MAINT: avoid using marker terminology

CHANGELOG.md

@@ -23,12 +23,12 @@
     - Rename section `dirs` to `paths`.
     - Remove `general.run_id`.
 - Rename some main modules to make naming more logical with non-cropclassification
-  markers being added (#162)
+  detections being added (#162)
 
 ### Improvements
 
-- Add feature "cross-prediction-models" to avoid markers being calculated on parcels
-  using a model that used this parcel in its training (#142, #143)
+- Add feature "cross-prediction-models" to be able to avoid classifications being
+  calculated on parcels using a model that used this parcel in its training (#142, #143)
 - Consolidated some landcover pre-processing ignore codes (#120)
 - Add some extra global accuracies (precision, recall, f1) to report (#119)
 - Add option `images.on_missing_images` to be able to ignore errors in the
@@ -77,8 +77,9 @@
 - Improve configurability + defaults of keras mlp classifier (#115)
 - Make image profiles to be used in a classification configurable in a config file (#56)
 - Add option to overrule configuration parameters at runtime (#92)
-- If image period is e.g. "weekly", align `start_date` of a marker to the next monday
-  instead of the previous one to avoid using data outside the dates provided (#83, #84)
+- If image period is e.g. "weekly", align `start_date` of the timeseries data used in a
+  detection to the next monday instead of the previous one to avoid using data outside
+  the dates provided (#83, #84)
 - Add method "best available pixel" on openeo for S2 (#70)
 - Add utility script to recalculate reports for an existing run + make recalculation
   more robust for old runs (#91, #102, #103, #104, #106)

README.md

@@ -45,4 +45,4 @@ Mind: the sentinel CARD image structure as expected for timeseries calculation d
 
 5. Start a crop classification
 
-Run `cropclassification -t <tasks_dir>`, with a 'calc_marker' type of task in the tasks dir.
+Run `cropclassification -t <tasks_dir>`, with a 'calc_cropclass' type of task in the tasks dir.

bin_util/calc_periodic_mosaic.py

@@ -41,7 +41,7 @@ def main():
 
     image_profiles_path = (
         Path(__file__).resolve().parent.parent
-        / "markers/_config/image_profiles.ini"
+        / "monitoring/_config/image_profiles.ini"
     )
     imageprofiles = conf._get_image_profiles(image_profiles_path)
 

cropclassification/calc_cropclass.py

@@ -25,7 +25,7 @@ def run_cropclass(
     default_basedir: Path,
     config_overrules: list[str] = [],
 ):
-    """Runs a crop classification marker using the setting in the config_paths.
+    """Runs a crop classification using the setting in the config_paths.
 
     Args:
         config_paths (List[Path]): the config files to load

cropclassification/general.ini

@@ -1,12 +1,12 @@
-# This is a config file with the shared/default settings for all markers. 
+# This is a config file with the shared/default settings for all detections. 
 
 # The task section contains information about the task you want to run 
 [task]
 
 # The action you want to run:
 #   - calc_timeseries: calculate a Sentinel timeseries for a file with polygons
-#   - calc_maker: calculate a marker
-#   - calc_periodic_mosaic: calculate periodic mosai
+#   - calc_cropclass: run a crop classification
+#   - calc_periodic_mosaic: create periodic mosaic images
 action = MUST_OVERRIDE
 
 # Extra config files to load, in addition to general defaults.
@@ -161,19 +161,19 @@ min_nb_pixels_train = ${marker:min_nb_pixels}
 
 # classes that will be ignored for training + won't receive a prediction
 classes_to_ignore = ${classes_to_ignore_default}
-# define default ignores here, so it is easy to ADD extra for specific markers
+# define default ignores here, so it is easy to ADD extra for specific classifications
 classes_to_ignore_default = IGNORE_DIFFICULT_PERMANENT_CLASS, IGNORE_UNIMPORTANT, IGNORE_NOT_ENOUGH_SAMPLES, IGNORE_EARLY_CROP, IGNORE_LATE_CROP, IGNORE_LATE_MAINCROP, IGNORE_NEW_GRASSLAND, IGNORE_NOT_DECLARED
 
 # classes that should be ignored for training, but have to get a prediction
 classes_to_ignore_for_train = ${classes_to_ignore_for_train_default}
-# define default ignores here, so it is easy to ADD extra for specific markers
+# define default ignores here, so it is easy to ADD extra for specific classifications
 classes_to_ignore_for_train_default = UNKNOWN
 
 # classes that should specified as unimportant in the reporting
 # Remark: this doesn't influence the training or predicting, these need to be set in 
 # the other paremeters!
 classes_to_ignore_unimportant = ${classes_to_ignore_unimportant_default}
-# define default ignores here, so it is easy to ADD extra for specific markers
+# define default ignores here, so it is easy to ADD extra for specific classifications
 classes_to_ignore_unimportant_default = IGNORE_UNIMPORTANT, IGNORE_LATE_MAINCROP, IGNORE_NOT_DECLARED
 
