From 05f39785e27045481131daab95af08967e210622 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 8 Apr 2025 12:56:54 +0200
Subject: [PATCH 01/40] use exactextract

---
 cropclassification/preprocess/_timeseries_calc_openeo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index 11439b3d..fe900fe5 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -91,6 +91,6 @@ def calculate_periodic_timeseries(
         rasters_bands=images_bands,
         output_dir=timeseries_periodic_dir,
         stats=["count", "mean", "median", "std", "min", "max"],
-        engine="pyqgis",
+        engine="exactextract",
         nb_parallel=nb_parallel,
     )

From fd1592f05714b2a81913c0e0783f9f2d44091b5b Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 8 Apr 2025 14:40:54 +0200
Subject: [PATCH 02/40] Test

---
 cropclassification/preprocess/_timeseries_calc_openeo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index fe900fe5..6aa18cd9 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -91,6 +91,6 @@ def calculate_periodic_timeseries(
         rasters_bands=images_bands,
         output_dir=timeseries_periodic_dir,
         stats=["count", "mean", "median", "std", "min", "max"],
-        engine="exactextract",
+        engine="exactextract",  # "pyqgis"
         nb_parallel=nb_parallel,
     )

From 5b0d6eda7a83e569f5ec083ac8bb35c77abea259 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 10 Apr 2025 12:51:51 +0200
Subject: [PATCH 03/40] use exactextract for zonal stats

---
 .../preprocess/_timeseries_calc_openeo.py     |  2 +-
 cropclassification/preprocess/timeseries.py   |  2 +-
 .../_zonal_stats_bulk_exactextract.py         | 40 ++++++++++++++-----
 tests/test_zonal_stats_bulk.py                | 16 ++------
 4 files changed, 34 insertions(+), 26 deletions(-)

diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index 6aa18cd9..fe900fe5 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -91,6 +91,6 @@ def calculate_periodic_timeseries(
         rasters_bands=images_bands,
         output_dir=timeseries_periodic_dir,
         stats=["count", "mean", "median", "std", "min", "max"],
-        engine="exactextract",  # "pyqgis"
+        engine="exactextract",
         nb_parallel=nb_parallel,
     )
diff --git a/cropclassification/preprocess/timeseries.py b/cropclassification/preprocess/timeseries.py
index 7441fe8b..171ac0f0 100644
--- a/cropclassification/preprocess/timeseries.py
+++ b/cropclassification/preprocess/timeseries.py
@@ -161,7 +161,7 @@ def collect_and_prepare_timeseries_data(
             continue
 
         # Determine the columns to be read from the file and which to rename.
-        info = gfo.get_layerinfo(curr_path, raise_on_nogeom=False)
+        info = gfo.get_layerinfo(curr_path, raise_on_nogeom=False, layer="info")
         columns = []
         columns_to_rename = {}
         for column in info.columns:
diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 2ee98f90..cb6a0e22 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -261,6 +261,17 @@ def zonal_stats_band_tofile(
                 output_path.unlink(missing_ok=True)
         return output_paths
 
+    # In stats replace 'std' with 'stdev' for exactextract
+    stats = [stat.replace("std", "stdev") for stat in stats]
+
+    # Add the operational arguments to the stats
+    min_coverage_frac = 0.8
+    coverage_weight = "none"
+    operation_arguments = (
+        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
+    )
+    stats = [stat + operation_arguments for stat in stats]
+
     stats_df = zonal_stats_band(
         vector_path=vector_path,
         raster_path=raster_path,
@@ -274,17 +285,24 @@ def zonal_stats_band_tofile(
     for band in bands:
         index = raster_info.bands[band].band_index
         band_columns = include_cols.copy()
-        band_columns.extend(
-            [f"band_{index}_{stat}" for stat in [stat.split("(")[0] for stat in stats]]
-        )
-        band_stats_df = stats_df[band_columns].copy()
-        band_stats_df.rename(
-            columns={
-                f"band_{index}_{stat}": stat
-                for stat in [stat.split("(")[0] for stat in stats]
-            },
-            inplace=True,
-        )
+        if len(bands) == 1:
+            band_columns.extend(stats)
+            band_stats_df = stats_df[band_columns].copy()
+        else:
+            band_columns.extend(
+                [
+                    f"band_{index}_{stat}"
+                    for stat in [stat.split("(")[0] for stat in stats]
+                ]
+            )
+            band_stats_df = stats_df[band_columns].copy()
+            band_stats_df.rename(
+                columns={
+                    f"band_{index}_{stat}": stat
+                    for stat in [stat.split("(")[0] for stat in stats]
+                },
+                inplace=True,
+            )
         # Add fid column to the beginning of the dataframe
         band_stats_df.insert(0, "fid", range(len(band_stats_df)))
 
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 6276a859..483eac5b 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -11,18 +11,8 @@
 
 
 @pytest.mark.parametrize(
-    "engine, stats",
-    [
-        ("pyqgis", ["mean", "count"]),
-        ("rasterstats", ["mean", "count"]),
-        (
-            "exactextract",
-            [
-                "mean(min_coverage_frac=0.5,coverage_weight=none)",
-                "count(min_coverage_frac=0.5,coverage_weight=none)",
-            ],
-        ),
-    ],
+    "engine",
+    ["pyqgis", "rasterstats", "exactextract"],
 )
 def test_zonal_stats_bulk(tmp_path, engine, stats):
     if engine == "pyqgis" and not HAS_QGIS:
@@ -58,7 +48,7 @@ def test_zonal_stats_bulk(tmp_path, engine, stats):
         id_column="UID",
         rasters_bands=images_bands,
         output_dir=tmp_path,
-        stats=stats,
+        stats=["mean", "count", "std"],
         engine=engine,
     )
 

From 89e7e6612c53a708824c5b3e8ac48d9ed7684731 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 10 Apr 2025 12:53:02 +0200
Subject: [PATCH 04/40] buffer = 0

---
 cropclassification/general.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index 2ba62990..563bce67 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -139,7 +139,7 @@ on_missing_image = calculate_raise
 [timeseries]
 
 # Negative buffer to apply to input parcels to account for mixels.
-buffer = 5
+buffer = 0
 
 # The maximum percentage cloudcover an (S2) image can have to be used.
 max_cloudcover_pct = 15

From ee6156a190f62459ea53c09ecaf77475d8db5e44 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 10 Apr 2025 12:57:59 +0200
Subject: [PATCH 05/40] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 65d27183..9a754e57 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -44,6 +44,7 @@
 - Add support to generate vvdvh index (#151)
 - Add support to generate sarrgb images and apply enhanced lee despeckling (#157)
 - General small improvements, e.g. save randomforest models compressed,.. (#144)
+- Use Exactextract for zonalstats calculation (#181)
 
 ### Bugs fixed
 

From 46345737c241c70147f9961636415d2b988a9ead Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 10 Apr 2025 13:22:41 +0200
Subject: [PATCH 06/40] removed stats as parameter

---
 tests/test_zonal_stats_bulk.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 483eac5b..b9297a01 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -14,7 +14,7 @@
     "engine",
     ["pyqgis", "rasterstats", "exactextract"],
 )
-def test_zonal_stats_bulk(tmp_path, engine, stats):
+def test_zonal_stats_bulk(tmp_path, engine):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
 

From 703cbe3e74468c6cf52df5476014a773d29310cc Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Wed, 7 May 2025 09:50:18 +0200
Subject: [PATCH 07/40] changed example

---
 .../_inputdata/Prc_BEFL_2023_2023-07-24.gpkg  | Bin 122880 -> 122880 bytes
 tests/test_end2end.py                         |   2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)

diff --git a/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg b/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg
index 610d5b0503354498fd200aee8a9be4dcb0c5a56d..b792eebc213c0cde89d13be4dc94dc4725cc7b01 100644
GIT binary patch
delta 644
zcmZoTz}|3xeS$Qj>O>i5R#gVQw3i!GQuRelbq#>XJjB4<%GlJ()I`tB)S&sU{`9;0
zjJj;RT3iwwf42)5Fn(iV4d`&5VLzSQm{CENZ%x(&&BM%&31;Gwhkmj-f~A0b@r>-(
zE4O<XGb%IjqNv$kValk%%$P8Jp#@_MXOmdh@o;g5rn2c5nHi<M9#)C03*W`;_+<Om
z$b!Ahj?<Dp-VyrD=E!w@alzj&Y>te~3=9m6K+FNev8S3gd;%(lDS~OLIV<3%KRw%$
zF_;fk$@VjrjAo213=B*f)7h*U3#`l{f28f+%<Q<%{b5xI(4@}y0YUCS>wtzcNB}(p
zw~hxW08=cYE&Y4e^bOXGlVzoOt{=Rx1)&dBNrDaIDb6O>uH!-C49#KFxw#pot@f_`
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kFrP8i!+iN0i1<}~57|FC9&(a@r*q6<RNL-0hjEuP02aaEKmY&$

delta 458
zcmZoTz}|3xeS$Qj;zSu|Rz(KAv{xHbQuRelbPY^(4UIz#jjT+}tPITbj4X|s@9Iy#
ztIw#*#vQ~Z!SQyxfC1w-rtQwYjC+~3A2wyY%fuKkeW3+o%ydszMiK9aRU+%ccQHFM
z071uIW=E$R$4`9y#OBC#eR09xFKmvC%s>f7Am#*OXSwoL{@n;gp2rlm>VTS9t$#N0
zeV$&!$rv>K9|xlVAF9IbXDk`b7+HAMFa%6zvt}%?x^>C=^OViZj_ceXR)qj9KlO5b
zy~1ZUup=aXB3a4<v=pZJpO8^b#q<r<jFV-rgzvOov<0CLRY`&k<Eiahyo@}IEI_B9
znr_9%Xtlk>j<L^CXcq$)|2zi%PyDa>pYY%1zs7%lyGR4$GJaG3pA4eR44epx56ENg
zUZoGBx_+sEspH`gDi}fqZGYd-c%NHn@g)!0Im<j`FD>yfpULcDe&WD%hdGRLTvzoy
XWdG!N$Vs<MSD3@7wq0)y<0WSR7o3_e

diff --git a/tests/test_end2end.py b/tests/test_end2end.py
index 2e89a95e..533e0383 100644
--- a/tests/test_end2end.py
+++ b/tests/test_end2end.py
@@ -46,7 +46,7 @@ def test_task_calc_marker(tmp_path, balancing_strategy, cross_pred_models):
     today_str = datetime.now().strftime("%Y-%m-%d")
     run_dir = markers_dir / f"2024_CROPGROUP/Run_{today_str}_001"
     assert run_dir.exists()
-    base_stem = "Prc_BEFL_2023_2023-07-24_bufm5_weekly_predict_all"
+    base_stem = "Prc_BEFL_2023_2023-07-24_bufm0_weekly_predict_all"
     assert (run_dir / f"{base_stem}.gpkg").exists()
     assert (run_dir / f"{base_stem}.sqlite_accuracy_report.html").exists()
     details_gpgk_path = (

