Minor fixes

lineage/LineageInputOutput.py

@@ -1,5 +1,6 @@
 """ The file contains the methods used to input lineage data from the Heiser lab. """
 
+import logging
 import math
 import pandas as pd
 from .CellVar import CellVar as c
@@ -250,7 +251,7 @@ def tryRecursion(
 
     # Check that the parent cell didn't get time censored (Likely divided in last frame)
     if divisionTime == exp_time:
-        print(
+        logging.info(
             f"Cell time censorship, but daughters were found in row {parentPos+1}, column {pColumn+1}. By default they will be set to None"
         )
 
@@ -263,7 +264,7 @@ def tryRecursion(
 
     # Creating daughter
     daughterCell = c(parent=parentCell)
-    daughterCell.obs = [0, 0, 0, 0, 0, 0]
+    daughterCell.obs = np.array([0.0, 0, 0, 0, 0, 0])
 
     # find upper daughter
     daughterCell.left = tryRecursion(

lineage/figures/common.py

@@ -1023,14 +1023,7 @@ def plot_all(ax, num_states, tHMMobj_list, Dname, cons, concsValues):
         (4, num_states, 2)
     )  # the avg lifetime: num_conc x num_states x num_phases
     bern_lpt = np.zeros((4, num_states, 2))  # bernoulli
-    # print parameters and estimated values
-    print(
-        Dname,
-        "\n the \u03C0: ",
-        tHMMobj_list[0].estimate.pi,
-        "\n the transition matrix: ",
-        tHMMobj_list[0].estimate.T,
-    )
+
     for idx, tHMMobj in enumerate(tHMMobj_list):  # for each concentration data
         for i in range(num_states):
             lpt_avg[idx, i, 0] = np.log10(

lineage/figures/figureS17.py

@@ -19,7 +19,7 @@ def makeFigure():
     """
     Makes figure 101.
     """
-    num_lins = [len(hgf_tHMMobj_list[i].X) for i in range(4)]
+    num_lins = [len(tM.X) for tM in hgf_tHMMobj_list]
     ax, f = getSetup((10, 20), (np.max(num_lins), 4))
 
     for i in range(4 * np.max(num_lins)):