Merge pull request #48 from SciKit-Surgery/46-use-headless

46 use headless

.github/workflows/ci.yml

@@ -9,20 +9,29 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest, macos-latest]
-        python-ver: [3.7, 3.8]
+        python-ver: [3.7]
         experimental: [false]
         include:
+          - python-ver: 3.8
+            os: ubuntu-latest
+            experimental: false
+          - python-ver: 3.8
+            os: windows-latest
+            experimental: true
+          - python-ver: 3.8
+            os: macos-latest
+            experimental: false
           - python-ver: 3.9
             os: ubuntu-latest
             experimental: true
-
           - python-ver: 3.9
             os: windows-latest
             experimental: true
           - python-ver: 3.9
             os: macos-latest
             experimental: true
 
+
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     timeout-minutes: 10

config/.gitignore

@@ -0,0 +1,17 @@
+# Pycharm
+/.idea
+
+# Generated files
+.tox
+.coverage
+*.pyc
+.pytest_cache/
+
+# PyInstaller
+build/
+dist/
+model2camera.spec
+
+# Mac Finder:
+.DS_Store
+

config/video_chessboard_conf.json

@@ -0,0 +1,8 @@
+{
+    "method": "chessboard",
+    "corners": [14, 10],
+    "square size in mm": 6,
+    "minimum number of views": 5,
+    "keypress delay in ms": 1000,
+    "sample frequency" : 1
+}

requirements-dev.txt

@@ -8,7 +8,7 @@ coverage
 mock
 pyfakefs
 parameterized
-pylint
+pylint<2.14
 sphinx
 sphinx_rtd_theme
 pyinstaller

requirements.txt

@@ -4,9 +4,10 @@
 # doc/requirements.rst
 six>=1.10
 numpy>=1.11
-opencv-contrib-python-headless>=4.1.1.26
-PySide2<5.15.0
+opencv-contrib-python-headless>=4.1.1.26,<4.6
 scikit-surgerycore>=0.1.7
-scikit-surgeryimage>=0.2.0
-scikit-surgeryvtk>=0.19.1
-scikit-surgeryarucotracker>=0.0.4
+scikit-surgeryimage>=0.10.1
+scikit-surgeryvtk>=1.0.6
+scikit-surgeryarucotracker>=0.2.7
+scikit-surgerycalibration>=0.2.1
+PySide2>=5.12.0

setup.py

@@ -14,7 +14,7 @@
     name='scikit-surgeryutils',
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-    description='scikit-surgeryutils - Tests/demos utilities, based around opencv-contrib and PySide2',
+    description='scikit-surgeryutils - Tests/demos utilities, based around opencv-contrib-python-headless and PySide2',
     long_description=long_description,
     long_description_content_type='text/x-rst',
     url='https://github.com/SciKit-Surgery/scikit-surgeryutils',
@@ -56,10 +56,10 @@
         'opencv-contrib-python-headless>=4.1.1.26',
         'PySide2<5.15.0',
         'scikit-surgerycore>=0.1.7',
-        'scikit-surgeryimage>=0.2.0',
-        'scikit-surgeryvtk>=0.19.1',
-        'scikit-surgeryarucotracker>=0.0.4'
-
+        'scikit-surgeryimage>=0.10.1',
+        'scikit-surgeryvtk>=1.0.6',
+        'scikit-surgeryarucotracker>=0.2.7',
+        'scikit-surgerycalibration>=0.2.1'
     ],
 
     entry_points={
@@ -71,6 +71,8 @@
             'sksurgeryreslice=sksurgeryutils.ui.sksurgeryreslice_command_line:main',
             'sksurgerytextoverlay=sksurgeryutils.ui.sksurgerytextoverlay_command_line:main',
             'sksurgerytransformpolydata=sksurgeryutils.ui.sksurgeryrendermodelslikecamera_command_line:main',
+            'sksurgeryvideocalibration=sksurgeryutils.ui.sksurgeryvideocalibration_command_line:main',
+            'sksurgeryvideocalibrationchecker=sksurgeryutils.ui.sksurgeryvideocalibrationchecker_command_line:main',
         ],
     },
 )

sksurgeryutils/common_overlay_apps.py

@@ -1,44 +1,70 @@
-"""Common use cases for vtk_overlay_window"""
+# coding=utf-8
+
+""" Common use cases for vtk_overlay_window """
 
