PyNOT-redux 2.2.3__tar.gz → 2.2.5__tar.gz

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.3
+Version: 2.2.5
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.3
+Version: 2.2.5
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

pynot_redux-2.2.5/PyNOT_redux.egg-info/top_level.txt

@@ -0,0 +1,5 @@
+build
+dist
+docs
+pynot
+tests

pynot_redux-2.2.5/pynot/VERSION

@@ -0,0 +1 @@
+2.2.5

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/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-2.2.3 → pynot_redux-2.2.5}/pynot/data/io.py

@@ -6,6 +6,7 @@ Input / Output functions for the DataSet class.
 
 from astropy.io import fits
 import numpy as np
+import warnings
 
 from pynot.data.organizer import TagDatabase
 from pynot import instrument
@@ -77,7 +78,10 @@ def save_database(database, output_fname):
 
 def load_database(input_fname):
     """Load file database from file."""
-    all_lines = np.loadtxt(input_fname, dtype=str, usecols=(0, 1), comments='##')
+    with warnings.catch_warnings():
+        # Suppress empty line warning from numpy 1.23+
+        warnings.simplefilter('ignore', UserWarning)
+        all_lines = np.loadtxt(input_fname, dtype=str, usecols=(0, 1), comments='##')
     # file_database = {key: val for key, val in all_lines}
     # inactive_files = {key: val for key, val in all_lines}
     file_database = {}

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/pynot/data/obs.py

@@ -2,6 +2,7 @@
 from collections import defaultdict
 import numpy as np
 import os
+import warnings
 
 from pynot.data import io
 from pynot.data import organizer as do
@@ -12,7 +13,10 @@ output_base_spec = 'spectra'
 class OBDatabase:
     def __init__(self, fname):
         if os.path.exists(fname):
-            data = np.loadtxt(fname, dtype=str, delimiter=':')
+            with warnings.catch_warnings():
+                # Suppress empty line warning from numpy 1.23+
+                warnings.simplefilter('ignore', UserWarning)
+                data = np.loadtxt(fname, dtype=str, delimiter=':')
             if len(data.shape) == 1:
                 data = np.array([data])
             self.data = {obid.strip(): status.strip() for obid, status in data}

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/pynot/functions.py

@@ -3,6 +3,7 @@ import numpy as np
 import yaml
 import os
 import glob
+import warnings
 
 from pynot import instrument
 
@@ -15,7 +16,10 @@ standard_stars = [fname.strip('.dat') for fname in _standard_star_files]
 # Look-up table from target-names -> star names
 # (mostly used for ALFOSC where TCSTGT is different)
 std_fname = os.path.join(path, 'calib/std/tcs_namelist.txt')
-calib_names = np.loadtxt(std_fname, dtype=str, delimiter=':')
+with warnings.catch_warnings():
+    # Suppress warning about empty rows not counting towards max_rows
+    warnings.simplefilter('ignore', UserWarning)
+    calib_names = np.loadtxt(std_fname, dtype=str, delimiter=':')
 tcs_standard_stars = {row[1].strip(): row[0].strip() for row in calib_names}
 
 

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/pynot/identify_gui.py

@@ -188,20 +188,20 @@ class ResidualView(object):
             line.set_visible(visible)
 
     def set_scatter(self, sig):
-        self.u68_line.set_ydata(self.mean + sig)
-        self.l68_line.set_ydata(self.mean - sig)
+        self.u68_line.set_ydata([self.mean + sig])
+        self.l68_line.set_ydata([self.mean - sig])
         self.scatter = sig
 
     def set_mean(self, mean):
-        self.u68_line.set_ydata(mean + self.scatter)
-        self.l68_line.set_ydata(mean - self.scatter)
+        self.u68_line.set_ydata([mean + self.scatter])
+        self.l68_line.set_ydata([mean - self.scatter])
         self.mean = mean
 
     def set_values(self, mean, scatter):
         self.mean = mean
         self.scatter = scatter
-        self.u68_line.set_ydata(mean + scatter)
-        self.l68_line.set_ydata(mean - scatter)
+        self.u68_line.set_ydata([mean + scatter])
+        self.l68_line.set_ydata([mean - scatter])
 
 
 def load_linelist(fname):
@@ -912,7 +912,7 @@ class GraphicInterface(QtWidgets.QMainWindow):
         item.setBackground(QtGui.QColor('lightgray'))
         self.linetable.setItem(idx, 0, item)
         self.pixel_list[idx] = x_cen
-        self.vlines[idx].set_xdata(x_cen)
+        self.vlines[idx].set_xdata([x_cen])
         self.update_plot()
 
     def refit_all(self):
@@ -1304,7 +1304,7 @@ class Image2DWindow(QtWidgets.QDialog):
     def update_loc(self):
         new_loc = int(self.loc_editor.text())
         self.loc = new_loc
-        self.loc_line.set_xdata(new_loc)
+        self.loc_line.set_xdata([new_loc])
         self.canvas.draw()
 
     def update_info(self):

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/pynot/main.py

@@ -15,7 +15,6 @@ import os
 import sys
 import numpy as np
 import warnings
-import distutils
 
 from pynot.functions import get_options, get_option_descr, get_version_number
 
@@ -38,6 +37,13 @@ def print_credits():
     print("  version %s\n" % __version__)
     print("")
 
