From f2002d4d7df2ec520c197bc6eeadc277284988a2 Mon Sep 17 00:00:00 2001
From: Hans Roelofsen <hans.roelofsen@wur.nl>
Date: Thu, 2 Feb 2023 10:56:38 +0100
Subject: [PATCH] mmmm
---
COMBINE.py => src/COMBINE.py | 39 ++++---
.../attribute_table.cpython-310.pyc | Bin 0 -> 1512 bytes
src/__pycache__/combinations.cpython-310.pyc | Bin 0 -> 1963 bytes
.../source_rasters.cpython-310.pyc | Bin 0 -> 5275 bytes
src/__pycache__/target_raster.cpython-310.pyc | Bin 0 -> 3652 bytes
src/__pycache__/windows.cpython-310.pyc | Bin 0 -> 2540 bytes
attribute_table.py => src/attribute_table.py | 5 +-
combinations.py => src/combinations.py | 9 +-
source_rasters.py => src/source_rasters.py | 64 +++++++++--
target_raster.py => src/target_raster.py | 36 +++----
src/windows.py | 100 ++++++++++++++++++
windows.py | 77 --------------
12 files changed, 206 insertions(+), 124 deletions(-)
rename COMBINE.py => src/COMBINE.py (70%)
create mode 100644 src/__pycache__/attribute_table.cpython-310.pyc
create mode 100644 src/__pycache__/combinations.cpython-310.pyc
create mode 100644 src/__pycache__/source_rasters.cpython-310.pyc
create mode 100644 src/__pycache__/target_raster.cpython-310.pyc
create mode 100644 src/__pycache__/windows.cpython-310.pyc
rename attribute_table.py => src/attribute_table.py (88%)
rename combinations.py => src/combinations.py (76%)
rename source_rasters.py => src/source_rasters.py (69%)
rename target_raster.py => src/target_raster.py (86%)
create mode 100644 src/windows.py
delete mode 100644 windows.py
diff --git a/COMBINE.py b/src/COMBINE.py
similarity index 70%
rename from COMBINE.py
rename to src/COMBINE.py
index fff2493..d188f82 100644
--- a/COMBINE.py
+++ b/src/COMBINE.py
@@ -18,11 +18,10 @@ except ModuleNotFoundError:
with Flow("COMBINE") as COMBINE:
destination = Parameter("destination")
- source_rasters = Parameter('sources')
- testing = Parameter('testing')
+ source_rasters = Parameter("sources")
+ testing = Parameter("testing")
source_rasters = get_source_rasters(source_rasters)
-
rw_windows = get_rw_windows(source_rasters=source_rasters, sample=testing)
combinations_per_window = get_combinations.map(rw_windows, unmapped(source_rasters))
@@ -43,12 +42,14 @@ with Flow("COMBINE") as COMBINE:
max_value = get_max_value(combination_dict)
max_value.set_dependencies(upstream_tasks=[attribute_table_to_file])
- target_raster_written = write_target_raster_chunk.map(rw_windows,
- unmapped(destination),
- unmapped(max_value),
- unmapped(combination_dict),
- unmapped(source_rasters))
- target_raster_written.set_dependencies(upstream_tasks=[combination_dict])
+ target_raster_written = write_target_raster_chunk.map(
+ rw_windows,
+ unmapped(destination),
+ unmapped(max_value),
+ unmapped(combination_dict),
+ unmapped(source_rasters),
+ )
+ target_raster_written.set_dependencies(upstream_tasks=[combination_dict, max_value])
if __name__ == "__main__":
@@ -61,7 +62,7 @@ if __name__ == "__main__":
Path to destination *.tif file
source_raster01: Path to first source raster
source_raster02: Path to second source raster
- ...: path to subsequent source rasters
+ ...: path to subsequent source rasters
Returns
-------
@@ -69,15 +70,21 @@ if __name__ == "__main__":
import argparse
- parser = argparse.ArgumentParser(prog='Open Source COMBINE alternative. By: Hans Roelofsen')
+ parser = argparse.ArgumentParser(
+ prog="Open Source COMBINE alternative. By: Hans Roelofsen"
+ )
parser.add_argument("destination", type=str, help="path to destination *.tif file")
- parser.add_argument("sources", type=str, help="path to destination source files", nargs='+')
- parser.add_argument('--test', action='store_true', help='test run with 20 windows')
+ parser.add_argument(
+ "sources", type=str, help="path to destination source files", nargs="+"
+ )
+ parser.add_argument("--test", action="store_true", help="test run with 20 windows")
args = parser.parse_args()
print("\n\nStarting COMBINE\n\n")
COMBINE.executor = LocalDaskExecutor()
- COMBINE.run(parameters=dict(destination=args.destination,
- sources=args.sources,
- testing=args.test))
+ COMBINE.run(
+ parameters=dict(
+ destination=args.destination, sources=args.sources, testing=args.test
+ )
+ )
diff --git a/src/__pycache__/attribute_table.cpython-310.pyc b/src/__pycache__/attribute_table.cpython-310.pyc
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diff --git a/src/__pycache__/target_raster.cpython-310.pyc b/src/__pycache__/target_raster.cpython-310.pyc
