PyNOT-redux 2.3__tar.gz → 2.4__tar.gz

{pynot_redux-2.3 → pynot_redux-2.4}/.gitignore

@@ -136,3 +136,4 @@ pynot/.instrument.cfg
 .DS_Store
 .DS_Store
 .DS_Store
+*.vscode

{pynot_redux-2.3 → pynot_redux-2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.3
+Version: 2.4
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

{pynot_redux-2.3 → pynot_redux-2.4}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.3
+Version: 2.4
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

pynot_redux-2.4/pynot/VERSION

@@ -0,0 +1 @@
+2.4

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/calib/default_options.yml

@@ -92,3 +92,5 @@ response:
   kappa:        2            # Threshold for the median filtering to remove outlying response points
   interactive:  False        # Interactively filter and fit the response function
   force:        False        # Overwrite existing response function?
+  match_date:   False        # Use only response functions taken on the same day as the science exposure?
+  match_slit:   False        # Match both GRISM and SLIT of the science observations?

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/data/io.py

@@ -44,7 +44,7 @@ def save_database(database, output_fname):
         for filetype, files in sorted(database.items()):
             output.write("## %s:\n" % filetype)
             file_list = list()
-            files += database.inactive.get(filetype, [])
+            files = files + database.inactive.get(filetype, [])
             sorted_files = sorted(files, key=lambda x: x[1:] if len(x) > 1 else x)
             for fname in sorted_files:
                 try:

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/data/organizer.py

@@ -81,7 +81,7 @@ def match_date(files, date_mjd):
 
     return matches
 
-def match_response(sci_img, file_list, exact_date=False):
+def match_response(sci_img, file_list, exact_date=False, match_slit=False):
     """
     Find response function that matches the grism of the input `sci_img`
     If `exact_date` is True, only return a match if the date matches exactly that of `sci_img`
@@ -89,17 +89,29 @@ def match_response(sci_img, file_list, exact_date=False):
     """
     target_grism = sci_img.grism
     target_mjd = sci_img.mjd
+    target_slit = sci_img.slit
     matches = list()
     date_diff = list()
     for fname in file_list:
         # These are PyNOT FITS files, so follows a slightly different Header Format
         hdr = fits.getheader(fname)
         this_grism = hdr['GRISM']
+        this_slit = hdr['SLIT']
         this_date = Time(hdr['DATE-OBS'])
-        if this_grism == target_grism:
+        if not match_slit:
+            slit_filter = True
+        elif match_slit and this_slit == target_slit:
+            slit_filter = True
+        else:
+            slit_filter = False
+
+        if this_grism == target_grism and slit_filter:
             matches.append(fname)
             date_diff.append(this_date.mjd - target_mjd)
 
+    if len(matches) == 0:
+        return ""
+
     # Find target with smallest time difference
     idx = np.argmin(np.abs(date_diff))
     match_fname = matches[idx]
@@ -540,7 +552,7 @@ class UnknownObservingMode(Exception):
     pass
 
 
-class RawImage(object):
+class RawImage:
     """
     Create a raw image instance from a FITS image.
 

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/extraction.py

@@ -8,7 +8,7 @@ from scipy.signal import find_peaks
 from numpy.polynomial import Chebyshev
 import warnings
 
-from lmfit import Parameters, minimize
+from lmfit import Parameters, minimize, MinimizerException
 
 from pynot.functions import mad, NN_moffat, NN_gaussian, fix_nans, get_version_number
 from pynot import instrument
@@ -158,8 +158,8 @@ def fit_trace(img2D, x, y, model_name='moffat', dx=50, kappa=10., ymin=5, ymax=-
 
     # Fit trace with N objects:
     msg.append("          - Fitting the spectral trace with a %s profile" % model_name.title())
-    trace_parameters = list()
-    x_binned = np.arange(0., img2D.shape[1], dx, dtype=np.float64)
+    trace_parameters = []
+    x_binned = []
     for num in range(0, img2D.shape[1], dx):
         pars = prep_parameters(peaks, prominences, size=img2D.shape[0], model_name=model_name)
         col = np.nanmean(img2D[:, num:num+dx], axis=1)
@@ -173,12 +173,19 @@ def fit_trace(img2D, x, y, model_name='moffat', dx=50, kappa=10., ymin=5, ymax=-
                 if par_val.stderr is None:
                     par_val.stderr = 100.
             trace_parameters.append(popt.params)
+            x_binned.append(num + dx/2)
+        except (OverflowError, RuntimeError, MinimizerException):
+            msg.append(f"[WARNING] - Fitting of the trace model using a {model_name} model failed!")
+            msg.append("            Consider using a 'tophat' model, increase `dx` and decrease `order_center`")
+            msg.append("[WARNING] - Skipping this location %i:%i" % (num, num+dx))
         except ValueError:
             for par_val in pars.values():
                 par_val.stderr = 100.
             trace_parameters.append(pars)
+            x_binned.append(num + dx/2)
     msg.append("          - Fitted %i points along the spectral trace" % len(trace_parameters))
     output_msg = "\n".join(msg)
+    x_binned = np.array(x_binned)
     return (x_binned, N_obj, trace_parameters, fwhm, output_msg)
 
 
@@ -262,6 +269,9 @@ def create_2d_profile(img2D, model_name='moffat', dx=25, width_scale=2, kappa_de
         fit_values = fit_trace(img2D, x, y, model_name=model_name, dx=dx, ymin=ymin, ymax=ymax, xmin=xmin, xmax=xmax, kappa=kappa_det)
     x_binned, N_obj, trace_parameters, fwhm, fit_msg = fit_values
     msg.append(fit_msg)
+    if len(trace_parameters) == 0:
+        msg.append(" [ERROR]  - Automated fitting of the trace failed!")
+        raise ValueError("Could not determine the trace position!")
 
     msg.append("          - Creating 2D spectral profile from fitted parameters")
     msg.append("          - Profile type: %s" % model_name)

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/phot.py

@@ -8,7 +8,6 @@ from matplotlib.patches import Ellipse
 from astropy.io import fits
 from astropy.modeling import models, fitting
 from astropy.table import Table
-from scipy.optimize import curve_fit
 import os
 
 from astropy.coordinates import SkyCoord
@@ -92,11 +91,11 @@ def source_detection(fname, zeropoint=0., threshold=5.0, aperture=10.0, kwargs_b
     data_sub = data - bkg
     msg.append("          - Subtracted sky background")
     msg.append("          - Background RMS: %.2e" % bkg.globalrms)
-    data_sub = data_sub.byteswap().newbyteorder()
-    error_image = error_image.byteswap().newbyteorder()
+    data_sub = data_sub.byteswap().view(data_sub.dtype.newbyteorder())
+    error_image = error_image.byteswap().view(error_image.dtype.newbyteorder())
     if data_sub.dtype.byteorder != '<':
-        data_sub = data_sub.byteswap().newbyteorder()
-        error_image = error_image.byteswap().newbyteorder()
+        data_sub = data_sub.byteswap().view(data_sub.dtype.newbyteorder())
+        error_image = error_image.byteswap().view(error_image.dtype.newbyteorder())
     extract_output = sep.extract(data_sub, threshold, err=bkg.globalrms, **kwargs_ext)
     if len(extract_output) == 2:
         objects, segmap = extract_output
@@ -366,9 +365,9 @@ def image_combine(corrected_images, output='', log_name='', fringe_image='', met
     msg.append("          - Registering input images:")
     shifted_images = [target]
     shifted_vars = [target_err**2]
-    target = target.byteswap().newbyteorder()
+    target = target.byteswap().view(target.dtype.newbyteorder())
     if target.dtype.byteorder != '<':
-        target = target.byteswap().newbyteorder()
+        target = target.byteswap().view(target.dtype.newbyteorder())
     final_exptime = exptime
     image_log = list()
     if len(corrected_images) > 1:
@@ -385,20 +384,20 @@ def image_combine(corrected_images, output='', log_name='', fringe_image='', met
                                                      max_control_points=max_control_points,
                                                      detection_sigma=detection_sigma,
                                                      min_area=min_area)
-            except:
+            except (TypeError, ValueError, aa.MaxIterError):
                 msg.append(" [ERROR]  - Failed to find image transformation!")
                 msg.append("          - Skipping image")
                 continue
 