From 8062e4aee47a70d38d1bd0a408004bb63271eb2d Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Wed, 7 May 2025 11:37:11 +0200
Subject: [PATCH 08/40] add force parameter to zonal_stats_band_tofile

---
 .../util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py      | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index cb6a0e22..851a8d31 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -136,6 +136,7 @@ def zonal_stats(
                 tmp_dir=tmp_dir,
                 include_cols=columns,
                 output_paths=output_paths,
+                force=force,
             )
             calc_queue[future] = {
                 "vector_path": vector_path,

From 6f9ce87cfef6a9b079bd93a85f3f4e79d8f668a9 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Wed, 7 May 2025 12:29:32 +0200
Subject: [PATCH 09/40] add force parameter to test

---
 debug.log                      | 9 +++++++++
 tests/test_zonal_stats_bulk.py | 9 ++++-----
 2 files changed, 13 insertions(+), 5 deletions(-)
 create mode 100644 debug.log

diff --git a/debug.log b/debug.log
new file mode 100644
index 00000000..11be91b6
--- /dev/null
+++ b/debug.log
@@ -0,0 +1,9 @@
+[0507/122314.187:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122315.996:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122323.090:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122334.963:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122456.210:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122457.711:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122502.946:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122514.849:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
+[0507/122823.970:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index b9297a01..54529fb4 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -10,11 +10,9 @@
 from tests.test_helper import SampleData
 
 
-@pytest.mark.parametrize(
-    "engine",
-    ["pyqgis", "rasterstats", "exactextract"],
-)
-def test_zonal_stats_bulk(tmp_path, engine):
+@pytest.mark.parametrize("engine", ["pyqgis", "rasterstats", "exactextract"])
+@pytest.mark.parametrize("force", [True, False])
+def test_zonal_stats_bulk(tmp_path, engine, force):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
 
@@ -50,6 +48,7 @@ def test_zonal_stats_bulk(tmp_path, engine):
         output_dir=tmp_path,
         stats=["mean", "count", "std"],
         engine=engine,
+        force=force,
     )
 
     result_paths = list(tmp_path.glob("*.sqlite"))

From 8e717276829bc36914c70f8c37c7927b1a48b028 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Wed, 7 May 2025 13:22:30 +0200
Subject: [PATCH 10/40] refactor

---
 .../util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 851a8d31..023107bb 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -257,10 +257,10 @@ def zonal_stats_band_tofile(
 ) -> dict[str, Path]:
     # Init
     if all(output_path.exists() for output_path in output_paths.values()):
-        if force:
-            for output_path in output_paths.values():
-                output_path.unlink(missing_ok=True)
         return output_paths
+    if force:
+        for output_path in output_paths.values():
+            output_path.unlink(missing_ok=True)
 
     # In stats replace 'std' with 'stdev' for exactextract
     stats = [stat.replace("std", "stdev") for stat in stats]

From 2f17bd25da3e87ef19fb765227b8453fc9dfe9d4 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Wed, 7 May 2025 16:00:08 +0200
Subject: [PATCH 11/40] refactor

---
 .../zonal_stats_bulk/_zonal_stats_bulk_exactextract.py     | 7 -------
 tests/test_zonal_stats_bulk.py                             | 4 +---
 2 files changed, 1 insertion(+), 10 deletions(-)

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 023107bb..d78d973c 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -255,13 +255,6 @@ def zonal_stats_band_tofile(
     include_cols: list[str],
     force: bool = False,
 ) -> dict[str, Path]:
-    # Init
-    if all(output_path.exists() for output_path in output_paths.values()):
-        return output_paths
-    if force:
-        for output_path in output_paths.values():
-            output_path.unlink(missing_ok=True)
-
     # In stats replace 'std' with 'stdev' for exactextract
     stats = [stat.replace("std", "stdev") for stat in stats]
 
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 54529fb4..01345452 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -11,8 +11,7 @@
 
 
 @pytest.mark.parametrize("engine", ["pyqgis", "rasterstats", "exactextract"])
-@pytest.mark.parametrize("force", [True, False])
-def test_zonal_stats_bulk(tmp_path, engine, force):
+def test_zonal_stats_bulk(tmp_path, engine):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
 
@@ -48,7 +47,6 @@ def test_zonal_stats_bulk(tmp_path, engine, force):
         output_dir=tmp_path,
         stats=["mean", "count", "std"],
         engine=engine,
-        force=force,
     )
 
     result_paths = list(tmp_path.glob("*.sqlite"))

From e38cfdeed8350d10b7bca451619433532af43c23 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 8 May 2025 16:08:16 +0200
Subject: [PATCH 12/40] refactor + add new test

---
 .../_zonal_stats_bulk_exactextract.py         |  20 ++++++-----
 ...eekly_2024-03-04_2024-03-10_vvdvh_last.tif | Bin 0 -> 10971 bytes
 ..._2024-03-04_2024-03-10_vvdvh_last.tif.json |  31 ++++++++++++++++++
 ...eekly_2024-03-11_2024-03-17_vvdvh_last.tif | Bin 0 -> 10986 bytes
 ..._2024-03-11_2024-03-17_vvdvh_last.tif.json |  31 ++++++++++++++++++
 ..._2024-03-04_2024-03-10_vvdvh_last.tif.json |  31 ++++++++++++++++++
 ..._2024-03-11_2024-03-17_vvdvh_last.tif.json |  31 ++++++++++++++++++
 tests/test_helper.py                          |  10 ++++++
 tests/test_zonal_stats_bulk.py                |  23 ++++++++++---
 9 files changed, 163 insertions(+), 14 deletions(-)
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
 create mode 100644 markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index d78d973c..3183a08c 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -227,6 +227,14 @@ def zonal_stats_band(
         dst_dir=tmp_dir,
     )
 
+    # Add the operational arguments to the stats
+    min_coverage_frac = 0.8
+    coverage_weight = "none"
+    operation_arguments = (
+        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
+    )
+    stats = [stat + operation_arguments for stat in stats]
+
     try:
         import exactextract
 
@@ -258,14 +266,6 @@ def zonal_stats_band_tofile(
     # In stats replace 'std' with 'stdev' for exactextract
     stats = [stat.replace("std", "stdev") for stat in stats]
 
-    # Add the operational arguments to the stats
-    min_coverage_frac = 0.8
-    coverage_weight = "none"
-    operation_arguments = (
-        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
-    )
-    stats = [stat + operation_arguments for stat in stats]
-
     stats_df = zonal_stats_band(
         vector_path=vector_path,
         raster_path=raster_path,
@@ -280,7 +280,9 @@ def zonal_stats_band_tofile(
         index = raster_info.bands[band].band_index
         band_columns = include_cols.copy()
         if len(bands) == 1:
-            band_columns.extend(stats)
+            band_columns.extend(
+                [f"{stat}" for stat in [stat.split("(")[0] for stat in stats]]
+            )
             band_stats_df = stats_df[band_columns].copy()
         else:
             band_columns.extend(
diff --git a/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif
new file mode 100644
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diff --git a/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
new file mode 100644
index 00000000..632a425a
--- /dev/null
+++ b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
@@ -0,0 +1,31 @@
+{
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+    "collection": null,
+    "index_type": "vvdvh",
+    "max_cloud_cover": null,
+    "image_source": "local",
+    "base_imageprofile": "s1-grd-sigma0-asc-weekly",
+    "pixel_type": "FLOAT32",
+    "satellite": "s1",
+    "roi_bounds": [
+        161400.0,
+        188000.0,
+        161900.0,
+        188500.0
+    ],
+    "roi_crs": "31370",
+    "start_date": "2024-03-04",
+    "end_date_incl": "2024-03-10",
+    "end_date": "2024-03-11",
+    "period_name": "weekly",
+    "weeks": [
+        10
+    ],
+    "bands": [
+        "vvdvh"
+    ],
+    "time_reducer": "last",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-5/test_task_calc_periodic_mosaic0/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif",
+    "job_options": null,
+    "process_options": null
+}
\ No newline at end of file
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zmRS@6ttHL%4(`d<Cdwt<5MlK}4cv~elE6ZG>B+a8;xZHF_HZb0b?spgw8a0421G{{
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literal 0
HcmV?d00001

