Squashed commit of the following:

commit 4a270e1
Merge: 64bd0b0 d14fce4
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Thu Jun 6 07:04:33 2024 -0700

    Merge branch 'pr-255' into new_release/1.2.6

commit 64bd0b0
Merge: 2f84fa2 e7d8e89
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Thu Jun 6 07:01:40 2024 -0700

    Merge branch 'issue/259/get_kmeans_cluster' into new_release/1.2.6

commit 2f84fa2
Merge: c0b2d01 606488f
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Thu Jun 6 07:01:25 2024 -0700

    Merge branch 'temp/issue/patch/251' into new_release/1.2.6

commit e7d8e89
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue Jun 4 15:38:46 2024 -0700

commit 7ffdf9d
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue Jun 4 13:11:09 2024 -0700

commit d14fce4
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue Jun 4 12:37:53 2024 -0700

commit 111d8ae
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue Jun 4 12:14:09 2024 -0700

    Fix the issue where ROI IDs were not converted to strings if passed as ints

commit 5e5da50
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue Jun 4 12:13:28 2024 -0700

commit 606488f
Merge: a366bb0 7a397c9
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Wed May 29 19:41:10 2024 -0700

    Merge branch 'fix/roi/id_issue' into temp/issue/patch/251

commit 7a397c9
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue May 21 13:57:55 2024 -0700

    fix preview available imagery to accept ids

commit 0b68d41
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue May 21 13:57:27 2024 -0700

    force roi to turn all incoming ids into type string

commit fdcc737
Author: Floris Calkoen <44444001+FlorisCalkoen@users.noreply.github.com>
Date:   Tue May 21 22:26:53 2024 +0200

     helper function to infer data dir

commit 441a06a
Author: floriscalkoen <floris_calkoen@hotmail.com>
Date:   Tue May 21 22:15:46 2024 +0200

    helper function to infer data dir

commit a366bb0
Author: Sharon Fitzpatrick <SF2309@Gmail.Com>
Date:   Tue May 21 13:15:21 2024 -0700

    add some docstrings, improve error messages and organize loading from config

1_download_imagery.py

@@ -1,25 +1,24 @@
+import os
 from coastseg import coastseg_logs
 from coastseg.common import initialize_gee
 from coastseg import coastseg_map
-import os
+from coastseg import core_utilities
 
+base_dir = core_utilities.get_base_dir()
+print(f"The base directory is {base_dir}")
+# path to Coastseg/data
+data_folder = base_dir / "data"
+print(f"The data directory is {data_folder}")
 
 # if you get an error here, enter your project id
 initialize_gee(auth_mode = "localhost",project='')
-
+# initialize the CoastSeg map
 coastsegmap=coastseg_map.CoastSeg_Map(create_map=False)
 
-# Get the directory of the current script
-script_dir = os.path.dirname(os.path.abspath(__file__))
-print(f"The script directory is {script_dir}")
 # Construct the path to rois.geojson
-rois_path = os.path.join(script_dir, 'examples',"rois.geojson")
+rois_path = os.path.join(os.path.abspath(base_dir), 'examples',"rois.geojson")
 print(f"Loading ROIs from {rois_path}")
 
-# path to Coastseg/data
-data_folder = os.path.join(script_dir, 'data')
-print(f"The data folder is {data_folder}")
-
 # sample ROI (Region of Interest) file
 roi = coastsegmap.load_feature_from_file('roi',rois_path)
 print(roi)
@@ -35,10 +34,11 @@
     "apply_cloud_mask": True,             # apply cloud mask to the imagery. If False, the cloud mask will not be applied.
     }
 
-# download the imagery for that ROI to the /data folder
+# # download the imagery for that ROI to the /data folder
 coastsegmap.download_imagery(rois=roi.gdf,selected_ids=roi_ids,settings=settings,file_path=data_folder)
 
