Edits to code formatting

Simple edits to improve compliance with PEP8 (https://www.python.org/dev/peps/pep-0008/). Top-level functions & classes surrounded by two blank lines. Imports reordered & split across separate lines.

hypro/AtmCorr.py

@@ -9,9 +9,14 @@
 
 """ Functions to do atmospheric corrections. """
 
-import logging, os, numpy as np
+import os
+import logging
+
+import numpy as np
+
 logger = logging.getLogger(__name__)
 
+
 def atm_corr_band(atm_lut_WVC, atm_lut_VIS, atm_lut_VZA, atm_lut_RAA, atm_lut,
                   wvc_image, vis_image, vza_image, raa_image, rdn_image,
                   bg_mask):
@@ -63,6 +68,7 @@ def atm_corr_band(atm_lut_WVC, atm_lut_VIS, atm_lut_VZA, atm_lut_RAA, atm_lut,
 
     return rho
 
+
 def atm_corr_image(flight_dict):
     """ Do atmospheric corrections on the whole image.
 

hypro/AtmLUT.py

@@ -9,7 +9,11 @@
 
 """ Functions to build an atmospheric lookup table (LUT). """
 
-import logging, os, numpy as np
+import os
+import logging
+
+import numpy as np
+
 logger = logging.getLogger(__name__)
 
 # Define atmosphere database parameters. Do not make any change to them.
@@ -23,6 +27,7 @@
 atm_db_VZA = np.array([0, 5, 10, 15, 20, 25, 30, 40]) # view zenith angle, in [deg]
 atm_db_RAA = np.array([0, 15, 30, 45, 60, 75, 90, 105, 120, 135, 150, 165, 180]) # relative azimuth angle, in [deg]
 
+
 def build_atm_lut(flight_dict):
     """ Make an atmospheric lookup table.
 
@@ -154,6 +159,7 @@ def build_atm_lut(flight_dict):
 
     logger.info('Write the raw ALT to %s.' %flight_dict['raw_atm_lut_file'])
 
+
 def resample_atm_lut(resampled_atm_lut_file, raw_atm_lut_file, rdn_header_file):
     """ Resample atmosphere lookup table radiance to sensor wavelengths.
 
@@ -218,6 +224,7 @@ def resample_atm_lut(resampled_atm_lut_file, raw_atm_lut_file, rdn_header_file):
 
     logger.info('Write the resampled ALT to %s.' %resampled_atm_lut_file)
 
+
 def write_binary_metadata(metadata_file, metadata):
     """ Write the metadata of a binary file.
 
@@ -246,6 +253,7 @@ def write_binary_metadata(metadata_file, metadata):
         fid.write('%s = %s\n' %(key, value))
     fid.close()
 
+
 def read_binary_metadata(metadata_file):
     """ Read the metadata of a binary file.
 
@@ -286,6 +294,7 @@ def read_binary_metadata(metadata_file):
 
     return metadata
 
+
 def get_interp_range(xs, x):
     """ Get the interpolation range. """
 
@@ -296,6 +305,7 @@ def get_interp_range(xs, x):
 
     return {x_index0: x_delta0, x_index1: x_delta1}
 
+
 def combos(indices):
     """ Return all combinations of indices in a list of index sublists.
 

hypro/Boresight.py

@@ -9,9 +9,14 @@
 
 """ Functions to do boresight calibration. """
 
-import logging, os, numpy as np
+import os
+import logging
+
+import numpy as np
+
 logger = logging.getLogger(__name__)
 
+
 def boresight_calibration(boresight_file, gcp_file, imugps_file, sensor_model_file, dem_image_file, boresight_options):
     """ Do boresight calibration.
 
@@ -145,6 +150,7 @@ def boresight_calibration(boresight_file, gcp_file, imugps_file, sensor_model_fi
 
     logger.info('Write boresight data to %s.' %boresight_file)
 
+
 def cost_fun(boresight_offsets, flight_xyz, flight_imu, flight_sensor_model, dem_image, dem_ulxy, dem_pixel_size, gcp_xyz, boresight_options):
     """ Cost function for boresight calibration.
 