diff --git a/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json
new file mode 100644
index 00000000..9087840d
--- /dev/null
+++ b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json
@@ -0,0 +1,31 @@
+{
+    "imageprofile": "s1-grd-sigma0-vvdvh-asc-weekly",
+    "collection": null,
+    "index_type": "vvdvh",
+    "max_cloud_cover": null,
+    "image_source": "local",
+    "base_imageprofile": "s1-grd-sigma0-asc-weekly",
+    "pixel_type": "FLOAT32",
+    "satellite": "s1",
+    "roi_bounds": [
+        161400.0,
+        188000.0,
+        161900.0,
+        188500.0
+    ],
+    "roi_crs": "31370",
+    "start_date": "2024-03-11",
+    "end_date_incl": "2024-03-17",
+    "end_date": "2024-03-18",
+    "period_name": "weekly",
+    "weeks": [
+        11
+    ],
+    "bands": [
+        "vvdvh"
+    ],
+    "time_reducer": "last",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-5/test_task_calc_periodic_mosaic0/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-asc-weekly/s1-grd-sigma0-vvdvh-asc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif",
+    "job_options": null,
+    "process_options": null
+}
\ No newline at end of file
diff --git a/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
new file mode 100644
index 00000000..3f0edb06
--- /dev/null
+++ b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.json
@@ -0,0 +1,31 @@
+{
+    "imageprofile": "s1-grd-sigma0-vvdvh-desc-weekly",
+    "collection": null,
+    "index_type": "vvvh",
+    "max_cloud_cover": null,
+    "image_source": "local",
+    "base_imageprofile": "s1-grd-sigma0-desc-weekly",
+    "pixel_type": "FLOAT32",
+    "satellite": "s1",
+    "roi_bounds": [
+        161400.0,
+        188000.0,
+        161900.0,
+        188500.0
+    ],
+    "roi_crs": "31370",
+    "start_date": "2024-03-04",
+    "end_date_incl": "2024-03-10",
+    "end_date": "2024-03-11",
+    "period_name": "weekly",
+    "weeks": [
+        10
+    ],
+    "bands": [
+        "vvdvh"
+    ],
+    "time_reducer": "last",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-5/test_task_calc_periodic_mosaic0/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif",
+    "job_options": null,
+    "process_options": null
+}
\ No newline at end of file
diff --git a/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json
new file mode 100644
index 00000000..1422516f
--- /dev/null
+++ b/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif.json
@@ -0,0 +1,31 @@
+{
+    "imageprofile": "s1-grd-sigma0-vvdvh-desc-weekly",
+    "collection": null,
+    "index_type": "vvvh",
+    "max_cloud_cover": null,
+    "image_source": "local",
+    "base_imageprofile": "s1-grd-sigma0-desc-weekly",
+    "pixel_type": "FLOAT32",
+    "satellite": "s1",
+    "roi_bounds": [
+        161400.0,
+        188000.0,
+        161900.0,
+        188500.0
+    ],
+    "roi_crs": "31370",
+    "start_date": "2024-03-11",
+    "end_date_incl": "2024-03-17",
+    "end_date": "2024-03-18",
+    "period_name": "weekly",
+    "weeks": [
+        11
+    ],
+    "bands": [
+        "vvdvh"
+    ],
+    "time_reducer": "last",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-5/test_task_calc_periodic_mosaic0/markers/_images_periodic/roi_test/s1-grd-sigma0-vvdvh-desc-weekly/s1-grd-sigma0-vvdvh-desc-weekly_2024-03-11_2024-03-17_vvdvh_last.tif",
+    "job_options": null,
+    "process_options": null
+}
\ No newline at end of file
diff --git a/tests/test_helper.py b/tests/test_helper.py
index 10a1eaa1..973e25b5 100644
--- a/tests/test_helper.py
+++ b/tests/test_helper.py
@@ -37,6 +37,16 @@ class SampleData:
         / "s2-agri-weekly"
         / "s2-agri-weekly_2024-03-04_2024-03-10_B02-B03-B04-B08-B11-B12_best.tif"
     )
+    image_s1_grd_vvdvh_asc_weekly_path = (
+        image_roi_dir
+        / "s1-grd-sigma0-vvdvh-asc-weekly"
+        / "s1-grd-sigma0-vvdvh-asc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.tif"
+    )
+    image_s1_grd_vvdvh_desc_weekly_path = (
+        image_roi_dir
+        / "s1-grd-sigma0-vvdvh-desc-weekly"
+        / "s1-grd-sigma0-vvdvh-desc-weekly_2024-03-04_2024-03-10_vvdvh_last.tif.tif"
+    )
 
     start_date = datetime(2024, 3, 4)
     end_date = datetime(2024, 3, 11)
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 01345452..31742311 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -11,7 +11,8 @@
 
 
 @pytest.mark.parametrize("engine", ["pyqgis", "rasterstats", "exactextract"])
-def test_zonal_stats_bulk(tmp_path, engine):
+@pytest.mark.parametrize("bands, exp_results_path", [(["vvdvh"], 2), (["VV", "VH"], 8)])
+def test_zonal_stats_bulk(tmp_path, engine, bands, exp_results_path):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
 
@@ -32,11 +33,23 @@ def test_zonal_stats_bulk(tmp_path, engine):
 
     # Make sure the s2-agri input file was copied
     test_image_roi_dir = test_dir / SampleData.image_dir.name / SampleData.roi_name
-    test_s1_asc_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name
-    test_s1_desc_dir = test_image_roi_dir / SampleData.image_s1_desc_path.parent.name
+    if bands == ["VV", "VH"]:
+        test_s1_asc_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name
+        test_s1_desc_dir = (
+            test_image_roi_dir / SampleData.image_s1_desc_path.parent.name
+        )
+    else:
+        test_s1_asc_dir = (
+            test_image_roi_dir
+            / SampleData.image_s1_grd_vvdvh_asc_weekly_path.parent.name
+        )
+        test_s1_desc_dir = (
+            test_image_roi_dir
+            / SampleData.image_s1_grd_vvdvh_desc_weekly_path.parent.name
+        )
     test_image_paths = list(test_s1_asc_dir.glob("*.tif"))
     test_image_paths.extend(test_s1_desc_dir.glob("*.tif"))
-    images_bands = [(path, ["VV", "VH"]) for path in test_image_paths]
+    images_bands = [(path, bands) for path in test_image_paths]
     vector_path = test_dir / SampleData.input_dir.name / "Prc_BEFL_2023_2023-07-24.gpkg"
     vector_info = gfo.get_layerinfo(vector_path)
 
@@ -50,7 +63,7 @@ def test_zonal_stats_bulk(tmp_path, engine):
     )
 
     result_paths = list(tmp_path.glob("*.sqlite"))
-    assert len(result_paths) == 8
+    assert len(result_paths) == exp_results_path
     for result_path in result_paths:
         result_df = pdh.read_file(result_path)
         # The result should have the same number of rows as the input vector file.

From f43273b6940884af99e64d20f2531577bb21b1b4 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Fri, 9 May 2025 10:21:55 +0200
Subject: [PATCH 13/40] refactor

---
 .../_zonal_stats_bulk_exactextract.py            | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 3183a08c..525292af 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -227,14 +227,6 @@ def zonal_stats_band(
         dst_dir=tmp_dir,
     )
 
-    # Add the operational arguments to the stats
-    min_coverage_frac = 0.8
-    coverage_weight = "none"
-    operation_arguments = (
-        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
-    )
-    stats = [stat + operation_arguments for stat in stats]
-
     try:
         import exactextract
 
@@ -266,6 +258,14 @@ def zonal_stats_band_tofile(
     # In stats replace 'std' with 'stdev' for exactextract
     stats = [stat.replace("std", "stdev") for stat in stats]
 
+    # Add the operational arguments to the stats
+    min_coverage_frac = 0.8
+    coverage_weight = "none"
+    operation_arguments = (
+        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
+    )
+    stats = [stat + operation_arguments for stat in stats]
+
     stats_df = zonal_stats_band(
         vector_path=vector_path,
         raster_path=raster_path,

From a73ec89bb42bc2ef26d6c10565b208026f123074 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Fri, 9 May 2025 15:28:13 +0200
Subject: [PATCH 14/40] refactor

---
 cropclassification/general.ini                | 12 +++++++++++
 .../preprocess/_timeseries_calc_openeo.py     | 10 ++++++++--
 cropclassification/preprocess/timeseries.py   |  2 ++
 .../util/zonal_stats_bulk/__init__.py         | 10 ++++++----
 .../_zonal_stats_bulk_exactextract.py         | 11 ----------
 tests/test_zonal_stats_bulk.py                | 20 ++++++++++++++++---
 6 files changed, 45 insertions(+), 20 deletions(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index 563bce67..c2f06fdc 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -138,6 +138,18 @@ on_missing_image = calculate_raise
 # Configuration on how/which periodic images/timeseries statistics should be generated.
 [timeseries]
 
+# Engine to use for the timeseries calculation.
+# Possible values are pyqgis, rasterstats and exactextract.
+engine = exactextract
+
+# Stats to calculate for the timeseries. The following stats are available:
+stats = count(min_coverage_frac=0.8,coverage_weight=none),
+        mean(min_coverage_frac=0.8,coverage_weight=none) ,
+        median(min_coverage_frac=0.8,coverage_weight=none),
+        stdev(min_coverage_frac=0.8,coverage_weight=none),
+        min(min_coverage_frac=0.8,coverage_weight=none),
+        max(min_coverage_frac=0.8,coverage_weight=none),
+
 # Negative buffer to apply to input parcels to account for mixels.
 buffer = 0
 
diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index fe900fe5..0ed9e75c 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -26,6 +26,8 @@ def calculate_periodic_timeseries(
     imageprofiles: dict[str, ImageProfile],
     images_periodic_dir: Path,
     timeseries_periodic_dir: Path,
+    engine: str,
+    stats: list[str],
     nb_parallel: int,
     on_missing_image: str,
 ):
@@ -44,6 +46,10 @@ def calculate_periodic_timeseries(
         images_periodic_dir (Path): directory where the images are stored.
         timeseries_periodic_dir (Path): directory where the timeseries data will be
             saved.
+        engine (str): the engine to use for the calculation. Options are
+            "exactextract", "rasterstats" and "pyqgis".
+        stats (list[str]): statistics to calculate. Available statistics and
+            special options are dependent on the `engine` specified:
         nb_parallel (int): number of parallel processes to use.
         on_missing_image (str): what to do when an image is missing. Options are:
 