 #pylint: disable=no-member, no-name-in-module, protected-access
-# coding=utf-8
+
 import datetime
 import logging
 import cv2
 
+from PySide2.QtWidgets import QWidget, QHBoxLayout
 from PySide2.QtCore import QTimer
 from sksurgeryimage.acquire.video_source import TimestampedVideoSource
 from sksurgeryimage.acquire.video_writer import TimestampedVideoWriter
-
 from sksurgeryvtk.widgets.vtk_overlay_window import VTKOverlayWindow
 from sksurgeryvtk.models.vtk_surface_model_directory_loader \
     import VTKSurfaceModelDirectoryLoader
 
-class OverlayBaseApp():
+
+class OverlayBaseWidget(QWidget):
     """
     Base class for applications that use vtk_overlay_window.
     The update() method should be implemented in the child
     class.
 
     :param video_source: OpenCV compatible video source (int or filename)
+    :param dims: size of video feed
     """
     def __init__(self, video_source, dims=None):
+        super().__init__()
+
+        self.layout = QHBoxLayout(self)
+        self.layout.setContentsMargins(0, 0, 0, 0)
+        self.layout.setSpacing(0)
+
         self.vtk_overlay_window = VTKOverlayWindow()
+        self.layout.addWidget(self.vtk_overlay_window)
+
         self.video_source = TimestampedVideoSource(video_source, dims)
+
+        self.timer = QTimer()
+        self.timer.timeout.connect(self.update_view)
+
         self.update_rate = 30
         self.img = None
-        self.timer = None
         self.save_frame = None
 
     def start(self):
-        """Show the overlay widget and
-        set a timer running"""
-        self.vtk_overlay_window.show()
-
-        self.timer = QTimer()
-        self.timer.timeout.connect(self.update)
+        """
+        Starts the timer, which repeatedly triggers the update_view() method.
+        """
         self.timer.start(1000.0 / self.update_rate)
 
+    def stop(self):
+        """
+        Stops the timer.
+        """
+        self.timer.stop()
+
+    def terminate(self):
+        """
+        Make sure that the VTK Interactor terminates nicely, otherwise
+        it can throw some error messages, depending on the usage.
+        """
+        self.vtk_overlay_window._RenderWindow.Finalize()
+        self.vtk_overlay_window.TerminateApp()
+
     def add_vtk_models_from_dir(self, directory):
         """
         Add VTK models to the foreground.
@@ -47,34 +73,28 @@ def add_vtk_models_from_dir(self, directory):
         model_loader = VTKSurfaceModelDirectoryLoader(directory)
         self.vtk_overlay_window.add_vtk_models(model_loader.models)
 
-    def update(self):
+    def update_view(self):
         """ Update the scene background and/or foreground.
             Should be implemented by sub class """
 
         raise NotImplementedError('Should have implemented this method.')
 
-    def stop(self):
-        """
-        Make sure that the VTK Interactor terminates nicely, otherwise
-        it can throw some error messages, depending on the usage.
-        """
-        self.vtk_overlay_window._RenderWindow.Finalize()
-        self.vtk_overlay_window.TerminateApp()
 
-class OverlayOnVideoFeed(OverlayBaseApp):
+class OverlayOnVideoFeed(OverlayBaseWidget):
     """
     Uses the acquired video feed as the background image,
     with no additional processing.
     """
-
-    def update(self):
-        """ Get the next frame of input and display it. """
+    def update_view(self):
+        """
+        Get the next frame of input and display it.
+        """
         _, self.img = self.video_source.read()
         self.vtk_overlay_window.set_video_image(self.img)
-        self.vtk_overlay_window._RenderWindow.Render()
+        self.vtk_overlay_window.Render()
 
 
-class OverlayOnVideoFeedCropRecord(OverlayBaseApp):
+class OverlayOnVideoFeedCropRecord(OverlayBaseWidget):
     """ Add cropping of the incoming video feed, and the ability to
         record the vtk_overlay_window.
 
