Merge branch 'hotfix/1.3.1'

CMakeLists.txt

@@ -19,7 +19,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake")
 
 set(${PROJECT_NAME}_VERSION_MAJOR 1)
 set(${PROJECT_NAME}_VERSION_MINOR 3)
-set(${PROJECT_NAME}_VERSION_PATCH 0)
+set(${PROJECT_NAME}_VERSION_PATCH 1)
 set(${PROJECT_NAME}_VERSION
         ${${PROJECT_NAME}_VERSION_MAJOR}.${${PROJECT_NAME}_VERSION_MINOR}.${${PROJECT_NAME}_VERSION_PATCH})
 

doc/source/conf.py

@@ -22,7 +22,7 @@ copyright = '2021, Grégoire MALANDAIN'
 author = 'Grégoire MALANDAIN'
 
 # The full version, including alpha/beta/rc tags
-release = '1.3.0'
+release = '1.3.1'
 
 
 # -- General configuration ---------------------------------------------------

pkg/env/vt-python.yaml

@@ -15,4 +15,4 @@ dependencies:
   - numpy-base
   - pooch
   - pytest
-  - vt >=1.6.0
+  - vt >=1.6.1

setup.cfg

@@ -2,7 +2,7 @@
 
 [metadata]
 name = vtpython
-version = 1.3.0
+version = 1.3.1
 author = Gregoire Malandain
 author_email = gregoire.malandain@inria.fr
 description = Python wrappers for the vt library

tst/test_pointmatching.py

@@ -6,11 +6,13 @@ from os.path import dirname
 from os.path import join
 from pathlib import Path
 
+import numpy as np
+
 import vt
 from vt.dataset import shared_data_path
 
 
-class TestPointmatching(unittest.TestCase):
+class TestPointmatchingFromFiles(unittest.TestCase):
 
     @classmethod
     def setUpClass(cls):
@@ -50,3 +52,28 @@ class TestPointmatching(unittest.TestCase):
 
     def test_pointmatching_vectorfield(self):
         self._pointmatching(params='-trsf-type vectorfield -no-verbose')
+
+class TestPointmatchingFromArrays(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        flo_pts = [[0, 0, 0], [0, 0, 1], [0, 1, 0], [1, 0, 0]]
+        ref_pts = [[0, 0, 0], [0, 0, 2], [0, 2, 0], [2, 0, 0]]
+        cls._ref_points = vt.vtPointList(ref_pts)
+        cls._flo_points = vt.vtPointList(flo_pts)
+        cls._template_path = shared_data_path("flower_confocal_ds2x", 0)
+        cls._template = vt.vtImage(str(cls._template_path))
+
+    def _pointmatching(self, params=""):
+        out_trsf = vt.pointmatching(self._flo_points, self._ref_points,
+                                    self._template, params=params)
+        self.assertIsNotNone(out_trsf)
+
+    def test_pointmatching_rigid(self):
+        self._pointmatching(params='-trsf-type rigid -no-verbose')
+
+    def test_pointmatching_affine(self):
+        self._pointmatching(params='-trsf-type affine -no-verbose')
+
+    def test_pointmatching_vectorfield(self):
+        self._pointmatching(params='-trsf-type vectorfield -no-verbose')

tst/test_vt_pointlist.py

@@ -6,6 +6,7 @@ import unittest
 from pathlib import Path
 
 import numpy as np
+from vt.tools import random_array
 
 import vt
 
@@ -17,20 +18,18 @@ class TestVtPointList(unittest.TestCase):
         cls._points_path = os.path.abspath(os.path.join(os.path.dirname(__file__), "..", "data",
                                                         "cell_barycenters_landmarks-t0.txt"))
         cls.file_points = vt.vtPointList(cls._points_path)
-
-        cls.rand_double_points = np.ndarray(dtype='double', shape=[12, 3])
-        for i in range(cls.rand_double_points.shape[0]):
-            for j in range(cls.rand_double_points.shape[1]):
-                cls.rand_double_points[i, j] = random.random()
-
-        cls.rand_float_points = np.ndarray(dtype='float', shape=[15, 3])
-        for i in range(cls.rand_float_points.shape[0]):
-            for j in range(cls.rand_float_points.shape[1]):
-                cls.rand_float_points[i, j] = random.random()
+        # Create two random arrays
+        cls.rand_double_points = random_array(dtype='double', shape=[12, 3])
+        cls.rand_float_points = random_array(dtype='float', shape=[15, 3])
 
     def _vt_np_vt(self, pts):
         a = pts.copy_to_array()
         l = vt.vtPointList(a)
+        # Test unit default value:
+        self.assertEqual(l.unit(), "real")
+        # Test spacing default value:
+        np.testing.assert_array_equal(l.spacing(), [1., 1., 1.])
+        # Save file from `vtPointList` and compare to original:
         with tempfile.NamedTemporaryFile(delete=False) as pts_file, tempfile.NamedTemporaryFile(
                 delete=False) as array_file:
             pts.write(pts_file.name)
@@ -41,6 +40,11 @@ class TestVtPointList(unittest.TestCase):
 
     def _np_vt_np(self, a):
         pts = vt.vtPointList(a)
+        # Test unit default value:
+        self.assertEqual(pts.unit(), "real")
+        # Test spacing default value:
+        np.testing.assert_array_equal(pts.spacing(), [1., 1., 1.])
+        # Copy array of point and compare to original
         b = pts.copy_to_array()
         self.assertTrue((a == b).all())
 

wrp/python/vtPointListBridgePython.cpp

@@ -154,6 +154,9 @@ void vtPointListWrapper(py::module m) {
             // Bind the method to get the spacing from the `vtPointListBridge` object
             .def("spacing", &vtPointList::spacing)
 
+            // Bind the method to get the unit from the `vtPointListBridge` object
+            .def("unit", &vtPointList::unit)
+
             // Bind the `__repr__` method to provide a string representation of the object
             .def("__repr__", &vtPointList::toString)