@@ -90,7 +96,7 @@ def calculate_periodic_timeseries(
         id_column=conf.columns["id"],
         rasters_bands=images_bands,
         output_dir=timeseries_periodic_dir,
-        stats=["count", "mean", "median", "std", "min", "max"],
-        engine="exactextract",
+        stats=stats,
+        engine=engine,
         nb_parallel=nb_parallel,
     )
diff --git a/cropclassification/preprocess/timeseries.py b/cropclassification/preprocess/timeseries.py
index 171ac0f0..cef2ceed 100644
--- a/cropclassification/preprocess/timeseries.py
+++ b/cropclassification/preprocess/timeseries.py
@@ -84,6 +84,8 @@ def calc_timeseries_data(
             imageprofiles=conf.image_profiles,
             images_periodic_dir=conf.paths.getpath("images_periodic_dir"),
             timeseries_periodic_dir=timeseries_periodic_dir,
+            engine=conf.timeseries.get("engine"),
+            stats=conf.timeseries.get("stats"),
             nb_parallel=conf.general.getint("nb_parallel", -1),
             on_missing_image=conf.images.get("on_missing_image", "calculate_raise"),
         )
diff --git a/cropclassification/util/zonal_stats_bulk/__init__.py b/cropclassification/util/zonal_stats_bulk/__init__.py
index 00ee2c7a..30b72bd2 100644
--- a/cropclassification/util/zonal_stats_bulk/__init__.py
+++ b/cropclassification/util/zonal_stats_bulk/__init__.py
@@ -11,10 +11,10 @@ def zonal_stats(
     id_column: str,
     rasters_bands: list[tuple[Path, list[str]]],
     output_dir: Path,
-    stats: Union[list[str], str] = ["count", "median"],
+    engine: str,
+    stats: Union[list[str], str],
     cloud_filter_band: Optional[str] = None,
     calc_bands_parallel: bool = True,
-    engine: str = "rasterstats",
     nb_parallel: int = -1,
     force: bool = False,
 ):
@@ -39,8 +39,10 @@ def zonal_stats(
             supported for engine "rasterstats". Defaults to None.
         calc_bands_parallel (bool, optional): True to calculate the bands in parallel.
             Only supported for engine "rasterstats". Defaults to True.
-        engine (str, optional): the engine to use for the calculation. Options are
-            "exactextract", "rasterstats" and "pyqgis". Defaults to "rasterstats".
+        engine (str): the engine to use for the calculation. Options are
+            "exactextract", "rasterstats" and "pyqgis".
+        stats (list[str]): statistics to calculate. Available statistics and
+            special options are dependent on the `engine` specified:
         nb_parallel (int, optional): the number of parallel processes to use.
             Defaults to -1: use all available processors.
         force (bool, optional): False to skip calculating existing output files. True to
diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 525292af..8787a900 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -255,17 +255,6 @@ def zonal_stats_band_tofile(
     include_cols: list[str],
     force: bool = False,
 ) -> dict[str, Path]:
-    # In stats replace 'std' with 'stdev' for exactextract
-    stats = [stat.replace("std", "stdev") for stat in stats]
-
-    # Add the operational arguments to the stats
-    min_coverage_frac = 0.8
-    coverage_weight = "none"
-    operation_arguments = (
-        f"(min_coverage_frac={min_coverage_frac},coverage_weight={coverage_weight})"
-    )
-    stats = [stat + operation_arguments for stat in stats]
-
     stats_df = zonal_stats_band(
         vector_path=vector_path,
         raster_path=raster_path,
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 31742311..b151a1d5 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -10,9 +10,23 @@
 from tests.test_helper import SampleData
 
 
-@pytest.mark.parametrize("engine", ["pyqgis", "rasterstats", "exactextract"])
+@pytest.mark.parametrize(
+    "engine, stats",
+    [
+        ("pyqgis", ["mean", "count", "std"]),
+        ("rasterstats", ["mean", "count", "std"]),
+        (
+            "exactextract",
+            [
+                "mean(min_coverage_frac=0.8,coverage_weight=none)",
+                "count(min_coverage_frac=0.8,coverage_weight=none)",
+                "stdev(min_coverage_frac=0.8,coverage_weight=none)",
+            ],
+        ),
+    ],
+)
 @pytest.mark.parametrize("bands, exp_results_path", [(["vvdvh"], 2), (["VV", "VH"], 8)])
-def test_zonal_stats_bulk(tmp_path, engine, bands, exp_results_path):
+def test_zonal_stats_bulk(tmp_path, engine, stats, bands, exp_results_path):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
 
@@ -58,7 +72,7 @@ def test_zonal_stats_bulk(tmp_path, engine, bands, exp_results_path):
         id_column="UID",
         rasters_bands=images_bands,
         output_dir=tmp_path,
-        stats=["mean", "count", "std"],
+        stats=stats,
         engine=engine,
     )
 

From fccb369b6de40b9c062115a6c3b5bfaeba4a62ee Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Sat, 10 May 2025 08:53:01 +0200
Subject: [PATCH 15/40] refactor

---
 cropclassification/general.ini                |  7 +----
 .../util/zonal_stats_bulk/__init__.py         |  6 ----
 .../_zonal_stats_bulk_exactextract.py         |  7 +++--
 tests/test_zonal_stats_bulk.py                | 29 ++++++++++++-------
 4 files changed, 24 insertions(+), 25 deletions(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index c2f06fdc..124567c2 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -143,12 +143,7 @@ on_missing_image = calculate_raise
 engine = exactextract
 
 # Stats to calculate for the timeseries. The following stats are available:
-stats = count(min_coverage_frac=0.8,coverage_weight=none),
-        mean(min_coverage_frac=0.8,coverage_weight=none) ,
-        median(min_coverage_frac=0.8,coverage_weight=none),
-        stdev(min_coverage_frac=0.8,coverage_weight=none),
-        min(min_coverage_frac=0.8,coverage_weight=none),
-        max(min_coverage_frac=0.8,coverage_weight=none),
+stats = count(min_coverage_frac=0.8,coverage_weight=none),mean(min_coverage_frac=0.8,coverage_weight=none),median(min_coverage_frac=0.8,coverage_weight=none),stdev(min_coverage_frac=0.8,coverage_weight=none),min(min_coverage_frac=0.8,coverage_weight=none),max(min_coverage_frac=0.8,coverage_weight=none)
 
 # Negative buffer to apply to input parcels to account for mixels.
 buffer = 0
diff --git a/cropclassification/util/zonal_stats_bulk/__init__.py b/cropclassification/util/zonal_stats_bulk/__init__.py
index 30b72bd2..c02af049 100644
--- a/cropclassification/util/zonal_stats_bulk/__init__.py
+++ b/cropclassification/util/zonal_stats_bulk/__init__.py
@@ -29,12 +29,6 @@ def zonal_stats(
         output_dir (Path): directory to write the results to.
         stats (List[str]): statistics to calculate. Available statistics and
             special options are dependent on the `engine` specified:
-
-                - "rasterstats": `rasterstats documentation <https://pythonhosted.org/rasterstats/manual.html#statistics>`_
-                - "pyqgis": "count", "sum", "mean", "median", "std", "min", "max",
-                        "range", "minority", "majority" and "variance".
-                - "exactextract": `exactextract documentation <https://isciences.github.io/exactextract/operations.html>`_
-
         cloud_filter_band (str, optional): the band to use as a cloud filter. Only
             supported for engine "rasterstats". Defaults to None.
         calc_bands_parallel (bool, optional): True to calculate the bands in parallel.
diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 8787a900..7ee20894 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -238,9 +238,10 @@ def zonal_stats_band(
             output="pandas",
             include_cols=include_cols,
         )
-
-    except Exception:
-        raise
+    except Exception as ex:
+        message = f"Error calculating zonal stats {stats}: {ex}"
+        logger.error(message)
+        raise Exception(message) from ex
 
     return stats_df
 
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index b151a1d5..5f0ba2ef 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -25,7 +25,14 @@
         ),
     ],
 )
-@pytest.mark.parametrize("bands, exp_results_path", [(["vvdvh"], 2), (["VV", "VH"], 8)])
+@pytest.mark.parametrize(
+    "bands, exp_results_path",
+    [
+        (["vvdvh"], 2),
+        (["VV", "VH"], 8),
+        (["B02", "B03", "B04", "B08", "B11", "B12"], 18),
+    ],
+)
 def test_zonal_stats_bulk(tmp_path, engine, stats, bands, exp_results_path):
     if engine == "pyqgis" and not HAS_QGIS:
         pytest.skip("QGIS is not available on this system.")
@@ -48,21 +55,23 @@ def test_zonal_stats_bulk(tmp_path, engine, stats, bands, exp_results_path):
     # Make sure the s2-agri input file was copied
     test_image_roi_dir = test_dir / SampleData.image_dir.name / SampleData.roi_name
     if bands == ["VV", "VH"]:
-        test_s1_asc_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name
-        test_s1_desc_dir = (
-            test_image_roi_dir / SampleData.image_s1_desc_path.parent.name
-        )
-    else:
-        test_s1_asc_dir = (
+        image1_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name
+        image2_dir = test_image_roi_dir / SampleData.image_s1_desc_path.parent.name
+    elif bands == ["vvdvh"]:
+        image1_dir = (
             test_image_roi_dir
             / SampleData.image_s1_grd_vvdvh_asc_weekly_path.parent.name
         )
-        test_s1_desc_dir = (
+        image2_dir = (
             test_image_roi_dir
             / SampleData.image_s1_grd_vvdvh_desc_weekly_path.parent.name
         )
-    test_image_paths = list(test_s1_asc_dir.glob("*.tif"))
-    test_image_paths.extend(test_s1_desc_dir.glob("*.tif"))
+    elif bands == ["B02", "B03", "B04", "B08", "B11", "B12"]:
+        image1_dir = test_image_roi_dir / SampleData.image_s2_mean_path.parent.name
+        image2_dir = None
+    test_image_paths = list(image1_dir.glob("*.tif"))
+    if image2_dir:
+        test_image_paths.extend(image2_dir.glob("*.tif"))
     images_bands = [(path, bands) for path in test_image_paths]
     vector_path = test_dir / SampleData.input_dir.name / "Prc_BEFL_2023_2023-07-24.gpkg"
     vector_info = gfo.get_layerinfo(vector_path)

From bd292e1d272bdc6147b79919458bb1482a0d973b Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 08:36:25 +0200
Subject: [PATCH 16/40] refactor stats as list of strings

---
 cropclassification/general.ini              | 10 ++++++++--
 cropclassification/helpers/config_helper.py |  1 +
 cropclassification/preprocess/timeseries.py |  2 +-
 3 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index 090e4a0d..911a0e67 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -143,8 +143,14 @@ on_missing_image = calculate_raise
 engine = exactextract
 
 # Stats to calculate for the timeseries. The following stats are available:
-stats = count(min_coverage_frac=0.8,coverage_weight=none),mean(min_coverage_frac=0.8,coverage_weight=none),median(min_coverage_frac=0.8,coverage_weight=none),stdev(min_coverage_frac=0.8,coverage_weight=none),min(min_coverage_frac=0.8,coverage_weight=none),max(min_coverage_frac=0.8,coverage_weight=none)
-
+stats = [
+             "count(min_coverage_frac=0.5,coverage_weight=none)",
+             "mean(min_coverage_frac=0.5,coverage_weight=none)",
+             "median(min_coverage_frac=0.5,coverage_weight=none)",
+             "stdev(min_coverage_frac=0.5,coverage_weight=none)",
+             "min(min_coverage_frac=0.5,coverage_weight=none)",
+             "max(min_coverage_frac=0.5,coverage_weight=none)"
+        ]
 # Negative buffer to apply to input parcels to account for mixels.
 buffer = 0
 
diff --git a/cropclassification/helpers/config_helper.py b/cropclassification/helpers/config_helper.py
index a422467e..b5d088fa 100644
--- a/cropclassification/helpers/config_helper.py
+++ b/cropclassification/helpers/config_helper.py
@@ -143,6 +143,7 @@ def read_config(
             "list": lambda x: [i.strip() for i in x.split(",")],
             "listint": lambda x: [int(i.strip()) for i in x.split(",")],
             "listfloat": lambda x: [float(i.strip()) for i in x.split(",")],
+            "jsonlist": lambda x: None if x is None else json.loads(x),
             "dict": lambda x: None if x is None else json.loads(x),
             "path": lambda x: None if x is None else Path(x),
         },
diff --git a/cropclassification/preprocess/timeseries.py b/cropclassification/preprocess/timeseries.py
index 6bad3c0b..032f4007 100644
--- a/cropclassification/preprocess/timeseries.py
+++ b/cropclassification/preprocess/timeseries.py
@@ -85,7 +85,7 @@ def calc_timeseries_data(
             images_periodic_dir=conf.paths.getpath("images_periodic_dir"),
             timeseries_periodic_dir=timeseries_periodic_dir,
             engine=conf.timeseries.get("engine"),
-            stats=conf.timeseries.get("stats"),
+            stats=conf.timeseries.getjsonlist("stats"),
             nb_parallel=conf.general.getint("nb_parallel", -1),
             on_missing_image=conf.images.get("on_missing_image", "calculate_raise"),
         )

