pyreduce-astro 0.7a5__tar.gz → 0.7a7__tar.gz

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/.gitignore

@@ -20,3 +20,4 @@ docs/_build/
 .claude
 debug/
 idl/
+logs/

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/CHANGELOG.md

@@ -1,6 +1,27 @@
 # Changelog
 
 
+## [0.7a7] - 2026-01-04
+
+### Added
+- `--settings` option for CLI to override reduction parameters from JSON file
+
+### Changed
+- Rename `extraction_width` to `extraction_height` in settings (clarifies coordinate system)
+- Rename `orders` to `traces` in extract.py internal API
+
+## [0.7a6] - 2026-01-03
+
+### Added
+- `--file` option for CLI step commands to bypass file discovery
+- NEID instrument with multi-amplifier support
+
+### Changed
+- Rename `orders` step to `trace` throughout codebase (CLI, API, configs)
+
+### Fixed
+- test_normflat to use column_range returned by extract
+
 ## [0.7a5] - 2025-12-30
 
 ### Changed

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/CLAUDE.md

@@ -19,7 +19,7 @@ uv run reduce download UVES
 PYREDUCE_PLOT=0 uv run python examples/uves_example.py
 
 # Or use CLI
-uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 ```
 
 ## Package Structure
@@ -54,6 +54,16 @@ pyreduce/
     └── slit_func_2d_xi_zeta_bd.c
 ```
 
+## Image Coordinate Convention
+
+PyReduce uses the convention that **dispersion runs horizontally (along x-axis)** and **cross-dispersion runs vertically (along y-axis)**. The `clipnflip()` function in `instruments/common.py` rotates and flips raw images to ensure this orientation.
+
+This means:
+- **Columns (x)** = wavelength/dispersion direction
+- **Rows (y)** = spatial/cross-dispersion direction
+- **Traces** are polynomial functions of x, giving y-position
+- **`extraction_height`** refers to pixels above/below each trace (in y)
+
 ## Pipeline Steps
 
 The reduction pipeline consists of these steps (in typical order):
@@ -63,7 +73,7 @@ The reduction pipeline consists of these steps (in typical order):
 | `mask` | `Mask` | Load bad pixel mask for detector |
 | `bias` | `Bias` | Combine bias frames into master bias |
 | `flat` | `Flat` | Combine flat frames, subtract bias |
-| `orders` | `OrderTracing` | Trace echelle order positions on flat |
+| `trace` | `OrderTracing` | Trace echelle order positions on flat |
 | `curvature` | `SlitCurvatureDetermination` | Measure slit tilt/shear from arc lamp |
 | `scatter` | `BackgroundScatter` | Model inter-order scattered light |
 | `norm_flat` | `NormalizeFlatField` | Normalize flat, extract blaze function |
@@ -138,14 +148,14 @@ Defines HOW to reduce - algorithm parameters per step:
   "bias": {
     "degree": 0
   },
-  "orders": {
+  "trace": {
     "degree": 4,
     "noise": 100,
     "min_cluster": 500,
     "filter_size": 120
   },
   "norm_flat": {
-    "extraction_width": 0.5,
+    "extraction_height": 0.5,
     "smooth_slitfunction": 1,
     "oversampling": 10
   },
@@ -156,7 +166,7 @@ Defines HOW to reduce - algorithm parameters per step:
   },
   "science": {
     "extraction_method": "optimal",
-    "extraction_width": 0.5,
+    "extraction_height": 0.5,
     "oversampling": 10
   }
 }
@@ -176,7 +186,7 @@ result = Pipeline.from_instrument(
     target="HD132205",
     night="2010-04-01",
     channel="middle",
-    steps=("bias", "flat", "orders", "science"),
+    steps=("bias", "flat", "trace", "science"),
     base_dir="/data",
     plot=1,
 ).run()
@@ -221,11 +231,11 @@ pyreduce.reduce.main(
 
 ```bash
 # Full pipeline
-uv run reduce run UVES HD132205 --steps bias,flat,orders
+uv run reduce run UVES HD132205 --steps bias,flat,trace
 
 # Individual steps (top-level commands)
 uv run reduce bias UVES HD132205
-uv run reduce orders UVES HD132205
+uv run reduce trace UVES HD132205
 uv run reduce wavecal UVES HD132205
 