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diff --git a/attribute_table.py b/src/attribute_table.py
similarity index 88%
rename from attribute_table.py
rename to src/attribute_table.py
index 4723dcb..d85d74e 100644
--- a/attribute_table.py
+++ b/src/attribute_table.py
@@ -29,7 +29,9 @@ def make_attribute_table(
index=[v for v in combi_dict.values()],
)
tab.to_clipboard(excel=True)
- tab.to_csv(f"{os.path.splitext(destination)[0]}.csv", index=True, index_label="Value")
+ tab.to_csv(
+ f"{os.path.splitext(destination)[0]}.csv", index=True, index_label="Value"
+ )
@task
@@ -40,4 +42,3 @@ def get_max_value(combi_dict: dict) -> int:
:return:
"""
return len(combi_dict)
-
diff --git a/combinations.py b/src/combinations.py
similarity index 76%
rename from combinations.py
rename to src/combinations.py
index eefd3b0..7ccdde8 100644
--- a/combinations.py
+++ b/src/combinations.py
@@ -11,6 +11,7 @@ except ModuleNotFoundError:
from src.windows import CombineWindow
from src.source_rasters import SourceRasters
+
@task
def get_combinations(
read_window: CombineWindow,
@@ -25,7 +26,7 @@ def get_combinations(
logger = prefect.context.get("logger")
logger.info(
- f"Finding unique combinations in window {read_window.nr:004}"
+ f"Finding unique combinations in window {read_window.nr} out of {read_window.total}"
)
arrays = [
@@ -34,7 +35,9 @@ def get_combinations(
]
unique_combinations = set(list(zip(*arrays)))
- logger.info(f'lowest value in window {read_window.nr:004}: {np.min(np.array(unique_combinations))}')
+ logger.info(
+ f"lowest value in window {read_window.nr:004}: {np.min(np.array(unique_combinations))}"
+ )
read_window.set_unique_combinations(uc=unique_combinations)
@@ -46,5 +49,3 @@ def make_combination_dict(read_windows: list) -> dict:
return {combi: n for n, combi in enumerate(all_combinations, start=1)}
-src = r'w:\PROJECTS\Nvk_bdb\b_HDB\b_scenarios\2_regionaal\brondata\Regionaal_Geworteld_Subsector_rel_Y2050\25m\Regionaal_Geworteld_Subsector_rel_Y2050.tif'
-arr = rio.open(src, window=Window(0, 0, 100, 150)).read(1).flatten()
\ No newline at end of file
diff --git a/source_rasters.py b/src/source_rasters.py
similarity index 69%
rename from source_rasters.py
rename to src/source_rasters.py
index 27371c5..4526d55 100644
--- a/source_rasters.py
+++ b/src/source_rasters.py
@@ -7,14 +7,16 @@ from abc import ABC, abstractmethod
from prefect.engine import signals
import pandas as pd
-class SourceRasters:
+class SourceRasters:
def __init__(self, source_list: list):
self.source_list = [s for s in source_list]
- self.procedures = [VerifyAsGeospatialRaster(source_list=self.source_list),
- VerifyMatchingBounds(source_list=self.source_list)]
- self.geospatial_profile = getattr(rio.open(self.source_list[0]), 'profile')
+ self.procedures = [
+ VerifyAsGeospatialRaster(source_list=self.source_list),
+ VerifyMatchingBounds(source_list=self.source_list),
+ VerifyMatchingResolution(source_list=self.source_list),
+ ]
def verify_input(self):
for procedure in self.procedures:
@@ -39,7 +41,7 @@ class VerificationProcedure(ABC):
pass
-class VerifyAsGeospatialRaster(ABC):
+class VerifyAsGeospatialRaster(VerificationProcedure):
def __init__(self, source_list):
self.rasters = source_list
self.status = True
@@ -53,10 +55,10 @@ class VerifyAsGeospatialRaster(ABC):
logger.info(message)
else:
logger.error(message)
- self.status=False
+ self.status = False
-class VerifyMatchingBounds(ABC):
+class VerifyMatchingBounds(VerificationProcedure):
def __init__(self, source_list):
self.rasters = source_list
self.status = True
@@ -72,6 +74,27 @@ class VerifyMatchingBounds(ABC):
self.status = False
+class VerifyMatchingResolution(VerificationProcedure):
+
+ def __init__(self, source_list):
+ self.rasters = source_list
+ self.status = True
+
+ def execute(self):
+ logger = prefect.context.get("logger")
+
+ reference_resolution = getattr(getattr(rio.open(self.rasters[0]), 'transform'), 'a')
+ resolutions = []
+ messages = []
+ for raster in self.rasters:
+ has_resolution, msg = raster_has_resolution(raster, reference_resolution)
+ resolutions.append(has_resolution)
+ messages.append(msg)
+
+ if not all(resolutions):
+ logger.error('Rasters have unequal resolutions')
+ self.status = False
+
def is_geospatial_raster(file_path: str, msg=False) -> (bool, str):
"""
Is a file a gdal compatible geospatial raster?
