Multi devices and temperature biopoint #123
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* Update feature extraction for heatmap visualization Modified feature extraction to use new FeatureExtractor interface. * Change features to fe in OnlineStreamer Replaced list of features with FeatureExtractor. This allows the user to pass in a FeatureExtractor object with feature parameters + standardization. * Offline regression example Added offline regression example .md and .rst files. Also added link to this example in index.rst. * Example for new streamer * Revert "Example for new streamer" This reverts commit 353e286. * Rename ColumnFetch to ColumnFetcher Class name was accidentally changed during a previous commit. Reverted so its name is more consistent with other classes. * Remove duplicate method Previous commit added a duplicate write_output method definition in OnlineStreamer. * Add feature queue for time series models Some time series models operate by predicting on a sequence of windows instead of raw EMG data. Added option to queue windows instead of just passing in a single window. * Move constructor docstrings outside __init__ sphinx-doc parsing wasn't detecting classes that didn't have docstrings before the constructor. Moved constructor docstrings to reflect this. * Regression explanation Added regression details to tabs that just described classification. * Add explicit conditional check instead of relying on casting * Only pop if queue is at max length * Add feature queue parameter to child classes Feature queue parameter was in OnlineStreamer, but not the online classifier and regressor. Added documentation to those classes and implemented parameters to create models that feature queue. * Add online channel mask Channels could not be isolated for online data. Added functionality to only grab certain channels online. * Revert "Revert "Rework FeatureExtractor"" This reverts commit ec52763. * Add skip until buffer fills up * Add TODO * Add wildcard to regex helper Default value for regex helper function often threw an error when searching for a pattern. Replaced the default value with the wildcard, so users can use this to grab the potential values without knowing them. * Add check for None in RegexFilter Since the regex helper function can take None values, users may pass in None to RegexFilter. This wouldn't work since we store metadata as an index of the values they pass in. Added a check to ensure this doesn't happen. * Add wildcard to regex helper Default value for regex helper function often threw an error when searching for a pattern. Replaced the default value with the wildcard, so users can use this to grab the potential values without knowing them. * Add check for None in RegexFilter Since the regex helper function can take None values, users may pass in None to RegexFilter. This wouldn't work since we store metadata as an index of the values they pass in. Added a check to ensure this doesn't happen. * Add MEC24 workshop to landing page * Add post-processing visual to regression example * Add skip until buffer fills up * Regression visualization * Handle coordinates without steady state frames An error was thrown if our method of calculating steady state frames failed (like in cases where there weren't any steady state frames). Added a try catch to deal with this. * Animation documentation Added an animation tab to Modules and described some of the animations you can make. * Add heatmap visualization * Add string parameters for common metadata operations Users could pass in function handles to change metadata operations, but there are some operations that are very common and require users to define function handles (like grabbing the last sample). Added ability to pass in strings for some common operations. * ninapro db2 dataglove support added * Revert "Revert "Revert "Rework FeatureExtractor""" This reverts commit 19f2049. * Add online standardization method Data could not be standardized online. Added a method to install standardization to online models. * Use proper FeatureExtractor interface Some changes were not reverted properly, causing the FeatureExtractor in OnlineStreamer to use the old interface. Updated to use the current interface (no breaking API). * Fix heatmap feature extraction Feature extraction in visualize_heatmap used old modified API for FeatureExtractor. Reverted to expected version. * Add clarification to install_standardization docstring * Fix online regressor visualize lag Online regressor method visualize() had lag when plotting. Modified so it uses the matplotlib animation API instead. * Add docstring to OnlineEMGRegressor.visualize * Skeleton for Controller class Added skeleton for Controller class and potential ideas for implementation. * Check for correct MacOS string * ninapro db2 * Remove unnecessary pop of oldest window There was a check for when the queue reached the max length that would manually pop the oldest window. This functionality is already built into deque by specifying the maxlen parameter, so replaced the check with maxlen. * Create SocketController Created base Controller class that all controllers (including keyboard) will inherit from. Also created a SocketController class that all controllers communicating over a port will inherit from. * Add comment idea * Add abstract