@@ -178,6 +184,7 @@ def cost_fun(boresight_offsets, flight_xyz, flight_imu, flight_sensor_model, dem
 
     return cost
 
+
 def estimate_gcp_xyz(boresight_offsets, flight_xyz, flight_imu, flight_sensor_model, dem_image, dem_ulxy, dem_pixel_size, boresight_options):
     """ Cestimate GCP map coordinates.
 

hypro/Classification.py

@@ -9,11 +9,16 @@
 
 """ Functions to do image classifications. """
 
-import logging, os, numpy as np
+import os
+import logging
+
+import numpy as np
+
 logger = logging.getLogger(__name__)
 
 solar_flux_file = os.path.join(os.path.dirname(os.path.realpath(__file__)),'data','solar_flux.dat')
 
+
 def pre_classification(pre_class_image_file, rdn_image_file, sun_zenith, distance, background_mask_file=None):
     """ Pre-classify the image.
 

hypro/CreateSCA.py

@@ -7,9 +7,10 @@
 # Dept. of Forest and Wildlife Ecology
 # University of Wisconsin - Madison
 
-from ENVI import read_envi_header, write_envi_header
 import numpy as np
 
+from ENVI import read_envi_header, write_envi_header
+
 if __name__ == "__main__":
 
     raw_sca_file = '/media/nanfeng/My Passport/Hyspex/Output/CEDAR-CREEK-EW_20180724_01/merge/CEDAR-CREEK-EW_20180724_01_SCA'

hypro/DEM.py

@@ -9,10 +9,15 @@
 
 """ Functions to process DEM data. """
 
+import os
+import logging
+
+import numpy as np
 from osgeo import gdal
-import logging, os, numpy as np
+
 logger = logging.getLogger(__name__)
 
+
 def get_avg_elev(dem_image_file):
     """ Get the average elevation of a DEM image.
 
@@ -39,6 +44,7 @@ def get_avg_elev(dem_image_file):
 
     return avg_elev
 
+
 def prepare_dem(dem_image_file, dem, imugps_file, fov, map_crs, pixel_size):
     """ Prepare DEM data.
 

hypro/ENVI.py

@@ -113,6 +113,7 @@
                'z plot range',
                'z plot titles']
 
+
 def read_envi_header(file):
     """ Read ENVI header.
 
@@ -164,6 +165,7 @@ def read_envi_header(file):
 
     return header
 
+
 def check_envi_required_fields(header):
     """ Check ENVI required fields.
 
@@ -183,6 +185,7 @@ def check_envi_required_fields(header):
         if header[field] is None:
             raise ValueError('No value for %s!' %field)
 
+
 def empty_envi_header():
     """ Generate an empty ENVI header.
 
@@ -198,6 +201,7 @@ def empty_envi_header():
 
     return header
 
+
 def write_envi_header(file, header):
     """ Write ENVI header.
 

hypro/Figure.py

@@ -9,13 +9,18 @@
 
 """ Functions to make figures. """
 
-import logging, os, matplotlib.pyplot as plt, numpy as np
+import os
+import logging
+
+import numpy as np
 from osgeo import gdal
+import matplotlib.pyplot as plt
 
 mpl_logger = logging.getLogger('matplotlib')
 mpl_logger.setLevel(logging.WARNING)
 logger = logging.getLogger(__name__)
 
+
 def plot_angle_geometry(angle_geometry_figure_file, sca_image_file):
     """ Plot the sun-target-view geometry in a polar coordinate system.
 
@@ -60,6 +65,7 @@ def plot_angle_geometry(angle_geometry_figure_file, sca_image_file):
 
     logger.info('Save the angle geometry figure to %s.' %angle_geometry_figure_file)
 
+
 def plot_image_area(image_area_figure_file, dem_image_file, igm_image_file, imugps_file):
     """ Plot image area (DEM is used as the background).
 
@@ -124,6 +130,7 @@ def plot_image_area(image_area_figure_file, dem_image_file, igm_image_file, imug
 
     logger.info('Save the image-area figure to %s.' %image_area_figure_file)
 
+
 def linear_percent_stretch(raw_image):
     """ Do linear percent stretch.
 
@@ -153,6 +160,7 @@ def linear_percent_stretch(raw_image):
 
     return stretched_image
 
+
 def make_quicklook(quicklook_figure_file, rdn_image_file, glt_image_file):
     """ Make a RGB quicklook image.
 
@@ -235,6 +243,7 @@ def make_quicklook(quicklook_figure_file, rdn_image_file, glt_image_file):
 
     logger.info('Save the quicklook figure to %s.' %quicklook_figure_file)
 
+
 def plot_avg_rdn(avg_rdn_figure_file, avg_rdn_file):
     """ Plot average radiance to a figure.
 
@@ -273,6 +282,7 @@ def plot_avg_rdn(avg_rdn_figure_file, avg_rdn_file):
 
     logger.info('Save the average radiance spectra figure to %s.' %avg_rdn_figure_file)
 
+
 def plot_wvc_model(wvc_model_figure_file, wvc_model_file):
     """ Plot the WVC model to a figure.
 
@@ -312,6 +322,7 @@ def plot_wvc_model(wvc_model_figure_file, wvc_model_file):
 
     logger.info('Save the WVC model figure to %s.' %wvc_model_file)
 
+
 def plot_smile_effect(smile_effect_at_atm_features_figure_file, smile_effect_at_atm_features_file):
     """ Plot smile effects at different atmosphere absorption features.
 
