flares/changelog.md

# Version 1.6.0

- This is potentially a save-changing release due to adding more data into the save file, renaming existing data, and changing what part of the code saves data. Please update your project files to ensure compatibility
- It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
- Optimized calculations being performed when calculating the Heart Rate to speed up step 5 by up to ~35% on a per-file basis
- Optimized calculations being performed when running the General Linear Model to speed up step 5 by up to ~35% on a per-file basis
- The Group Stats Viewer windows will now properly load the Right/Left or Front/Back fallback ROIs if JSON_LOCATION is not set
- Changed the warning message for lots of short channels to be percentage based (25%) instead of numerical based (6)
- Renames GENDER to SEX to better represent the values that the field expects and to be more BIDS compliant
- Changed the Assign Groups by AGE window to now be the Assign Groups by Metadata window and added support for grouping by other metadata values
- Added a new metadata value of HAND to allow for grouping participants based on their handiness
- Updated the layout of the participant metadata area to better accommodate current and future metadata values
- Updated the message displayed when "Why are these useful?" is clicked to better represent what the values are used for and to accommodate the new metadata values
- Changed the application title to now show what project you are working on. If you are not working on a project, it will display 'Untitled'
- Tracking of current save states is now present and an asterisk will now appear in the title bar when a project has not been saved
- Currently tracking is only supported on loaded files, parameters on the right side of the screen, and when processing has completed. Per-file metadata or processing stages are not currently implemented
- Clicking close on the Main Window will now properly close all sub windows when closing the application and closing the application with unsaved changes will now prompt to save a project or discard changes. Fixes [Issue 87](https://git.research.dezeeuw.ca/tyler/flares/issues/87)
- The Save button under the File menu no longer asks for a destination if a saved project was already loaded. Fixes [Issue 72](https://git.research.dezeeuw.ca/tyler/flares/issues/72)
- The popup that appeared when a project was saved has now been moved to a message displayed from the status bar
- Moved all loading of files, loading of folders, loading of projects, and saving of projects to a new file for easier future development
- Changed the working of some messages on the status bar to better reflect what has occurred
- Fixed an issue where the two Group Stats Viewer windows would crash the application once attempted to be opened if JSON_LOCATION was not set
- Fixed an issue where participants could be skipped when processing multiple participants at once which could prevent overall processing from completing
- Fixed an issue where when loading a save file some list dropdowns could go blue and bold even if the value was default
- Fixed an issue where the Analysis button would not be clickable if the user had previously pushed Clear. Fixes [Issue 83](https://git.research.dezeeuw.ca/tyler/flares/issues/83)
- Fixed an issue where some popup windows would not properly display the application name when they would open
- Fixed instances of the word MacOS to now read macOS to match Apple branding
- Fixed welcom dialog application image not displaying correctly on macOS


