diff --git a/dataloader.py b/dataloader.py index 305880a9545f396303614dbc35c070488beae596..574264735f4386daac98dd30cfe12d784184bc3e 100644 --- a/dataloader.py +++ b/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", diff --git a/plotting.py b/plotting.py index 3ce04827a66788c0937553461ddf13949ebe0157..5ca2ba6699e21d81b914bc7ae77574a3d4011686 100644 --- a/plotting.py +++ b/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)