+def combine_1d(files, output=None, method='mean', scale=False, table_output=True, imin=0, imax=None):
     """Combine a list of 1d-spectra using either median or mean combination.
     For median combination, only the overlapping parts of the spectra will be
     combined. The mean combination uses a weighted average over the entire
@@ -368,6 +376,12 @@ def combine_1d(files, output=None, method='mean', scale=False, table_output=True
 
     table_output : bool   [default=True]
         Use FITS table for the output format? Otherwise use a MultiExtension Fits File
+
+    imin : int
+        Apply slicing to each spectrum from imin to imax.
+
+    imax : int | None
+        Apply slicing to each spectrum from imin to imax.
     """
 
     wl_all = list()
@@ -377,6 +391,7 @@ def combine_1d(files, output=None, method='mean', scale=False, table_output=True
     size_all = list()
     scales = list()
 
+    cut = slice(imin, imax)
     msg = list()
     for fname in files:
         if fname.endswith('.fits') or fname.endswith('.fit'):
@@ -393,11 +408,11 @@ def combine_1d(files, output=None, method='mean', scale=False, table_output=True
                 msg.append(load_msg)
             msg.append("          - Loaded ASCII spectrum: %s" % fname)
 
-        wl_all.append(wl)
-        flux_all.append(flux)
-        err_all.append(err)
-        mask_all.append(mask)
-        size_all.append(len(wl))
+        wl_all.append(wl[cut])
+        flux_all.append(flux[cut])
+        err_all.append(err[cut])
+        mask_all.append(mask[cut])
+        size_all.append(len(wl[cut]))
         if scale:
             nonzero = flux.nonzero()[0]
             idx_0 = min(nonzero) + len(nonzero)/2

{pynot_redux-2.1.2 → pynot_redux-2.2}/pynot/skysub.py

@@ -30,6 +30,7 @@ def fit_background_row(x, row, mask=None, order_bg=3, med_kernel=15, kappa=5):
         mask = np.ones(len(row), dtype=bool)
 
     # Median filter the data to remove outliers:
+    row = row.astype(np.float64)
     med_row = median_filter(row, med_kernel)
     noise = mad(row) * 1.4826
     this_mask = mask * (np.abs(row - med_row) < kappa*noise)