# Version 1.5.2

- Opening both a file or a folder now contains support for reading some metadata from the BIDS structure. Both options will still function if this metadata is not present
- Currently only the AGE metadata is grabbed and is auto populated into the participants AGE field and displayed on their bubble
- If the participants have metadata, a popup will be displayed asking if the user wants to group the participants by their metadata
- If the user wants to create groups, a dialog box is presented allowing them to do so. Once completed, the GROUP value will be automatically applied to all applicable participants
- A new options menu item has been added: Regroup Files from Metadata. This will allow the dialog to be opened at a later time with a popup appearing if there is no metadata present
- Added two new options to the Export to CSV Viewer: Export Configuration to CSV and Paragraph of Configuration
- Export Configuration to CSV will export the parameters utilized for each file into a CSV formatted file to provide additional validation of what parameters were used
- Paragraph of Configuration will generate a ready-to-go paragraph explaining in a more friendly and easy to follow manner of what parameters were used
- Chunked the loading of folders to provide more feedback to the user instead of hanging the application waiting for all files to load
- New parameters have been added to the right side of the screen! This allows for more flexibility and customizability when processing
- A new Preference Menu option has been added: Show Advanced Parameters. This keeps some of the parameters hidden when not checked. Since this is a preference, it will be saved when reopening the application
- Advanced parameters should only be changed if you know what you are doing, and will have a yellow warning symbol next to them to avoid potential confusion on what parameters are advanced
- Optimized some of the calculations in Scalp Coupling Index to speed up Step 6 by up to ~25% on a per-file basis
- Removed duplicate/redundant calculations in Peak Spectral Power to speed up Step 8 by up to ~50% on a per-file basis
- Changed how the figures are generated when processing to speed up Step 28 by up to ~85% on a per-file basis
- Removed unused methods inside the processing file to slightly speed up application load time
- Fixed an issue with the build script not properly updating the version string causing the application to falsely think that an update was always available
- Fixed an issue where parameters that were dependent on SHORT_CHANNELS were not properly being updated
- Fixed an issue where files that failed processing were not having their progress bar turn red at the step that failed
- Fixed an issue where progress bars were not updating when MAX_WORKERS was set to a value higher than default
- Fixed an issue where a high value of MAX_WORKERS was never hit the targeted value due to not being able to spawn the workers fast enough
- Fixed an issue causing numerous 'Invalid File' popups to appear upon closing the application while files were still having their initial metadata being grabbed
- Fixed an issue where both 'Update events in snirf file...' windows could not be open at the same time
- Fixed an issue where externally updating a participant's metadata when they were selected would cause the application to crash
- Fixed an issue where there was a redundant checking of dependencies when the parameters on the right side of the screen were being calculated
- Fixed an issue in which clicking menu options too fast would cause the application to hard crash
- Added a time elapsed message to the status bar denoting how long processing has been going on for. When processing is complete, it will change to be the time elapsed
- Added a speedup multiplier to show how much time was saved by having MAX_WORKERS not set to 1. This multiplier is calculated using a naive approach and may not be accurate
- Removed redundant font styling when parameters were changed from their default values


# Version 1.5.1

- Opening a folder is now minimally BIDS compatible. It will recursively go through all folders, but not load external metadata
- Renamed options in the Viewer Launcher window to better denote what actions they can perform
- 2 new analysis options have been added in the viewer launcher window: Inter-Group Stats and Cross-Group Stats
- Each of these analysis options have lots of text explaining what they do when their respective windows are opened
- The parameter input dialog in the analysis windows will now be able to scroll down when lots of parameters are required
- When a project is saved, it automatically will populate into the Recent Projects menu. Fixes [Issue 86](https://git.research.dezeeuw.ca/tyler/flares/issues/86)
- The description when clicking "Why are these useful?" underneath the per-file parameters is no longer placeholder text. Fixes [Issue 85](https://git.research.dezeeuw.ca/tyler/flares/issues/85)
- Added a new parameter section "Region of Interest". It has one parameter of "JSON_LOCATION", a json file containing Region of Interest data
- Temporarily removed the parameter REMOVE_EVENTS due to its functionality being removed because of a memory leak
- Fixed participant metadata remaining in the background when the participant was removed. Fixes [Issue 82](https://git.research.dezeeuw.ca/tyler/flares/issues/82)
- Fixed processing remaining active hidden in the background when the "Clear" button was pushed. Fixes [Issue 81](https://git.research.dezeeuw.ca/tyler/flares/issues/81)
- Now when "Clear" is pushed while data is processing, a popup will appear ensuring that the user understands that pushing "Clear" will stop processing
- Reset to Default Configuration will now properly reset all of the parameters to their default values. Fixes [Issue 90](https://git.research.dezeeuw.ca/tyler/flares/issues/90)
- A confirmation popup will now display once the application has been reset to default in addition to the status bar message
- Changed the improper display text of "Cross Validation" to now properly read as "Coefficient of Variation"
- Changed the parameters "CV" and "CV_THRESHOLD" to now be "COEFF_VAR and COEFF_VAR_THRESHOLD"
- Changed the improper display text of "Mean Absolute Deviation" to now properly read as "Median Absolute Deviation"
- Changed the parameters "SHORT_CHANNEL", "SHORT_CHANNEL_THRESH", and "LONG_CHANNEL_THRESH" to now be "SHORT_CHANNELS", "SHORT_CHANNELS_THRESHOLD", and "LONG_CHANNELS_THRESHOLD"
- Changed the parameter section "Channel Variance" to now be "Sensor Dropout" to better reflect the action it performs, not the method employed to calculate it
- Changed the parameters "CHANNEL_VAR" and "CHANNEL_THRESH" to now be "SENSOR_DROPOUT" and "SENSOR_DROPOUT_VARIANCE_THRESHOLD"
- Changed the messaged displayed when the application crashes to better reflect what occurred
- Changed the processing stages 25-27 and updates their messages to better reflect their actions that they now perform
- Changed stage 25 from "Generate Channel Significance" to "Generate Channel Results"
- Changed stage 26 from "Generate Channel, Region of Interest, and Contrast Results" to "Generate Region of Interest Results"
- Changed stage 27 from "Compute Contrast Results" to "Generate Contrast Results"
- Changed backend code to only load required methods and not load all methods every time
- Fixed string parameters not going blue and bold when their value was different than default
- Fixed all parameters not going blue and bold when a save file is loaded containing values that differ from default
- Fixed a crucial bug where short channels were not being processed and filtered the same way as long channels before being used as regressors
- Fixed a crucial bug where short channels were being presented to the design matrix as normal long channels
- Fixed a crucial bug where long channels could be interpolated from short channels. Short channels are still potentially interpolated from long channels. See [this link](https://git.research.dezeeuw.ca/tyler/flares/issues/80) for more information regarding this issue.
- Decreased unnecessary processing time when fOLDing channels by an order of magnitude. Fixes [Issue 84](https://git.research.dezeeuw.ca/tyler/flares/issues/84)
- Added a welcome message when the terminal is opened, resized the terminal, and added more commands


# Version 1.5.0

- This release introduces a new configuration file that may break existing installs. If your application does not update correctly, please download fresh from [this link.](https://git.research.dezeeuw.ca/tyler/flares/releases/)
- This release features an almost complete rewrite of backend files. If you encounter any problems, please raise an issue at [this link.](https://git.research.dezeeuw.ca/tyler/flares/issues/new)
- New configuration file has been added! Now your choices of preferences will be saved when the application is closed and re-opened. If the configuration file is missing, a new one will be generated
- Recent files and recent projects are now saved and appear under the File menu for quick resuming
- The new option "Reset to Default Configuration" under the Options menu will reset the configuration file back to its default values and remove any recent files
- A welcome dialog will now display the changelog on first startup and after every update. This popup will only appear once but can be reopened under the Options menu through the button "Show Update Changelog"
- Changed the hotkey for "Update optodes in snirf file..." to be F9 instead of F6
- Revamped the fOLD channels window. Images containing the pie charts are now interactable! Click whitespace to expand the whole image and click a chart to expand it.
- fOLD progress bar when processing now updates the percentages live. Fixes [Issue 76](https://git.research.dezeeuw.ca/tyler/flares/issues/76)
- Overall pie charts on an individual and global basis are now generated. Fixes [Issue 78](https://git.research.dezeeuw.ca/tyler/flares/issues/78)
- Brodmann images are now available when examining a pie chart to understand which area is being reported. Fixes [Issue 77](https://git.research.dezeeuw.ca/tyler/flares/issues/77)
- Added a new option 'Folding Bypass' to the Preferences Menu. This skips most processing steps and the only analysis option available will be to fold. Parameters on the right will be ignored. Fixes [Issue 75](https://git.research.dezeeuw.ca/tyler/flares/issues/75)
- Fixed an issue where the fOLD analysis progress window would go unresponsive before processing participants. Fixes [Issue 45](https://git.research.dezeeuw.ca/tyler/flares/issues/45), Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34)
- Added a feature to hover over the 28-stage progress bar and see which state the progress bar is at. Fixes [Issue 74](https://git.research.dezeeuw.ca/tyler/flares/issues/74)
- Loading a broken snirf file no longer hangs its processing and can now be removed from the list. Fixes [Issue 73](https://git.research.dezeeuw.ca/tyler/flares/issues/73)


# Version 1.4.3

- Fixed an issue where the fOLD files could not be located
- Added better support for updating events from external software


# Version 1.4.2

- Fixed AGE, GENDER, GROUP not visually appearing on a bubble after the metadata has been set. Fixes [Issue 42](https://git.research.dezeeuw.ca/tyler/flares/issues/42)
- Fixed first stage of progress bar going yellow after loading from an unprocessed save
- Fixed AGE, GENDER, GROUP not visually appearing on a bubble when loading from a save 
- Group images involving an optode template will now be the average of all participants selected in the group and not the last processed participant. Fixes [Issue 62](https://git.research.dezeeuw.ca/tyler/flares/issues/62)
- Group images will no longer crash if being made with participants that have a different number of channels
- Changed CSV files to now save to the same folder rather than asking each time for each file. Fixes [Issue 39](https://git.research.dezeeuw.ca/tyler/flares/issues/39)


# Version 1.4.1

- Hotfix to fix a recursive child loop that would cause the macOS version to not open


# Version 1.4.0

- This is potentially a save-changing release due to changes in how file paths and parameters are stored. Please update your project files to ensure compatibility
- It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
- AGE, GENDER, GROUP, loaded files, and all the parameters on the right side of the screen can now be saved before any data has been processed
- If processing has not been completed, the process button will be visible. If processing has completed, the analysis button will be visible
- If the values fail to load, they will fallback to the previous logic of retrieving these values after processing has occurred. Fixes [Issue 66](https://git.research.dezeeuw.ca/tyler/flares/issues/66)
- Added new parameters to the right side of the screen: MAX_SHIFT, T_MIN, T_MAX, MAX_BAD_CHANNELS. Fixes [Issue 69](https://git.research.dezeeuw.ca/tyler/flares/issues/69)
- Participants that are bad on channels will no longer continue to the GLM stage. Fixes [Issue 18](https://git.research.dezeeuw.ca/tyler/flares/issues/18)
- Added new sections to the right side of the screen to mark bad channels: Cross Validation, Median Absolute Deviation, PSD Noise, & Channel Variance
- These sections come with the new parameters CV, CV_THRESHOLD, MAD, MAD_THRESHOLD, PSD_NOISE, TARGET_FREQ_DIV, DB_LIMIT, CHANNEL_VAR, & CHANNEL_THRESH
- Changed number of rectangles in the progress bar to 28 to account for the new options and updated the User Guide with the new stages
- Added feedback when clicking an analysis option that opens up a new window. Fixes [Issue 20](https://git.research.dezeeuw.ca/tyler/flares/issues/20)
- Fixed an issue where projects can not be saved to a different drive letter on windows. Fixes [Issue 71](https://git.research.dezeeuw.ca/tyler/flares/issues/71)
- Fixed an issue where the fOLD files were not included in the Windows version. Fixes [Issue 60](https://git.research.dezeeuw.ca/tyler/flares/issues/60)
- Fixed an issue where the macOS version would fail to perform some analysis options. Fixes [Issue 63](https://git.research.dezeeuw.ca/tyler/flares/issues/63)
- Fixed an issue where processing too many participants would cause the analysis button to not appear. Fixes [Issue 61](https://git.research.dezeeuw.ca/tyler/flares/issues/61)
- Fixed an issue where the error message when a participant fails would not appear. Fixes [Issue 68](https://git.research.dezeeuw.ca/tyler/flares/issues/68)
- Fixed an issue where changes would not be saved if a project was originally loaded from a save. Fixes [Issue 44](https://git.research.dezeeuw.ca/tyler/flares/issues/44)
- Fixed an issue where the significance image would be empty in the Inter-Group Viewer if only one participant was selected. Fixes [Issue 32](https://git.research.dezeeuw.ca/tyler/flares/issues/32)
- Fixed an issue where pressing the 'Clear' button after loading a save would cause the application to crash. Fixes [Issue 67](https://git.research.dezeeuw.ca/tyler/flares/issues/67)
- Fixed an issue where group dropdowns in the Cross-Group viewer would not be updated correctly based on the other groups selected value. Fixes [Issue 49](https://git.research.dezeeuw.ca/tyler/flares/issues/49)
- Fixed an issue where scrollbars were still present after clearing all data. Fixes [Issue 70](https://git.research.dezeeuw.ca/tyler/flares/issues/70)
- Fixed an issue where 'Missing Events Bypass' did not work on the Cross-Group viewer. Fixes [Issue 64](https://git.research.dezeeuw.ca/tyler/flares/issues/64)
- Fixed an issue where bubbles loaded from a save would not resize correctly. Fixes [Issue 14](https://git.research.dezeeuw.ca/tyler/flares/issues/14)


# Version 1.3.0

- This is potentially a save-changing release due to a new parameter being saved. Please update your project files to ensure compatibility
- It is still possible to load older saves by enabling 'Incompatible Save Bypass' from the Preferences menu, but your mileage may vary
- Fixed workers not releasing memory when processing multiple participants. Fixes [Issue 55](https://git.research.dezeeuw.ca/tyler/flares/issues/55)
- Fixed part of an issue where memory could increase over time despite clicking the clear button. There are still some edge cases where this can occur 
- Fixed an issue when clearing a bubble, reloading the same file, and clicking it again would cause the app to crash. Fixes [Issue 57](https://git.research.dezeeuw.ca/tyler/flares/issues/57)
- Picking a .txt or .xlsx file now has both in the same file selection instead of having to select which extension was desired
- Added a new parameter to the right side of the screen: EPOCH_HANDLING. Fixes [Issue 58](https://git.research.dezeeuw.ca/tyler/flares/issues/58)
- EPOCH_HANDLING defaults to 'shift' compared to previous versions where the default would have been equivalent to 'strict'
- The label for ENHANCE_NEGATIVE_CORRELATION no longer gets cut off by its dropdown selection
- Loading in files and folders have changes to immediately show their bubbles having a respective loading symbol on each bubble
- Once the file has been completely loaded and processed, the loading symbol will change to a green checkmark and clicking will be enabled
- The metadata in the File information widget is now saved to prevent recalculations every time the bubble is selected
- The status bar will now say loading while the bubbles are being processed, and loaded once the processing has completed
- This new loading method will prevent the application from hanging when loading lots of files at once. Fixes [Issue 59](https://git.research.dezeeuw.ca/tyler/flares/issues/59)
- Fixed text alignment for the first paragraph when a bubble is selected in the 'File information' widget
- The three main widgets are now resizable! All of them have minimum widths to ensure they do not get too squished
- Added a new option 'Reset Window Layout' under the View menu that will resize all widgets back to their default sizes
- Added a new terminal command 'version' that will print the applications current version


# Version 1.2.2

- Added 'Update events in snirf file (BLAZES)...' and renamed 'Update events in snirf file...' to 'Update events in snirf file (BORIS)...' under the Options menu
- The BLAZES option will assign events that are exported directly from the software [BLAZES](https://git.research.dezeeuw.ca/tyler/blazes)
- Moved the updating logic to a separate file for better reusability and generalization
- Fixed 'Toggle Status Bar' having no effect on the visibility of the status bar
- Fixed a bug when updating optode positions that would prevent .txt files from being selected. Fixes [Issue 54](https://git.research.dezeeuw.ca/tyler/flares/issues/54)
- Fixed a missing dependency in the standalone application when attempting to use an .xlsx file to update optode positions


# Version 1.2.1

- Added a requirements.txt file to ensure compatibility
- Added new options 'Missing Events Bypass' and 'Analysis Clearing Bypass' to the Preferences Menu
- Missing Events Bypass allows comparing events in the Group Viewers even if not all participants in the group have the event present. Fixes [Issue 28](https://git.research.dezeeuw.ca/tyler/flares/issues/28)
- Clicking Process after an analysis has been performed will now clear the existing analysis by default with a popup warning that the analysis will be cleared
- Analysis Clearing Bypass will prevent the popup and will not clear the existing analysis data. Fixes [Issue 41](https://git.research.dezeeuw.ca/tyler/flares/issues/41)
- Clicking 'Clear' should now actually properly clear all data. Hopefully fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9) for good
- Setting SHORT_CHANNEL to False will now grey out SHORT_CHANNEL_REGRESSION, as it is impossible to regress what does not exist. Sets SHORT_CHANNEL_REGRESSION to False under the hood when it is greyed out regardless of what is displayed. Fixes [Issue 47](https://git.research.dezeeuw.ca/tyler/flares/issues/47)
- Projects can now be saves if files have different parent folders. Fixes [Issue 48](https://git.research.dezeeuw.ca/tyler/flares/issues/48)
- It is no longer possible to attempt a save before any data has been processed. A popup will now display if a save is attempted with nothing to save
- Fixed a bug where LONG_CHANNEL_THRESH was not being applied in the processing steps
- Added a new option in the Analysis window for Group Functional Connectivity. Implements [Issue 50](https://git.research.dezeeuw.ca/tyler/flares/issues/50)
- Group Functional connectivity is still in development and the results should currently be taken with a grain of salt
- A warning is displayed when entering the Group Functional Connectivity Viewer disclosing this
- Fixed a bug when updating optode positions that would prevent .txt files from being selected. Fixes [Issue 54](https://git.research.dezeeuw.ca/tyler/flares/issues/54)
- Fixed a bug where the secondary download server would never get contacted if the primary failed
- Automatic downloads will now ignore prerelease versions. Fixes [Issue 52](https://git.research.dezeeuw.ca/tyler/flares/issues/52)


# Version 1.2.0

- This is a save-breaking release due to a new save file format. Please update your project files to ensure compatibility. Fixes [Issue 30](https://git.research.dezeeuw.ca/tyler/flares/issues/30)
- Added new parameters to the right side of the screen
- These parameters include SHOW_OPTODE_NAMES, SECONDS_TO_STRIP_HR, MAX_LOW_HR, MAX_HIGH_HR, SMOOTHING_WINDOW_HR, HEART_RATE_WINDOW, BAD_CHANNELS_HANDLING, MAX_DIST, MIN_NEIGHBORS, L_TRANS_BANDWIDTH, H_TRANS_BANDWIDTH, RESAMPLE, RESAMPLE_FREQ, STIM_DUR, HRF_MODEL, HIGH_PASS, DRIFT_ORDER, FIR_DELAYS, MIN_ONSET, OVERSAMPLING, SHORT_CHANNEL_REGRESSION, NOISE_MODEL, BINS, and VERBOSITY.
- Certain parameters now have dependencies on other parameters and will now grey out if they are not used
- All the new parameters have default values matching the underlying values in version 1.1.7
- The order of the parameters has been changed to match the order that the code runs when the Process button is clicked
- Moved TIME_WINDOW_START and TIME_WINDOW_END to the 'Other' category
- Fixed a bug causing SCI to not work when HEART_RATE was set to False
- Bad channels can now be dealt with by taking no action, removing them completely, or interpolating them based on their neighbours. Interpolation remains the default option
- Fixed an underlying deprecation warning
- Fixed an issue causing some overlay elements to not render on the brain for certain devices
- Fixed a crash when rendering some Inter-Group images with only one participant in a group
- Fixed a crash when attempting to fOLD channels without the fOLD dataset installed
- Lowered the number of rectangles in the progress bar to 24 after combining some actions
- Fixed the User Guide window to properly display information about the 24 stages and added a link to the Git wiki page
- MAX_WORKERS should now properly respect the value set
- Added a new CSV export option to be used by other applications
- Added support for updating optode positions directly from an .xlsx file from a Polhemius system
- Fixed an issue where the dropdowns in the Viewer windows would immediately open and close when using a trackpad
- glover and spm HRF models now function as intended without crashing. Currently, group analysis is still only supported by fir. Fixes [Issue 8](https://git.research.dezeeuw.ca/tyler/flares/issues/8)
- Clicking 'Clear' should now properly clear all data. Fixes [Issue 9](https://git.research.dezeeuw.ca/tyler/flares/issues/9)
- Revamped the fold channels viewer to not hang the application and to better process multiple participants at once. Fixes [Issue 34](https://git.research.dezeeuw.ca/tyler/flares/issues/34), [Issue 31](https://git.research.dezeeuw.ca/tyler/flares/issues/31)
- Added a Preferences menu to the navigation bar
- Two preferences have been added allowing to bypass the warning of 2D data detected and save files being from previous, potentially breaking versions
- Fixed a typo when saving a CSV that stated a SNIRF was being saved
- Loading a save file now properly restores AGE, GENDER, and GROUP. Fixes [Issue 40](https://git.research.dezeeuw.ca/tyler/flares/issues/40)
- Saving a project now no longer makes the main window go not responding. Fixes [Issue 43](https://git.research.dezeeuw.ca/tyler/flares/issues/43)
- Memory usage should no longer grow when generating lots of images multiple times. Fixes [Issue 36](https://git.research.dezeeuw.ca/tyler/flares/issues/36)
- Added a new option in the Analysis window for Functional Connectivity
- Functional connectivity is still in development and the results should currently be taken with a grain of salt
- A warning is displayed when entering the Functional Connectivity Viewer disclosing this


