Merge pull request #106 from SciKit-Surgery/101-skutils

101 skutils

requirements-dev.txt

@@ -9,7 +9,7 @@ coveralls
 mock
 pyfakefs
 parameterized
-pylint<2.14
+pylint>2.13
 sphinx
 sphinx_rtd_theme
 pyinstaller

requirements.txt

@@ -5,9 +5,9 @@
 numpy
 glob2
 PySide2<5.15.0
-scikit-surgerycalibration<=0.1.11
+scikit-surgerycalibration>=0.1.9
 scikit-surgerycore>=0.6.8
-scikit-surgeryutils<1.2
+scikit-surgeryutils>=1.2.1
 scikit-surgeryvtk
 scikit-surgeryarucotracker>=0.2.5
 opencv-contrib-python-headless

setup.py

@@ -59,8 +59,8 @@
         'PySide2<5.15.0',
         'opencv-contrib-python-headless',
         'scikit-surgerycore>=0.6.8',
-        'scikit-surgerycalibration<=0.1.11',
-        'scikit-surgeryutils<1.2',
+        'scikit-surgerycalibration>=0.1.9',
+        'scikit-surgeryutils>=1.2.1',
         'scikit-surgeryvtk',
         'scikit-surgeryarucotracker>=0.2.5',
     ],

sksurgerybard/ui/sksurgerybard_command_app.py

@@ -2,7 +2,6 @@
 
 """ Demo app, to show OpenCV video and PySide2 widgets together."""
 
-import sys
 from PySide2.QtWidgets import QApplication
 from sksurgerycore.configuration.configuration_manager import \
         ConfigurationManager
@@ -22,6 +21,11 @@ def run_demo(config_file, calib_dir):
 
     viewer = BARDOverlayApp(configuration, calib_dir)
 
+    viewer.vtk_overlay_window.Initialize()
+    viewer.vtk_overlay_window.Start()
+    viewer.show()
     viewer.start()
 
-    sys.exit(app.exec_())
+    app.exec_()
+
+    viewer.vtk_overlay_window.Finalize()

sksurgerybard/widgets/bard_overlay_app.py

@@ -7,7 +7,7 @@
 import cv2
 
 from sksurgeryvtk.utils.matrix_utils import create_vtk_matrix_from_numpy
-from sksurgeryutils.common_overlay_apps import OverlayBaseApp
+from sksurgeryutils.common_overlay_apps import OverlayBaseWidget
 from sksurgeryarucotracker.arucotracker import ArUcoTracker
 from sksurgerybard.algorithms.bard_config_algorithms import \
     configure_interaction, configure_camera, replace_calibration_dir
@@ -19,7 +19,7 @@
 from sksurgerybard.algorithms.decimation import decimate_actor
 from sksurgerybard.tracking.bard_tracking import setup_tracker
 
-class BARDOverlayApp(OverlayBaseApp):
+class BARDOverlayApp(OverlayBaseWidget):
     """
     Inherits from OverlayBaseApp, and adds methods to
     detect aruco tags and move the model to follow.
@@ -57,7 +57,7 @@ def __init__(self, configuration = None, calib_dir = None):
 
         # call the constructor for the base class
         try:
-            super().__init__(video_source, dims)
+            super().__init__(video_source, dims, init_vtk_widget=False)
         except RuntimeError:
             raise RuntimeError("Failed to create overlay window, check you " +
                                "have access to video source: ", video_source) \
@@ -160,7 +160,7 @@ def position_model_actors(self, increment = None):
                     self._model_list['target anatomy']:
                 actor.SetUserMatrix(matrix)
 
-    def update(self):
+    def update_view(self):
         """
         Update the background render with a new frame
         """

tests/interaction/test_interaction.py

@@ -29,7 +29,7 @@ class StartTrackingEvent(Exception):#pylint: disable=missing-class-docstring
 
 
 class _FakePointerWriter:
-    def write_pointer_tip(self): # pylint: disable=no-self-use
+    def write_pointer_tip(self):
         """Raises an exception so we know when it's run"""
         raise WritePointerEvent
 
@@ -58,28 +58,28 @@ def GetSize(self):# pylint: disable=invalid-name
 
 
 class _FakeVisualisationControl:
-    def cycle_visible_anatomy_vis(self): # pylint: disable=no-self-use
+    def cycle_visible_anatomy_vis(self):
         """Raises an error so we know when it's run"""
         raise CycleAnatomyEvent
 
-    def next_target(self): # pylint: disable=no-self-use
+    def next_target(self):
         """Raises an error so we know when it's run"""
         raise NextTargetEvent
 
