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Merge pull request #307 from GispoCoding/293-add-smoothingfilter-cli-…
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…functions

293 add smoothing / filter cli functions
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@nmaarnio
nmaarnio committed Mar 4, 2024
2 parents a261d5f + 0e078ae commit 5813e55
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Showing 2 changed files with 297 additions and 6 deletions.
291 changes: 291 additions & 0 deletions eis_toolkit/cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -200,6 +200,27 @@ class NodataHandling(str, Enum):
remove = "remove"


class FocalFilterMethod(str, Enum):
"""Focal filter methods."""

mean = "mean"
median = "median"


class FocalFilterShape(str, Enum):
"""Shape of the filter window."""

square = "square"
circle = "circle"


class MexicanHatFilterDirection(str, Enum):
"""Direction of calculating kernel values."""

rectangular = "rectangular"
circular = "circular"


class LocalMoranWeightType(str, Enum):
"""Weight type for Local Moran's I."""

Expand Down Expand Up @@ -533,6 +554,276 @@ def local_morans_i_cli(
# --- RASTER PROCESSING ---


# FOCAL FILTER
@app.command()
def focal_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
method: FocalFilterMethod = FocalFilterMethod.mean,
size: int = 3,
shape: FocalFilterShape = FocalFilterShape.circle,
):
"""Apply a basic focal filter to the input raster."""
from eis_toolkit.raster_processing.filters.focal import focal_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = focal_filter(raster=raster, method=method, size=size, shape=shape)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Focal filter applied, output raster written to {output_raster}.")


# GAUSSIAN FILTER
@app.command()
def gaussian_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
sigma: float = 1.0,
truncate: float = 4.0,
size: int = None,
):
"""Apply a gaussian filter to the input raster."""
from eis_toolkit.raster_processing.filters.focal import gaussian_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = gaussian_filter(raster=raster, sigma=sigma, truncate=truncate, size=size)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Gaussial filter applied, output raster written to {output_raster}.")


# MEXICAN HAT FILTER
@app.command()
def mexican_hat_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
sigma: float = 1.0,
truncate: float = 4.0,
size: int = None,
direction: MexicanHatFilterDirection = MexicanHatFilterDirection.circular,
):
"""Apply a mexican hat filter to the input raster."""
from eis_toolkit.raster_processing.filters.focal import mexican_hat_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = mexican_hat_filter(
raster=raster, sigma=sigma, truncate=truncate, size=size, direction=direction
)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Mexican hat filter applied, output raster written to {output_raster}.")


# LEE ADDITIVE NOISE FILTER
@app.command()
def lee_additive_noise_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
add_noise_var: float = 0.25,
):
"""Apply a Lee filter considering additive noise components in the input raster."""
from eis_toolkit.raster_processing.filters.speckle import lee_additive_noise_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = lee_additive_noise_filter(raster=raster, size=size, add_noise_var=add_noise_var)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Additive Lee noise filter applied, output raster written to {output_raster}.")


# LEE MULTIPLICATIVE NOISE FILTER
@app.command()
def lee_multiplicative_noise_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
multi_noise_mean: float = 1.0,
n_looks: int = 1,
):
"""Apply a Lee filter considering multiplicative noise components in the input raster."""
from eis_toolkit.raster_processing.filters.speckle import lee_multiplicative_noise_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = lee_multiplicative_noise_filter(
raster=raster, size=size, mult_noise_mean=multi_noise_mean, n_looks=n_looks
)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Multiplicative Lee noise filter applied, output raster written to {output_raster}.")


# LEE ADDITIVE MULTIPLICATIVE NOISE FILTER
@app.command()
def lee_additive_multiplicative_noise_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
add_noise_var: float = 0.25,
add_noise_mean: float = 0,
multi_noise_mean: float = 1.0,
):
"""Apply a Lee filter considering both additive and multiplicative noise components in the input raster."""
from eis_toolkit.raster_processing.filters.speckle import lee_additive_multiplicative_noise_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = lee_additive_multiplicative_noise_filter(
raster=raster,
size=size,
add_noise_var=add_noise_var,
add_noise_mean=add_noise_mean,
mult_noise_mean=multi_noise_mean,
)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Additive multiplicative Lee noise filter applied, output raster written to {output_raster}.")


