PyNOT-redux 2.2.2__tar.gz → 2.2.4__tar.gz

{pynot_redux-2.2.2 → pynot_redux-2.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.2
+Version: 2.2.4
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

{pynot_redux-2.2.2 → pynot_redux-2.2.4}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.2.2
+Version: 2.2.4
 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.egg-info/top_level.txt

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

pynot_redux-2.2.4/pynot/VERSION

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

{pynot_redux-2.2.2 → pynot_redux-2.2.4}/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-2.2.2 → pynot_redux-2.2.4}/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-2.2.2 → pynot_redux-2.2.4}/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-2.2.2 → pynot_redux-2.2.4}/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-2.2.2 → pynot_redux-2.2.4}/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)
 

{pynot_redux-2.2.2 → pynot_redux-2.2.4}/pynot/viewer/notes.py

@@ -62,7 +62,7 @@ class TargetNote:
 
 
 REDSHIFT_NAMES = ['REDSHIFT', 'Z_SPEC', 'ZBEST', 'Z_PIPE', 'ZSPEC', 'Z', 'ZFIT', 'Z_VI']
-ID_NAMES = ['OBJ_NME', 'OBJ_UID', 'SPECUID', 'NAME', 'OBJECT', 'TARGET', 'TARGETID', 'ID', 'UID', 'FILENAME']
+ID_NAMES = ['SPECUID', 'FILENAME', 'PROV', 'OBJ_NME', 'OBJ_UID', 'NAME', 'OBJECT', 'TARGET', 'TARGETID', 'ID', 'UID']
 CLASS_NAMES = ['TYPE', 'ZBESTTYPE', 'SPECTYPE', 'CLASS', 'CLASSIFICATION', 'OBJ_CLS']
 
 
@@ -162,7 +162,7 @@ def redshift_table_lookup(redshift_table, spectrum):
     """
     name_column = redshift_table.meta['NAME_COLUMN']
 
-    if name_column.upper() == 'FILENAME':
+    if name_column.upper() == 'FILENAME' or name_column.upper() == 'PROV':
         name = spectrum.filename
 
     else:

{pynot_redux-2.2.2 → pynot_redux-2.2.4}/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-2.2.2 → pynot_redux-2.2.4}/pynot/viewer/viewer.py

@@ -46,11 +46,11 @@ from pynot.viewer.linelists import LineManagerDialog
 
 
 color_list = cycle([
-    "#3949AB",
-    "#D81B60",
-    "#009688",
-    "#8E24AA",
-    "#CCA000",
+    # "#3949AB",
+    # "#D81B60",
+    # "#009688",
+    # "#8E24AA",
+    # "#CCA000",
     "#202020",
 ])
 
@@ -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([])
@@ -706,6 +706,13 @@ 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 +720,10 @@ 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 +797,24 @@ 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 +927,7 @@ 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-2.2.2 → pynot_redux-2.2.4}/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-2.2.2/PyNOT_redux.egg-info/top_level.txt

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

pynot_redux-2.2.2/pynot/VERSION

@@ -1 +0,0 @@
-2.2.2