ngiab-data-preprocess 4.5.1__py3-none-any.whl → 4.6.1__py3-none-any.whl

map_app/views.py

@@ -2,12 +2,14 @@ import json
 import logging
 from datetime import datetime
 from pathlib import Path
+import os
+import threading
 
 import geopandas as gpd
 from data_processing.create_realization import create_realization
 from data_processing.dataset_utils import save_and_clip_dataset
 from data_processing.datasets import load_aorc_zarr, load_v3_retrospective_zarr
-from data_processing.file_paths import file_paths
+from data_processing.file_paths import FilePaths
 from data_processing.forcings import create_forcings
 from data_processing.graph_utils import get_upstream_cats, get_upstream_ids
 from data_processing.subset import subset
@@ -23,24 +25,35 @@ logger = logging.getLogger(__name__)
 def index():
     return render_template("index.html")
 
-
+# this subset does not include the downstream nexus
 @main.route("/get_upstream_catids", methods=["POST"])
 def get_upstream_catids():
     cat_id = json.loads(request.data.decode("utf-8"))
     # give wb_id to get_upstream_cats because the graph search is 1000x faster
     wb_id = "wb-" + cat_id.split("-")[-1]
-    upstream_cats = get_upstream_cats(wb_id)
-    if cat_id in upstream_cats:
-        upstream_cats.remove(cat_id)
-    return list(upstream_cats), 200
-
-
+    upstream_cats = get_upstream_ids(wb_id, include_outlet=False)
+    cleaned_upstreams = set()
+    for id in upstream_cats:
+        if id.startswith("wb-"):
+            cleaned_upstreams.add("cat-" + id.split("-")[-1])
+    if cat_id in cleaned_upstreams:
+        cleaned_upstreams.remove(cat_id)
+    return list(cleaned_upstreams), 200
+
+# this subset includes the downstream nexus
 @main.route("/get_upstream_wbids", methods=["POST"])
 def get_upstream_wbids():
     cat_id = json.loads(request.data.decode("utf-8"))
-    upstream_ids = get_upstream_ids(cat_id)
-    # remove the selected cat_id from the set
-    return [id for id in upstream_ids if id.startswith("wb")], 200
+    # give wb_id to get_upstream_cats because the graph search is 1000x faster
+    wb_id = "wb-" + cat_id.split("-")[-1]
+    upstream_cats = get_upstream_ids(wb_id)
+    cleaned_upstreams = set()
+    for id in upstream_cats:
+        if id.startswith("wb-"):
+            cleaned_upstreams.add("cat-" + id.split("-")[-1])
+    if cat_id in cleaned_upstreams:
+        cleaned_upstreams.remove(cat_id)
+    return list(cleaned_upstreams), 200
 
 
 @main.route("/subset_check", methods=["POST"])
@@ -48,20 +61,28 @@ def subset_check():
     cat_ids = list(json.loads(request.data.decode("utf-8")))
     logger.info(cat_ids)
     subset_name = cat_ids[0]
-    run_paths = file_paths(subset_name)
+    run_paths = FilePaths(subset_name)
     if run_paths.geopackage_path.exists():
-        return "check required", 409
+        return str(run_paths.geopackage_path), 409
     else:
-        return "success", 200
+        return "no conflict",200
 
 
 @main.route("/subset", methods=["POST"])
 def subset_selection():
-    cat_ids = list(json.loads(request.data.decode("utf-8")))
+    #body: JSON.stringify({ 'cat_id': [cat_id], 'subset_type': subset_type})
+    data = json.loads(request.data.decode("utf-8"))
+    cat_ids = data.get("cat_id")
+    subset_type = data.get("subset_type")
     logger.info(cat_ids)
+    logger.info(subset_type)
     subset_name = cat_ids[0]
-    run_paths = file_paths(subset_name)
-    subset(cat_ids, output_gpkg_path=run_paths.geopackage_path, override_gpkg=True)
+
+    run_paths = FilePaths(subset_name)
+    if subset_type == "nexus":
+        subset(cat_ids, output_gpkg_path=run_paths.geopackage_path, override_gpkg=True)
+    else:
+        subset(cat_ids, output_gpkg_path=run_paths.geopackage_path, include_outlet=False, override_gpkg=True)
     return str(run_paths.geopackage_path), 200
 
 
@@ -72,21 +93,57 @@ def subset_to_file():
     logger.info(cat_ids)
     subset_name = cat_ids[0]
     total_subset = get_upstream_ids(cat_ids)
-    subset_paths = file_paths(subset_name)
+    subset_paths = FilePaths(subset_name)
     output_file = subset_paths.subset_dir / "subset.txt"
     output_file.parent.mkdir(parents=True, exist_ok=True)
     with open(output_file, "w") as f:
         f.write("\n".join(total_subset))
     return str(subset_paths.subset_dir), 200
 