@@ -161,6 +184,33 @@ def rasters_have_identical_bounds(rasters: list) -> (bool, str):
return out, msg
+def raster_has_resolution(file_path: str, target_resolution) -> (bool, str):
+ """
+ Check if a raster has target resolution
+ Parameters
+ ----------
+ file_path: target file path
+ target_resolution: expected resolution of the raster
+
+ Returns
+ -------
+
+ """
+
+ if is_geospatial_raster(file_path):
+ raster_resolution = getattr(rio.open(file_path), "res")[0]
+ has_target_resolution = raster_resolution == target_resolution
+ if has_target_resolution:
+ out = True
+ msg = f"{os.path.basename(file_path)} has target resolution."
+ else:
+ out = False
+ msg = f"{os.path.basename(file_path)} resolution {raster_resolution}m does not meet target resolution {target_resolution}."
+ return out, msg
+ else:
+ return False, f"{os.path.basename} is not a geospatial raster"
+
+
@task
def get_source_rasters(source_list: list) -> SourceRasters:
diff --git a/target_raster.py b/src/target_raster.py
similarity index 86%
rename from target_raster.py
rename to src/target_raster.py
index 2c37b26..7431809 100644
--- a/target_raster.py
+++ b/src/target_raster.py
@@ -12,31 +12,30 @@ except ModuleNotFoundError:
from src.source_rasters import SourceRasters
from src.windows import CombineWindow
+
@task
def write_target_raster_chunk(
- rw_window: CombineWindow,
- destination: str,
- max_value: int,
- combi_dict: dict,
- source_rasters: SourceRasters
+ rw_window: CombineWindow,
+ destination: str,
+ max_value: int,
+ combi_dict: dict,
+ source_rasters: SourceRasters,
):
- """
- Write target raster for a single RW Window
- """
+
logger = prefect.context.get("logger")
with rio.open(
- destination,
- "w",
- driver="GTiff",
- width=rw_window.rio_window.width,
- height=rw_window.rio_window.height,
- count=1,
- dtype=rio.dtypes.get_minimum_dtype([0, max_value]),
- transform=source_rasters.geospatial_profile["transform"],
- compress="LZW",
- crs=source_rasters.geospatial_profile["crs"],
+ f"{os.path.splitext(destination)[0]}_{rw_window.nr:05}.tif",
+ "w",
+ driver="GTiff",
+ width=rw_window.rio_window.width,
+ height=rw_window.rio_window.height,
+ count=1,
+ dtype=rio.dtypes.get_minimum_dtype([0, max_value]),
+ transform=rw_window.transform,
+ compress="LZW",
+ crs=source_rasters.geospatial_profile["crs"],
) as dest:
dest.update_tags(
creation_date=datetime.datetime.now().strftime("%d-%b-%Y_%H:%M:%S"),
@@ -73,6 +72,7 @@ def write_target_raster_chunk(
indexes=1,
)
+ logger.info(f"Writing chunk {rw_window.nr} out of {rw_window.total} to file.")
