ecoscape-utilities 0.0.32__py3-none-any.whl → 0.0.34__py3-none-any.whl

ecoscape_utilities/ebird_db.py

@@ -486,42 +486,12 @@ A module for common functionality in the validaiton process using ebird data
 """
 class Validation(object):
 
-    def __init__(self, obs_fn, geotiff_fn):
+    def __init__(self, obs_fn):
         """
         Generates a class for validation.
-        It first tries to read the cached version of obs_fn for the specified geotiff_fn.
-        If the cached version is not found, it is created.
-        The cached version contains pre-translated coordinates to pixel values.
         :param obs_fn: Observations filename.
-        :param geotiff_fn: name of a geotiff (repopulation is preferred) used
-            for translating coordinates to pixel coordinates.
         """
         self.obs_fn = obs_fn
-        self.geotiff_fn = geotiff_fn
-        h = hashlib.sha1(obs_fn.encode('utf-8'))
-        h.update(geotiff_fn.encode('utf-8'))
-        cached_fn = obs_fn + "." + h.hexdigest() + ".csv"
-        if not os.path.exists(cached_fn):
-            self._create_cached_observations(cached_fn)
-        self.observations = pd.read_csv(cached_fn)
-
-
-    def _create_cached_observations(self, cached_fn):
-        """Creates a cached version of the observations that also contains
-        pixel coordinates."""
-        geotiff = GeoTiff.from_file(self.geotiff_fn)
-        def f(row):
-            square = row["Square"]
-            if (isinstance(square, str)):
-                coords = format_coords(square)
-            else:
-                coords = square
-            lat, lng = coords
-            pix_x, pix_y = transform_coords(geotiff, coords)
-            return lat, lng, pix_x, pix_y
-        df = pd.read_csv(self.obs_fn)
-        df["lat"], df["lng"], df["pix_x"], df["pix_y"] = zip(*df.apply(f, axis=1))
-        df.to_csv(cached_fn)
 
 
     def filter_CA_rectangle(self, observation_ratios, bigsquare=False):
@@ -594,8 +564,6 @@ class Validation(object):
         :param weighted_tile_size: size of the tile to attribute grouped weights to
         :returns: a dataframe with columns repopulation, observation ratio, and weights
         '''
-        assert repop_tif.crs == hab.crs, "Repopulation and habitat geotiffs must have the same CRS"
-        assert repop_tif.size == hab.size, "Repopulation and habitat geotiffs must have the same size"
         df = pd.DataFrame(columns=['repop', 'hab', 'max_repop', 'max_hab', 'obs_ratio', 'lat', 'lng', 'x', 'y', ])
         count = defaultdict(int)
         for (square, ratio) in observation_ratios:
@@ -604,9 +572,10 @@ class Validation(object):
             else:
                 coords = square
             lat, lng = coords
-            coords = transform_coords(repop_tif, coords)
-            repop_tile = repop_tif.get_tile_from_coord(coords, tile_scale=tile_scale)
-            hab_tile = hab.get_tile_from_coord(hab, coords, tile_scale=tile_scale)
+            repop_pix_coords = transform_coords(repop_tif, coords)
+            hab_pix_coords = transform_coords(hab, coords)
+            repop_tile = repop_tif.get_tile_from_coord(repop_pix_coords, tile_scale=tile_scale)
+            hab_tile = hab.get_tile_from_coord(hab_pix_coords, tile_scale=tile_scale)
             if repop_tile is None or hab_tile is None:
                 continue
             x, y = repop_tif.get_pixel_from_coord(coords)
@@ -638,11 +607,18 @@ class Validation(object):
         :param hab_tif: habitat geotiff used to compute repop
         :param tile_scale: size of the tile around square
         """
-        df = self.observations.copy()
+        df = pd.read_csv(self.obs_fn)
         def f(row):
-            coords = (row["pix_x"], row["pix_y"])
-            repop_tile = repop_tif.get_tile_from_coord(coords, tile_scale=tile_scale)
-            hab_tile = hab_tif.get_tile_from_coord(coords, tile_scale=tile_scale)
+            square = row["Square"]
+            if (isinstance(square, str)):
+                coords = format_coords(square)
+            else:
+                coords = square
+            lat, lng = coords
+            repop_pix_coords = transform_coords(repop_tif, coords)
+            hab_pix_coords = transform_coords(hab_tif, coords)
+            repop_tile = repop_tif.get_tile_from_coord(repop_pix_coords, tile_scale=tile_scale)
+            hab_tile = hab_tif.get_tile_from_coord(hab_pix_coords, tile_scale=tile_scale)
             if repop_tile is None or hab_tile is None:
                 return pd.NA, pd.NA, pd.NA, pd.NA
             avg_repop = np.average(repop_tile.m)
@@ -652,7 +628,7 @@ class Validation(object):
             if div_by_255:
                 avg_repop /= 255.
                 max_repop /= 255.
-            return avg_repop, avg_hab, max_repop, max_hab
-        df["avg_repop"], df["avg_hab"], df["max_repop"], df["max_hab"] = zip(*df.apply(f, axis=1))
+            return avg_repop, avg_hab, max_repop, max_hab, lat, lng
+        df["avg_repop"], df["avg_hab"], df["max_repop"], df["max_hab"], df["lat"], df["lng"] = zip(*df.apply(f, axis=1))
         return df
 

