Merge branch 'master' into am/pin-gee

.github/workflows/publish.yml

@@ -118,7 +118,7 @@ jobs:
       - name: Create channel
         run: mkdir -p /tmp/ecoscope/release/artifacts
       - name: Build prefix release
-        uses: prefix-dev/[email protected].26
+        uses: prefix-dev/[email protected].29
         with:
           recipe-path: publish/recipes/release/ecoscope.yaml
           build-args: --output-dir /tmp/ecoscope/release/artifacts --channel https://prefix.dev/ecoscope-workflows --channel conda-forge

.github/workflows/tests.yml

@@ -24,7 +24,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Setup Micromamba
-        uses: mamba-org/[email protected].3
+        uses: mamba-org/[email protected].4
         with:
           environment-file: environment.yml
           cache-environment: true

doc/source/notebooks/01. IO/EarthRanger_IO.ipynb

@@ -30,7 +30,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/01. IO/GEE_IO.ipynb

@@ -28,7 +28,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/01. IO/Landscape Dynamics Data.ipynb

@@ -30,7 +30,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/02. Relocations & Trajectories/Relocations_and_Trajectories.ipynb

@@ -37,7 +37,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/03. Home Range & Movescape/EcoGraph.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/03. Home Range & Movescape/Elliptical Time Density (ETD).ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {
@@ -49,6 +49,7 @@
     "import ecoscope\n",
     "from ecoscope.analysis.UD import calculate_etd_range\n",
     "from ecoscope.analysis.percentile import get_percentile_area\n",
+    "from ecoscope.io.raster import RasterData\n",
     "\n",
     "ecoscope.init()"
    ]
@@ -255,7 +256,12 @@
    "outputs": [],
    "source": [
     "percentiles = pd.concat(\n",
-    "    [get_percentile_area(percentile_levels=[50, 99.9, 100.0], raster_path=v, subject_id=k) for k, v in etd.items()]\n",
+    "    [\n",
+    "        get_percentile_area(\n",
+    "            percentile_levels=[50, 99.9, 100.0], raster_data=RasterData.from_raster_file(v), subject_id=k\n",
+    "        )\n",
+    "        for k, v in etd.items()\n",
+    "    ]\n",
     ").reset_index(drop=True)\n",
     "\n",
     "percentiles"
@@ -301,7 +307,7 @@
    "source": [
     "salif = get_percentile_area(\n",
     "    percentile_levels=[50, 60, 70, 80, 90, 99.9],\n",
-    "    raster_path=etd.at[\"Salif Keita\"],\n",
+    "    raster_data=RasterData.from_raster_file(etd.at[\"Salif Keita\"]),\n",
     "    subject_id=\"Salif Keita\",\n",
     ")"
    ]

doc/source/notebooks/03. Home Range & Movescape/Reduce Regions.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/04. EcoMap & EcoPlot/EcoMap.ipynb

@@ -37,7 +37,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {
@@ -496,9 +496,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "raster_data = ecoscope.io.raster.RasterData.from_raster_file(etd.at[\"Salif Keita\"])\n",
     "percentile_areas = get_percentile_area(\n",
     "    percentile_levels=[50, 60, 70, 80, 90, 99.9],\n",
-    "    raster_path=etd.at[\"Salif Keita\"],\n",
+    "    raster_data=raster_data,\n",
     "    subject_id=\"Salif Keita\",\n",
     ").to_crs(4326)\n",
     "\n",

doc/source/notebooks/04. EcoMap & EcoPlot/EcoPlot.ipynb

@@ -37,7 +37,7 @@
    "outputs": [],
    "source": [
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/05. Environmental Analyses/Landscape Grid.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/05. Environmental Analyses/Remote Sensing Time Series Anomaly.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/05. Environmental Analyses/Seasonal Calculation.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

doc/source/notebooks/06. Data Management/Tracking Data Gantt Chart.ipynb

@@ -30,7 +30,7 @@
     "ECOSCOPE_RAW = \"https://raw.githubusercontent.com/wildlife-dynamics/ecoscope/master\"\n",
     "\n",
     "%pip install \\\n",
-    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].17' &> /dev/null"
+    "    'ecoscope[analysis,mapping,plotting] @ git+https://github.com/wildlife-dynamics/[email protected].19' &> /dev/null"
    ]
   },
   {

