Merge pull request #448 from courtois-neuromod/fix/huge_memleaks_perfs_issues

Improve performance by using numpy for trigger detection and closing matplotlib figures to avoid memleaks.

Author: smoia

phys2bids/physio_obj.py

@@ -524,9 +524,7 @@ def check_trigger_amount(self, thr=None, num_timepoints_expected=0, tr=0):
             thr = np.mean(trigger)
             flag = 1
         timepoints = trigger > thr
-        num_timepoints_found = len(
-            [is_true for is_true, _ in groupby(timepoints, lambda x: x != 0) if is_true]
-        )
+        num_timepoints_found = np.count_nonzero(np.ediff1d(timepoints.astype(np.int8)) > 0)
         if flag == 1:
             LGR.info(
                 f"The number of timepoints according to the std_thr method "

phys2bids/tests/test_viz.py

@@ -20,6 +20,7 @@ def test_plot_all(samefreq_full_acq_file):
     assert os.path.isfile(
         os.path.join(test_path, os.path.splitext(os.path.basename(test_filename))[0] + ".png")
     )
+    assert len(viz.plt.get_fignums()) == 0, "plots are not closed, this can cause memory leaks"
 
 
 # Expected to fail due to trigger plot issue
@@ -33,3 +34,4 @@ def test_plot_trigger(samefreq_full_acq_file):
         phys_obj.timeseries[0], phys_obj.timeseries[chtrig], out, 1.5, 1.6, 60, test_filename
     )
     assert os.path.isfile(out + "_trigger_time.png")
+    assert len(viz.plt.get_fignums()) == 0, "plots are not closed, this can cause memory leaks"

phys2bids/viz.py

@@ -267,3 +267,4 @@ def plot_all(ch_name, timeseries, units, freq, infile, outfile, dpi=SET_DPI, siz
     outfile = os.path.join(outfile, os.path.splitext(os.path.basename(infile))[0] + ".png")
     LGR.info(f"saving channel plot to {outfile}")
     fig.savefig(outfile, dpi=dpi, bbox_inches="tight")
+    plt.close()