import os
import numpy as np
from polsartools.utils.proc_utils import process_chunks_parallel
from polsartools.utils.utils import conv2d,time_it
from polsartools.utils.convert_matrices import T3_C3_mat
from .fp_infiles import fp_c3t3files
[docs]
@time_it
def shannon_h_fp(in_dir, win=1, fmt="tif", cog=False,
ovr = [2, 4, 8, 16], comp=False,
max_workers=None,block_size=(512, 512),
progress_callback=None, # for QGIS plugin
):
"""Calculate Shannon Entropy parameters from full-pol SAR data.
This function computes three Shannon Entropy-based parameters from full-polarimetric
SAR data: total Shannon Entropy (H), intensity contribution (HI), and polarimetric
contribution (HP). These parameters provide information about the complexity and
disorder of the scattered wave field.
Examples
--------
>>> # Basic usage with default parameters
>>> shannon_h_fp("/path/to/fullpol_data")
>>> # Advanced usage with custom parameters
>>> shannon_h_fp(
... in_dir="/path/to/fullpol_data",
... win=5,
... fmt="tif",
... cog=True,
... block_size=(1024, 1024)
... )
Parameters
----------
in_dir : str
Path to the input folder containing full-pol T3 or C3 matrix files.
window_size : int, default=1
Size of the spatial averaging window. Larger windows provide better
entropy estimation but decrease spatial resolution.
fmt : {'tif', 'bin'}, default='tif'
Output file format:
- 'tif': GeoTIFF format with georeferencing information
- 'bin': Raw binary format
cog : bool, default=False
If True, creates Cloud Optimized GeoTIFF (COG) outputs with internal tiling
and overviews for efficient web access.
ovr : list[int], default=[2, 4, 8, 16]
Overview levels for COG creation. Each number represents the
decimation factor for that overview level.
comp : bool, default=False
If True, uses LZW compression for GeoTIFF outputs.
max_workers : int | None, default=None
Maximum number of parallel processing workers. If None, uses
CPU count - 1 workers.
block_size : tuple[int, int], default=(512, 512)
Size of processing blocks (rows, cols) for parallel computation.
Larger blocks use more memory but may be more efficient.
Returns
-------
None
Writes three output files to disk:
1. H_Shannon: Total Shannon Entropy
2. HI_Shannon: Intensity contribution
3. HP_Shannon: Polarimetric contribution
"""
write_flag=True
input_filepaths = fp_c3t3files(in_dir)
output_filepaths = []
if fmt == "bin":
output_filepaths.append(os.path.join(in_dir, "H_Shannon.bin"))
output_filepaths.append(os.path.join(in_dir, "HI_Shannon.bin"))
output_filepaths.append(os.path.join(in_dir, "HP_Shannon.bin"))
else:
output_filepaths.append(os.path.join(in_dir, "H_Shannon.tif"))
output_filepaths.append(os.path.join(in_dir, "HI_Shannon.tif"))
output_filepaths.append(os.path.join(in_dir, "HP_Shannon.tif"))
process_chunks_parallel(input_filepaths, list(output_filepaths),
window_size=win, write_flag=write_flag,
processing_func=proc_shannon_h_fp,block_size=block_size,
max_workers=max_workers, num_outputs=len(output_filepaths),
cog=cog, ovr=ovr, comp=comp,
progress_callback=progress_callback
)
def proc_shannon_h_fp(chunks, window_size, input_filepaths, *args):
# additional_arg1 = args[0] if len(args) > 0 else None
# additional_arg2 = args[1] if len(args) > 1 else None
if 'T11' in input_filepaths[0] and 'T22' in input_filepaths[5] and 'T33' in input_filepaths[8]:
t11_T1 = np.array(chunks[0])
t12_T1 = np.array(chunks[1])+1j*np.array(chunks[2])
t13_T1 = np.array(chunks[3])+1j*np.array(chunks[4])
t21_T1 = np.conj(t12_T1)
t22_T1 = np.array(chunks[5])
t23_T1 = np.array(chunks[6])+1j*np.array(chunks[7])
t31_T1 = np.conj(t13_T1)
t32_T1 = np.conj(t23_T1)
t33_T1 = np.array(chunks[8])
T_T1 = np.array([[t11_T1, t12_T1, t13_T1],
[t21_T1, t22_T1, t23_T1],
[t31_T1, t32_T1, t33_T1]])
# T_T1 = T3_C3_mat(T3)
elif 'C11' in input_filepaths[0] and 'C22' in input_filepaths[5] and 'C33' in input_filepaths[8]:
C11 = np.array(chunks[0])
C12 = np.array(chunks[1])+1j*np.array(chunks[2])
C13 = np.array(chunks[3])+1j*np.array(chunks[4])
C21 = np.conj(C12)
C22 = np.array(chunks[5])
C23 = np.array(chunks[6])+1j*np.array(chunks[7])
C31 = np.conj(C13)
C32 = np.conj(C23)
C33 = np.array(chunks[8])
T_T1 = np.array([[C11, C12, C13],
[C21, C22, C23],
[C31, C32, C33]])
else:
raise ValueError("Invalid input matrices. Ensure the input is either T3 or C3 matrix folder.")