@@ -412,6 +423,7 @@ def plot_smile_effect(smile_effect_at_atm_features_figure_file, smile_effect_at_
 
     logger.info('Save smile effect at atmosphere absorption features figure to %s.' %smile_effect_at_atm_features_figure_file)
 
+
 def plot_wvc_histogram(wvc_histogram_figure_file, water_vapor_column_image_file):
     """ Plot water vapor column histogram.
 

hypro/GeoRectification.py

@@ -9,9 +9,14 @@
 
 """ Functions to do geo-rectification. """
 
-import logging, os, numpy as np
+import os
+import logging
+
+import numpy as np
+
 logger = logging.getLogger(__name__)
 
+
 def orthorectify_sca(ortho_sca_image_file, sca_image_file, glt_image_file):
     """ Do orthorectifications on SCA.
 
@@ -88,6 +93,7 @@ def orthorectify_sca(ortho_sca_image_file, sca_image_file, glt_image_file):
 
     logger.info('Write the geo-rectified SCA image to %s.' %ortho_sca_image_file)
 
+
 def orthorectify_dem(ortho_dem_image_file, igm_image_file, glt_image_file):
     """ Do orthorectifications on DEM.
 
@@ -160,6 +166,7 @@ def orthorectify_dem(ortho_dem_image_file, igm_image_file, glt_image_file):
 
     logger.info('Write the geo-rectified DEM image to %s.' %ortho_dem_image_file)
 
+
 def orthorectify_rdn(ortho_rdn_image_file, rdn_image_file, glt_image_file):
     """ Do orthorectifications on radiance.
 

hypro/GeoReferencing.py

@@ -9,13 +9,20 @@
 
 """ Functions to do geo-referencing. """
 
+import os
+import logging
+import warnings
+
+import numpy as np
 from osgeo import gdal
-import logging, os, numpy as np
-logger = logging.getLogger(__name__)
 from numba import guvectorize, jit
-import warnings
+
+
+logger = logging.getLogger(__name__)
+
 warnings.filterwarnings("ignore")
 
+
 def calculate_igm(igm_image_file, imugps_file, sensor_model_file, dem_image_file, boresight_options):
     """ Create an input geometry (IGM) image.
 
@@ -137,6 +144,7 @@ def calculate_igm(igm_image_file, imugps_file, sensor_model_file, dem_image_file
 
     logger.info('Write the IGM to %s.' %igm_image_file)
 
+
 def calculate_sca(sca_image_file, imugps_file, igm_image_file, sun_angles):
     """ Create a scan angle (SCA) image.
 
@@ -223,6 +231,7 @@ def calculate_sca(sca_image_file, imugps_file, igm_image_file, sun_angles):
 
     logger.info('Write the SCA to %s.' %sca_image_file)
 
+
 def build_glt(glt_image_file, igm_image_file, pixel_size, map_crs):
     """ Create a geographic lookup table (GLT) image.
 
@@ -417,6 +426,7 @@ def build_glt(glt_image_file, igm_image_file, pixel_size, map_crs):
 
     logger.info('Write the GLT to %s.' %glt_image_file)
 
+
 def get_scan_vectors(imu, sensor_model):
     """ Get scan vectors.
 
@@ -507,6 +517,7 @@ def get_scan_vectors(imu, sensor_model):
 
     return L0
 
+
 def get_xyz0_xyz1(xyz, L0, h_min, h_max):
     """ Get the starting and ending locations of ray tracing.
 
@@ -548,6 +559,7 @@ def get_xyz0_xyz1(xyz, L0, h_min, h_max):
 
     return xyz0, xyz1
 
+
 @guvectorize(['void(f8[:,:,:], f8[:,:,:], f8[:,:,:], f8[:,:], f8[:], f8[:,:,:])'],
              '(b,n,m), (b,n,m), (b,n,m), (u,v), (c) -> (b,m,n)', cache=True)
 def ray_tracer_ufunc(xyz0, xyz1, L0, dem, dem_gt, output):
@@ -596,6 +608,7 @@ def ray_tracer_ufunc(xyz0, xyz1, L0, dem, dem_gt, output):
         for j in range(xyz0.shape[2]): # Iterate over scanlines
             output[:,j,i] = ray_tracing(xyz0[:,i,j], xyz1[:,i,j], L0[:,i,j], dem, dem_origin, resolution)
 
+
 @jit
 def ray_tracing(XYZ0, XYZ1, V, DEM, DEM_X0Y0, DEM_Resolution):
     """ Implement ray-tracing to get the pixel's geo-location and elevation.