timestamp parsing function Added another abstract parsing function because messages should also include a timestamp, so the user may want to parse those as well. * RegressorController Implementation of a regressor controller. Hasn't been tested yet. * updates sifi streamer to accept bridge version. forked sifi bridge into bp and ba * Remove model from RegressorController Users may not have access to the model itself in a script, so passing in the model may not work. Modified so users just pass in the IP and port. * db2 dataglove support limited to NinaproDB2 class * ClassifierController implementation Created concept for ClassifierController, but still hasn't been tested. * Fix online regressor visualize lag Online regressor method visualize() had lag when plotting. Modified so it uses the matplotlib animation API instead. * Add option to parse timestamp Added ability to grab timestamp when calling get_data. * Remove OnlineEMGRegressor.parse_output and references This method was essentially a copy of the RegressorController functionality. Replaced it with a call to the RegressorController. * documentation for NinaproDB2 * Remove duplicate method Removed a duplicate method that parent class already had. * Throw error when streaming stops during SGT * Update .gitignore .gitignore didn't ignore all .pyc files. * Convert methods to private Controller had many methods that the user shouldn't call. Converted these methods to private. * Regression Fitts task Added class for Fitts task using regression. Needs to be modified for classification. * Added sifi-bridge-py to dependencies. Renamed executable to sifibridge * cleanup init and sifibridge configurations * Change raw writes to sbp methods * Updated some redundant parameters and docstrings * Remove executable from repo * Fixed sifibridge process launch, added sifibridge to gitignore * Fix gitignore * Fixed cleanup * make streamer function more in-line with sifi-breakout * docstring, change 'device' to 'name' * Remove metric calculation functions * Implement classifier controller for visualization * Add check for data not being received * Add EMG hero legacy code * Replace deque with multiprocessing Queue SocketController used a deque, which isn't thread-safe and meant that the SocketController's data parameter didn't update in all threads when it was updated in another. Replaced deque with multiprocessing queue, which is thread safe. * Fix online ClassifierController parsing ClassifierController was not parsing all messages properly. Added parameters to allow for definite parsing and some checks to tell the user if they set something up incorrectly. * Fix OnlineEMGClassifier.visualize OnlineEMGClassifier.visualize hadn't been updated since shared memory changes. Modified to use new ClassifierController. * Automatically start Controller in Environment * Classifier working in FittsLawTest Regression worked in Fitts environment, but not classification. Modified data parsing to handle classification properly. Also added a parameter that the user can pass in to customize which commands cause which directions. * Rename FittsLawTest to IsoFitts * Move common functionality to run method Replaced abstract run method with abstract _run_helper method. * Update OnlineEMGClassifier visualize docstring Description for the legend parameterr didn't fully explain what user should pass in. * Hide pygame welcome message * Move functionality to Environment class and Fitts parameters Moved shared functionality into common parent class and added some helpful parameters to IsoFitts. * Rework prediction map Having commands be the keys made it a bit tedious to grab the commands. Reverted so the controller outputs are the keys and we grab the commands from that. * Convert EMGHero to Environment Modified legacy EMGHero code to fit Environment interface. * Rework _get_action for queue Blocking until we grabbed the desired value sometimes caused the program to stop. Replaced this so action will just be set to None if no data was received. * Remove _parse_timestamp from Controller class This method was only needed for the SocketController, so moved it there. * Fix prediction map for IsoFitts Prediction map had hand open/close swapped. * Implemented KeyboardController Added KeyboardController to allow users to test out environments with a keyboard first. * Properly receive None in EMGHero EMGHero didn't properly handle None b/c previous implementation used blocking with multiprocessing Queue. Setting key pressed to -1 on each loop meant that the notes flickered because the while loop updated quicker than the environment FPS. The key pressed is now only updated when data are received. * Split environments.py into multiple files Having all environments in one module would result in a massive file. Split into a submodule where each environment can get their own file. * Add environments to __init__ * Fix environment imports * Hide pygame welcome message * IsoFitts direction fix IsoFitts up/down directions were okay for classification/keyboard, but not regression due to pygame treating down as +. * Convert IsoFitts methods to hidden methods Only the run method should be public to the user, so all other methods were hidden. * Environments documentation Added docstrings and explanations for all added environments and controllers. * Rework SocketController SocketController used a multiprocessing Queue, which randomly caused issues when different threads tried to pop/put out of sync. Replaced with a multiprocessing Value to avoid this. * Add wait in OnlineEMGRegressor.visualize Without waiting for predictions to be received an error would be thrown. Added a while loop to wait until predictions are received. * fixed windows compilation target * Override terminate method Overriding terminate method to gracefully close the socket before stopping the process. * Allow non-callable dtypes Some numpy dtypes aren't callable without extra parameters, so added support for those. * Convert Manager to SharedMemory Previous implementation used a multiprocessing.Value and a string array, which is different from other low level memory interfaces in libemg (e.g., streamers) and isn't as fast. Replaced with straight shared memory. This way it uses the same interface as the streamers, has a fixed buffer size, and is quicker. * Add proportional control flag to IsoFitts * Automatically create parent directories when saving coordinates * Update Fitts example with regression Modified Fitts example documentation to include regressor comparisons. * added sifi bridge to setup * Launch the subprocess in run method for pickling issues * Update streamers.py * removed version from sifi bridge import * added more checks for creating variables * SocketController Lock Fix SocketController created a new Lock in the run method, which meant that the Lock wasn't actually serving its purpose (i.e., locking down that block of memory so we couldn't read in one process and write in another). Replaced it so the run method uses self.lock as well. * Add pygame to setup.py * Simplify SocketController Changing Controllers so they don't need a Process. * Make socket non-blocking Socket default behaviour is blocking, which means the FPS of an environment is tied to how often it is receiving data (i.e., the window increment). Made socket non-blocking so the FPS is always the same. * Replace classifier_smm_writes with model_smm_writes Old SMM key was still using classifier instead of model, which threw an error in the regressor. * Pass model timestamp instead of current time Model timestamp is needed for adaptation. * Fixed saving of IMU data data structure changed for the IMU. Previously it was acc_x, now it is ax. * Remove Delsys pasted docstring * Add numpy import to Delsys API streamer * Add check for num_channels in delsys_api_streamer Delsys API streamer required num_channels to be passed, but didn't explain this in the docstring or check. * Add support for .json when logging environment Some users may not want to read a .pkl file, so add support for json. * Add target and distance radii parameters * Add option to redo final rep * Show "Rep X of Y" during data collection * Automatically calculate rep time for videos * Find labels files and move to corresponding data directory * Throw ConnectionError during start callback * GUI docstring update Added information on convenience changes and behaviour when searching for media files. * Add game time parameter * Removed unused dependencies in sifibridge streamer. Set EDA to 0Hz by default. Removed version parameter. Set all modalities to Off except EMG by default. * Add regression info to docstring * Add timestamps to KeyboardController * Draw cursor for RotationalIsoFitts * WIP: converting to using polygons * Rename isofitts module to fitts * Rename IsoFitts class to ISOFitts * Create PolarFitts * Fitts base class * Remove duplicated code from ISOFitts * Inherit from Fitts instead of ISOFitts for PolarFitts * Remove dead code * Create Fitts targets in uniform circle * Handle different target sizes * Custom directions for PolarFitts prediction_map * Set minimum target size based on cursor * Reimplement feature parameters online Installing feature parameters online had been removed at some point. Reimplemented this by passing feature parameters from the offline model. * Only add to smm_items list if tag has not already been provided * Fix check for cursor being on new goal target * Keep radius on screen * Fix incorrect polar to cartesian action map * Restrict PolarFitts to a single side * Removed unused dependencies in sifibridge streamer. Set EDA to 0Hz by default. Removed version parameter. Set all modalities to Off except EMG by default. * Stop targets from generating in the center of the screen * Set theta pointed at bottom of screen instead of right * Docstring for PolarFitts * Initialize theta to pi/2 * Remap theta direction to correspond to prediction direction * Fix visualize_heatmap throwing error for feature lists of length 1 * WIP: Functional conversion from Cartesian to Polar space * Remove dead code * Pass in rect when drawing to polar space * Add fill parameter for drawing polar circle * Fix logical error when checking if new target is on cursor * Combine PolarFitts into parent Fitts class With the changes so everything is the same under the hood and the cursor is rendered differently, the PolarFitts class could be removed and replaced with a parameter in the Fitts class. This way ISOFitts gets this functionality for free. * Fix check for cursor remaining on screen * Update Fitts and ISOFitts docstrings * Add option to draw radius in polar Fitts * Extract origin to variable * Improve check for cursor staying in bounds * Add check in ISOFitts for target distance radius and screen size * Improve error handling for small screen size error * Fix fstring formatting in error message * Use full screen size when possible * Switch polar Fitts to vertical layout instead of horizontal * Change default num_targets in ISOFitts * Add parameters for target and cursor color * Extract Fitts parameters to config dataclass Managing contructor parameters and docstrings for Fitts and ISOFitts was quite tedious and would only get worse when adding more Fitts environments. Extracted many configuration parameters (e.g., target size and color) to a dataclass. Now the docstring and parameters of the dataclass can be changed to update both environments. * Update colors Changed colors to use a color-blind friendly palette. Also added parameters to change timer color, background color, and cursor in target color. * Make OnlineDataHandler processes daemons Processes are created for visualize and log_to_file, but they weren't created as daemon processes. This meant that users had to manually call stop_log() and stop_visualize(). Otherwise, the script would hang because these processes would continue even after the main script was finished. Created these as daemons so they will be killed when the parent process is killed. * Dataset Updates (LibEMG#85) * Dataset updates * Updates * Added Grab Myo * Updates * Changed pathing * Update OneSubjectEMaGerDataset to new format Added in OneSubjectEMaGerDataset for regression tasks. Updated for new Dataset format. * Add split parameter to prepare_data Return value of prepare_data was changed to a dictionary, which would be a breaking change. Modified this so users can pass in a flag that will determine if it is returned as a dictionary or a data handler. * Updates * Updates * Fixed Grab Myo * Added resp to EPN * Updated the data handler to run faster * Made them all parse fast * Sped up window parsing * Fixed data handler * Updated ref * Made faster * Fixed * Updated * Updates * Updates * Updates * Added cropping * Updated to crop better * Updates * Undo * Hyser dataset Started working on Hyser dataset. Created parent class and started 1DOF class. Both classes still need to be tested. * Updated libemg * Fix zoom logical error Parameter passed to scipy zoom created a value for each column instead of one for each axis. This didn't throw an error in the past because most data that had been tested was also 2 DOF. Modified to proper zoom factor. * Add regex filter packaging and .hea support to FilePackager FilePackager could not read .hea files and creating a package function to match based on filename was tedious. Added the option to pass in a list of RegexFilters that will match the regex metadata from two files to package them. * Add check in regex package function Some metadata files would throw an error when calling get_metadata because the file didn't match the original regex filter. Added a check so False is returned if it doesn't match the RegexFilters. * Fix Hyser1DOF Added correct RegexFilters, package function, and data split. * Added CI dataset * Updates * Updates * UpdaTes * added limb position * radman->radmand * added h5py req * added kaufmannMD * created kaufmann class * added submodules to _dataset * Updated myodisco * Updates * added h5py * HyserNDOF and HyserRandom Classes Added classes for Hyser NDOF and random datasets. * Add type hint to RegexFilter Specified that values should be a list of strings. * Handle single values from MetadataFetcher MetadatFetcher stated in the docs that it expected an N x M array, but didn't throw an error as long as an array was returned. Added a check to ensure that single values aren't being returned. If a single value array is returned, it is cast to an N x 1 array. * Hyser PR Dataset Implemented pattern recognition Hyser dataset. * Remove subject 10 from random task dataset Subject 10 is missing a labels file, so removed this subjects from the random task dataset. * Rename Hyser to _Hyser Added _ to signify that this is a hidden class. * Hyser documentation Added documentation to Hyser dataset classes. * Don't do any processing on the dataset * Add NinaproDB8 * Add note to NinaproDB8 * Add OneSubjectEMaGerDataset import to datasets.py * Add OneSubjectEMaGerDataset to dataset list * Fix parse_windows for 2D metadata parse_windows call np.hstack to stack metadata, which works for 1D arrays but throws an error for 2D arrays since different files likely won't have the exact same number of samples. We also don't want this behaviour anyways since we want to stack along the sample axis. Replaced np.hstack with np.concatenate so metadata is always concatenated along the 0th axis. * Reimplement NinaPro cyberglove data Parsing cyberglove data wasn't brought over when modifying datasets. Reimplemented cyberglove parsing. * Allow empty strings in RegexFilter Added option to pass in an empty string as a description for a RegexFilter for cases where you want to filter files, like finding a labels file, but don't necessarily want that metadata to be stored. * Properly handle cyberglove data Previous implementation didn't consider that some files are skipped because they don't have cyberglove data. Added logic to parse all data, and then allow user to select what they want to grab based