refactoring

water-bodies/command-line-tools/norm_diff/Dockerfile

@@ -1,21 +1,9 @@
-FROM mambaorg/micromamba
+FROM docker.io/python:3.10-slim
 
-USER root
+RUN pip install --no-cache-dir rasterio click loguru && \
+ python -c "import rasterio"
 
-ENV PATH=/opt/conda/envs/env_norm_diff/bin:$PATH
-
-RUN apt-get update -y && \
- apt-get upgrade -y && \
- apt-get install -y --no-install-recommends \
- ca-certificates \
- curl gcc build-essential && \
- apt-get clean
-
-RUN mkdir -p /app && chown -R mambauser:mambauser /app
-
-USER mambauser
+ADD app.py /app/app.py
 
-RUN micromamba create -n env_norm_diff -c conda-forge gdal click loguru && \
- micromamba clean -a
+ENTRYPOINT []
 
-ADD app.py /app/app.py

water-bodies/command-line-tools/norm_diff/app.py

@@ -1,10 +1,11 @@
 """Normalized difference"""
 import click
+import rasterio
 import numpy as np
-from osgeo import gdal
 from loguru import logger
 
-gdal.UseExceptions()
+np.seterr(divide="ignore", invalid="ignore")
+
 
 @click.command(
  short_help="Normalized difference",
@@ -16,35 +17,18 @@ def normalized_difference(rasters):
 
  logger.info(f"Processing the normalized image with {rasters[0]} and {rasters[1]}")
 
- # Allow division by zero
- np.seterr(divide="ignore", invalid="ignore")
-
- ds1 = gdal.Open(rasters[0])
- ds2 = gdal.Open(rasters[1])
-
- driver = gdal.GetDriverByName("GTiff")
-
- dst_ds = driver.Create(
- "norm_diff.tif",
- ds1.RasterXSize,
- ds1.RasterYSize,
- 1,
- gdal.GDT_Float32,
- options=["TILED=YES", "COMPRESS=DEFLATE", "INTERLEAVE=BAND"],
- )
-
- dst_ds.SetGeoTransform(ds1.GetGeoTransform())
- dst_ds.SetProjection(ds1.GetProjectionRef())
-
- array1 = ds1.GetRasterBand(1).ReadAsArray().astype(float)
- array2 = ds2.GetRasterBand(1).ReadAsArray().astype(float)
+ with rasterio.open(rasters[0]) as ds1:
+ array1 = ds1.read(1)
+ out_meta = ds1.meta.copy()
 
- norm_diff = (array1 - array2) / (array1 + array2)
+ with rasterio.open(rasters[0]) as ds2:
+ array2 = ds2.read(1)
 
- dst_ds.GetRasterBand(1).WriteArray(norm_diff)
+ out_meta.update({'dtype': "float32"})
 
- dst_ds = None
- ds1 = ds2 = None
+ with rasterio.open("norm_diff.tif", 'w', **out_meta) as dst_dataset:
+ logger.info(f"Write norm_diff.tif")
+ dst_dataset.write((array1 - array2) / (array1 + array2), indexes=1)
 
  logger.info("Done!")
 

water-bodies/command-line-tools/otsu/Dockerfile

@@ -1,20 +1,8 @@
-FROM mambaorg/micromamba
+FROM docker.io/python:3.10-slim
 
-USER root
-
-ENV PATH=/opt/conda/envs/env_otsu/bin:$PATH
-
-RUN apt-get update -y && \
- apt-get upgrade -y && \
- apt-get install -y --no-install-recommends \
- ca-certificates \
- curl gcc build-essential && \
- apt-get clean
-
-RUN mkdir -p /app && chown -R mambauser:mambauser /app
-
-USER mambauser
-
-RUN micromamba create -n env_otsu -c conda-forge gdal scikit-image click loguru
+RUN pip install --no-cache-dir rasterio scikit-image click loguru && \
+ python -c "import rasterio"
 
 ADD app.py /app/app.py
+
+ENTRYPOINT []

water-bodies/command-line-tools/otsu/app.py

@@ -1,12 +1,10 @@
 """Command line tool to apply the Otsu threshold to a raster"""
 import click
+import rasterio
 import numpy as np
-from osgeo import gdal
 from skimage.filters import threshold_otsu
 from loguru import logger
 
-gdal.UseExceptions()
-
 def threshold(data):
  """Returns the Otsu threshold of a numpy array"""
  return data > threshold_otsu(data[np.isfinite(data)])
@@ -20,30 +18,15 @@ def threshold(data):
 def otsu(raster):
  """Applies the Otsu threshold"""
 
- logger.info(f"Applying the Otsu threshold to {raster}")
- ds = gdal.Open(raster)
-
- driver = gdal.GetDriverByName("GTiff")
-
- dst_ds = driver.Create(
- "otsu.tif",
- ds.RasterXSize,
- ds.RasterYSize,
- 1,
- gdal.GDT_Byte,
- options=["TILED=YES", "COMPRESS=DEFLATE", "INTERLEAVE=BAND"],
- )
+ with rasterio.open(raster) as ds:
+ array = ds.read(1)
+ out_meta = ds.meta.copy()
 
- dst_ds.SetGeoTransform(ds.GetGeoTransform())
- dst_ds.SetProjection(ds.GetProjectionRef())
-
- array = ds.GetRasterBand(1).ReadAsArray().astype(float)
-
- dst_ds.GetRasterBand(1).WriteArray(threshold(array))
- dst_ds.GetRasterBand(1).SetNoDataValue(0)
+ logger.info(f"Applying the Otsu threshold to {raster}")
 
- dst_ds = None
- ds = None
+ with rasterio.open("otsu.tif", 'w', **out_meta) as dst_dataset:
+ logger.info(f"Write otsu.tif")
+ dst_dataset.write(threshold(array), indexes=1)
 
  logger.info("Done!")
 

water-bodies/command-line-tools/stac/Dockerfile

@@ -1,21 +1,8 @@
-FROM mambaorg/micromamba
+FROM docker.io/python:3.10-slim
 
-USER root
-
-ENV PATH=/opt/conda/envs/env_stac/bin:$PATH
-
-RUN apt-get update -y && \
- apt-get upgrade -y && \
- apt-get install -y --no-install-recommends \
- ca-certificates \
- curl gcc build-essential && \
- apt-get clean
-
-USER mambauser
-
-RUN micromamba create -n env_stac -c conda-forge pystac python=3.9 pip loguru && \
- /opt/conda/envs/env_stac/bin/pip install rio_stac
+RUN pip install --no-cache-dir pystac rio_stac loguru click && \
+ python -c "import rio_stac"
 
 ADD app.py /app/app.py
 
-WORKDIR /home/mambauser
+ENTRYPOINT []