Merge pull request #20 from BrainLesion/clean_niftyreg

Clean niftyreg

brainles_preprocessing/registration/functional.py

@@ -1,4 +1,3 @@
-from .niftyreg import niftyreg_caller
 from .niftyreg import NiftyRegRegistrator
 
 

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)

example_modality_centric.py

@@ -33,10 +33,10 @@ def preprocess(inputDir):
         flair_file = btk_raw_dir.files("*fla.nii.gz")
 
         if len(t1_file) == len(t1c_file) == len(t2_file) == len(flair_file) == 1:
-            print(t1_file)
-            print(t1c_file)
-            print(t2_file)
-            print(flair_file)
+            # print(t1_file)
+            # print(t1c_file)
+            # print(t2_file)
+            # print(flair_file)
 
             t1File = t1_file[0]
             t1cFile = t1c_file[0]
@@ -107,5 +107,5 @@ def preprocess(inputDir):
     exams = EXAMPLE_DATA_DIR.dirs()
 
     for exam in tqdm(exams):
-        print(exam)
+        print("processing:", exam)
         preprocess(exam)

pyproject.toml

@@ -7,7 +7,7 @@ enable = true
 
 [tool.poetry]
 name = "brainles_preprocessing"
-version = "0.0.0" # will be overwritten by poetry-dynamic-versioning but needs to be set
+version = "0.0.0"               # will be overwritten by poetry-dynamic-versioning but needs to be set
 description = "TODO."
 license = "AGPL-3.0"
 
@@ -27,11 +27,17 @@ readme = "README.md"
 repository = "https://github.com/BrainLesion/preprocessing"
 #documentation = ""
 
-keywords = ["brain tumor", "glioma", "BraTS", "skullstripping", "brain extraction"]
+keywords = [
+  "brain tumor",
+  "glioma",
+  "BraTS",
+  "skullstripping",
+  "brain extraction",
+]
 classifiers = [
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: GNU Affero General Public License v3",
-    "Operating System :: OS Independent",
+  "Programming Language :: Python :: 3",
+  "License :: OSI Approved :: GNU Affero General Public License v3",
+  "Operating System :: OS Independent",
 ]
 
 
@@ -49,7 +55,7 @@ BrainLes-HD-BET = ">=0.0.5"
 
 # utils
 tqdm = "^4.64.1"
-auxiliary = "^0.0.35"
+auxiliary = "^0.0.37"
 rich = "^13.6.0"
 
 [tool.poetry.dev-dependencies]