Merge branch 'master' of https://git.ecdf.ed.ac.uk/swain-lab/wela

dataloader.py

@@ -79,12 +79,10 @@ class dataloader:
             "extraction/cy5/max/median": "cy5",
             "extraction/GFP/max/median": "median_GFP",
             "extraction/GFP/max/mean": "mean_GFP",
-            "extraction/GFP/max/max5px": "max5px_GFP",
-            "extraction/GFP/max/max5px_med": "max5px_med_GFP",
+            "extraction/GFP/max/max5px_median": "max5px_median_GFP",
             "extraction/mCherry/max/median": "median_mCherry",
             "extraction/mCherry/max/mean": "mean_mCherry",
-            "extraction/mCherry/max/max5px": "max5px_mCherry",
-            "extraction/mCherry/max/max5px_med": "max5px_med_mCherry",
+            "extraction/mCherry/max/max5px_median": "max5px_median_mCherry",
             "extraction/general/None/area": "area",
             "extraction/general/None/volume": "volume",
             "extraction/Flavin_bgsub/max/mean": "flavin",

plotting.py

@@ -233,9 +233,9 @@ def plot_lineage(
             plt.grid()
             splt += 1
         else:
-            s = df[df.id == idx][signal].to_numpy()
+            m_sig = df[df.id == idx][signal].to_numpy()
             plt.subplot(nosubplots, 1, splt)
-            plt.plot(t, s)
+            plt.plot(t, m_sig)
             plt.ylabel(signal)
             add_shading(shade_times, shade_colour)
             plt.grid()
@@ -247,7 +247,7 @@ def plot_lineage(
             and signal not in ["volume", "growth_rate"]
         ):
             for bpt in b_pts:
-                plt.plot(t[bpt], bud_sig[bpt], "k.")
+                plt.plot(t[bpt], m_sig[bpt], "k.")
     plt.xlabel("time (hours)")
     # share the x axis
     ax_list = fig.axes
@@ -259,7 +259,7 @@ def plot_lineage(
 def add_shading(shade_times, shade_colour):
     """Shade vertically between each pair of shade_times."""
     if shade_times is not None:
-        for (tstart, tend) in shade_times:
+        for tstart, tend in shade_times:
             plt.axvspan(tstart, tend, facecolor=shade_colour, alpha=0.1)