From a1c9ec70af9325a7ccc92f50947d1b6ded6e19f6 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 11:44:44 +0200
Subject: [PATCH 17/40] new version of prc_befl_2023_2023_07_24.gpkg

---
 .../_inputdata/Prc_BEFL_2023_2023-07-24.gpkg  | Bin 122880 -> 106496 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg b/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg
index b792eebc213c0cde89d13be4dc94dc4725cc7b01..b3cca2d7f02f852a4f1a223cfd82dff5fa38d088 100644
GIT binary patch
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EKSJuNY5)KL


From bbafed8901f230512582b122abebef78f6d9e7e7 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 12:48:00 +0200
Subject: [PATCH 18/40] add zonal_stats_bulk_invalid test

---
 tests/test_zonal_stats_bulk.py | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 5f0ba2ef..9a3e27b5 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -93,3 +93,22 @@ def test_zonal_stats_bulk(tmp_path, engine, stats, bands, exp_results_path):
         assert len(result_df) == vector_info.featurecount
         # The calculates stats should not be nan for any row.
         assert not any(result_df["mean"].isna())
+
+
+def test_zonal_stats_bulk_invalid(tmp_path):
+    # Prepare test data
+    sample_dir = SampleData.markers_dir
+    test_dir = tmp_path / sample_dir.name
+    shutil.copytree(sample_dir, test_dir)
+
+    vector_path = test_dir / SampleData.input_dir.name / "Prc_BEFL_2023_2023-07-24.gpkg"
+
+    with pytest.raises(ValueError):
+        zonal_stats_bulk.zonal_stats(
+            vector_path=vector_path,
+            id_column="UID",
+            rasters_bands=["vvdvh"],
+            output_dir=tmp_path,
+            stats=["means"],
+            engine="exactextract",
+        )

From ca64d33bfff3f764d313886582f9660e93e2bf2a Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 13:59:06 +0200
Subject: [PATCH 19/40] min_coverage_frac = 0.8

---
 cropclassification/general.ini | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index 911a0e67..c1cacbcc 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -144,12 +144,12 @@ engine = exactextract
 
 # Stats to calculate for the timeseries. The following stats are available:
 stats = [
-             "count(min_coverage_frac=0.5,coverage_weight=none)",
-             "mean(min_coverage_frac=0.5,coverage_weight=none)",
-             "median(min_coverage_frac=0.5,coverage_weight=none)",
-             "stdev(min_coverage_frac=0.5,coverage_weight=none)",
-             "min(min_coverage_frac=0.5,coverage_weight=none)",
-             "max(min_coverage_frac=0.5,coverage_weight=none)"
+             "count(min_coverage_frac=0.8,coverage_weight=none)",
+             "mean(min_coverage_frac=0.8,coverage_weight=none)",
+             "median(min_coverage_frac=0.8,coverage_weight=none)",
+             "stdev(min_coverage_frac=0.8,coverage_weight=none)",
+             "min(min_coverage_frac=0.8,coverage_weight=none)",
+             "max(min_coverage_frac=0.8,coverage_weight=none)"
         ]
 # Negative buffer to apply to input parcels to account for mixels.
 buffer = 0

From 260216c1e04223dd1c755299c33eaa50b254cc02 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 16:23:22 +0200
Subject: [PATCH 20/40] refactor zonal_stats_bulk_invalid test

---
 .../_zonal_stats_bulk_exactextract.py                |  2 +-
 tests/test_zonal_stats_bulk.py                       | 12 ++++++------
 2 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
index 7ee20894..6d7dbb00 100644
--- a/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
+++ b/cropclassification/util/zonal_stats_bulk/_zonal_stats_bulk_exactextract.py
@@ -241,7 +241,7 @@ def zonal_stats_band(
     except Exception as ex:
         message = f"Error calculating zonal stats {stats}: {ex}"
         logger.error(message)
-        raise Exception(message) from ex
+        raise ValueError(message) from ex
 
     return stats_df
 
diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 9a3e27b5..5e0ac217 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -6,6 +6,7 @@
 from cropclassification.helpers import config_helper as conf
 from cropclassification.helpers import pandas_helper as pdh
 from cropclassification.util import zonal_stats_bulk
+from cropclassification.util.zonal_stats_bulk import _zonal_stats_bulk_exactextract
 from cropclassification.util.zonal_stats_bulk._zonal_stats_bulk_pyqgis import HAS_QGIS
 from tests.test_helper import SampleData
 
@@ -103,12 +104,11 @@ def test_zonal_stats_bulk_invalid(tmp_path):
 
     vector_path = test_dir / SampleData.input_dir.name / "Prc_BEFL_2023_2023-07-24.gpkg"
 
-    with pytest.raises(ValueError):
-        zonal_stats_bulk.zonal_stats(
+    with pytest.raises(ValueError, match="Error calculating zonal stats"):
+        _zonal_stats_bulk_exactextract.zonal_stats_band(
             vector_path=vector_path,
-            id_column="UID",
-            rasters_bands=["vvdvh"],
-            output_dir=tmp_path,
+            raster_path=test_dir / SampleData.image_s1_asc_path,
+            tmp_dir=tmp_path,
             stats=["means"],
-            engine="exactextract",
+            include_cols=["index", "UID", "x_ref"],
         )

From cfa604900884d8e754b164e4df7420701a5128e5 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 12 May 2025 17:04:00 +0200
Subject: [PATCH 21/40] addressed review comments

---
 CHANGELOG.md                                             | 2 +-
 cropclassification/general.ini                           | 3 +++
 cropclassification/preprocess/_timeseries_calc_openeo.py | 6 ++++++
 cropclassification/util/zonal_stats_bulk/__init__.py     | 5 +++++
 debug.log                                                | 9 ---------
 5 files changed, 15 insertions(+), 10 deletions(-)
 delete mode 100644 debug.log

diff --git a/CHANGELOG.md b/CHANGELOG.md
index eed44ea7..fc00c104 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -45,7 +45,7 @@
 - Add support to generate sarrgb images and apply enhanced lee despeckling (#157)
 - Add POC (not for operational use) of a cover/bare soil marker (#168)
 - General small improvements, e.g. save randomforest models compressed,.. (#144)
-- Use Exactextract for zonalstats calculation (#181)
+- Use Exactextract as default engine for zonalstats calculation (#181)
 
 ### Bugs fixed
 
diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index c1cacbcc..b311b748 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -143,6 +143,9 @@ on_missing_image = calculate_raise
 engine = exactextract
 
 # Stats to calculate for the timeseries. The following stats are available:
+#     - "rasterstats": documentation: https://pythonhosted.org/rasterstats/manual.html#statistics
+#     - "pyqgis": "count", "sum", "mean", "median", "std", "min", "max", "range", "minority", "majority" and "variance".
+#     - "exactextract": documentation: https://isciences.github.io/exactextract/operations.html
 stats = [
              "count(min_coverage_frac=0.8,coverage_weight=none)",
              "mean(min_coverage_frac=0.8,coverage_weight=none)",
diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index cc5e2de0..4d72b28c 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -50,6 +50,12 @@ def calculate_periodic_timeseries(
             "exactextract", "rasterstats" and "pyqgis".
         stats (list[str]): statistics to calculate. Available statistics and
             special options are dependent on the `engine` specified:
+
+                - "rasterstats": `rasterstats documentation <https://pythonhosted.org/rasterstats/manual.html#statistics>`_
+                - "pyqgis": "count", "sum", "mean", "median", "std", "min", "max",
+                        "range", "minority", "majority" and "variance".
+                - "exactextract": `exactextract documentation <https://isciences.github.io/exactextract/operations.html>`_
+
         nb_parallel (int): number of parallel processes to use.
         on_missing_image (str): what to do when an image is missing. Options are:
 
diff --git a/cropclassification/util/zonal_stats_bulk/__init__.py b/cropclassification/util/zonal_stats_bulk/__init__.py
index c02af049..3d36ccc6 100644
--- a/cropclassification/util/zonal_stats_bulk/__init__.py
+++ b/cropclassification/util/zonal_stats_bulk/__init__.py
@@ -37,6 +37,11 @@ def zonal_stats(
             "exactextract", "rasterstats" and "pyqgis".
         stats (list[str]): statistics to calculate. Available statistics and
             special options are dependent on the `engine` specified:
+                - "rasterstats": `rasterstats documentation <https://pythonhosted.org/rasterstats/manual.html#statistics>`_
+                - "pyqgis": "count", "sum", "mean", "median", "std", "min", "max",
+                        "range", "minority", "majority" and "variance".
+                - "exactextract": `exactextract documentation <https://isciences.github.io/exactextract/operations.html>`_
+
         nb_parallel (int, optional): the number of parallel processes to use.
             Defaults to -1: use all available processors.
         force (bool, optional): False to skip calculating existing output files. True to
diff --git a/debug.log b/debug.log
deleted file mode 100644
index 11be91b6..00000000
--- a/debug.log
+++ /dev/null
@@ -1,9 +0,0 @@
-[0507/122314.187:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122315.996:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122323.090:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122334.963:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122456.210:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122457.711:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122502.946:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122514.849:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)
-[0507/122823.970:ERROR:registration_protocol_win.cc(108)] CreateFile: Het systeem kan het opgegeven bestand niet vinden. (0x2)

From af936dcbb31c50a34729070d0b67fc2a403598c8 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Fri, 23 May 2025 13:00:01 +0200
Subject: [PATCH 22/40] added test exactextract

---
 tests/test_zonal_stats_bulk.py | 90 ++++++++++++++++++++++++++++++++++
 1 file changed, 90 insertions(+)

diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index 5e0ac217..f911d6bd 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -1,7 +1,9 @@
 import shutil
 
 import geofileops as gfo
+import geopandas as gpd
 import pytest
+import shapely
 
 from cropclassification.helpers import config_helper as conf
 from cropclassification.helpers import pandas_helper as pdh
@@ -112,3 +114,91 @@ def test_zonal_stats_bulk_invalid(tmp_path):
             stats=["means"],
             include_cols=["index", "UID", "x_ref"],
         )
+
+
+@pytest.mark.parametrize(
+    "min_coverage_frac, exp_count",
+    [
+        (0.0, [49, 42, 42, 42]),
+        (0.2, [25, 30, 30, 30]),
+        (0.5, [25, 30, 30, 20]),
+        (0.8, [25, 20, 30, 20]),
+        (1.0, [25, 20, 20, 20]),
+    ],
+)
+def test_zonal_stats_bulk_exactextract(tmp_path, min_coverage_frac, exp_count):
+    # Prepare test data
+    sample_dir = SampleData.markers_dir
+    test_dir = tmp_path / sample_dir.name
+    shutil.copytree(sample_dir, test_dir)
+
+    geoms = [
+        (
+            "POLYGON ((161405.210003 188506.174464, 161456.432668 188505.089414,"
+            " 161455.476062 188453.597478, 161403.717327 188454.559035, 161405.210003"
+            " 188506.174464))"
+        ),
+        (
+            "POLYGON ((161495.16002 188499.432483, 161546.38515 188498.480826,"
+            " 161545.277792 188446.05759, 161493.919267 188447.011718, 161495.16002"
+            " 188499.432483))"
+        ),
+        (
+            "POLYGON ((161433.705572 188423.843391, 161484.794828 188422.760828,"
+            " 161483.986074 188364.860805, 161432.368184 188366.22007, 161433.705572"
+            " 188423.843391))"
+        ),
+        (
+            "POLYGON ((161513.51231 188417.022976, 161565.006707 188416.199771,"
+            " 161563.840308 188367.780984, 161512.222428 188369.140255, 161513.51231"
+            " 188417.022976))"
+        ),
+    ]
+
+    box_geoms = shapely.from_wkt(geoms)
+
+    gdf_geoms = gpd.GeoDataFrame(geometry=box_geoms, crs="EPSG:31370")
+
+    # write the geofile to a file
+    vector_path = tmp_path / "vector.gpkg"
+    gfo.to_file(gdf=gdf_geoms, path=vector_path)
+    expression = """
+        CASE
+            WHEN fid = 1
+                THEN -0.2
+            WHEN fid = 2
+                THEN 0.5
+            WHEN fid = 3
+                THEN 0.8
+            WHEN fid = 4
+                THEN 0.2
+            ELSE NULL
+        END
+    """
+    gfo.add_column(path=vector_path, name="UID", type="TEXT", expression=expression)
+
+    test_image_roi_dir = test_dir / SampleData.image_dir.name / SampleData.roi_name
+    image1_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name
+    image2_dir = test_image_roi_dir / SampleData.image_s1_desc_path.parent.name
+    test_image_paths = list(image1_dir.glob("*.tif"))
+    if image2_dir:
+        test_image_paths.extend(image2_dir.glob("*.tif"))
+    bands = ["VV", "VH"]
+    images_bands = [(path, bands) for path in test_image_paths]
+    output_path = tmp_path / f"min_cov_frac_{min_coverage_frac}"
+    stats = [f"count(min_coverage_frac={min_coverage_frac},coverage_weight=none)"]
+
+    zonal_stats_bulk.zonal_stats(
+        vector_path=vector_path,
+        id_column="UID",
+        rasters_bands=images_bands,
+        output_dir=output_path,
+        stats=stats,
+        engine="exactextract",
+    )
+
+    result_paths = list(output_path.glob("*.sqlite"))
+    result_df = pdh.read_file(result_paths[0])
+    for index in range(4):
+        count = result_df[result_df["index"] == index]["count"].values[0]
+        assert count == exp_count[index]

From 7def42dbac3a836f171a5b1964c53c931f386eed Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:07:03 +0200
Subject: [PATCH 23/40] Avoid very high commited memory being reserved

---
 .../util/zonal_stats_bulk/_processing_util.py             | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/cropclassification/util/zonal_stats_bulk/_processing_util.py b/cropclassification/util/zonal_stats_bulk/_processing_util.py
index c6432cf3..9408334a 100644
--- a/cropclassification/util/zonal_stats_bulk/_processing_util.py
+++ b/cropclassification/util/zonal_stats_bulk/_processing_util.py
@@ -44,6 +44,14 @@ def __exit__(self, type, value, traceback):
 
 
 def initialize_worker():
+    """Some default inits."""
+    # Reduce OpenMP threads to avoid the committed memory usage becoming huge when using
+    # multiprocessing.
+    # Should work for any numeric library used (openblas, mkl,...).
+    # Ref: https://stackoverflow.com/questions/77764228/pandas-scipy-high-commit-memory-usage-windows
+    if os.environ.get("OMP_NUM_THREADS") is None:
+        os.environ["OMP_NUM_THREADS"] = "1"
+
     # We don't want the workers to block the entire system, so make them nice
     # if they aren't quite nice already.
     # Remark: on linux, depending on system settings it is not possible to

From 1cafab4841a079a1cb2ecdd060ce36ceef937b90 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:08:05 +0200
Subject: [PATCH 24/40] Small improvement to logging

---
 cropclassification/preprocess/_timeseries_calc_openeo.py | 1 -
 cropclassification/util/zonal_stats_bulk/__init__.py     | 7 +++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/cropclassification/preprocess/_timeseries_calc_openeo.py b/cropclassification/preprocess/_timeseries_calc_openeo.py
index 4d72b28c..55ee2da8 100644
--- a/cropclassification/preprocess/_timeseries_calc_openeo.py
+++ b/cropclassification/preprocess/_timeseries_calc_openeo.py
@@ -98,7 +98,6 @@ def calculate_periodic_timeseries(
     if temp_dir == "None":
         temp_dir = Path(tempfile.gettempdir())
 
-    logger.info(f"Calculating timeseries for {len(images_bands)} images")
     zonal_stats_bulk.zonal_stats(
         vector_path=input_parcel_path,
         id_column=conf.columns["id"],
diff --git a/cropclassification/util/zonal_stats_bulk/__init__.py b/cropclassification/util/zonal_stats_bulk/__init__.py
index 9728871e..a7fe70b3 100644
--- a/cropclassification/util/zonal_stats_bulk/__init__.py
+++ b/cropclassification/util/zonal_stats_bulk/__init__.py
@@ -1,5 +1,6 @@
 """Calculate zonal statistics for a vector file with many raster files."""
 
+import logging
 from pathlib import Path
 from typing import Optional, Union
 
@@ -10,6 +11,8 @@
 )
 from ._raster_helper import *  # noqa: F403
 
+logger = logging.getLogger(__name__)
+
 
 def zonal_stats(
     vector_path: Path,
@@ -52,6 +55,10 @@ def zonal_stats(
         force (bool, optional): False to skip calculating existing output files. True to
             recalculate and overwrite existing output files. Defaults to False.
     """
+    logger.info(
+        f"Calculate zonal statistics for {len(rasters_bands)} rasters ({nb_parallel=})"
+    )
+
     if isinstance(stats, str):
         stats = [stats]
 

From bed1b87e8e68377f75cf20591aad546c3ff922e6 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:09:12 +0200
Subject: [PATCH 25/40] Adapt min_parcels_with_data_prc to avoid s1 being lost
 due to buffer=0

---
 cropclassification/general.ini | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/cropclassification/general.ini b/cropclassification/general.ini
index 0515fca6..ec158e1c 100644
--- a/cropclassification/general.ini
+++ b/cropclassification/general.ini
@@ -147,13 +147,13 @@ engine = exactextract
 #     - "pyqgis": "count", "sum", "mean", "median", "std", "min", "max", "range", "minority", "majority" and "variance".
 #     - "exactextract": documentation: https://isciences.github.io/exactextract/operations.html
 stats = [
-             "count(min_coverage_frac=0.8,coverage_weight=none)",
-             "mean(min_coverage_frac=0.8,coverage_weight=none)",
-             "median(min_coverage_frac=0.8,coverage_weight=none)",
-             "stdev(min_coverage_frac=0.8,coverage_weight=none)",
-             "min(min_coverage_frac=0.8,coverage_weight=none)",
-             "max(min_coverage_frac=0.8,coverage_weight=none)"
-        ]
+        "count(min_coverage_frac=1,coverage_weight=none)",
+        "mean(min_coverage_frac=1,coverage_weight=none)",
+        "median(min_coverage_frac=1,coverage_weight=none)",
+        "stdev(min_coverage_frac=1,coverage_weight=none)",
+        "min(min_coverage_frac=1,coverage_weight=none)",
+        "max(min_coverage_frac=1,coverage_weight=none)"
+    ]
 # Negative buffer to apply to input parcels to account for mixels.
 buffer = 0
 
@@ -161,7 +161,7 @@ buffer = 0
 max_cloudcover_pct = 15
 
 # The min percentage of parcels that need to have valid data for a time+sensor to use it 
-min_parcels_with_data_pct = 80
+min_parcels_with_data_pct = 75
 
 # Configuration specific to the marker being calculated.
 [marker]

From 61cccb575ee16b1bde800ca1a6872363cc5d21d3 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:09:22 +0200
Subject: [PATCH 26/40] Update calc_cropclass.py

---
 cropclassification/calc_cropclass.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/cropclassification/calc_cropclass.py b/cropclassification/calc_cropclass.py
index 2d2d006f..28253f29 100644
--- a/cropclassification/calc_cropclass.py
+++ b/cropclassification/calc_cropclass.py
@@ -189,6 +189,7 @@ def run_cropclass(
     parceldata_aggregations_to_use = conf.marker.getlist(
         "parceldata_aggregations_to_use"
     )
+
     ts.calc_timeseries_data(
         input_parcel_path=imagedata_input_parcel_path,
         roi_bounds=tuple(conf.roi.getlistfloat("roi_bounds")),

From 306f1726dc1afbce497ce85367c69383a0e1ab31 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:09:45 +0200
Subject: [PATCH 27/40] Disable botocore.credentions info logging

