further variable changes

flares.py

@@ -90,7 +90,7 @@ from mne_nirs.io.fold import fold_channel_specificity  # type: ignore
 from mne_nirs.preprocessing import peak_power  # type: ignore
 from mne_nirs.statistics._glm_level_first import RegressionResults  # type: ignore
 
-# Needs to be set for men
+# Needs to be set for mne
 os.environ["SUBJECTS_DIR"] = str(data_path()) + "/subjects" # type: ignore
 
 # TODO: Tidy this up
@@ -167,6 +167,8 @@ H_FREQ: float
 L_TRANS_BANDWIDTH: float
 H_TRANS_BANDWIDTH: float
 
+RESAMPLE: bool
+RESAMPLE_FREQ: int
 STIM_DUR: float
 HRF_MODEL: str
 DRIFT_MODEL: str
@@ -184,8 +186,8 @@ N_JOBS: int
 
 TIME_WINDOW_START: int
 TIME_WINDOW_END: int
-
-VERBOSITY = True
+MAX_WORKERS: int
+VERBOSITY: bool
 
 AGE = 25    # Assume 25 if not set from the GUI. This will result in a reasonable PPF
 GENDER = ""
@@ -1252,7 +1254,7 @@ def epochs_calculations(raw_haemo, events, event_dict):
                 continue
 
             data = evoked.data[picks_idx, :].mean(axis=0)
-            t_start, t_end = 0, 15
+            t_start, t_end = 0, 15 #TODO: Is this in seconds? or is it 1hz input that makes it 15s?
             times_mask = (evoked.times >= t_start) & (evoked.times <= t_end)
             data_segment = data[times_mask]
             times_segment = evoked.times[times_mask]
@@ -1314,11 +1316,16 @@ def make_design_matrix(raw_haemo, short_chans):
     # Set the new annotations
     raw_haemo.set_annotations(new_annot)
 
-    raw_haemo.resample(1, npad="auto")
-    raw_haemo._data = raw_haemo._data * 1e6
+    if RESAMPLE:
+        raw_haemo.resample(RESAMPLE_FREQ, npad="auto")
+        raw_haemo._data = raw_haemo._data * 1e6
+        try:
+            short_chans.resample(RESAMPLE_FREQ)
+        except:
+            pass
+
     # 2) Create design matrix
-    if SHORT_CHANNEL:
-        short_chans.resample(1)
+    if SHORT_CHANNEL_REGRESSION:
         design_matrix = make_first_level_design_matrix(
             raw=raw_haemo,
             stim_dur=STIM_DUR,