ecoscape-utilities 0.0.3__py3-none-any.whl → 0.0.25__py3-none-any.whl

ecoscape_utilities/bird_runs.py

@@ -1,9 +1,12 @@
 import os
 from collections import namedtuple
+import shutil
 
-BirdRunDef = namedtuple('BirdRun', [
+BirdRunInfo = namedtuple('BirdRunInfo', [
     'nickname', # 6-letter ebird name.
     'name', # official name.
+    'state', # State for the analysis. 
+    'run_name', # Name of the run.
     'terrain_fn', # File for the terrain
     'habitat_fn', # File for the habitat.
     'transmission_fn', # Terrain transmission.
@@ -14,50 +17,46 @@ BirdRunDef = namedtuple('BirdRun', [
     'validation_fn',
     'obs_path',
     'obs_csv_path',
-    'do_gradient', 'do_validation',
-    'hop_distance', 'num_spreads', 'num_simulations'])
+    ])
 
+def delete_run(base_path, nickname, state, run_name="Standard"):
+    """Deletes the files for the given run."""
+    p = os.path.join(base_path, f"{nickname}/{state}/Output/{run_name}")
+    print("Deleting", p)
+    shutil.rmtree(p, ignore_errors=True)
 
 class BirdRun(object):
 
     def __init__(self, data_path):
         """Initializes a bird run, given a data path"""
         self.files_path = data_path
-
-    def get_bird_run(self, nickname, bird_name, run_name=None, do_gradient=False, do_validation=False,
-                     hop_distance=4, num_spreads=5, num_simulations=2, transmission_exponent=1):
+        
+    def get_bird_run(self, nickname, bird_name, run_name=None, state="US-CA"):
         """Given a bird name in 6-letter ebird format, returns the BirdRun object for the bird."""
         d = {"bird": nickname,
              "run_name": run_name or "Standard",
-             "num_spreads": num_spreads,
-             "hop_distance": hop_distance,
-             "num_simulations": num_simulations,
-             "transmission_exponent": transmission_exponent}
-        self.createdir(os.path.join(self.files_path, "{bird}/Output/{run_name}".format(**d)))
-        return BirdRunDef(
+             "state": state}
+        self.createdir(os.path.join(self.files_path, "{bird}/{state}/Output/{run_name}".format(**d)))
+        return BirdRunInfo(
             nickname = nickname,
             name = bird_name,
+            state = state,
+            run_name = run_name or "Standard",
             # Input ,
-            terrain_fn = os.path.join(self.files_path, "Terrain/iucn_habclass_lvl2_us_300_near_cropped.tif"),
-            habitat_fn = os.path.join(self.files_path, "{bird}/habitat.tif".format(**d)),
-            transmission_fn = os.path.join(self.files_path, "{bird}/transmission_refined_{transmission_exponent}.csv".format(**d)),
+            terrain_fn = os.path.join(self.files_path, "{bird}/{state}/terrain.tif".format(**d)),
+            habitat_fn = os.path.join(self.files_path, "{bird}/{state}/habitat.tif".format(**d)),
+            transmission_fn = os.path.join(self.files_path, "{bird}/{state}/transmission_refined_1.csv".format(**d)),
             resistance_original_fn = os.path.join(self.files_path, "{bird}/resistance.csv".format(**d)),
-            terrain_histogram_json_fn = os.path.join(self.files_path, "{bird}/terrain_hist.json".format(**d)),
-            terrain_histogram_csv_fn = os.path.join(self.files_path, "{bird}/terrain_hist.csv".format(**d)),
+            terrain_histogram_json_fn = os.path.join(self.files_path, "{bird}/{state}/terrain_hist.json".format(**d)),
+            terrain_histogram_csv_fn = os.path.join(self.files_path, "{bird}/{state}/terrain_hist.csv".format(**d)),
             # Validation files.
-            validation_fn = os.path.join(self.files_path, "{bird}/Ratios".format(**d)),
+            validation_fn = os.path.join(self.files_path, "{bird}/{state}/Ratios".format(**d)),
             # Output files
-            repopulation_fn = os.path.join(self.files_path, "{bird}/Output/{run_name}/repopulation_spreads_{num_spreads}_hop_{hop_distance}_sims_{num_simulations}_texp_{transmission_exponent}.tif".format(**d)),
-            gradient_fn = os.path.join(self.files_path, "{bird}/Output/{run_name}/gradient_spreads_{num_spreads}_hop_{hop_distance}_sims_{num_simulations}_texp_{transmission_exponent}.tif".format(**d)),
-            log_fn = os.path.join(self.files_path, "{bird}/Output/{run_name}/log_spreads_{num_spreads}_hop_{hop_distance}_sims_{num_simulations}_texp_{transmission_exponent}.json".format(**d)),
-            obs_path = os.path.join(self.files_path, "{bird}/Observations".format(**d)),
-            obs_csv_path = os.path.join(self.files_path, "{bird}/Output/{run_name}/obs_{num_spreads}_hop_{hop_distance}_sims_{num_simulations}_texp_{transmission_exponent}.csv".format(**d)),
-            # Run parameters
-            do_gradient=do_gradient,
-            do_validation = do_validation,
-            hop_distance = hop_distance,
-            num_spreads = num_spreads,
-            num_simulations = num_simulations
+            repopulation_fn = os.path.join(self.files_path, "{bird}/{state}/Output/{run_name}/repopulation.tif".format(**d)),
+            gradient_fn = os.path.join(self.files_path, "{bird}/{state}/Output/{run_name}/gradient.tif".format(**d)),
+            log_fn = os.path.join(self.files_path, "{bird}/{state}/Output/{run_name}/log.json".format(**d)),
+            obs_path = os.path.join(self.files_path, "{bird}/{state}/Observations".format(**d)),
+            obs_csv_path = os.path.join(self.files_path, "{bird}/{state}/Output/{run_name}/observations.csv".format(**d)),
         )
 
