pyreduce-astro 0.7a4__cp314-cp314-win_amd64.whl

pyreduce/settings/settings_METIS_LSS.json

@@ -0,0 +1,77 @@
+{
+    "__instrument__": "METIS_IFU",
+    "flat":{
+        "bias_scaling": "number_of_files",
+        "plot": false
+    },
+    "orders": {
+        "degree": 4,
+        "degree_before_merge": "best",
+        "bias_scaling": "number_of_files",
+        "filter_y": 20,
+        "min_cluster": 100,
+        "noise": 120,
+        "border_width": 6,
+        "auto_merge_threshold": 0.9,
+        "merge_min_threshold": 0.01,
+        "manual": false,
+        "min_width": 0,
+        "plot": false
+    },
+    "scatter": {
+        "bias_scaling": "number_of_files",
+        "extraction_width": 0.45,
+        "border_width": 20
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 1e3,
+        "smooth_spectrum": 1e-7,
+        "extraction_width": 0.14,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "curvature": {
+        "extraction_method": "arc",
+        "dimensionality": "1D",
+        "curv_degree": 2,
+        "collapse_function": "mean",
+        "extraction_width": 0.77,
+        "extraction_cutoff": 20,
+        "curvature_cutoff": 3,
+        "peak_threshold": 0.9725,
+        "peak_width": 1,
+        "window_width": 1,
+        "peak_function": "lorentzian",
+        "bias_scaling": "exposure_time",
+        "degree": 2
+    },
+    "wavecal_master": {
+        "extraction_method": "arc",
+        "collapse_function": "median",
+        "extraction_width": 0.7825,
+        "extraction_cutoff": 10,
+        "bias_scaling": "exposure_time"
+    },
+     "wavecal": {
+        "extraction_method": "optimal",
+        "bias_scaling": "exposure_time",
+        "threshold": 70,
+        "iterations": 3,
+        "dimensionality": "2D",
+        "extraction_width": 0.7825,
+        "degree": [
+            4,
+            4
+        ],
+        "manual": true,
+        "shift_window": 0.1
+    },
+    "science": {
+        "oversampling": 10,
+        "extraction_width": 0.14235,
+        "swath_width": 400,
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0.5e-5
+    }
+}

pyreduce/settings/settings_MICADO.json

@@ -0,0 +1,78 @@
+{
+    "__instrument__": "MICADO",
+    "flat":{
+        "bias_scaling": "number_of_files"
+    },
+    "orders": {
+        "degree": 5,
+        "degree_before_merge": "best",
+        "bias_scaling": "exposure_time",
+        "filter_y": 300,
+        "min_cluster": 500,
+        "noise": 100,
+        "border_width": 5,
+        "auto_merge_threshold": 0.9,
+        "merge_min_threshold": 0.01,
+        "manual": true,
+        "min_width": 0
+    },
+    "scatter": {
+        "bias_scaling": "number_of_files",
+        "extraction_width": 0.45,
+        "border_width": 20
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 1e3,
+        "smooth_spectrum": 1e-7,
+        "extraction_width": 0.14,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "curvature": {
+        "extraction_method": "arc",
+        "dimensionality": "2D",
+        "curv_degree": 1,
+        "collapse_function": "mean",
+        "extraction_width": 350,
+        "extraction_cutoff": 10,
+        "curvature_cutoff": 10,
+        "peak_threshold": 10,
+        "peak_width":2,
+        "window_width": 5,
+        "peak_function": "lorentzian",
+        "bias_scaling": "exposure_time",
+        "degree": [
+            1,
+            1
+        ]
+    },
+    "wavecal_master": {
+        "extraction_method": "arc",
+        "collapse_function": "mean",
+        "extraction_width": 350,
+        "extraction_cutoff": 20,
+        "bias_scaling": "exposure_time"
+    },
+     "wavecal": {
+        "extraction_method": "optimal",
+        "bias_scaling": "number_of_files",
+        "threshold": 80,
+        "iterations": 3,
+        "dimensionality": "2D",
+        "extraction_width": 350,
+        "degree": [
+            5,
+            5
+        ],
+        "manual": true,
+        "shift_window": 0.1
+    },
+    "science": {
+        "oversampling": 10,
+        "extraction_width": 0.14235,
+        "swath_width": 400,
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0.5e-5
+    }
+}

