PyNOT-redux 2.4.1__tar.gz → 2.4.2__tar.gz

{pynot_redux-2.4.1 → pynot_redux-2.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.4.1
+Version: 2.4.2
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

{pynot_redux-2.4.1 → pynot_redux-2.4.2}/PyNOT_redux.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: PyNOT-redux
-Version: 2.4.1
+Version: 2.4.2
 Summary: Data Reduction Pipeline for NOT/ALFOSC
 Home-page: https://github.com/jkrogager/PyNOT
 Author: Jens-Kristian Krogager

pynot_redux-2.4.2/pynot/VERSION

@@ -0,0 +1 @@
+2.4.2

{pynot_redux-2.4.1 → pynot_redux-2.4.2}/pynot/fitsio.py

@@ -4,7 +4,7 @@ __author__ = "Jens-Kristian Krogager"
 import warnings
 from astropy.io import fits
 from astropy import units as u
-from astropy.table import QTable
+from astropy.table import Table
 import numpy as np
 import os
 
@@ -165,7 +165,7 @@ def get_spectrum_fits_table(table_hdu):
         Numpy boolean array of pixel mask. `True` if the pixel is 'good',
         `False` if the pixel is bad and should not be used.
     """
-    tbdata = QTable.read(table_hdu)
+    tbdata = Table.read(table_hdu)
     # table_names = [name.lower() for name in tbdata.names]
     for colname in tbdata.colnames:
         tbdata.rename_column(colname, colname.lower())

{pynot_redux-2.4.1 → pynot_redux-2.4.2}/pynot/viewer/notes.py

@@ -3,8 +3,9 @@ import logging
 import json
 import numpy as np
 from enum import IntFlag
-from dataclasses import dataclass
+from dataclasses import dataclass, fields
 import datetime
+import os
 
 from PyQt5.QtWidgets import QFileDialog
 
@@ -64,6 +65,10 @@ class TargetNote:
         return row
 
 
+target_note_fields = [f.name for f in fields(TargetNote)]
+target_note_defaults = {f.name: f.type for f in fields(TargetNote)}
+
+
 REDSHIFT_NAMES = ['REDSHIFT', 'Z_SPEC', 'ZBEST', 'Z_PIPE', 'ZSPEC', 'Z', 'ZFIT', 'Z_VI']
 ID_NAMES = ['PROV', 'FILENAME', 'PROV', 'OBJ_NME', 'OBJ_UID', 'NAME', 'OBJECT', 'TARGET', 'TARGETID', 'ID', 'UID']
 CLASS_NAMES = ['TYPE', 'ZBESTTYPE', 'SPECTYPE', 'CLASS', 'CLASSIFICATION', 'OBJ_CLS']
@@ -170,7 +175,7 @@ def redshift_table_lookup(redshift_table, spectrum):
     name_column = redshift_table.meta['NAME_COLUMN']
 
     if name_column.upper() == 'FILENAME' or name_column.upper() == 'PROV':
-        name = spectrum.filename
+        name = os.path.basename(spectrum.filename)
 
     else:
         if not spectrum.meta:
@@ -272,3 +277,64 @@ def write_notes_to_file(notes: dict[str, TargetNote], flags: dict[str, DataFlag]
 
     file_saved = writer(rows, filename)
     return file_saved
+
+
+def load_json(filename):
+    with open(filename) as f:
+        rows = json.load(f)
+    return Table(rows)
+
+
+def load_table(filename):
+    return Table.read(filename)
+
+
+def parse_masked_values(key, val):
+    if hasattr(val, 'mask') and val.mask:
+        return target_note_defaults[key]()
+    else:
+        return val
+
+
+def target_note_from_row(**kwargs):
+    pars = {}
+    for key, val in kwargs.items():
+        if key in target_note_fields and key == 'filenames':
+            pars[key] = val.split(';')
+        elif key in target_note_fields and key != 'filenames':
+            pars[key] = parse_masked_values(key, val)
+        else:
+            continue
+    return TargetNote(**pars)
+
+
+def data_flag_from_row(row):
+    try:
+        flag = DataFlag(row['flag'])
+    except ValueError:
+        flag = DataFlag(0)
+        logging.error(f"Could not parse flag value: {row['flag']}. The flags must have changed")
+    return flag
+
+
+def validate_table(tab: Table):
+    mandatory_columns = [f.name for f in fields(TargetNote)]
+    mandatory_columns.append('flag')
+    valid = all([key in tab.colnames for key in mandatory_columns])
+    return valid
+
+
+def load_notes_from_file(filename):
+    if '.json' in filename:
+        loader = load_json
+    else:
+        loader = load_table
+
+    tab = loader(filename)
+    valid = validate_table(tab)
+    if not valid:
+        logging.error(f"Error loading notes from file: {filename}. Unexpected format!")
+
+    target_notes = {row['name']: target_note_from_row(**row) for row in tab}
+    target_flags = {row['name']: data_flag_from_row(row) for row in tab}
+    return target_notes, target_flags

{pynot_redux-2.4.1 → pynot_redux-2.4.2}/pynot/viewer/viewer.py

@@ -17,7 +17,11 @@ import os
 import warnings
 
 from pynot.fitsio import load_fits_spectrum, save_fits_spectrum
-from pynot.viewer.notes import load_redshift_table, redshift_table_lookup, TargetNote, DataFlag, write_notes_to_file
+from pynot.viewer.notes import (load_redshift_table,
+                                redshift_table_lookup,
+                                TargetNote, DataFlag,
+                                write_notes_to_file,
+                                load_notes_from_file)
 from pynot.viewer.tablemodels import TableModel, ActiveTableModel, AbstractIndex
 from pynot.viewer.spectrum import Spectrum, join_spectra, Template, ModelSpectrum
 from pynot.viewer.messages import QtLogHandler, LogViewerDialog
@@ -967,6 +971,21 @@ class MainWindow(QtWidgets.QMainWindow):
             self.notes_filename = str(notes_filename)
             logging.info(f"Saved target notes to file: {notes_filename}")
 
+    def load_notes(self, filename=None):
+        current_dir = "./"
+        filters = "CSV Files (*.csv);; JSON Files (*.json);; FITS Files (*.fits)"
+        fname, selected_filter = QtWidgets.QFileDialog.getOpenFileName(
+                                                self,
+                                                'Load Target Notes',
+                                                current_dir,
+                                                filters)
+        if not fname:
+            return
+        loaded_notes, loaded_flags = load_notes_from_file(fname)
+        self.target_notes = loaded_notes
+        self.target_flags = loaded_flags
+        logging.info(f"Loaded target notes from file: {fname}")
+
     def create_menubar(self):
         self.main_menu = self.menuBar()
 
@@ -979,11 +998,16 @@ class MainWindow(QtWidgets.QMainWindow):
         save_action.triggered.connect(lambda x: self.write_notes())
         save_action.setShortcut("Ctrl+S")
 
+        load_action = QtWidgets.QAction("Load Notes", self)
+        load_action.triggered.connect(lambda x: self.load_notes())
+        load_action.setShortcut("Ctrl+L")
+
         # Exit QAction
         exit_action = QtWidgets.QAction("Exit", self)
         exit_action.triggered.connect(self.close)
         
         self.file_menu.addAction(save_action)
+        self.file_menu.addAction(load_action)
         self.file_menu.addAction(exit_action)
 
         # -- Models Menu

pynot_redux-2.4.1/pynot/VERSION

@@ -1 +0,0 @@
-2.4.1