---
 cropclassification/__init__.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/cropclassification/__init__.py b/cropclassification/__init__.py
index cce4f0c2..afa44509 100644
--- a/cropclassification/__init__.py
+++ b/cropclassification/__init__.py
@@ -1 +1,7 @@
 """Package with functionalities to support agricultural parcel monitoring."""
+
+import logging
+
+# Disable info logging pf botocore.credentials
+logger_botocore_credentials = logging.getLogger("botocore.credentials")
+logger_botocore_credentials.setLevel(logging.WARNING)

From 268ceff294be02ce88e0cfb16cd3f763efa65598 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:10:31 +0200
Subject: [PATCH 28/40] Small improvements to tests

---
 tests/test_zonal_stats_bulk.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index f911d6bd..bfcfcaff 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -98,7 +98,7 @@ def test_zonal_stats_bulk(tmp_path, engine, stats, bands, exp_results_path):
         assert not any(result_df["mean"].isna())
 
 
-def test_zonal_stats_bulk_invalid(tmp_path):
+def test_exactextract_invalid_stats(tmp_path):
     # Prepare test data
     sample_dir = SampleData.markers_dir
     test_dir = tmp_path / sample_dir.name
@@ -106,7 +106,7 @@ def test_zonal_stats_bulk_invalid(tmp_path):
 
     vector_path = test_dir / SampleData.input_dir.name / "Prc_BEFL_2023_2023-07-24.gpkg"
 
-    with pytest.raises(ValueError, match="Error calculating zonal stats"):
+    with pytest.raises(ValueError, match="Unsupported stat: means"):
         _zonal_stats_bulk_exactextract.zonal_stats_band(
             vector_path=vector_path,
             raster_path=test_dir / SampleData.image_s1_asc_path,
@@ -126,7 +126,7 @@ def test_zonal_stats_bulk_invalid(tmp_path):
         (1.0, [25, 20, 20, 20]),
     ],
 )
-def test_zonal_stats_bulk_exactextract(tmp_path, min_coverage_frac, exp_count):
+def test_exactextract_min_coverage_frac(tmp_path, min_coverage_frac, exp_count):
     # Prepare test data
     sample_dir = SampleData.markers_dir
     test_dir = tmp_path / sample_dir.name

From fda5432c088fb785a68d0a5c42bf58ff4464af30 Mon Sep 17 00:00:00 2001
From: Pieter Roggemans <pieter.roggemans@gmail.com>
Date: Sun, 24 Aug 2025 17:10:59 +0200
Subject: [PATCH 29/40] Simplify test

---
 tests/test_zonal_stats_bulk.py | 15 +--------------
 1 file changed, 1 insertion(+), 14 deletions(-)

diff --git a/tests/test_zonal_stats_bulk.py b/tests/test_zonal_stats_bulk.py
index bfcfcaff..9448113b 100644
--- a/tests/test_zonal_stats_bulk.py
+++ b/tests/test_zonal_stats_bulk.py
@@ -162,20 +162,7 @@ def test_exactextract_min_coverage_frac(tmp_path, min_coverage_frac, exp_count):
     # write the geofile to a file
     vector_path = tmp_path / "vector.gpkg"
     gfo.to_file(gdf=gdf_geoms, path=vector_path)
-    expression = """
-        CASE
-            WHEN fid = 1
-                THEN -0.2
-            WHEN fid = 2
-                THEN 0.5
-            WHEN fid = 3
-                THEN 0.8
-            WHEN fid = 4
-                THEN 0.2
-            ELSE NULL
-        END
-    """
-    gfo.add_column(path=vector_path, name="UID", type="TEXT", expression=expression)
+    gfo.add_column(path=vector_path, name="UID", type="TEXT", expression="fid")
 
     test_image_roi_dir = test_dir / SampleData.image_dir.name / SampleData.roi_name
     image1_dir = test_image_roi_dir / SampleData.image_s1_asc_path.parent.name

From aa4c702c493e002382b4c0a5d1a4fccd77d4bb1f Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 27 Apr 2026 15:20:47 +0200
Subject: [PATCH 30/40] updated version

---
 .../_inputdata/Prc_BEFL_2023_2023-07-24.gpkg  | Bin 106496 -> 131072 bytes
 1 file changed, 0 insertions(+), 0 deletions(-)

diff --git a/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg b/markers/_inputdata/Prc_BEFL_2023_2023-07-24.gpkg
index b3cca2d7f02f852a4f1a223cfd82dff5fa38d088..222223acb2055e36612fbe3f1399078ed7eb9d43 100644
GIT binary patch
delta 10851
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z^Ay>;cEMq1NAu%tAzEaiP~^gmhhUZT_IP|+9;uoxps$zgPTJWTSlZdvDTZlhv%~)Z
DfpSS3


From f8d67a148a102ac8799c407381d0ebe6dee88c1a Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 30 Apr 2026 07:33:55 +0200
Subject: [PATCH 31/40] expect float16 in stead of float32

---
 tests/test_raster_index_util.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index 12e3e0ab..8f6ac23f 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -236,20 +236,20 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
     [
         ("ndvi", "BYTE", gdal.GDT_UInt16, 32676, ["B04", "B08", "b1"], "uint8", 255),
         ("ndvi", "BYTE", gdal.GDT_Float32, np.nan, ["B04", "B08"], "uint8", 255),
-        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float32", np.nan),
+        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float16", np.nan),
         (
             "ndvi",
             "FLOAT16",
             gdal.GDT_Float32,
             np.nan,
             ["B04", "B08"],
-            "float32",
+            "float16",
             np.nan,
         ),
         ("dprvi", "BYTE", gdal.GDT_UInt16, 32676, ["VH", "VV"], "uint8", 255),
         ("dprvi", "BYTE", gdal.GDT_Float32, np.nan, ["VH", "VV"], "uint8", 255),
-        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float32", np.nan),
-        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float32", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float16", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float16", np.nan),
     ],
 )
 def test_calc_index_by_gdal_raster(

From 0811a8a121561ebcd61f0f3ac324449e0da11fd3 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Thu, 30 Apr 2026 07:56:47 +0200
Subject: [PATCH 32/40] undo the changes

---
 tests/test_raster_index_util.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index 8f6ac23f..12e3e0ab 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -236,20 +236,20 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
     [
         ("ndvi", "BYTE", gdal.GDT_UInt16, 32676, ["B04", "B08", "b1"], "uint8", 255),
         ("ndvi", "BYTE", gdal.GDT_Float32, np.nan, ["B04", "B08"], "uint8", 255),
-        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float16", np.nan),
+        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float32", np.nan),
         (
             "ndvi",
             "FLOAT16",
             gdal.GDT_Float32,
             np.nan,
             ["B04", "B08"],
-            "float16",
+            "float32",
             np.nan,
         ),
         ("dprvi", "BYTE", gdal.GDT_UInt16, 32676, ["VH", "VV"], "uint8", 255),
         ("dprvi", "BYTE", gdal.GDT_Float32, np.nan, ["VH", "VV"], "uint8", 255),
-        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float16", np.nan),
-        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float16", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float32", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float32", np.nan),
     ],
 )
 def test_calc_index_by_gdal_raster(

From 6e8b0b97a9a19fa90ca6acb22b019a5121c03fc4 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 4 May 2026 10:39:45 +0200
Subject: [PATCH 33/40] redo changes

---
 tests/test_raster_index_util.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index 12e3e0ab..8f6ac23f 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -236,20 +236,20 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
     [
         ("ndvi", "BYTE", gdal.GDT_UInt16, 32676, ["B04", "B08", "b1"], "uint8", 255),
         ("ndvi", "BYTE", gdal.GDT_Float32, np.nan, ["B04", "B08"], "uint8", 255),
-        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float32", np.nan),
+        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float16", np.nan),
         (
             "ndvi",
             "FLOAT16",
             gdal.GDT_Float32,
             np.nan,
             ["B04", "B08"],
-            "float32",
+            "float16",
             np.nan,
         ),
         ("dprvi", "BYTE", gdal.GDT_UInt16, 32676, ["VH", "VV"], "uint8", 255),
         ("dprvi", "BYTE", gdal.GDT_Float32, np.nan, ["VH", "VV"], "uint8", 255),
-        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float32", np.nan),
-        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float32", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float16", np.nan),
+        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float16", np.nan),
     ],
 )
 def test_calc_index_by_gdal_raster(

From b4b70b994ea3007a4341f49d6761caf7452a295d Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Mon, 4 May 2026 13:15:39 +0200
Subject: [PATCH 34/40] pinned version rasterio and tests with minimal python
 3.12

---
 .github/workflows/tests.yml | 4 ++--
 ci/envs/latest.yml          | 2 +-
 ci/envs/minimal.yml         | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 3e7c2268..17443b7e 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -28,7 +28,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         dev: [false]
-        python: ["3.10", "3.11", "3.12"]
+        python: ["3.12"]
         env: ["latest"]
         # Use openblas instead of mkl saves 600 MB. Linux OK, 50% slower on Windows and OSX!
         extra: ["nomkl"]
@@ -36,7 +36,7 @@ jobs:
           - env: minimal
             os: ubuntu-latest
             dev: false
-            python: "3.10"
+            python: "3.12"
           - env: latest
             os: macos-latest
             dev: false
diff --git a/ci/envs/latest.yml b/ci/envs/latest.yml
index 5cc83c7c..336634fb 100644
--- a/ci/envs/latest.yml
+++ b/ci/envs/latest.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio
+  - rasterio >=1.5
   - rasterstats
   - rioxarray
   - scikit-learn
diff --git a/ci/envs/minimal.yml b/ci/envs/minimal.yml
index 9d8f287a..2d5d1f75 100644
--- a/ci/envs/minimal.yml
+++ b/ci/envs/minimal.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio
+  - rasterio =1.5
   - rasterstats
   - rioxarray
   - scikit-learn

From 94645468352ed7dfa057e1c3c07d62566d99f675 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 10:04:19 +0200
Subject: [PATCH 35/40] use python 3.13 for macos-latest test

---
 .github/workflows/tests.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 17443b7e..96f92e30 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -28,7 +28,7 @@ jobs:
       matrix:
         os: [ubuntu-latest]
         dev: [false]
-        python: ["3.12"]
+        python: ["3.10", "3.11", "3.12", "3.13"]
         env: ["latest"]
         # Use openblas instead of mkl saves 600 MB. Linux OK, 50% slower on Windows and OSX!
         extra: ["nomkl"]
@@ -40,7 +40,7 @@ jobs:
           - env: latest
             os: macos-latest
             dev: false
-            python: "3.12"
+            python: "3.13"
           - env: latest
             os: windows-latest
             dev: false

