Configuration Options
This document describes information about configuration options for GridMet. Please see the other documentation pages for GridMet to have its recommended use explained. For example, the overview describes pages that are a part of the documentation.
Config.txt options
px2cm
Conversion of each pixel to a centimeter lenth in an environment.
nonfld_filt_perc
Non-field filter percentage threshold.
load_plot_from_file
Load a neural data plot from individual file (1; plot_filepath) or instead pick a file from a numbered list (0; heat_maps_list or heat_maps_ac_list). A note is that one must run the source code, not runtime version of GridMet, to edit these lists.
plot_filepath
File path to plot to load from a file when load_plot_from_file is enabled.
use_binary_input
Select to use (1) or not (0) binary input files as opposed to text input files.
heat_map_selection
Index number of plot file on heat_maps_list or heat_maps_ac_list to use with this software if load_plot_from_file is set to 0.
use_ac
Choose to use autocorrelogram (ac) (1) or standard rate map (0).
convert_to_ac
Automatically convert rate map input into an autocorrelogram. If this option is not selected and use_ac is set to 1 then a user must supply a previously generated autocorrelogram data file as the plot to load.
use_dist_thresh
This is an experimental feature that may not yet work correctly. This is designed to filter out fields that are too distant from other fields
dist_thresh
Distance threshold parameter in pixels for use_dist_thresh
use_fld_sz_thresh
This is an experimental feature that may not yet work correctly. This is designed to automatically filter out fields at plot borders without enough pixel points in their area. This can try to automatically detect fields the are cut off too much at the border of plots. This could aid in automatically excluding fields in addition to a user being able to manually exclude fields.
fld_sz_thresh
This is a threshold for use_fld_sz_thresh of the minimum number of pixels in a feild’s area to allow not filtering the field out.
manual_field_exclud
Choose to enable (1) or disable (0) manually excluding fields from statistical analyses.
load_px2cm_conv
Load saved px2cm settings based on file number. saved_px2cm_conv.m is the file the settings are saved in.
dbscan_epsilon
DBSCAN’s epsilon parameter value. See https://www.mathworks.com/help/stats/dbscan.html for more info.
dbscan_min_pts
DBSCAN’s minpts (minimum number of neighbors required for core point) parameter value. See https://www.mathworks.com/help/stats/dbscan.html for more info.
load_custom_rm
Load rate map data from the heat_maps_real_custom_list.mat file. This is an alternative to using load_plot_from_file to load data.
load_custom_ac
Load autocorrelogram data from the heat_maps_ac_custom_list.mat file. This is an alternative to using load_plot_from_file to load data.
only_center_seven
Filter out fields except for the seven closest to the center of the plot.
inout_excl
Filter out fields detected beyond the center seven in the calculation of the in_out_fields_ratio. Note: this does not use advanced field detection to detect the fields outside the central seven. This option can only be used if only_center_seven is enabled.
use_tophat_filter
This is an experimental feature that may not yet work correctly. This feature is designed to filter neural firing through a tophat filter.
use_centsurr_filter
This is an experimental feature that may not yet work correctly. This feature is designed to filter neural firing through a center-surround filter.
minimal_plotting_mode
Preset plotting window size configuration
auto_export_plots
Automatically save generated plots
plot_fields_detected
Enables the plotting of detected fields.
plot_orig_firing
Enables the plotting of the original cell firing data.
plot_legend
Include a legend in the plot.
print_angles
This is an experimental feature that may not yet work correctly. This is designed to print the frequency of angles that are found between field centroids.
control_window_size
Preset plotting window size configuration.
custom
A group of custom configuration settings.
custom2
A group of custom configuration settings.
custom3
A group of custom configuration settings.
custom4
A group of custom configuration settings.
sml_ang_cnt_fld
Smallest angle from the center field. Default value for this is 361, which is beyond 360, and that is intended to be beyond the highest angle possible.
sml_ang_cent_num
Centriod number of sml_ang_cnt_fld match.
advanced_detection
Enable (1) or disable (0) advanced field detection.
advanced_detection_maxdist
Maximum advanced detection distance to test. This is the distance from the centroid to a point beyond that, e.g., 50 pixels. This is used in the scanning of each angle from the centroid to find where field boundaries are detected.
advanced_detection_ang_inc
Angle to increment radar scan in advanced grid field detection.
com_centroids
Use center of mass to find centroids.
in_out_fields_ratio
Report the ratio of firing intensity within fields compared to outside of them.
cov_between_fields_reporting
Report the mean of the coefficient of variation of the firing rate (or correlation values in the case of autocorrelograms) across fields.
report_gridscore
Report grid score metrics. “HD grid score” is a score previously introduced to quantify experimental data in Dannenberg, H.; Lazaro, H.; Nambiar, P.; Hoyland, A.; Hasselmo, M.E. Effects of Visual Inputs on Neural Dynamics for Coding of Location and Running Speed in Medial Entorhinal Cortex. eLife 2020. https://doi.org/10.7554/eLife.62500. The Gridness3Score is based on a grid score metric found in the software CMBHome at https://github.com/hasselmonians/CMBHOME.
report_orientation2
Report Opexebo methods based orientation measurement.
min_orientation2
Value of the minimum angle used in the orientation2 measurement.
report_centroid_positions
Report on the coordinates of centroid positions.
report_centroid_positions_python
Report on the coordinates of centroid positions in a Python syntax format. This can be used to test comparing results with Opexebo, which is in Python.
outlier_removal
Enable automatic removal of outlier points in fields. This can only be used if advanced_detection is enabled.
outlier_allowance
This is a parameter value for use with outlier_removal. This is an amount, as a percentage, of outlier distance from each median field radius to field boundary points to allow. Value is relative to 1.0 being 100%, e.g., 0.25 is 25% and 2 is 200%. Boundary points found beyond this value are converted into the closest maximum value this parameter allows. For instance, a boundary coordinate being 200% beyond the median with a limit of 25% will be converted into being a point 25% beyond the median.
spac_exclud
Grid feilds to exclude from field spacing statistics. Format should be “1|2|3” that is delimited by “|”. No exclusion should be described as “[]”.
size_exclud
Grid feilds to exclude from field sizes statistics. Format should be “1|2|3” that is delimited by “|”. No exclusion should be described as “[]”.
ang_exclud
Grid feilds to exclude from field angles statistics. Format should be “1|2|3” that is delimited by “|”. No exclusion should be described as “[]”.