fixes #37

doc/00_Introduction.rst

@@ -42,62 +42,24 @@ guide the user in creating an augmented reality application in around 70 lines o
 
 Installation
 ~~~~~~~~~~~~
-Step 1:
-You'll need SciKit-SurgeryUtils installed on your system. Provided you have Python installed on 
-your system you should be able to run ...
-::
- 
-  pip install scikit-surgeryutils
-
-to install SciKit-SurgeryUtils and its dependencies (including SciKit-SurgeryCore).
-For the third part of the tutorial you'll also need SciKit-SurgeryArUcoTracker
-
-::
 
-  pip install scikit-surgeryarucotracker
+Packages, other requirements, and virtual environments
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-If you don't have Python installed, we 
-recommend downloading an installer for your platform directly from `python.org`_.
-
-Virtual environments
+Python virtual environments
 ~~~~~~~~~~~~
 Virtualenv, venv, conda or pyenv can be used to create virtual environments to manage python packages.
-You can use conda env by installing conda for your OS (`conda_installation`_) and use the following yml file with all dependencies.
+If you don't have Python installed, we recommend downloading an installer for your platform directly from `python.org`_.
+For the case of conda, please create a VE using the following commands in your terminal:
+
 ::
-   ## Create scikit-surgerytutorial01VE.yml in your favorite location with the following content:
-   ##
-   ##  scikit-surgerytutorial01VE.yml
-   ##
-   ## Some useful commands to manage your conda env:
-   ## LIST CONDA ENVS: conda list -n *VE # show list of installed packages
-   ## UPDATE CONDA: conda update -n base -c defaults conda
-   ## INSTALL CONDA EV: conda env create -f *VE.yml
-   ## UPDATE CONDA ENV: conda env update --file *VE.yml --prune
-   ## ACTIVATE CONDA ENV: conda activate *VE
-   ## REMOVE CONDA ENV: conda remove -n *VE --all
-
-   name: scikit-surgerytutorial01VE
-   channels:
-     - defaults
-     - conda-forge #vtk; tox;
-     - anaconda #coverage; scipy;
-   dependencies:
-     - python=3.7
-     - numpy>=1.17.4
-     - vtk=8.1.2
-     - tox>=3.26.0
-     - pytest>=7.1.2
-     - pylint>=2.14.5
-     - pip>=22.2.2
-     - pip:
-        - PySide2>=5.14.2.3
-        - scikit-surgerycore>=0.1.7
-        - scikit-surgeryutils>=1.2.0
-        - scikit-surgeryarucotracker>=0.1.1
-        - opencv-python-headless
-
-Step 2: 
-You should now be able to follow the tutorial, using the code snippets contained herein.
+
+   conda update -n base -c defaults conda
+   conda create -n sst01VE python=3.8 pip -c conda-forge #try3.7
+   conda activate sst01VE
+   pip install -r requirements.txt
+   pip install -r requirements-dev.txt
+
 
 .. _`python.org`: https://www.python.org/downloads/
 .. _`SmartLiver`: https://link.springer.com/article/10.1007/s11548-018-1761-3

requirements-dev.txt

@@ -2,7 +2,6 @@
 # for development.
 # It is used by pip to manage software dependencies. It is not to be
 # confused with the software requirements, which are listed in
-# doc/requirements.rst
 -r requirements.txt
 coverage
 mock

requirements.txt

@@ -4,7 +4,9 @@
 # confused with the software requirements, which are listed in
 # doc/requirements.rst
 numpy>=1.17.4
-PySide2
+vtk>=9.2.6
+PySide6>=6.5.1.1
+opencv-contrib-python-headless>=4.2.0.32
 scikit-surgerycore>=0.1.7
 scikit-surgeryutils>=1.2.0
-scikit-surgeryarucotracker>= 0.2.7
+scikit-surgeryarucotracker>= 0.2.7

sksurgerytutorial01/vtk_aruco_app.py

@@ -1,12 +1,15 @@
-# coding=utf-8
+"""
+Script to create a viewer window with a movable surface
+model overlaid in a live video feed
 
-"""Script to create a viewer window with a movable surface
-model overlaid in a live video feed"""
+USAGE:
+python vtk_aruco_app.py
+"""
 
 import sys
 #add an import for numpy, to manipulate arrays
 import numpy
-from PySide2.QtWidgets import QApplication
+from PySide6.QtWidgets import QApplication
 from sksurgeryutils.common_overlay_apps import OverlayBaseWidget
 from sksurgerycore.transforms.transform_manager import TransformManager
 from sksurgeryarucotracker.arucotracker import ArUcoTracker
@@ -60,6 +63,8 @@ def update_view(self):
         #see what happens.
         self.vtk_overlay_window.set_camera_state({"ClippingRange": [10, 800]})
         self.vtk_overlay_window.set_video_image(image)
+        self.vtk_overlay_window.Initialize() # Allows the interactor to initialize itself.
+        self.vtk_overlay_window.Start()  # Start the event loop.
         self.vtk_overlay_window.Render()
 
     def _aruco_detect_and_follow(self, image):
@@ -104,4 +109,4 @@ def _move_camera(self, tag2camera):
     viewer.show()
     viewer.start()
 
-    sys.exit(app.exec_())
+    sys.exit(app.exec())

sksurgerytutorial01/vtkoverlay_app.py

@@ -1,10 +1,13 @@
-# coding=utf-8
+"""
+Script to create a viewer window with a static surface 
+model overlaid in a live video feed
 
-"""Script to create a viewer window with a static surface
-model overlaid in a live video feed"""
+USAGE:
+python vtkoverlay_app.py
+"""
 
 import sys
-from PySide2.QtWidgets import QApplication
+from PySide6.QtWidgets import QApplication
 from sksurgeryutils.common_overlay_apps import OverlayBaseWidget
 
 #create an OverlayApp class, that inherits from OverlayBaseApp
@@ -16,6 +19,8 @@ def update_view(self):
         and render"""
         _, image = self.video_source.read()
         self.vtk_overlay_window.set_video_image(image)
+        self.vtk_overlay_window.Initialize() # Allows the interactor to initialize itself.
+        self.vtk_overlay_window.Start()  # Start the event loop.
         self.vtk_overlay_window.Render()
 
 #the following line prevents the code below from running unless
@@ -43,4 +48,4 @@ def update_view(self):
     viewer.start()
 
     #start the application
-    sys.exit(app.exec_())
+    sys.exit(app.exec())

sksurgerytutorial01/vtkoverlay_with_movement_app.py

@@ -1,10 +1,13 @@
-# coding=utf-8
+"""
+Script to create a viewer window with a moving surface
+model overlaid in a live video feed
 
-"""Script to create a viewer window with a moving surface
-model overlaid in a live video feed"""
+USAGE:
+python vtkoverlay_with_movement_app.py
+"""
 
 import sys
-from PySide2.QtWidgets import QApplication
+from PySide6.QtWidgets import QApplication
 from sksurgeryutils.common_overlay_apps import OverlayBaseWidget
 
 class OverlayApp(OverlayBaseWidget):
@@ -20,6 +23,8 @@ def update_view(self):
         self._move_model()
 
         self.vtk_overlay_window.set_video_image(image)
+        self.vtk_overlay_window.Initialize() # Allows the interactor to initialize itself.
+        self.vtk_overlay_window.Start()  # Start the event loop.
         self.vtk_overlay_window.Render()
 
     def _move_model(self):
@@ -48,4 +53,4 @@ def _move_model(self):
     viewer.show()
     viewer.start()
 
-    sys.exit(app.exec_())
+    sys.exit(app.exec())

tests/conftest.py

@@ -1,10 +1,10 @@
 # -*- coding: utf-8 -*-
 import pytest
-from PySide2.QtWidgets import QApplication
+from PySide6.QtWidgets import QApplication
 
 @pytest.fixture(scope="session")
 def setup_qt():
 
     """ Create the QT application. """
     app = QApplication([])
-    return app
+    return app

tests/test_sksurgerytorial01.py

@@ -1,6 +1,9 @@
-# coding=utf-8
+"""
+sksurgerytutorial01 vtkoverlay tests
 
-"""sksurgerytutorial01 vtkoverlay tests"""
+USAGE:
+python -m pytest -v -s tests
+"""
 
 import pytest