ecoscape-utilities 0.0.35__tar.gz → 0.0.37__tar.gz

{ecoscape_utilities-0.0.35 → ecoscape_utilities-0.0.37}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ecoscape-utilities
-Version: 0.0.35
+Version: 0.0.37
 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-0.0.35 → ecoscape_utilities-0.0.37}/ecoscape_utilities/ebird_db.py

@@ -72,35 +72,39 @@ class EbirdObservations(Connection):
         super().__init__(db_file)
 
     def get_all_squares(self, state=None,
-                        breeding=True, date_range=None,
-                        lat_range=None, lng_range=None, max_dist=2,
+                        breeding=None, date_range=None,
+                        lat_range=None, lng_range=None, max_dist=2, min_time=None,
                         verbose=False):
         """
         Gets all squares with bird (any bird) observations, for a certain state,
         and withing certain lat, lng, and date ranges.
         :param state (str): state code
-        :param breeding (boolean): whether to filter observations by breeding months (getting only apr-june)
+        :param breeding: None, or pair of months delimiting the breeding season, e.g. ("04", "06").
         :param date_range: tuple of 2 date-strings in format "YYYY-MM-DD" to get only observations in this date range
         :param lat_range: tuple of 2 floats for the lower and upper bounds for latitude
         :param lng_range: tuple of 2 floats for the lower and upper bounds for longitude
         :param max_dist (int): max kilometers traveled for the checklist for any observation we consider
             (any of further distance will be too noisy, and should be disreguarded)
+        :param min_time (int): minimum time in minutes for the checklist for any observation we consider
         :returns: list of squares which fall within the query parameters
         """
         query_string=['select DISTINCT SQUARE from checklist where "ALL SPECIES REPORTED" = 1']
         query_string.append('and "PROTOCOL TYPE" != "Incidental"')
         query_string.append('and "EFFORT DISTANCE KM" <= :dist')
         d = {"dist": max_dist}
+        if min_time is not None:
+            query_string.append('and "DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         if state is not None:
             query_string.append('and "STATE CODE" = :state')
             d['state'] = state
         # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr("OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and "OBSERVATION DATE" >= :min_date')
             query_string.append('and "OBSERVATION DATE" <= :max_date')
@@ -120,20 +124,21 @@ class EbirdObservations(Connection):
         return [sq[0] for sq in squares_list]
 
     def get_square_observations(self, square, bird,
-                          breeding=True, date_range=None,
-                          lat_range=None, lng_range=None, max_dist=2,
+                          breeding=None, date_range=None,
+                          lat_range=None, lng_range=None, max_dist=2, min_time=None,
                           verbose=False):
         """
         Get the number of checklists, number of checklists with a bird,
         total time, total distance, and total bird sightings, for a square.
         :param square: tuple of 2 floats, representing (lat, lng) of the square
         :param bird: bird
-        :param breeding (boolean): whether to filter observations by breeding months (getting only apr-june)
+        :param breeding: pair of months delimiting breeding season, or None (e.g., ("04", "06")). 
         :param date_range: tuple of 2 date-strings in format "YYYY-MM-DD" to get only observations in this date range
         :param lat_range: tuple of 2 floats for the lower and upper bounds for latitude
         :param lng_range: tuple of 2 floats for the lower and upper bounds for longitude
         :param max_dist (int): max kilometers traveled for the checklist for any observation we consider
             (any of further distance will be too noisy, and should be disreguarded)
+        :param min_time (int): minimum time in minutes for the checklist for any observation we consider
         :returns: num_checklists, num_bird_checklists, num_birds for the given square.
         """
         # Gets the number of checklists, the total time, the total distance, and the total number of birds.
@@ -144,13 +149,16 @@ class EbirdObservations(Connection):
         query_string.append('and "PROTOCOL TYPE" != "Incidental"')
         query_string.append('and "EFFORT DISTANCE KM" <= :dist')
         d["dist"] = max_dist
+        if min_time is not None:
+            query_string.append('and "DURATION MINUTES" >= :min_time')
+            d["min_time"] = min_time
         # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr("OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and "OBSERVATION DATE" >= :min_date')
             query_string.append('and "OBSERVATION DATE" <= :max_date')
@@ -187,12 +195,12 @@ class EbirdObservations(Connection):
         query_string.append('and checklist."EFFORT DISTANCE KM" <= :dist')
         d["dist"] = max_dist
         # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr(checklist."OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
@@ -229,7 +237,7 @@ class EbirdObservations(Connection):
         )
 
