AK Lidar + AK Bonnell GPR Add (#28)

* Updated minor things in the readme

* Added in script published lidar canopy height and snow depth for farmers-creamers AK

* Added in CSU gpr for farmers-creamers in AK.

* Fixed  #27

README.rst

@@ -36,7 +36,7 @@ Features
 * Interpret and upload csv, rasters, uavsar files,
 * Full provenance for download and upload
 * Manage Site, Point, Profile and Raster Data
-* PostgreSQL Database end point for researchers
+* Postgres SQL Database end point for researchers
 
 
 Installing
@@ -49,7 +49,7 @@ Mac OS
 
 First ensure you have following prerequisites:
 
-* Python3.7 +
+* Python3.8 +
 * HomeBrew
 
 Then to install the postgres database with postgis functionality run:
@@ -64,7 +64,7 @@ Ubuntu
 
 First ensure you have following prerequisites:
 
-* Python3.7 +
+* Python3.8 +
 * wget
 
 Then to install the postgres database with postgis functionality run:
@@ -121,7 +121,7 @@ Quickly test your installation by running:
 This will run a series of tests that create a small database and confirm
 that samples of the data sets references in `./scripts/upload` folder can be
 uploaded seamlessly. These tests can serve as a nice way to see how to
-interact with the database but also serve to confirm our reproduciblity.
+interact with the database but also serve to confirm our reproducibility.
 
 The goal of this project is to have high fidelity in data
 interpretation/submission to the database. To see the current

scripts/download/nsidc_sources.txt

@@ -9,3 +9,5 @@ https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX20_SD_TLI.001/2019.09.29/SNEX20_SD_TLI
 https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX20_TS_SP.002/
 https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX21_TS_SP.001/
 https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX_Met.001/
+https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX23_Lidar.001/2022.10.24/SNEX23_Lidar_FLCF_CH_0.25M_20221024_V01.0.tif
+https://n5eil01u.ecs.nsidc.org/SNOWEX/SNEX23_Lidar.001/2023.03.11/SNEX23_Lidar_FLCF_SD_0.25M_20230311_V01.0.tif

scripts/upload/add_AK_lidar.py

@@ -0,0 +1,77 @@
+"""
+Upload the SnowEx AK lidar products from Farmers and Creamers field
+for now.
+
+# To run with all the scripts
+python run.py
+
+# To run individually
+python add_AK_lidar.py
+"""
+import os
+from datetime import date
+from pathlib import Path
+from subprocess import Popen
+
+from snowex_db.batch import UploadRasterBatch
+
+
+def main():
+    """
+    Uploader script partial SnowEx Lidar
+    """
+
+    # Typical kwargs for the dataset
+    kwargs = {'instrument': 'lidar',
+              'observers': 'chris larsen',
+              'description': '0.5m products', # Datasheet says 0.25 but data is actually 0.5
+              'tiled': True,
+              'epsg': 26906, # Alaska is Zone 6
+              'no_data': -9999,
+              'in_timezone': 'AKST',
+              'doi':'https://doi.org/10.5067/BV4D8RRU1H7U',
+              "site_name": "farmers-creamers"
+              }
+    # Build a list of uploaders and then execute them
+    uploaders = []
+
+    # Directory of SNOWEX products
+    lidar_dir = Path('../download/data/SNOWEX/SNEX23_Lidar.001/')
+    reprojected = lidar_dir.joinpath('reprojected')
+
+    if not reprojected.is_dir():
+        os.mkdir(reprojected)
+
+
+    # Reproject using GDAL
+    print('Reprojecting files...')
+    raw_files = lidar_dir.glob('*/*.tif')
+    for f in raw_files:
+        # Watch out for files already in the reprojection
+        if f.parent != reprojected:
+            output = reprojected.joinpath(f.name)
+            cmd = f'gdalwarp -overwrite -t_srs EPSG:{kwargs["epsg"]} {f} {output}'
+            print(cmd)
+            p = Popen(cmd,shell=True)
+            p.wait()
+
+    ######################################## Farmers/Creamers Field (FLCF) ###################################################
+    # Snow off - canopy height
+    f = reprojected.joinpath("SNEX23_Lidar_FLCF_CH_0.25M_20221024_V01.0.tif")
+    uploaders.append(UploadRasterBatch([f], date=date(2022, 10, 24),
+                                       type="canopy_height", units="meters", **kwargs))
+
+    # Snow Depth
+    f =  reprojected.joinpath(reprojected, "SNEX23_Lidar_FLCF_SD_0.25M_20230311_V01.0.tif")
+    uploaders.append(UploadRasterBatch([f], date=date(2023, 3, 11),
+                                       type="depth", units="meters", **kwargs))
+
+    errors = 0
+    for u in uploaders:
+        u.push()
+        errors += len(u.errors)
+
+
+# Add this so you can run your script directly without running run.py
+if __name__ == '__main__':
+    main()

scripts/upload/add_csu_gpr_AK.py

@@ -0,0 +1,66 @@
+"""
+Read in the SnowEx 2023 CSU GPR data collected at Farmers Loop and Creamers Field.
+
+1. Data is preliminary and currently only available via email from Randall B.
+2A. python run.py # To run all together all at once
+2B. python add_gpr.py # To run individually
+
+"""
+
+from pathlib import Path
+from snowexsql.db import get_db
+from snowex_db.upload import PointDataCSV
+import pandas as pd
+
+
+def main():
+    file = Path('../download/data/SnowEx223_FLCF_1GHz_GPR_CSU.csv')
+
+    # Fix quirks
+    df = pd.read_csv(file, dtype=str)
+
+    # Upload is not able to handle the Notes col. So just remove it for now
+    modified = file.parent.joinpath(file.stem + f'_mod{file.suffix}')
+    print(f"Removing Notes Column prior to upload. Writing to {modified}")
+
+    coi = [c for c in df.columns if c != 'Notes']
+
+    # No time is a problem. Use 12 AKST == 9pm (21:00) UTC
+    df['Time[HHMM]'] = '21:00'
+
+    # Write out the modified version
+    df[coi].to_csv(modified, index=False)
+
+
+    kwargs = {
+        # Keyword argument to upload depth measurements
+        'depth_is_metadata': False,
+
+        # Constant Metadata for the GPR data
+        'site_name': 'farmers-creamers',
+        'observers': 'Randall Bonnell',
+        'instrument': 'pulseEkko pro 1 GHz GPR',
+        'in_timezone': 'UTC',
+        'out_timezone': 'UTC',
+        'doi': None, # Data is preliminary
+        'epsg': 26906
+    }
+
+    # Grab a db connection to a local db named snowex
+    db_name = 'localhost/snowex'
+    engine, session = get_db(db_name, credentials='./credentials.json')
+
+    # Instantiate the point uploader
+    csv = PointDataCSV(modified, **kwargs)
+    # Push it to the database
+    csv.submit(session)
+
+    # Close out the session with the DB
+    session.close()
+
+    # return the number of errors for run.py can report it
+    return len(csv.errors)
+
+
+if __name__ == '__main__':
+    main()

snowex_db/metadata.py

@@ -336,7 +336,7 @@ class ExtendedSnowExProfileVariables(SnowExProfileVariables):
     )
     ELEVATION = MeasurementDescription(
         'elevation', "Elevation",
-        ['elev_m', 'elevation']
+        ['elev_m', 'elevation', 'elevationwgs84']
     )
     EQUIPMENT = MeasurementDescription(
         'equipment', "Equipment",

snowex_db/upload.py

@@ -515,6 +515,7 @@ def persist_cog(self):
         if exists(self._cog_path):
             if self.use_s3:
                 self._key_name = join(self.s3_prefix, self._cog_path.name)
+                LOG.info(f'Uploading {self._cog_path} to {self.s3_bucket}/{self._key_name}')
                 s3 = boto3.resource('s3', region_name=self.AWS_REGION)
                 s3.meta.client.upload_file(
                     str(self._cog_path),  # local file