[routines] Unit scaling argument

Specifying a sampling period via the sampling_period argument duplicated
multiplying the horizontal axes by a scaling factor.

This is because recent changes to postprocessor (see last paragraph of
commit) makes the columns of DataFrames show absolute time units (e.g. [0, 5,
10, 15...] if the images were taken every 5 minutes).  Previously,
columns showed time points (e.g. [0, 1, 2, 3...]).  All routines relied
on column labels to define the horizontal axis.  This issue would
have been addressed more timely if the commit in question had a more
informative description; 'add tiniterval property' tells me nothing and
does not inform me that it affects the column labels.

These recent changes mean that the sampling_period argument is no longer
necessary.  However, instead of deleting this argument, I've decided to
repurpose it for unit scaling, e.g. from minutes to hours.
Operationally, nothing has changed, but the meaning of the argument has
changed, and I've updated the docstrings accordingly.

This commit may affect horizontal axes of plots affected; users should
inspect the axes carefully, especially if the source data relies on
postprocessor.grouper.

This bug was likely caused by 17e13b59
on 2022-06-16 14:21.  It is unclear from the commit message, but I
suspect that this commit attempted to incorporate the image sampling
interval into defining the DataFrame columns produced by postprocessor.
This commit addresses issue #20.

routines/mean_plot.py

@@ -13,7 +13,7 @@ class _MeanPlotter(BasePlotter):
         self,
         trace_df,
         trace_name,
-        sampling_period,
+        unit_scaling,
         label,
         mean_color,
         error_color,
@@ -22,7 +22,7 @@ class _MeanPlotter(BasePlotter):
         ylabel,
         plot_title,
     ):
-        super().__init__(trace_name, sampling_period, xlabel, plot_title)
+        super().__init__(trace_name, unit_scaling, xlabel, plot_title)
         # Define attributes from arguments
         self.trace_df = trace_df
         self.label = label
@@ -35,7 +35,7 @@ class _MeanPlotter(BasePlotter):
         self.ylabel = ylabel
 
         # Mean and standard error
-        self.trace_time = np.array(self.trace_df.columns) * self.sampling_period
+        self.trace_time = np.array(self.trace_df.columns) * self.unit_scaling
         self.mean_ts = self.trace_df.mean(axis=0)
         self.stderr = self.trace_df.std(axis=0) / np.sqrt(len(self.trace_df))
 
@@ -64,7 +64,7 @@ class _MeanPlotter(BasePlotter):
 def mean_plot(
     trace_df,
     trace_name="flavin",
-    sampling_period=5,
+    unit_scaling=1,
     label="wild type",
     mean_color="b",
     error_color="lightblue",
@@ -82,8 +82,8 @@ def mean_plot(
         Time series of traces (rows = cells, columns = time points).
     trace_name : string
         Name of trace being plotted, e.g. 'flavin'.
-    sampling_period : int or float
-        Sampling period, in unit time.
+    unit_scaling : int or float
+        Unit scaling factor, e.g. 1/60 to convert minutes to hours.
     label : string
         Name of group being plotted, e.g. a strain name.
     mean_color : string
@@ -109,7 +109,7 @@ def mean_plot(
     plotter = _MeanPlotter(
         trace_df,
         trace_name,
-        sampling_period,
+        unit_scaling,
         label,
         mean_color,
         error_color,

routines/median_plot.py

@@ -13,7 +13,7 @@ class _MedianPlotter(BasePlotter):
         self,
         trace_df,
         trace_name,
-        sampling_period,
+        unit_scaling,
         label,
         median_color,
         error_color,
@@ -22,7 +22,7 @@ class _MedianPlotter(BasePlotter):
         ylabel,
         plot_title,
     ):
-        super().__init__(trace_name, sampling_period, xlabel, plot_title)
+        super().__init__(trace_name, unit_scaling, xlabel, plot_title)
         # Define attributes from arguments
         self.trace_df = trace_df
         self.label = label
@@ -35,7 +35,7 @@ class _MedianPlotter(BasePlotter):
         self.ylabel = ylabel
 
         # Median and interquartile range
-        self.trace_time = np.array(self.trace_df.columns) * self.sampling_period
+        self.trace_time = np.array(self.trace_df.columns) * self.unit_scaling
         self.median_ts = self.trace_df.median(axis=0)
         self.quartile1_ts = self.trace_df.quantile(0.25)
         self.quartile3_ts = self.trace_df.quantile(0.75)
@@ -65,7 +65,7 @@ class _MedianPlotter(BasePlotter):
 def median_plot(
     trace_df,
     trace_name="flavin",
-    sampling_period=5,
+    unit_scaling=1,
     label="wild type",
     median_color="b",
     error_color="lightblue",
@@ -83,8 +83,8 @@ def median_plot(
         Time series of traces (rows = cells, columns = time points).
     trace_name : string
         Name of trace being plotted, e.g. 'flavin'.
-    sampling_period : int or float
-        Sampling period, in unit time.
+    unit_scaling : int or float
+        Unit scaling factor, e.g. 1/60 to convert minutes to hours.
     label : string
         Name of group being plotted, e.g. a strain name.
     median_color : string
@@ -110,7 +110,7 @@ def median_plot(
     plotter = _MedianPlotter(
         trace_df,
         trace_name,
-        sampling_period,
+        unit_scaling,
         label,
         median_color,
         error_color,

routines/plottingabc.py

@@ -6,10 +6,10 @@ from abc import ABC
 class BasePlotter(ABC):
     """Base class for plotting handler classes"""
 