ecoscope/analysis/UD/etd_range.py

@@ -1,24 +1,28 @@
+import logging
 import math
 import os
 import typing
 from dataclasses import dataclass
 
 import numpy as np
+
 from ecoscope.base import Trajectory
 from ecoscope.io import raster
 
 try:
     import numba as nb
     import scipy
-    from sklearn import neighbors
     from scipy.optimize import minimize
     from scipy.stats import weibull_min
+    from sklearn import neighbors
 except ModuleNotFoundError:
     raise ModuleNotFoundError(
         'Missing optional dependencies required by this module. \
          Please run pip install ecoscope["analysis"]'
     )
 
+logger = logging.getLogger(__name__)
+
 
 @nb.cfunc("double(intc, CPointer(double))")
 def __etd__(_, a):
@@ -84,13 +88,14 @@ class Weibull3Parameter(WeibullPDF):
 
 def calculate_etd_range(
     trajectory_gdf: Trajectory,
-    output_path: typing.Union[str, bytes, os.PathLike],
+    output_path: typing.Union[str, bytes, os.PathLike, None] = None,
     max_speed_kmhr: float = 0.0,
     max_speed_percentage: float = 0.9999,
     raster_profile: raster.RasterProfile = None,
     expansion_factor: float = 1.3,
     weibull_pdf: typing.Union[Weibull2Parameter, Weibull3Parameter] = Weibull2Parameter(),
-) -> None:
+    grid_threshold: int = 100,
+) -> raster.RasterData:
     """
     The ETDRange class provides a trajectory-based, nonparametric approach to estimate the utilization distribution (UD)
     of an animal, using model parameters derived directly from the movement behaviour of the species.
@@ -100,12 +105,13 @@ def calculate_etd_range(
     Parameters
     ----------
     trajectory_gdf : geopandas.GeoDataFrame
-    output_path : str or PathLike
+    output_path : str or PathLike or None
     max_speed_kmhr : float
     max_speed_percentage : 0.999
     raster_profile : raster.RasterProfile
     expansion_factor : float
     weibull_pdf : Weibull2Parameter or Weibull3Parameter
+    grid_threshold: int
 
     Returns
     -------
@@ -169,8 +175,20 @@ def calculate_etd_range(
     grid_centroids[1, 0] = y_max - raster_profile.pixel_size * 0.5
 
     centroids_coords = np.dot(grid_centroids, np.mgrid[1:2, :num_columns, :num_rows].T.reshape(-1, 3, 1))
+    centroids_coords = centroids_coords.squeeze().T
+
+    if centroids_coords.size < grid_threshold:
+        logger.warning(
+            f"Centroid size {centroids_coords.size} is too small to calculate density. "
+            f"The threshold value is {grid_threshold}. "
+            "Check if there’s a data issue or decrease pixel size"
+        )
+        return raster.RasterData(data=np.array([]), crs=raster_profile.crs, transform=raster_profile.transform)
+
+    if centroids_coords.ndim != 2:
+        centroids_coords = centroids_coords.reshape(1, -1)
 
-    tr = neighbors.KDTree(centroids_coords.squeeze().T)
+    tr = neighbors.KDTree(centroids_coords)
 
     del centroids_coords
 
@@ -206,12 +224,17 @@ def calculate_etd_range(
     # Normalize the grid values
     raster_ndarray = raster_ndarray / raster_ndarray.sum()
 
-    # Set the null data values
-    raster_ndarray[raster_ndarray == 0] = raster_profile.nodata_value
+    ndarray = raster_ndarray.reshape(num_rows, num_columns)
 
     # write raster_ndarray to GeoTIFF file.
-    raster.RasterPy.write(
-        ndarray=raster_ndarray.reshape(num_rows, num_columns),
-        fp=output_path,
-        **raster_profile,
-    )
+    if output_path:
+        # Set the null data values
+        raster_ndarray[np.isnan(raster_ndarray) | (raster_ndarray == 0)] = raster_profile.nodata_value
+
+        raster.RasterPy.write(
+            ndarray,
+            fp=output_path,
+            **raster_profile,
+        )
+
+    return raster.RasterData(data=ndarray.astype("float32"), crs=raster_profile.crs, transform=raster_profile.transform)