Merge pull request #48 from sdss/twilights

Implementing reduction sequence for twilights

bin/drp

@@ -5,6 +5,7 @@
 import os
 import pathlib
 import shutil
+from typing import Tuple
 
 import click
 import cloup
@@ -15,6 +16,48 @@ from lvmdrp.functions.skyMethod import configureSkyModel_drp
 from lvmdrp.utils.metadata import get_frames_metadata, get_master_metadata
 
 from lvmdrp.functions.run_quickdrp import quick_science_reduction
+from lvmdrp.functions.run_twilights import reduce_twilight_sequence
+
+
+class IntRangeType(click.ParamType):
+    name = 'int_list'
+
+    def convert(self, value, param, ctx):
+        try:
+            # Split the input value by commas
+            parts = value.split(',')
+
+            if len(parts) == 1:
+                # If only one part, treat it as a single integer
+                return [int(parts[0])]
+            elif len(parts) == 2:
+                # If two parts, treat them as initial and final values for a range
+                start, end = map(int, parts)
+                return list(range(start, end + 1))
+            else:
+                self.fail(f'{value} is not a valid input', param, ctx)
+
+        except ValueError:
+            self.fail(f'{value} is not a valid input', param, ctx)
+
+
+class WaveRange(click.ParamType):
+    name = 'wave_ranges'
+
+    def convert(self, value, param, ctx):
+        try:
+            # Split the input value by commas
+            waves = value.split(',')
+
+            if len(waves) == 2:
+                # Only if two parts, treat them as initial and final values for a range
+                iwave, fwave = map(float, waves)
+                return iwave, fwave
+            else:
+                self.fail(f'{value} is not a valid input', param, ctx)
+
+        except ValueError:
+            self.fail(f'{value} is not a valid input', param, ctx)
 
 
 @click.group('drp', short_help='CLI for the LVM data reduction')
@@ -128,6 +171,42 @@ def quick_reduction(expnum: int, use_fiducial_master: bool, skip_sky_subtraction
 cli.add_command(quick_reduction)
 
 
+@click.command('twilight', short_help='Run the twilight sequence reduction')
+@click.option('-e', '--expnums', type=IntRangeType(), multiple=True, help='a list of exposure numbers to reduce')
+@click.option('-b', '--median-box', type=int, default=5, help='the median box size')
+@click.option('-n', '--niter', type=int, default=1000, help='the number of iterations')
+@click.option('-t', '--threshold', type=tuple, default=(0.5,2.0), help='the thresholds (lower,upper) for the sigma clipping')
+@click.option('-k', '--nknots', type=int, default=80, help='the number of knots for the spline')
+@cloup.option_group(
+    'Channel masks',
+    'Options for masking wavelength ranges for each spectrograph channel',
+    cloup.option('--b-mask', type=WaveRange(), multiple=True, help='the wavelength ranges to mask for b channel'),
+    cloup.option('--r-mask', type=WaveRange(), multiple=True, help='the wavelength ranges to mask for r channel'),
+    cloup.option('--z-mask', type=WaveRange(), multiple=True, help='the wavelength ranges to mask for z channel')
+)
+@click.option('-d', '--display-plots', is_flag=True, default=False, help='Flag to display the plots')
+def twilight_reduction(expnums: list, median_box: int, niter: int, threshold: Tuple[float,float],
+                       nknots: int, b_mask: list, r_mask: list, z_mask: list,
+                       display_plots: bool) -> None:
+    """ Run the twilight sequence reduction """
+    # parse multiple exposure number lists into a single list
+    expnums = [expnum for expnum_list in expnums for expnum in expnum_list]
+    reduce_twilight_sequence(
+        expnums=expnums,
+        median_box=median_box,
+        niter=niter,
+        threshold=threshold,
+        nknots=nknots,
+        b_mask=b_mask,
+        r_mask=r_mask,
+        z_mask=z_mask,
+        display_plots=display_plots)
+
+
+# register twilight sequence reduction
+cli.add_command(twilight_reduction)
+
+
 @cli.command('erase', short_help='Remove the DRP reductions')
 @click.option('-d', '--drpver', type=str, help='the DRP version', required=True)
 def erase(drpver: str):