# Version 1.1.7

- Fixed a bug where having both a L_FREQ and H_FREQ would cause only the L_FREQ to be used
- Changed the default H_FREQ from 0.7 to 0.3
- Added a PSD graph, along with 2 heart rate images to the individual participant viewer
- The PSD graph is used to help calculate the heart rate, whereas the other 2 are currently just for show
- SCI is now done using a .6hz window around the calculated heart rate compared to a window around an average heart rate
- Fixed an issue with some epochs figures not showing under the participant analysis
- Removed SECONDS_TO_STRIP from the preprocessing options
- Added new parameters to the right side of the screen
- These parameters include TRIM, SECONDS_TO_KEEP, OPTODE_PLACEMENT, HEART_RATE, WAVELET, IQR, WAVELET_TYPE, WAVELET_LEVEL, ENHANCE_NEGATIVE_CORRELATION, SHORT_CHANNEL_THRESH, LONG_CHANNEL_THRESH, and DRIFT_MODEL
- Changed number of rectangles in the progress bar to 25 to account for the new options


# Version 1.1.6

- Fixed Process button from appearing when no files are selected
- Fixed a bug that would cause an instant child process crash on Windows
- Added L_FREQ and H_FREQ parameters for more user control over low and high pass filtering


# Version 1.1.5

- Fixed Windows saves not being able to be opened by a Mac (hopefully the other way too!)
- Added the option to right click loaded snirf files to reveal them in a file browser or delete them if they are no longer desired
- Changed the way folders are opened to store the files separately rather than the folder as a whole to allow for the removal of files
- Fixed issues with dropdowns and bubbles not populating correctly when opening a single file and temporarily removed the option to open multiple folders
- Improved crash handling and the message that is displayed to the user if the application crashes
- Progress bar will now colour the stage that fails as red if a file fails during processing
- A warning message will be displayed when a file fails to process with information on what went wrong. This message does not halt the rest of the processing of the other files
- Fixed the number of rectangles in the progress bar to 20 (was incorrect in v1.1.1)
- Added validation to ensure loaded files do not have 2-dimensional data when clicking process to prevent inaccurate results from being generated
- Added more metadata information to the top left information panel
- Changed the Status Bar message when processing is complete to state how many were successful and how many were not
- Added a clickable link below the selected file's metadata explaining the independent parameters and why they are useful
- Updated some tooltips to provide better, more accurate information
- Added details about the processing steps and their order into the user guide
- Changed the default bandpass filtering parameters


