PyNOT-redux 2.2.4__tar.gz → 2.3__tar.gz

{pynot_redux-2.2.4 → pynot_redux-2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.4
+Version: 2.3
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

{pynot_redux-2.2.4 → pynot_redux-2.3}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.4
+Version: 2.3
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

pynot_redux-2.3/pynot/VERSION

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

{pynot_redux-2.2.4 → pynot_redux-2.3}/pynot/calibs.py

@@ -62,6 +62,9 @@ def combine_bias_frames(bias_frames, output='', kappa=15, method='mean', overwri
     """
     msg = list()
 
+    if len(bias_frames) == 1:
+        msg.append("[WARNING] - Only 1 frame provided! More than 1 frame is expected!!\n")
+
     bias = list()
     for frame in bias_frames:
         msg.append("          - Loaded bias frame: %s" % frame)
@@ -172,6 +175,10 @@ def combine_flat_frames(raw_frames, output, mbias='', mode='spec', dispaxis=None
         The log of the function steps and errors
     """
     msg = list()
+
+    if len(raw_frames) == 1:
+        msg.append("[WARNING] - Only 1 frame provided! More than 1 frame is expected!!\n")
+
     if mbias and exists(mbias):
         bias = fits.getdata(mbias)
         # bias_hdr = instrument.get_header(mbias)
@@ -380,7 +387,7 @@ def normalize_spectral_flat(fname, output='', fig_dir='', dispaxis=None, order=2
         if len(edges) != 2:
             msg.append("[WARNING] - Automatic edge detection failed. Using full frame!")
             edges = [0, len(x)]
-    except:
+    except Exception:
         msg.append("[WARNING] - Automatic edge detection failed. Using full frame!")
         edges = [0, len(x)]
 

{pynot_redux-2.2.4 → pynot_redux-2.3}/pynot/main.py

@@ -653,13 +653,13 @@ def main(inspect=False):
     elif task == 'bias':
         from pynot.calibs import combine_bias_frames
         print("Running task: Bias combination")
-        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
         _, log = combine_bias_frames(input_list, args.output, kappa=args.kappa, method=args.method)
 
     elif task == 'sflat':
         from pynot.calibs import combine_flat_frames, normalize_spectral_flat
         print("Running task: Spectral flat field combination and normalization")
-        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
         flatcombine, log = combine_flat_frames(input_list, output='', mbias=args.bias, mode='spec',
                                                dispaxis=args.axis, kappa=args.kappa, method=args.method)
 
@@ -783,10 +783,14 @@ def main(inspect=False):
             if '*' in input_arg or '?' in input_arg:
                 filelist = glob(input_arg)
             else:
-                filelist = np.loadtxt(input_arg, usecols=(0,), dtype=str)
+                filelist = np.loadtxt(input_arg, usecols=(0,), dtype=str, ndmin=1)
         else:
             filelist = args.input
 
+        if len(filelist) == 1:
+            print("Must provide more than one frame to combine!\n")
+            sys.exit()
+
         # Check if data are 1D or 2D:
         try:
             data = fits.getdata(filelist[0])
@@ -864,7 +868,7 @@ def main(inspect=False):
     elif task == 'imflat':
         print("Running task: Combination of Imaging Flat Fields")
         from pynot.calibs import combine_flat_frames
-        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
         _, log = combine_flat_frames(input_list, output=args.output, mbias=args.bias, mode='img',
                                      kappa=args.kappa, method=args.method)
 
@@ -884,7 +888,7 @@ def main(inspect=False):
         if args.input.endswith('.fits'):
             input_list = [args.input]
         else:
-            input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+            input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
 
         for fname in input_list:
             print("  Trimming image: %s" % fname)
@@ -893,7 +897,10 @@ def main(inspect=False):
     elif task == 'imcombine':
         print("Running task: Image Combination")
         from pynot.phot import image_combine
-        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
+        if len(input_list) == 1:
+            print("Must provide more than one frame to combine!\n")
+            sys.exit()
         options = copy(vars(args))
         vars_to_remove = ['task', 'input', 'output', 'log', 'fringe']
         for varname in vars_to_remove:
@@ -903,7 +910,7 @@ def main(inspect=False):
     elif task == 'fringe':
         print("Running task: Creating Average Fringe Image")
         from pynot.phot import create_fringe_image
-        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,))
+        input_list = np.loadtxt(args.input, dtype=str, usecols=(0,), ndmin=1)
         log = create_fringe_image(input_list, output=args.output, fig_fname=args.fig, threshold=args.sigma)
 
     elif task == 'sep':

{pynot_redux-2.2.4 → pynot_redux-2.3}/pynot/viewer/notes.py

@@ -23,6 +23,7 @@ class DataFlag(IntFlag):
     BAL_QSO           = 2**9    # Broad absorption line quasar
     ABS_QSO           = 2**10   # Absorption associated with quasar
     DLA_INTERVENING   = 2**11   # Damped Lyman Alpha absorption
+    STAR              = 2**12   # Stellar classification
 
 
     def get_flags(self):

{pynot_redux-2.2.4 → pynot_redux-2.3}/pynot/viewer/viewer.py

@@ -610,6 +610,8 @@ class MainWindow(QtWidgets.QMainWindow):
         note_text = self.note_input.text()
         target: Target = self.active_targets._data[0]
         target_note = TargetNote.from_target(target, note=note_text)
+        if self.redshift_table is not None:
+            target_note.redshift = float(self.z_input.text())
 
         target_flag = self.target_flags.get(target.name, DataFlag(0))
         if DataFlag.Z_VI_CONFIRM in target_flag:
@@ -627,6 +629,7 @@ class MainWindow(QtWidgets.QMainWindow):
         if len(self.active_targets._data) != 1:
             logging.error("Cannot add flags to more than one target at a time. Remove other targets.")
             return
+
         target_flag = DataFlag(0)
         for checkbox, val in zip(self.flag_inputs, DataFlag):
             if checkbox.isChecked():
@@ -634,16 +637,18 @@ class MainWindow(QtWidgets.QMainWindow):
 
         target: Target = self.active_targets._data[0]
         self.target_flags[target.name] = target_flag
-        target_note = self.target_notes.get(target.name, None)
+        if target.name not in self.target_notes:
+            target_note = TargetNote.from_target(target, "")
+            if self.redshift_table is not None:
+                target_note.redshift = float(self.z_input.text())
 
-        if DataFlag.Z_VI_CONFIRM in target_flag:
-            if target.name not in self.target_notes:
-                target_note = TargetNote.from_target(target, "Visually updated redshift")
+            if DataFlag.Z_VI_CONFIRM in target_flag:
+                target_note.redshift = float(self.z_input.text())
+            self.target_notes[target.name] = target_note
+        else:
+            target_note = self.target_notes.get(target.name)
+            if DataFlag.Z_VI_CONFIRM in target_flag:
                 target_note.redshift = float(self.z_input.text())
-                self.target_notes[target.name] = target_note
-        elif target_note and target_note.note == "Visually updated redshift":
-            target_note.note = ""
-            self.note_input.setText("")
 
     def create_notes_toolbar(self):
         notes_toolbar = QtWidgets.QToolBar()

pynot_redux-2.2.4/pynot/VERSION

@@ -1 +0,0 @@
-2.2.4