-    def turn_on_all_targets(self): # pylint: disable=no-self-use
+    def turn_on_all_targets(self):
         """Raises an error so we know when it's run"""
         raise TurnOnAllEvent
 
-    def visibility_toggle(self, _): # pylint: disable=no-self-use
+    def visibility_toggle(self, _):
         """Raises an error so we know when it's run"""
         raise VisibilityToggleEvent
 
-    def change_opacity(self, _): # pylint: disable=no-self-use
+    def change_opacity(self, _):
         """Raises an error so we know when it's run"""
         raise ChangeOpacityEvent
 
 class _FakeBardWidget:
-    def position_model_actors(self, increment): # pylint: disable=no-self-use
+    def position_model_actors(self, increment):
         """Raises and error so we know it's run"""
         raise PositionModelEvent(increment)
     class transform_manager: #pylint: disable=invalid-name

tests/interaction/test_speech_interation.py

@@ -43,23 +43,23 @@ class ChangeOpacityEvent(Exception):#pylint: disable=missing-class-docstring
     pass
 
 class _FakeVisualisationControl:
-    def cycle_visible_anatomy_vis(self): # pylint: disable=no-self-use
+    def cycle_visible_anatomy_vis(self):
         """Raises an error so we know when it's run"""
         raise CycleAnatomyEvent
 
-    def next_target(self): # pylint: disable=no-self-use
+    def next_target(self):
         """Raises an error so we know when it's run"""
         raise NextTargetEvent
 
-    def turn_on_all_targets(self): # pylint: disable=no-self-use
+    def turn_on_all_targets(self):
         """Raises an error so we know when it's run"""
         raise TurnOnAllEvent
 
-    def visibility_toggle(self, _): # pylint: disable=no-self-use
+    def visibility_toggle(self, _):
         """Raises an error so we know when it's run"""
         raise VisibilityToggleEvent
 
-    def change_opacity(self, _): # pylint: disable=no-self-use
+    def change_opacity(self, _):
         """Raises an error so we know when it's run"""
         raise ChangeOpacityEvent
 

tests/pylintrc

@@ -34,15 +34,6 @@ unsafe-load-any-extension=no
 # run arbitrary code
 extension-pkg-whitelist=numpy,aruco
 
-# Allow optimization of some AST trees. This will activate a peephole AST
-# optimizer, which will apply various small optimizations. For instance, it can
-# be used to obtain the result of joining multiple strings with the addition
-# operator. Joining a lot of strings can lead to a maximum recursion error in
-# Pylint and this flag can prevent that. It has one side effect, the resulting
-# AST will be different than the one from reality. This option is deprecated
-# and it will be removed in Pylint 2.0.
-optimize-ast=no
-
 
 [MESSAGES CONTROL]
 
@@ -56,31 +47,13 @@ confidence=
 # it should appear only once). See also the "--disable" option for examples.
 #enable=
 
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once).You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use"--disable=all --enable=classes
-# --disable=W"
-disable=long-suffix,standarderror-builtin,indexing-exception,delslice-method,unichr-builtin,dict-view-method,parameter-unpacking,unicode-builtin,cmp-builtin,intern-builtin,round-builtin,backtick,nonzero-method,xrange-builtin,coerce-method,raw_input-builtin,old-division,filter-builtin-not-iterating,old-octal-literal,input-builtin,map-builtin-not-iterating,buffer-builtin,basestring-builtin,zip-builtin-not-iterating,using-cmp-argument,unpacking-in-except,old-raise-syntax,coerce-builtin,dict-iter-method,hex-method,range-builtin-not-iterating,useless-suppression,cmp-method,print-statement,reduce-builtin,file-builtin,long-builtin,getslice-method,execfile-builtin,no-absolute-import,metaclass-assignment,oct-method,reload-builtin,import-star-module-level,suppressed-message,apply-builtin,raising-string,next-method-called,setslice-method,old-ne-operator,arguments-differ,wildcard-import,locally-disabled
-
-
 [REPORTS]
 
 # Set the output format. Available formats are text, parseable, colorized, msvs
 # (visual studio) and html. You can also give a reporter class, eg
 # mypackage.mymodule.MyReporterClass.
 output-format=text
 
-# Put messages in a separate file for each module / package specified on the
-# command line instead of printing them on stdout. Reports (if any) will be
-# written in a file name "pylint_global.[txt|html]". This option is deprecated
-# and it will be removed in Pylint 2.0.
-files-output=no
-
 # Tells whether to display a full report or only the messages
 reports=yes
 
