Adding functionality for split timing

Author: djsmith17

basic_phenotyper_lib.py

@@ -633,16 +633,14 @@ def perform_spatialUMAP(spatial_umap, bc, umap_subset_per_fit, umap_subset_toggl
     spatial_umap.set_train_test(n_fit=n_fit, n_tra = n_tra, groupby_label = 'TMA_core_id', seed=54321, umap_subset_toggle = umap_subset_toggle)
 
     # fit umap on training cells
-    bc.startTimer()
     print('Fitting Model')
     spatial_umap.umap_fit = umap.UMAP().fit(spatial_umap.density[spatial_umap.cells['umap_train'].values].reshape((spatial_umap.cells['umap_train'].sum(), -1)))
-    bc.printElapsedTime(f'      Fitting {np.sum(spatial_umap.cells["umap_train"] == 1)} points to a model')
+    bc.printElapsedTime(f'      Fitting {np.sum(spatial_umap.cells["umap_train"] == 1)} points to a model', split = True)
 
     # Transform test cells based on fitted model
-    bc.startTimer()
     print('Transforming Data')
     spatial_umap.umap_test = spatial_umap.umap_fit.transform(spatial_umap.density[spatial_umap.cells['umap_test'].values].reshape((spatial_umap.cells['umap_test'].sum(), -1)))
-    bc.printElapsedTime(f'      Transforming {np.sum(spatial_umap.cells["umap_test"] == 1)} points with the model')
+    bc.printElapsedTime(f'      Transforming {np.sum(spatial_umap.cells["umap_test"] == 1)} points with the model', split = True)
 
     spatial_umap.umap_completed = True
 

benchmark_collector.py

@@ -3,12 +3,11 @@
 Specifically to mark the time it takes for functions to run
 and save their values in a spreadsheet (if wanted)
 '''
-
+from datetime import datetime
 import os
 import time
 import numpy as np
 import pandas as pd
-from datetime import datetime
 
 class benchmark_collector:
     '''
@@ -56,36 +55,42 @@ def __init__(self, fiol = None):
         self.benchmarkDF.loc[0, 'id']       = datetime.now()
         self.benchmarkDF.loc[0, 'on_NIDAP'] = self.on_nidap
         self.stTimer = None
+        self.stTimer_split = None
         self.spTimer = None
 
     def startTimer(self):
         '''
         Set the Start time to the current date-time
         '''
         self.stTimer = time.time()
+        self.stTimer_split = self.stTimer
 
     def stopTimer(self):
         '''
         Set the Stop time to the current date-time
         '''
         self.spTimer = time.time()
 
-    def elapsedTime(self):
+    def elapsedTime(self, split = False):
         '''
         Calculate the elapsed time from the spTimer and the stTimer
         '''
-        if self.stTimer is not None:
+        if self.stTimer is not None and split is False:
+            self.stopTimer()
+            elapsed_time = np.round((self.spTimer - self.stTimer)/60, 2)
+        elif self.stTimer is not None and split is True:
             self.stopTimer()
-            elapsed_time =  np.round(self.spTimer - self.stTimer, 3)
+            elapsed_time = np.round((self.spTimer - self.stTimer_split)/60, 2)
+            self.stTimer_split = self.spTimer
         else:
             elapsed_time = None
         return elapsed_time
 
-    def printElapsedTime(self, msg):
+    def printElapsedTime(self, msg, split = False):
         '''
-        Print the current value of elapsed time 
+        Print the current value of elapsed time
         '''
-        print(f'{msg} took {self.elapsedTime()} s')
+        print(f'{msg} took {self.elapsedTime(split)} min')
 
     def check_df(self):
         '''