Initial commit

Flexbrdf/scripts/neon2envi.py

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+'''neon2envi.py
+
+TODO: Add phase and UTC time to ancillary output
+TODO: Implement progress bar like from this example:
+      https://docs.ray.io/en/master/auto_examples/progress_bar.html
+
+'''
+import argparse
+import os
+import ray
+import numpy as np
+import hytools as ht
+from hytools.io.envi import WriteENVI
+
+def main():
+    '''This command line tool exports NEON AOP HDF imaging spectroscopy data
+    to an ENVI formatted binary file, with the option of also exporting
+    ancillary data following formatting used by NASA JPL for AVIRIS
+    observables. The script utilizes ray to export images in parallel.
+
+    '''
+    parser = argparse.ArgumentParser(description = "Convert NEON AOP H5 to ENVI format")
+    parser.add_argument('images',help="Input image pathnames", nargs='*')
+    parser.add_argument('output_dir',help="Output directory", type = str)
+    parser.add_argument("-anc", help="Output ancillary", required=False, action='store_true')
+
+    args = parser.parse_args()
+
+    if not args.output_dir.endswith("/"):
+        args.output_dir+="/"
+
+    if ray.is_initialized():
+        ray.shutdown()
+    ray.init(num_cpus = len(args.images))
+
+    hytool = ray.remote(ht.HyTools)
+    actors = [hytool.remote() for image in args.images]
+    _ = ray.get([a.read_file.remote(image,'neon') for a,image in zip(actors,args.images)])
+
+    def neon_to_envi(hy_obj):
+        basemame = os.path.basename(os.path.splitext(hy_obj.file_name)[0])
+        print("Exporting %s " % basemame)
+        output_name = args.output_dir+ basemame
+        writer = WriteENVI(output_name,hy_obj.get_header())
+        iterator = hy_obj.iterate(by = 'chunk')
+        pixels_processed = 0
+        while not iterator.complete:
+            chunk = iterator.read_next()
+            pixels_processed += chunk.shape[0]*chunk.shape[1]
+            writer.write_chunk(chunk,iterator.current_line,iterator.current_column)
+            if iterator.complete:
+                writer.close()
+
+    def export_anc(hy_obj):
+        anc_header = hy_obj.get_header()
+        anc_header['bands'] = 10
+        anc_header['band_names'] = ['path length', 'to-sensor azimuth',
+                                    'to-sensor zenith','to-sun azimuth',
+                                      'to-sun zenith','phase', 'slope',
+                                      'aspect', 'cosine i','UTC time']
+        anc_header['wavelength units'] = np.nan
+        anc_header['wavelength'] = np.nan
+        anc_header['data type'] = 4
+
+        output_name = args.output_dir+ os.path.basename(os.path.splitext(hy_obj.file_name)[0])
+        writer = WriteENVI(output_name + "_ancillary", anc_header)
+        writer.write_band(hy_obj.get_anc("path_length"),0)
+        writer.write_band(hy_obj.get_anc("sensor_az",radians = False),1)
+        writer.write_band(hy_obj.get_anc("sensor_zn",radians = False),2)
+        writer.write_band(hy_obj.get_anc("solar_az",radians = False),3)
+        writer.write_band(hy_obj.get_anc("solar_zn",radians = False),4)
+        #writer.write_band(hy_obj.get_anc("phase placeholder"),5)
+        writer.write_band(hy_obj.get_anc("slope",radians = False),6)
+        writer.write_band(hy_obj.get_anc("aspect",radians = False),7)
+        writer.write_band(hy_obj.cosine_i(),8)
+        #writer.write_band('UTC time placeholder',9)
+        writer.close()
+
+    _ = ray.get([a.do.remote(neon_to_envi) for a in actors])
+
+    if args.anc:
+        print("\nExporting ancillary data")
+        _ = ray.get([a.do.remote(export_anc) for a in actors])
+
+    print("Export complete.")
+
+
+if __name__== "__main__":
+    main()