From c092ec4080794c0c29460458526a58b9d928db6d Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Wed, 22 Mar 2023 16:02:30 +0200 Subject: [PATCH 01/29] testing --- eis_toolkit/__main__.py | 4 ++ eis_toolkit/cli.py | 0 eis_toolkit/cli_click.py | 123 +++++++++++++++++++++++++++++++++++ eis_toolkit/cli_config.py | 64 ++++++++++++++++++ eis_toolkit/config_test.json | 22 +++++++ tests/cli_test.py | 83 +++++++++++++++++++++++ 6 files changed, 296 insertions(+) create mode 100644 eis_toolkit/__main__.py create mode 100644 eis_toolkit/cli.py create mode 100644 eis_toolkit/cli_click.py create mode 100644 eis_toolkit/cli_config.py create mode 100644 eis_toolkit/config_test.json create mode 100644 tests/cli_test.py diff --git a/eis_toolkit/__main__.py b/eis_toolkit/__main__.py new file mode 100644 index 00000000..f0363941 --- /dev/null +++ b/eis_toolkit/__main__.py @@ -0,0 +1,4 @@ +from eis_toolkit.cli_click import cli + +if __name__ == "__main__": + cli() diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py new file mode 100644 index 00000000..e69de29b diff --git a/eis_toolkit/cli_click.py b/eis_toolkit/cli_click.py new file mode 100644 index 00000000..33c16815 --- /dev/null +++ b/eis_toolkit/cli_click.py @@ -0,0 +1,123 @@ +"""Command-line interface for eis_toolkit.""" +from pathlib import Path +from typing import List, Tuple + +import click +import geopandas as gpd +import rasterio +from rasterio import warp + +from eis_toolkit.raster_processing.clipping import clip_raster +from eis_toolkit.raster_processing.gridding_check import gridding_check +from eis_toolkit.raster_processing.reprojecting import reproject_raster +from eis_toolkit.raster_processing.snapping import snap_with_raster +from eis_toolkit.raster_processing.windowing import extract_window + +EXISTING_CLICK_FILE = click.Path(exists=True, file_okay=True, dir_okay=False, readable=True) + + +@click.group() +def cli(): + """Click group to nest subcommands under one interface.""" + pass + + +# CLIP RASTER +@cli.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE, help="Input raster to be clipped") +@click.argument("geodataframe", nargs=1, type=EXISTING_CLICK_FILE, help="Clipping geometries") +@click.option("--output-raster-file", type=click.Path(), required=True, help="Output raster file path") +def clip_raster_cli(input_raster: str, geodataframe: str, output_raster_file: str): + """Clip the input raster with geometries in geodataframe.""" + raster_path, geodataframe_path, output_raster_path = ( + Path(input_raster), + Path(geodataframe), + Path(output_raster_file), + ) + + geodataframe = gpd.read_file(geodataframe_path) + with rasterio.open(raster_path) as raster: + out_image, out_meta = clip_raster( + raster=raster, + geodataframe=geodataframe, + ) + + click.echo(f"Clipping completed") + click.echo(f"Writing raster to {output_raster_path}.") + with rasterio.open(output_raster_path, "w", **out_meta) as dest: + dest.write(out_image) + + +# REPROJECT RASTER +@cli.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE, help="Input raster to be reprojected") +@click.option("--crs", type=int, required=True, help="Target CRS as an EPSG code") +@click.option( + "--output-raster-file", type=click.Path(), required=True, help="Path to the output reprojected raster file." +) +@click.option( + "--resampling-method", + type=click.Choice([m.name for m in warp.Resampling], case_sensitive=False), + default=warp.Resampling.nearest.name, + help="Resampling method to use. Defaults to 'nearest'.", +) +def reproject_raster_cli(input_raster: str, crs: str, output_raster_file: str, resampling_method: str): + """Reproject the input raster to given coordinate refrence system.""" + raster_path, output_raster_path = (Path(input_raster), Path(output_raster_file)) + + with rasterio.open(raster_path) as raster: + out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling_method) + + click.echo(f"Reprojecting completed") + click.echo(f"Writing raster to {output_raster_path}.") + with rasterio.open(output_raster_path, "w", **out_meta) as dest: + dest.write(out_image) + + +# SNAP WITH RASTER +@click.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.argument("snap_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--output-raster-file", type=click.Path(), required=True) +def snap_with_raster_cli(input_raster: str, snap_raster: str, output_raster_file: str): + """Snaps/aligns input raster to the given snap raster.""" + with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: + out_image, out_meta = snap_with_raster(src, snap_src) + click.echo(f"Snapping completed") + click.echo(f"Writing raster to {output_raster_file}") + with rasterio.open(output_raster_file, "w", **out_meta) as dst: + dst.write(out_image) + + +# EXTRACT WINDOW +@click.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--center-coords", type=(float, float), required=True) +@click.option("--height", type=int, required=True) +@click.option("--width", type=int, required=True) +@click.option("--output-raster-file", type=click.Path(), required=True) +def extract_window_cli( + input_raster: str, center_coords: Tuple[float, float], height: int, width: int, output_raster_file: str +): + """Extract a window from a raster.""" + with rasterio.open(input_raster) as raster: + out_image, out_meta = extract_window(raster, center_coords, height, width) + click.echo(f"Windowing completed") + click.echo(f"Writing raster to {output_raster_file}") + with rasterio.open(output_raster_file, "w", **out_meta) as dst: + dst.write(out_image) + + +# CHECK RASTER GRIDS +@click.command() +@click.argument("input-rasters", nargs=-1, type=EXISTING_CLICK_FILE) +@click.option("--same-extent", type=bool, default=False) +def check_matching_grids_cli(input_rasters, same_extent: bool): + """Check the set of input rasters for matching gridding and optionally matching bounds.""" + open_rasters = [] + for raster in input_rasters: + open_rasters.append(rasterio.open(raster)) + check = gridding_check(open_rasters, same_extent) + for raster in open_rasters: + raster.close() + click.echo(f"Gridding check returned {check}") diff --git a/eis_toolkit/cli_config.py b/eis_toolkit/cli_config.py new file mode 100644 index 00000000..4cc45e67 --- /dev/null +++ b/eis_toolkit/cli_config.py @@ -0,0 +1,64 @@ +import json +from pathlib import Path + +import geopandas as gpd +import rasterio + + +def convert_arguments(arg_data): + function_arguments = {} + for arg, arg_items in arg_data: + arg_type = arg_items["type"] + arg_value = arg_items["value"] + converted_arg = convert_argument(arg_value, arg_type) + function_arguments[arg] = converted_arg + + +def convert_argument(arg_value, arg_type): + if arg_type == "raster": + converted_arg = rasterio.open(arg_value) + elif arg_type == "geodataframe": + converted_arg = gpd.read_file(arg_value) + else: + raise Exception(f"Unknown argument type (arg type, arg value): {arg_type, arg_value}") + + return converted_arg + + +def write_outputs(output_definitions, output_data): + for arg, arg_items in output_definitions: + arg_type = arg_items["type"] + arg_value = arg_items["value"] + write_output(arg_value, arg_type, output_data) + + +def write_output(arg_value, arg_type, data): + if arg_type == "raster": + out_image = data[0] + out_meta = data[1] + with rasterio.open(arg_value, "w", **out_meta) as dest: + dest.write(out_image) + elif arg_type == "vector": + pass + + +def read_config(config_path): + config_path = Path(config_path) + loaded_config = json.loads(config_path.read_text()) + + +def execute_workflow(config): + for function_name, func_items in config["workflow"].items(): + function = locals()[function_name] + function_arguments = convert_arguments(func_items["inputs"].items()) + output_data = function(**function_arguments) + write_outputs(func_items["outputs"].items(), output_data) + + +def interface(): + config_path = "/home/niko/code/plugin_dev/eis_toolkit/eis_toolkit/config_test.json" + loaded_config = read_config(config_path) + execute_workflow(loaded_config) + + +interface() diff --git a/eis_toolkit/config_test.json b/eis_toolkit/config_test.json new file mode 100644 index 00000000..b77936fb --- /dev/null +++ b/eis_toolkit/config_test.json @@ -0,0 +1,22 @@ +{ + "workflow": { + "clip_raster": { + "inputs": { + "raster": { + "type": "raster", + "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/remote/small_raster.tif" + }, + "geodataframe": { + "type": "geodataframe", + "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/remote/small_area.shp" + } + }, + "outputs": { + "output_raster:": { + "type": "raster", + "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/local/cli_clip_test_output.tif" + } + } + } + } +} diff --git a/tests/cli_test.py b/tests/cli_test.py new file mode 100644 index 00000000..6e5f5e06 --- /dev/null +++ b/tests/cli_test.py @@ -0,0 +1,83 @@ +"""Tests for eis_toolkit.cli.""" +import json +from contextlib import nullcontext +from pathlib import Path +from traceback import print_tb +from typing import ContextManager + +import pytest +import rasterio +from click.testing import CliRunner, Result + +from eis_toolkit.cli_click import cli + +CLICK_RUNNER = CliRunner() + +RASTER_FILE_PATH = Path("tests/data/remote/small_raster.tif") +GEODATAFRAME_FILE_PATH = Path("tests/data/remote/small_area.shp") + + +def click_error_print(result: Result): + """Print click result traceback.""" + # If exit_code is zero then the cli execution succeeded + # If it is not zero then the execution failed + if result.exit_code == 0: + return + + # Print the Python traceback related to failed execution + assert result.exc_info is not None + _, _, tb = result.exc_info + print_tb(tb) + + # Print the stdout of the execution + print(result.output) + assert result.exception is not None + + # Raise the collected Python exception that was raised + raise result.exception + + +@pytest.mark.parametrize( + "raster_file_path,geodataframe_file_path,raises", + [ + # Using the contextmanagers nullcontext and pytest.raises, the tests + # can be conditionalized to both error and succeed based on the + # parameter (nullcontext == succeed) + (RASTER_FILE_PATH, GEODATAFRAME_FILE_PATH, nullcontext()), + (Path("invalid/path/to/nowhere.tif"), Path("invalid/path/to/nowhere.shp"), pytest.raises(SystemExit)), + ], +) +def test_cli_clip_raster(raster_file_path: Path, geodataframe_file_path: Path, raises: ContextManager, tmp_path: Path): + """Test cli_clip_raster click entrypoint.""" + # tmp_path is a pytest fixture that is always a temporary directory path on + # the file system if is put in the function signature + output_raster_path = tmp_path / "clipped_raster.tif" + + # Define the arguments for the command-line execution + args = [ + # The first arg defines which subcommand to use + "cli-clip-raster", + str(raster_file_path), + str(geodataframe_file_path), + f"--output-raster-file={output_raster_path}", + ] + # Run the eis_toolkit.cli:cli click entrypoint function + result = CLICK_RUNNER.invoke(cli=cli, args=args) + + # If error is expected, raises will equal to pytest.raises() + # where the can e.g. be FileNotFoundError. For click executions + # is is always/usually SystemExit + with raises: + # This function will error and print tracebacks and exceptions if the + # execution fails + click_error_print(result=result) + + # Check that the expected result occurred + assert output_raster_path.exists() + assert output_raster_path.is_file() + + with rasterio.open(output_raster_path, mode="r") as out_raster, rasterio.open( + raster_file_path, mode="r" + ) as src_raster: + # Check that coordinate reference system is maintained + assert out_raster.meta["crs"] == src_raster.meta["crs"] From 7f0105c58f97ea8d7b191d8c4ffc28ba12c817dc Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Fri, 24 Mar 2023 10:49:38 +0200 Subject: [PATCH 02/29] Now Click CLI uses setuptools, interfaces for some algs and some placeholders --- eis_toolkit/cli_click.py | 127 +++++++++++++++++++++++++++++++++------ setup.py | 15 +++++ 2 files changed, 122 insertions(+), 20 deletions(-) create mode 100644 setup.py diff --git a/eis_toolkit/cli_click.py b/eis_toolkit/cli_click.py index 33c16815..d58a0209 100644 --- a/eis_toolkit/cli_click.py +++ b/eis_toolkit/cli_click.py @@ -1,6 +1,6 @@ """Command-line interface for eis_toolkit.""" from pathlib import Path -from typing import List, Tuple +from typing import Tuple import click import geopandas as gpd @@ -13,9 +13,24 @@ from eis_toolkit.raster_processing.snapping import snap_with_raster from eis_toolkit.raster_processing.windowing import extract_window +# from eis_toolkit.raster_processing.unifying import unify_rasters + EXISTING_CLICK_FILE = click.Path(exists=True, file_okay=True, dir_okay=False, readable=True) +resampling_mapping = { + "nearest": warp.Resampling.nearest, + "bilinear": warp.Resampling.bilinear, + "cubic": warp.Resampling.cubic, + "average": warp.Resampling.average, + "gauss": warp.Resampling.gauss, + "max": warp.Resampling.max, + "min": warp.Resampling.min, +} +# NOTE: Use the mapping below if all variants are wanted +# resampling_mapping = {method.name.lower(): method for method in warp.Resampling} + + @click.group() def cli(): """Click group to nest subcommands under one interface.""" @@ -24,25 +39,25 @@ def cli(): # CLIP RASTER @cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE, help="Input raster to be clipped") -@click.argument("geodataframe", nargs=1, type=EXISTING_CLICK_FILE, help="Clipping geometries") +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.argument("geometries", nargs=1, type=EXISTING_CLICK_FILE) @click.option("--output-raster-file", type=click.Path(), required=True, help="Output raster file path") -def clip_raster_cli(input_raster: str, geodataframe: str, output_raster_file: str): - """Clip the input raster with geometries in geodataframe.""" - raster_path, geodataframe_path, output_raster_path = ( +def clip_raster_cli(input_raster: str, geometries: str, output_raster_file: str): + """Clip the input raster with geometries in a geodataframe.""" + raster_path, geometries_path, output_raster_path = ( Path(input_raster), - Path(geodataframe), + Path(geometries), Path(output_raster_file), ) - geodataframe = gpd.read_file(geodataframe_path) + geodataframe = gpd.read_file(geometries_path) with rasterio.open(raster_path) as raster: out_image, out_meta = clip_raster( raster=raster, geodataframe=geodataframe, ) - click.echo(f"Clipping completed") + click.echo("Clipping completed") click.echo(f"Writing raster to {output_raster_path}.") with rasterio.open(output_raster_path, "w", **out_meta) as dest: dest.write(out_image) @@ -50,7 +65,7 @@ def clip_raster_cli(input_raster: str, geodataframe: str, output_raster_file: st # REPROJECT RASTER @cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE, help="Input raster to be reprojected") +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) @click.option("--crs", type=int, required=True, help="Target CRS as an EPSG code") @click.option( "--output-raster-file", type=click.Path(), required=True, help="Path to the output reprojected raster file." @@ -65,17 +80,18 @@ def reproject_raster_cli(input_raster: str, crs: str, output_raster_file: str, r """Reproject the input raster to given coordinate refrence system.""" raster_path, output_raster_path = (Path(input_raster), Path(output_raster_file)) + resampling = resampling_mapping[resampling_method.lower()] with rasterio.open(raster_path) as raster: - out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling_method) + out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling) - click.echo(f"Reprojecting completed") + click.echo("Reprojecting completed") click.echo(f"Writing raster to {output_raster_path}.") with rasterio.open(output_raster_path, "w", **out_meta) as dest: dest.write(out_image) # SNAP WITH RASTER -@click.command() +@cli.command() @click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) @click.argument("snap_raster", nargs=1, type=EXISTING_CLICK_FILE) @click.option("--output-raster-file", type=click.Path(), required=True) @@ -83,14 +99,14 @@ def snap_with_raster_cli(input_raster: str, snap_raster: str, output_raster_file """Snaps/aligns input raster to the given snap raster.""" with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: out_image, out_meta = snap_with_raster(src, snap_src) - click.echo(f"Snapping completed") + click.echo("Snapping completed") click.echo(f"Writing raster to {output_raster_file}") with rasterio.open(output_raster_file, "w", **out_meta) as dst: dst.write(out_image) # EXTRACT WINDOW -@click.command() +@cli.command() @click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) @click.option("--center-coords", type=(float, float), required=True) @click.option("--height", type=int, required=True) @@ -102,17 +118,17 @@ def extract_window_cli( """Extract a window from a raster.""" with rasterio.open(input_raster) as raster: out_image, out_meta = extract_window(raster, center_coords, height, width) - click.echo(f"Windowing completed") + click.echo("Windowing completed") click.echo(f"Writing raster to {output_raster_file}") with rasterio.open(output_raster_file, "w", **out_meta) as dst: dst.write(out_image) # CHECK RASTER GRIDS -@click.command() -@click.argument("input-rasters", nargs=-1, type=EXISTING_CLICK_FILE) +@cli.command() +@click.argument("input_rasters", nargs=-1, type=EXISTING_CLICK_FILE) @click.option("--same-extent", type=bool, default=False) -def check_matching_grids_cli(input_rasters, same_extent: bool): +def check_raster_grids_cli(input_rasters, same_extent: bool): """Check the set of input rasters for matching gridding and optionally matching bounds.""" open_rasters = [] for raster in input_rasters: @@ -120,4 +136,75 @@ def check_matching_grids_cli(input_rasters, same_extent: bool): check = gridding_check(open_rasters, same_extent) for raster in open_rasters: raster.close() - click.echo(f"Gridding check returned {check}") + click.echo(f"{check}") + # click.echo(f"Gridding check returned {check}") + return check + + +# PLACEHOLDER INTERFACES + +# PCA +@cli.command() +@click.argument("input-raster", nargs=-1, type=EXISTING_CLICK_FILE) +@click.option("--components", type=int, required=True) +@click.option("--output-raster-file", type=click.Path(), required=True) +def pca_cli(input_raster, components: int, output_raster_file: str): + """NOT IMPLEMENTED. Compute PCA with specified nr. of components.""" + raise Exception("Not implemented yet") + + +# FUZZY OVERLAY +@cli.command() +@click.argument("input_rasters", nargs=-1, type=EXISTING_CLICK_FILE) +@click.option("--fuzzy_method", type=str, required=True) +@click.option("--output-raster-file", type=click.Path(), required=True) +def fuzzy_overlay_cli(input_rasters, fuzzy_method: str, output_raster_file: str): + """NOT IMPLEMENTED. Calculate fuzzy overlay.""" + raise Exception("Not implemented yet") + + +# GERETATE DATA +@cli.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--output-raster-file", type=click.Path(), required=True) +def generate_data_cli(input_raster: str, output_raster_file: str): + """NOT IMPLEMENTED. Generate data for machine learning models.""" + raise Exception("Not implemented yet") + + +# RASTERIZE +@cli.command() +@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--output-raster-file", type=click.Path(), required=True) +def rasterize_cli(input_raster: str, output_raster_file: str): + """NOT IMPLEMENTED. Rasterize a given vector.""" + raise Exception("Not implemented yet") + + +# WEIGHTS OF EVIDENCE +@cli.command() +@click.argument("evidential_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.argument("deposit_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--weights-type", type=str) +@click.option("--contrast", type=int) +@click.option("--output-raster-file", type=click.Path(), required=True) +def weights_of_evidence_cli( + evidential_raster: str, deposit_raster: str, weights_type: str, contrast: int, output_raster_file: str +): + """NOT IMPLEMENTED. Calculate weights of evidence.""" + raise Exception("Not implemented yet") + + +# UNIFY RASTERS +@cli.command() +@click.argument("base_raster", nargs=1, type=EXISTING_CLICK_FILE) +@click.argument("rasters", nargs=1, type=EXISTING_CLICK_FILE) +@click.option("--same-extent", type=bool, default=False) +@click.option("--output-raster-file", type=click.Path(), required=True) +def unify_rasters_cli(base_raster: str, rasters, same_extent: bool, output_raster_file: str): + """NOT IMPLEMENTED. Unify given set of rasters.""" + raise Exception("Not implemented yet") + + +if __name__ == "__main__": + cli() diff --git a/setup.py b/setup.py new file mode 100644 index 00000000..fcb8cf74 --- /dev/null +++ b/setup.py @@ -0,0 +1,15 @@ +from setuptools import find_packages, setup + +setup( + name="eis_toolkit", + version="0.1", + packages=find_packages(), + install_requires=[ + # Add your package dependencies here + ], + entry_points={ + "console_scripts": [ + "eis=eis_toolkit.cli_click:cli", + ], + }, +) From 6268f1d18fb5e14621b3436c306bbf167347c29b Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Mon, 31 Jul 2023 13:46:36 +0300 Subject: [PATCH 03/29] First typer implementations --- eis_toolkit/cli_typer.py | 170 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 170 insertions(+) create mode 100644 eis_toolkit/cli_typer.py diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py new file mode 100644 index 00000000..45772a6f --- /dev/null +++ b/eis_toolkit/cli_typer.py @@ -0,0 +1,170 @@ +from enum import Enum +from pathlib import Path +from typing import Tuple + +import geopandas as gpd +import rasterio +import typer +from rasterio import warp +from typing_extensions import Annotated + +from eis_toolkit.raster_processing.clipping import clip_raster +from eis_toolkit.raster_processing.reprojecting import reproject_raster +from eis_toolkit.raster_processing.snapping import snap_with_raster +from eis_toolkit.raster_processing.windowing import extract_window +from eis_toolkit.vector_processing.reproject_vector import reproject_vector + +app = typer.Typer() + + +class ResamplingMethods(str, Enum): + """Resampling methods available.""" + + nearest = "nearest" + bilinear = "bilinear" + cubic = "cubic" + average = "average" + gauss = "gauss" + max = "max" + min = "min" + + +RESAMPLING_MAPPING = { + "nearest": warp.Resampling.nearest, + "bilinear": warp.Resampling.bilinear, + "cubic": warp.Resampling.cubic, + "average": warp.Resampling.average, + "gauss": warp.Resampling.gauss, + "max": warp.Resampling.max, + "min": warp.Resampling.min, +} + + +INPUT_FILE_OPTION = typer.Option( + exists=True, + file_okay=True, + dir_okay=False, + writable=False, + readable=True, + resolve_path=True, +) + +OUTPUT_FILE_OPTION = typer.Option( + exists=True, + file_okay=True, + dir_okay=False, + writable=False, + readable=True, + resolve_path=True, +) + + +# CLIP RASTER +@app.command() +def clip_raster_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + geometries: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Clip the input raster with geometries in a geodataframe.""" + geodataframe = gpd.read_file(geometries) + with rasterio.open(input_raster) as raster: + out_image, out_meta = clip_raster( + raster=raster, + geodataframe=geodataframe, + ) + + with rasterio.open(output_raster, "w", **out_meta) as dest: + dest.write(out_image) + + typer.echo("Clipping completed") + typer.echo(f"Writing raster to {output_raster}.") + + +# REPROJECT RASTER +@app.command() +def reproject_raster_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + crs: int = typer.Option(help="crs help"), + resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), +): + """Reproject the input raster to given CRS.""" + with rasterio.open(input_raster) as raster: + out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling_method) + + with rasterio.open(output_raster, "w", **out_meta) as dest: + dest.write(out_image) + + typer.echo("Reprojecting completed") + typer.echo(f"Writing raster to {output_raster}.") + + +# SNAP RASTER +@app.command() +def snap_with_raster_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + snap_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Snaps/aligns input raster to the given snap raster.""" + with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: + out_image, out_meta = snap_with_raster(src, snap_src) + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("Snapping completed") + typer.echo(f"Writing raster to {output_raster}") + + +# EXTRACT WINDOW +@app.command() +def extract_window_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + center_coords: Tuple[float, float] = typer.Option(), + height: int = typer.Option(), + width: int = typer.Option(), +): + """Extract window from raster.""" + with rasterio.open(input_raster) as raster: + out_image, out_meta = extract_window(raster, center_coords, height, width) + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("Windowing completed") + typer.echo(f"Writing raster to {output_raster}") + + +# RASTERIZE +@app.command() +def rasterize_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """NOT IMPLEMENTED. Rasterize a given vector.""" + raise Exception("Not implemented yet") + + +# REPROJECT VECTOR +@app.command() +def reproject_vector_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_vector: Annotated[Path, OUTPUT_FILE_OPTION], + crs: int = typer.Option(help="crs help"), +): + """Reproject the input vector to given CRS.""" + geodataframe = gpd.read_file(input_vector) + + reprojected_geodataframe = reproject_vector(geodataframe=geodataframe, target_EPSG=crs) + + reprojected_geodataframe.to_file(output_vector, driver="GeoJSON") + + typer.echo("Reprojecting completed") + typer.echo(f"Writing vector to {output_vector}") + + +if __name__ == "__main__": + app() From 48dfd7755d7cef80f3c0847d7352a1ce60480b92 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Wed, 2 Aug 2023 09:31:00 +0300 Subject: [PATCH 04/29] Add methods --- eis_toolkit/cli_typer.py | 144 ++++++++++++++++++++++++++++++++++++++- 1 file changed, 141 insertions(+), 3 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 45772a6f..c30dae69 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -1,6 +1,7 @@ from enum import Enum +from numbers import Number from pathlib import Path -from typing import Tuple +from typing import List, Literal, Tuple import geopandas as gpd import rasterio @@ -17,6 +18,31 @@ app = typer.Typer() +class VariogramModel(str, Enum): + """Variogram models for kriging interpolation.""" + + linear = "linear" + power = "power" + gaussian = "gaussian" + spherical = "spherical" + exponential = "exponential" + hole_effect = "hole-effect" + + +class KrigingMethod(str, Enum): + """Kriging methods.""" + + ordinary = "ordinary" + universal = "universal" + + +class MergeStrategy(str, Enum): + """Merge strategies for rasterizing.""" + + replace = "replace" + add = "add" + + class ResamplingMethods(str, Enum): """Resampling methods available.""" @@ -40,6 +66,19 @@ class ResamplingMethods(str, Enum): } +# def file_option(help: str = None, default: Any = None, read: bool = True, write: bool = False): +# return typer.Option( +# default=default, +# help=help, +# exists=True, +# file_okay=True, +# dir_okay=False, +# writable=write, +# readable=read, +# resolve_path=True, +# ) + + INPUT_FILE_OPTION = typer.Option( exists=True, file_okay=True, @@ -138,14 +177,53 @@ def extract_window_cli( typer.echo(f"Writing raster to {output_raster}") +# UNIFY RASTERS +@app.command() +def unify_rasters_cli( + base_raster: Annotated[Path, INPUT_FILE_OPTION], + rasters_to_unify: Annotated[List[float], INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), + same_extent: bool = False, +): + """Extract window from raster. NOT IMPLEMENTED YET.""" + pass + + # RASTERIZE @app.command() def rasterize_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + resolution: float = None, + value_column: str = None, + default_value: float = 1.0, + fill_value: float = 0.0, + base_raster_profile: Annotated[Path, INPUT_FILE_OPTION] = None, + buffer_value: float = None, + merge_strategy: MergeStrategy = MergeStrategy.replace, ): - """NOT IMPLEMENTED. Rasterize a given vector.""" - raise Exception("Not implemented yet") + """Rasterize input vector.""" + from eis_toolkit.vector_processing.rasterize_vector import rasterize_vector + + geodataframe = gpd.read_file(input_vector) + + out_image, out_meta = rasterize_vector( + geodataframe, + resolution, + value_column, + default_value, + fill_value, + base_raster_profile, + buffer_value, + merge_strategy, + ) + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("Rasterizing completed") + typer.echo(f"Writing raster to {output_raster}") # REPROJECT VECTOR @@ -166,5 +244,65 @@ def reproject_vector_cli( typer.echo(f"Writing vector to {output_vector}") +# KRIGING INTERPOLATION +@app.command() +def kriging_interpolation_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_vector: Annotated[Path, OUTPUT_FILE_OPTION], + target_column: str, + resolution: Tuple[Number, Number], + extent: Tuple[Number, Number, Number, Number], + variogram_model: Literal["linear", "power", "gaussian", "spherical", "exponential", "hole-effect"] = "linear", + method: Literal["ordinary", "universal"] = "ordinary", + drift_terms: list = ["regional_linear"], +): + """TODO. Reproject the input vector to given CRS.""" + # from eis_toolkit.vector_processing.kriging_interpolation import kriging + + pass + + # geodataframe = gpd.read_file(input_vector) + + # out_image, out_meta = kriging( + # geodataframe=geodataframe, + # target_column= + # ) + + # reprojected_geodataframe.to_file(output_vector, driver="GeoJSON") + + # typer.echo("Reprojecting completed") + # typer.echo(f"Writing vector to {output_vector}") + + +# DISTANCE COMPUTATION +@app.command() +def distance_computation_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + geometries: gpd.GeoDataFrame, + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Reproject the input vector to given CRS.""" + from eis_toolkit.spatial_analyses.distance_computation import distance_computation + + with rasterio.open(input_raster) as raster: + profile = raster.profile + + geodataframe = gpd.read_file(geometries) + + out_image = distance_computation(profile, geodataframe) + + with rasterio.open(output_raster, "w", **profile) as dst: + dst.write(out_image) + + typer.echo("Distance computation completed") + typer.echo(f"Writing raster to {output_raster}") + + +# DESCRIPTIVE STATISTICS +def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], column: str): + """Not implemented yet.""" + pass + + if __name__ == "__main__": app() From 8d8488ea516dac00b04a1078bb71fbbe5a5fb589 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Wed, 2 Aug 2023 12:34:07 +0300 Subject: [PATCH 05/29] Fix a few bugs, add typer to pyproject, poetry and conda env --- eis_toolkit/__main__.py | 3 +- eis_toolkit/cli_typer.py | 24 +- environment.yml | 1 + poetry.lock | 3706 ++++++++++++++++++++++---------------- pyproject.toml | 6 +- requirements.txt | 1 + 6 files changed, 2226 insertions(+), 1515 deletions(-) diff --git a/eis_toolkit/__main__.py b/eis_toolkit/__main__.py index f0363941..103befc2 100644 --- a/eis_toolkit/__main__.py +++ b/eis_toolkit/__main__.py @@ -1,4 +1,5 @@ -from eis_toolkit.cli_click import cli +# from eis_toolkit.cli_click import cli +from eis_toolkit.cli_typer import cli if __name__ == "__main__": cli() diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index c30dae69..505d129c 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -1,7 +1,6 @@ from enum import Enum -from numbers import Number from pathlib import Path -from typing import List, Literal, Tuple +from typing import List, Tuple import geopandas as gpd import rasterio @@ -181,7 +180,7 @@ def extract_window_cli( @app.command() def unify_rasters_cli( base_raster: Annotated[Path, INPUT_FILE_OPTION], - rasters_to_unify: Annotated[List[float], INPUT_FILE_OPTION], + rasters_to_unify: Annotated[List[Path], INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), same_extent: bool = False, @@ -250,11 +249,11 @@ def kriging_interpolation_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_vector: Annotated[Path, OUTPUT_FILE_OPTION], target_column: str, - resolution: Tuple[Number, Number], - extent: Tuple[Number, Number, Number, Number], - variogram_model: Literal["linear", "power", "gaussian", "spherical", "exponential", "hole-effect"] = "linear", - method: Literal["ordinary", "universal"] = "ordinary", - drift_terms: list = ["regional_linear"], + resolution: Tuple[float, float], + extent: Tuple[float, float, float, float], + variogram_model: VariogramModel = VariogramModel.linear, + method: KrigingMethod = KrigingMethod.ordinary, + drift_terms: Annotated[List[str], typer.Option()] = ["regional_linear"], ): """TODO. Reproject the input vector to given CRS.""" # from eis_toolkit.vector_processing.kriging_interpolation import kriging @@ -278,7 +277,7 @@ def kriging_interpolation_cli( @app.command() def distance_computation_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], - geometries: gpd.GeoDataFrame, + geometries: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], ): """Reproject the input vector to given CRS.""" @@ -304,5 +303,10 @@ def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], c pass -if __name__ == "__main__": +# if __name__ == "__main__": +def cli(): app() + + +if __name__ == "__main__": + app() \ No newline at end of file diff --git a/environment.yml b/environment.yml index 7049a9ae..520b3ff8 100755 --- a/environment.yml +++ b/environment.yml @@ -23,3 +23,4 @@ dependencies: # Dependencies for testing - pytest >=7.2.1 - rtree >=1.0.1 + - typer >=0.9.0 diff --git a/poetry.lock b/poetry.lock index b7b877d2..d4f8f7ef 100755 --- a/poetry.lock +++ b/poetry.lock @@ -2,48 +2,76 @@ [[package]] name = "absl-py" -version = "1.2.0" +version = "1.4.0" description = "Abseil Python Common Libraries, see https://github.com/abseil/abseil-py." optional = false python-versions = ">=3.6" files = [ - 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"e05daf49d78630aa2ee8ad1b7999d8cc34136721ca83d5078a6310fe32bbab80" diff --git a/pyproject.toml b/pyproject.toml index 65c01db8..49df6da5 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -8,7 +8,7 @@ license = "EUPL-1.2" readme = "README.md" homepage = "https://eis-he.eu" repository = "https://github.com/GispoCoding/eis_toolkit" -documentation = "" +# documentation = "" keywords = [ "Exploration", "Mineral prospectivity", @@ -17,6 +17,9 @@ keywords = [ "Packages" ] +[tool.poetry.scripts] +eis = "eis_toolkit.cli_typer:app" + [tool.poetry.dependencies] python = ">=3.8,<3.11" gdal = "3.4.3" @@ -34,6 +37,7 @@ beartype = "^0.13.1" seaborn = "^0.12.2" pykrige = "^1.7.0" rtree = "^1.0.1" +typer = {extras = ["all"], version = "^0.9.0"} [tool.poetry.dev-dependencies] jupyterlab = "^3.4.5" diff --git a/requirements.txt b/requirements.txt index 187cb73b..7e2095df 100644 --- a/requirements.txt +++ b/requirements.txt @@ -81,6 +81,7 @@ tensorflow-io-gcs-filesystem==0.26.0 ; python_version >= "3.8" and python_versio tensorflow==2.9.2 ; python_version >= "3.8" and python_version < "3.11" termcolor==1.1.0 ; python_version >= "3.8" and python_version < "3.11" threadpoolctl==3.1.0 ; python_version >= "3.8" and python_version < "3.11" +typer[all]==0.9.0 ; python_version >= "3.8" and python_version < "3.11" typing-extensions==4.3.0 ; python_version >= "3.8" and python_version < "3.11" urllib3==1.26.12 ; python_version >= "3.8" and python_version < "3.11" watchdog==2.1.9 ; python_version >= "3.8" and python_version < "3.11" From 01a1b447060237d55421d55432ef62e58c3b32a7 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Tue, 15 Aug 2023 11:11:34 +0300 Subject: [PATCH 06/29] Add functions, minor fixes --- eis_toolkit/cli_typer.py | 76 +++++++++++++++++++++++++++------------- 1 file changed, 51 insertions(+), 25 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 505d129c..0b207ebb 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -78,6 +78,7 @@ class ResamplingMethods(str, Enum): # ) +# TODO: Check this and output file option INPUT_FILE_OPTION = typer.Option( exists=True, file_okay=True, @@ -88,10 +89,9 @@ class ResamplingMethods(str, Enum): ) OUTPUT_FILE_OPTION = typer.Option( - exists=True, file_okay=True, dir_okay=False, - writable=False, + writable=True, readable=True, resolve_path=True, ) @@ -124,12 +124,13 @@ def clip_raster_cli( def reproject_raster_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - crs: int = typer.Option(help="crs help"), + target_crs: int = typer.Option(help="crs help"), resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), ): """Reproject the input raster to given CRS.""" + method = RESAMPLING_MAPPING[resampling_method] with rasterio.open(input_raster) as raster: - out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling_method) + out_image, out_meta = reproject_raster(raster=raster, target_crs=target_crs, resampling_method=method) with rasterio.open(output_raster, "w", **out_meta) as dest: dest.write(out_image) @@ -140,7 +141,7 @@ def reproject_raster_cli( # SNAP RASTER @app.command() -def snap_with_raster_cli( +def snap_raster_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], snap_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], @@ -198,7 +199,7 @@ def rasterize_cli( value_column: str = None, default_value: float = 1.0, fill_value: float = 0.0, - base_raster_profile: Annotated[Path, INPUT_FILE_OPTION] = None, + base_raster_profile_raster: Annotated[Path, INPUT_FILE_OPTION] = None, buffer_value: float = None, merge_strategy: MergeStrategy = MergeStrategy.replace, ): @@ -207,6 +208,10 @@ def rasterize_cli( geodataframe = gpd.read_file(input_vector) + if base_raster_profile_raster is not None: + with rasterio.open(base_raster_profile_raster) as raster: + base_raster_profile = raster.profile + out_image, out_meta = rasterize_vector( geodataframe, resolution, @@ -218,6 +223,13 @@ def rasterize_cli( merge_strategy, ) + out_meta.update( + { + "count": 1, + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else float, # TODO change this + } + ) + with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image) @@ -230,12 +242,12 @@ def rasterize_cli( def reproject_vector_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_vector: Annotated[Path, OUTPUT_FILE_OPTION], - crs: int = typer.Option(help="crs help"), + target_crs: int = typer.Option(help="crs help"), ): """Reproject the input vector to given CRS.""" geodataframe = gpd.read_file(input_vector) - reprojected_geodataframe = reproject_vector(geodataframe=geodataframe, target_EPSG=crs) + reprojected_geodataframe = reproject_vector(geodataframe=geodataframe, target_crs=target_crs) reprojected_geodataframe.to_file(output_vector, driver="GeoJSON") @@ -247,30 +259,43 @@ def reproject_vector_cli( @app.command() def kriging_interpolation_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], - output_vector: Annotated[Path, OUTPUT_FILE_OPTION], - target_column: str, - resolution: Tuple[float, float], - extent: Tuple[float, float, float, float], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + target_column: str = typer.Option(), + pixel_size_x: float = typer.Option(), + pixel_size_y: float = typer.Option(), + extent: Tuple[float, float, float, float] = None, variogram_model: VariogramModel = VariogramModel.linear, method: KrigingMethod = KrigingMethod.ordinary, drift_terms: Annotated[List[str], typer.Option()] = ["regional_linear"], ): - """TODO. Reproject the input vector to given CRS.""" - # from eis_toolkit.vector_processing.kriging_interpolation import kriging + """Apply kriging interpolation to input vector file.""" + from eis_toolkit.vector_processing.kriging_interpolation import kriging - pass + geodataframe = gpd.read_file(input_vector) - # geodataframe = gpd.read_file(input_vector) + out_image, out_meta = kriging( + data=geodataframe, + target_column=target_column, + resolution=(pixel_size_x, pixel_size_y), + extent=extent, + variogram_model=variogram_model, + method=method, + drift_terms=drift_terms, + ) - # out_image, out_meta = kriging( - # geodataframe=geodataframe, - # target_column= - # ) + out_meta.update( + { + "count": 1, + "driver": "GTiff", + "dtype": "float32", + } + ) - # reprojected_geodataframe.to_file(output_vector, driver="GeoJSON") + with rasterio.open(out_image, "w", **out_meta) as dst: + dst.write(out_image) - # typer.echo("Reprojecting completed") - # typer.echo(f"Writing vector to {output_vector}") + typer.echo("Kriging interpolation completed") + typer.echo(f"Writing raster to {output_raster}") # DISTANCE COMPUTATION @@ -291,7 +316,7 @@ def distance_computation_cli( out_image = distance_computation(profile, geodataframe) with rasterio.open(output_raster, "w", **profile) as dst: - dst.write(out_image) + dst.write(out_image, profile["count"]) typer.echo("Distance computation completed") typer.echo(f"Writing raster to {output_raster}") @@ -305,8 +330,9 @@ def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], c # if __name__ == "__main__": def cli(): + """CLI app.""" app() if __name__ == "__main__": - app() \ No newline at end of file + app() From 7db988edf95e21699f895155af987a1c804a3a3b Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Wed, 16 Aug 2023 09:36:36 +0300 Subject: [PATCH 07/29] Test progress echoes --- eis_toolkit/cli_typer.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 0b207ebb..a0f00437 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -105,18 +105,25 @@ def clip_raster_cli( output_raster: Annotated[Path, OUTPUT_FILE_OPTION], ): """Clip the input raster with geometries in a geodataframe.""" + + typer.echo("Progress: 10%") + geodataframe = gpd.read_file(geometries) + typer.echo("Progress: 40%") + with rasterio.open(input_raster) as raster: out_image, out_meta = clip_raster( raster=raster, geodataframe=geodataframe, ) + typer.echo("Progress: 70%") + with rasterio.open(output_raster, "w", **out_meta) as dest: dest.write(out_image) - typer.echo("Clipping completed") - typer.echo(f"Writing raster to {output_raster}.") + typer.echo("Progress: 100%") + typer.echo(f"Clipping completed, output raster written to {output_raster}.") # REPROJECT RASTER From 4b20377f1f197355b93e75fb612a2169681881f3 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 14 Sep 2023 12:49:40 +0300 Subject: [PATCH 08/29] Deleted files related to old implementation --- eis_toolkit/__main__.py | 5 - eis_toolkit/cli.py | 0 eis_toolkit/cli_click.py | 210 ----------------------------------- eis_toolkit/cli_config.py | 64 ----------- eis_toolkit/config_test.json | 22 ---- tests/cli_test.py | 83 -------------- 6 files changed, 384 deletions(-) delete mode 100644 eis_toolkit/__main__.py delete mode 100644 eis_toolkit/cli.py delete mode 100644 eis_toolkit/cli_click.py delete mode 100644 eis_toolkit/cli_config.py delete mode 100644 eis_toolkit/config_test.json delete mode 100644 tests/cli_test.py diff --git a/eis_toolkit/__main__.py b/eis_toolkit/__main__.py deleted file mode 100644 index 103befc2..00000000 --- a/eis_toolkit/__main__.py +++ /dev/null @@ -1,5 +0,0 @@ -# from eis_toolkit.cli_click import cli -from eis_toolkit.cli_typer import cli - -if __name__ == "__main__": - cli() diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py deleted file mode 100644 index e69de29b..00000000 diff --git a/eis_toolkit/cli_click.py b/eis_toolkit/cli_click.py deleted file mode 100644 index d58a0209..00000000 --- a/eis_toolkit/cli_click.py +++ /dev/null @@ -1,210 +0,0 @@ -"""Command-line interface for eis_toolkit.""" -from pathlib import Path -from typing import Tuple - -import click -import geopandas as gpd -import rasterio -from rasterio import warp - -from eis_toolkit.raster_processing.clipping import clip_raster -from eis_toolkit.raster_processing.gridding_check import gridding_check -from eis_toolkit.raster_processing.reprojecting import reproject_raster -from eis_toolkit.raster_processing.snapping import snap_with_raster -from eis_toolkit.raster_processing.windowing import extract_window - -# from eis_toolkit.raster_processing.unifying import unify_rasters - -EXISTING_CLICK_FILE = click.Path(exists=True, file_okay=True, dir_okay=False, readable=True) - - -resampling_mapping = { - "nearest": warp.Resampling.nearest, - "bilinear": warp.Resampling.bilinear, - "cubic": warp.Resampling.cubic, - "average": warp.Resampling.average, - "gauss": warp.Resampling.gauss, - "max": warp.Resampling.max, - "min": warp.Resampling.min, -} -# NOTE: Use the mapping below if all variants are wanted -# resampling_mapping = {method.name.lower(): method for method in warp.Resampling} - - -@click.group() -def cli(): - """Click group to nest subcommands under one interface.""" - pass - - -# CLIP RASTER -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.argument("geometries", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--output-raster-file", type=click.Path(), required=True, help="Output raster file path") -def clip_raster_cli(input_raster: str, geometries: str, output_raster_file: str): - """Clip the input raster with geometries in a geodataframe.""" - raster_path, geometries_path, output_raster_path = ( - Path(input_raster), - Path(geometries), - Path(output_raster_file), - ) - - geodataframe = gpd.read_file(geometries_path) - with rasterio.open(raster_path) as raster: - out_image, out_meta = clip_raster( - raster=raster, - geodataframe=geodataframe, - ) - - click.echo("Clipping completed") - click.echo(f"Writing raster to {output_raster_path}.") - with rasterio.open(output_raster_path, "w", **out_meta) as dest: - dest.write(out_image) - - -# REPROJECT RASTER -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--crs", type=int, required=True, help="Target CRS as an EPSG code") -@click.option( - "--output-raster-file", type=click.Path(), required=True, help="Path to the output reprojected raster file." -) -@click.option( - "--resampling-method", - type=click.Choice([m.name for m in warp.Resampling], case_sensitive=False), - default=warp.Resampling.nearest.name, - help="Resampling method to use. Defaults to 'nearest'.", -) -def reproject_raster_cli(input_raster: str, crs: str, output_raster_file: str, resampling_method: str): - """Reproject the input raster to given coordinate refrence system.""" - raster_path, output_raster_path = (Path(input_raster), Path(output_raster_file)) - - resampling = resampling_mapping[resampling_method.lower()] - with rasterio.open(raster_path) as raster: - out_image, out_meta = reproject_raster(src=raster, target_EPSG=crs, resampling_method=resampling) - - click.echo("Reprojecting completed") - click.echo(f"Writing raster to {output_raster_path}.") - with rasterio.open(output_raster_path, "w", **out_meta) as dest: - dest.write(out_image) - - -# SNAP WITH RASTER -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.argument("snap_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--output-raster-file", type=click.Path(), required=True) -def snap_with_raster_cli(input_raster: str, snap_raster: str, output_raster_file: str): - """Snaps/aligns input raster to the given snap raster.""" - with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: - out_image, out_meta = snap_with_raster(src, snap_src) - click.echo("Snapping completed") - click.echo(f"Writing raster to {output_raster_file}") - with rasterio.open(output_raster_file, "w", **out_meta) as dst: - dst.write(out_image) - - -# EXTRACT WINDOW -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--center-coords", type=(float, float), required=True) -@click.option("--height", type=int, required=True) -@click.option("--width", type=int, required=True) -@click.option("--output-raster-file", type=click.Path(), required=True) -def extract_window_cli( - input_raster: str, center_coords: Tuple[float, float], height: int, width: int, output_raster_file: str -): - """Extract a window from a raster.""" - with rasterio.open(input_raster) as raster: - out_image, out_meta = extract_window(raster, center_coords, height, width) - click.echo("Windowing completed") - click.echo(f"Writing raster to {output_raster_file}") - with rasterio.open(output_raster_file, "w", **out_meta) as dst: - dst.write(out_image) - - -# CHECK RASTER GRIDS -@cli.command() -@click.argument("input_rasters", nargs=-1, type=EXISTING_CLICK_FILE) -@click.option("--same-extent", type=bool, default=False) -def check_raster_grids_cli(input_rasters, same_extent: bool): - """Check the set of input rasters for matching gridding and optionally matching bounds.""" - open_rasters = [] - for raster in input_rasters: - open_rasters.append(rasterio.open(raster)) - check = gridding_check(open_rasters, same_extent) - for raster in open_rasters: - raster.close() - click.echo(f"{check}") - # click.echo(f"Gridding check returned {check}") - return check - - -# PLACEHOLDER INTERFACES - -# PCA -@cli.command() -@click.argument("input-raster", nargs=-1, type=EXISTING_CLICK_FILE) -@click.option("--components", type=int, required=True) -@click.option("--output-raster-file", type=click.Path(), required=True) -def pca_cli(input_raster, components: int, output_raster_file: str): - """NOT IMPLEMENTED. Compute PCA with specified nr. of components.""" - raise Exception("Not implemented yet") - - -# FUZZY OVERLAY -@cli.command() -@click.argument("input_rasters", nargs=-1, type=EXISTING_CLICK_FILE) -@click.option("--fuzzy_method", type=str, required=True) -@click.option("--output-raster-file", type=click.Path(), required=True) -def fuzzy_overlay_cli(input_rasters, fuzzy_method: str, output_raster_file: str): - """NOT IMPLEMENTED. Calculate fuzzy overlay.""" - raise Exception("Not implemented yet") - - -# GERETATE DATA -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--output-raster-file", type=click.Path(), required=True) -def generate_data_cli(input_raster: str, output_raster_file: str): - """NOT IMPLEMENTED. Generate data for machine learning models.""" - raise Exception("Not implemented yet") - - -# RASTERIZE -@cli.command() -@click.argument("input_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--output-raster-file", type=click.Path(), required=True) -def rasterize_cli(input_raster: str, output_raster_file: str): - """NOT IMPLEMENTED. Rasterize a given vector.""" - raise Exception("Not implemented