From 16c7b7402e97b648f167c6eaa5a6faff4442c514 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 10:05:02 +0200
Subject: [PATCH 36/40] skip tests when certain rasterio version

---
 environment-dev.yml             |  2 +-
 tests/test_raster_index_util.py | 92 +++++++++++++++++++++++++++++++--
 2 files changed, 89 insertions(+), 5 deletions(-)

diff --git a/environment-dev.yml b/environment-dev.yml
index be31ac47..93f95dbc 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -16,7 +16,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio
+  - rasterio <1.5
   - rasterstats
   - requests
   - rioxarray
diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index 8f6ac23f..197e2861 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -236,8 +236,19 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
     [
         ("ndvi", "BYTE", gdal.GDT_UInt16, 32676, ["B04", "B08", "b1"], "uint8", 255),
         ("ndvi", "BYTE", gdal.GDT_Float32, np.nan, ["B04", "B08"], "uint8", 255),
-        ("ndvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["B04", "B08"], "float16", np.nan),
-        (
+        pytest.param(
+            "ndvi",
+            "FLOAT16",
+            gdal.GDT_UInt16,
+            32676,
+            ["B04", "B08"],
+            "float16",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ < "1.5", reason="Requires rasterio 1.5 or higher"
+            ),
+        ),
+        pytest.param(
             "ndvi",
             "FLOAT16",
             gdal.GDT_Float32,
@@ -245,11 +256,84 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
             ["B04", "B08"],
             "float16",
             np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ < "1.5", reason="Requires rasterio 1.5 or higher"
+            ),
+        ),
+        pytest.param(
+            "ndvi",
+            "FLOAT16",
+            gdal.GDT_UInt16,
+            32676,
+            ["B04", "B08"],
+            "float32",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+            ),
+        ),
+        pytest.param(
+            "ndvi",
+            "FLOAT16",
+            gdal.GDT_Float32,
+            np.nan,
+            ["B04", "B08"],
+            "float32",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+            ),
         ),
         ("dprvi", "BYTE", gdal.GDT_UInt16, 32676, ["VH", "VV"], "uint8", 255),
         ("dprvi", "BYTE", gdal.GDT_Float32, np.nan, ["VH", "VV"], "uint8", 255),
-        ("dprvi", "FLOAT16", gdal.GDT_UInt16, 32676, ["VH", "VV"], "float16", np.nan),
-        ("dprvi", "FLOAT16", gdal.GDT_Float32, np.nan, ["VH", "VV"], "float16", np.nan),
+        pytest.param(
+            "dprvi",
+            "FLOAT16",
+            gdal.GDT_UInt16,
+            32676,
+            ["VH", "VV"],
+            "float16",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ < "1.5", reason="Requires rasterio 1.5 or higher"
+            ),
+        ),
+        pytest.param(
+            "dprvi",
+            "FLOAT16",
+            gdal.GDT_Float32,
+            np.nan,
+            ["VH", "VV"],
+            "float16",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ < "1.5", reason="Requires rasterio 1.5 or higher"
+            ),
+        ),
+        pytest.param(
+            "dprvi",
+            "FLOAT16",
+            gdal.GDT_UInt16,
+            32676,
+            ["VH", "VV"],
+            "float32",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+            ),
+        ),
+        pytest.param(
+            "dprvi",
+            "FLOAT16",
+            gdal.GDT_Float32,
+            np.nan,
+            ["VH", "VV"],
+            "float32",
+            np.nan,
+            marks=pytest.mark.skipif(
+                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+            ),
+        ),
     ],
 )
 def test_calc_index_by_gdal_raster(

From 77090f6d3e94f8219aa9666497a25880088d638d Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 10:45:22 +0200
Subject: [PATCH 37/40] rasterio not pinned

---
 ci/envs/latest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ci/envs/latest.yml b/ci/envs/latest.yml
index 336634fb..5cc83c7c 100644
--- a/ci/envs/latest.yml
+++ b/ci/envs/latest.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio >=1.5
+  - rasterio
   - rasterstats
   - rioxarray
   - scikit-learn

From 0b61113902f6fa2da028bd3e3cca4ec2f5073399 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 10:52:43 +0200
Subject: [PATCH 38/40] set minimal python version to 3.10

---
 .github/workflows/tests.yml | 2 +-
 ci/envs/minimal.yml         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index 96f92e30..b5fc907c 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -36,7 +36,7 @@ jobs:
           - env: minimal
             os: ubuntu-latest
             dev: false
-            python: "3.12"
+            python: "3.10"
           - env: latest
             os: macos-latest
             dev: false
diff --git a/ci/envs/minimal.yml b/ci/envs/minimal.yml
index 2d5d1f75..9d8f287a 100644
--- a/ci/envs/minimal.yml
+++ b/ci/envs/minimal.yml
@@ -15,7 +15,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio =1.5
+  - rasterio
   - rasterstats
   - rioxarray
   - scikit-learn

From e7507089a14a49cceacfbd68f532c93b98c828f7 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 12:20:36 +0200
Subject: [PATCH 39/40] refactor yml

---
 .github/workflows/tests.yml     |  4 +--
 environment-dev.yml             |  2 +-
 tests/test_raster_index_util.py | 45 ++++++++++++++++++++++++++++-----
 3 files changed, 41 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
index b5fc907c..a010a076 100644
--- a/.github/workflows/tests.yml
+++ b/.github/workflows/tests.yml
@@ -40,11 +40,11 @@ jobs:
           - env: latest
             os: macos-latest
             dev: false
-            python: "3.13"
+            python: "3.12"
           - env: latest
             os: windows-latest
             dev: false
-            python: "3.12"
+            python: "3.13"
             
     steps:
       - uses: actions/checkout@v6
diff --git a/environment-dev.yml b/environment-dev.yml
index 93f95dbc..be31ac47 100644
--- a/environment-dev.yml
+++ b/environment-dev.yml
@@ -16,7 +16,7 @@ dependencies:
   - pandas
   - psutil
   - pyproj
-  - rasterio <1.5
+  - rasterio
   - rasterstats
   - requests
   - rioxarray
diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index 197e2861..fd6d8c26 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -126,11 +126,38 @@ def test_calc_index_invalid(tmp_path):
     "index, pixel_type, process_options, expected_bands",
     [
         ("dprvi", "BYTE", {}, ["dprvi"]),
-        ("dprvi", "FLOAT16", None, ["dprvi"]),
+        pytest.param(
+            "dprvi",
+            "FLOAT16",
+            None,
+            ["dprvi"],
+            marks=pytest.mark.skipif(
+                rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio <> 1.4.4",
+            ),
+        ),
         ("dprvi", "FLOAT32", {}, ["dprvi"]),
         ("rvi", "BYTE", {}, ["rvi"]),
-        ("vvdvh", "FLOAT16", {}, ["vvdvh"]),
-        ("sarrgb", "FLOAT16", {}, ["vv", "vh", "vvdvh"]),
+        pytest.param(
+            "vvdvh",
+            "FLOAT16",
+            {},
+            ["vvdvh"],
+            marks=pytest.mark.skipif(
+                rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio <> 1.4.4",
+            ),
+        ),
+        pytest.param(
+            "sarrgb",
+            "FLOAT16",
+            {},
+            ["vv", "vh", "vvdvh"],
+            marks=pytest.mark.skipif(
+                rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio <> 1.4.4",
+            ),
+        ),
         ("sarrgb", "FLOAT32", {"log10": True}, ["vvdb", "vhdb", "vvdvhdb"]),
         ("sarrgb", "BYTE", {"log10": True}, ["vvdb", "vhdb", "vvdvhdb"]),
         (
@@ -269,7 +296,8 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
             "float32",
             np.nan,
             marks=pytest.mark.skipif(
-                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+                rasterio.__version__ >= "1.5" or rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio < 1.5",
             ),
         ),
         pytest.param(
@@ -281,7 +309,8 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
             "float32",
             np.nan,
             marks=pytest.mark.skipif(
-                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+                rasterio.__version__ >= "1.5" or rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio < 1.5",
             ),
         ),
         ("dprvi", "BYTE", gdal.GDT_UInt16, 32676, ["VH", "VV"], "uint8", 255),
@@ -319,7 +348,8 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
             "float32",
             np.nan,
             marks=pytest.mark.skipif(
-                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+                rasterio.__version__ >= "1.5" or rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio < 1.5",
             ),
         ),
         pytest.param(
@@ -331,7 +361,8 @@ def test_calc_index_s2(tmp_path, index, pixel_type):
             "float32",
             np.nan,
             marks=pytest.mark.skipif(
-                rasterio.__version__ >= "1.5", reason="Requires rasterio < 1.5"
+                rasterio.__version__ >= "1.5" or rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio < 1.5",
             ),
         ),
     ],

From 6f2bdc6c61b4f6ff4eb8037f5b30ec1977c39c61 Mon Sep 17 00:00:00 2001
From: KriWay <kris.vanwayenberge@lv.vlaanderen.be>
Date: Tue, 5 May 2026 12:38:41 +0200
Subject: [PATCH 40/40] refactor yml

---
 tests/test_raster_index_util.py | 21 ++++++++++++++++++++-
 1 file changed, 20 insertions(+), 1 deletion(-)

diff --git a/tests/test_raster_index_util.py b/tests/test_raster_index_util.py
index fd6d8c26..b7e64022 100644
--- a/tests/test_raster_index_util.py
+++ b/tests/test_raster_index_util.py
@@ -238,7 +238,26 @@ def test_calc_index_s1_error(
 
 
 @pytest.mark.parametrize(
-    "index, pixel_type", [("ndvi", "BYTE"), ("ndvi", "FLOAT16"), ("bsi", "FLOAT16")]
+    "index, pixel_type",
+    [
+        ("ndvi", "BYTE"),
+        pytest.param(
+            "ndvi",
+            "FLOAT16",
+            marks=pytest.mark.skipif(
+                rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio <> 1.4.4",
+            ),
+        ),
+        pytest.param(
+            "bsi",
+            "FLOAT16",
+            marks=pytest.mark.skipif(
+                rasterio.__version__ == "1.4.4",
+                reason="Requires rasterio <> 1.4.4",
+            ),
+        ),
+    ],
 )
 def test_calc_index_s2(tmp_path, index, pixel_type):
     # Prepare test data