# Version 1.1.4

- Fixed some display text to now display the correct information
- A new option under Analysis has been added to export the data from a specified participant as a csv file. Fixes [Issue 19](https://git.research.dezeeuw.ca/tyler/flares/issues/19), [Issue 27](https://git.research.dezeeuw.ca/tyler/flares/issues/27)
- Added 2 new parameters - TIME_WINDOW_START and TIME_WINDOW_END. Fixes [Issue 29](https://git.research.dezeeuw.ca/tyler/flares/issues/29)
- These parameters affect the visualization of the significance and contrast images but do not change the total time modeled underneath
- Fixed the duration of annotations edited from a BORIS file from 0 seconds to their proper duration
- Added the annotation information to each participant under their "File information" window
- Fixed Macs not being able to save snirfs attempting to be updated from BORIS files, and in general the updated files not respecting the path chosen by the user


# Version 1.1.3

- Added back the ability to use the fOLD dataset. Fixes [Issue 23](https://git.research.dezeeuw.ca/tyler/flares/issues/23)
- 5th option has been added under Analysis to get to fOLD channels per participant
- Added an option to cancel the running process. Fixes [Issue 15](https://git.research.dezeeuw.ca/tyler/flares/issues/15)
- Prevented graph images from showing when participants are being processed. Fixes [Issue 24](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
- Allow the option to remove all events of a type from all loaded snirfs. Fixes [Issue 25](https://git.research.dezeeuw.ca/tyler/flares/issues/25)
- Added new icons in the menu bar
- Added a terminal to interact with the app in a more command-like form
- Currently the terminal has no functionality but some features for batch operations will be coming soon!
- Inter-Group viewer now has the option to visualize the average response on the brain of all participants in the group. Fixes [Issue 26](https://git.research.dezeeuw.ca/tyler/flares/issues/24)
- Fixed the description under "Update events in snirf file..."


# Version 1.1.2

- Fixed incorrect colormaps being applied
- Added functionality to utilize external event markers from a file. Fixes [Issue 6](https://git.research.dezeeuw.ca/tyler/flares/issues/6)


# Version 1.1.1

- Fixed the number of rectangles in the progress bar to 19
- Fixed a crash when attempting to load a brain image on Windows
- Removed hardcoded event annotations. Fixes [Issue 16](https://git.research.dezeeuw.ca/tyler/flares/issues/16)


# Version 1.1.0

- Revamped the Analysis window
- 4 Options of Participant, Participant Brain, Inter-Group, and Cross Group Brain are available.
- Customization is present to query different participants, images, events, brains, etc.
- Removed preprocessing options and reorganized their order to correlate with the actual order.
- Most preprocessing options removed will be coming back soon
- Added a group option when clicking on a participant's file
- If no group is specified, the participant will be added to the "Default" group
- Added option to update the optode positions in a snirf file from the Options menu (F6)
- Fixed [Issue 3](https://git.research.dezeeuw.ca/tyler/flares/issues/3), [Issue 5](https://git.research.dezeeuw.ca/tyler/flares/issues/5), [Issue 17](https://git.research.dezeeuw.ca/tyler/flares/issues/17), [Issue 21](https://git.research.dezeeuw.ca/tyler/flares/issues/21), [Issue 22](https://git.research.dezeeuw.ca/tyler/flares/issues/22)


# Version 1.0.1

- Two new options have been added when clicking on a participant's file.
- First new option is Age which allows the option to specify age on a per-file basis to calculate DPF by using the Scholkmann & Wolf calculation instead of having one DPF for all files. Fixes [Issue 1](https://git.research.dezeeuw.ca/tyler/flares/issues/1). This also allows for proper calculation of DPF for the two separate wavelengths.
- If no age is set by the user, the code will fall back to the age of 25
- Second new option is Gender to be used in future analysis options (currently not implemented).
- UI elements have been shuffled to make room for the new parameters.
- Removed the process button from being available until a file or project is opened. Fixes [Issue 2](https://git.research.dezeeuw.ca/tyler/flares/issues/2).
- Removed the option for PPF under Haemoglobin Concentration as it is no longer used.
- Added a new category in the options called Other
- Added MAX_WORKERS to the Other category. This is how many files should be processed at once. Fixes [Issue 13](https://git.research.dezeeuw.ca/tyler/flares/issues/13).
- Added more information about the snirf file to be displayed when selected


# Version 1.0.0

- Initial release.