on if they're using the cyberglove. * added tmr data * Updates * Updated logging * Updates * Updates * Add UserComplianceDataset * Updates * Updates * Convert labels field to classes in HyserPR * added CIIL_WS. Fixed dataset exist check for regression & WS * initial commit for CIIL_WS * added onedrive download method * added onedrive download method * added one drive downloader * added arguments for unzip and clean * now downloads * Fixed one site bio * Hyser labels fix * Add subjects to Hyser classes * Continuous transitions debugging * Add subjects to OneSubjectEMaGerDataset * Evaluate method fixes * Fixed continuous * Fix subject indexing with Hyser * Handle default subject values for Hyser datasets * Fixed DB8 * Hyser missing subject fixes * added onesiteBP * Fixed continuous transitions * Biopoint * Fixed hyser * Fixed fougner * Add linear mapping to NinaproDB8 * Normalize NinaProDB8 labels * Add parameter to normalize NinaProDB8 labels * Replace string concatenation with fstring String concatenation only worked when strings were passed in. * fxied some docs * Small fixes * Updated doc * Changed to fast by default * Added cross_user evaluation * Trying to fix grab * Updates * Changed to just one session * Fixed error * Trying to fix grab myo * Fixed cross user * Updates * Added option for CNN * datasets * Added nomralization * added subject to prepare method * Updated docs * Fixed cross-user * Add subjects parameter to UserComplianceDataset * Partially fixed the memory issue * Fixed EPN * Fixed * Removed disco * Updates * Fixed FORS-EMG * Updated hyser * Hopefully fixed hyser * Fixed hyser part 2 * Updates * Added meta * Fixes * Fixed all regression datasets * Upadted meta * Update UserComplianceDataset subject IDs UserComplianceDataset subject IDs were reverted to original. Updated full subject list to reflect this. * Updated all to split Ture * fixed * cross user * Updated EPN * Update UserComplianceDataset baseline analysis This dataset was made to train on poor data and test on good, so having the default use just baseline data didn't make sense. * Added docs for most classification datasets * Just need to add Hyser and references * Doc changes * updated docs to include datasets * Updates * More doc updates * Updates and fixed offline metrics * Updated offline metrics * Updated TMR * Remove Hyser workaround A previous commit had added a hacky workaround for dealing with subject IDs that were removed in the Hyser dataset. Removed this change as it has been fixed by new subject indexing. --------- Co-authored-by: Christian Morrell <cmorrell@unb.ca> Co-authored-by: ECEEvanCampbell <evan.campbell1@unb.ca> * Fixed setup issue * Remove incorrect docstring * Reset dwell timer in _get_new_goal_target * Add HyserMVC Dataset (LibEMG#105) * Add HyserMVC Dataset All Hyser datasets had been included except for MVC. Added MVC in case users wanted it for normalization. * Fix train/test split for HyserMVC * Wait to start timers until data have been received * Add cursor_radius parameter to FittsConfig * Updated the normalization in the feature extractor * Modify FittsConfig default parameters Many of these parameters were for testing and/or primarily for regression. Reduced dwell time and made timeout default to None to apply to most use cases. Also made num_trials a required parameter. * Update _delsys_streamer.py adding axis to the delsys streamer was done to the wrong location * Added option for dictionary list * Added option for dictionary list * Added a fix feature errors to feature extractor * Changed feature_extractor to default to fix errors is false * Changed dataset names * Updated feature dictionary * Updates * Remove old calls to Controller.start * Fixed code example for feature performance (LibEMG#118) * added pca visualization to online data handler (LibEMG#110) * Regressor Visualize On One Axis (LibEMG#112) * Add single_axis parameter * Remove manual y-axis limits Some labels may not be in the range (-1, 1) so manually setting labels wasn't best. * Add docstring for visualize method * Streamer Cleanup (LibEMG#115) * Add mindrove to requirements * Add MindroveStreamer * Rename mindrove.py to _mindrove.py * Pass correct append method to smm * Add comment * Add comment * Add mindrove streamer function * Add cleanup to MindroveStreamer * Improve variable name * Cleanup Mindrove streamer * Add proper cleanup for MyoStreamer * Handle proper cleanup for EMaGer streamer * Add MindRove to documentation * Updated README * Updated yaml * Added option to configure BLE Power and Memory Mode (LibEMG#121) Added parameters ble_power and memory_mode to function configure and in the __init__ as this is an important parameter that users should be able to set when using the devices. Co-authored-by: ulysseTM <156504252+ulysseTM@users.noreply.github.com> * Updated version --------- Co-authored-by: Christian Morrell <cmorrell@unb.ca> Co-authored-by: Evan Campbell <evan.campbell1@unb.ca> Co-authored-by: Amir Reza Hariri <amirrezahariri2000@gmail.com> Co-authored-by: Gabriel Gagne <gabrielpgagne@gmail.com> Co-authored-by: Gabriel Gagne <gagag158@ulaval.ca> Co-authored-by: ulysseTM <156504252+ulysseTM@users.noreply.github.com>
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Enable multiple biopoints and bioarmbands as well as temperature readings for both devices.