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Flexbrdf/scripts/configs/plsr_model_format_v0_1.py

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+# -*- coding: utf-8 -*-
+"""
+HyTools:  Hyperspectral image processing library
+
+Copyright (C) 2021 University of Wisconsin
+
+Authors: Adam Chlus, Zhiwei Ye, Philip Townsend.
+
+This program is free software: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation, version 3 of the License.
+This program is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+You should have received a copy of the GNU General Public License
+along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+JSON format for PLSR trait models v0.1
+
+This version assumes that all transforms are applied using all model wavelengths.
+
+TODO: Develop standard codes for spectrometer, both airborne/spaceborne and field.
+TODO: Allow for more options for specifying wavelength subsets
+
+"""
+
+
+import json
+
+model_dict = {}
+
+# Metadata
+#####################################
+'''
+    trait : Trait name (str)
+    units : Trait units (str)
+    description: Model description (str)
+    wavelength_units: Wavelength units (str)
+    wavelengths : Model wavelengths (list)
+        Only wavelengths used in the model should be
+        included in the list of wavelengths.
+    fwhm : Model fwhm (list)
+    type : Model type (str)
+'''
+model_dict["name"] = ''
+model_dict["units"] = ''
+model_dict["description"] = ''
+model_dict["wavelength_units"] = ''
+model_dict["wavelengths"] = []
+model_dict["fwhm"] = []
+model_dict["spectrometer"] = ''
+model_dict["type"] =  ''
+
+# Diagnostics
+#####################################
+'''Currently the only required diagnostics are 'min'
+and 'max', these are the min and max values of the
+dataset used to build the model and are used to generate
+the data range mask, which identifies pixels with predictions
+outside of the model dataset range.
+
+'''
+model_dict["model_diagnostics"] = {}
+model_dict["model_diagnostics"]["rmse"] = 0.0
+model_dict["model_diagnostics"]["r_squared"] = 0.0
+model_dict["model_diagnostics"]["min"] = 0.0
+model_dict["model_diagnostics"]["max"] = 0.0
+
+# Model
+#####################################
+'''
+transform:  List of transforms to be applied in order of application.
+            Options:
+                - 'vector': vector norm using np.linalg.norm
+                - 'mean' : Normalize to mean
+                - 'absorb' : log(1/R)
+            Examples:
+                ['vector','absorb']
+            Empty list for no transforms ([])
+coefficients: List of lists, sublists are the coefficients for
+                model iterations.
+
+intercepts : Permuted model intercepts (list)
+components : Number of model component (int)
+'''
+
+model_dict['model'] = {}
+model_dict['model']["components"] =  0
+model_dict['model']["transform"] = ['mean']
+model_dict['model']["intercepts"] = []
+model_dict['model']["coefficients"] =[[],[]]
+
+model_path = '*.json'
+with open(model_path, 'w') as outfile:
+    json.dump(model_dict,outfile)
+
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