-            source = source.byteswap().newbyteorder()
-            source_err = source_err.byteswap().newbyteorder()
-            source_mask = source_mask.byteswap().newbyteorder()
+            source = source.byteswap().view(source.dtype.newbyteorder())
+            source_err = source_err.byteswap().view(source_err.dtype.newbyteorder())
+            source_mask = source_mask.byteswap().view(source_mask.dtype.newbyteorder())
             if source.dtype.byteorder != '<':
-                source = source.byteswap().newbyteorder()
+                source = source.byteswap().view(source.dtype.newbyteorder())
             if source_err.dtype.byteorder != '<':
-                source_err = source_err.byteswap().newbyteorder()
+                source_err = source_err.byteswap().view(source_err.dtype.newbyteorder())
             if source_mask.dtype.byteorder != '<':
-                source_mask = source_mask.byteswap().newbyteorder()
+                source_mask = source_mask.byteswap().view(source_mask.dtype.newbyteorder())
 
             registered_image, _ = aa.apply_transform(transf, source, target, fill_value=0)
             registered_error, _ = aa.apply_transform(transf, source_err, target, fill_value=0)
@@ -584,11 +583,13 @@ def match_phot_catalogs(sep, phot, match_radius=1.):
 
 def get_sdss_catalog(ra, dec, radius=4.):
     """Download the SDSS photometry using astroquery for a circular region of radius in deg."""
+    # astroquery enforces radius < 3 arcmin when photoobj_fields are requested
+    radius = min(radius, 2.9)
     catalog_fname = 'sdss_phot_%.2f%+.2f.csv' % (ra, dec)
     fields = ['ra', 'dec', 'psfMag_u', 'psfMag_g', 'psfMag_r', 'psfMag_i', 'psfMag_z',
               'psfMagErr_u', 'psfMagErr_g', 'psfMagErr_r', 'psfMagErr_i', 'psfMagErr_z']
     field_center = SkyCoord(ra, dec, frame='icrs', unit='deg')
-    sdss_result = SDSS.query_region(field_center, radius*u.arcmin, photoobj_fields=fields)
+    sdss_result = SDSS.query_region(field_center, radius=radius*u.arcmin, photoobj_fields=fields)
     if sdss_result is not None:
         sdss_result.write(os.path.join(obs.output_base_phot, catalog_fname), format='ascii.csv', overwrite=True)
     return sdss_result
@@ -641,14 +642,12 @@ def flux_calibration_sdss(img_fname, sep_fname, fig_fname='', q_lim=0.8, kappa=3
     msg.append("          - Downloading SDSS photometric catalog...")
     try:
         sdss_cat = get_sdss_catalog(hdr['CRVAL1'], hdr['CRVAL2'], radius)
-    except:
+    except Exception as e:
         msg.append(" [ERROR]  - Could not connect to SDSS server. Check your internet connection.")
         msg.append("")
+        msg.append(str(e))
         return "\n".join(msg)
 
-    def line(x, zp):
-        return zp + x
-
     if sdss_cat is None:
         msg.append(" [ERROR]  - No data found in SDSS. No zero point calculated")
         msg.append("")
@@ -708,8 +707,14 @@ def flux_calibration_sdss(img_fname, sep_fname, fig_fname='', q_lim=0.8, kappa=3
     m_inst = match_sep['mag_auto']
     k = ext_coeffs[band]
 
+    # Reject non-finite measurements (e.g. negative fluxes giving NaN magnitudes):
+    finite = np.isfinite(mag) & np.isfinite(mag_err) & np.isfinite(m_inst) & (mag_err > 0)
+    mag = mag[finite]
+    mag_err = mag_err[finite]
+    m_inst = m_inst[finite]
+
     # Get first estimate using the median:
-    zp0, _ = curve_fit(line, m_inst+k*airmass, mag, p0=[27], sigma=mag_err)
+    zp0 = np.median(mag - m_inst - k*airmass)
 
