Merge pull request #69 from SciKit-Surgery/68-quaternion-fix

68 quaternion fix

.github/workflows/ci.yml

@@ -9,11 +9,11 @@ jobs:
       fail-fast: false
       matrix:
         python-ver: [3.7]
-        os: [ubuntu-18.04, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-latest]
         experimental: [false]
         include:
           - python-ver: 3.8
-            os: ubuntu-18.04
+            os: ubuntu-latest
             experimental: false 
           - python-ver: 3.8
             os: macos-latest
@@ -22,7 +22,7 @@ jobs:
             os: windows-latest
             experimental: true
           - python-ver: 3.9
-            os: ubuntu-18.04
+            os: ubuntu-latest
             experimental: true
           - python-ver: 3.9
             os: macos-latest
@@ -55,16 +55,15 @@ jobs:
           coveralls
 
   deploy:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-latest
     needs: test
     steps:
       - uses: actions/checkout@v2
       - uses: actions/checkout@master
       - name: Set up Python
         uses: actions/setup-python@v1
         with:
-          # TODO: python version for deploy?
-          python-version: 3.6
+          python-version: 3.9
 
       - name: Install dependencies
         run: python -m pip install wheel twine setuptools

sksurgerycore/algorithms/tracking_smoothing.py

@@ -118,7 +118,7 @@ def __init__(self, buffer_size=1):
         """
         super().__init__(4, buffer_size)
 
-    def pop(self, rvector, is_quaternion = False):
+    def pop(self, vector, is_quaternion = False):
         """
         Adds a new vector to the buffer, removing the oldest one.
 
@@ -128,9 +128,9 @@ def pop(self, rvector, is_quaternion = False):
         """
         quaternion = None
         if is_quaternion:
-            quaternion = rvector
+            quaternion = vector
         else:
-            quaternion = _rvec_to_quaternion(rvector)
+            quaternion = _rvec_to_quaternion(vector)
         super().pop(quaternion)
 
     def getmean(self):

sksurgerycore/baseclasses/tracker.py

@@ -54,7 +54,8 @@ def get_smooth_frame(self, port_handles):
 
             tracking : list of 4x4 tracking matrices, rotation and position,
             or if use_quaternions is true, a list of tracking quaternions,
-            column 0-2 is x,y,z column 3-6 is the rotation as a quaternion.
+            column 0-3 is the rotation as a quaternion (qw, qx, qy, qz),
+            column 4-6 is the translation (x,y,z).
 
             tracking_quality : list the tracking quality, one per tool.
         """
@@ -74,9 +75,9 @@ def get_smooth_frame(self, port_handles):
                 smth_qual.append(self.qualities[my_index].getmean()[0])
 
                 if self.use_quaternions:
-                    output_matrix = np.full((7,1), np.nan)
-                    output_matrix[0:3,0] = mean_tvec
-                    output_matrix[3:7,0] = mean_quat
+                    output_matrix = np.full((1,7), np.nan)
+                    output_matrix[0,0:4] = mean_quat
+                    output_matrix[0,4:7] = mean_tvec
                     smth_tracking.append(output_matrix)
 
                 else:
@@ -155,7 +156,8 @@ def get_frame(self):
 
             tracking : list of 4x4 tracking matrices, rotation and position,
             or if use_quaternions is true, a list of tracking quaternions,
-            column 0-2 is x,y,z column 3-6 is the rotation as a quaternion.
+            column 0-3 is the rotation as a quaternion (qw, qx, qy, qz),
+            column 4-6 is the translation (x,y,z).
 
             tracking_quality : list the tracking quality, one per tool.
             """

tests/baseclasses/test_tracker.py

@@ -208,10 +208,10 @@ def test_tracker_quaternions():
     test_index = port_handles_out.index("test rb")
     assert time_stamps[test_index] == 1.3
     assert frame_numbers[test_index] == 0
-    transform = np.full((7,1), np.nan)
+    transform = np.full((1,7), np.nan)
     rotation = _rvec_to_quaternion([1.0, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [0.0, 100.0, 200.0]
+    transform[0,0:4] = rotation
+    transform[0,4:7] = [0.0, 100.0, 200.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.5
 
@@ -244,8 +244,8 @@ def test_tracker_quaternions():
     assert frame_numbers[test_index] == 1
 
     rotation = _rvec_to_quaternion([0.6, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [5.0, 75.0, 200.0]
+    transform[0,0:4] = rotation
+    transform[0,4:7] = [5.0, 75.0, 200.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.65
 
@@ -254,8 +254,8 @@ def test_tracker_quaternions():
     assert frame_numbers[test_index] == 0
 
     rotation = _rvec_to_quaternion([0.0, 0.0, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [50.0, -100.0, 70.0]
+    transform[0,0:4] = rotation
+    transform[0,4:7] = [50.0, -100.0, 70.0]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 1.0
 
@@ -284,8 +284,8 @@ def test_tracker_quaternions():
     assert time_stamps[test_index] == 1.4
     assert frame_numbers[test_index] == 2
     rotation = _rvec_to_quaternion([0.0, 0.45, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [50.0, -100.0, 70.0]
+    transform[0,4:7] = [50.0, -100.0, 70.0]
+    transform[0,0:4] = rotation
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 1.0
 
@@ -300,7 +300,7 @@ def test_tracker_quaternions():
     assert math.isclose(time_stamps[test_index],1.4)
     assert frame_numbers[test_index] == 2
     rotation = _rvec_to_quaternion([0.6, 0.00, 0.0])
-    transform[3:7,0] = rotation
-    transform[0:3,0] = [3.333333, 83.33333, 166.666667]
+    transform[0,0:4] = rotation
+    transform[0,4:7] = [3.333333, 83.33333, 166.666667]
     assert np.allclose(tracking[test_index], transform)
     assert tracking_quality[test_index] == 0.6

tests/pylintrc

@@ -34,16 +34,6 @@ unsafe-load-any-extension=no
 # run arbitrary code
 extension-pkg-whitelist=numpy
 
-# 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]
 
 # Only show warnings with the listed confidence levels. Leave empty to show
@@ -56,17 +46,6 @@ 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]
 
@@ -75,12 +54,6 @@ disable=long-suffix,standarderror-builtin,indexing-exception,delslice-method,uni
 # 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
 
@@ -118,63 +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 +145,6 @@ 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
 
@@ -404,4 +341,4 @@ analyse-fallback-blocks=no
 
 # Exceptions that will emit a warning when being caught. Defaults to
 # "Exception"
-overgeneral-exceptions=Exception
+overgeneral-exceptions=builtins.Exception