-
+@main.route("/make_forcings_progress_file", methods=["POST"])
+def make_forcings_progress_file():
+    data = json.loads(request.data.decode("utf-8"))
+    subset_gpkg = Path(data.split("subset to ")[-1])
+    paths = FilePaths(subset_gpkg.stem.split("_")[0])
+    paths.forcing_progress_file.parent.mkdir(parents=True, exist_ok=True)
+    with open(paths.forcing_progress_file, "w") as f:
+        json.dump({"total_steps": 0, "steps_completed": 0}, f)
+    return str(paths.forcing_progress_file), 200
+
+@main.route("/forcings_progress", methods=["POST"])
+def forcings_progress_endpoint():
+    progress_file = Path(json.loads(request.data.decode("utf-8")))
+    with open(progress_file, "r") as f:
+        forcings_progress = json.load(f)
+    forcings_progress_all = forcings_progress['total_steps']
+    forcings_progress_completed = forcings_progress['steps_completed']
+    try:
+        percent = int((forcings_progress_completed / forcings_progress_all) * 100)
+    except ZeroDivisionError:
+        percent = "NaN"
+    return str(percent), 200
+
+def download_forcings(data_source, start_time, end_time, paths):
+    if data_source == "aorc":
+        raw_data = load_aorc_zarr(start_time.year, end_time.year)
+    elif data_source == "nwm":
+        raw_data = load_v3_retrospective_zarr()
+    else:
+        raise ValueError(f"Unknown data source: {data_source}")
+    gdf = gpd.read_file(paths.geopackage_path, layer="divides")
+    cached_data = save_and_clip_dataset(raw_data, gdf, start_time, end_time, paths.cached_nc_file)
+    return cached_data
+
+def compute_forcings(cached_data, paths):
+    create_forcings(cached_data, paths.output_dir.stem)  # type: ignore
+    
 @main.route("/forcings", methods=["POST"])
 def get_forcings():
     # body: JSON.stringify({'forcing_dir': forcing_dir, 'start_time': start_time, 'end_time': end_time}),
     data = json.loads(request.data.decode("utf-8"))
     subset_gpkg = Path(data.get("forcing_dir").split("subset to ")[-1])
     output_folder = Path(subset_gpkg.parent.parent)
-    paths = file_paths(output_dir=output_folder)
+    paths = FilePaths(output_dir=output_folder)
 
     start_time = data.get("start_time")
     end_time = data.get("end_time")
@@ -102,22 +159,14 @@ def get_forcings():
     app.debug = False
     logger.debug(f"get_forcings() disabled debug mode at {datetime.now()}")
     logger.debug(f"forcing_dir: {output_folder}")
-    try:
-        if data_source == "aorc":
-            data = load_aorc_zarr(start_time.year, end_time.year)
-        elif data_source == "nwm":
-            data = load_v3_retrospective_zarr()
-        gdf = gpd.read_file(paths.geopackage_path, layer="divides")
-        cached_data = save_and_clip_dataset(data, gdf, start_time, end_time, paths.cached_nc_file)
-
-        create_forcings(cached_data, paths.output_dir.stem)  # type: ignore
-    except Exception as e:
-        logger.info(f"get_forcings() failed with error: {str(e)}")
-        return jsonify({"error": str(e)}), 500
     app.debug = debug_enabled
 
-    return "success", 200
-
+    cached_data = download_forcings(data_source, start_time, end_time, paths)
+    # threading implemented so that main process can periodically poll progress file
+    thread = threading.Thread(target=compute_forcings,
+                              args=(cached_data, paths))
+    thread.start()
+    return "started", 200
 
 @main.route("/realization", methods=["POST"])
 def get_realization():

ngiab_data_cli/__main__.py

@@ -9,13 +9,14 @@ with rich.status.Status("loading") as status:
     import subprocess
     import time
     from multiprocessing import cpu_count
+    from pathlib import Path
 
     import geopandas as gpd
     from data_processing.create_realization import create_lstm_realization, create_realization
     from data_processing.dask_utils import shutdown_cluster
     from data_processing.dataset_utils import save_and_clip_dataset
     from data_processing.datasets import load_aorc_zarr, load_v3_retrospective_zarr
-    from data_processing.file_paths import file_paths
+    from data_processing.file_paths import FilePaths
     from data_processing.forcings import create_forcings
     from data_processing.gpkg_utils import get_cat_from_gage_id, get_catid_from_point
     from data_processing.graph_utils import get_upstream_cats
@@ -23,57 +24,63 @@ with rich.status.Status("loading") as status:
     from data_sources.source_validation import validate_hydrofabric, validate_output_dir
     from ngiab_data_cli.arguments import parse_arguments
     from ngiab_data_cli.custom_logging import set_logging_to_critical_only, setup_logging
-    
 
 
 def validate_input(args: argparse.Namespace) -> Tuple[str, str]:
     """Validate input arguments."""
 
+    feature_name = None
+    output_folder = None
+
     if args.vpu:
         if not args.output_name:
             args.output_name = f"vpu-{args.vpu}"
             validate_output_dir()
         return args.vpu, args.output_name
 
-    input_feature = args.input_feature.replace("_", "-")
-
-    # look at the prefix for autodetection, if -g or -l is used then there is no prefix
-    if len(input_feature.split("-")) > 1:
-        prefix = input_feature.split("-")[0]
-        if prefix.lower() == "gage":
-            args.gage = True
-        elif prefix.lower() == "wb":
-            logging.warning("Waterbody IDs are no longer supported!")
-            logging.warning(f"Automatically converting {input_feature} to catid")
-            time.sleep(2)
-
-    # always add or replace the prefix with cat if it is not a lat lon or gage
-    if not args.latlon and not args.gage:
-        input_feature = "cat-" + input_feature.split("-")[-1]
-
-    if args.latlon and args.gage:
-        raise ValueError("Cannot use both --latlon and --gage options at the same time.")
-
-    if args.latlon:
-        validate_hydrofabric()
-        feature_name = get_cat_id_from_lat_lon(input_feature)
-        logging.info(f"Found {feature_name} from {input_feature}")
-    elif args.gage:
-        validate_hydrofabric()
-        feature_name = get_cat_from_gage_id(input_feature)
-        logging.info(f"Found {feature_name} from {input_feature}")
-    else:
-        feature_name = input_feature
-
-    if args.output_name:
-        output_folder = args.output_name
-        validate_output_dir()
-    elif args.gage:
-        output_folder = input_feature
-        validate_output_dir()
-    else:
-        output_folder = feature_name
-        validate_output_dir()
+    if args.input_feature:
+        input_feature = args.input_feature.replace("_", "-")
+
+        if args.gage and not input_feature.startswith("gage-"):
+            input_feature = "gage-" + input_feature
+
+        # look at the prefix for autodetection, if -g or -l is used then there is no prefix
+        if len(input_feature.split("-")) > 1:
+            prefix = input_feature.split("-")[0]
+            if prefix.lower() == "gage":
+                args.gage = True
+            elif prefix.lower() == "wb":
+                logging.warning("Waterbody IDs are no longer supported!")
+                logging.warning(f"Automatically converting {input_feature} to catid")
+                time.sleep(2)
+
+        # always add or replace the prefix with cat if it is not a lat lon or gage
+        if not args.latlon and not args.gage:
+            input_feature = "cat-" + input_feature.split("-")[-1]
+
+        if args.latlon and args.gage:
+            raise ValueError("Cannot use both --latlon and --gage options at the same time.")
+
+        if args.latlon:
+            validate_hydrofabric()
+            feature_name = get_cat_id_from_lat_lon(input_feature)
+            logging.info(f"Found {feature_name} from {input_feature}")
+        elif args.gage:
+            validate_hydrofabric()
+            feature_name = get_cat_from_gage_id(input_feature)
+            logging.info(f"Found {feature_name} from {input_feature}")
+        else:
+            feature_name = input_feature
+
+        if args.output_name:
+            output_folder = args.output_name
+            validate_output_dir()
+        elif args.gage:
+            output_folder = input_feature
+            validate_output_dir()
+        else:
+            output_folder = feature_name
+            validate_output_dir()
 
     return feature_name, output_folder
 
@@ -87,7 +94,7 @@ def get_cat_id_from_lat_lon(input_feature: str) -> str:
         raise ValueError("Lat Lon input must be comma separated e.g. -l 54.33,-69.4")
 
 
-def set_dependent_flags(args, paths: file_paths):
+def set_dependent_flags(args, paths: FilePaths):
     # if validate is set, run everything that is missing
     if args.validate:
         logging.info("Running all missing steps required to run ngiab.")
@@ -109,7 +116,7 @@ def set_dependent_flags(args, paths: file_paths):
     return args
 
 
-def validate_run_directory(args, paths: file_paths):
+def validate_run_directory(args, paths: FilePaths):
     # checks the folder that is going to be run, enables steps that are needed to populate the folder
     if not paths.subset_dir.exists():
         logging.info("Subset folder does not exist, enabling subset, forcings, and realization.")
@@ -134,8 +141,23 @@ def main() -> None:
         args = parse_arguments()
         if args.debug:
             logging.getLogger("data_processing").setLevel(logging.DEBUG)
+
+        if args.output_root:
+            with open(FilePaths.config_file, "w") as config_file:
+                config_file.write(str(Path(args.output_root).expanduser().absolute()))
+            logging.info(
+                f"Changed default directory where outputs are stored to {args.output_root}"
+            )
+
         feature_to_subset, output_folder = validate_input(args)
-        paths = file_paths(output_folder)
+
+        if (feature_to_subset, output_folder) == (
+            None,
+            None,
+        ):  # in case someone just passes an argument to change default output dir
+            return
+
+        paths = FilePaths(output_folder)
         args = set_dependent_flags(args, paths)  # --validate
         if feature_to_subset:
             logging.info(f"Processing {feature_to_subset} in {paths.output_dir}")
@@ -186,9 +208,14 @@ def main() -> None:
             gage_id = None
             if args.gage:
                 gage_id = args.input_feature
-            if args.lstm:
+                if not gage_id.startswith("gage-"):
+                    gage_id = "gage-" + gage_id
+            if args.lstm or args.lstm_rust:
                 create_lstm_realization(
-                    output_folder, start_time=args.start_date, end_time=args.end_date
+                    output_folder,
+                    start_time=args.start_date,
+                    end_time=args.end_date,
+                    use_rust=args.lstm_rust,
                 )
             else:
                 create_realization(
@@ -202,7 +229,7 @@ def main() -> None:
 
         if args.run:
             logging.info("Running Next Gen using NGIAB...")
-            
+
             try:
                 subprocess.run("docker pull awiciroh/ciroh-ngen-image:latest", shell=True)
             except:

ngiab_data_cli/arguments.py

@@ -11,7 +11,14 @@ def parse_arguments() -> argparse.Namespace:
     parser = argparse.ArgumentParser(
         description="Subsetting hydrofabrics, forcing generation, and realization creation"
     )
-    group = parser.add_mutually_exclusive_group(required=True)
+    group = parser.add_mutually_exclusive_group(required=False)
+
+    parser.add_argument(
+        "--output_root",
+        type=str,
+        help="Path to new default directory where outputs in the future will be stored",
+    )
+
     group.add_argument(
         "-i",
         "--input_feature",
@@ -97,7 +104,7 @@ def parse_arguments() -> argparse.Namespace:
         "-o",
         "--output_name",
         type=str,
-        help="Name of the output folder",
+        help="Custom data output folder name in lieu of the default, which is the ID of the input feature",
     )
     parser.add_argument(
         "-D",
@@ -105,11 +112,17 @@ def parse_arguments() -> argparse.Namespace:
         action="store_true",
         help="enable debug logging",
     )
-    parser.add_argument(
+    lstm_group = parser.add_mutually_exclusive_group(required=False)
+    lstm_group.add_argument(
         "--lstm",
         action="store_true",
         help="enable LSTM model realization and forcings",
     )
+    lstm_group.add_argument(
+        "--lstm_rust",
+        action="store_true",
+        help="enable experimental high speed Rust bindings of LSTM model realization and forcings",
+    )
     parser.add_argument(
         "--nwm_gw",
         action="store_true",

{ngiab_data_preprocess-4.5.1.dist-info → ngiab_data_preprocess-4.6.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ngiab_data_preprocess
-Version: 4.5.1
+Version: 4.6.1
 Summary: Graphical Tools for creating Next Gen Water model input data.
 Author-email: Josh Cunningham <jcunningham8@ua.edu>
 Project-URL: Homepage, https://github.com/CIROH-UA/NGIAB_data_preprocess

ngiab_data_preprocess-4.6.1.dist-info/RECORD

@@ -0,0 +1,43 @@
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+data_processing/dataset_utils.py,sha256=0FhspUlGUs0iJLwYY0dl_1fjt0_zwhe9Hl-jikIgrpk,8312
+data_processing/datasets.py,sha256=_EJ1uZSWTU1HWpvF7TQSikneJqWZFikTrdo9usCV8A0,4665
+data_processing/file_paths.py,sha256=7MpwfIQewLRrDpAw1dxTjTperUwOk3EC_kthmnJSRII,4851
+data_processing/forcings.py,sha256=8WY3w-TrhuCexnvUtvNCaUM9Uu3F5IaSO2qpIsUEtyg,21527
+data_processing/gpkg_utils.py,sha256=VoQG53zaGcdmkU9M_7kRrk_vygRGJV9E-wX-T48Rzj8,20576
+data_processing/graph_utils.py,sha256=4D72wMSiCRKCPC7JUz7XCoaISRGLuqDx6wpeO_VP8fk,8301
+data_processing/s3fs_utils.py,sha256=ki1EmA0ezV0r26re6dRWIGzL5FudGdwF9Qw1eVLR0Bc,2747
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