pyreduce/settings/settings_NEID.json

@@ -0,0 +1,73 @@
+{
+    "__instrument__": "HARPN",
+    "instrument": {
+        "fiber": "A"
+    },
+    "orders": {
+        "degree": 4,
+        "filter_y": 80,
+        "min_cluster": 2000,
+        "noise": 8,
+        "manual": false
+    },
+    "scatter": {
+        "extraction_width": 10
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 1e-7,
+        "extraction_width": 10,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "wavecal_master": {
+        "extraction_width": 5,
+        "collapse_function" : "median",
+        "bias_scaling" : "number_of_files"
+    },
+    "wavecal_init": {
+        "element": "thar",
+        "medium": "vac"
+    },
+    "wavecal": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "degree": [
+            5,
+            5
+        ],
+        "manual": false,
+        "element": "thar",
+        "medium": "vac",
+        "correlate_cols": 0
+    },
+    "freq_comb_master": {
+        "extraction_width": 10
+    },
+    "freq_comb": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "nstep": 7,
+        "degree": [
+            9,
+            7
+        ]
+    },
+    "curvature": {
+        "extraction_width": 10,
+        "peak_threshold": 0,
+        "peak_width": 3,
+        "window_width": 5,
+        "dimensionality": "1D",
+        "curv_degree": 1,
+        "degree": 3
+    },
+    "science": {
+        "oversampling": 10,
+        "extraction_width": 10,
+        "swath_width": 300,
+        "smooth_slitfunction": 1,
+        "smooth_spectrum": 0
+    }
+}

pyreduce/settings/settings_NIRSPEC.json

@@ -0,0 +1,58 @@
+{
+    "__instrument__": "NIRSPEC",
+    "instrument": {
+        "#": "The calibration dir points to the location of the calibration data, since the default data download seperates the science and the calibration into different directories. It is relative to the science directory.",
+        "calibration_dir": ""
+    },
+    "orders": {
+        "degree": 4,
+        "filter_y": 50,
+        "min_cluster": 2000,
+        "border_width": 0,
+        "noise": 40,
+        "merge_min_threshold": 0.2,
+        "manual": true
+    },
+    "scatter": {
+        "extraction_width": 35
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0,
+        "extraction_width": 35,
+        "oversampling": 12,
+        "swath_width": 300,
+        "threshold": 1000
+    },
+    "wavecal_master": {
+        "extraction_width": 0.25
+    },
+    "wavecal": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "degree": [2, 6],
+        "manual": false
+    },
+    "freq_comb_master": {
+        "extraction_width": 0.25
+    },
+    "freq_comb": {
+        "dimensionality": "2D",
+        "degree": [6, 6]
+    },
+    "curvature": {
+        "extraction_width": 35,
+        "dimensionality": "1D",
+        "degree": 2
+    },
+    "science": {
+        "oversampling": 10,
+        "extraction_width": [35, 35],
+        "swath_width": 300,
+        "smooth_slitfunction": 0.3,
+        "smooth_spectrum": 0
+    },
+    "finalize": {
+        "filename": "{input}.fits"
+    }
+}

pyreduce/settings/settings_NTE.json

@@ -0,0 +1,60 @@
+{
+    "$schema": "./settings_schema.json",
+    "__instrument__": "NTE",
+    "orders": {
+        "degree": 5,
+        "filter_y": 80,
+        "min_cluster": 200,
+        "noise": 8,
+        "manual": false
+    },
+    "scatter": {
+        "extraction_width": 0.5,
+        "scatter_degree": 2
+    },
+    "norm_flat": {
+        "threshold": 1000,
+        "extraction_width": 0.45,
+        "smooth_slitfunction": 10,
+        "maxiter": 100,
+        "swath_width": 512,
+        "threshold_lower": 0.001
+    },
+    "wavecal_master": {
+        "collapse_function": "sum",
+        "extraction_width": 0.5
+    },
+    "wavecal_init": {
+        "element": "sky"
+    },
+    "wavecal": {
+    },
+    "freq_comb_master":{
+        "extraction_method": "optimal",
+        "extraction_width": 0.45,
+        "oversampling": 10,
+        "swath_width": 300,
+        "maxiter": 20,
+        "smooth_slitfunction": 0.1,
+        "smooth_spectrum": 1e-7,
+        "extraction_cutoff": 20,
+        "norm_scaling": "none"
+    },
+    "freq_comb": {
+    },
+    "curvature": {
+        "extraction_method": "arc",
+        "collapse_function": "sum",
+        "extraction_width": 0.5,
+        "peak_threshold": 0.1,
+        "peak_width": 1,
+        "window_width": 5,
+        "dimensionality": "2D",
+        "degree": [1, 1],
+        "curv_degree": 1,
+        "peak_function": "gaussian",
+        "bias_scaling": "exposure_time"
+    },
+    "science": {
+    }
+}

pyreduce/settings/settings_UVES.json

@@ -0,0 +1,54 @@
+{
+    "$schema": "./settings_schema.json",
+    "__instrument__": "UVES",
+    "orders": {
+        "degree": 5,
+        "filter_y": 80,
+        "min_cluster": 2000,
+        "noise": 8,
+        "manual": true,
+        "split_sigma": 5
+    },
+    "scatter": {
+        "extraction_width": 0.45,
+        "border_width": 20
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0,
+        "extraction_width": 0.45,
+        "oversampling": 8,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "wavecal_master": {
+    },
+    "wavecal_init": {
+    },
+    "wavecal": {
+        "threshold": 100,
+        "dimensionality": "2D",
+        "degree": [6, 6],
+        "shift_window": 0.01,
+        "manual": false
+    },
+    "freq_comb_master":{
+    },
+    "freq_comb": {
+        "dimensionality": "2D",
+        "degree": [6, 6]
+    },
+    "curvature": {
+        "dimensionality": "1D",
+        "degree": 1,
+        "curv_degree": 1,
+        "peak_width": 1
+    },
+    "science": {
+        "oversampling": 8,
+        "extraction_width": 0.2,
+        "swath_width": 300,
+        "smooth_slitfunction": 0.1,
+        "smooth_spectrum": 0
+    }
+}

pyreduce/settings/settings_XSHOOTER.json

@@ -0,0 +1,78 @@
+{
+    "__instrument__": "XSHOOTER",
+    "bias": {
+        "degree": 1
+    },
+    "flat":{
+        "bias_scaling": "exposure_time"
+    },
+    "orders": {
+        "degree": 5,
+        "degree_before_merge": 2,
+        "bias_scaling": "exposure_time",
+        "filter_y": 20,
+        "min_cluster": 500,
+        "noise": 10,
+        "border_width": 50,
+        "auto_merge_threshold": 0.7,
+        "merge_min_threshold": 0.4,
+        "manual": true,
+        "min_width": 0
+    },
+    "scatter": {
+        "bias_scaling": "exposure_time",
+        "extraction_width": 0.45,
+        "border_width": 20
+    },
+    "norm_flat": {
+        "smooth_slitfunction": 1e3,
+        "smooth_spectrum": 1e-7,
+        "extraction_width": 0.5,
+        "oversampling": 12,
+        "swath_width": 200,
+        "threshold": 1000
+    },
+    "curvature": {
+        "bias_scaling": "exposure_time",
+        "dimensionality": "2D",
+        "curv_degree": 1,
+        "extraction_width": 0.45,
+        "degree": [
+            1,
+            1
+        ]
+    },
+    "wavecal_master": {
+        "extraction_method": "arc",
+        "bias_scaling": "exposure_time"
+    },
+    "wavecal": {
+        "threshold": 200,
+        "iterations": 3,
+        "dimensionality": "2D",
+        "degree": [
+            7,
+            8
+        ],
+        "manual": false,
+        "shift_window": 0
+    },
+    "freq_comb_master": {
+        "bias_scaling": "exposure_time"
+    },
+    "freq_comb": {
+        "dimensionality": "2D",
+        "degree": [
+            6,
+            6
+        ]
+    },
+    "science": {
+        "bias_scaling": "exposure_time",
+        "oversampling": 10,
+        "extraction_width": 0.45,
+        "swath_width": 400,
+        "smooth_slitfunction": 2,
+        "smooth_spectrum": 0.5e-5
+    }
+}

