Configuration¶
When you initialize a Experiment, raw data is extracted from
the .csv(s) and cleaned-up. Then, additional analyses are performed. You can
fine tune the clean up and the analyses by changing default parameters.
Upon importing pyfim, defaults are loaded from config.py in the pyFIM directory. You can either change the defaults in the file which will affect all subsequent sessions (persistent, does not work on-the-fly!) or change the defaults in the current session (temporary, only for this session).
Making lasting changes¶
Open a Python session, import pyFIM and get it’s location:
>>> import pyfim
>>> pyfim.__file__
... '/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/pyfim/__init__.py'
Next, navigate to the pyFIM directory, open config.py and make your changes.
Making temporary changes¶
You can change defaults for the current session.
>>> import pyfim
>>> # Defaults are stored as dictionary
>>> pyfim.defaults
... {'AREA_PARAMS': ['area'],
... 'BENDING_ANGLE_THRESHOLD': 45,
... 'BENDING_ANGLE_THRESHOLD_FOR_BENDING_STRENGTH': 20,
... 'CUT_TABLE_HEAD': False, ...
>>> # Change some parameter
>>> pyfim.defaults['MIN_STOP_TIME'] = 10
What is what¶
The config.py is well documented and superseeds this document but here is a list of relevant parameters:
| Function | Variable | Desciption |
|---|---|---|
| Import | FILE_FORMAT | File format to search for |
| Import | DELIMITER | Delimiter in CSV file |
| Import | PIXEL2MM | If True pixel coords are converted to mm or mm^2 |
| Import | PIXEL_PER_MM | Adjust this according to your setup |
| Import | SPATIAL_PARAMS | List parameters that can be converted to mm |
| Import | AREA_PARAMS | List parameters that can be converted to mm^2 |
| Import | FPS | Frames per second |
| Import | CUT_TABLE_HEAD | Remove first N Frames |
| Import | CUT_TABLE_TAIL | Remove last N Frames |
| Import | REMOVE_NANS | Remove objects without any values |
| Import | MIN_TRACK_LENGTH | Minimum track length in frames |
| Import | FILL_GAPS | Fill sub-threshold gaps within thresholded columns: [0 1 1 0 0 1 1] -> [0 1 1 1 1 1 1] |
| Import | MAX_GAP_SIZE | Max gap size |
| Import | THRESHOLDED_PARAMS | Parameters to fill gaps for |
| Head bends | BENDING_ANGLE_THRESHOLD | Minimum angle to be counted as bend |
| Head bends | MIN_BENDED_PHASE | Minimum consecutive frames spend bent |
| Stops | MIN_STOP_PHASE | Minimum number of frames for a stop |
| Peristalses | MIN_PEAK_DIST | Minimum frames between peristalses |
| Pause-turns | MIN_STOP_TIME | Minimum length of pause in frames |
| Pause-turns | MIN_GO_TIME | Minimum frames of go phase before and after pause |
| Pause-turns | TURN_ANGLE_THRESHOLD | Minimum anglular difference in movement direction before vs after pause |
| Pause-turns | DIRECTION_SMOOTHING | Direction will be smoother over X frames |
| Bend strength | BENDING_ANGLE_THRESHOLD_FOR_BENDING_STRENGTH | Minimum angle for bending strength |
| Two-Choice | TC_PARAM | Parameter used to split data (e.g. “mom_x” for split along x-axis) |
| Two-Choice | TC_BOUNDARY | Boundary between control and experiment |
| Two-Choice | TC_CONTROL_SIDE | Defines which side is the control |
| PreferenceIndex | TC_COUNT_WINDOW | Rolling window over which to count objects on either side |
| PreferenceIndex | TC_SMOOTHING_WINDOW | Rolling window over which to smooth preference index (PI) |
| PreferenceIndex | TC_CUT_HEAD | Ignore the first X frames for PI calculation |
| PreferenceIndex | TC_CUT_TAIL | Ignore the last X frames for PI calculation |