@@ -118,64 +91,33 @@ property-classes=abc.abstractproperty
 # Regular expression matching correct variable names
 variable-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for variable names
-variable-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct class attribute names
 class-attribute-rgx=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
 
-# Naming hint for class attribute names
-class-attribute-name-hint=([A-Za-z_][A-Za-z0-9_]{2,30}|(__.*__))$
-
 # Regular expression matching correct argument names
 argument-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for argument names
-argument-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct module names
 module-rgx=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
 
-# Naming hint for module names
-module-name-hint=(([a-z_][a-z0-9_]*)|([A-Z][a-zA-Z0-9]+))$
-
 # Regular expression matching correct constant names
 const-rgx=(([A-Z_][A-Z0-9_]*)|(__.*__))$
 
-# Naming hint for constant names
-const-name-hint=(([A-Z_][A-Z0-9_]*)|(__.*__))$
-
 # Regular expression matching correct inline iteration names
 inlinevar-rgx=[A-Za-z_][A-Za-z0-9_]*$
 
-# Naming hint for inline iteration names
-inlinevar-name-hint=[A-Za-z_][A-Za-z0-9_]*$
-
 # Regular expression matching correct method names
 method-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for method names
-method-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct function names
 function-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for function names
-function-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct attribute names
 attr-rgx=[a-z_][a-z0-9_]{2,30}$
 
-# Naming hint for attribute names
-attr-name-hint=[a-z_][a-z0-9_]{2,30}$
-
 # Regular expression matching correct class names
 class-rgx=[A-Z_][a-zA-Z0-9]+$
 
-# Naming hint for class names
-class-name-hint=[A-Z_][a-zA-Z0-9]+$
-
-# Regular expression which should only match function or class names that do
 # not require a docstring.
 #no-docstring-rgx=^test_
 
@@ -202,12 +144,6 @@ ignore-long-lines=^\s*(# )?<?https?://\S+>?$
 # else.
 single-line-if-stmt=y
 
-# List of optional constructs for which whitespace checking is disabled. `dict-
-# separator` is used to allow tabulation in dicts, etc.: {1  : 1,\n222: 2}.
-# `trailing-comma` allows a space between comma and closing bracket: (a, ).
-# `empty-line` allows space-only lines.
-no-space-check=trailing-comma,dict-separator
-
 # Maximum number of lines in a module
 max-module-lines=1000
 

tests/widgets/test_bard_overlay.py

@@ -66,7 +66,7 @@ def test_valid_config():
             bard_overlay.transform_manager.get("pointerref2camera"),
             np.eye(4, dtype = np.float64))
 
-    bard_overlay.update()
+    bard_overlay.update_view()
 
     cam2model_regression = np.array([
        [-0.85007277,  0.51807849, -0.09471516, -8.06235428e+01],
@@ -100,7 +100,7 @@ def test_valid_config():
 
     #skip 5 frames
     for _ in range(5):
-        bard_overlay.update()
+        bard_overlay.update_view()
 
     cam2model_regression = np.array([
         [-8.50551488e-01,  5.17049795e-01, -9.60295592e-02, -8.10664190e+01],
@@ -131,8 +131,8 @@ def test_valid_config():
         dtype=np.float32)
 
     assert matrices_equivalent(pointer2model_regression,
-                bard_overlay.transform_manager.get("pointerref2modelreference")
-                ,tolerance = 13.0)
+                bard_overlay.transform_manager.get("pointerref2modelreference"),
+                tolerance = 13.0)
 
 
 def test_with_no_pointer():
@@ -168,7 +168,7 @@ def test_with_no_pointer():
     with pytest.raises(ValueError):
         bard_overlay.transform_manager.get("pointerref2camera")
 
-    bard_overlay.update()
+    bard_overlay.update_view()
 
     cam2model_regression = np.array([
        [-0.85007277,  0.51807849, -0.09471516, -8.06235428e+01],
@@ -206,7 +206,7 @@ def test_with_camera_only():
     with pytest.raises(ValueError):
         bard_overlay.transform_manager.get("pointerref2camera")
 
-    bard_overlay.update()
+    bard_overlay.update_view()
 
 
 def test_with_model_no_tracking():

tox.ini

@@ -11,7 +11,7 @@ python =
 [testenv]
 passenv = *
 deps=-rrequirements-dev.txt
-whitelist_externals=git
+allowlist_externals=git
 # See .coveragerc for list of omitted files
 commands = versioneer install
            git restore --staged  sksurgerybard/_version.py