Merge pull request #36 from neuronflow/cli-citation-reminder

Cli citation reminder

brats_toolkit/cli.py

@@ -11,6 +11,7 @@
 import pprint
 import argparse
 
+
 from . import segmentor, fusionator, preprocessor
 
 
@@ -41,7 +42,7 @@ def list_docker_cpu():
         if seg.config[id]["runtime"] == "runc":
             print(id)
 
-
+    
 def fusion():
     parser = argparse.ArgumentParser(
         description="Runs the Docker orchestra to fuse segmentations. All inputs have to have equal shape and label values"
@@ -83,7 +84,6 @@ def fusion():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
-
 def segmentation():
     parser = argparse.ArgumentParser(
         description="Runs the Docker orchestra to segment and fuse segmentations based on the"
@@ -179,7 +179,6 @@ def segmentation():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
-
 def batchpreprocess():
     parser = argparse.ArgumentParser(
         description="Runs the preprocessing for MRI scans on a folder of images."
@@ -243,7 +242,6 @@ def batchpreprocess():
     except Exception as e:
         print("ERROR DETAIL: ", e)
 
-
 def singlepreprocess():
     parser = argparse.ArgumentParser(
         description="Runs the preprocessing for MRI scans on a single set of images."

brats_toolkit/fusionator.py

@@ -13,9 +13,12 @@
 import os.path as op
 from .util import own_itk as oitk
 from .util import filemanager as fm
+from .util.citation_reminder import citation_reminder
 
 
 class Fusionator(object):
+
+    @citation_reminder
     def __init__(self, verbose=True):
         self.verbose = verbose
 

brats_toolkit/preprocessor.py

@@ -5,10 +5,13 @@
 from pathlib import Path
 
 from brats_toolkit.util.prep_utils import tempFiler
+from brats_toolkit.util.citation_reminder import citation_reminder
 import sys
 
 
 class Preprocessor(object):
+
+    @citation_reminder
     def __init__(self, noDocker=False):
         # settings
         self.clientVersion = "0.0.1"
@@ -45,7 +48,7 @@ def message(data):
 
         @self.sio.on("status")
         def on_status(data):
-            print("status reveived: ", data)
+            print("status received: ", data)
             if data["message"] == "client ID json generation finished!":
                 self._inspect_input()
             elif data["message"] == "input inspection finished!":
@@ -85,7 +88,7 @@ def outdated(data):
 
         @self.sio.on("ipstatus")
         def on_ipstatus(data):
-            print("image processing status reveived:")
+            print("image processing status received:")
             print(data["examid"], ": ", data["ipstatus"])
 
     def single_preprocess(
@@ -161,7 +164,7 @@ def batch_preprocess(
 
         # setup connection
         # TODO do this in a more elegant way and somehow check whether docker is up and running before connect
-        self.sio.sleep(5)  # wait 5 secs for docker to start
+        self.sio.sleep(8)  # wait 8 secs for docker to start
         self._connect_client()
         self.sio.wait()
 

brats_toolkit/segmentor.py

@@ -24,13 +24,15 @@
 from . import fusionator
 from .util import filemanager as fm
 from .util import own_itk as oitk
+from .util.citation_reminder import citation_reminder
 
 
 class Segmentor(object):
     """
     Now does it all!
     """
 
+    @citation_reminder
     def __init__(
         self,
         config=None,

brats_toolkit/util/citation_reminder.py

@@ -0,0 +1,14 @@
+from rich.console import Console
+
+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("Thank you!", justify="center")
+        console.rule()
+        console.line()
+        func(*args, **kwargs)
+    return wrapper

pyproject.toml

@@ -39,7 +39,8 @@ dependencies = [
     'numpy==1.22.0',
     'python-engineio==3.14.2',
     'python-socketio==4.6.1',
-    'requests==2.24.0'
+    'requests==2.24.0',
+    'rich==13.6.0'
 ]
 
 [project.optional-dependencies]