     # Filter outliers:
     cut = np.abs(zp0 + m_inst + k*airmass - mag) < kappa*mad(zp0 + m_inst + k*airmass - mag)

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/phot_redux.py

@@ -123,7 +123,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                                               overwrite=True)
             log.commit(bias_msg)
             log.add_linebreak()
-        except:
+        except Exception:
             log.error("Median combination of bias frames failed!")
             log.fatal_error()
             print("Unexpected error:", sys.exc_info()[0])
@@ -143,7 +143,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                                               overwrite=True, mode='img')
             log.commit(flat_msg)
             master_flat[filter_name] = comb_flat_fname
-        except:
+        except Exception:
             log.error("Flat field combination failed for filter: %s" % filter_name)
             log.fatal_error()
             print("Unexpected error:", sys.exc_info()[0])
@@ -156,7 +156,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
             log.write("Detected edges on Y-axis: %i  ;  %i" % (y1, y2))
             log.add_linebreak()
             filter_edges[filter_name] = (x1, x2, y1, y2)
-        except:
+        except Exception:
             log.error("Automatic edge detection failed!")
             log.fatal_error()
             print("Unexpected error:", sys.exc_info()[0])
@@ -217,7 +217,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                                        output=corrected_fname, overwrite=True, mode='img')
                     log.commit("          - bias+flat ")
                     temp_images.append(corrected_fname)
-                except:
+                except Exception:
                     log.error("Bias and flat field correction failed!")
                     log.fatal_error()
                     print("Unexpected error:", sys.exc_info()[0])
@@ -228,7 +228,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                 try:
                     _ = trim_filter_edge(corrected_fname, *image_region, output=trim_fname)
                     log.commit(" trim ")
-                except:
+                except Exception:
                     log.error("Image trim failed!")
                     log.fatal_error()
                     print("Unexpected error:", sys.exc_info()[0])
@@ -242,7 +242,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                         log.commit("  [done]")
                         corrected_images.append(crr_fname)
                         temp_images.append(trim_fname)
-                    except:
+                    except Exception:
                         log.error("Cosmic ray correction failed!")
                         log.fatal_error()
                         print("Unexpected error:", sys.exc_info()[0])
@@ -265,7 +265,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                                               threshold=3)
                     log.commit(msg)
                     log.add_linebreak()
-                except:
+                except Exception:
                     log.error("Image combination failed!")
                     log.fatal_error()
                     print("Unexpected error:", sys.exc_info()[0])
@@ -294,8 +294,8 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                 log.error(str(e))
                 log.fatal_error()
                 return
-            except:
-                log.datal_error()
+            except Exception:
+                log.fatal_error()
                 print("Unexpected error:", sys.exc_info()[0])
                 raise
 
@@ -308,7 +308,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                                                             kwargs_ext=options['sep-extract'])
                 log.commit(output_msg)
                 log.add_linebreak()
-            except:
+            except Exception:
                 log.error("Source extraction failed!")
                 log.fatal_error()
                 print("Unexpected error:", sys.exc_info()[0])
@@ -321,7 +321,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                 output_msg = correct_wcs(combined_fname, sep_fname, **options['wcs'])
                 log.commit(output_msg)
                 log.add_linebreak()
-            except:
+            except Exception:
                 log.error("WCS calibration failed!")
                 log.fatal_error()
                 print("Unexpected error:", sys.exc_info()[0])
@@ -335,7 +335,7 @@ def run_pipeline(options_fname, verbose=False, force_restart=False):
                     output_msg = flux_calibration_sdss(combined_fname, sep_fname, **options['sdss_flux'])
                     log.commit(output_msg)
                     log.add_linebreak()
-                except:
+                except Exception:
                     log.error("Zero point calibration failed!")
                     log.fatal_error()
                     print("Unexpected error:", sys.exc_info()[0])

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/redux.py

@@ -463,7 +463,10 @@ def run_pipeline(options_fname, object_id=None, verbose=True, interactive=False,
 
                     # Flux Calibration:
                     if database.has_tag('RESPONSE'):
-                        response_fname = do.match_response(sci_img, database['RESPONSE'], exact_date=False)
+                        response_fname = do.match_response(sci_img, database['RESPONSE'],
+                                                           exact_date=task_options['response']['match_date'],
+                                                           match_slit=task_options['response']['match_slit'],
+                                                           )
                     else:
                         response_fname = ''
 
@@ -483,6 +486,8 @@ def run_pipeline(options_fname, object_id=None, verbose=True, interactive=False,
                     else:
                         log.warn("Could not find a response function that matches the observations!")
                         log.warn("The spectra will not be flux clibrated!")
+                        log.warn("Response functions in the database:")
+                        log.warn(", ".join(database['RESPONSE']))
                         status['FLUX2D'] = crr_fname
 
 