 # name the session where you want to save the extracted shorelines
+# session_name = 'sample_session1'
 session_name = 'sample_session1'
 coastsegmap.set_session_name(session_name)
 
@@ -47,15 +47,14 @@
 # - a minimum beach area of 500 m^2
 # - a minimum length of 20 m
 # - a maximum distance from the reference shoreline of 300 m
-coastsegmap.set_settings(min_beach_area=500,min_length_sl=20,max_dist_ref=300)
+coastsegmap.set_settings(min_beach_area=100,min_length_sl=20,max_dist_ref=300)
 
 # load a shoreline file from the examples folder
-script_dir = os.path.dirname(os.path.abspath(__file__))
-shoreline_path = os.path.join(script_dir, 'examples', "shoreline.geojson")
+shoreline_path = os.path.join(base_dir, 'examples', "shoreline.geojson")
 shoreline = coastsegmap.load_feature_from_file('shoreline',shoreline_path)
 
 # load transects from the examples folder
-transect_path = os.path.join(script_dir,'examples', "transects.geojson")
+transect_path = os.path.join(base_dir,'examples', "transects.geojson")
 transects = coastsegmap.load_feature_from_file('transects', transect_path)
 
 # extract the shorelines for the selected ROI and save them to the /sessions/session_name folder

2_extract_shorelines.py

@@ -1,6 +1,9 @@
+import os
 from coastseg import coastseg_logs
 from coastseg import coastseg_map
-import os
+from coastseg import core_utilities
+
+base_dir = core_utilities.get_base_dir()
 
 # Run this script only after running 1_download_imagery.py 
 
@@ -10,7 +13,7 @@
 # Enter the name of the session you want to load here
 session_name = 'sample_session1'
 # session_name = 'paper_dfg2_extract_shorelines_buffer_62'
-session_path = os.path.join(os.getcwd(),'sessions', session_name)
+session_path = os.path.join(os.path.abspath(base_dir),'sessions', session_name)
 print(f"Loading session from {session_path}")
 # r"C:\development\doodleverse\coastseg\CoastSeg\sessions\paper_dfg2_extract_shorelines_buffer_62"
 coastsegmap.load_fresh_session(session_path)

src/coastseg/coastseg_logs.py

@@ -1,14 +1,14 @@
 import os
 from datetime import datetime
 import logging
-
+from coastseg import core_utilities
 # DESCRIPTION: Sets up a logging system that writes logs to a file named with the current timestamp in a "logs" directory.
 
 
 def prepare_logging():
     """create a directory named 'logs' in the current working directory if a 'logs' directory does not exist"""
-    if not os.path.exists(os.path.abspath(os.path.join(os.getcwd(), "logs"))):
-        os.mkdir(os.path.abspath(os.path.join(os.getcwd(), "logs")))
+    if not os.path.exists(os.path.abspath(os.path.join(core_utilities.get_base_dir(), "logs"))):
+        os.mkdir(os.path.abspath(os.path.join(core_utilities.get_base_dir(), "logs")))
 
 
 def clear_default_handlers() -> None:
@@ -22,10 +22,10 @@ def create_root_logger():
     log_<year>-<month>-<day>-<hour>-<minute>. This log file will  be written to by all the other loggers
     """
     log_filename = "log_" + datetime.now().strftime("%m-%d-%y-%I_%M_%S") + ".txt"
-    log_file = os.path.abspath(os.path.join(os.getcwd(), "logs", log_filename))
+    log_file = os.path.abspath(os.path.join(core_utilities.get_base_dir(), "logs", log_filename))
     # configure the logger
     log_format = "%(asctime)s - %(filename)s at line %(lineno)s in %(funcName)s() - %(levelname)s : %(message)s"
-    os.path.abspath(os.path.join(os.getcwd(), "logs"))
+    os.path.abspath(os.path.join(core_utilities.get_base_dir(), "logs"))
     # Use FileHandler() to log to a file
     file_handler = logging.FileHandler(log_file, mode="a")
     formatter = logging.Formatter(log_format)