     def get_square_individual_checklists(self, square, bird,
-                          breeding=True, date_range=None,
+                          breeding=None, date_range=None,
                           lat_range=None, lng_range=None, max_dist=2,
                           verbose=False):
         """
@@ -239,7 +247,7 @@ class EbirdObservations(Connection):
         and total bird sightings, for a square.
         :param square: tuple of 2 floats, representing (lat, lng) of the square
         :param bird (str): name of bird
-        :param breeding (boolean): whether to filter observations by breeding months (getting only apr-june)
+        :param breeding: None, or pair of months delimiting breeding season ("04", "06"). 
         :param date_range: tuple of 2 date-strings in format "YYYY-MM-DD" to get only observations in this date range
         :param lat_range: tuple of 2 floats for the lower and upper bounds for latitude
         :param lng_range: tuple of 2 floats for the lower and upper bounds for longitude
@@ -256,12 +264,12 @@ class EbirdObservations(Connection):
         query_string.append('and "EFFORT DISTANCE KM" <= :dist')
         d["dist"] = max_dist
         # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr("OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and "OBSERVATION DATE" >= :min_date')
             query_string.append('and "OBSERVATION DATE" <= :max_date')
@@ -291,12 +299,12 @@ class EbirdObservations(Connection):
         query_string.append('and checklist."EFFORT DISTANCE KM" <= :dist')
         d["dist"] = max_dist
         # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr(checklist."OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
@@ -323,14 +331,14 @@ class EbirdObservations(Connection):
         checklists_df["Count"] = checklists_df.apply(lambda row : counts[row["SAMPLING EVENT IDENTIFIER"]], axis=1)
         return checklists_df
 
-    def get_squares_with_bird(self, bird, max_dist=1, breeding=False,
+    def get_squares_with_bird(self, bird, max_dist=1, breeding=None,
                               date_range=None, lat_range=None, lng_range=None,
                               state=None, verbose=False):
         """Gets all the squares where a bird has been sighted.  This is used
         primarily to refine the terrain resistance.
         :param bird: Common name of the bird
         :param max_dist: max length of the checklist in Km
-        :param breeding: whether to consider only the breeding period or not
+        :param breeding: pair of months delimiting breeding season, or None. 
         :param date_range: date range in years, as a string tuple of yyyy-mm-dd dates
         :param lat_range: range of latitudes to consider, as number tuple, optional.
         :param lng_range: range of longitudes to consider, as number tuple, optional.
@@ -350,12 +358,12 @@ class EbirdObservations(Connection):
         query_string.append('and checklist."PROTOCOL TYPE" != "Incidental"')
         query_string.append('and checklist."EFFORT DISTANCE KM" <= :dist')
          # Adds breeding portion
-        if breeding:
+        if breeding is not None:
             query_string.extend([
-                'and (substr(checklist."OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "06")'
+                'and substr("OBSERVATION DATE", 6, 2) >= ":br1"',
+                'and substr("OBSERVATION DATE", 6, 2) <= ":br2"',
                 ])
+            d['br1'], d['br2'] = breeding
         if date_range is not None:
             query_string.append('and checklist."OBSERVATION DATE" >= :min_date')
             query_string.append('and checklist."OBSERVATION DATE" <= :max_date')
@@ -376,78 +384,6 @@ class EbirdObservations(Connection):
         return [row[0] for row in r]
 