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/viewer/containers.py

@@ -1,6 +1,7 @@
 import os
 import numpy as np
 from astropy.io import fits
+from astropy.table import Table
 import astropy.units as u
 
 from pynot.viewer.spectrum import Spectrum
@@ -47,6 +48,8 @@ class QMEC:
         with fits.open(self.filename) as hdu:
             data = hdu['SPECTAB'].data[index]
             hdr = hdu['SPECTAB'].header
+            fibinfo = dict(Table.read(hdu['FIBMETATAB'])[index])
+            prov = hdu['PROVTAB'].data[::3][index]['ESOFILENAME']
 
             flux = data['FLUX'].flatten()
             try:
@@ -62,9 +65,9 @@ class QMEC:
             spectrum = Spectrum(wavelength=wavelength,
                                 flux=flux*flux_unit,
                                 error=error*flux_unit,
-                                name=f"[{index}]",
-                                filename=self.filename+f"[{index}]",
-                                meta=dict(hdr))
+                                name=fibinfo['OBJ_NME'],
+                                filename=prov,
+                                meta=fibinfo)
             target.add_spectrum(spectrum)
             return target
 

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/viewer/notes.py

@@ -63,7 +63,7 @@ class TargetNote:
 
 
 REDSHIFT_NAMES = ['REDSHIFT', 'Z_SPEC', 'ZBEST', 'Z_PIPE', 'ZSPEC', 'Z', 'ZFIT', 'Z_VI']
-ID_NAMES = ['SPECUID', 'FILENAME', 'PROV', 'OBJ_NME', 'OBJ_UID', 'NAME', 'OBJECT', 'TARGET', 'TARGETID', 'ID', 'UID']
+ID_NAMES = ['PROV', 'FILENAME', 'PROV', 'OBJ_NME', 'OBJ_UID', 'NAME', 'OBJECT', 'TARGET', 'TARGETID', 'ID', 'UID']
 CLASS_NAMES = ['TYPE', 'ZBESTTYPE', 'SPECTYPE', 'CLASS', 'CLASSIFICATION', 'OBJ_CLS']
 
 
@@ -152,6 +152,10 @@ def load_redshift_table(filename, z_col=None, name_col=None, cls_col=None):
     redshift_table['TYPE'] = spectype
     redshift_table.meta['NAME_COLUMN'] = name_column
     redshift_table.add_index('NAME')
+    if 'ZBESTPROB' in tab.colnames:
+        redshift_table['ZPROB'] = tab['ZBESTPROB']
+    else:
+        redshift_table['ZPROB'] = np.nan
     return redshift_table
 
 
@@ -169,29 +173,31 @@ def redshift_table_lookup(redshift_table, spectrum):
     else:
         if not spectrum.meta:
             logging.error("Could not find a redshift. Spectrum has no metadata")
-            return np.nan, ""
+            return np.nan, "", np.nan
 
         try:
             name = spectrum.meta[name_column]
         except KeyError:
             logging.error(f"Could not find a redshift. Spectrum has no {name_column} meta data")
-            return np.nan, ""
+            return np.nan, "", np.nan
 
     try:
         row = redshift_table.loc[name]
         if isinstance(row, Table):
             z = row['REDSHIFT'][0]
             spectype = row['TYPE'][0]
+            zprob = row['ZPROB'][0]
             logging.warning(f"Multiple matches for name: {name}. Redshifts: {row['REDSHIFT']}")
             logging.warning(f"Multiple redshifts: Choosing the first: z = {z}, spectral type: {spectype}")
         else:
             z = row['REDSHIFT']
             spectype = row['TYPE']
-        return z, spectype
+            zprob = row['ZPROB']
+        return z, spectype, zprob
 
     except KeyError:
         logging.error(f"No matching redshift for name: {name}")
-        return np.nan, ""
+        return np.nan, "", np.nan
 
 
 def to_json(target: TargetNote):

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/viewer/viewer.py

@@ -511,8 +511,9 @@ class MainWindow(QtWidgets.QMainWindow):
         self.plot_spectrum(target)
 
         if self.redshift_table and len(target.spectra) > 0:
-            z, spectype = redshift_table_lookup(self.redshift_table, target.spectra[0])
+            z, spectype, zprob = redshift_table_lookup(self.redshift_table, target.spectra[0])
             self.update_redshift(z)
+            self.update_zprob(zprob)
         self.sync_target_notes()
         self.sync_target_flags()
         target_flag: DataFlag = self.target_flags.get(target.name, DataFlag(0))
@@ -711,24 +712,36 @@ class MainWindow(QtWidgets.QMainWindow):
         self.slider_scale = 100_000
         self.slider.setRange(int(-0.1*self.slider_scale), int(7*self.slider_scale))
 