{ecoscape_utilities-0.0.32.dist-info → ecoscape_utilities-0.0.34.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ecoscape-utilities
-Version: 0.0.32
+Version: 0.0.34
 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-0.0.34.dist-info/RECORD

@@ -0,0 +1,8 @@
+ecoscape_utilities/__init__.py,sha256=LXt1rL9JVsjnCmsNZwZ2aoElphIK-koaEDdW6ffZsMQ,50
+ecoscape_utilities/bird_runs.py,sha256=v43PfH_4ojpkTE-EFOJxr0oOW3M9suNm_1zMjZ9P-eI,5409
+ecoscape_utilities/ebird_db.py,sha256=4c7QihjkO_sqygtQKlk-GdOojTaYq8ZkU1S5q0UqfSQ,30124
+ecoscape_utilities-0.0.34.dist-info/licenses/LICENSE.md,sha256=3vh2mpA_XIR3FJot6a5F9DqktAoq45sEGIRkYjvAEeU,1304
+ecoscape_utilities-0.0.34.dist-info/METADATA,sha256=Aj9MAVUYgt_vM7TG1Yp1H46I0BLOBuxPpKiM-bdomB4,1382
+ecoscape_utilities-0.0.34.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
+ecoscape_utilities-0.0.34.dist-info/top_level.txt,sha256=jLf7iMlySaJg0Vh8z4lbAaqOc5W5ruMgKFvp797CryQ,19
+ecoscape_utilities-0.0.34.dist-info/RECORD,,

ecoscape_utilities-0.0.32.dist-info/RECORD

@@ -1,8 +0,0 @@
-ecoscape_utilities/__init__.py,sha256=LXt1rL9JVsjnCmsNZwZ2aoElphIK-koaEDdW6ffZsMQ,50
-ecoscape_utilities/bird_runs.py,sha256=v43PfH_4ojpkTE-EFOJxr0oOW3M9suNm_1zMjZ9P-eI,5409
-ecoscape_utilities/ebird_db.py,sha256=A3xoeymVIZbnxhYwlS9Ex22NJdeUVJDI_PATT0BGL3k,31321
-ecoscape_utilities-0.0.32.dist-info/licenses/LICENSE.md,sha256=3vh2mpA_XIR3FJot6a5F9DqktAoq45sEGIRkYjvAEeU,1304
-ecoscape_utilities-0.0.32.dist-info/METADATA,sha256=7o3bGeSdY49LAM57i-Cknxwt3hHBGMdAHZNTfszgMw0,1382
-ecoscape_utilities-0.0.32.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-ecoscape_utilities-0.0.32.dist-info/top_level.txt,sha256=jLf7iMlySaJg0Vh8z4lbAaqOc5W5ruMgKFvp797CryQ,19
-ecoscape_utilities-0.0.32.dist-info/RECORD,,