Merge pull request #117 from SciKit-Surgery/115-final-release-2.0.0

115 - final release 1.0.0

.github/workflows/ci.yml

@@ -86,6 +86,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install xvfb
           sudo apt-get install libegl-dev
+          sudo apt-get install libxcb-cursor-dev
           ## Qt for X11 Requirements> https://doc.qt.io/qt-6/linux-requirements.html
           sudo apt-get install libfontconfig1-dev libfreetype6-dev
           sudo apt-get install libx11-dev libx11-xcb-dev
@@ -99,6 +100,7 @@ jobs:
           export DISPLAY=:1
           sudo Xvfb $DISPLAY -screen 0 1024x768x24 </dev/null &
           export QT_DEBUG_PLUGINS=0
+          export QT_QPA_PLATFORM=xcb
           export LD_LIBRARY_PATH=$pythonLocation"/lib/python${{ matrix.python-version }}/site-packages/PySide6/Qt/plugins/platforms"
           coverage erase
           coverage run -a --source ./sksurgerybard -m pytest -v -s

.gitignore

@@ -13,3 +13,6 @@ build/
 dist/
 tests/output/
 pointer_positions/
+
+# Generated bard models with tox
+bard_model2modelref.txt

.readthedocs.yaml

@@ -0,0 +1,23 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+  configuration: doc/conf.py
+  fail_on_warning: false
+
+# Optionally declare the Python requirements required to build your docs
+python:
+  install:
+    - requirements: requirements-docs.txt

README.rst

@@ -34,8 +34,8 @@ Basic Augmented Reality Demo.
    :alt: Follow scikit_surgery on twitter
 
 
-Author(s): Stephen Thompson and Matt Clarkson;
-Contributor(s): Miguel Xochicale, Thomas Dowrick, and Mian Ahmad.
+Author(s): Miguel Xochicale, Thomas Dowrick, Stephen Thompson and Matt Clarkson;
+Contributor(s): Mian Ahmad.
 
 Basic Augmented Reality Demo (BARD) is part of the `SciKit-Surgery`_ software project, developed at the `Wellcome EPSRC Centre for Interventional and Surgical Sciences`_, part of `University College London (UCL)`_.
 

doc/02_0_Build_Your_Own_Systems.rst

@@ -17,43 +17,51 @@ Build Your Own Image Guided Surgery System
 
 3. Get B.A.R.D.
 ::
+
   git clone https://github.com/SciKit-Surgery/scikit-surgerybard.git
 
 or navigate to https://github.com/SciKit-Surgery/scikit-surgerybard
 and use the download button
 
 navigate to the scikit-surgerybard directory and run
 ::
+
   pip install .
 
 You may need to add
 ::
+
   pip install --user
 
 if you don't have administrative permissions.
 
 **Another method to get BARD and all its dependant packages is the following**
 ::
+
   git clone https://github.com/SciKit-Surgery/scikit-surgerybard.git
 
 Change directory to the newly created `scikit-surgerybard` by
 ::
+
   cd scikit-surgerybard
 
 Run the tox commands
 ::
+
   tox
 
 If tox run successfully,
 For Mac and Linux, activate the virtual environment using command
 ::
+
   source .tox/py36/bin/activate
 
 If all goes well the prompt should be preceded by (py36).
 
 
 For Windows, activate the virtual environment using command
 ::
+
   .tox\py36\Scripts\activate
 
 If all goes well the prompt should be preceded by (py36).

doc/02_1_Calibrate_Your_Camera.rst

@@ -30,6 +30,7 @@ or write a script to make one.
 
 Take 5-20 pictures of chessboard using:
 ::
+
   python bardVideoCalibration.py -c config/video_calib_chessboard.json
 
 Hit the 'c' key to capture an image. Press the 'q' key to quite the application.
@@ -48,12 +49,14 @@ in the terminal window.
 Often, in a research setting, it is best to save the data for later
 analysis. The same program can be used to save the data to a given folder.
 
-Use the '-s' option to specify a directory to save to, and the
-'-p' option to specify a filename prefix.
+Use the '-o' option to specify a directory to save to, the
+'-p' option to specify a filename prefix, and '-h' option to show help message and exit.
 