 # Combine reduced spectra
@@ -283,3 +293,43 @@ uv run ruff check --fix .            # Lint and fix
 | `pyreduce/instruments/models.py` | Pydantic config models |
 | `pyreduce/clib/*.c` | C code for slit function decomposition |
 | `hatch_build.py` | CFFI extension build hook |
+
+## Release Process
+
+To release a new version (e.g., `0.7a6`):
+
+1. **Update documentation** for any renamed steps, new CLI options, etc:
+   - `README.md` - Quick start examples
+   - `docs/cli.md` - CLI reference
+   - `docs/index.md`, `docs/howto.md`, `docs/examples.md` - Usage examples
+   - `docs/configuration_file.md` - Config key names
+
+2. **Update CHANGELOG.md** with release date and changes
+
+3. **Update version** in `pyproject.toml`
+
+3a. **sync** - run `uv sync` to get the new version into uv.lock
+
+4. **Update example headers** - all `examples/*.py` have PEP 723 metadata:
+   ```python
+   # /// script
+   # dependencies = ["pyreduce-astro>=0.7a6"]
+   # ///
+   ```
+
+5. **Commit, tag, and push**:
+   ```bash
+   git add -A && git commit -m "Release v0.7a6"
+   git tag v0.7a6
+   git push && git push --tags
+   ```
+
+6. **Monitor GitHub Actions** - the tag push triggers:
+   - Tests on Python 3.13
+   - Wheel builds (Linux, Windows, macOS)
+   - PyPI upload
+   - GitHub Release creation
+
+   ```bash
+   gh run watch  # watch the triggered workflow
+   ```

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyreduce-astro
-Version: 0.7a5
+Version: 0.7a7
 Summary: A data reduction package for echelle spectrographs
 Project-URL: Homepage, https://github.com/ivh/PyReduce
 Project-URL: Documentation, https://pyreduce-astro.readthedocs.io
@@ -76,7 +76,7 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
 uv run reduce bias UVES HD132205
@@ -101,4 +101,4 @@ Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
 
 ## Output
 
-PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/README.md

@@ -34,7 +34,7 @@ uv sync
 uv run reduce download UVES
 
 # Run reduction
-uv run reduce run UVES HD132205 --steps bias,flat,orders,science
+uv run reduce run UVES HD132205 --steps bias,flat,trace,science
 
 # Or run individual steps
 uv run reduce bias UVES HD132205
@@ -59,4 +59,4 @@ Full documentation at [ReadTheDocs](https://pyreduce-astro.readthedocs.io/).
 
 ## Output
 
-PyReduce creates `.ech` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.
+PyReduce creates `.fits` files (standard FITS with binary table extension). Headers include original keywords plus PyReduce-specific ones prefixed with `e_`.

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/aj_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 AJ instrument example: Fiber bundle tracing with direct function calls.
@@ -26,6 +26,7 @@ import os
 
 import numpy as np
 
+from pyreduce.extract import extract
 from pyreduce.instruments.instrument_info import load_instrument
 from pyreduce.trace import group_and_refit, merge_traces, trace
 
@@ -41,6 +42,7 @@ orders_file = os.path.join(raw_dir, "ANDES_75fibre_J_orders.npz")
 # Output
 output_dir = os.path.expanduser("~/REDUCE_DATA/AJ/reduced")
 output_file = os.path.join(output_dir, "fiber_traces.npz")
+output_blaze = os.path.join(output_dir, "fiber_blaze.npz")
 
 # Load order centers from npz file
 orders_data = np.load(orders_file)
@@ -65,7 +67,7 @@ trace_params = {
     "border_width": 0,
     "manual": False,
     "auto_merge_threshold": 1.0,
-    "merge_min_threshold": 0.1,
+    "merge_min_threshold": 1.0,  # 1.0 disables merging entirely
     "sigma": 0,
     "plot": 1,
 }
@@ -90,6 +92,10 @@ print(f"  Shape: {img_even.shape}, dtype: {img_even.dtype}")
 print(f"Loading {file_odd}...")
 img_odd, head_odd = instrument.load_fits(file_odd, channel=channel, extension=0)
 
+# Combine even and odd flats for extraction
+img_combined = img_even.astype(np.float64) + img_odd.astype(np.float64)
+print(f"Combined flat shape: {img_combined.shape}")
+
 # --- Step 2: Trace each flat independently ---
 print("\nTracing even-illuminated fibers...")
 traces_even, cr_even = trace(
@@ -166,4 +172,38 @@ else:
     save_dict["column_range"] = all_cr
 