 
-    def get_observation_ratios(self, bird, min_checklists, bigsquare=False,
-                               max_dist=1, verbose=False,
-                               state=None, breeding=True):
-        """This function is not used now.  It was the old, deprecated way of
-        doing validation, and we are keeping the code for reference only."""
-        # First, I create a dictionary of squares to checklist counts.
-        query_string = [
-            'select "SAMPLING EVENT IDENTIFIER",',
-            'BIGSQUARE' if bigsquare else 'SQUARE',
-            'from checklist where',
-            '"ALL SPECIES REPORTED" = 1',
-        ]
-        d = {'dist': max_dist}
-        query_string.append('and "PROTOCOL TYPE" != "Incidental"')
-        query_string.append('and "EFFORT DISTANCE KM" <= :dist')
-        if state is not None:
-            query_string.append('and "STATE CODE" = :state')
-            d['state'] = state
-        # Adds breeding portion
-        if breeding:
-            query_string.extend([
-                'and (substr("OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr("OBSERVATION DATE", 6, 2) = "06")'
-                ])
-        query_string = " ".join(query_string)
-        if verbose:
-            print("Query:", query_string)
-        observations = self.execute_query((query_string, d))
-        checklists_per_square = defaultdict(int)
-        for _, sq in observations:
-            checklists_per_square[sq] += 1
-        # Now I keep only the squares with a minimum of checklists.
-        checklists_per_square = {sq: c for sq, c in checklists_per_square.items() if c >= min_checklists}
-        # Ok, I care only about these squares.
-        # Now I want to know, for each of these squares, how many checklists there are that
-        # contain the bird.
-        query_string = [
-            'select DISTINCT checklist."SAMPLING EVENT IDENTIFIER",',
-            'checklist.BIGSQUARE' if bigsquare else 'checklist.SQUARE',
-            'from checklist join observation on',
-            'checklist."SAMPLING EVENT IDENTIFIER" = observation."SAMPLING EVENT IDENTIFIER"',
-            'where observation."COMMON NAME" = :bird',
-            'and checklist."ALL SPECIES REPORTED" = 1',
-        ]
-        d = {'dist': max_dist ,'bird': bird}
-        query_string.append('and checklist."PROTOCOL TYPE" != "Incidental"')
-        query_string.append('and checklist."EFFORT DISTANCE KM" <= :dist')
-        if state is not None:
-            query_string.append('and checklist."STATE CODE" = :state')
-            d['state'] = state
-        if breeding:
-            query_string.extend([
-                'and (substr(checklist."OBSERVATION DATE", 6, 2) = "04"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "05"',
-                'OR substr(checklist."OBSERVATION DATE", 6, 2) = "06")',
-                ])
-        query_string = " ".join(query_string)
-        if verbose:
-            print("Query:", query_string)
-        observations = self.execute_query((query_string, d))
-        good_checklists_per_square = defaultdict(int)
-        for _, sq in observations:
-            if sq in checklists_per_square: # Otherwise, too few observations.
-                good_checklists_per_square[sq] += 1
-        for sq in checklists_per_square:
-            if good_checklists_per_square[sq] > checklists_per_square[sq]:
-                print("Too many checklists at", sq, good_checklists_per_square[sq], checklists_per_square[sq])
-        return {sq: (good_checklists_per_square[sq] / checklists_per_square[sq])
-                for sq in checklists_per_square}
-
-
 def format_coords(coords, bigsquare=False):
     """
     formats coords from the eBird database format '4406;-12131' to

{ecoscape_utilities-0.0.35 → ecoscape_utilities-0.0.37}/ecoscape_utilities.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ecoscape-utilities
-Version: 0.0.35
+Version: 0.0.37
 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-0.0.35 → ecoscape_utilities-0.0.37}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "ecoscape-utilities"
-version = "0.0.35"
+version = "0.0.37"
 authors = [
   {name="Luca de Alfaro", email="luca@ucsc.edu"},
   {name="Coen Adler", email="ctadler@ucsc.edu"},