     def get_observations_fn(self, obs_path, bigsquare=False, **kwargs):
@@ -66,7 +65,7 @@ class BirdRun(object):
         """
         d = dict(**kwargs)
         d["isbig"] = "_big" if bigsquare else ""
-        return os.path.join(obs_path, "CA_min_{min_checklists}_len_{max_distance}{isbig}.json".format(**d))
+        return os.path.join(obs_path, "OBS_min_{min_checklists}_len_{max_distance}{isbig}.json".format(**d))
 
     def get_observations_display_fn(self, obs_path, bigsquare=False, **kwargs):
         """Completes the name of an observation ratio tif file, adding the information on minimum number of observations,
@@ -74,21 +73,28 @@ class BirdRun(object):
         """
         d = dict(**kwargs)
         d["isbig"] = "_big" if bigsquare else ""
-        return os.path.join(obs_path, "CA_min_{min_checklists}_len_{max_distance}{isbig}.tif".format(**d))
+        return os.path.join(obs_path, "OBS_min_{min_checklists}_len_{max_distance}{isbig}.tif".format(**d))
 
     def get_observations_all_fn(self, obs_path, **kwargs):
         """Completes the name of an observation ratio file, adding the information on minimum number of observations,
         and maximum length walked.
         """
         d = dict(**kwargs)
-        return os.path.join(obs_path, "CA_all_len_{max_distance}_{date_range}_{num_squares}.csv".format(**d))
+        return os.path.join(obs_path, "OBS_all_len_{max_distance}_{date_range}_{num_squares}.csv".format(**d))
+
+    def get_terrain_occurrences_fn(self, obs_path, **kwargs):
+        """Completes the name of an observation ratio file, adding the information on minimum number of observations,
+        and maximum length walked.
+        """
+        d = dict(**kwargs)
+        return os.path.join(obs_path, "TEROBS_all_len_{max_distance}_{date_range}_{num_squares}.csv".format(**d))
 
     def get_observations_all_display_fn(self, obs_path, **kwargs):
         """Completes the name of an observation ratio tif file, adding the information on minimum number of observations,
         and maximum length walked.
         """
         d = dict(**kwargs)
-        return os.path.join(obs_path, "CA_all_len_{max_distance}_{date_range}_{num_squares}.tif".format(**d))
+        return os.path.join(obs_path, "OBS_all_len_{max_distance}_{date_range}_{num_squares}.tif".format(**d))
 
     def createdir_for_file(self, fn):
         """Ensures that the path to a file exists."""

{ecoscape_utilities-0.0.3.dist-info → ecoscape_utilities-0.0.25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ecoscape-utilities
-Version: 0.0.3
+Version: 0.0.25
 Summary: A collection of EcoScape utilities.
 Author-email: Luca de Alfaro <luca@ucsc.edu>, Coen Adler <ctadler@ucsc.edu>, Artie Nazarov <anazarov@ucsc.edu>, Natalia Ocampo-Peñuela <nocampop@ucsc.edu>, Jasmine Tai <cjtai@ucsc.edu>, Natalie Valett <nvalett@ucsc.edu>
 Project-URL: Homepage, https://github.com/ecoscape-earth/ecoscape-utilities

ecoscape_utilities-0.0.25.dist-info/RECORD

@@ -0,0 +1,7 @@
+ecoscape_utilities/__init__.py,sha256=Zk3uTyqbLTdAUiTEutTKG9vI82XD-DQ7SvEB-6h4pcM,26
+ecoscape_utilities/bird_runs.py,sha256=v43PfH_4ojpkTE-EFOJxr0oOW3M9suNm_1zMjZ9P-eI,5409
+ecoscape_utilities-0.0.25.dist-info/LICENSE.md,sha256=3vh2mpA_XIR3FJot6a5F9DqktAoq45sEGIRkYjvAEeU,1304
+ecoscape_utilities-0.0.25.dist-info/METADATA,sha256=8ilvkRRwtKfmhQgmVmpGf-9v4ALdjEQesZkMLig-ycs,1246
+ecoscape_utilities-0.0.25.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
+ecoscape_utilities-0.0.25.dist-info/top_level.txt,sha256=jLf7iMlySaJg0Vh8z4lbAaqOc5W5ruMgKFvp797CryQ,19
+ecoscape_utilities-0.0.25.dist-info/RECORD,,

{ecoscape_utilities-0.0.3.dist-info → ecoscape_utilities-0.0.25.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

ecoscape_utilities-0.0.3.dist-info/RECORD

@@ -1,7 +0,0 @@
-ecoscape_utilities/__init__.py,sha256=Zk3uTyqbLTdAUiTEutTKG9vI82XD-DQ7SvEB-6h4pcM,26
-ecoscape_utilities/bird_runs.py,sha256=bkgm0H2dRcKP_9PzzSoIwWx4QMRHrpY9M_mLjzI-Oe0,5514
-ecoscape_utilities-0.0.3.dist-info/LICENSE.md,sha256=3vh2mpA_XIR3FJot6a5F9DqktAoq45sEGIRkYjvAEeU,1304
-ecoscape_utilities-0.0.3.dist-info/METADATA,sha256=3g7VHV9-usoDQkDgBOmop8BKPOEOnkLEdn3W-ECp8Sw,1245
-ecoscape_utilities-0.0.3.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-ecoscape_utilities-0.0.3.dist-info/top_level.txt,sha256=jLf7iMlySaJg0Vh8z4lbAaqOc5W5ruMgKFvp797CryQ,19
-ecoscape_utilities-0.0.3.dist-info/RECORD,,