repic.utils.common
==================

.. py:module:: repic.utils.common

.. autoapi-nested-parse::

   Common functions and libraries shared across REPIC scripts



Attributes
----------

.. autoapisummary::

   repic.utils.common.print
   repic.utils.common.box_id


Functions
---------

.. autoapisummary::

   repic.utils.common.adjust_plot_attributes
   repic.utils.common.is_float
   repic.utils.common.create_dir
   repic.utils.common.del_dir
   repic.utils.common.get_box_coords
   repic.utils.common.get_box_vertex_entry
   repic.utils.common.get_multi_in_coords
   repic.utils.common.write_pickle


Module Contents
---------------

.. py:data:: print

   partial function to have all print statements flush buffer

   :type: func

.. py:data:: box_id
   :value: 0


   NetworkX initial vertex (particle bounding box) ID

   :type: int

.. py:function:: adjust_plot_attributes(ax, xlabel, ylabel, fontsize=32)

   Adjusts general Matplotlib plot parameters

   :param ax: Matplotlib axis object
   :type ax: obj
   :param xlabel: x-axis label
   :type xlabel: str
   :param ylabel: y-axis label
   :type ylabel: str

   :keyword fontsize: font size of plot text
   :kwtype fontsize: int, default=32

   :returns: None


.. py:function:: is_float(val)

   Checks if Python object can be converted to float datatype

   :param val: Python object
   :type val: obj

   :returns: True if string can be converted (False otherwise)
   :rtype: bool


.. py:function:: create_dir(dir_path)

   Creates directory at provided location

   :param dir_path: file path to directory
   :type dir_path: str

   :returns: file path to directory
   :rtype: str


.. py:function:: del_dir(dir_path)

   Deletes directory if it exists

   :param dir_path: file path to directory
   :type dir_path: str

   :returns: file path to directory
   :rtype: str


.. py:function:: get_box_coords(pattern, key=1.0, size=None, return_weights=False)

   Parses particle bounding box file and returns particle bounding box coordinates

   :param pattern: filename RegEx pattern
   :type pattern: str

   :keyword key: method key for k-d tree building
   :kwtype key: float, default=1.
   :keyword size: restrict the number of coordinates returned to this value
   :kwtype size: int or None
   :keyword return_weight: flag to include particle bounding box score or confidence in return
   :kwtype return_weight: bool, default=False

   :returns: list of particle bounding box coordinates
   :rtype: list


.. py:function:: get_box_vertex_entry(coord, clique_size, index)

   Returns particle bounding box coordinates of a clique as a vector

   :param coord: particle bounding box coordinates
   :type coord: list
   :param clique_size: size of clique
   :type clique_size: int
   :param index: position of particle bounding boxes in clique (determined by order of particle picking algorithms)
   :type index: int

   :returns: particle coordinates formatted for multi-out output
   :rtype: list


.. py:function:: get_multi_in_coords(in_file)

   Parses a particle bounding box file that contains multiple boxes per line (optimal cliques) and returns their coordinates, labels, and weights

   :param in_file: filepath to particle bounding box file
   :type in_file: str

   :returns: lists of particle bounding box coordinates, labels, and weights
   :rtype: list, list, list


.. py:function:: write_pickle(data, out_file)

   Writes provided data to storage in Pickle format

   :param data: NumPy array object
   :type data: obj
   :param out_file: filepath for output file
   :type out_file: str

   :returns: None