yet") - - -# WEIGHTS OF EVIDENCE -@cli.command() -@click.argument("evidential_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.argument("deposit_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--weights-type", type=str) -@click.option("--contrast", type=int) -@click.option("--output-raster-file", type=click.Path(), required=True) -def weights_of_evidence_cli( - evidential_raster: str, deposit_raster: str, weights_type: str, contrast: int, output_raster_file: str -): - """NOT IMPLEMENTED. Calculate weights of evidence.""" - raise Exception("Not implemented yet") - - -# UNIFY RASTERS -@cli.command() -@click.argument("base_raster", nargs=1, type=EXISTING_CLICK_FILE) -@click.argument("rasters", nargs=1, type=EXISTING_CLICK_FILE) -@click.option("--same-extent", type=bool, default=False) -@click.option("--output-raster-file", type=click.Path(), required=True) -def unify_rasters_cli(base_raster: str, rasters, same_extent: bool, output_raster_file: str): - """NOT IMPLEMENTED. Unify given set of rasters.""" - raise Exception("Not implemented yet") - - -if __name__ == "__main__": - cli() diff --git a/eis_toolkit/cli_config.py b/eis_toolkit/cli_config.py deleted file mode 100644 index 4cc45e67..00000000 --- a/eis_toolkit/cli_config.py +++ /dev/null @@ -1,64 +0,0 @@ -import json -from pathlib import Path - -import geopandas as gpd -import rasterio - - -def convert_arguments(arg_data): - function_arguments = {} - for arg, arg_items in arg_data: - arg_type = arg_items["type"] - arg_value = arg_items["value"] - converted_arg = convert_argument(arg_value, arg_type) - function_arguments[arg] = converted_arg - - -def convert_argument(arg_value, arg_type): - if arg_type == "raster": - converted_arg = rasterio.open(arg_value) - elif arg_type == "geodataframe": - converted_arg = gpd.read_file(arg_value) - else: - raise Exception(f"Unknown argument type (arg type, arg value): {arg_type, arg_value}") - - return converted_arg - - -def write_outputs(output_definitions, output_data): - for arg, arg_items in output_definitions: - arg_type = arg_items["type"] - arg_value = arg_items["value"] - write_output(arg_value, arg_type, output_data) - - -def write_output(arg_value, arg_type, data): - if arg_type == "raster": - out_image = data[0] - out_meta = data[1] - with rasterio.open(arg_value, "w", **out_meta) as dest: - dest.write(out_image) - elif arg_type == "vector": - pass - - -def read_config(config_path): - config_path = Path(config_path) - loaded_config = json.loads(config_path.read_text()) - - -def execute_workflow(config): - for function_name, func_items in config["workflow"].items(): - function = locals()[function_name] - function_arguments = convert_arguments(func_items["inputs"].items()) - output_data = function(**function_arguments) - write_outputs(func_items["outputs"].items(), output_data) - - -def interface(): - config_path = "/home/niko/code/plugin_dev/eis_toolkit/eis_toolkit/config_test.json" - loaded_config = read_config(config_path) - execute_workflow(loaded_config) - - -interface() diff --git a/eis_toolkit/config_test.json b/eis_toolkit/config_test.json deleted file mode 100644 index b77936fb..00000000 --- a/eis_toolkit/config_test.json +++ /dev/null @@ -1,22 +0,0 @@ -{ - "workflow": { - "clip_raster": { - "inputs": { - "raster": { - "type": "raster", - "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/remote/small_raster.tif" - }, - "geodataframe": { - "type": "geodataframe", - "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/remote/small_area.shp" - } - }, - "outputs": { - "output_raster:": { - "type": "raster", - "value": "/home/niko/code/plugin_dev/eis_toolkit/tests/data/local/cli_clip_test_output.tif" - } - } - } - } -} diff --git a/tests/cli_test.py b/tests/cli_test.py deleted file mode 100644 index 6e5f5e06..00000000 --- a/tests/cli_test.py +++ /dev/null @@ -1,83 +0,0 @@ -"""Tests for eis_toolkit.cli.""" -import json -from contextlib import nullcontext -from pathlib import Path -from traceback import print_tb -from typing import ContextManager - -import pytest -import rasterio -from click.testing import CliRunner, Result - -from eis_toolkit.cli_click import cli - -CLICK_RUNNER = CliRunner() - -RASTER_FILE_PATH = Path("tests/data/remote/small_raster.tif") -GEODATAFRAME_FILE_PATH = Path("tests/data/remote/small_area.shp") - - -def click_error_print(result: Result): - """Print click result traceback.""" - # If exit_code is zero then the cli execution succeeded - # If it is not zero then the execution failed - if result.exit_code == 0: - return - - # Print the Python traceback related to failed execution - assert result.exc_info is not None - _, _, tb = result.exc_info - print_tb(tb) - - # Print the stdout of the execution - print(result.output) - assert result.exception is not None - - # Raise the collected Python exception that was raised - raise result.exception - - -@pytest.mark.parametrize( - "raster_file_path,geodataframe_file_path,raises", - [ - # Using the contextmanagers nullcontext and pytest.raises, the tests - # can be conditionalized to both error and succeed based on the - # parameter (nullcontext == succeed) - (RASTER_FILE_PATH, GEODATAFRAME_FILE_PATH, nullcontext()), - (Path("invalid/path/to/nowhere.tif"), Path("invalid/path/to/nowhere.shp"), pytest.raises(SystemExit)), - ], -) -def test_cli_clip_raster(raster_file_path: Path, geodataframe_file_path: Path, raises: ContextManager, tmp_path: Path): - """Test cli_clip_raster click entrypoint.""" - # tmp_path is a pytest fixture that is always a temporary directory path on - # the file system if is put in the function signature - output_raster_path = tmp_path / "clipped_raster.tif" - - # Define the arguments for the command-line execution - args = [ - # The first arg defines which subcommand to use - "cli-clip-raster", - str(raster_file_path), - str(geodataframe_file_path), - f"--output-raster-file={output_raster_path}", - ] - # Run the eis_toolkit.cli:cli click entrypoint function - result = CLICK_RUNNER.invoke(cli=cli, args=args) - - # If error is expected, raises will equal to pytest.raises() - # where the can e.g. be FileNotFoundError. For click executions - # is is always/usually SystemExit - with raises: - # This function will error and print tracebacks and exceptions if the - # execution fails - click_error_print(result=result) - - # Check that the expected result occurred - assert output_raster_path.exists() - assert output_raster_path.is_file() - - with rasterio.open(output_raster_path, mode="r") as out_raster, rasterio.open( - raster_file_path, mode="r" - ) as src_raster: - # Check that coordinate reference system is maintained - assert out_raster.meta["crs"] == src_raster.meta["crs"] From 213fd40a521f065a6f30868166b6283fd93a5c0c Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 14 Sep 2023 12:55:06 +0300 Subject: [PATCH 09/29] Added CLI implementations for multiple tools, updated some implementations --- eis_toolkit/cli_typer.py | 349 ++++++++++++++++++++++++++++++++++----- 1 file changed, 309 insertions(+), 40 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index a0f00437..116f1a62 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -1,19 +1,15 @@ +import json from enum import Enum from pathlib import Path from typing import List, Tuple import geopandas as gpd +import pandas as pd import rasterio import typer from rasterio import warp from typing_extensions import Annotated -from eis_toolkit.raster_processing.clipping import clip_raster -from eis_toolkit.raster_processing.reprojecting import reproject_raster -from eis_toolkit.raster_processing.snapping import snap_with_raster -from eis_toolkit.raster_processing.windowing import extract_window -from eis_toolkit.vector_processing.reproject_vector import reproject_vector - app = typer.Typer() @@ -28,6 +24,13 @@ class VariogramModel(str, Enum): hole_effect = "hole-effect" +class CoordinatesType(str, Enum): + """Coordinates type for kriging interpolation.""" + + euclidean = "euclidean" + geographic = "geographic" + + class KrigingMethod(str, Enum): """Kriging methods.""" @@ -42,6 +45,13 @@ class MergeStrategy(str, Enum): add = "add" +class VectorDensityStatistic(str, Enum): + """Vector density statistic.""" + + density = "density" + count = "count" + + class ResamplingMethods(str, Enum): """Resampling methods available.""" @@ -97,6 +107,13 @@ class ResamplingMethods(str, Enum): ) +# --- RASTER PROCESSING --- + + +# CHECK RASTER GRIDS +# TODO + + # CLIP RASTER @app.command() def clip_raster_cli( @@ -105,6 +122,7 @@ def clip_raster_cli( output_raster: Annotated[Path, OUTPUT_FILE_OPTION], ): """Clip the input raster with geometries in a geodataframe.""" + from eis_toolkit.raster_processing.clipping import clip_raster typer.echo("Progress: 10%") @@ -126,6 +144,90 @@ def clip_raster_cli( typer.echo(f"Clipping completed, output raster written to {output_raster}.") +# CREATE CONSTANT RASTER +@app.command() +def create_constant_raster_cli( + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + constant_value: float = typer.Option(), + template_raster: Annotated[Path, INPUT_FILE_OPTION] = None, + coord_west: float = None, + coord_north: float = None, + coord_east: float = None, + coord_south: float = None, + target_epsg: int = None, + target_pixel_size: int = None, + raster_width: int = None, + raster_height: int = None, + nodata_value: float = None, +): + """ + Create a constant raster with the given value. + + There are 3 methods for raster creation: + - Set extent and coordinate system based on a template raster. + - Set extent from origin, based on the western and northern coordinates and the pixel size. + - Set extent from bounds, based on western, northern, eastern and southern points. + """ + from eis_toolkit.raster_processing.create_constant_raster import create_constant_raster + + if template_raster is not None: + with rasterio.open(template_raster) as raster: + out_image, out_meta = create_constant_raster( + constant_value, + raster, + coord_west, + coord_north, + coord_east, + coord_south, + target_epsg, + target_pixel_size, + raster_width, + raster_height, + nodata_value, + ) + else: + out_image, out_meta = create_constant_raster( + constant_value, + template_raster, + coord_west, + coord_north, + coord_east, + coord_south, + target_epsg, + target_pixel_size, + raster_width, + raster_height, + nodata_value, + ) + + with rasterio.open(output_raster, "w", **out_meta) as dest: + dest.write(out_image) + + typer.echo("Creating constant raster completed") + typer.echo(f"Writing raster to {output_raster}.") + + +# EXTRACT VALUES FROM RASTER +@app.command() +def extract_values_from_raster_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + geometries: Annotated[Path, INPUT_FILE_OPTION], + output_vector: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Extract raster values using point data to a DataFrame.""" + from eis_toolkit.raster_processing.extract_values_from_raster import extract_values_from_raster + + geodataframe = gpd.read_file(geometries) + + with rasterio.open(input_raster) as raster: + df = extract_values_from_raster(raster=[raster], geodataframe=geodataframe) + + df.to_csv(output_vector) + + typer.echo("Extracting values from raster completed") + typer.echo(f"Writing vector to {output_vector}.") + + # REPROJECT RASTER @app.command() def reproject_raster_cli( @@ -135,6 +237,8 @@ def reproject_raster_cli( resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), ): """Reproject the input raster to given CRS.""" + from eis_toolkit.raster_processing.reprojecting import reproject_raster + method = RESAMPLING_MAPPING[resampling_method] with rasterio.open(input_raster) as raster: out_image, out_meta = reproject_raster(raster=raster, target_crs=target_crs, resampling_method=method) @@ -154,6 +258,8 @@ def snap_raster_cli( output_raster: Annotated[Path, OUTPUT_FILE_OPTION], ): """Snaps/aligns input raster to the given snap raster.""" + from eis_toolkit.raster_processing.snapping import snap_with_raster + with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: out_image, out_meta = snap_with_raster(src, snap_src) @@ -164,6 +270,20 @@ def snap_raster_cli( typer.echo(f"Writing raster to {output_raster}") +# UNIFY RASTERS +@app.command() +def unify_rasters_cli( + base_raster: Annotated[Path, INPUT_FILE_OPTION], + rasters_to_unify: Annotated[List[Path], INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), + same_extent: bool = False, +): + """Extract window from raster. NOT IMPLEMENTED YET.""" + # TODO + pass + + # EXTRACT WINDOW @app.command() def extract_window_cli( @@ -174,6 +294,8 @@ def extract_window_cli( width: int = typer.Option(), ): """Extract window from raster.""" + from eis_toolkit.raster_processing.windowing import extract_window + with rasterio.open(input_raster) as raster: out_image, out_meta = extract_window(raster, center_coords, height, width) @@ -184,17 +306,89 @@ def extract_window_cli( typer.echo(f"Writing raster to {output_raster}") -# UNIFY RASTERS +# --- VECTOR PROCESSING --- + + +# IDW INTERPOLATION @app.command() -def unify_rasters_cli( - base_raster: Annotated[Path, INPUT_FILE_OPTION], - rasters_to_unify: Annotated[List[Path], INPUT_FILE_OPTION], +def idw_interpolation_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), - same_extent: bool = False, + target_column: str = typer.Option(), + pixel_size_x: float = typer.Option(), + pixel_size_y: float = typer.Option(), + power: float = 2.0, + extent: Tuple[float, float, float, float] = None, ): - """Extract window from raster. NOT IMPLEMENTED YET.""" - pass + """Apply kriging interpolation to input vector file.""" + from eis_toolkit.vector_processing.idw_interpolation import idw + + geodataframe = gpd.read_file(input_vector) + + out_image, out_meta = idw( + geodataframe=geodataframe, + target_column=target_column, + resolution=(pixel_size_x, pixel_size_y), + extent=extent, + power=power, + ) + + out_meta.update( + { + "count": 1, + "driver": "GTiff", + "dtype": "float32", + } + ) + + with rasterio.open(out_image, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("IDW interpolation completed") + typer.echo(f"Writing raster to {output_raster}") + + +# KRIGING INTERPOLATION +@app.command() +def kriging_interpolation_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + target_column: str = typer.Option(), + pixel_size_x: float = typer.Option(), + pixel_size_y: float = typer.Option(), + extent: Tuple[float, float, float, float] = None, + variogram_model: VariogramModel = VariogramModel.linear, + coordinates_type: CoordinatesType = CoordinatesType.geographic, + method: KrigingMethod = KrigingMethod.ordinary, +): + """Apply kriging interpolation to input vector file.""" + from eis_toolkit.vector_processing.kriging_interpolation import kriging + + geodataframe = gpd.read_file(input_vector) + + out_image, out_meta = kriging( + data=geodataframe, + target_column=target_column, + resolution=(pixel_size_x, pixel_size_y), + extent=extent, + variogram_model=variogram_model, + coordinates_type=coordinates_type, + method=method, + ) + + out_meta.update( + { + "count": 1, + "driver": "GTiff", + "dtype": "float32", + } + ) + + with rasterio.open(out_image, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("Kriging interpolation completed") + typer.echo(f"Writing raster to {output_raster}") # RASTERIZE @@ -252,6 +446,8 @@ def reproject_vector_cli( target_crs: int = typer.Option(help="crs help"), ): """Reproject the input vector to given CRS.""" + from eis_toolkit.vector_processing.reproject_vector import reproject_vector + geodataframe = gpd.read_file(input_vector) reprojected_geodataframe = reproject_vector(geodataframe=geodataframe, target_crs=target_crs) @@ -262,49 +458,50 @@ def reproject_vector_cli( typer.echo(f"Writing vector to {output_vector}") -# KRIGING INTERPOLATION +# VECTOR DENSITY @app.command() -def kriging_interpolation_cli( +def vector_density_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - target_column: str = typer.Option(), - pixel_size_x: float = typer.Option(), - pixel_size_y: float = typer.Option(), - extent: Tuple[float, float, float, float] = None, - variogram_model: VariogramModel = VariogramModel.linear, - method: KrigingMethod = KrigingMethod.ordinary, - drift_terms: Annotated[List[str], typer.Option()] = ["regional_linear"], + resolution: float = None, + base_raster_profile_raster: Annotated[Path, INPUT_FILE_OPTION] = None, + buffer_value: float = None, + statistic: VectorDensityStatistic = VectorDensityStatistic.density, ): - """Apply kriging interpolation to input vector file.""" - from eis_toolkit.vector_processing.kriging_interpolation import kriging + """Reproject the input vector to given CRS.""" + from eis_toolkit.vector_processing.vector_density import vector_density geodataframe = gpd.read_file(input_vector) - out_image, out_meta = kriging( - data=geodataframe, - target_column=target_column, - resolution=(pixel_size_x, pixel_size_y), - extent=extent, - variogram_model=variogram_model, - method=method, - drift_terms=drift_terms, + if base_raster_profile_raster is not None: + with rasterio.open(base_raster_profile_raster) as raster: + base_raster_profile = raster.profile + + out_image, out_meta = vector_density( + geodataframe=geodataframe, + resolution=resolution, + base_raster_profile=base_raster_profile, + buffer_value=buffer_value, + statistic=statistic, ) out_meta.update( { "count": 1, - "driver": "GTiff", - "dtype": "float32", + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else float, # TODO change this } ) - with rasterio.open(out_image, "w", **out_meta) as dst: + with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image) - typer.echo("Kriging interpolation completed") + typer.echo("Vector density computation completed") typer.echo(f"Writing raster to {output_raster}") +# --- SPATIAL ANALYSES --- + + # DISTANCE COMPUTATION @app.command() def distance_computation_cli( @@ -329,10 +526,82 @@ def distance_computation_cli( typer.echo(f"Writing raster to {output_raster}") +# CBA +# TODO + + +# --- STATISTICAL ANALYSES --- + + # DESCRIPTIVE STATISTICS -def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], column: str): - """Not implemented yet.""" - pass +@app.command() +def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], column: str = None): + """Generate descriptive statistics from raster, vector or tabular data.""" + from eis_toolkit.statistical_analyses.descriptive_statistics import ( + descriptive_statistics_dataframe, + descriptive_statistics_raster, + ) + + # TODO modify input file detection + try: + raster = rasterio.open(input_file) + results_dict = descriptive_statistics_raster(raster) + except: # noqa: E722 # TODO Which exception? Applies to the 2 below as well + try: + gdf = gpd.read_file(input_file) + results_dict = descriptive_statistics_dataframe(gdf, column) + except: # noqa: E722 + try: + df = pd.read_csv(input_file) + results_dict = descriptive_statistics_dataframe(df, column) + except: # noqa: E722 + raise Exception("Could not read input file as raster or dataframe") + + json_str = json.dumps(results_dict) + typer.echo(f"Results: {json_str}") + typer.echo("Descriptive statistics completed") + + +# --- PREDICTION --- + + +# FUZZY OVERLAY +# TODO + + +# WOFE +# TODO + + +# --- TRANSFORMATIONS --- + + +# BINARIZE +# TODO + + +# CLIPPING (PROBLEMATIC NAME, CHANGE!) +# TODO + + +# LINEAR +# TODO + + +# LOGARITHMIC +# TODO + + +# SIGMOID +# TODO + + +# WINSORIZE +# TODO + + +# ---VALIDATION --- +# TODO # if __name__ == "__main__": From c3a3e21c2fcbefe5254824a17946830e9f6d77ed Mon Sep 17 00:00:00 2001 From: msorvoja Date: Thu, 14 Sep 2023 15:14:22 +0300 Subject: [PATCH 10/29] Fix docstrings --- eis_toolkit/cli_typer.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 116f1a62..09f89677 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -21,7 +21,6 @@ class VariogramModel(str, Enum): gaussian = "gaussian" spherical = "spherical" exponential = "exponential" - hole_effect = "hole-effect" class CoordinatesType(str, Enum): @@ -279,7 +278,7 @@ def unify_rasters_cli( resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), same_extent: bool = False, ): - """Extract window from raster. NOT IMPLEMENTED YET.""" + """Unify given rasters relative to base raster. NOT IMPLEMENTED YET.""" # TODO pass @@ -320,7 +319,7 @@ def idw_interpolation_cli( power: float = 2.0, extent: Tuple[float, float, float, float] = None, ): - """Apply kriging interpolation to input vector file.""" + """Apply inverse distance weighting (IDW) interpolation to input vector file.""" from eis_toolkit.vector_processing.idw_interpolation import idw geodataframe = gpd.read_file(input_vector) @@ -468,7 +467,7 @@ def vector_density_cli( buffer_value: float = None, statistic: VectorDensityStatistic = VectorDensityStatistic.density, ): - """Reproject the input vector to given CRS.""" + """Compute density of geometries within raster.""" from eis_toolkit.vector_processing.vector_density import vector_density geodataframe = gpd.read_file(input_vector) @@ -509,7 +508,7 @@ def distance_computation_cli( geometries: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], ): - """Reproject the input vector to given CRS.""" + """Calculate distance from raster cell to nearest geometry.""" from eis_toolkit.spatial_analyses.distance_computation import distance_computation with rasterio.open(input_raster) as raster: From c0161288ae11ef2583f7b87351d12153166dc04f Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 14 Sep 2023 15:42:55 +0300 Subject: [PATCH 11/29] Separated raster and vector descriptive stats to different interaces in CLI --- eis_toolkit/cli_typer.py | 43 ++++++++++-------- tests/data/remote/point.gpkg | Bin 98304 -> 98304 bytes tests/data/remote/smaller_raster.tif.aux.xml | 11 +++++ .../remote/snapping/snap_raster.tif.aux.xml | 11 +++++ 4 files changed, 47 insertions(+), 18 deletions(-) create mode 100644 tests/data/remote/smaller_raster.tif.aux.xml create mode 100644 tests/data/remote/snapping/snap_raster.tif.aux.xml diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 116f1a62..fab4c11a 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -533,33 +533,40 @@ def distance_computation_cli( # --- STATISTICAL ANALYSES --- -# DESCRIPTIVE STATISTICS +# DESCRIPTIVE STATISTICS (RASTER) @app.command() -def descriptive_statistics_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], column: str = None): - """Generate descriptive statistics from raster, vector or tabular data.""" - from eis_toolkit.statistical_analyses.descriptive_statistics import ( - descriptive_statistics_dataframe, - descriptive_statistics_raster, - ) +def descriptive_statistics_raster_cli(input_file: Annotated[Path, INPUT_FILE_OPTION]): + """Generate descriptive statistics from raster data.""" + from eis_toolkit.statistical_analyses.descriptive_statistics import descriptive_statistics_raster + + with rasterio.open(input_file) as raster: + results_dict = descriptive_statistics_raster(raster) + + json_str = json.dumps(results_dict) + typer.echo(f"Results: {json_str}") + typer.echo("Descriptive statistics (raster) completed") + + +# DESCRIPTIVE STATISTICS (VECTOR) +@app.command() +def descriptive_statistics_vector_cli(input_file: Annotated[Path, INPUT_FILE_OPTION], column: str = None): + """Generate descriptive statistics from vector or tabular data.""" + from eis_toolkit.statistical_analyses.descriptive_statistics import descriptive_statistics_dataframe # TODO modify input file detection try: - raster = rasterio.open(input_file) - results_dict = descriptive_statistics_raster(raster) - except: # noqa: E722 # TODO Which exception? Applies to the 2 below as well + gdf = gpd.read_file(input_file) + results_dict = descriptive_statistics_dataframe(gdf, column) + except: # noqa: E722 try: - gdf = gpd.read_file(input_file) - results_dict = descriptive_statistics_dataframe(gdf, column) + df = pd.read_csv(input_file) + results_dict = descriptive_statistics_dataframe(df, column) except: # noqa: E722 - try: - df = pd.read_csv(input_file) - results_dict = descriptive_statistics_dataframe(df, column) - except: # noqa: E722 - raise Exception("Could not read input file as raster or dataframe") + raise Exception("Could not read input file as raster or dataframe") json_str = json.dumps(results_dict) typer.echo(f"Results: {json_str}") - typer.echo("Descriptive statistics completed") + typer.echo("Descriptive statistics (vector) completed") # --- PREDICTION --- diff --git a/tests/data/remote/point.gpkg b/tests/data/remote/point.gpkg index 2eaa958a2785e01a2ec8c155ff42cb47dbe9b190..5226357388fb27de4225251daad142c16eeacc90 100755 GIT binary patch delta 26 hcmZo@U~6b#n;^|7GEv5vRfIt=+^aEVYYO9>dH`cP2fqLS delta 26 hcmZo@U~6b#n;^|7G*QNxRfs{){$^v!))dA$^#Ep}2r>Ww diff --git a/tests/data/remote/smaller_raster.tif.aux.xml b/tests/data/remote/smaller_raster.tif.aux.xml new file mode 100644 index 00000000..5c061d65 --- /dev/null +++ b/tests/data/remote/smaller_raster.tif.aux.xml @@ -0,0 +1,11 @@ + + + + 9.131 + 4.9635555555556 + 2.507 + 1.3273457218511 + 100 + + + diff --git a/tests/data/remote/snapping/snap_raster.tif.aux.xml b/tests/data/remote/snapping/snap_raster.tif.aux.xml new file mode 100644 index 00000000..697ae396 --- /dev/null +++ b/tests/data/remote/snapping/snap_raster.tif.aux.xml @@ -0,0 +1,11 @@ + + + + 6.399 + 5.450775 + 3.15 + 0.70932369153652 + 100 + + + From ae9106195413b3a425a49f3df3e59ac72902a425 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 08:13:04 +0300 Subject: [PATCH 12/29] Small fix for create_constant_raster_cli --- eis_toolkit/cli_typer.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index cd2b3aa0..f45d6af0 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -198,9 +198,9 @@ def create_constant_raster_cli( raster_height, nodata_value, ) - with rasterio.open(output_raster, "w", **out_meta) as dest: - dest.write(out_image) + for band_n in range(1, out_meta["count"] + 1): + dest.write(out_image, band_n) typer.echo("Creating constant raster completed") typer.echo(f"Writing raster to {output_raster}.") From 47971674170251329024893b0bdbee5aa7108fdc Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 08:50:22 +0300 Subject: [PATCH 13/29] Small fix for extract_values_from_raster_cli --- eis_toolkit/cli_typer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index f45d6af0..37215aef 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -219,7 +219,7 @@ def extract_values_from_raster_cli( geodataframe = gpd.read_file(geometries) with rasterio.open(input_raster) as raster: - df = extract_values_from_raster(raster=[raster], geodataframe=geodataframe) + df = extract_values_from_raster(raster_list=[raster], geodataframe=geodataframe) df.to_csv(output_vector) From c483ec2c68d6d1b0707e86e49c9254abae7959b8 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 09:51:03 +0300 Subject: [PATCH 14/29] Small fix for rasterize_cli --- eis_toolkit/cli_typer.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 37215aef..0b6085e6 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -411,6 +411,8 @@ def rasterize_cli( if base_raster_profile_raster is not None: with rasterio.open(base_raster_profile_raster) as raster: base_raster_profile = raster.profile + else: + base_raster_profile = base_raster_profile_raster out_image, out_meta = rasterize_vector( geodataframe, @@ -431,7 +433,7 @@ def rasterize_cli( ) with rasterio.open(output_raster, "w", **out_meta) as dst: - dst.write(out_image) + dst.write(out_image, 1) typer.echo("Rasterizing completed") typer.echo(f"Writing raster to {output_raster}") From d8a2c7fad2cc7ee5a4af0d3decd053a6d43c50f0 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 10:30:35 +0300 Subject: [PATCH 15/29] Small fixes --- eis_toolkit/cli_typer.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 0b6085e6..ddd41ecf 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -433,7 +433,8 @@ def rasterize_cli( ) with rasterio.open(output_raster, "w", **out_meta) as dst: - dst.write(out_image, 1) + for band_n in range(1, out_meta["count"]): + dst.write(out_image, band_n) typer.echo("Rasterizing completed") typer.echo(f"Writing raster to {output_raster}") @@ -477,6 +478,8 @@ def vector_density_cli( if base_raster_profile_raster is not None: with rasterio.open(base_raster_profile_raster) as raster: base_raster_profile = raster.profile + else: + base_raster_profile = base_raster_profile_raster out_image, out_meta = vector_density( geodataframe=geodataframe, @@ -494,7 +497,8 @@ def vector_density_cli( ) with rasterio.open(output_raster, "w", **out_meta) as dst: - dst.write(out_image) + for band_n in range(1, out_meta["count"]): + dst.write(out_image, band_n) typer.echo("Vector density computation completed") typer.echo(f"Writing raster to {output_raster}") From 892846000f4581b4ce1853507b3565141a8dc1b8 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 11:38:14 +0300 Subject: [PATCH 16/29] Small fixes --- eis_toolkit/cli_typer.py | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index ddd41ecf..380ed2ec 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -4,6 +4,7 @@ from typing import List, Tuple import geopandas as gpd +import numpy as np import pandas as pd import rasterio import typer @@ -403,7 +404,11 @@ def rasterize_cli( buffer_value: float = None, merge_strategy: MergeStrategy = MergeStrategy.replace, ): - """Rasterize input vector.""" + """ + Rasterize input vector. + + Either resolution or base-raster-profile-raster must be provided. + """ from eis_toolkit.vector_processing.rasterize_vector import rasterize_vector geodataframe = gpd.read_file(input_vector) @@ -428,7 +433,7 @@ def rasterize_cli( out_meta.update( { "count": 1, - "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else float, # TODO change this + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else np.float64, # TODO change this } ) @@ -470,7 +475,11 @@ def vector_density_cli( buffer_value: float = None, statistic: VectorDensityStatistic = VectorDensityStatistic.density, ): - """Compute density of geometries within raster.""" + """ + Compute density of geometries within raster. + + Either resolution or base_raster_profile_raster must be provided. + """ from eis_toolkit.vector_processing.vector_density import vector_density geodataframe = gpd.read_file(input_vector) @@ -492,7 +501,7 @@ def vector_density_cli( out_meta.update( { "count": 1, - "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else float, # TODO change this + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else np.float64, # TODO change this } ) From e82b0f466d028cd94f05a47f42ce501569aac8b9 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 12:10:42 +0300 Subject: [PATCH 17/29] Small fixes --- eis_toolkit/cli_typer.py | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 380ed2ec..8814f5ee 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -4,7 +4,6 @@ from typing import List, Tuple import geopandas as gpd -import numpy as np import pandas as pd import rasterio import typer @@ -315,8 +314,7 @@ def idw_interpolation_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], target_column: str = typer.Option(), - pixel_size_x: float = typer.Option(), - pixel_size_y: float = typer.Option(), + resolution: float = typer.Option(), power: float = 2.0, extent: Tuple[float, float, float, float] = None, ): @@ -328,7 +326,7 @@ def idw_interpolation_cli( out_image, out_meta = idw( geodataframe=geodataframe, target_column=target_column, - resolution=(pixel_size_x, pixel_size_y), + resolution=(resolution, resolution), extent=extent, power=power, ) @@ -354,8 +352,7 @@ def kriging_interpolation_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], target_column: str = typer.Option(), - pixel_size_x: float = typer.Option(), - pixel_size_y: float = typer.Option(), + resolution: float = typer.Option(), extent: Tuple[float, float, float, float] = None, variogram_model: VariogramModel = VariogramModel.linear, coordinates_type: CoordinatesType = CoordinatesType.geographic, @@ -369,7 +366,7 @@ def kriging_interpolation_cli( out_image, out_meta = kriging( data=geodataframe, target_column=target_column, - resolution=(pixel_size_x, pixel_size_y), + resolution=(resolution, resolution), extent=extent, variogram_model=variogram_model, coordinates_type=coordinates_type, @@ -433,7 +430,7 @@ def rasterize_cli( out_meta.update( { "count": 1, - "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else np.float64, # TODO change this + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else "float32", # TODO change this } ) @@ -501,7 +498,7 @@ def vector_density_cli( out_meta.update( { "count": 1, - "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else np.float64, # TODO change this + "dtype": base_raster_profile["dtype"] if base_raster_profile_raster else "float32", # TODO change this } ) From 8e60db4ecc561d7ee3899cf47e5187a4c4413385 Mon Sep 17 00:00:00 2001 From: msorvoja Date: Fri, 15 Sep 2023 13:37:02 +0300 Subject: [PATCH 18/29] Minor fixes --- eis_toolkit/cli_typer.py | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 8814f5ee..3fb6708b 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -316,11 +316,14 @@ def idw_interpolation_cli( target_column: str = typer.Option(), resolution: float = typer.Option(), power: float = 2.0, - extent: Tuple[float, float, float, float] = None, + extent: Tuple[float, float, float, float] = (None, None, None, None), # TODO Change this ): """Apply inverse distance weighting (IDW) interpolation to input vector file.""" from eis_toolkit.vector_processing.idw_interpolation import idw + if extent == (None, None, None, None): + extent = None + geodataframe = gpd.read_file(input_vector) out_image, out_meta = idw( @@ -339,8 +342,8 @@ def idw_interpolation_cli( } ) - with rasterio.open(out_image, "w", **out_meta) as dst: - dst.write(out_image) + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, 1) typer.echo("IDW interpolation completed") typer.echo(f"Writing raster to {output_raster}") @@ -353,7 +356,7 @@ def kriging_interpolation_cli( output_raster: Annotated[Path, OUTPUT_FILE_OPTION], target_column: str = typer.Option(), resolution: float = typer.Option(), - extent: Tuple[float, float, float, float] = None, + extent: Tuple[float, float, float, float] = (None, None, None, None), # TODO Change this variogram_model: VariogramModel = VariogramModel.linear, coordinates_type: CoordinatesType = CoordinatesType.geographic, method: KrigingMethod = KrigingMethod.ordinary, @@ -361,6 +364,9 @@ def kriging_interpolation_cli( """Apply kriging interpolation to input vector file.""" from eis_toolkit.vector_processing.kriging_interpolation import kriging + if extent == (None, None, None, None): + extent = None + geodataframe = gpd.read_file(input_vector) out_image, out_meta = kriging( @@ -381,8 +387,8 @@ def kriging_interpolation_cli( } ) - with rasterio.open(out_image, "w", **out_meta) as dst: - dst.write(out_image) + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, 1) typer.echo("Kriging interpolation completed") typer.echo(f"Writing raster to {output_raster}") From 03b58ba86b021ab62fc39c1b63ed1aef130b26af Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 28 Sep 2023 09:45:20 +0300 Subject: [PATCH 19/29] Added binarize algorithm --- eis_toolkit/cli_typer.py | 23 ++++++++++++++++++++++- 1 file changed, 22 insertions(+), 1 deletion(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 3fb6708b..0dfadf5c 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -601,7 +601,28 @@ def descriptive_statistics_vector_cli(input_file: Annotated[Path, INPUT_FILE_OPT # BINARIZE -# TODO +@app.command() +def binarize_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + threshold: float = typer.Option(), +): + """ + Binarize data based on a given threshold. + + Replaces values less or equal threshold with 0. + Replaces values greater than the threshold with 1. + """ + from eis_toolkit.transformations.binarize import binarize + + with rasterio.open(input_raster) as raster: + out_image, out_meta, _ = binarize(raster=raster, thresholds=[threshold]) + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + + typer.echo("Binarizing completed") + typer.echo(f"Writing raster to {output_raster}") # CLIPPING (PROBLEMATIC NAME, CHANGE!) From 2d2793269534762f9f8a63f7c8a5cde634ef9c92 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 5 Oct 2023 10:34:40 +0300 Subject: [PATCH 20/29] Renamed clipping (transform) to clip transform, added simple progress updates to CLI, added transformations CLI --- eis_toolkit/cli_typer.py | 304 +++++++++++++++--- .../transformations/{clipping.py => clip.py} | 8 +- .../{clipping_test.py => clip_test.py} | 32 +- 3 files changed, 288 insertions(+), 56 deletions(-) rename eis_toolkit/transformations/{clipping.py => clip.py} (94%) rename tests/transformations/{clipping_test.py => clip_test.py} (61%) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 0dfadf5c..df1a4341 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -1,7 +1,7 @@ import json from enum import Enum from pathlib import Path -from typing import List, Tuple +from typing import List, Optional, Tuple import geopandas as gpd import pandas as pd @@ -51,6 +51,14 @@ class VectorDensityStatistic(str, Enum): count = "count" +class LogarithmTransforms(str, Enum): + """Logarithm choices for log transform.""" + + ln = "ln" + log2 = "log2" + log10 = "log10" + + class ResamplingMethods(str, Enum): """Resampling methods available.""" @@ -126,20 +134,19 @@ def clip_raster_cli( typer.echo("Progress: 10%") geodataframe = gpd.read_file(geometries) - typer.echo("Progress: 40%") with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") out_image, out_meta = clip_raster( raster=raster, geodataframe=geodataframe, ) - - typer.echo("Progress: 70%") + typer.echo("Progress: 75%") with rasterio.open(output_raster, "w", **out_meta) as dest: dest.write(out_image) - typer.echo("Progress: 100%") + typer.echo(f"Clipping completed, output raster written to {output_raster}.") @@ -169,8 +176,11 @@ def create_constant_raster_cli( """ from eis_toolkit.raster_processing.create_constant_raster import create_constant_raster + typer.echo("Progress: 10%") + if template_raster is not None: with rasterio.open(template_raster) as raster: + typer.echo("Progress: 25%") out_image, out_meta = create_constant_raster( constant_value, raster, @@ -185,6 +195,7 @@ def create_constant_raster_cli( nodata_value, ) else: + typer.echo("Progress: 25%") out_image, out_meta = create_constant_raster( constant_value, template_raster, @@ -198,12 +209,14 @@ def create_constant_raster_cli( raster_height, nodata_value, ) + typer.echo("Progress: 75%") + with rasterio.open(output_raster, "w", **out_meta) as dest: for band_n in range(1, out_meta["count"] + 1): dest.write(out_image, band_n) + typer.echo("Progress: 100%") - typer.echo("Creating constant raster completed") - typer.echo(f"Writing raster to {output_raster}.") + typer.echo(f"Creating constant raster completed, writing raster to {output_raster}.") # EXTRACT VALUES FROM RASTER @@ -216,15 +229,19 @@ def extract_values_from_raster_cli( """Extract raster values using point data to a DataFrame.""" from eis_toolkit.raster_processing.extract_values_from_raster import extract_values_from_raster + typer.echo("Progress: 10%") + geodataframe = gpd.read_file(geometries) with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") df = extract_values_from_raster(raster_list=[raster], geodataframe=geodataframe) + typer.echo("Progress: 75%") df.to_csv(output_vector) + typer.echo("Progress: 100%") - typer.echo("Extracting values from raster completed") - typer.echo(f"Writing vector to {output_vector}.") + typer.echo(f"Extracting values from raster completed, writing vector to {output_vector}.") # REPROJECT RASTER @@ -238,15 +255,19 @@ def reproject_raster_cli( """Reproject the input raster to given CRS.""" from eis_toolkit.raster_processing.reprojecting import reproject_raster + typer.echo("Progress: 10%") + method = RESAMPLING_MAPPING[resampling_method] with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") out_image, out_meta = reproject_raster(raster=raster, target_crs=target_crs, resampling_method=method) + typer.echo("Progress: 75%") with rasterio.open(output_raster, "w", **out_meta) as dest: dest.write(out_image) + typer.echo("Progress: 100%") - typer.echo("Reprojecting completed") - typer.echo(f"Writing raster to {output_raster}.") + typer.echo(f"Reprojecting completed, writing raster to {output_raster}.") # SNAP RASTER @@ -259,14 +280,18 @@ def snap_raster_cli( """Snaps/aligns input raster to the given snap raster.""" from eis_toolkit.raster_processing.snapping import snap_with_raster + typer.echo("Progress: 10%") + with rasterio.open(input_raster) as src, rasterio.open(snap_raster) as snap_src: + typer.echo("Progress: 25%") out_image, out_meta = snap_with_raster(src, snap_src) + typer.echo("Progress: 75%") with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image) + typer.echo("Progress: 100%") - typer.echo("Snapping completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Snapping completed, writing raster to {output_raster}.") # UNIFY RASTERS @@ -295,14 +320,18 @@ def extract_window_cli( """Extract window from raster.""" from eis_toolkit.raster_processing.windowing import extract_window + typer.echo("Progress: 10%") + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") out_image, out_meta = extract_window(raster, center_coords, height, width) + typer.echo("Progress: 75%") with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image) + typer.echo("Progress: 100%") - typer.echo("Windowing completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Windowing completed, writing raster to {output_raster}") # --- VECTOR PROCESSING --- @@ -321,10 +350,13 @@ def idw_interpolation_cli( """Apply inverse distance weighting (IDW) interpolation to input vector file.""" from eis_toolkit.vector_processing.idw_interpolation import idw + typer.echo("Progress: 10%") + if extent == (None, None, None, None): extent = None geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") out_image, out_meta = idw( geodataframe=geodataframe, @@ -333,6 +365,7 @@ def idw_interpolation_cli( extent=extent, power=power, ) + typer.echo("Progress: 75%") out_meta.update( { @@ -344,9 +377,9 @@ def idw_interpolation_cli( with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image, 1) + typer.echo("Progress: 100%") - typer.echo("IDW interpolation completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"IDW interpolation completed, writing raster to {output_raster}.") # KRIGING INTERPOLATION @@ -364,10 +397,13 @@ def kriging_interpolation_cli( """Apply kriging interpolation to input vector file.""" from eis_toolkit.vector_processing.kriging_interpolation import kriging + typer.echo("Progress: 10%") + if extent == (None, None, None, None): extent = None geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") out_image, out_meta = kriging( data=geodataframe, @@ -378,6 +414,7 @@ def kriging_interpolation_cli( coordinates_type=coordinates_type, method=method, ) + typer.echo("Progress: 75%") out_meta.update( { @@ -389,9 +426,9 @@ def kriging_interpolation_cli( with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image, 1) + typer.echo("Progress: 100%") - typer.echo("Kriging interpolation completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Kriging interpolation completed, writing raster to {output_raster}.") # RASTERIZE @@ -414,6 +451,8 @@ def rasterize_cli( """ from eis_toolkit.vector_processing.rasterize_vector import rasterize_vector + typer.echo("Progress: 10%") + geodataframe = gpd.read_file(input_vector) if base_raster_profile_raster is not None: @@ -421,6 +460,7 @@ def rasterize_cli( base_raster_profile = raster.profile else: base_raster_profile = base_raster_profile_raster + typer.echo("Progress: 25%") out_image, out_meta = rasterize_vector( geodataframe, @@ -432,6 +472,7 @@ def rasterize_cli( buffer_value, merge_strategy, ) + typer.echo("Progress: 75%") out_meta.update( { @@ -443,9 +484,9 @@ def rasterize_cli( with rasterio.open(output_raster, "w", **out_meta) as dst: for band_n in range(1, out_meta["count"]): dst.write(out_image, band_n) + typer.echo("Progress: 100%") - typer.echo("Rasterizing completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Rasterizing completed, writing raster to {output_raster}.") # REPROJECT VECTOR @@ -458,14 +499,18 @@ def reproject_vector_cli( """Reproject the input vector to given CRS.""" from eis_toolkit.vector_processing.reproject_vector import reproject_vector + typer.echo("Progress: 10%") + geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") reprojected_geodataframe = reproject_vector(geodataframe=geodataframe, target_crs=target_crs) + typer.echo("Progress: 75%") reprojected_geodataframe.to_file(output_vector, driver="GeoJSON") + typer.echo("Progress: 100%") - typer.echo("Reprojecting completed") - typer.echo(f"Writing vector to {output_vector}") + typer.echo(f"Reprojecting completed, writing vector to {output_vector}.") # VECTOR DENSITY @@ -485,6 +530,8 @@ def vector_density_cli( """ from eis_toolkit.vector_processing.vector_density import vector_density + typer.echo("Progress: 10%") + geodataframe = gpd.read_file(input_vector) if base_raster_profile_raster is not None: @@ -492,6 +539,7 @@ def vector_density_cli( base_raster_profile = raster.profile else: base_raster_profile = base_raster_profile_raster + typer.echo("Progress: 25%") out_image, out_meta = vector_density( geodataframe=geodataframe, @@ -500,6 +548,7 @@ def vector_density_cli( buffer_value=buffer_value, statistic=statistic, ) + typer.echo("Progress: 75%") out_meta.update( { @@ -511,9 +560,9 @@ def vector_density_cli( with rasterio.open(output_raster, "w", **out_meta) as dst: for band_n in range(1, out_meta["count"]): dst.write(out_image, band_n) + typer.echo("Progress: 100%") - typer.echo("Vector density computation completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Vector density computation completed, writing raster to {output_raster}.") # --- SPATIAL ANALYSES --- @@ -529,18 +578,22 @@ def distance_computation_cli( """Calculate distance from raster cell to nearest geometry.""" from eis_toolkit.spatial_analyses.distance_computation import distance_computation + typer.echo("Progress: 10%") + with rasterio.open(input_raster) as raster: profile = raster.profile geodataframe = gpd.read_file(geometries) + typer.echo("Progress: 25%") out_image = distance_computation(profile, geodataframe) + typer.echo("Progress: 75%") with rasterio.open(output_raster, "w", **profile) as dst: dst.write(out_image, profile["count"]) + typer.echo("Progress: 100%") - typer.echo("Distance computation completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Distance computation completed, writing raster to {output_raster}.") # CBA @@ -556,10 +609,15 @@ def descriptive_statistics_raster_cli(input_file: Annotated[Path, INPUT_FILE_OPT """Generate descriptive statistics from raster data.""" from eis_toolkit.statistical_analyses.descriptive_statistics import descriptive_statistics_raster + typer.echo("Progress: 10%") + with rasterio.open(input_file) as raster: + typer.echo("Progress: 25%") results_dict = descriptive_statistics_raster(raster) + typer.echo("Progress: 75%") json_str = json.dumps(results_dict) + typer.echo("Progress: 100%") typer.echo(f"Results: {json_str}") typer.echo("Descriptive statistics (raster) completed") @@ -570,18 +628,25 @@ def descriptive_statistics_vector_cli(input_file: Annotated[Path, INPUT_FILE_OPT """Generate descriptive statistics from vector or tabular data.""" from eis_toolkit.statistical_analyses.descriptive_statistics import descriptive_statistics_dataframe + typer.echo("Progress: 10%") + # TODO modify input file detection try: gdf = gpd.read_file(input_file) + typer.echo("Progress: 25%") results_dict = descriptive_statistics_dataframe(gdf, column) except: # noqa: E722 try: df = pd.read_csv(input_file) + typer.echo("Progress: 25%") results_dict = descriptive_statistics_dataframe(df, column) except: # noqa: E722 raise Exception("Could not read input file as raster or dataframe") + typer.echo("Progress: 75%") json_str = json.dumps(results_dict) + typer.echo("Progress: 10%") + typer.echo(f"Results: {json_str}") typer.echo("Descriptive statistics (vector) completed") @@ -615,34 +680,201 @@ def binarize_cli( """ from eis_toolkit.transformations.binarize import binarize + typer.echo("Progress: 10%") + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") out_image, out_meta, _ = binarize(raster=raster, thresholds=[threshold]) + typer.echo("Progress: 70%") with rasterio.open(output_raster, "w", **out_meta) as dst: dst.write(out_image) + typer.echo("Progress: 100%") - typer.echo("Binarizing completed") - typer.echo(f"Writing raster to {output_raster}") + typer.echo(f"Binarizing completed, writing raster to {output_raster}.") -# CLIPPING (PROBLEMATIC NAME, CHANGE!) -# TODO +# CLIP TRANSFORM +@app.command() +def clip_transform_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + limits: Tuple[Optional[float], Optional[float]] = typer.Option(), +): + """ + Clips data based on specified upper and lower limits. + Replaces values below the lower limit and above the upper limit with provided values, respecively. + Works both one-sided and two-sided but raises error if no limits provided. + """ + from eis_toolkit.transformations.clip import clip_transform -# LINEAR -# TODO + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = clip_transform(raster=raster, limits=limits) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Clip transform completed, writing raster to {output_raster}.") + + +# Z-SCORE NORMALIZATION +@app.command() +def z_score_normalization_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """ + Normalize data based on mean and standard deviation. + + Results will have a mean = 0 and standard deviation = 1. + """ + from eis_toolkit.transformations.linear import z_score_normalization + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = z_score_normalization(raster=raster) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Z-score normalization completed, writing raster to {output_raster}.") + + +# MIX_MAX SCALING +@app.command() +def min_max_scaling_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + new_range: Tuple[float, float] = (0, 1), +): + """ + Normalize data based on a specified new range. + + Uses the provided new minimum and maximum to transform data into the new interval. + """ + from eis_toolkit.transformations.linear import min_max_scaling + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = min_max_scaling(raster=raster, new_range=[new_range]) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Min-max scaling completed, writing raster to {output_raster}.") # LOGARITHMIC -# TODO +@app.command() +def log_transform_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + log_type: LogarithmTransforms = LogarithmTransforms.log2, +): + """ + Perform a logarithmic transformation on the provided data. + + Logarithm base can be "ln", "log" or "log10". + Negative values will not be considered for transformation and replaced by the specific nodata value. + """ + from eis_toolkit.transformations.logarithmic import log_transform + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = log_transform(raster=raster, log_transform=[log_type]) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Logarithm transform completed, writing raster to {output_raster}.") # SIGMOID -# TODO +@app.command() +def sigmoid_transform_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + bounds: Tuple[float, float] = (0, 1), + slope: float = 1, + center: bool = True, +): + """ + Transform data into a sigmoid-shape based on a specified new range. + + Uses the provided new minimum and maximum, shift and slope parameters to transform the data. + """ + from eis_toolkit.transformations.sigmoid import sigmoid_transform + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = sigmoid_transform(raster=raster, bounds=[bounds], slope=[slope], center=center) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Sigmoid transform completed, writing raster to {output_raster}.") # WINSORIZE -# TODO +@app.command() +def winsorize_transform_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + percentiles: Tuple[Optional[float], Optional[float]] = typer.Option(), + inside: bool = False, +): + """ + Winsorize data based on specified percentile values. + + Replaces values between [minimum, lower percentile] and [upper percentile, maximum] if provided. + Works both one-sided and two-sided but raises error if no percentile values provided. + + Percentiles are symmetrical, i.e. percentile_lower = 10 corresponds to the interval [min, 10%]. + And percentile_upper = 10 corresponds to the intervall [90%, max]. + I.e. percentile_lower = 0 refers to the minimum and percentile_upper = 0 to the data maximum. + + Calculation of percentiles is ambiguous. Users can choose whether to use the value + for replacement from inside or outside of the respective interval. Example: + Given the np.array[5 10 12 15 20 24 27 30 35] and percentiles(10, 10), the calculated + percentiles are (5, 35) for inside and (10, 30) for outside. + This results in [5 10 12 15 20 24 27 30 35] and [10 10 12 15 20 24 27 30 30], respectively. + """ + from eis_toolkit.transformations.winsorize import winsorize + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + typer.echo("Progress: 25%") + out_image, out_meta, _ = winsorize(raster=raster, percentiles=percentiles, inside=inside) + typer.echo("Progress: 70%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Winsorize transform completed, writing raster to {output_raster}.") # ---VALIDATION --- diff --git a/eis_toolkit/transformations/clipping.py b/eis_toolkit/transformations/clip.py similarity index 94% rename from eis_toolkit/transformations/clipping.py rename to eis_toolkit/transformations/clip.py index 3a284daa..afb9d341 100644 --- a/eis_toolkit/transformations/clipping.py +++ b/eis_toolkit/transformations/clip.py @@ -22,7 +22,7 @@ @beartype -def _clipping( # type: ignore[no-any-unimported] +def _clip_transform( # type: ignore[no-any-unimported] in_array: np.ndarray, limits: Tuple[Optional[Number], Optional[Number]], ) -> np.ndarray: @@ -40,14 +40,14 @@ def _clipping( # type: ignore[no-any-unimported] @beartype -def clipping( # type: ignore[no-any-unimported] +def clip_transform( # type: ignore[no-any-unimported] raster: rasterio.io.DatasetReader, limits: Sequence[Tuple[Optional[Number], Optional[Number]]], bands: Optional[Sequence[int]] = None, nodata: Optional[Number] = None, ) -> Tuple[np.ndarray, dict, dict]: """ - Clipping data based on specified upper and lower limits. + Clips data based on specified upper and lower limits. Takes one nodata value that will be ignored in calculations. Replaces values below the lower limit and above the upper limit with provided values, respecively. @@ -101,7 +101,7 @@ def clipping( # type: ignore[no-any-unimported] band_array = cast_array_to_float(band_array, cast_int=True) band_array = nodata_to_nan(band_array, nodata_value=nodata) - band_array = _clipping(band_array, limits=limits[i]) + band_array = _clip_transform(band_array, limits=limits[i]) band_array = nan_to_nodata(band_array, nodata_value=nodata) band_array = cast_array_to_int(band_array, scalar=nodata, initial_dtype=inital_dtype) diff --git a/tests/transformations/clipping_test.py b/tests/transformations/clip_test.py similarity index 61% rename from tests/transformations/clipping_test.py rename to tests/transformations/clip_test.py index c0db0d18..5d0fbbe0 100644 --- a/tests/transformations/clipping_test.py +++ b/tests/transformations/clip_test.py @@ -9,14 +9,14 @@ InvalidRasterBandException, NonMatchingParameterLengthsException, ) -from eis_toolkit.transformations.clipping import _clipping, clipping +from eis_toolkit.transformations.clip import _clip_transform, clip_transform from tests.transformations import check_transformation_outputs parent_dir = Path(__file__).parent raster_path = parent_dir.joinpath("../data/remote/small_raster_multiband.tif") -def test_clipping(): +def test_clip_transform(): """Test that transformation works as intended.""" bands = None limits = [(-1, 1)] @@ -24,49 +24,49 @@ def test_clipping(): nodata = 3.748 with rasterio.open(raster_path) as raster: - out_array, out_meta, out_settings = clipping(raster=raster, bands=bands, limits=limits, nodata=nodata) + out_array, out_meta, out_settings = clip_transform(raster=raster, bands=bands, limits=limits, nodata=nodata) # Output shapes and types check_transformation_outputs(out_array, out_meta, out_settings, raster, nodata) -def test_clipping_core(): +def test_clip_transform_core(): """Test for core functionality with small example computation.""" in_array = np.array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]) - transformation = _clipping(in_array, limits=(2, 8)) + transformation = _clip_transform(in_array, limits=(2, 8)) expected = np.array([2, 2, 2, 3, 4, 5, 6, 7, 8, 8, 8]) np.testing.assert_array_equal(transformation, expected) -def test_clipping_band_selection(): +def test_clip_transform_band_selection(): """Tests that invalid parameter value for band selection raises the correct exception.""" with pytest.raises(InvalidRasterBandException): with rasterio.open(raster_path) as raster: - clipping(raster=raster, bands=[0], limits=[(-1, 1)], nodata=None) - clipping(raster=raster, bands=list(range(1, 100)), percentiles=[(-1, 1)], nodata=None) + clip_transform(raster=raster, bands=[0], limits=[(-1, 1)], nodata=None) + clip_transform(raster=raster, bands=list(range(1, 100)), percentiles=[(-1, 1)], nodata=None) -def test_clipping_parameter_length(): +def test_clip_transform_parameter_length(): """Tests that invalid length for provided parameters raises the correct exception.""" with pytest.raises(NonMatchingParameterLengthsException): with rasterio.open(raster_path) as raster: - clipping(raster=raster, bands=[1, 2, 3], limits=[(-1, 1), (-2, 2)], nodata=None) - clipping(raster=raster, bands=[1, 2], limits=[(-1, 1), (-2, 2), (-3, 3)], nodata=None) + clip_transform(raster=raster, bands=[1, 2, 3], limits=[(-1, 1), (-2, 2)], nodata=None) + clip_transform(raster=raster, bands=[1, 2], limits=[(-1, 1), (-2, 2), (-3, 3)], nodata=None) -def test_clipping_percentile_parameter(): +def test_clip_transform_percentile_parameter(): """Tests that invalid percentile values raises the correct exception.""" with pytest.raises(InvalidParameterValueException): with rasterio.open(raster_path) as raster: # All None - clipping(raster=raster, bands=None, limits=[(None, None)], nodata=None) + clip_transform(raster=raster, bands=None, limits=[(None, None)], nodata=None) -def test_clipping_min_max_position(): +def test_clip_transform_min_max_position(): """Tests that invalid min-max positions for provided parameters raises the correct exception.""" with pytest.raises(InvalidParameterValueException): with rasterio.open(raster_path) as raster: # Invalid position of minimum and maximum values for limits - clipping(raster=raster, bands=None, limits=[(1, 0)], nodata=None) - clipping(raster=raster, bands=[1, 2, 3], limits=[(0, 0), (1, 0), (2, 0)], nodata=None) + clip_transform(raster=raster, bands=None, limits=[(1, 0)], nodata=None) + clip_transform(raster=raster, bands=[1, 2, 3], limits=[(0, 0), (1, 0), (2, 0)], nodata=None) From ef27725ab06acc75a6a5794dc4b8641ba2ed8384 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 5 Oct 2023 11:15:53 +0300 Subject: [PATCH 21/29] Add to CLI: check raster grids, fuzzy overlays, unify rasters (WIP) --- eis_toolkit/cli_typer.py | 177 +++++++++++++++++++++++++++++++++++++-- 1 file changed, 170 insertions(+), 7 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index df1a4341..8cff17fa 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -118,7 +118,24 @@ class ResamplingMethods(str, Enum): # CHECK RASTER GRIDS -# TODO +@app.command() +def check_raster_grids_cli(input_rasters: Annotated[List[Path], INPUT_FILE_OPTION], same_extent: bool = False): + """Check all input rasters for matching gridding and optionally matching bounds.""" + from eis_toolkit.checks.raster import check_raster_grids + + typer.echo("Progress: 10%") + + open_rasters = [rasterio.open(raster) for raster in input_rasters] + typer.echo("Progress: 25%") + + result = check_raster_grids(input_rasters=open_rasters, same_extent=same_extent) + typer.echo("Progress: 75%") + + [raster.close() for raster in open_rasters] + typer.echo("Progress: 100%") + + typer.echo(f"Result: {str(result)}") + typer.echo("Checking raster grids completed.") # CLIP RASTER @@ -299,13 +316,30 @@ def snap_raster_cli( def unify_rasters_cli( base_raster: Annotated[Path, INPUT_FILE_OPTION], rasters_to_unify: Annotated[List[Path], INPUT_FILE_OPTION], - output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + output_directory: Annotated[Path, OUTPUT_FILE_OPTION], # Directory path? resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), same_extent: bool = False, ): - """Unify given rasters relative to base raster. NOT IMPLEMENTED YET.""" - # TODO - pass + """Unify given rasters relative to base raster. WIP.""" + from eis_toolkit.raster_processing.unifying import unify_raster_grids + + typer.echo("Progress: 10%") + + with rasterio.open(base_raster) as raster: + to_unify = [rasterio.open(rstr) for rstr in rasters_to_unify] # Open all rasters to be unfiied + unified = unify_raster_grids( + base_raster=raster, rasters_to_unify=to_unify, resampling_method=resampling_method, same_extent=same_extent + ) + [rstr.close() for rstr in to_unify] # Close all rasters + typer.echo("Progress: 75%") + + for i, (out_image, out_meta) in enumerate(unified[1:]): # Skip writing base raster + output_raster = output_directory.joinpath(f"unified_raster {i+1}.tif") + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image) + typer.echo("Progress: 100%") + + typer.echo(f"Unifying completed, writing rasters to {output_directory}.") # EXTRACT WINDOW @@ -654,8 +688,137 @@ def descriptive_statistics_vector_cli(input_file: Annotated[Path, INPUT_FILE_OPT # --- PREDICTION --- -# FUZZY OVERLAY -# TODO +# FUZZY OVERLAYS + +# AND OVERLAY +@app.command() +def and_overlay_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Compute an 'and' overlay operation with fuzzy logic.""" + from eis_toolkit.prediction.fuzzy_overlay import and_overlay + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + data = raster.read() # NOTE: Overlays take in data while for example transforms rasters, consistentency? + typer.echo("Progress: 25%") + out_image = and_overlay(data) + out_meta = raster.meta.copy() + out_meta["count"] = 1 + typer.echo("Progress: 75%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, out_meta["count"]) + typer.echo("Progress: 100%") + + typer.echo(f"'And' overlay completed, writing raster to {output_raster}.") + + +# OR OVERLAY +@app.command() +def or_overlay_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Compute an 'or' overlay operation with fuzzy logic.""" + from eis_toolkit.prediction.fuzzy_overlay import or_overlay + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + data = raster.read() # NOTE: Overlays take in data while for example transforms rasters, consistentency? + typer.echo("Progress: 25%") + out_image = or_overlay(data) + out_meta = raster.meta.copy() + out_meta["count"] = 1 + typer.echo("Progress: 75%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, out_meta["count"]) + typer.echo("Progress: 100%") + + typer.echo(f"'Or' overlay completed, writing raster to {output_raster}.") + + +# PRODUCT OVERLAY +@app.command() +def product_overlay_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Compute a 'product' overlay operation with fuzzy logic.""" + from eis_toolkit.prediction.fuzzy_overlay import product_overlay + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + data = raster.read() # NOTE: Overlays take in data while for example transforms rasters, consistentency? + typer.echo("Progress: 25%") + out_image = product_overlay(data) + out_meta = raster.meta.copy() + out_meta["count"] = 1 + typer.echo("Progress: 75%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, out_meta["count"]) + typer.echo("Progress: 100%") + + typer.echo(f"'Product' overlay completed, writing raster to {output_raster}.") + + +# SUM OVERLAY +@app.command() +def sum_overlay_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], +): + """Compute a 'sum' overlay operation with fuzzy logic.""" + from eis_toolkit.prediction.fuzzy_overlay import sum_overlay + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + data = raster.read() # NOTE: Overlays take in data while for example transforms rasters, consistentency? + typer.echo("Progress: 25%") + out_image = sum_overlay(data) + out_meta = raster.meta.copy() + out_meta["count"] = 1 + typer.echo("Progress: 75%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, out_meta["count"]) + typer.echo("Progress: 100%") + + typer.echo(f"'Sum' overlay completed, writing raster to {output_raster}.") + + +# GAMMA OVERLAY +@app.command() +def gamme_overlay_cli( + input_raster: Annotated[Path, INPUT_FILE_OPTION], + output_raster: Annotated[Path, OUTPUT_FILE_OPTION], + gamma: float = typer.Option(), +): + """Compute a 'gamma' overlay operation with fuzzy logic.""" + from eis_toolkit.prediction.fuzzy_overlay import gamma_overlay + + typer.echo("Progress: 10%") + + with rasterio.open(input_raster) as raster: + data = raster.read() # NOTE: Overlays take in data while for example transforms rasters, consistentency? + typer.echo("Progress: 25%") + out_image = gamma_overlay(data, gamma) + out_meta = raster.meta.copy() + out_meta["count"] = 1 + typer.echo("Progress: 75%") + + with rasterio.open(output_raster, "w", **out_meta) as dst: + dst.write(out_image, out_meta["count"]) + typer.echo("Progress: 100%") + + typer.echo(f"'Gamma' overlay completed, writing raster to {output_raster}.") # WOFE From b7b677118f958415a52497f19e6227d5a1c2859e Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 5 Oct 2023 12:39:34 +0300 Subject: [PATCH 22/29] Add to CLI: dbscan, k-means clustering, parallel_coordinates, compute_pca --- eis_toolkit/cli_typer.py | 118 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 118 insertions(+) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 8cff17fa..41d49fec 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -114,6 +114,124 @@ class ResamplingMethods(str, Enum): ) +# --- EXPLORATORY ANALYSES --- + + +# DBSCAN +@app.command() +def dbscan_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_vector: Annotated[Path, OUTPUT_FILE_OPTION], + max_distance: float = 0.5, + min_samples: int = 5, +): + """Perform DBSCAN clustering on the input data.""" + from eis_toolkit.exploratory_analyses.dbscan import dbscan + + typer.echo("Progress: 10%") + + geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") + + output_geodataframe = dbscan(data=geodataframe, max_distance=max_distance, min_samples=min_samples) + typer.echo("Progress: 75%") + + output_geodataframe.to_file(output_vector, driver="GeoJSON") + typer.echo("Progress: 100%") + + typer.echo(f"DBSCAN completed, output vector written to {output_vector}.") + + +# K-MEANS CLUSTERING +@app.command() +def k_means_clustering_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_vector: Annotated[Path, OUTPUT_FILE_OPTION], + number_of_clusters: Optional[float] = None, + random_state: int = None, # NOTE: Check typing +): + """Perform k-means clustering on the input data.""" + from eis_toolkit.exploratory_analyses.k_means_cluster import k_means_clustering + + typer.echo("Progress: 10%") + + geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") + + output_geodataframe = k_means_clustering( + data=geodataframe, number_of_clusters=number_of_clusters, random_state=random_state + ) + typer.echo("Progress: 75%") + + output_geodataframe.to_file(output_vector, driver="GeoJSON") + typer.echo("Progress: 100%") + + typer.echo(f"K-means clustering completed, output vector written to {output_vector}.") + + +# PARALLEL COORDINATES +@app.command() +def parallel_coordinates_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_file: Optional[Annotated[Path, OUTPUT_FILE_OPTION]] = None, + color_column_name: str = typer.Option(), + plot_title: Optional[str] = None, + palette_name: Optional[str] = None, + curved_lines: bool = True, + show_plot: bool = False, + save_dpi: Optional[int] = None, +): + """Perform k-means clustering on the input data.""" + import matplotlib as plt + + from eis_toolkit.exploratory_analyses.parallel_coordinates import plot_parallel_coordinates + + typer.echo("Progress: 10%") + + geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") + + figure = plot_parallel_coordinates( + geodataframe, + color_column_name=color_column_name, + plot_title=plot_title, + palette_name=palette_name, + curved_lines=curved_lines, + ) + typer.echo("Progress: 75%") + if show_plot: + plt.show(figure) + + echo_str_end = "." + if output_file is not None: + dpi = "figure" if save_dpi is None else save_dpi + plt.savefig(output_file, dpi=dpi) + echo_str_end = f", output figure saved to {output_file}." + typer.echo("Progress: 100%") + + typer.echo("Parallel coordinates plot completed" + echo_str_end) + + +# PCA +@app.command() +def compute_pca_cli( + input_vector: Annotated[Path, INPUT_FILE_OPTION], + output_file: Annotated[Path, OUTPUT_FILE_OPTION], + number_of_components: int = typer.Option(), +): + """Compute principal components for the input data.""" + from eis_toolkit.exploratory_analyses.pca import compute_pca + + typer.echo("Progress: 10%") + + geodataframe = gpd.read_file(input_vector) + typer.echo("Progress: 25%") + + pca_df, variance_ratios = compute_pca(data=geodataframe, number_of_components=number_of_components) + + pca_df.to_csv(output_file) + + # --- RASTER PROCESSING --- From 7ad48435054398873517bf08429b14f20d4d564e Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 5 Oct 2023 13:04:44 +0300 Subject: [PATCH 23/29] Separate complex tuple parameters --- eis_toolkit/cli_typer.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 41d49fec..49beb5fb 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -980,7 +980,8 @@ def binarize_cli( def clip_transform_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - limits: Tuple[Optional[float], Optional[float]] = typer.Option(), + limit_lower: Optional[float] = None, + limit_higher: Optional[float] = None, ): """ Clips data based on specified upper and lower limits. @@ -994,7 +995,7 @@ def clip_transform_cli( with rasterio.open(input_raster) as raster: typer.echo("Progress: 25%") - out_image, out_meta, _ = clip_transform(raster=raster, limits=limits) + out_image, out_meta, _ = clip_transform(raster=raster, limits=[(limit_lower, limit_higher)]) typer.echo("Progress: 70%") with rasterio.open(output_raster, "w", **out_meta) as dst: @@ -1123,7 +1124,8 @@ def sigmoid_transform_cli( def winsorize_transform_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - percentiles: Tuple[Optional[float], Optional[float]] = typer.Option(), + percentile_lower: Optional[float] = None, + percentile_higher: Optional[float] = None, inside: bool = False, ): """ @@ -1148,7 +1150,9 @@ def winsorize_transform_cli( with rasterio.open(input_raster) as raster: typer.echo("Progress: 25%") - out_image, out_meta, _ = winsorize(raster=raster, percentiles=percentiles, inside=inside) + out_image, out_meta, _ = winsorize( + raster=raster, percentiles=[(percentile_lower, percentile_higher)], inside=inside + ) typer.echo("Progress: 70%") with rasterio.open(output_raster, "w", **out_meta) as dst: From 39a953b1c94cfacebf6d402d8eadd71234dd98ba Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 5 Oct 2023 13:23:33 +0300 Subject: [PATCH 24/29] Modify docstring --- eis_toolkit/cli_typer.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli_typer.py index 49beb5fb..d327a3f7 100644 --- a/eis_toolkit/cli_typer.py +++ b/eis_toolkit/cli_typer.py @@ -181,7 +181,7 @@ def parallel_coordinates_cli( show_plot: bool = False, save_dpi: Optional[int] = None, ): - """Perform k-means clustering on the input data.""" + """Generate a parallel coordinates plot.""" import matplotlib as plt from eis_toolkit.exploratory_analyses.parallel_coordinates import plot_parallel_coordinates From 2ccc917a82b32f18a1f68d2d764ee1a381191752 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Wed, 11 Oct 2023 17:31:23 +0300 Subject: [PATCH 25/29] Rename cli file --- eis_toolkit/{cli_typer.py => cli.py} | 0 pyproject.toml | 2 +- setup.py | 2 +- 3 files changed, 2 insertions(+), 2 deletions(-) rename eis_toolkit/{cli_typer.py => cli.py} (100%) diff --git a/eis_toolkit/cli_typer.py b/eis_toolkit/cli.py similarity index 100% rename from eis_toolkit/cli_typer.py rename to eis_toolkit/cli.py diff --git a/pyproject.toml b/pyproject.toml index 49df6da5..cd9dc14a 100755 --- a/pyproject.toml +++ b/pyproject.toml @@ -18,7 +18,7 @@ keywords = [ ] [tool.poetry.scripts] -eis = "eis_toolkit.cli_typer:app" +eis = "eis_toolkit.cli:app" [tool.poetry.dependencies] python = ">=3.8,<3.11" diff --git a/setup.py b/setup.py index fcb8cf74..28756e29 100644 --- a/setup.py +++ b/setup.py @@ -9,7 +9,7 @@ ], entry_points={ "console_scripts": [ - "eis=eis_toolkit.cli_click:cli", + "eis=eis_toolkit.cli:cli", ], }, ) From a926dd2eaff03c3b5dd85500466376ed8ec3b771 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 12 Oct 2023 11:41:34 +0300 Subject: [PATCH 26/29] Modifications to gdf/df inputs --- eis_toolkit/cli.py | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py index d327a3f7..61039884 100644 --- a/eis_toolkit/cli.py +++ b/eis_toolkit/cli.py @@ -147,7 +147,7 @@ def dbscan_cli( def k_means_clustering_cli( input_vector: Annotated[Path, INPUT_FILE_OPTION], output_vector: Annotated[Path, OUTPUT_FILE_OPTION], - number_of_clusters: Optional[float] = None, + number_of_clusters: Optional[int] = None, random_state: int = None, # NOTE: Check typing ): """Perform k-means clustering on the input data.""" @@ -187,12 +187,12 @@ def parallel_coordinates_cli( from eis_toolkit.exploratory_analyses.parallel_coordinates import plot_parallel_coordinates typer.echo("Progress: 10%") - geodataframe = gpd.read_file(input_vector) + dataframe = pd.DataFrame(geodataframe.drop(columns="geometry")) typer.echo("Progress: 25%") figure = plot_parallel_coordinates( - geodataframe, + dataframe, color_column_name=color_column_name, plot_title=plot_title, palette_name=palette_name, @@ -224,10 +224,11 @@ def compute_pca_cli( typer.echo("Progress: 10%") - geodataframe = gpd.read_file(input_vector) + geodataframe = gpd.read_file(input_vector) # TODO: Check if gdf to df handling in tool itself + dataframe = pd.DataFrame(geodataframe.drop(columns="geometry")) typer.echo("Progress: 25%") - pca_df, variance_ratios = compute_pca(data=geodataframe, number_of_components=number_of_components) + pca_df, variance_ratios = compute_pca(data=dataframe, number_of_components=number_of_components) pca_df.to_csv(output_file) From 4204f9c73380202fa54ed59ba6608111a692a894 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Thu, 12 Oct 2023 16:55:39 +0300 Subject: [PATCH 27/29] Add documentation to CLI, check that input data is 3D for overlay --- eis_toolkit/cli.py | 6 ++++++ eis_toolkit/prediction/fuzzy_overlay.py | 10 ++++++---- 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py index 61039884..7852e771 100644 --- a/eis_toolkit/cli.py +++ b/eis_toolkit/cli.py @@ -1,3 +1,9 @@ +# --- ! --- +# NOTE! Work in progress in the implementation of command-line interface +# Note also, that this CLI is primarily created for other applications to +# utilize EIS Toolkit, such as EIS QGIS Plugin +# --- ! --- + import json from enum import Enum from pathlib import Path diff --git a/eis_toolkit/prediction/fuzzy_overlay.py b/eis_toolkit/prediction/fuzzy_overlay.py index 75404685..87800fe8 100644 --- a/eis_toolkit/prediction/fuzzy_overlay.py +++ b/eis_toolkit/prediction/fuzzy_overlay.py @@ -1,12 +1,14 @@ import numpy as np from beartype import beartype -from eis_toolkit.exceptions import InvalidParameterValueException +from eis_toolkit import exceptions -def _check_input_data(data): +def _check_input_data(data: np.ndarray): if data.min() < 0 or data.max() > 1: - raise InvalidParameterValueException("All data must be in range [0, 1]") + raise exceptions.InvalidParameterValueException("All data must be in range [0, 1].") + if data.ndim != 3: + raise exceptions.InvalidParameterValueException("Input data for overlay should be 3D numpy array.") @beartype @@ -103,7 +105,7 @@ def gamma_overlay(data: np.ndarray, gamma: float) -> np.ndarray: InvalidParameterValueException: If data values or gamma are not in range [0, 1]. """ if gamma < 0 or gamma > 1: - raise InvalidParameterValueException("The gamma parameter must be in range [0, 1]") + raise exceptions.InvalidParameterValueException("The gamma parameter must be in range [0, 1]") sum = sum_overlay(data=data) product = product_overlay(data=data) From 780b0320debe69c910bdeae5cf6414be7c52e3b2 Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Mon, 16 Oct 2023 11:50:00 +0300 Subject: [PATCH 28/29] Modify transformation cli params --- eis_toolkit/cli.py | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py index 7852e771..9fde1678 100644 --- a/eis_toolkit/cli.py +++ b/eis_toolkit/cli.py @@ -1044,7 +1044,8 @@ def z_score_normalization_cli( def min_max_scaling_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - new_range: Tuple[float, float] = (0, 1), + min: float = 0.0, + max: float = 1.0, ): """ Normalize data based on a specified new range. @@ -1057,7 +1058,7 @@ def min_max_scaling_cli( with rasterio.open(input_raster) as raster: typer.echo("Progress: 25%") - out_image, out_meta, _ = min_max_scaling(raster=raster, new_range=[new_range]) + out_image, out_meta, _ = min_max_scaling(raster=raster, new_range=[(min, max)]) typer.echo("Progress: 70%") with rasterio.open(output_raster, "w", **out_meta) as dst: @@ -1101,7 +1102,8 @@ def log_transform_cli( def sigmoid_transform_cli( input_raster: Annotated[Path, INPUT_FILE_OPTION], output_raster: Annotated[Path, OUTPUT_FILE_OPTION], - bounds: Tuple[float, float] = (0, 1), + limit_lower: float = 0.0, + limit_upper: float = 1.0, slope: float = 1, center: bool = True, ): @@ -1116,7 +1118,9 @@ def sigmoid_transform_cli( with rasterio.open(input_raster) as raster: typer.echo("Progress: 25%") - out_image, out_meta, _ = sigmoid_transform(raster=raster, bounds=[bounds], slope=[slope], center=center) + out_image, out_meta, _ = sigmoid_transform( + raster=raster, bounds=[(limit_lower, limit_upper)], slope=[slope], center=center + ) typer.echo("Progress: 70%") with rasterio.open(output_raster, "w", **out_meta) as dst: From 5268234e1ef2ffd88f106f3234e23609ba4486fd Mon Sep 17 00:00:00 2001 From: Niko Aarnio Date: Mon, 16 Oct 2023 19:26:09 +0300 Subject: [PATCH 29/29] Fix unify cli function, add output dir option, changes to parallel coordinates plot --- eis_toolkit/cli.py | 21 ++++++++++---- .../parallel_coordinates.py | 29 ++++++++++++++----- 2 files changed, 37 insertions(+), 13 deletions(-) diff --git a/eis_toolkit/cli.py b/eis_toolkit/cli.py index 9fde1678..894b807a 100644 --- a/eis_toolkit/cli.py +++ b/eis_toolkit/cli.py @@ -119,6 +119,14 @@ class ResamplingMethods(str, Enum): resolve_path=True, ) +OUTPUT_DIR_OPTION = typer.Option( + file_okay=False, + dir_okay=True, + writable=True, + readable=True, + resolve_path=True, +) + # --- EXPLORATORY ANALYSES --- @@ -188,7 +196,7 @@ def parallel_coordinates_cli( save_dpi: Optional[int] = None, ): """Generate a parallel coordinates plot.""" - import matplotlib as plt + import matplotlib.pyplot as plt from eis_toolkit.exploratory_analyses.parallel_coordinates import plot_parallel_coordinates @@ -197,7 +205,7 @@ def parallel_coordinates_cli( dataframe = pd.DataFrame(geodataframe.drop(columns="geometry")) typer.echo("Progress: 25%") - figure = plot_parallel_coordinates( + _ = plot_parallel_coordinates( dataframe, color_column_name=color_column_name, plot_title=plot_title, @@ -206,7 +214,7 @@ def parallel_coordinates_cli( ) typer.echo("Progress: 75%") if show_plot: - plt.show(figure) + plt.show() echo_str_end = "." if output_file is not None: @@ -440,8 +448,8 @@ def snap_raster_cli( @app.command() def unify_rasters_cli( base_raster: Annotated[Path, INPUT_FILE_OPTION], + output_directory: Annotated[Path, OUTPUT_DIR_OPTION], # Directory path? rasters_to_unify: Annotated[List[Path], INPUT_FILE_OPTION], - output_directory: Annotated[Path, OUTPUT_FILE_OPTION], # Directory path? resampling_method: ResamplingMethods = typer.Option(help="resample help", default=ResamplingMethods.nearest), same_extent: bool = False, ): @@ -453,7 +461,10 @@ def unify_rasters_cli( with rasterio.open(base_raster) as raster: to_unify = [rasterio.open(rstr) for rstr in rasters_to_unify] # Open all rasters to be unfiied unified = unify_raster_grids( - base_raster=raster, rasters_to_unify=to_unify, resampling_method=resampling_method, same_extent=same_extent + base_raster=raster, + rasters_to_unify=to_unify, + resampling_method=RESAMPLING_MAPPING[resampling_method], + same_extent=same_extent, ) [rstr.close() for rstr in to_unify] # Close all rasters typer.echo("Progress: 75%") diff --git a/eis_toolkit/exploratory_analyses/parallel_coordinates.py b/eis_toolkit/exploratory_analyses/parallel_coordinates.py index 3f966be3..10dd73da 100644 --- a/eis_toolkit/exploratory_analyses/parallel_coordinates.py +++ b/eis_toolkit/exploratory_analyses/parallel_coordinates.py @@ -17,8 +17,8 @@ def _normalize_data(data: np.ndarray) -> Tuple[np.ndarray, float, float]: - y_min = data.min(axis=0) - y_max = data.max(axis=0) + y_min = np.nanmin(data, axis=0) + y_max = np.nanmax(data, axis=0) dy = y_max - y_min y_min -= dy * 0.05 y_max += dy * 0.05 @@ -108,8 +108,8 @@ def _plot_parallel_coordinates( # Create the colorbar for numerical data colorbar_mappable = ScalarMappable(cmap=cmap, norm=norm) colorbar_mappable.set_array([]) - colorbar = plt.colorbar(colorbar_mappable) - colorbar.set_label(color_column_name, fontsize=14) + # colorbar = plt.colorbar(colorbar_mappable) + # colorbar.set_label(color_column_name, fontsize=14) # Draw lines for i in range(data.shape[0]): @@ -141,6 +141,10 @@ def plot_parallel_coordinates( ) -> matplotlib.figure.Figure: """Plot a parallel coordinates plot. + Automatically removes all rows containing null/nan values. Tries to convert columns to numeric + to be able to plot them. If more than 8 columns are present (after numeric filtering), keeps only + the first 8 to plot. + Args: df: The DataFrame to plot. color_column_name: The name of the column in df to use for color encoding. @@ -165,21 +169,30 @@ def plot_parallel_coordinates( f"The provided color column {color_column_name} is not found in the DataFrame." ) + df = df.convert_dtypes() + df = df.apply(pd.to_numeric, errors="ignore") + color_data = df[color_column_name].to_numpy() if len(set([type(elem) for elem in color_data])) != 1: raise exceptions.InconsistentDataTypesException( "The color column should have a consistent datatype. Multiple data types detected in the color column." ) + df = df.select_dtypes(include=np.number) + # Drop non-numeric columns and the column used for coloring columns_to_drop = [color_column_name] for column in df.columns.values: - if not np.issubdtype(df[column].dtype, np.number): + if df[column].isnull().all(): columns_to_drop.append(column) - filtered_df = df.loc[:, ~df.columns.isin(columns_to_drop)] + df = df.loc[:, ~df.columns.isin(columns_to_drop)] + + # Keep only first 8 columns if more are still present + if len(df.columns.values) > 8: + df = df.iloc[:, :8] - data_labels = filtered_df.columns.values - data = filtered_df.to_numpy() + data_labels = df.columns.values + data = df.to_numpy() fig = _plot_parallel_coordinates( data=data,