 For example:
 ::
+
   python bardVideoCalibration.py -c config/video_calib_chessboard.json -s tests/output -p myresults
+  #usage: bardVideoCalibration.py [-h] -c CONFIG [-s SOURCE] [-o OUTPUT] [-p PREFIX] [-ni] [-v]
 
 Then, each time the program recalibrates, the results will be saved to the 'tests/output' folder, with the filename prefix 'myresults'.
 

doc/02_2_Tracking_With_AuRcoTags.rst

@@ -14,6 +14,7 @@ OpenCV.
 
 1. Try running the following, and check that the USB camera can track the reference marker
 ::
+
    python sksurgerybard.py --config config/example_config.json
 
 
@@ -36,7 +37,8 @@ a registration to be performed once. Here we have glued the marker to the phanto
 so model2reference should not change.
 
 Now try running
-:: 
+::
+
    python sksurgerybard.py --config config/reference_with_model.json
 
 Move the webcam so that the reference markers are visible, and you should see

doc/02_3_Make_Your_Own_Pointer.rst

@@ -18,6 +18,7 @@ can be reliably located in both the model (e.g. CT scan) and patient (i.e. physi
 Within the data directory there are files based on a CT scan of the
 pelvis phantom. 
 ::
+
   ls data/PelvisPhantom
   CT_Fiduicial_Markers.txt  
   FullPelvis.vtk  
@@ -36,6 +37,7 @@ pointer, using the "pointer" markers, a pen, some cardboard and some sort of adh
 
 Now run this:
 ::
+
   python sksurgerybard.py --config config/pointer_markers.json
 
 Move the pointer around in front of the camera. You should be able to see that 
@@ -49,6 +51,7 @@ move either the pointer tip or the tracking system (webcam).
 
 When you have a directory of pointer matrices you can run this;
 ::
+
   python bardPivotCalibration.py --help
   python bardPivotCalibration.py --input pointer_positions/bard_pointer_matrices
 
@@ -63,13 +66,15 @@ less pointer poses.
 
 Now edit config/pointer_markers.json to include the the pointer_tag_to_tip transform, within the pointerData entry:
 ::
+
     "pointerData": {
         "pointer_tag_file": "data/pointer.txt",
         "pointer_tag_to_tip": "data/pointer_tip.txt"
     },
 
 Now run; 
 ::
+
   python sksurgerybard.py --config config/pointer_markers.json
 
 When you place the pointer in front of the camera, you should now see an additional sphere

doc/02_4_Register_And_Ovelay.rst

@@ -10,12 +10,14 @@ Create a plain text-file containing the coordinates of the prostate phantom fidu
 
 Compute the registration of CT points in CT_Fiduicial_Markers.txt to your world points, run this;
 ::
+
   python bardProcrustes.py -f world.txt -m data/PelvisPhantom/CT_Fiduicial_Markers.txt
 
 So here -f stands for "fixed" points, also called "target" points in the literature, and -m stands for "moving" points, also called "source" points in the literature.
 This will output a rotation, a translation, and Fiducial Registration Error.
 Cut and paste the rotation and translation into a CT_to_world.txt file as 
 ::
+
   R11 R12 R13 T1
   R21 R22 R23 T2
   R31 R31 R33 T3
@@ -25,6 +27,7 @@ and edit config/reference_with_model.json to use this file instead of data/id.tx
 
 Rerun BARD using this configuration file, using:
 ::
+
    python sksurgerybard.py --config config/reference_with_model.json
 
 and see what happens.

doc/conf.py

@@ -55,27 +55,6 @@
 html_static_path = [static_folder]
 