@@ -89,14 +109,15 @@ def __init__(self, video_source, output_filename=None, dims=None):
         self.output_filename = output_filename
         self.video_writer = None
 
-    def update(self):
-        """ Get the next frame of input, crop and/or
-            write to file (if either enabled). """
+    def update_view(self):
+        """
+        Get the next frame of input, crop and/or
+        write to file (if either enabled).
+        """
         _, self.img = self.video_source.read()
 
         self.vtk_overlay_window.set_video_image(self.img)
-
-        self.vtk_overlay_window._RenderWindow.Render()
+        self.vtk_overlay_window.Render()
 
         if self.save_frame:
             output_frame = self.get_output_frame()
@@ -144,46 +165,3 @@ def on_record_stop(self):
         self.save_frame = False
         self.video_writer.close()
         logging.debug("Recording stopped.")
-
-
-class DuplicateOverlayWindow(OverlayOnVideoFeedCropRecord):
-    """
-    Set the background of vtk_overlay_window to duplicate
-    that of another vtk_overlay_window.
-
-    Example usage:
-    video_source = 0
-    source_window = OverlayOnVideoFeedCropRecord(video_source)
-
-    duplicate_window = DuplicateOverlayWindow()
-    duplicate_window.set_source_window(source_window)
-
-    """
-    def __init__(self):
-
-        #pylint: disable=super-init-not-called
-        self.vtk_overlay_window = VTKOverlayWindow()
-        self.update_rate = 30
-        self.img = None
-        self.timer = None
-        self.source_window = None
-
-    def set_source_window(self, source_window):
-        """ Set the source window.
-        :param source_window: The window that contains the image to copy. """
-        self.source_window = source_window
-
-    def update(self):
-        """ Update the frame with a new background image."""
-
-        self.img = self.source_window.vtk_overlay_window.input
-        self.vtk_overlay_window.set_video_image(self.img)
-
-        self.vtk_overlay_window._RenderWindow.Render()
-
-    def on_record_start(self):
-        """ Don't want to call the base class version, so override."""
-
-
-    def on_record_stop(self):
-        """ Don't want to call the base class version, so override."""

sksurgeryutils/ui/sksurgeryreslice_demo.py

@@ -5,6 +5,7 @@
 
 from sksurgeryarucotracker.arucotracker import ArUcoTracker
 
+
 def run_demo(tracked, dicom_dir):
 
     """ Demo """

sksurgeryutils/ui/sksurgerytextoverlay_demo.py

@@ -12,7 +12,9 @@
 
 logging.basicConfig(level=logging.INFO)
 LOGGER = logging.getLogger(__name__)
-#pylint:disable=line-too-long, invalid-name, unused-argument
+
+
+# pylint:disable=line-too-long, invalid-name, unused-argument
 class TextOverlayDemo(common_overlay_apps.OverlayOnVideoFeed):
     """ Demo app, to show text overlay"""
     def __init__(self, video_source):
@@ -50,6 +52,7 @@ def mouse_click_callback(self, obj, ev):
         vtk_text.set_parent_window(self.vtk_overlay_window)
         self.vtk_overlay_window.add_vtk_actor(vtk_text.text_actor, 2)
 
+
 def run_demo():
     """ Run demo """
     app = QApplication([])

sksurgeryutils/ui/sksurgerytransformpolydata_demo.py

@@ -9,7 +9,8 @@
 import sksurgeryvtk.utils.matrix_utils as mu
 import sksurgeryvtk.models.vtk_surface_model as sm
 
-#pylint:disable=no-member
+# pylint:disable=no-member
+
 
 def run_demo(input_file,
              output_file,