pyreduce/settings/settings_pyreduce.json

@@ -0,0 +1,184 @@
+{
+    "$schema": "./settings_schema.json",
+    "__instrument__": "DEFAULT",
+    "reduce": {
+        "base_dir": "./",
+        "input_dir": "raw",
+        "output_dir": "reduced"
+    },
+    "instrument": {},
+    "mask": {},
+    "bias": {
+        "degree": 0,
+        "plot": true,
+        "plot_title": "Bias"
+    },
+    "flat": {
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "none",
+        "plot": true,
+        "plot_title": "Flat"
+    },
+    "orders": {
+        "degree": 4,
+        "degree_before_merge": 2,
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "none",
+        "regularization": 0,
+        "closing_shape": [
+            5,
+            5
+        ],
+        "opening_shape": [
+            2,
+            2
+        ],
+        "auto_merge_threshold": 0.9,
+        "merge_min_threshold": 0.1,
+        "split_sigma": 0,
+        "filter_x": 0,
+        "filter_y": null,
+        "filter_type": "boxcar",
+        "min_cluster": null,
+        "min_width": null,
+        "noise": null,
+        "border_width": null,
+        "manual": true,
+        "plot": true,
+        "plot_title": "Order Tracing"
+    },
+    "scatter": {
+        "scatter_degree": 4,
+        "scatter_cutoff": 2,
+        "border_width": null,
+        "extraction_width": 0.3,
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "divide",
+        "plot": true,
+        "plot_title": "Background Scatter"
+    },
+    "norm_flat": {
+        "extraction_method": "normalize",
+        "smooth_slitfunction": 4,
+        "smooth_spectrum": 1e-7,
+        "oversampling": 10,
+        "maxiter": 20,
+        "swath_width": 200,
+        "extraction_width": 0.2,
+        "threshold": 0.6,
+        "threshold_lower": 0,
+        "extraction_cutoff": 20,
+        "plot": true,
+        "plot_title": "Normalized Flat"
+    },
+    "wavecal_master": {
+        "extraction_method": "arc",
+        "collapse_function": "median",
+        "extraction_width": 0.5,
+        "extraction_cutoff": 20,
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "divide",
+        "maxiter": 20,
+        "plot": true,
+        "plot_title": "Wavelength Calibration Spectrum"
+    },
+    "wavecal_init": {
+        "degree": 2,
+        "element": "thar",
+        "medium": "vac",
+        "wave_delta": 20,
+        "nwalkers": 100,
+        "steps": 50000,
+        "resid_delta": 1000,
+        "cutoff": 0.01,
+        "smoothing": 0,
+        "plot": true,
+        "plot_title": "Wavelength Calibration Initial"
+    },
+    "wavecal": {
+        "manual": false,
+        "threshold": 100,
+        "iterations": 3,
+        "dimensionality": "2D",
+        "degree": [
+            6,
+            6
+        ],
+        "nstep": 0,
+        "correlate_cols": 0,
+        "shift_window": 0.01,
+        "element": "thar",
+        "medium": "vac",
+        "plot": true,
+        "plot_title": "Wavelength Calibration"
+    },
+    "freq_comb_master":{
+        "extraction_method": "arc",
+        "collapse_function": "median",
+        "extraction_width": 0.5,
+        "extraction_cutoff": 20,
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "divide",
+        "plot": true,
+        "plot_title": "Frequency Comb Spectrum"
+    },
+    "freq_comb": {
+        "lfc_peak_width": 3,
+        "dimensionality": "2D",
+        "nstep": 0,
+        "degree": [
+            6,
+            6
+        ],
+        "threshold": 100,
+        "plot": true,
+        "plot_title": "Frequency Comb"
+    },
+    "curvature": {
+        "dimensionality": "1D",
+        "degree": 2,
+        "curv_degree": 2,
+        "extraction_method": "arc",
+        "collapse_function": "median",
+        "extraction_width": 0.2,
+        "curvature_cutoff": 3,
+        "extraction_cutoff": 20,
+        "peak_threshold": 10,
+        "peak_width": 1,
+        "window_width": 9,
+        "peak_function": "gaussian",
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "divide",
+        "plot": true,
+        "plot_title": "Slit Curvature"
+    },
+    "rectify": {
+        "extraction_width": 0.5,
+        "input_files": "science",
+        "plot": true,
+        "plot_title": "Rectified Image"
+    },
+    "science": {
+        "extraction_method": "optimal",
+        "extraction_width": 0.25,
+        "oversampling": 10,
+        "swath_width": 300,
+        "maxiter": 20,
+        "smooth_slitfunction": 0.1,
+        "smooth_spectrum": 1e-7,
+        "extraction_cutoff": 20,
+        "bias_scaling": "number_of_files",
+        "norm_scaling": "divide",
+        "plot": true,
+        "plot_title": "Science Data"
+    },
+    "continuum": {
+        "plot": true,
+        "plot_title": "Continuum Normalization"
+    },
+    "finalize": {
+        "filename": "{instrument}.{night}_{number}.final.fits",
+        "plot": true,
+        "plot_title": "Final Science Product"
+    }
+}