 # strategy to balance the training dataset for the marker. Possible values:

markers/_images_periodic/roi_test/s1-grd-sigma0-asc-weekly/s1-grd-sigma0-asc-weekly_2024-03-04_2024-03-10_VV-VH_last.tif.json

@@ -23,6 +23,6 @@
         "VH"
     ],
     "time_reducer": "first",
-    "path": "C:/Users/local_PIEROG/Temp/1/pytest-of-PIEROG/pytest-5/test_calc_periodic_mosaic_loca0/markers/periodic_mosaic/roi_test/s1-grd-sigma0-asc/s1-grd-sigma0-asc_2024-03-04_2024-03-10_VV-VH_first.tif",
+    "path": "C:/Users/local_PIEROG/Temp/1/pytest-of-PIEROG/pytest-5/test_calc_periodic_mosaic_loca0/monitoring/periodic_mosaic/roi_test/s1-grd-sigma0-asc/s1-grd-sigma0-asc_2024-03-04_2024-03-10_VV-VH_first.tif",
     "orbit": "asc"
 }

markers/_images_periodic/roi_test/s1-grd-sigma0-asc-weekly/s1-grd-sigma0-asc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif.json

@@ -25,7 +25,7 @@
         "VH"
     ],
     "time_reducer": "last",
-    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/markers/_images_periodic/BEFL/s1-grd-sigma0-asc-weekly/s1-grd-sigma0-asc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/monitoring/_images_periodic/BEFL/s1-grd-sigma0-asc-weekly/s1-grd-sigma0-asc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif",
     "job_options": null,
     "process_options": null
 }

markers/_images_periodic/roi_test/s1-grd-sigma0-desc-weekly/s1-grd-sigma0-desc-weekly_2024-03-04_2024-03-10_VV-VH_last.tif.json

@@ -23,6 +23,6 @@
         "VH"
     ],
     "time_reducer": "first",
-    "path": "C:/Users/local_PIEROG/Temp/1/pytest-of-PIEROG/pytest-5/test_calc_periodic_mosaic_loca0/markers/periodic_mosaic/roi_test/s1-grd-sigma0-desc/s1-grd-sigma0-desc_2024-03-04_2024-03-10_VV-VH_first.tif",
+    "path": "C:/Users/local_PIEROG/Temp/1/pytest-of-PIEROG/pytest-5/test_calc_periodic_mosaic_loca0/monitoring/periodic_mosaic/roi_test/s1-grd-sigma0-desc/s1-grd-sigma0-desc_2024-03-04_2024-03-10_VV-VH_first.tif",
     "orbit": "desc"
 }

markers/_images_periodic/roi_test/s1-grd-sigma0-desc-weekly/s1-grd-sigma0-desc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif.json

@@ -25,7 +25,7 @@
         "VH"
     ],
     "time_reducer": "last",
-    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/markers/_images_periodic/BEFL/s1-grd-sigma0-desc-weekly/s1-grd-sigma0-desc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/monitoring/_images_periodic/BEFL/s1-grd-sigma0-desc-weekly/s1-grd-sigma0-desc-weekly_2024-03-11_2024-03-17_VV-VH_last.tif",
     "job_options": null,
     "process_options": null
 }

markers/_images_periodic/roi_test/s2-agri-weekly/s2-agri-weekly_2024-03-11_2024-03-17_B02-B03-B04-B08-B11-B12_mean.tif.json

@@ -29,7 +29,7 @@
         "B12"
     ],
     "time_reducer": "mean",
-    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/markers/_images_periodic/BEFL/s2-agri-weekly/s2-agri-weekly_2024-03-11_2024-03-17_B02-B03-B04-B08-B11-B12_mean.tif",
+    "path": "C:/Users/local_KRIWAY/Temp/1/pytest-of-KRIWAY/pytest-36/test_end2end0/monitoring/_images_periodic/BEFL/s2-agri-weekly/s2-agri-weekly_2024-03-11_2024-03-17_B02-B03-B04-B08-B11-B12_mean.tif",
     "job_options": {
         "driver-memoryOverhead": "5G"
     },

tests/test_config_helper.py

@@ -39,7 +39,7 @@ def test_read_config():
     ]
     conf.read_config(
         config_paths=config_paths,
-        default_basedir=SampleData.markers_dir,
+        default_basedir=SampleData.base_dir,
         overrules=[
             "paths.images_periodic_dir=_satellite_periodic/BEFL",
         ],
@@ -80,7 +80,7 @@ def test_read_config_overrule():
     config_paths = SampleData.config_dir / "cropgroup.ini"
     conf.read_config(
         config_paths=config_paths,
-        default_basedir=SampleData.markers_dir,
+        default_basedir=SampleData.base_dir,
         overrules=[
             "roi.roi_name=ROI_NAME_TEST",
             "paths.images_periodic_dir=_satellite_periodic/BEFL",

tests/test_end2end.py

@@ -24,11 +24,11 @@ def test_task_calc_marker(tmp_path, balancing_strategy, cross_pred_models):
     if not HAS_QGIS:
         pytest.skip("QGIS is needed for timeseries calculation, but is not available.")
 