 np.savez(output_file, **save_dict)
-print(f"\nSaved to: {output_file}")
+print(f"\nSaved traces to: {output_file}")
+
+# --- Step 6: Extract spectra from all fiber traces ---
+# Flatten all traces into a single orders array for extraction
+all_traces = np.vstack([traces_by_order[k] for k in sorted(traces_by_order.keys())])
+all_cr = np.vstack([cr_by_order[k] for k in sorted(cr_by_order.keys())])
+print(f"\nExtracting {len(all_traces)} fiber traces...")
+
+# Extraction parameters
+extract_params = {
+    "extraction_height": 0.5,
+    "lambda_sf": 0.1,  # smooth_slitfunction
+    "lambda_sp": 0,  # smooth_spectrum
+    "osample": 10,  # oversampling
+    "swath_width": 200,
+    "plot": 1,
+}
+
+norm, spec, blaze, unc = extract(
+    img_combined,
+    all_traces,
+    column_range=all_cr,
+    extraction_type="normalize",
+    gain=1.0,
+    readnoise=0.0,
+    dark=0.0,
+    **extract_params,
+)
+
+print(f"  Extracted blaze shape: {blaze.shape}")
+print(f"  Normalized flat shape: {norm.shape}")
+
+# Save extraction results
+np.savez(output_blaze, blaze=blaze, norm=norm, spec=spec, unc=unc)
+print(f"Saved blaze to: {output_blaze}")

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/crires_plus_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "J1228_det1"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/custom_instrument_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -32,7 +32,7 @@ instrument.info["prescan_x"] = "PRESCAN X"
 # For loading the config we specify pyreduce as the source, since this is the default
 config = get_configuration_for_instrument("pyreduce")
 # Define your own configuration
-config["orders"]["degree"] = 5
+config["trace"]["degree"] = 5
 
 # Since we can't find the files ourselves (at least not without defining the criteria we are looking for)
 # We need to manually define which files go where
@@ -53,7 +53,7 @@ channel = ""
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/harpn_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "HARPN"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "norm_flat",
     # "wavecal_master",
     "wavecal",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/harps_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "red"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     "scatter",
     "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/harps_gridsearch.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import os.path
 
@@ -71,7 +71,7 @@ kwargs_comb["nstep"] = 0
 kwargs["plot"] = False
 
 
-for key in ["extraction_method", "extraction_width", "extraction_cutoff"]:
+for key in ["extraction_method", "extraction_height", "extraction_cutoff"]:
     del kwargs_comb[key]
     del kwargs[key]
 

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/just_one_swath.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import matplotlib.pyplot as plt
 import numpy as np

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/jwst_miri_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "LRS_SLITLESS"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/jwst_niriss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "GR700XD"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/lick_apf_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = ""
 steps = (
     "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "norm_flat",
     # "wavecal",
     # "curvature",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/mcdonald_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -19,7 +19,7 @@ channel = "CS23"
 steps = (
     # "bias",
     # "flat",
-    # "orders",
+    # "trace",
     # "curvature",
     "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/metis_ifu_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "IFU_NOMINAL"
 steps = (
     # "bias",
     # "flat",
-    "orders",
+    "trace",
     "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/metis_lss_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -20,7 +20,7 @@ channel = "LSS_M"
 steps = (
     # "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     # "scatter",
     # "norm_flat",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/micado_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -17,7 +17,7 @@ channel = ""
 steps = (
     # "bias",
     "flat",
-    "orders",
+    "trace",
     "curvature",
     # # "scatter",
     # "norm_flat",
@@ -47,12 +47,12 @@ config = pyreduce.configuration.get_configuration_for_instrument(instrument)
 # Once you are satisfied with a certain parameter, you can update it in settings_MICADO.json.
 
 
-# config["orders"]["noise"] = 100
-# config["curvature"]["extraction_width"] = 350 # curvature can still be improved with this and the following parameters
+# config["trace"]["noise"] = 100
+# config["curvature"]["extraction_height"] = 350 # curvature can still be improved with this and the following parameters
 # config["curvature"]["peak_threshold"] =10
 # config["curvature"]["peak_width"] =2 #CHECK 6 also works and detects one less line
 # config["curvature"]["window_width"] = 5
-# config["wavecal"]["extraction_width"] = 350
+# config["wavecal"]["extraction_height"] = 350
 
 # NOTE: micado.thar_master.fits (created and controlled by wavecal_master) is NOT overwritten if any parameter in the steps in or before it are changed. Thus it has to be deleted before running PyReduce again.
 

