From 487c3ddf67fa7de6fb27786f0df2ba892e3529b5 Mon Sep 17 00:00:00 2001
From: Ansgar Wehrhahn <31626864+AWehrhahn@users.noreply.github.com>
Date: Thu, 19 Aug 2021 10:20:55 +0200
Subject: [PATCH] wavelength additions

---
 pyreduce/reduce.py                 | 12 +++++++++++-
 pyreduce/wavelength_calibration.py | 10 +++++-----
 2 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/pyreduce/reduce.py b/pyreduce/reduce.py
index 870310b7..86c8b482 100755
--- a/pyreduce/reduce.py
+++ b/pyreduce/reduce.py
@@ -841,10 +841,11 @@ def __init__(self, *args, **config):
         self.iterations = config["iterations"]
         #:{'1D', '2D'}: Whether to use 1d or 2d polynomials
         self.dimensionality = config["dimensionality"]
+        #:int: Number of detector offset steps, due to detector design
         self.nstep = config["nstep"]
         #:float: fraction of columns, to allow individual orders to shift
         self.shift_window = config["shift_window"]
-
+        #:{'number_of_files', 'exposure_time', 'mean', 'median'}: how to adjust for diferences between the bias and flat field exposure times
         self.bias_scaling = config["bias_scaling"]
 
     @property
@@ -852,6 +853,11 @@ def savefile(self):
         """str: Name of the wavelength echelle file"""
         return join(self.output_dir, self.prefix + ".thar.npz")
 
+    @property
+    def savefile_thar(self):
+        """str: Name of the wavelength echelle file"""
+        return join(self.output_dir, self.prefix + ".thar_only.npz")
+
     def run(self, files, orders, mask, curvature, bias, config):
         """Perform wavelength calibration
 
@@ -913,6 +919,10 @@ def run(self, files, orders, mask, curvature, bias, config):
             **self.extraction_kwargs,
         )
 
+        # Save the extracted wavecal spectrum only
+        # This can be useful for creating a calibration file in IDL
+        np.savez(self.savefile_thar, thar=thar)
+
         # load reference linelist
         reference = self.instrument.get_wavecal_filename(
             thead, self.mode, **config["instrument"]
diff --git a/pyreduce/wavelength_calibration.py b/pyreduce/wavelength_calibration.py
index 273fb760..18426831 100644
--- a/pyreduce/wavelength_calibration.py
+++ b/pyreduce/wavelength_calibration.py
@@ -148,7 +148,7 @@ class LineList:
                 (("posm", "POSM"), ">f8"), # Pixel Position (after fit)
                 (("xfirst", "XFIRST"), ">i2"), # first pixel of the line
                 (("xlast", "XLAST"), ">i2"), # last pixel of the line
-                (("approx", "APPROX"), "O"), # ???
+                (("approx", "APPROX"), "O"), # Not used. Describes the shape used to approximate the line. "G" for Gaussian
                 (("width", "WIDTH"), ">f8"), # width of the line in pixels
                 (("height", "HEIGHT"), ">f8"), # relative strength of the line
                 (("order", "ORDER"), ">i2"), # echelle order the line is found in
@@ -183,14 +183,14 @@ def add_line(self, wave, order, pos, width, height, flag):
         lines = np.array(lines, dtype=self.dtype)
         self.data = np.append(self.data, lines)
 
-    @staticmethod
-    def from_list(wave, order, pos, width, height, flag):
+    @classmethod
+    def from_list(cls, wave, order, pos, width, height, flag):
         lines = [
             (w, w, p, p, p - wi / 2, p + wi / 2, b"G", wi, h, o, f)
             for w, o, p, wi, h, f in zip(wave, order, pos, width, height, flag)
         ]
-        lines = np.array(lines, dtype=LineList.dtype)
-        return LineList(lines)
+        lines = np.array(lines, dtype=cls.dtype)
+        return cls(lines)
 
 
 class WavelengthCalibration: