Update Repository links

leonelluiscorado · Nov 8, 2024 · ddf8137 · ddf8137
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diff --git a/README.md b/README.md
@@ -57,10 +57,6 @@ You may create a Conda/Mamba environment specifically for this project, requirin
 
 You can execute the pipeline script by running `python3 gedi_pipeline.py`. Additional commands must be provided for the pipeline to work, such as GEDI product, version, start date and end date query and the output directory. You can run `python3 gedi_pipeline.py --help` for more information.
 
-## Modules as separate classes (WIP)
-
-You can also import the classes used by the Pipeline, as well as the Pipeline itself. Check the `example_notebook.ipynb` for a quick tutorial.
-
 ## Available GEDI Products
 
 - GEDI L1B Geolocated Waveform Data Global Footprint Level - [GEDI01_B](https://lpdaac.usgs.gov/products/gedi01_bv001/)

diff --git a/pipeline/finder.py b/pipeline/finder.py
@@ -4,9 +4,9 @@
 
 # Set up dictionary where key is GEDI shortname + version
 concept_ids = {
-    'GEDI01_B.002': 'C1908344278-LPDAAC_ECS', 
-    'GEDI02_A.002': 'C1908348134-LPDAAC_ECS', 
-    'GEDI02_B.002': 'C1908350066-LPDAAC_ECS',
+    'GEDI01_B.002': 'C2142749196-LPCLOUD', 
+    'GEDI02_A.002': 'C2142771958-LPCLOUD', 
+    'GEDI02_B.002': 'C2142776747-LPCLOUD',
     'GEDI04_A.002': 'C2237824918-ORNL_CLOUD'
 }
 
@@ -65,7 +65,6 @@ def __find_all_granules(self):
         try:
             # Send GET request to CMR granule search endpoint w/ product concept ID, bbox & page number, format return as json
             cmr_response = r.get(f"{cmr}{concept_ids[product]}&bounding_box={bbox}&pageNum={page}").json()['feed']['entry']
-
             # If 2000 features are returned, move to the next page and submit another request, and append to the response
             while len(cmr_response) % 2000 == 0:
                 page += 1

diff --git a/pipeline/subsetter.py b/pipeline/subsetter.py
@@ -13,14 +13,14 @@
 from utils.utils import get_date_from_gedi_fn
 
 # Default layers to be subset and exported, see README for information on how to add additional layers
-l1b_subset = ['/geolocation/latitude_bin0', '/geolocation/longitude_bin0', '/channel', '/shot_number',
+l1b_subset = ['/geolocation/latitude_bin0', '/geolocation/longitude_bin0', '/channel', '/shot_number', '/rx_sample_start_index',
              '/rxwaveform','/rx_sample_count', '/stale_return_flag', '/tx_sample_count', '/txwaveform',
              '/geolocation/degrade', '/geolocation/delta_time', '/geolocation/digital_elevation_model',
               '/geolocation/solar_elevation',  '/geolocation/local_beam_elevation',  '/noise_mean_corrected',
-             '/geolocation/elevation_bin0', '/geolocation/elevation_lastbin', '/geolocation/surface_type', '/geolocation/digital_elevation_model_srtm']
+             '/geolocation/elevation_bin0', '/geolocation/elevation_lastbin', '/geolocation/surface_type', '/geolocation/digital_elevation_model_srtm' '/geolocation/degrade']
 
 l2a_subset = ['/lat_lowestmode', '/lon_lowestmode', '/channel', '/shot_number', '/degrade_flag', '/delta_time', 
-             '/digital_elevation_model', '/elev_lowestmode', '/quality_flag', '/rh', '/sensitivity', '/digital_elevation_model_srtm', 
+             '/digital_elevation_model', '/elev_lowestmode', '/quality_flag', '/rh', '/sensitivity', '/rx_cumulative', '/digital_elevation_model_srtm', 
              '/elevation_bias_flag', '/surface_flag',  '/num_detectedmodes',  '/selected_algorithm',  '/solar_elevation']
 
 
@@ -224,7 +224,7 @@ def _select_sds_variables(self, gedi_file, gedi_df, beams, gedi_sds):
                     surfaces = ['land', 'ocean', 'sea_ice', 'land_ice', 'inland_water']
                     all_data = gedi_file[s][()]
 
-                    for i in range(gedi[s].shape[0]):
+                    for i in range(gedi_file[s].shape[0]):
                         beam_df[f'{surfaces[i]}'] = all_data[i][mindex:maxdex]
 
                     del all_data
@@ -322,4 +322,4 @@ def subset(self, granule):
         except ValueError:
             print(f"[Subsetter] {granule_name} intersects the bounding box of the input ROI, but no shots intersect final clipped ROI.")
 
-        return out_df
+        return out_df