Renaming library to platipy

.devcontainer.json

@@ -1,8 +1,8 @@
 {
-	"name": "IMPIT Development",
+	"name": "PlatiPy Development",
 	"dockerComposeFile": "./docker-compose.yml",
-	"service": "impit",
-	"workspaceFolder": "/impit",
+	"service": "platipy",
+	"workspaceFolder": "/platipy",
 	"shutdownAction": "stopCompose",
 	"appPort": [ 8001, 7777 ],
 

.vscode/settings.json

@@ -9,7 +9,6 @@
         "--disable=W0102",
         "--disable=W0105",
         "--init-hook",
-        "import sys; sys.path.append('..')",
         "--extension-pkg-whitelist=vtk"
     ],
     "python.formatting.blackArgs": [

Dockerfile

@@ -15,7 +15,7 @@ RUN pip install -r requirements.txt
 COPY requirements-dev.txt requirements-dev.txt
 RUN pip install -r requirements-dev.txt
 
-COPY . impit
+COPY . platipy
 
 COPY entrypoint.sh /entrypoint.sh
 
@@ -31,9 +31,9 @@ ENV WORK C.UTF-8
 ARG dicom_listen_port=7777
 
 ENV DICOM_LISTEN_PORT ${dicom_listen_port}
-ENV DICOM_LISTEN_AET IMPIT_SERVICE
+ENV DICOM_LISTEN_AET PLATIPY_SERVICE
 
-RUN printf '#!/bin/bash\npython3 -m impit.framework.manage $@\n' > /usr/bin/manage && chmod +x /usr/bin/manage
+RUN printf '#!/bin/bash\npython3 -m platipy.framework.manage $@\n' > /usr/bin/manage && chmod +x /usr/bin/manage
 
 EXPOSE 8000
 EXPOSE ${dicom_listen_port}

README.md

@@ -1,9 +1,8 @@
-# IMPIT (Ingham Medical Physics Imaging Toolbox)
+# PlatiPy (Processing Library and Analysis Toolkit for Medical Imaging in Python)
 
-This toolbox contains tools and scripts used for image processing within the Medical Physics group
-at Ingham Institute in Liverpool, Australia. The code makes use of ITK and VTK and is written in
-Python. Jupyter notebooks are provided where possible, mainly for guidance on getting started with
-using the tools.
+This library contains tools and scripts used for image processing and analysis of medical images.
+The code makes use of ITK and VTK and is written in Python. Jupyter notebooks are provided where
+possible, mainly for guidance on getting started with using the tools.
 
 ## Getting Started
 

bootstrap.sh

@@ -13,15 +13,15 @@ sudo apt-get install -y orthanc
 mkdir ~/environments
 cd ~/environments
 
-python3 -m venv impit_env
+python3 -m venv platipy_env
 
-source ~/environments/impit_env/bin/activate
-echo ". ~/environments/impit_env/bin/activate" > ~/.profile
+source ~/environments/platipy_env/bin/activate
+echo ". ~/environments/platipy_env/bin/activate" > ~/.profile
 
 export PYTHONPATH="${PYTHONPATH}:/"
 echo 'export PYTHONPATH="${PYTHONPATH}:/"' >> ~/.profile
 
-pip install -r /impit/requirements.txt
+pip install -r /platipy/requirements.txt
 
 
 # Install Docker

dicom/nifti_to_rtstruct/convert.py

@@ -4,8 +4,8 @@
 import argparse
 import nibabel
 import os
-from impit.dicom.nifti_to_rtstruct.export_to_rtstruct import export_to_rtstruct
-from impit.dicom.nifti_to_rtstruct.gen_contours import gen_contours
+from platipy.dicom.nifti_to_rtstruct.export_to_rtstruct import export_to_rtstruct
+from platipy.dicom.nifti_to_rtstruct.gen_contours import gen_contours
 import pydicom
 from collections import OrderedDict
 from loguru import logger

dicom/tests/test_convert_nifti.py

@@ -2,7 +2,7 @@
 import pydicom
 import numpy as np
 
-from impit.dicom.nifti_to_rtstruct.convert import convert_nifti
+from platipy.dicom.nifti_to_rtstruct.convert import convert_nifti
 
 def test_convert_nifti():
 

dicom/tests/test_convert_rtstruct.py

@@ -1,7 +1,7 @@
 import os
 import SimpleITK as sitk
 
-from impit.dicom.rtstruct_to_nifti.convert import convert_rtstruct
+from platipy.dicom.rtstruct_to_nifti.convert import convert_rtstruct
 
 def test_convert_rtstruct():
 

docker-compose.yml

@@ -1,19 +1,19 @@
 version: '3'
 
 services:
-  impit:
-    image: impit
+  platipy:
+    image: platipy
     ports:
       - "8001:8000"
       - "7777:7777"
     volumes:
-      - .:/impit
-      - impit_data:/data
+      - .:/platipy
+      - platipy_data:/data
     links:
       - redis:redis
     entrypoint: /bin/sh -c "while sleep 1000; do :; done"
     environment:
-      PYTHONPATH: "/"
+      PYTHONPATH: "/platipy"
     deploy:
       resources:
         limits:
@@ -26,5 +26,5 @@ services:
       - redis_data:/data
 
 volumes:
-  impit_data:
+  platipy_data:
   redis_data:

entrypoint.sh

@@ -11,7 +11,7 @@ celery beat --app=service:celery --loglevel=INFO &
 celery worker --app=service:celery --loglevel=INFO &
 
 # Start the Dicom listen celery task
-python3 -c "from impit.framework.tasks import listen_task; listen_task.apply_async([$DICOM_LISTEN_PORT, '$DICOM_LISTEN_AET'])"
+python3 -c "from platipy.framework.tasks import listen_task; listen_task.apply_async([$DICOM_LISTEN_PORT, '$DICOM_LISTEN_AET'])"
 
 exec gunicorn -b :8000 --timeout 300 --graceful-timeout 60 --access-logfile - --error-logfile - service:app
 

framework/__init__.py

@@ -6,7 +6,7 @@
 from flask_restful import Api
 from celery import Celery
 
-from impit.framework.application import FlaskApp
+from platipy.framework.application import FlaskApp
 
 from loguru import logger
 
@@ -45,9 +45,9 @@
 
 # Configure API
 api = Api(app)
-app.config.from_object('impit.framework.api.CustomConfig')
+app.config.from_object('platipy.framework.api.CustomConfig')
 
-import impit.framework.views
-import impit.framework.api
-import impit.framework.tasks
-from impit.framework.models import DataObject
+import platipy.framework.views
+import platipy.framework.api
+import platipy.framework.tasks
+from platipy.framework.models import DataObject

framework/api.py

@@ -1,4 +1,4 @@
-from impit.framework import app, api
+from platipy.framework import app, api
 from loguru import logger
 
 import flask_restful

framework/application.py

@@ -29,7 +29,7 @@ class FlaskApp(Flask):
     celery_started = False
     beat_started = False
     dicom_listener_port = 7777
-    dicom_listener_aetitle = "IMPIT_SERVICE"
+    dicom_listener_aetitle = "PLATIPY_SERVICE"
 
     api = None # Holds reference to api for extensibility
 
@@ -81,7 +81,7 @@ def run_beat(self):
 
     def run(self, host=None, port=None, debug=None,
             dicom_listener_port=7777,
-            dicom_listener_aetitle="IMPIT_SERVICE",
+            dicom_listener_aetitle="PLATIPY_SERVICE",
             load_dotenv=True, **options):
 
         logger.info('Starting APP!')

framework/client.py

@@ -1,5 +1,5 @@
 """
-Provides a client to interact with IMPITs framework
+Provides a client to interact with PlatiPy's framework
 """
 import time
 import os
@@ -20,8 +20,8 @@
 API_DOWNLOAD_OBJECT = "{0}/api/dataobject/download"
 
 
-class IMPITClient:
-    """Client to help iteract with the framework implemented within IMPIT.
+class PlatiPyClient:
+    """Client to help iteract with the framework implemented within PlatiPy.
     """
 
     def __init__(self, host, port, api_key, algorithm_name):

framework/models.py

@@ -1,4 +1,4 @@
-from impit.framework import db
+from platipy.framework import db
 import datetime
 import json
 

framework/sample/sample.py

@@ -3,8 +3,8 @@
 
 from loguru import logger
 
-from impit.framework import app, DataObject
-from impit.dicom.nifti_to_rtstruct.convert import convert_nifti
+from platipy.framework import app, DataObject
+from platipy.dicom.nifti_to_rtstruct.convert import convert_nifti
 
 import SimpleITK as sitk
 import pydicom

framework/tasks.py

@@ -1,4 +1,4 @@
-from impit.framework import celery, db, app
+from platipy.framework import celery, db, app
 from celery.schedules import crontab
 
 from loguru import logger
@@ -16,7 +16,7 @@
 celery.conf.beat_schedule = {
     # Executes every hour
     'clean-up-every-hour': {
-        'task': 'impit.framework.tasks.clean_up_task',
+        'task': 'platipy.framework.tasks.clean_up_task',
         'schedule': crontab(minute=0),
         'args': (),
     },

framework/tests/test_framework.py

@@ -2,7 +2,7 @@
 import os
 import json
 import tempfile
-from impit.framework import app
+from platipy.framework import app
 
 
 @pytest.fixture

framework/views.py

@@ -1,4 +1,4 @@
-from impit.framework import app, celery, log_file_path
+from platipy.framework import app, celery, log_file_path
 from ..dicom.communication import DicomConnector
 from .models import db, APIKey
 

jupyter/Dockerfile

@@ -1,4 +1,4 @@
-FROM impit:latest
+FROM platipy:latest
 
 RUN pip3 install matplotlib==3.1.0 jupyterlab pandas itkwidgets seaborn gitpython
 

jupyter/README

@@ -1,7 +1,7 @@
 ## Jupyter Tools
 
 A Dockerfile is provided to create a useful Jupyter environment to develop and 
-work with these impit tools. It can be launched using ```docker-compose up -d```
+work with these platipy tools. It can be launched using ```docker-compose up -d```
 
 Work in progress.
 

segmentation/bronchus/bronchus.py

@@ -19,7 +19,7 @@
 
 import SimpleITK as sitk
 
-from impit.segmentation.common.tools import detect_holes, get_lung_mask
+from platipy.segmentation.common.tools import detect_holes, get_lung_mask
 
 
 def fast_mask(img, start, end):

segmentation/bronchus/run.py

@@ -5,7 +5,7 @@
 
 from loguru import logger
 
-from impit.segmentation.bronchus.bronchus import (
+from platipy.segmentation.bronchus.bronchus import (
     generate_lung_mask,
     generate_airway_mask,
     default_settings,