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Add MOSAIC VIS quadrant support (VIS1-VIS4 channels)
VIS detector is a 12788x12394 mosaic with 4 quadrants separated by gaps. Each quadrant is processed as a separate channel with its own bundle centers. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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examples/mosaic_example.py renamed to examples/mosaic_nir.py

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# - Groups 630 traces into 90 bundles of 7
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# - Selects center fiber from each bundle
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# - Uses grouped traces for curvature and science steps
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# pipe.trace_orders([flat_file])
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# pipe.curvature([thar_file])
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pipe.trace_orders([flat_file])
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pipe.curvature([thar_file])
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pipe.extract([thar_file, flat_file])
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print("\n=== Running Pipeline ===")

‎examples/mosaic_vis.py‎

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# /// script
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# requires-python = ">=3.13"
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# dependencies = ["pyreduce-astro>=0.7b3"]
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# ///
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"""
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MOSAIC VIS spectrograph example.
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The VIS detector is a 4-quadrant mosaic (12788x12394 pixels total).
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Each quadrant is processed as a separate channel:
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- VIS1: lower-left quadrant
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- VIS2: lower-right quadrant
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- VIS3: upper-left quadrant
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- VIS4: upper-right quadrant
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This example processes VIS1. Run with different channel values for other quadrants.
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"""
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import os
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from os.path import join
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from pyreduce import util
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from pyreduce.configuration import load_config
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from pyreduce.pipeline import Pipeline
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# Parameters
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# Change channel to VIS2, VIS3, or VIS4 for other quadrants
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instrument_name = "MOSAIC"
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target = "MOSAIC_VIS"
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night = ""
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channel = "VIS1"
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plot = 1
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# Handle plot environment variables
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if "PYREDUCE_PLOT" in os.environ:
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plot = int(os.environ["PYREDUCE_PLOT"])
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plot_dir = os.environ.get("PYREDUCE_PLOT_DIR")
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util.set_plot_dir(plot_dir)
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# Data location
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data_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
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base_dir = join(data_dir, "MOSAIC", "REF_E2E", "VIS")
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output_dir = join(data_dir, "MOSAIC", "reduced", channel)
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# File paths (simulated data)
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flat_file = join(
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base_dir,
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"E2E_as_built_FLAT_DIT_20s_MOSAIC_VIS_c01_FOCAL_PLANE_000.fits",
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)
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thar_file = join(
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base_dir,
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"E2E_as_built_ThAr_DIT_20s_MOSAIC_VIS_c01_FOCAL_PLANE.fits",
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)
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# Verify files exist
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for fpath in [flat_file, thar_file]:
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if not os.path.exists(fpath):
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raise FileNotFoundError(f"Data file not found: {fpath}")
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print(f"FLAT: {flat_file}")
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print(f"ThAr: {thar_file}")
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# Load configuration
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config = load_config(None, instrument_name, plot)
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# Create pipeline - fiber grouping is handled by config.yaml
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pipe = Pipeline(
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instrument=instrument_name,
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output_dir=output_dir,
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target=target,
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channel=channel,
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night=night,
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config=config,
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plot=plot,
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)
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# Run pipeline steps
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pipe.trace_orders([flat_file])
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pipe.curvature([thar_file])
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pipe.extract([thar_file, flat_file])
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print("\n=== Running Pipeline ===")
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results = pipe.run()
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print("\n=== Results ===")
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orders, column_range = results["trace"]
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print(f"Raw traces: {len(orders)}")
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if "trace_groups" in results and results["trace_groups"]:
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group_traces, group_cr = results["trace_groups"]
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print(
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f"Fiber groups: {list(group_traces.keys())[:5]}... ({len(group_traces)} total)"
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)

‎pyreduce/instruments/MOSAIC/__init__.py‎

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MOSAIC instrument - ELT multi-object spectrograph with 630 fibers.
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NIR channel: 90 fiber groups (7 fibers each), 4096x4096 H4RG detector.
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VIS channel: 4 quadrants (VIS1-VIS4) from a 12788x12394 mosaic detector.
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Fibers split into two halves with a gap in the middle.
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"""
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from ..common import Instrument
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class MOSAIC(Instrument):
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pass
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# VIS detector quadrant boundaries (from gap analysis)
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# Full VIS frame: 12788 (height) x 12394 (width) pixels
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# Horizontal gap: rows 6144-6644, Vertical gap: cols 6144-6250
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# Active region: rows 2038-10734
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VIS_QUADRANTS = {
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"VIS1": {"xlo": 0, "xhi": 6144, "ylo": 2038, "yhi": 6144}, # lower-left
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"VIS2": {"xlo": 6250, "xhi": 12394, "ylo": 2038, "yhi": 6144}, # lower-right
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"VIS3": {"xlo": 0, "xhi": 6144, "ylo": 6644, "yhi": 10734}, # upper-left
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"VIS4": {"xlo": 6250, "xhi": 12394, "ylo": 6644, "yhi": 10734}, # upper-right
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}
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def add_header_info(self, header, channel, **kwargs):
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"""Override to handle VIS quadrant extraction."""
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# Let parent populate all standard header info
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header = super().add_header_info(header, channel, **kwargs)
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# For VIS quadrants, override the clip bounds
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channel_upper = channel.upper()
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if channel_upper in self.VIS_QUADRANTS:
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q = self.VIS_QUADRANTS[channel_upper]
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header["e_xlo"] = q["xlo"]
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header["e_xhi"] = q["xhi"]
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header["e_ylo"] = q["ylo"]
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header["e_yhi"] = q["yhi"]
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return header

pyreduce/instruments/MOSAIC/bundle_centers.yaml renamed to pyreduce/instruments/MOSAIC/bundle_centers_nir.yaml

File renamed without changes.

‎pyreduce/instruments/MOSAIC/bundle_centers_vis1.yaml‎

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# Bundle centers for MOSAIC VIS1 (70 bundles)
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# Bundle ID -> y-position at detector center
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1: 39.0
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2: 100.0
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3: 160.5
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4: 221.0
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5: 281.5
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‎pyreduce/instruments/MOSAIC/bundle_centers_vis2.yaml‎

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# Bundle centers for MOSAIC VIS2 (70 bundles)
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# Bundle ID -> y-position at detector center
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1: 84.0
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2: 144.0
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3: 203.5
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4: 263.5
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5: 324.0
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‎pyreduce/instruments/MOSAIC/bundle_centers_vis3.yaml‎

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# Bundle centers for MOSAIC VIS3 (85 bundles)
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# Bundle ID -> y-position at detector center
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1: 9.5
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2: 51.5
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3: 111.5
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4: 172.5
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5: 233.0
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