Metadata-Version: 1.1
Name: biotracks
Version: 0.4.0
Summary: Data package representation for cell migration tracking data
Home-page: https://github.com/CellMigStandOrg/biotracks
Author: paola masuzzo
Author-email: paola.masuzzo@ugent.be
License: BSD
Description-Content-Type: UNKNOWN
Description: Biotracks: a standard format for cell migration-derived tracking files
        ======================================================================
        
        .. image:: https://travis-ci.org/CellMigStandOrg/biotracks.svg?branch=master
            :target: https://travis-ci.org/CellMigStandOrg/biotracks
        
        .. image:: https://badge.fury.io/py/biotracks.svg
            :target: https://badge.fury.io/py/biotracks
        
        Biotracks provides a standard format for cell migration tracking files and a series of converters from popular tracking sofware packages to the biotracks format, which is a specialization of the `Frictionless Tabular Data Package <http://specs.frictionlessdata.io/tabular-data-package/>`_ .
        
        
        Installation (Python 3 only)
        ----------------------------
        
        .. code-block::
        
           python setup.py install
        
        
        Usage
        -----
        
        Move to the ``scripts`` directory and run:
        
        .. code-block:: bash
        
          python create_dpkg.py your_tracking_file
        
        This will create a tabular data package directory containing:
        
        + a csv file for the **objects** (e.g., cells)
        + a csv file for the **links** (linear collections of objects)
        + the json descriptor file for the data package
        
        The latter will look like this:
        
        .. code-block:: json
        
          {
              "name": "cmso_tracks",
              "resources": [
                  {
                      "name": "cmso_objects_table",
                      "path": "objects.csv",
                      "schema": {
                          "fields": [
                              {
                                  "constraints": {
                                      "unique": true
                                  },
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_object_id",
                                  "title": "",
                                  "type": "integer"
                              },
                              {
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_frame_id",
                                  "title": "",
                                  "type": "integer"
                              },
                              {
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_x_coord",
                                  "title": "",
                                  "type": "number"
                              },
                              {
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_y_coord",
                                  "title": "",
                                  "type": "number"
                              }
                          ],
                          "primaryKey": "cmso_object_id"
                      }
                  },
                  {
                      "name": "cmso_links_table",
                      "path": "links.csv",
                      "schema": {
                          "fields": [
                              {
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_link_id",
                                  "title": "",
                                  "type": "integer"
                              },
                              {
                                  "description": "",
                                  "format": "default",
                                  "name": "cmso_object_id",
                                  "title": "",
                                  "type": "integer"
                              }
                          ],
                          "foreignKeys": [
                              {
                                  "fields": "cmso_object_id",
                                  "reference": {
                                      "datapackage": "",
                                      "fields": "cmso_object_id",
                                      "resource": "cmso_objects_table"
                                  }
                              }
                          ]
                      }
                  }
              ]
          }
        
        The script also creates plots of trajectories and turning angles.
        
        
        Configuration
        -------------
        
        Some formats require a configuration file that specifies how to map object IDs, coordinate names, etc. This file must be in the `INI <https://en.wikipedia.org/wiki/INI_file>`_ format with two sections:
        
        + TOP_LEVEL_INFO: specifies a name for the data package and additional (optional) information
        + TRACKING_DATA: specifies how to map information from the source format to the biotracks column headers
        
        You can provide a configuration file by passing it via the ``-c`` option to ``create_dpkg.py``; if this option is not set, the script will look for a ``biotracks.ini`` file in the same directory as your tracking file; if this is not found, the script will use default names for both the overall package and the column headers.
        
        Example:
        
        .. code-block::
        
          [TOP_LEVEL_INFO]
          author = the author of the dp
          title = a title describing the dp
          name = a name for the dp
          author_institute = the insitute of the author
          author_email = a valid email address
        
          [TRACKING_DATA]
          cmso_x_coord = the column name pointing to the x coordinate
          cmso_y_coord = the column name pointing to the y coordinate
          cmso_z_coord = the column name pointing to the z coordinate
          cmso_frame_id = the column name pointing to the frame information
          cmso_object_id = the object identifier
          cmso_link_id = the link identifier
          
          
          Examples
          --------
          
          `CELLMIA <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/CELLMIA>`_ .
          `CellProfiler <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/CellProfiler>`_ .
          `ICY <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/ICY>`_ .
          `Mosaic <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/Mosaic>`_ .
          `TrackMate <https://github.com/CellMigStandOrg/biotracks/tree/master/examples/TrackMate>`_ .
          
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Intended Audience :: Science/Research
