add envi reformat, fix some ortho read issues

spectral_util/__main__.py

@@ -6,6 +6,7 @@
 from spectral_util.mosaic import mosaic
 from spectral_util.ea_assist import earthaccess_helpers_AV3, earthaccess_helpers_EMIT
 from spectral_util import ea_assist
+from spectral_util.spec_io import reformat
 
 @click.group()
 def cli():
@@ -15,6 +16,7 @@ def cli():
 cli.add_command(mosaic.cli, name='mosaic')
 cli.add_command(common.cli_quicklook, name='quicklooks')
 cli.add_command(common.cli_plot, name='plot')
+cli.add_command(reformat.cli, name='reformat')
 
 if __name__ == '__main__':
     cli()

spectral_util/common/quicklooks.py

@@ -52,6 +52,7 @@ def ndvi(input_file, output_file, ortho, red_wl, nir_wl, red_width, nir_width):
     """
     Calculate NDVI.
 
+    \b
     Args:
         input_file (str): Path to the input file.
         output_file (str): Path to the output file.
@@ -77,6 +78,7 @@ def nbr(input_file, output_file, ortho, nir_wl, swir_wl, nir_width, swir_width):
     """
     Calculate NBR.
 
+    \b
     Args:
         input_file (str): Path to the input file.
         output_file (str): Path to the output file.

spectral_util/ea_assist/download.py

@@ -77,6 +77,8 @@ def get_scene(outdir: str,
 def get_fid(outdir, short_name, fid, subfile, version, overwrite):
     """
     Download Earth Data granules based on search criteria.
+
+    \b
     Args:
         outdir (str): Directory to save downloaded files.
         short_name (str): Short name of the dataset to search for.

spectral_util/mosaic/mosaic.py

@@ -179,6 +179,7 @@ def stack_glts(glt_files, obs_file_lists, output_glt_file, output_file_list):
     """
     Stack the GLTs from the input files.
 
+    \b
     Args:
         glt_files (list): List of GLT files to stack, in order.
         obs_file_lists (list): List of observation file lists, matching order to glt_files.
@@ -239,6 +240,7 @@ def build_obs_nc(output_file, input_file_list, ignore_file_list, x_resolution, y
     """
     Build a mosaic from the input file.
 
+    \b
     Args:
         output_file (str): Path to the output file.
         input_file_list (str): Path to the input file.
@@ -384,6 +386,7 @@ def apply_glt(glt_file, raw_files, output_file, nodata_value, bands, output_form
     """
     Apply the GLT to the input files.
 
+    \b
     Args:
         glt_file (str): Path to the GLT file.
         raw_files (str): Path to the raw files.

spectral_util/spec_io/reformat.py

@@ -0,0 +1,53 @@
+import click
+import os
+import numpy as np
+from scipy.spatial import KDTree
+from scipy.signal import convolve2d
+
+import time
+import spectral_util.spec_io as spec_io
+from osgeo import osr
+import pyproj
+import logging
+from tqdm import tqdm
+from copy import deepcopy
+osr.UseExceptions()
+
+@click.command()
+@click.argument('nc_file')
+@click.argument('output_file')
+@click.option('--ortho', is_flag=True)
+@click.option('--overwrite', is_flag=True)
+def nc_to_envi(nc_file: str, output_file: str, ortho=False, overwrite=False):
+    """Convert a NetCDF file to ENVI format.
+
+    \b
+    Args:
+        nc_file (str): Path to the input NetCDF file.
+        output_file (str): Path to the output ENVI file.
+        ortho (bool, optional): Whether to orthorectify the data. Defaults to False.
+    """
+    meta, dat = spec_io.load_data(nc_file, load_glt=True)
+    dat = np.array(dat)
+
+    if ortho and meta.orthoable:
+        dat = spec_io.ortho_data(dat, meta.glt)
+
+    if os.path.isfile(output_file) and not overwrite:
+        raise FileExistsError(f'Output file {output_file} already exists. Use --overwrite to overwrite it.')
+
+    spec_io.write_envi_file(dat, meta, output_file)
+
+
+
+
+
+@click.group()
+def cli():
+    pass
+
+
+cli.add_command(nc_to_envi)
+
+if __name__ == '__main__':
+    cli()

spectral_util/spec_io/spec_io.py

@@ -458,7 +458,7 @@ def open_loc_l1b_rad_nc(input_file, lazy=True, load_glt=False, load_loc=False):
     loc_plus_elev = np.stack([ds_loc['lat'], ds_loc['lon'], ds_loc['elev']], axis = -1)
 
     meta = GenericGeoMetadata([ds_loc['lat'].long_name, ds_loc['lon'].long_name, ds_loc['elev'].long_name], 
-                              trans, proj, glt=glt, pre_orthod=True, nodata_value=nodata_value, loc=loc)
+                              trans, proj, glt=glt, pre_orthod=False, nodata_value=nodata_value, loc=loc)
 
     return meta, loc_plus_elev
 
@@ -532,7 +532,7 @@ def open_emit_l2a_mask_nc(input_file, mask_type, lazy=True, load_glt=False, load
 
     mask = np.array(ds[mask_type][...])
 
-    meta = GenericGeoMetadata(mask_names, trans, proj, glt=glt, pre_orthod=True, nodata_value=nodata_value, loc=loc)
+    meta = GenericGeoMetadata(mask_names, trans, proj, glt=glt, pre_orthod=False, nodata_value=nodata_value, loc=loc)
 
     return meta, mask
 
@@ -568,7 +568,7 @@ def open_emit_obs_nc(input_file, lazy=True, load_glt=False, load_loc=False):
         logging.warning("Lazy loading not supported for observation data.")
     obs = ds['obs'][...]
 
-    meta = GenericGeoMetadata(obs_names, trans, proj, glt=glt, pre_orthod=True, nodata_value=nodata_value, loc=loc)
+    meta = GenericGeoMetadata(obs_names, trans, proj, glt=glt, pre_orthod=False, nodata_value=nodata_value, loc=loc)
 
     return meta, obs
 
@@ -670,7 +670,7 @@ def open_airborne_obs(input_file, lazy=True, load_glt=False, load_loc=False):
         logging.warning("Lazy loading not supported for observation data.")
     obs = np.stack([ds['observation_parameters'][on] for on in obs_names], axis=-1)
 
-    meta = GenericGeoMetadata(obs_names, trans, proj, glt=glt, pre_orthod=True, nodata_value=nodata_value, loc=loc)
+    meta = GenericGeoMetadata(obs_names, trans, proj, glt=glt, pre_orthod=False, nodata_value=nodata_value, loc=loc)
 
     return meta, obs