Merge pull request #48 from neuronflow/deprecated_prep

Deprecated prep

0_preprocessing_batch.py

@@ -1,6 +1,3 @@
-import os
-from path import Path
-
 from brats_toolkit.preprocessor import Preprocessor
 
 # instantiate

1_segmentation.py

@@ -1,9 +1,7 @@
-import os
 import datetime
 
 from brats_toolkit.segmentor import Segmentor
 
-
 # log
 starttime = str(datetime.datetime.now().time())
 print("*** starting at", starttime, "***")

2_fusion.py

@@ -1,5 +1,3 @@
-import os
-from path import Path
 import datetime
 
 from brats_toolkit.fusionator import Fusionator
@@ -12,7 +10,7 @@
 fus = Fusionator(verbose=True)
 
 # input
-SOURCEDIR = Path("example_data/output_segmentor/TCGA-DU-7294/")
+SOURCEDIR = "example_data/output_segmentor/TCGA-DU-7294/"
 # output
 OUTPUTDIR = "example_data/output_fusionator/TCGA-DU-7294/"
 

brats_toolkit/preprocessor.py

@@ -1,17 +1,21 @@
-import socketio
-from brats_toolkit.util.docker_functions import start_docker, stop_docker, update_docker
 import os
+import sys
 import tempfile
 from pathlib import Path
 
+import socketio
+
+from brats_toolkit.util.citation_reminder import (
+    citation_reminder,
+    deprecated_preprocessor,
+)
+from brats_toolkit.util.docker_functions import start_docker, stop_docker, update_docker
 from brats_toolkit.util.prep_utils import tempFiler
-from brats_toolkit.util.citation_reminder import citation_reminder
-import sys
 
 
 class Preprocessor(object):
-
     @citation_reminder
+    @deprecated_preprocessor
     def __init__(self, noDocker=False):
         # settings
         self.clientVersion = "0.0.1"

brats_toolkit/util/citation_reminder.py

@@ -1,14 +1,44 @@
 from rich.console import Console
 
-def citation_reminder(func):
 
+def citation_reminder(func):
     def wrapper(*args, **kwargs):
         console = Console()
         console.rule("[bold red]Friendly citation reminder[/bold red]")
-        console.print("If you use this software in your research, please [bold cyan]cite[/bold cyan] BraTS Toolkit and the original authors of the algorithms who make this repository and tool possible.", justify="center")
-        console.print("Details can be found at https://github.com/neuronflow/BraTS-Toolkit#citation", justify="center")
+        console.print(
+            "If you use this software in your research, please [bold cyan]cite[/bold cyan] BraTS Toolkit and the original authors of the algorithms who make this repository and tool possible.",
+            justify="center",
+        )
+        console.print(
+            "Details can be found at https://github.com/neuronflow/BraTS-Toolkit#citation",
+            justify="center",
+        )
         console.print("Thank you!", justify="center")
         console.rule()
         console.line()
         func(*args, **kwargs)
-    return wrapper
+
+    return wrapper
+
+
+def deprecated_preprocessor(func):
+    def wrapper(*args, **kwargs):
+        console = Console()
+        console.rule("[bold red]Deprecation note[/bold red]")
+        console.print(
+            "Support for BraTS Toolkit's preprocessor will be deprecated soon, even though it should continue working.",
+            justify="center",
+        )
+        console.print(
+            "You can already beta test the new BrainLes preprocessing pipeline which allows for arbitrary sequences and implements multiple backends for registration and brain extration and. Furthermore it does not require docker",
+            justify="center",
+        )
+        console.print(
+            "visit https://github.com/BrainLesion/preprocessing to learn more",
+            justify="center",
+        )
+        console.rule()
+        console.line()
+        func(*args, **kwargs)
+
+    return wrapper