pyreduce_astro-0.7a7/examples/neid_example.py

@@ -0,0 +1,65 @@
+# /// script
+# requires-python = ">=3.13"
+# dependencies = ["pyreduce-astro>=0.7a7"]
+# ///
+"""
+NEID reduction example
+
+NEID is a fiber-fed, high-resolution (R~110,000) spectrograph on the
+WIYN 3.5m telescope at Kitt Peak. L0 data has 16 amplifiers that are
+automatically assembled during loading.
+
+This example reduces HD 4628 observations from night 2024-09-19.
+Note: Observations before 12:00 UTC belong to the previous night.
+"""
+
+import os
+
+from pyreduce.configuration import get_configuration_for_instrument
+from pyreduce.pipeline import Pipeline
+
+# Define parameters
+instrument = "NEID"
+target = "HD 4628"
+night = "2024-09-19"  # Observations before 12:00 UTC belong to previous night
+channel = "HR"
+
+# Reduction steps to run
+# Start with basic steps; add wavecal/science once calibration files are set up
+steps = (
+    "flat",
+    "trace",
+    # "curvature",
+    # "norm_flat",
+    # "wavecal_master",
+    # "wavecal_init",
+    # "wavecal",
+    # "science",
+    # "continuum",
+    # "finalize",
+)
+
+# Data paths
+# Set REDUCE_DATA environment variable or modify base_dir
+base_dir = os.environ.get("REDUCE_DATA", os.path.expanduser("~/REDUCE_DATA"))
+base_dir = os.path.join(base_dir, "NEID")
+input_dir = ""  # Files directly in base_dir
+output_dir = "reduced"
+
+# Load default configuration
+config = get_configuration_for_instrument(instrument)
+
+# Run the pipeline
+if __name__ == "__main__":
+    Pipeline.from_instrument(
+        instrument,
+        target,
+        night=night,
+        channel=channel,
+        steps=steps,
+        base_dir=base_dir,
+        input_dir=input_dir,
+        output_dir=output_dir,
+        configuration=config,
+        plot=1,
+    ).run()

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/nirspec_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 """
 Simple usage example for PyReduce
@@ -18,7 +18,7 @@ channel = "NIRSPEC"
 steps = (
     "bias",
     "flat",
-    "orders",
+    "trace",
     "norm_flat",
     "wavecal",
     "freq_comb",

{pyreduce_astro-0.7a5 → pyreduce_astro-0.7a7}/examples/toes_example.py

@@ -1,6 +1,6 @@
 # /// script
 # requires-python = ">=3.13"
-# dependencies = ["pyreduce-astro>=0.7a5"]
+# dependencies = ["pyreduce-astro>=0.7a7"]
 # ///
 import numpy as np
 
@@ -81,16 +81,16 @@ instrument.info["wavelength_range"] = [
 # For loading the config we specify pyreduce as the source, since this is the default
 config = get_configuration_for_instrument("pyreduce")
 # Define your own configuration
-config["orders"]["filter_y"] = 20  # smoothing along cross-dispersion
-config["orders"]["degree"] = 4
-config["orders"]["degree_before_merge"] = 2
-config["orders"]["noise"] = 5.5
-config["orders"]["min_cluster"] = 3000
-config["orders"]["min_width"] = 200
-config["orders"]["manual"] = True
+config["trace"]["filter_y"] = 20  # smoothing along cross-dispersion
+config["trace"]["degree"] = 4
+config["trace"]["degree_before_merge"] = 2
+config["trace"]["noise"] = 5.5
+config["trace"]["min_cluster"] = 3000
+config["trace"]["min_width"] = 200
+config["trace"]["manual"] = True
 config["norm_flat"]["oversampling"] = 8  # Subpixel scale for slit function modelling
 config["norm_flat"]["swath_width"] = 400  # Extraction swath width (columns)
-config["wavecal_master"]["extraction_width"] = 2
+config["wavecal_master"]["extraction_height"] = 2
 config["wavecal_master"]["collapse_function"] = "sum"
 config["wavecal_master"]["bias_scaling"] = "number_of_files"
 config["wavecal"]["medium"] = "vac"
@@ -102,7 +102,7 @@ config["science"]["oversampling"] = 8  # Subpixel scale for slit function modell
 config["science"]["swath_width"] = 400  # Extraction swath width (columns)
 config["science"]["smooth_slitfunction"] = 1.0  # Smoothing of the slit function
 config["science"]["smooth_spectrum"] = 1.0e-6  # Smoothing in spectral direction
-config["science"]["extraction_width"] = [5, 5]  # Extraction slit height (rows)
+config["science"]["extraction_height"] = [5, 5]  # Extraction slit height (rows)
 config["science"]["bias_scaling"] = "number_of_files"
 
 # Since we can't find the files ourselves (at least not without defining the criteria we are looking for)
@@ -110,7 +110,7 @@ config["science"]["bias_scaling"] = "number_of_files"
 files = {
     "bias": ["Bias_0s_20240621_221716-%d.fit" % i for i in np.arange(1, 11)],
     "flat": ["Flat_5s_20240621_222912-%d.fit" % i for i in np.arange(1, 5)],
-    "orders": [flat_file],
+    "trace": [flat_file],
     "science": ["Vega_Object_25s_20240621_224908-%d.fit" % i for i in np.arange(1, 2)],
     "wavecal_master": [
         "Sun_Calibration_35s_20240621_184136-%d.fit" % i for i in np.arange(1, 2)
@@ -138,7 +138,7 @@ channel = ""
 steps = (
     #    "bias",
     #    "flat",
-    #    "orders",
+    #    "trace",
     #    "norm_flat",
     "wavecal_master",
     "wavecal",