@task
diff --git a/src/windows.py b/src/windows.py
new file mode 100644
index 0000000..2764858
--- /dev/null
+++ b/src/windows.py
@@ -0,0 +1,100 @@
+import random
+import prefect
+import affine
+import numpy as np
+import rasterio as rio
+from prefect import task
+from rasterio.windows import Window
+
+try:
+ from source_rasters import SourceRasters
+except ModuleNotFoundError:
+ from src.source_rasters import SourceRasters
+
+
+class CombineWindow:
+ """
+ A single read/write window and its associated unique combinations
+ """
+
+ def __init__(
+ self,
+ row_start: int,
+ row_stop: int,
+ column_start: int,
+ column_stop: int,
+ nr: int,
+ totals: int,
+ top_left_x: int,
+ top_left_y: int,
+ resolution: int,
+ ):
+ self.rio_window = Window.from_slices(
+ (row_start, row_stop), (column_start, column_stop)
+ )
+ self.unique_combinations = None
+ self.nr = nr
+ self.total = totals
+
+ self.transform = affine.Affine(
+ a=resolution, b=0, c=top_left_x, d=0, e=resolution * -1, f=top_left_y
+ )
+
+ def set_unique_combinations(self, uc: set):
+ self.unique_combinations = uc
+
+ def get_unique_combinations(self):
+ return self.unique_combinations
+
+
+@task
+def get_rw_windows(
+ source_rasters: SourceRasters,
+ window_height: int = 2000,
+ window_width: int = 2000,
+ sample: bool = False,
+) -> list:
+ """ """
+
+ logger = prefect.context.get("logger")
+
+ row_starts = range(
+ 0, (source_rasters.geospatial_profile["height"] - window_height), window_height
+ )
+ column_starts = range(
+ 0, (source_rasters.geospatial_profile["width"] - window_width), window_width
+ )
+ windows = []
+ n = 0
+ total_windows = np.multiply(len(row_starts), len(column_starts))
+ for row_start in row_starts:
+ for column_start in column_starts:
+ windows.append(
+ CombineWindow(
+ row_start=row_start,
+ row_stop=row_start + window_height,
+ column_start=column_start,
+ column_stop=column_start + window_width,
+ nr=n,
+ totals=total_windows,
+ top_left_x=(
+ getattr(rio.open(source_rasters.source_list[0]), "transform")
+ * (column_start, row_start)
+ )[0],
+ top_left_y=(
+ getattr(rio.open(source_rasters.source_list[0]), "transform")
+ * (column_start, row_start)
+ )[1],
+ resolution=getattr(
+ getattr(rio.open(source_rasters.source_list[0]), "transform"),
+ "a",
+ ),
+ )
+ )
+ n += 1
+ logger.info(f"Created {n} windows of size {window_height}X{window_width}")
+
+ if sample:
+ return random.sample(windows, 20)
+ else:
+ return windows
diff --git a/windows.py b/windows.py
deleted file mode 100644
index 973c26f..0000000
--- a/windows.py
+++ /dev/null
@@ -1,77 +0,0 @@
-import random
-import prefect
-import affine
-import rasterio as rio
-from prefect import task
-from rasterio.windows import Window
-
-try:
- from source_rasters import SourceRasters
-except ModuleNotFoundError:
- from src.source_rasters import SourceRasters
-
-
-class CombineWindow:
- """
- A single read/write window and its associated unique combinations
- """
-
- def __init__(self, row_start: int, row_stop: int, column_start: int, column_stop: int, nr: int,
- top_left_x: int, top_left_y: int, resolution: int):
- self.rio_window = Window.from_slices(
- (row_start, row_stop), (column_start, column_stop)
- )
- self.unique_combinations = None
- self.nr = nr
- self.transform = affine.Affine(a=resolution,
- b=0,
- c=top_left_x,
- d=0,
- e=resolution*-1,
- f=top_left_y)
-
-
- def set_unique_combinations(self, uc: set):
- self.unique_combinations = uc
-
- def get_unique_combinations(self):
- return self.unique_combinations
-
-
-@task
-def get_rw_windows(
- source_rasters: SourceRasters,
- window_rows: int = 2000,
- window_columns: int = 2000,
- sample: bool = False,
-) -> list:
-
- logger = prefect.context.get("logger")
-
- row_starts = range(0, (source_rasters.geospatial_profile['height'] - window_rows), window_rows)
- column_starts = range(0, (source_rasters.geospatial_profile['width'] - window_columns), window_columns)
- windows = []
- n = 0
- for row_start in row_starts:
- for column_start in column_starts:
- windows.append(
- CombineWindow(
- row_start=row_start,
- row_stop=row_start + window_rows,
- column_start=column_start,
- column_stop=column_start + window_columns,
- nr=n,
- top_left_x=(getattr(rio.open(source_rasters.src_list[0]), 'transform') * (column_start, row_start))[0],
- top_left_y=(getattr(rio.open(source_rasters.src_list[0]), 'transform') * (column_start, row_start))[1],
- resolution=getattr(getattr(rio.open(source_rasters.src_list[0]), 'transform'), 'a'),
- )
- )
- n += 1
- logger.info(
- f"Created {n} windows of size {window_rows}X{window_columns}"
- )
-
- if sample:
- return random.sample(windows, 20)
- else:
- return windows
--
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