+        self.z_plusplus_btn = QtWidgets.QPushButton("++")
+        self.z_minusminus_btn = QtWidgets.QPushButton("--")
+        self.z_plusplus_btn.clicked.connect(lambda x: self.z_increment(0.001))
+        self.z_minusminus_btn.clicked.connect(lambda x: self.z_increment(-0.001))
         self.z_plus_btn = QtWidgets.QPushButton("+")
         self.z_minus_btn = QtWidgets.QPushButton("-")
-        self.z_plus_btn.clicked.connect(self.z_increment)
-        self.z_minus_btn.clicked.connect(self.z_decrement)
+        self.z_plus_btn.clicked.connect(lambda x: self.z_increment(0.0005))
+        self.z_minus_btn.clicked.connect(lambda x: self.z_increment(-0.0005))
         self.z_reset_btn = QtWidgets.QPushButton("Reset z")
         self.z_reset_btn.clicked.connect(self.reset_table_redshift)
 
         self.z_input = QtWidgets.QLineEdit("0.0")
         self.z_input.setFixedWidth(60)
 
+        self.zprob_text = QtWidgets.QLineEdit("0.0")
+        self.zprob_text.setFixedWidth(45)
+        self.zprob_text.setReadOnly(True)
+
         lines_toolbar.addWidget(self.linelist_combo)
         lines_toolbar.addWidget(self.linelist_edit_btn)
         lines_toolbar.addWidget(QtWidgets.QLabel("Redshift: "))
         lines_toolbar.addWidget(self.slider)
-        lines_toolbar.addWidget(self.z_plus_btn)
+        # lines_toolbar.addWidget(self.z_minusminus_btn)
         lines_toolbar.addWidget(self.z_minus_btn)
+        lines_toolbar.addWidget(self.z_plus_btn)
+        # lines_toolbar.addWidget(self.z_plusplus_btn)
         lines_toolbar.addWidget(self.z_input)
         lines_toolbar.addWidget(self.z_reset_btn)
+        lines_toolbar.addWidget(QtWidgets.QLabel("P(z):"))
+        lines_toolbar.addWidget(self.zprob_text)
         self.slider.valueChanged.connect(self.update_from_slider)
         self.z_input.editingFinished.connect(self.update_from_text)
         self.addToolBar(lines_toolbar)
@@ -802,13 +815,13 @@ class MainWindow(QtWidgets.QMainWindow):
         except (ValueError, TypeError):
             logging.error("Invalid redshift input: {z}. Must be a numeral")
 
-    def z_increment(self):
+    def z_increment(self, dz):
         z = float(self.z_input.text())
-        self.update_redshift(z + 0.0001)
+        self.update_redshift(z + dz)
 
     def z_decrement(self):
         z = float(self.z_input.text())
-        self.update_redshift(z - 0.0001)
+        self.update_redshift(z - 0.0005)
 
     def reset_table_redshift(self):
         targets = self.get_real_active_targets()
@@ -817,8 +830,12 @@ class MainWindow(QtWidgets.QMainWindow):
 
         target = targets[0]
         if self.redshift_table and len(target.spectra) > 0:
-            z, spectype = redshift_table_lookup(self.redshift_table, target.spectra[0])
+            z, spectype, zprob = redshift_table_lookup(self.redshift_table, target.spectra[0])
             self.update_redshift(z)
+            self.update_zprob(zprob)
+
+    def update_zprob(self, zprob):
+        self.zprob_text.setText(f"{zprob:.3f}")
 
     def toggle_gridlines(self):
         show_grid = self.grid_radio_button.isChecked()

