replace urlretrieve with requests

Author: tompollard

wfdb/_rdann.py

@@ -34,22 +34,22 @@ def rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1):
     if sampto and sampto<=sampfrom:
         raise ValueError("sampto must be greater than sampfrom")
 
-    #fields=readheader(recordname) # Get the info from the header file
+    # Get the info from the header file
+    #fields=readheader(recordname) 
     dirname, baserecordname=os.path.split(recordname)
-
-    f=open(recordname+'.'+annot, 'rb')
-    filebytes=np.fromfile(f, '<u1').reshape([-1, 2]) # Read the file's byte pairs.
-    f.close()
+    
+    # Read the file's byte pairs.
+    with open(recordname+'.'+annot, 'rb') as f:
+        filebytes=np.fromfile(f, '<u1').reshape([-1, 2])
 
     # Allocate for the maximum possible number of annotations contained in the file. 
-    annsamp=np.zeros(filebytes.shape[0])
-    anntype=np.zeros(filebytes.shape[0])
-    subtype=np.zeros(filebytes.shape[0])
-    chan=np.zeros(filebytes.shape[0])
-    num=np.zeros(filebytes.shape[0])
+    annsamp=np.empty(filebytes.shape[0])
+    anntype=np.empty(filebytes.shape[0])
+    subtype=np.empty(filebytes.shape[0])
+    chan=np.empty(filebytes.shape[0])
+    num=np.empty(filebytes.shape[0])
     aux=['']*filebytes.shape[0] 
-    
-    annfs=[] # Stores the fs written in the annotation file if it exists. 
+    annfs=[] # Stores the frequencies written in the annotation file if it exists. 
     ai=0 # Annotation index, the number of annotations processed. Not to be comfused with the 'num' field of an annotation.
     bpi=0 # Byte pair index, for searching through bytes of the annotation file. 
 
@@ -165,7 +165,6 @@ def rdann(recordname, annot, sampfrom=0, sampto=[], anndisp=1):
         elif anndisp==2:
             anntype=[anncodes[code] for code in anntype]
 
-        
     return (annsamp, anntype, subtype, chan, num, aux, annfs)
 
 

wfdb/_rdsamp.py

@@ -4,8 +4,8 @@
 import math
 import sys
 import configparser 
-from urllib import urlretrieve
 import configparser
+import requests
 
 def checkrecordfiles(recordname, filedirectory):
     """Check a local directory along with the database cache directory specified in 'config.ini' for all necessary files required to read a WFDB record. Calls pbdownload.dlrecordfiles to download any missing files into the database cache directory. Returns the base record name if all files were present, or a full path record name specifying where the downloaded files are to be read, and a list of files downloaded. 
@@ -132,8 +132,12 @@ def dlrecordfiles(pbrecname, targetdir):
     if not os.path.isfile(os.path.join(targetdir, baserecname+".hea")):
         # Not calling dlorexit here. Extra instruction of removing the faulty created directory.
         try:
-            urlretrieve("http://physionet.org/physiobank/database/"+pbrecname+".hea", os.path.join(targetdir, baserecname+".hea")) 
-            dledfiles.append(os.path.join(targetdir, baserecname+".hea"))
+            remotefile = "http://physionet.org/physiobank/database/"+pbrecname+".hea"
+            targetfile = os.path.join(targetdir, baserecname+".hea")
+            r = requests.get(remotefile)
+            with open(targetfile, "w") as text_file:
+                text_file.write(r.text)
+            dledfiles.append(targetfile)
         except HTTPError:
             if madetargetdir:
                 os.rmdir(targetdir) # Remove the recently created faulty directory. 
@@ -165,7 +169,9 @@ def dlrecordfiles(pbrecname, targetdir):
 # Helper function for dlrecordfiles. Download the file from the specified 'url' as the 'filename', or exit with warning. 
 def dlorexit(url, filename, dledfiles):
     try:
-        urlretrieve(url, filename)
+        r = requests.get(url)
+        with open(filename, "w") as text_file:
+            text_file.write(r.text)
         dledfiles.append(filename)
         return dledfiles
     except HTTPError: