changed the changelog

changelog.md

@@ -1,3 +1,34 @@
+# 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

flares.py

@@ -50,12 +50,12 @@ from scipy.spatial.distance import cdist
 
 # Backen visualization needed to be defined for pyinstaller
 import pyvistaqt # type: ignore
-import vtkmodules.util.data_model
+# import vtkmodules.util.data_model
-import vtkmodules.util.execution_model
+# import vtkmodules.util.execution_model
 
 # External library imports for mne
 from mne import (
-    EvokedArray, SourceEstimate, Info, Epochs, Label,
+    EvokedArray, SourceEstimate, Info, Epochs, Label, Annotations,
     events_from_annotations, read_source_spaces,
     stc_near_sensors, pick_types, grand_average, get_config, set_config, read_labels_from_annot
 )  # type: ignore
@@ -132,6 +132,11 @@ ENHANCE_NEGATIVE_CORRELATION: bool
 
 SHORT_CHANNEL: bool
 
+REMOVE_EVENTS: list
+
+TIME_WINDOW_START: int
+TIME_WINDOW_END: int
+
 VERBOSITY = True
 
 # FIXME: Shouldn't need each ordering - just order it before checking
@@ -179,6 +184,9 @@ REQUIRED_KEYS: dict[str, Any] = {
     "PSP_THRESHOLD": float,
     
     "SHORT_CHANNEL": bool,
+    "REMOVE_EVENTS": list,
+    "TIME_WINDOW_START": int,
+    "TIME_WINDOW_END": int
     # "REJECT_PAIRS": bool,
     # "FORCE_DROP_ANNOTATIONS": list,
     # "FILTER_LOW_PASS": float,
@@ -1074,7 +1082,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
 
     # Plot drop log
     # TODO: Why show this if we never use epochs2?
-    fig_epochs_dropped = epochs2.plot_drop_log()
+    fig_epochs_dropped = epochs2.plot_drop_log(show=False)
     fig_epochs.append(("fig_epochs_dropped", fig_epochs_dropped))
 
     # Plot for each condition
@@ -1108,7 +1116,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
     evokeds3 = []
     colors = []
     conditions = list(epochs.event_id.keys())
-    cmap = plt.cm.get_cmap("tab10", len(conditions))
+    cmap = plt.get_cmap("tab10", len(conditions))
 
     for idx, cond in enumerate(conditions):
         evoked = epochs[cond].average(picks="hbo")
@@ -1470,9 +1478,15 @@ def resource_path(relative_path):
 
 def fold_channels(raw: BaseRaw) -> None:
 
+    # if getattr(sys, 'frozen', False):
+    path = os.path.expanduser("~") + "/mne_data/fOLD/fOLD-public-master/Supplementary"
+    logger.info(path)
+    set_config('MNE_NIRS_FOLD_PATH', resource_path(path)) # type: ignore
 
-    # Locate the fOLD excel files
+    # # Locate the fOLD excel files
-    set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
+    # else:
+    #     logger.info("yabba")
+    #     set_config('MNE_NIRS_FOLD_PATH', resource_path("../../mne_data/fOLD/fOLD-public-master/Supplementary")) # type: ignore
 
     output = None
 
@@ -1534,8 +1548,8 @@ def fold_channels(raw: BaseRaw) -> None:
             "Brain_Outside",
         ]
 
-        cmap1 = plt.cm.get_cmap('tab20')  # First 20 colors
+        cmap1 = plt.get_cmap('tab20')  # First 20 colors
-        cmap2 = plt.cm.get_cmap('tab20b')  # Next 20 colors
+        cmap2 = plt.get_cmap('tab20b')  # Next 20 colors
 
         # Combine the colors from both colormaps
         colors = [cmap1(i) for i in range(20)] + [cmap2(i) for i in range(20)]  # Total 40 colors
@@ -1611,6 +1625,7 @@ def fold_channels(raw: BaseRaw) -> None:
     for ax in axes[len(hbo_channel_names):]:
         ax.axis('off')
     
+    plt.show()
     return fig, legend_fig
 
                 
@@ -2935,6 +2950,19 @@ def process_participant(file_path, progress_callback=None):
     logger.info("14")
 
     # Step 14: Design Matrix
+    events_to_remove = REMOVE_EVENTS
+        
+    filtered_annotations = [ann for ann in raw.annotations if ann['description'] not in events_to_remove]
+    
+    new_annot = Annotations(
+        onset=[ann['onset'] for ann in filtered_annotations],
+        duration=[ann['duration'] for ann in filtered_annotations],
+        description=[ann['description'] for ann in filtered_annotations]
+    )
+    
+    # Set the new annotations
+    raw_haemo.set_annotations(new_annot)
+
     design_matrix, fig_design_matrix = make_design_matrix(raw_haemo, short_chans)
     fig_individual["Design Matrix"] = fig_design_matrix
     if progress_callback: progress_callback(15)
@@ -3008,7 +3036,11 @@ def process_participant(file_path, progress_callback=None):
     contrast_dict = {}
 
     for condition in all_conditions:
-        delay_cols = [col for col in all_delay_cols if col.startswith(f"{condition}_delay_")]
+        delay_cols = [
+            col for col in all_delay_cols
+            if col.startswith(f"{condition}_delay_") and
+            TIME_WINDOW_START <= int(col.split("_delay_")[-1]) <= TIME_WINDOW_END
+        ]
 
         if not delay_cols:
             continue  # skip if no columns found (shouldn't happen?)

icons/terminal_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M160-160q-33 0-56.5-23.5T80-240v-480q0-33 23.5-56.5T160-800h640q33 0 56.5 23.5T880-720v480q0 33-23.5 56.5T800-160H160Zm0-80h640v-400H160v400Zm140-40-56-56 103-104-104-104 57-56 160 160-160 160Zm180 0v-80h240v80H480Z"/></svg>

icons/upgrade_24dp_1F1F1F.svg

@@ -0,0 +1 @@
+<svg xmlns="http://www.w3.org/2000/svg" height="24px" viewBox="0 -960 960 960" width="24px" fill="#1f1f1f"><path d="M280-160v-80h400v80H280Zm160-160v-327L336-544l-56-56 200-200 200 200-56 56-104-103v327h-80Z"/></svg>