'plotter.py' updaten

Complete description

README.md

@@ -0,0 +1,27 @@
+In this folder you can find 4 scripts that can be used to transfrom 24/7 .csv accelerometer data to intensity plots. The methods are based on the Rowland et al. 2018 article 'Beyond Cut Points: Accelerometer Metrics that Capture the Physical Activity Profile. 
+
+The scripts should be run in the following order:
+
+1. DailyCutter.py   -   This script is used to transform single week .csv files (input) into individual day-files (output)
+                        The WeekPath should be set to the folder containing the week-files of the patient 
+                        The ScriptPath should be set to the folder containing the 'formules.py' script. This script holds
+                        all functions used in the analysis.
+
+2. plotter.py       -   This is the second script used in the analysis and is the script that performs the most. 
+                        Before getting started, the os.chdir() should be set to the 'formules.py' pathway
+                        The rootdir should be set to the folder containing 7 individual .csv day-files
+                        The PtName variable should be set accordingly to the name of the files used. This possibly changes 
+                        between different weeks/different patients.
+                        Finally, the CheckWeel.to_csv() should be filled with the used weeknumber, to save the 
+                        parameters of the trendline for each different week.
+                        After changing these variables to your liking, the script should run automatically, using the 
+                        folder with individual days as input and saving the plots for individual days as well as an 
+                        overview of the entire week as output.
+
+3. Totalplotter.py  -   After running the plotter.py script you should have ended up with 6 .csv files with parameters 
+                        of the trendlines. Make sure that these files are saved within the same folder and set the path
+                        of this folder as the rootdir in this script.
+                        Change the names in the plt.title() and plt.savefig() commands accordingly and run the scripts
+                        The output will be a plot of all 6 weeks in one figure.
+
+

formules.py

@@ -4,7 +4,7 @@ Created on Wed Jun 16 09:34:35 2021
 
 @author: -
 """
-import osa
+import os
 import pandas as pd
 import numpy as np
 import matplotlib.pyplot as plt
@@ -115,7 +115,7 @@ def SlopeWeeker(Keylist, Dict):
             PtName = PtName.replace('resampled-','') 
             PtName = PtName.replace('.csv','')
             
-            plt.figure()
+            plt.figure(dpi=720)
             plt.ylim(0,1440)
             plt.xlim(0,(ENMOmax+10))
             plt.title('Intensity plot ' + PtName)
@@ -124,10 +124,11 @@ def SlopeWeeker(Keylist, Dict):
             plt.grid()
             plt.scatter(Xscale, y=Counter)
             plt.plot(Xscale, Trendline, 'r--')
-            plt.show()
             
             PtName = (PtName + '.png')
             plt.savefig(fname=PtName)
+
+            plt.show()
             
     except:
         print(PtName + ' could not be used')

plotter.py

@@ -54,7 +54,7 @@ for i in Length:
    
     Xscale = np.arange(0,CheckWeek['ENMOmax'].max(), 5)
    
-    plt.figure()
+    plt.figure(dpi=720)
     plt.ylim(0,1440)
     plt.xlim(0,CheckWeek['ENMOmax'].max())
     plt.title('All weekdays and average plotted ' + PtName)
@@ -69,6 +69,7 @@ for i in Length:
         else:
             plt.plot(Xscale, Y, 'k--')
             
-    plt.show()
     plt.savefig(fname=('Weekplot ' + PtName+ '.png'))
+    plt.show()
+