 
-def generate_apidocs(*args):
-    """Generate API docs automatically by trawling the available modules"""
-
-    global working_dir, module_path
-    output_path = working_dir
-    apidoc_command_path = 'sphinx-apidoc'
-    if hasattr(sys, 'real_prefix'):  # called from a virtualenv
-        apidoc_command_path = os.path.join(sys.prefix, 'bin', 'sphinx-apidoc')
-        apidoc_command_path = os.path.abspath(apidoc_command_path)
-    subprocess.check_call(
-        [apidoc_command_path, '--force', '--separate'] +
-        ['-o', output_path, module_path] +
-        [os.path.join(root_dir_abs, pattern) for pattern in exclude_patterns])
-
-
-def setup(app):
-    # Hook to allow for automatic generation of API docs
-    # before doc deployment begins.
-    app.connect('builder-inited', generate_apidocs)
-
-
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
@@ -115,9 +94,9 @@ def setup(app):
 # built documents.
 #
 # The short X.Y version.
-version = u''
+version = u'1.0.0'
 # The full version, including alpha/beta/rc tags.
-release = u''
+release = u'1.0.0'
 
 # The short X.Y version.
 # version = sksurgerybard.__version__
@@ -129,7 +108,7 @@ def setup(app):
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+# language = None
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'

requirements-dev.txt

@@ -10,8 +10,6 @@ mock
 pyfakefs
 parameterized
 pylint<=2.17.0
-sphinx
-sphinx_rtd_theme
 pyinstaller
 pytest
 tox

requirements-docs.txt

@@ -0,0 +1,5 @@
+-r requirements.txt
+six
+docutils
+sphinx
+sphinx_rtd_theme

requirements.txt

@@ -4,11 +4,11 @@
 # doc/requirements.rst
 numpy
 glob2
-pyside6>=6.4.2
+pyside6>=6.5.1.1
 scikit-surgerycalibration>=0.2.4
 scikit-surgerycore>=0.6.10
-scikit-surgeryutils==2.0rc0
-scikit-surgeryvtk==2.0rc0
+scikit-surgeryutils>=2.0.0
+scikit-surgeryvtk>=2.0.1
 scikit-surgeryarucotracker>=1.0.1
 opencv-contrib-python-headless>=4.2.0.32
 #scikit-surgeryspeech>=0.2.0 #uncomment this to use speech interface

setup.py

@@ -18,13 +18,13 @@
                 'based on scikit-surgery (SNAPPY)',
     long_description=long_description,
     long_description_content_type='text/x-rst',
-    url='https://github.com/SciKit-Surgery/'
-        'scikit-surgerybard',
+    url='https://github.com/SciKit-Surgery/scikit-surgerybard',
+    # Authors: Miguel Xochicale, Thomas Dowrick, Stephen Thompson, Matt Clarkson
     author='Stephen Thompson',
     author_email='[email protected]',
     license='BSD-3 license',
     classifiers=[
-        'Development Status :: 3 - Alpha',
+        'Development Status :: 5 - Production/Stable',
 
         'Intended Audience :: Developers',
         'Intended Audience :: Healthcare Industry',
@@ -36,7 +36,7 @@
 
 
         'Programming Language :: Python',
-        'Programming Language :: Python :: 3',
+        'Programming Language :: Python :: 3.8',
 
         'Topic :: Scientific/Engineering :: Information Analysis',
         'Topic :: Scientific/Engineering :: Medical Science Apps.',
@@ -55,12 +55,12 @@
     install_requires=[
         'numpy',
         'glob2',
-        'pyside6>=6.4.2',
+        'pyside6>=6.5.1.1',
         'opencv-contrib-python-headless>=4.2.0.32',
         'scikit-surgerycore>=0.6.10',
         'scikit-surgerycalibration>=0.2.4',
-        'scikit-surgeryutils==2.0rc0',
-        'scikit-surgeryvtk==2.0rc0',
+        'scikit-surgeryutils>=2.0.0',
+        'scikit-surgeryvtk>=2.0.1',
         'scikit-surgeryarucotracker>=1.0.1',
     ],
 

tox.ini

@@ -29,6 +29,7 @@ commands=pylint --rcfile=tests/pylintrc --extension-pkg-whitelist=PySide6,vtk,cv
 [testenv:docs]
 basepython=python3.8
 changedir = doc
+deps=-rrequirements-docs.txt
 commands = sphinx-build -M html . build
 
 [testenv:installer]