{pynot_redux-2.3 → pynot_redux-2.4}/pynot/wcs.py

@@ -87,10 +87,15 @@ def get_gaia_catalog(ra, dec, radius=4., limit=2000, catalog_fname='', database=
     limit: max number of targets to retrieve
     """
     from astroquery.gaia import Gaia
-    query_args = {'limit': limit, 'ra': ra, 'dec': dec, 'radius': radius/60., 'dr': database}
-    query = """SELECT TOP {limit} ra, dec, phot_g_mean_mag, bp_rp FROM gaia{dr}.gaia_source
-    WHERE CONTAINS(POINT('ICRS', gaia{dr}.gaia_source.ra, gaia{dr}.gaia_source.dec),
-                   CIRCLE('ICRS', {ra}, {dec}, {radius}))=1;""".format(**query_args)
+    size = radius / 60.
+    query_args = {'limit': limit, 'ra_lower': ra-size, 'ra_upper': ra+size,
+                  'dec_lower': dec-size, 'dec_upper': dec+size, 'dr': database}
+    query = """
+    SELECT TOP {limit} ra, dec, phot_g_mean_mag, bp_rp
+    FROM gaia{dr}.gaia_source
+    WHERE ra BETWEEN {ra_lower} AND {ra_upper}
+      AND dec BETWEEN {dec_lower} AND {dec_upper}
+    """.format(**query_args)
     job = Gaia.launch_job_async(query, dump_to_file=True,
                                 output_format='csv', verbose=False,
                                 output_file=catalog_fname)
@@ -187,9 +192,10 @@ def correct_wcs(img_fname, sep_fname, output='', fig_fname='', min_num=6, G_lim=
             ref_cat = get_gaia_catalog(hdr['CRVAL1'], hdr['CRVAL2'],
                                        radius=radius, catalog_fname=gaia_cat_name, database=gaia_dr)
             msg.append("          - Saving Gaia source catalog: %s" % gaia_cat_name)
-        except:
+        except Exception as e:
             msg.append(" [ERROR]  - Could not reach Gaia server! Check your internet connection.")
             msg.append("")
+            msg.append(str(e))
             return "\n".join(msg)
 
     # reject brightest sources:
@@ -234,7 +240,7 @@ def correct_wcs(img_fname, sep_fname, output='', fig_fname='', min_num=6, G_lim=
     # Reject outliers:
     msg.append("          - Performing initial cross identification")
     msg.append("          - Found %s source%s" % (len(matched_ref),
-                                                  '' if len(matched_ref)==1 else 's'))
+                                                  '' if len(matched_ref) == 1 else 's'))
     dist = np.sqrt(np.sum((matched_ref - matched_sep)**2, axis=1))*3600
     dxdy = np.abs(matched_sep - matched_ref)
     theta = np.arctan2(dxdy[:, 1], dxdy[:, 0])
@@ -280,7 +286,7 @@ def correct_wcs(img_fname, sep_fname, output='', fig_fname='', min_num=6, G_lim=
         msg.append("")
         return "\n".join(msg)
 
-    # Fit the WCS transformation:    
+    # Fit the WCS transformation:
     _, crval, CD, _ = get_WCS(hdr)
     msg.append("          - Fitting WCS transformation using %i sources" % len(matched_ref))
     wcs_keys = update_WCS(matched_sep, matched_ref, crval, CD)
@@ -299,12 +305,12 @@ def correct_wcs(img_fname, sep_fname, output='', fig_fname='', min_num=6, G_lim=
         ax = fig.add_subplot(111, projection=wcs_new)
         med_val = np.median(img)
         ax.imshow(img, vmin=med_val-1*mad(img), vmax=med_val+10*mad(img),
-                origin='lower', cmap=plt.cm.gray_r)
+                  origin='lower', cmap=plt.cm.gray_r)
         ax.scatter(matched_ref[:, 0], matched_ref[:, 1],
-                transform=ax.get_transform('fk5'), edgecolor='r', facecolor='none', s=50)
+                   transform=ax.get_transform('fk5'), edgecolor='r', facecolor='none', s=50)
         if debug:
             ax.scatter(matched_sep[:, 0], matched_sep[:, 1],
-                    transform=ax.get_transform('fk5'), edgecolor='green', facecolor='none', s=10, alpha=0.7)
+                       transform=ax.get_transform('fk5'), edgecolor='green', facecolor='none', s=10, alpha=0.7)
             for i, r in zip(matched_sep, matched_ref):
                 ax.plot([i[0], r[0]], [i[1], r[1]], 'k', alpha=0.5, transform=ax.get_transform('fk5'))
         ax.set_xlabel("Right Ascension")

pynot_redux-2.3/pynot/VERSION

@@ -1 +0,0 @@
-2.3