Update MOSAIC VIS example and settings

- Add flat step to mosaic_vis.py pipeline
- Use standard data paths and env vars
- VIS3 inherits from VIS1 settings
- Increase VIS1 trace filter_y to 8

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: ivh

examples/mosaic_vis.py

@@ -36,8 +36,6 @@
     plot = int(os.environ["PYREDUCE_PLOT"])
 plot_dir = join(data_dir, "pyreduce_plots", channel)
 util.set_plot_dir(plot_dir)
-# to not show plots during processing:
-# PYREDUCE_PLOT_SHOW=off uv run...
 
 # File paths (simulated data)
 flat_file = join(
@@ -72,8 +70,9 @@
 )
 
 # Run pipeline steps
-pipe.trace([flat_file])
-pipe.curvature([thar_file])
+# pipe.trace([flat_file])
+# pipe.curvature([thar_file])
+pipe.flat([flat_file])
 pipe.normalize_flat()
 pipe.wavecal_master([thar_file])
 pipe.wavecal_init()

pyreduce/instruments/MOSAIC/bundle_centers_vis1.yaml

@@ -66,4 +66,4 @@
   64:       3874.4365
   65:       3935.0129
   66:       3995.5693
-  67:       4056.2100
+  67:       4056.2100

pyreduce/instruments/MOSAIC/bundle_centers_vis3.yaml

@@ -66,4 +66,4 @@
 64: 3873.05
 65: 3934.25
 66: 3993.05
-67: 4055.45
+67: 4055.45

pyreduce/instruments/MOSAIC/bundle_centers_vis4.yaml

@@ -67,86 +67,3 @@
 65: 3883.35
 66: 3943.07
 67: 4004.18
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pyreduce/instruments/MOSAIC/settings_VIS1.json

@@ -7,7 +7,7 @@
         "noise_relative": 0.05,
         "min_cluster": 100,
         "min_width": 0.6,
-        "filter_y": 5,
+        "filter_y": 8,
         "border_width": [0, 0,0,0],
         "closing_shape": [1, 50],
         "opening_shape": [1, 5]