+def _strtobool(val: str) -> bool:
+    val = val.lower()
+    if val in ('y', 'yes', 't', 'true', 'on', '1'):
+        return True
+    if val in ('n', 'no', 'f', 'false', 'off', '0'):
+        return False
+    raise ValueError(f"Invalid truth value {val!r}")
 
 def set_default_pars(parser, *, section, default_type, ignore_pars=[], mode='spec'):
     if mode == 'spec':
@@ -56,7 +62,7 @@ def set_default_pars(parser, *, section, default_type, ignore_pars=[], mode='spe
         if val is None:
             value_type = default_type
         if isinstance(val, bool):
-            value_type = lambda x: bool(distutils.util.strtobool(x))
+            value_type = lambda x: bool(_strtobool(x))
         else:
             value_type = type(val)
 
@@ -647,13 +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)
 
@@ -777,10 +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])
@@ -858,7 +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)
 
@@ -878,7 +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)
@@ -887,7 +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:
@@ -897,7 +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-2.2.3 → pynot_redux-2.2.5}/pynot/viewer/spectrum.py

@@ -83,9 +83,9 @@ class Spectrum:
         plot_graph.setLabel("bottom", f"Spectral Axis  [{self.wavelength.unit}]")
         self.plot_line = line
         if yerr is not None:
-            err_color = QtGui.QColor(color)
+            err_color = QtGui.QColor('red')
             h, s, l, a = err_color.getHsl()
-            err_color.setHsl(h, int(s*0.5), 192, 128)
+            err_color.setHsl(h, int(s*0.8), l, 200)
             err_pen = pg.mkPen(color=err_color, style=ls)
             error_line = plot_graph.plot(self.wavelength, yerr, pen=err_pen,
                                          name=f"{self.parent.name} {self.name} 1σ")

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/pynot/viewer/viewer.py

@@ -81,7 +81,7 @@ class MainWindow(QtWidgets.QMainWindow):
         self.linelists["All"] = superset
         self.line_objects = []
         self.active_lines = []
-        self.linePen = pg.mkPen(color=(100, 100, 100, 150))
+        self.linePen = pg.mkPen(color='RoyalBlue')
 
         self.all_targets = TableModel([])
         self.active_targets = ActiveTableModel([])
@@ -627,6 +627,7 @@ 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 +635,12 @@ 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 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 target.name not in self.target_notes:
+            target_note = TargetNote.from_target(target, "")
+            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("")
+                target_note.note = "Visually updated redshift"
+            self.target_notes[target.name] = target_note
 
     def create_notes_toolbar(self):
         notes_toolbar = QtWidgets.QToolBar()
@@ -706,6 +703,13 @@ 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_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_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)
 
@@ -713,7 +717,10 @@ class MainWindow(QtWidgets.QMainWindow):
         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_minus_btn)
         lines_toolbar.addWidget(self.z_input)
+        lines_toolbar.addWidget(self.z_reset_btn)
         self.slider.valueChanged.connect(self.update_from_slider)
         self.z_input.editingFinished.connect(self.update_from_text)
         self.addToolBar(lines_toolbar)
@@ -787,6 +794,24 @@ class MainWindow(QtWidgets.QMainWindow):
         except (ValueError, TypeError):
             logging.error("Invalid redshift input: {z}. Must be a numeral")
 
+    def z_increment(self):
+        z = float(self.z_input.text())
+        self.update_redshift(z + 0.0001)
+
+    def z_decrement(self):
+        z = float(self.z_input.text())
+        self.update_redshift(z - 0.0001)
+
+    def reset_table_redshift(self):
+        targets = self.get_real_active_targets()
+        if len(targets) != 1:
+            return
+
+        target = targets[0]
+        if self.redshift_table and len(target.spectra) > 0:
+            z, spectype = redshift_table_lookup(self.redshift_table, target.spectra[0])
+            self.update_redshift(z)
+
     def toggle_gridlines(self):
         show_grid = self.grid_radio_button.isChecked()
         self.plot_graph.showGrid(x=show_grid, y=show_grid)
@@ -899,6 +924,7 @@ class MainWindow(QtWidgets.QMainWindow):
     def resample_target(self):
         current = self.active_table.selectedIndexes()
         logging.info(f"Currently selected target(s): {current}")
+        logging.info("Resampling is not implemented yet")
 
     def show_log_window(self, event):
         self.log_dialog.show()

{pynot_redux-2.2.3 → pynot_redux-2.2.5}/setup.py

@@ -6,7 +6,7 @@ https://github.com/pypa/sampleproject
 """
 
 # Always prefer setuptools over distutils
-from setuptools import setup, find_packages
+from setuptools import setup, find_namespace_packages
 # To use a consistent encoding
 from codecs import open
 from os import path
@@ -87,7 +87,7 @@ setup(
 
     # You can just specify the packages manually here if your project is
     # simple. Or you can use find_packages().
-    packages=find_packages(exclude=['docs', 'tests']),
+    packages=find_namespace_packages(exclude=['docs', 'tests']),
 
     # Alternatively, if you want to distribute just a my_module.py, uncomment
     # this:

pynot_redux-2.2.3/PyNOT_redux.egg-info/top_level.txt

@@ -1 +0,0 @@
-pynot

pynot_redux-2.2.3/pynot/VERSION

@@ -1 +0,0 @@
-2.2.3