if window_size>1:
kernel = np.ones((window_size,window_size),np.float32)/(window_size*window_size)
t11f = conv2d(T_T1[0,0,:,:],kernel)
t12f = conv2d(np.real(T_T1[0,1,:,:]),kernel)+1j*conv2d(np.imag(T_T1[0,1,:,:]),kernel)
t13f = conv2d(np.real(T_T1[0,2,:,:]),kernel)+1j*conv2d(np.imag(T_T1[0,2,:,:]),kernel)
t21f = np.conj(t12f)
t22f = conv2d(T_T1[1,1,:,:],kernel)
t23f = conv2d(np.real(T_T1[1,2,:,:]),kernel)+1j*conv2d(np.imag(T_T1[1,2,:,:]),kernel)
t31f = np.conj(t13f)
t32f = np.conj(t23f)
t33f = conv2d(T_T1[2,2,:,:],kernel)
T_T1 = np.array([[t11f, t12f, t13f], [t21f, t22f, t23f], [t31f, t32f, t33f]])
_,_,rows,cols = np.shape(T_T1)
T_T1 = T_T1.reshape(9, rows, cols)
# Indices for vectorized access
i, j = np.indices((rows, cols))
T_T1 = np.dstack((T_T1[0,:,:],T_T1[1,:,:],T_T1[2,:,:],
T_T1[3,:,:],T_T1[4,:,:],T_T1[5,:,:],T_T1[6,:,:],T_T1[7,:,:],T_T1[8,:,:]))
data = T_T1.reshape( T_T1.shape[0]*T_T1.shape[1], T_T1.shape[2]).reshape((-1,3,3))
# infinity, nan handling
data = np.nan_to_num(data, nan=0.0, posinf=0, neginf=0)
# data = np.nan_to_num(data, nan=np.nan, posinf=np.nan, neginf=np.nan)
evals_, evecs_ = np.linalg.eig(data.reshape(-1, 3, 3))
# Sort eigenvalues for each pixel in descending order;
sorted_indices = np.argsort(evals_, axis=-1)[:, ::-1]
# Reorder eigenvalues and eigenvectors based on sorted indices
evals = np.take_along_axis(evals_, sorted_indices, axis=-1) # Reorder eigenvalues
eps = 1e-8
D = evals[:,0]*evals[:,1]*evals[:,2]
I = evals[:,0]+evals[:,1]+evals[:,2]
#Barakat Degree of Polarization
DoP = np.ones(rows*cols).astype(np.float32) - 27* D / (I*I*I + eps)
HSP = np.zeros(rows*cols).astype(np.float32)
# HSI = np.zeros(rows*cols).astype(np.float32)
# HS = np.zeros(rows*cols).astype(np.float32)
condition = (np.ones(rows*cols) - DoP) < eps
HSP = np.where(condition, 0, np.log(np.abs(np.ones(rows*cols) - DoP)))
HSP[np.isinf(HSP)] = np.nan
HSP[HSP==0] = np.nan
with np.errstate(divide='ignore', invalid='ignore'):
HSI = 3 * np.log(np.exp(1) * np.pi * I / 3)
HSI[np.isinf(HSI)] = np.nan
HSI[HSI==0] = np.nan
HS = np.nansum(np.dstack((HSP, HSI)), 2)
return np.real(HS).reshape(rows,cols).astype(np.float32),\
np.real(HSI).reshape(rows,cols).astype(np.float32) ,\
np.real(HSP).reshape(rows,cols).astype(np.float32)#,np.real(HS_norm).reshape(rows,cols),np.real(HSI_norm).reshape(rows,cols),np.real(HSP_norm).reshape(rows,cols)