-    markers_dir = tmp_path / test_helper.SampleData.markers_dir.name
-    shutil.copytree(test_helper.SampleData.markers_dir, markers_dir)
+    base_dir = tmp_path / test_helper.SampleData.base_dir.name
+    shutil.copytree(test_helper.SampleData.base_dir, base_dir)
 
     # Create configparser and read task file!
-    tasks_dir = markers_dir / "_tasks"
+    tasks_dir = base_dir / "_tasks"
     ignore_dir = tasks_dir / "ignore"
     task_ini = "task_test_calc_marker.ini"
 
@@ -44,7 +44,7 @@ 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"
+    run_dir = base_dir / f"2024_CROPGROUP/Run_{today_str}_001"
     assert run_dir.exists()
     base_stem = "Prc_BEFL_2023_2023-07-24_bufm5_weekly_predict_all"
     assert (run_dir / f"{base_stem}.gpkg").exists()
@@ -71,10 +71,10 @@ def test_task_calc_marker(tmp_path, balancing_strategy, cross_pred_models):
 
 
 def test_task_calc_periodic_mosaic(tmp_path):
-    markers_dir = tmp_path / test_helper.SampleData.markers_dir.name
-    shutil.copytree(test_helper.SampleData.markers_dir, markers_dir)
+    base_dir = tmp_path / test_helper.SampleData.base_dir.name
+    shutil.copytree(test_helper.SampleData.base_dir, base_dir)
     # Create configparser and read task file!
-    tasks_dir = markers_dir / "_tasks"
+    tasks_dir = base_dir / "_tasks"
     ignore_dir = tasks_dir / "ignore"
     task_ini = "task_test_calc_periodic_mosaic.ini"
 
@@ -83,6 +83,6 @@ def test_task_calc_periodic_mosaic(tmp_path):
     taskrunner.run_tasks(tasksdir=tasks_dir)
 
     # Check if a log file was written
-    log_dir = markers_dir / "log"
+    log_dir = base_dir / "log"
     assert log_dir.exists()
     assert len(list(log_dir.glob("*.log"))) == 1

tests/test_helper.py

@@ -7,13 +7,13 @@
 
 
 class SampleData:
-    markers_dir = Path(__file__).resolve().parent.parent / "markers"
-    tasks_dir = markers_dir / "_tasks"
-    config_dir = markers_dir / "_config"
-    inputdata_dir = markers_dir / "_inputdata"
-    refe_dir = markers_dir / "_refe"
-    image_dir = markers_dir / "_images_periodic"
-    input_dir = markers_dir / "_inputdata"
+    base_dir = Path(__file__).resolve().parent.parent / "monitoring"
+    tasks_dir = base_dir / "_tasks"
+    config_dir = base_dir / "_config"
+    inputdata_dir = base_dir / "_inputdata"
+    refe_dir = base_dir / "_refe"
+    image_dir = base_dir / "_images_periodic"
+    input_dir = base_dir / "_inputdata"
     roi_name = "roi_test"
     image_roi_dir = image_dir / roi_name
 

tests/test_mosaic_util.py

@@ -11,7 +11,7 @@
 
 def test_calc_periodic_mosaic_s2(tmp_path):
     # Prepare test data
-    sample_dir = SampleData.markers_dir
+    sample_dir = SampleData.base_dir
     test_dir = tmp_path / sample_dir.name
     shutil.copytree(sample_dir, test_dir)
 
@@ -48,7 +48,7 @@ def test_calc_periodic_mosaic_s2(tmp_path):
 
 def test_calc_periodic_mosaic_s1_local_index_dprvi(tmp_path):
     # Prepare test data
-    sample_dir = SampleData.markers_dir
+    sample_dir = SampleData.base_dir
     test_dir = tmp_path / sample_dir.name
     shutil.copytree(sample_dir, test_dir)
 

tests/test_zonal_stats_bulk.py

@@ -15,7 +15,7 @@ def test_zonal_stats_bulk(tmp_path, engine):
         pytest.skip("QGIS is not available on this system.")
 
     # Prepare test data
-    sample_dir = SampleData.markers_dir
+    sample_dir = SampleData.base_dir
     test_dir = tmp_path / sample_dir.name
     shutil.copytree(sample_dir, test_dir)