-    def __init__(self, trace_name, sampling_period, xlabel, plot_title):
+    def __init__(self, trace_name, unit_scaling, xlabel, plot_title):
         """Common attributes"""
         self.trace_name = trace_name
-        self.sampling_period = sampling_period
+        self.unit_scaling = unit_scaling
 
         self.xlabel = xlabel
         self.ylabel = None

routines/single_birth_plot.py

@@ -14,7 +14,7 @@ class _SingleBirthPlotter(_SinglePlotter):
         trace_values,
         trace_name,
         birth_mask,
-        sampling_period,
+        unit_scaling,
         trace_color,
         birth_color,
         trace_linestyle,
@@ -27,7 +27,7 @@ class _SingleBirthPlotter(_SinglePlotter):
             trace_timepoints,
             trace_values,
             trace_name,
-            sampling_period,
+            unit_scaling,
             trace_color,
             trace_linestyle,
             xlabel,
@@ -40,7 +40,7 @@ class _SingleBirthPlotter(_SinglePlotter):
 
     def plot(self, ax):
         """Draw the line plots on the provided Axes."""
-        trace_time = self.trace_timepoints * self.sampling_period
+        trace_time = self.trace_timepoints * self.unit_scaling
         super().plot(ax)
         birth_mask_bool = self.birth_mask.astype(bool)
         for occurence, birth_time in enumerate(trace_time[birth_mask_bool]):
@@ -62,7 +62,7 @@ def single_birth_plot(
     trace_values,
     trace_name="flavin",
     birth_mask=None,
-    sampling_period=5,
+    unit_scaling=1,
     trace_color="b",
     birth_color="k",
     trace_linestyle="-",
@@ -84,8 +84,8 @@ def single_birth_plot(
     birth_mask : array_like
         Mask to indicate where births are. Expect values of '0' and '1' or
         'False' and 'True' in the elements.
-    sampling_period : int or float
-        Sampling period, in unit time.
+    unit_scaling : int or float
+        Unit scaling factor, e.g. 1/60 to convert minutes to hours.
     trace_color : string
         matplotlib colour string for the trace
     birth_color : string
@@ -116,7 +116,7 @@ def single_birth_plot(
         trace_values,
         trace_name,
         birth_mask,
-        sampling_period,
+        unit_scaling,
         trace_color,
         birth_color,
         trace_linestyle,

routines/single_plot.py

@@ -13,13 +13,13 @@ class _SinglePlotter(BasePlotter):
         trace_timepoints,
         trace_values,
         trace_name,
-        sampling_period,
+        unit_scaling,
         trace_color,
         trace_linestyle,
         xlabel,
         plot_title,
     ):
-        super().__init__(trace_name, sampling_period, xlabel, plot_title)
+        super().__init__(trace_name, unit_scaling, xlabel, plot_title)
         # Define attributes from arguments
         self.trace_timepoints = trace_timepoints
         self.trace_values = trace_values
@@ -33,7 +33,7 @@ class _SinglePlotter(BasePlotter):
         """Draw the line plot on the provided Axes."""
         super().plot(ax)
         ax.plot(
-            self.trace_timepoints * self.sampling_period,
+            self.trace_timepoints * self.unit_scaling,
             self.trace_values,
             color=self.trace_color,
             linestyle=self.trace_linestyle,
@@ -45,7 +45,7 @@ def single_plot(
     trace_timepoints,
     trace_values,
     trace_name="flavin",
-    sampling_period=5,
+    unit_scaling=1,
     trace_color="b",
     trace_linestyle="-",
     xlabel="Time (min)",
@@ -62,8 +62,8 @@ def single_plot(
         Trace to plot.
     trace_name : string
         Name of trace being plotted, e.g. 'flavin'.
-    sampling_period : int or float
-        Sampling period, in unit time.
+    unit_scaling : int or float
+        Unit scaling factor, e.g. 1/60 to convert minutes to hours.
     trace_color : string
         matplotlib colour string, specifies colour of line plot.
     trace_linestyle : string
@@ -89,7 +89,7 @@ def single_plot(
         trace_timepoints,
         trace_values,
         trace_name,
-        sampling_period,
+        unit_scaling,
         trace_color,
         trace_linestyle,
         xlabel,