:py:mod:`ecoscope.analysis`
===========================

.. py:module:: ecoscope.analysis


Subpackages
-----------
.. toctree::
   :titlesonly:
   :maxdepth: 3

   UD/index.rst


Submodules
----------
.. toctree::
   :titlesonly:
   :maxdepth: 1

   astronomy/index.rst
   ecograph/index.rst
   geofence/index.rst
   immobility/index.rst
   percentile/index.rst
   proximity/index.rst
   seasons/index.rst
   speed/index.rst


Package Contents
----------------

.. py:class:: Ecograph(trajectory, resolution=15, radius=2, cutoff=None, tortuosity_length=3)


   A class that analyzes movement tracking data using Network Theory.

   :param trajectory: Trajectory dataframe
   :type trajectory: ecoscope.base.Trajectory
   :param resolution: Pixel size, in meters
   :type resolution: float
   :param radius: Radius to compute Collective Influence (Default : 2)
   :type radius: int
   :param cutoff: Cutoff to compute an approximation of betweenness index if the standard algorithm is
                  too slow. Can be useful for very large graphs (Default : None)
   :type cutoff: int
   :param tortuosity_length: The number of steps used to compute the two tortuosity metrics (Default : 3 steps)
   :type tortuosity_length: int

   .. py:method:: to_csv(output_path)

      Saves the features of all nodes in a CSV file

      :param output_path: Output path for the CSV file
      :type output_path: str, Pathlike


   .. py:method:: to_geotiff(feature, output_path, individual='all', interpolation=None, transform=None)

      Saves a specific node feature as a GeoTIFF

      :param feature: Feature of interest
      :type feature: str
      :param output_path: Output path for the GeoTIFF file
      :type output_path: str, Pathlike
      :param individual: The individual for which we want to output the node feature (Default : "all")
      :type individual: str
      :param interpolation: Whether to interpolate the feature for each step in the trajectory (Default : None). If
                            provided, has to be one of those four types of interpolation : "mean", "median", "max"
                            or "min"
      :type interpolation: str or None
      :param transform: A feature transform method (Default : None)
      :type transform: sklearn.base.TransformerMixin or None


   .. py:method:: _get_ecograph(self, trajectory_gdf, individual_name, radius, cutoff, tortuosity_length)
      :staticmethod:


   .. py:method:: _update_node(G, node_id, attributes)
      :staticmethod:


   .. py:method:: _get_day_night_value(day_night_value)
      :staticmethod:


   .. py:method:: _initialize_node(G, node_id, attributes, empty=False)
      :staticmethod:


   .. py:method:: _get_dot_product(x, y, z, w)
      :staticmethod:


   .. py:method:: _get_tortuosities(self, lines, time_delta)
      :staticmethod:


   .. py:method:: _compute_network_metrics(self, G, radius, cutoff)
      :staticmethod:


   .. py:method:: _compute_degree(G)
      :staticmethod:


   .. py:method:: _compute_collective_influence(self, G, radius)
      :staticmethod:


   .. py:method:: _get_collective_influence(G, start, radius)
      :staticmethod:


   .. py:method:: _compute_betweenness(G, cutoff)
      :staticmethod:


   .. py:method:: _get_feature_mosaic(self, feature, interpolation=None)
      :staticmethod:


   .. py:method:: _get_feature_map(self, feature, individual, interpolation)
      :staticmethod:


   .. py:method:: _get_regular_feature_map(self, feature, individual)
      :staticmethod:


   .. py:method:: _get_interpolated_feature_map(self, feature, individual, interpolation)
      :staticmethod:



.. py:function:: get_feature_gdf(input_path)

   Convert a GeoTIFF feature map into a GeoDataFrame

   :param input_path: Input path for the GeoTIFF file
   :type input_path: str, Pathlike


.. py:function:: get_percentile_area(percentile_levels, raster_path, subject_id = '')

   :param percentile_levels: list of k-th percentile scores.
   :type percentile_levels: Typing.List[Int]
   :param raster_path: file path to where the raster is stored.
   :type raster_path: str or os.PathLike
   :param subject_id: unique identifier for the subject
   :type subject_id: str

   :rtype: GeoDataFrame


.. py:class:: SpeedDataFrame(data=None, *args, **kwargs)


   Bases: :py:obj:`ecoscope.base.EcoDataFrame`

   `EcoDataFrame` extends `geopandas.GeoDataFrame` to provide customizations and allow for simpler extension.

   .. py:method:: from_trajectory(trajectory, classification_method = 'equal_interval', num_classes = 6, bins = None, speed_colors = None)
      :classmethod: