clean niftyreg

Signed-off-by: neuronflow <[email protected]>

brainles_preprocessing/registration/niftyreg.py

@@ -1,7 +1,4 @@
-import datetime
 import os
-import shlex
-import subprocess
 
 from auxiliary.runscript import ScriptRunner
 from auxiliary.turbopath import turbopath
@@ -70,8 +67,6 @@ def register(
             turbopath(__file__).parent + "/niftyreg_scripts/reg_aladin",
         )
 
-        print("niftyreg_executable:", niftyreg_executable)
-
         input_params = [
             turbopath(niftyreg_executable),
             turbopath(fixed_image),
@@ -80,10 +75,9 @@ def register(
             turbopath(matrix),
         ]
 
-        print("Input Params:", input_params)
-
         # Call the run method to execute the script and capture the output in the log file
         success, error = runner.run(input_params)
+
         # if success:
         #     print("Script executed successfully. Check the log file for details.")
         # else:
@@ -116,105 +110,18 @@ def transform(
             turbopath(__file__).parent + "/niftyreg_scripts/reg_resample",
         )
 
-        # print("niftyreg_executable:", niftyreg_executable)
-
         input_params = [
             turbopath(niftyreg_executable),
             turbopath(fixed_image),
             turbopath(moving_image),
             turbopath(transformed_image),
             turbopath(matrix),
         ]
-        print("Input Params:", input_params)
 
         # Call the run method to execute the script and capture the output in the log file
         success, error = runner.run(input_params)
 
-
-def run_bash_script_in_subprocess_and_log():
-    pass
-
-
-# TODO consider removing this legacy function
-def niftyreg_caller(
-    fixed_image,
-    moving_image,
-    transformed_image,
-    matrix,
-    log_file,
-    mode,
-):
-    """calls niftyreg for registration and transforms"""
-
-    the_shell = "/bin/bash"
-    registration_abspath = os.path.dirname(os.path.abspath(__file__))
-
-    if mode == "registration":
-        shell_script = os.path.join(
-            registration_abspath, "niftyreg_scripts", "rigid_reg.sh"
-        )
-    elif mode == "transformation":
-        shell_script = os.path.join(
-            registration_abspath, "niftyreg_scripts", "transform.sh"
-        )
-    else:
-        raise NotImplementedError("this mode is not implemented:", mode)
-
-    # let's try to call it
-    try:
-        starttime = str(datetime.datetime.now())
-        print("** starting: " + moving_image.name + " at: " + starttime)
-        t = Timer()  # TicToc("name")
-        t.start()
-        # your code ...
-        # first we create the output dir
-        # os.makedirs(output_dir, exist_ok=True)
-
-        # generate subprocess call
-        readableCmd = (
-            the_shell,
-            shell_script,
-            fixed_image,
-            moving_image,
-            transformed_image,
-            matrix,
-        )
-        readableCmd = " ".join(readableCmd)
-        print(readableCmd)
-        command = shlex.split(readableCmd)
-        print(command)
-
-        # cwd = pathlib.Path(__file__).resolve().parent
-        cwd = registration_abspath
-        print("*** cwd:", cwd)
-
-        with open(log_file, "w") as outfile:
-            subprocess.run(
-                command,
-                stdout=outfile,
-                stderr=outfile,
-                cwd=cwd,
-            )
-
-        endtime = str(datetime.datetime.now().time())
-
-        elapsed = t.stop("call")
-        print(elapsed)
-
-        with open(log_file, "a") as file:
-            file.write("\n" + "************************************************" + "\n")
-            file.write("cwd: " + str(cwd) + "\n")
-            file.write("CALL: " + readableCmd + "\n")
-            file.write("************************************************" + "\n")
-            file.write("************************************************" + "\n")
-            file.write("start time: " + starttime + "\n")
-            file.write("end time: " + endtime + "\n")
-            file.write("time elapsed: " + str(int(elapsed) / 60) + " minutes" + "\n")
-            file.write("************************************************" + "\n")
-
-    except Exception as e:
-        print("error: " + str(e))
-        print("registration error for: " + moving_image.name)
-
-    endtime = str(datetime.datetime.now())
-    print("** finished: " + moving_image.name + " at: " + endtime)
+        # if success:
+        #     print("Script executed successfully. Check the log file for details.")
+        # else:
+        #     print("Script execution failed:", error)