print and save both stdout and stderr in real time

Author: mavel101

python/bart.py

@@ -10,6 +10,7 @@
 import tempfile as tmp
 import os
 import sys
+import threading
 
 if __spec__.parent:
     from . import cfl
@@ -171,33 +172,34 @@ def bart_postprocess(nargout, ERR, infiles, infiles_kw, outfiles):
 def execute_cmd(cmd):
     """
     Execute a command in a shell.
-    Print and catch the output.
+    Print and catch the output (stdout + stderr) in real time.
     """
 
-    errcode = 0
-    stdout = ""
-    stderr = ""
-
     # remove empty strings from cmd
     cmd = [item for item in cmd if len(item)]
 
     # execute cmd
     proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE, universal_newlines=True)
 
-    # print to stdout
-    for stdout_line in iter(proc.stdout.readline, ""):
-        stdout += stdout_line
-        print(stdout_line, end="")
-    proc.stdout.close()
+    def read_stream(stream, buffer, prefix=""):
+        for line in iter(stream.readline, ""):
+            buffer.append(line)
+            print(prefix + line, end="")
+        stream.close()
 
-    # in case of error, print to stderr
-    errcode = proc.wait()
-    if errcode:
-        stderr = "".join(proc.stderr.readlines())
-        print(stderr)
-    proc.stderr.close()
+    stdout_lines, stderr_lines = [], []
+
+    t_out = threading.Thread(target=read_stream, args=(proc.stdout, stdout_lines))
+    t_err = threading.Thread(target=read_stream, args=(proc.stderr, stderr_lines))
 
-    return errcode, stdout, stderr
+    t_out.start()
+    t_err.start()
+
+    t_out.join()
+    t_err.join()
+
+    errcode = proc.wait()
+    return errcode, "".join(stdout_lines), "".join(stderr_lines)