Initial commit: GasFlux project with core processing pipelines

src/gasflux/gasflux_config.yaml

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+# gasflux_config.yaml
+
+output_dir: ~/gasflux_reports
+
+# required columns and maximum ranges
+required_cols:
+  latitude: [-90, 90]
+  longitude: [-180, 180]
+  height_ato: [-200, 500] # meters above takeoff
+  windspeed: [0, 50] # m/s
+  winddir: [0, 360] # degrees
+  temperature: [-50, 60] # degrees Celsius
+  pressure: [900, 1100] # hPa/mb
+
+# optional gas columns and maximum ppm ranges. Relative concentrations are used so offset can be wrong as long as gain and linearity are correct.
+gases:
+  ch4: [1.5, 500]
+  co2: [300, 5000]
+  c2h6: [-0.5, 10]
+
+strategies:
+  background: "algorithm" # currently only algorithm (via pybaselines) is supported
+  sensor: "insitu" # currently only insitu is supported
+  spatial: "curtain" # currently "curtain" and "spiral" are supported
+  interpolation: "kriging" # currently only kriging is supported
+
+# baseline settings. 
+algorithmic_baseline_settings:
+  algorithm: fastchrom
+  fastchrom: {
+    "half_window": 6, 
+    "threshold": "custom", #
+    "min_fwhm": ~,
+    "interp_half_window": 3, 
+    "smooth_half_window": 3, 
+    "weights": ~, 
+    "max_iter": 100, 
+    "min_length": 2}
+  fabc : {
+    "lam": 10000,  # The smoothing parameter. Larger values will create smoother baselines. Default is 1e6.
+    "scale": 10,  # The scale at which to calculate the continuous wavelet transform. Should be approximately equal to the index-based full-width-at-half-maximum of the peaks or features in the data.  Default is None, which will use half of the value from optimize_window(), which is not always a good value, but at least scales with the number of data points and gives a starting point for tuning the parameter.
+    "diff_order": 2}  # The order of the differential matrix. Must be greater than 0. Default is 2 (second order differential matrix). Typical values are 2 or 1.
+  dietrich : {
+    "poly_order": 5,
+    "smooth_half_window": 5,}
+  golotvin : {
+    "half_window": 2, 
+    "sections": 10}
+
+# kriging settings
+semivariogram_settings:
+  model: spherical
+  estimator: cressie
+  n_lags: 20
+  bin_func: even
+  fit_method: lm
+  ### Size of the search window; if the algorithm complains about not having enough neighbours, consider increasing these
+  maxlag: 100 # in meters. 
+  tolerance: 10 # in degrees
+  azimuth: 0 # in degrees (0 is right/horizontal)
+  bandwidth: 20 # in meters 
+   # fit_sigma: linear # this should allow for a spatial uncertainty but currently producing bugs
+ordinary_kriging_settings:
+  min_points: 3 
+  max_points: 100
+  grid_resolution: 500
+  min_nodes: 10
+  y_min: ~  # manual override for the minimum y value. Leave blank or ~ to use ymin.
+  cut_ground: True # cuts everything below the ground level in the krig (need height_agl to work at the moment)