# LEE ENHANCED FILTER
@app.command()
def lee_enhanced_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
n_looks: int = 1,
damping_factor: float = 1.0,
):
"""Apply an enhanced Lee filter to the input raster."""
from eis_toolkit.raster_processing.filters.speckle import lee_enhanced_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = lee_enhanced_filter(
raster=raster, size=size, n_looks=n_looks, damping_factor=damping_factor
)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Enhanced Lee filter applied, output raster written to {output_raster}.")


# GAMMA FILTER
@app.command()
def gamma_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
n_looks: int = 1,
):
"""Apply a Gamma filter to the input raster."""
from eis_toolkit.raster_processing.filters.speckle import gamma_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = gamma_filter(raster=raster, size=size, n_looks=n_looks)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Gamma filter applied, output raster written to {output_raster}.")


# FROST FILTER
@app.command()
def frost_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
damping_factor: float = 1.0,
):
"""Apply a Frost filter to the input raster."""
from eis_toolkit.raster_processing.filters.speckle import frost_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("Progress: 25%")
out_image, out_meta = frost_filter(raster=raster, size=size, damping_factor=damping_factor)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Frost filter applied, output raster written to {output_raster}.")


# KUAN FILTER
@app.command()
def kuan_filter_cli(
input_raster: Annotated[Path, INPUT_FILE_OPTION],
output_raster: Annotated[Path, OUTPUT_FILE_OPTION],
size: int = 3,
n_looks: int = 1,
):
"""Apply a Kuan filter to the input raster."""
from eis_toolkit.raster_processing.filters.speckle import kuan_filter

typer.echo("Progress: 10%")

with rasterio.open(input_raster) as raster:
typer.echo("progress: 25%")
out_image, out_meta = kuan_filter(raster=raster, size=size, n_looks=n_looks)
typer.echo("Progress: 75%")

with rasterio.open(output_raster, "w", **out_meta) as dest:
dest.write(out_image, 1)
typer.echo("Progress: 100%")

typer.echo(f"Kuan filter applied, output raster written to {output_raster}.")


# CHECK RASTER GRIDS
@app.command()
def check_raster_grids_cli(input_rasters: INPUT_FILES_ARGUMENT, same_extent: bool = False):
Expand Down
12 changes: 6 additions & 6 deletions eis_toolkit/raster_processing/filters/speckle.py
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Original file line number Diff line number Diff line change
Expand Up @@ -179,7 +179,7 @@ def _gamma(window: np.ndarray, n_looks: int) -> np.ndarray:


@beartype
def _frost(window: np.ndarray, damping_factor: int) -> Number:
def _frost(window: np.ndarray, damping_factor: Number) -> Number:
"""
Calculate the weighted value for a Frost filter from a window of pixels.
Expand Down Expand Up @@ -381,8 +381,8 @@ def lee_additive_multiplicative_noise_filter(
def lee_enhanced_filter(
raster: rasterio.io.DatasetReader,
size: int = 3,
n_looks: Number = 1,
damping_factor: Number = 1,
n_looks: int = 1,
damping_factor: Number = 1.0,
) -> tuple[np.ndarray, dict]:
"""
Apply an enhanced Lee filter to the input raster.
Expand Down Expand Up @@ -431,7 +431,7 @@ def lee_enhanced_filter(
def gamma_filter(
raster: rasterio.io.DatasetReader,
size: int = 3,
n_looks: Number = 1,
n_looks: int = 1,
) -> tuple[np.ndarray, dict]:
"""
Apply a Gamma filter to the input raster.
Expand Down Expand Up @@ -476,7 +476,7 @@ def gamma_filter(
def frost_filter(
raster: rasterio.io.DatasetReader,
size: int = 3,
damping_factor: Number = 1,
damping_factor: Number = 1.0,
) -> tuple[np.ndarray, dict]:
"""
Apply a Frost filter to the input raster.
Expand Down Expand Up @@ -521,7 +521,7 @@ def frost_filter(
def kuan_filter(
raster: rasterio.io.DatasetReader,
size: int = 3,
n_looks: Number = 1,
n_looks: int = 1,
) -> tuple[np.ndarray, dict]:
"""
Apply a Kuan filter to the input raster.
Expand Down

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