update readme

Author: samuelbray32

README.md

@@ -1,21 +1,25 @@
 # ndx-franklab-novela Extension for NWB
 
 # About
+
 ndx-franklab-novela is a python package containing NWB custom extensions for Loren Frank's Lab.
 
 # How to install
 
 Add ndx-franklab-novela to your conda environment:
+
 ```
 pip install ndx-franklab-novela
 ```
 
 Or install the latest version from the repository:
+
 ```
 pip install git+git://github.com/LorenFrankLab/ndx-franklab-novela
 ```
 
 The original published extension maintained by NovelaNeuro can be installed using:
+
 ```
 conda install -c conda-forge -c novelakrk ndx-franklab-novela
 ```
@@ -29,17 +33,21 @@ Loading `ndx-franklab-novela` by importing `ndx_franklab_novela` will also load
 # Extensions
 
 ## AssociatedFiles
+
 Representation of associated files in NWB.
 
 **Attributes:**
+
 - **description**  `string`: description of associated file
 - **content**  `string`: content of associated file
 - **task_epochs**  `string`: id of epochs with task that is descripted by associated files
 
 ## HeaderDevice
+
 Representation of HeaderDevice in NWB.
 
 **Attributes:**
+
 - **headstage_serial**  `string`: headstage_serial from header global configuration
 - **headstage_smart_ref_on**  `string`: headstage_smart_ref_on from header global configuration
 - **realtime_mode**  `string`: realtime_mode from header global configuration
@@ -62,25 +70,31 @@ Representation of HeaderDevice in NWB.
 - **file_path**  `string`: file_path from header global configuration
 
 ## ShanksElectrode
+
 Representation of electrodes of a shank in NWB.
 
 **Attributes:**
+
 - **name**  `string`: name of the shank
 - **rel_x**  `float`: the rel_x value of this electrode
 - **rel_y**  `float`: the rel_y value of this electrode
 - **rel_z**  `float`: the rel_z value of this electrode
 
 ## Shank
+
 Representation of a shank in NWB.
 
 **Attributes:**
+
 - **name**  `string`: name of the shank
 - **shanks_electrodes**  `dict`: electrodes in the shank
 
 ## Probe
+
 Representation of a probe in NWB.
 
 **Attributes:**
+
 - **id**  `int`: unique id of the probe
 - **probe_type**  `string`: type of probe
 - **units**  `string`: units in device
@@ -90,27 +104,33 @@ Representation of a probe in NWB.
 - **shanks**  `dict`: shanks in the probe
 
 ## DataAcqDevice
+
 Representation of data acquisition device in NWB.
 
 **Attributes:**
+
 - **system**  `string`: system of device
 - **amplifier**  `string`: amplifier (optional)
 - **adc_circuit**  `string`: adc_circuit (optional)
 
 ## CameraDevice
+
 Representation of a camera device in NWB.
 
 **Attributes:**
+
 - **meters_per_pixel**  `float`: meters per pixel
 - **model**  `string`: model of this camera device
 - **lens**  `string`: info about lens in this camera
 - **camera_name**  `string`: name of this camera
 - **frame_rate**  `float`: frame rate of this camera (optional)
 
 ## FrankLabOptogeneticEpochsTable
+
 An extension of the `OptogeneticEpochsTable` from [ndx-optogenetics](https://github.com/rly/ndx-optogenetics) with the following columns:
 
 **Columns:**
+
 - **epoch_name**  `string`: name of this epoch
 - **epoch_number**  `int`: 1-indexed number of this epoch
 - **convenience_code**  `string`: convenience code of this epoch
@@ -121,15 +141,20 @@ An extension of the `OptogeneticEpochsTable` from [ndx-optogenetics](https://git
 - **theta_filter_reference_ntrode**  `int`: reference ntrode for theta filter (optional)
 - **spatial_filter_on**  `bool`: whether the spatial filter was on (optional)
 - **spatial_filter_lockout_period_in_samples**  `int`: lockout period in samples for spatial filter (optional)
-- **spatial_filter_bottom_left_coord_in_pixels**  `float`, shape `(2, )`: bottom left coordinate in pixels for spatial filter (optional)
-- **spatial_filter_top_right_coord_in_pixels**  `float`, shape `(2, )`: top right coordinate in pixels for spatial filter (optional)
+- **spatial_filter_region_node_coordinates_in_pixels** `float`, shape `(n_region, n_nodes, 2,)`: If the spatial filter was used, the (x, y) coordinate of each boundary-defining node for each region. _Note:_ all regions must have the same number of nodes. For regions with fewer nodes, use (-1, -1) to fill the additional xy values.'
 - **spatial_filter_cameras_index**  `int`: index column for spatial filter cameras (optional)
 - **spatial_filter_cameras** : references to `CameraDevice` objects used for spatial filter (optional)
 - **spatial_filter_cameras_cm_per_pixel**  `float`: cm per pixel for spatial filter cameras (optional)
 - **ripple_filter_on**  `bool`: whether the ripple filter was on (optional)
 - **ripple_filter_lockout_period_in_samples**  `int`: lockout period in samples for ripple filter (optional)
 - **ripple_filter_threshold_sd**  `float`: threshold in standard deviations for ripple filter (optional)
 - **ripple_filter_num_above_threshold**  `int`: number of tetrodes above threshold for ripple filter (optional)
+- **speed_filter_on** `bool`: Whether the speed filter was on. Closed-loop stimulation based on whether
+      the animal is moving fast/slow enough. (optional)
+- **speed_filter_threshold_in_cm_per_s** `float`: If the speed filter was used, the threshold for detecting a fast/slow animal (optional)
+- **speed_filter_on_above_threshold** `bool`: If the speed filter was used, True if active when speed above threshold. (optional)
+- **stimulus_signal** `TimeSeries`: Timeseries of the delivered stimulus. Can be continuous values or time of
+      digital on/off events.
 
 ---
 This extension was created using [ndx-template](https://github.com/nwb-extensions/ndx-template).