Merge pull request #146 from fcollman/scale_thinplate

Scale thinplate

renderapi/transform/leaf/thin_plate_spline.py

@@ -394,10 +394,8 @@ def adaptive_mesh_estimate(
 
         mn = self.srcPts.min(axis=1)
         mx = self.srcPts.max(axis=1)
-        xt, yt = np.meshgrid(
-                np.linspace(mn[0], mx[0], starting_grid),
-                np.linspace(mn[1], mx[1], starting_grid))
-        new_src = np.vstack((xt.flatten(), yt.flatten())).transpose()
+        new_src = self.src_array(
+                mn[0], mn[1], mx[0], mx[1], starting_grid, starting_grid)
         old_src = self.srcPts.transpose()
         old_dst = self.tform(old_src)
 
@@ -411,3 +409,82 @@ def adaptive_mesh_estimate(
                 max_iter=max_iter,
                 nworst=nworst,
                 niter=0)
+
+    @staticmethod
+    def src_array(xmin, ymin, xmax, ymax, nx, ny):
+        """create N x 2 array of regularly spaced points
+
+        Parameters
+        ----------
+        xmin : float
+            minimum of x grid
+        ymin : float
+            minimum of y grid
+        xmax : float
+            maximum of x grid
+        ymax : float
+            maximum of y grid
+        nx : int
+            number of points in x axis
+        ny : int
+            number of points in y axis
+
+        Returns
+        -------
+        src : :class:`numpy.ndarray`
+            (nx * ny) x 2 array of coordinated.
+
+        """
+        src = np.mgrid[xmin:xmax:nx*1j, ymin:ymax:ny*1j].reshape(2, -1).T
+        return src
+
+    def scale_coordinates(
+            self,
+            factor,
+            ngrid=20,
+            preserve_srcPts=False):
+        """estimates a new ThinPlateSplineTransform from the current one
+           in a scaled transform space.
+
+        Parameters
+        ----------
+        factor : float
+            the factor by which to scale the space
+        ngrid : int
+            number of points per axis for the estimation grid
+        preserve_srcPts : bool
+            one might want to keep the original scaled srcPts
+            for example, if pts were made specially for a mask
+            or a crack or fold
+
+        Returns
+        -------
+        new_tform : :class:`renderapi.transform.ThinPlateSplineTransform`
+            the new transform in the scaled space
+
+        """
+
+        new_tform = ThinPlateSplineTransform()
+        computeAffine = True
+        if self.aMtx is None:
+            computeAffine = False
+
+        mn = self.srcPts.min(axis=1)
+        mx = self.srcPts.max(axis=1)
+        src = self.src_array(mn[0], mn[1], mx[0], mx[1], ngrid, ngrid)
+
+        if preserve_srcPts:
+            # do not repeat close points
+            dist = scipy.spatial.distance.cdist(
+                    src,
+                    self.srcPts.transpose(),
+                    metric='euclidean')
+            ind = np.invert(np.any(dist < 1e-3, axis=0))
+            src = np.vstack((src, self.srcPts.transpose()[ind]))
+
+        new_tform.estimate(
+                src * factor,
+                self.tform(src) * factor,
+                computeAffine=computeAffine)
+
+        return new_tform

test/rendersettings.py

@@ -36,6 +36,9 @@
 TEST_THINPLATESPLINE_FILE = os.path.join(
         TEST_FILES_DIR,
         'thin_plate_spline.json')
+TEST_THINPLATEROUGH_FILE = os.path.join(
+        TEST_FILES_DIR,
+        'thin_plate_from_rough.json')
 TEST_THINPLATESPLINEAFFINE_FILE = os.path.join(
         TEST_FILES_DIR,
         'thin_plate_spline_affine.json')

test/test_files/thin_plate_from_rough.json

@@ -0,0 +1 @@
+{"type": "leaf", "className": "mpicbg.trakem2.transform.ThinPlateSplineTransform", "dataString": "ThinPlateSplineR2LogR 2 25 eJwBMADP/78yLRWQifN2vw/ErHm04Cs/IqdJx765j78ab8sN7GLJwCCjMIEXaI2/9qEQnRU3FUt4FyU= 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"}

test/test_transform.py

@@ -5,6 +5,8 @@
 import rendersettings
 import importlib
 import pytest
+from scipy.spatial.distance import cdist
+
 
 EPSILON = 0.0000000001
 EPSILON2 = 0.000000001
@@ -1037,3 +1039,47 @@ def test_polynomial_shear():
         assert atf.shear == ptf.shear
         assert atf.rotation == ptf.rotation
         assert atf.translation == ptf.translation
+
+
+@pytest.mark.parametrize('ngrid', [5, 20])
+@pytest.mark.parametrize('preserve_srcPts', [True, False])
+@pytest.mark.parametrize('computeAffine', [True, False])
+@pytest.mark.parametrize('factor', [1e-3, 1e3, 1e5])
+def test_scale_thinplate(factor, computeAffine, preserve_srcPts, ngrid):
+    # use case is to scale a rough alignment thinplate spline
+    with open(rendersettings.TEST_THINPLATEROUGH_FILE, 'r') as f:
+        tform = renderapi.transform.load_transform_json(
+                json.load(f))
+
+    if not computeAffine:
+        tform.aMtx = None
+        tform.bVec = None
+
+    mn = tform.srcPts.min(axis=0)
+    mx = tform.srcPts.max(axis=0)
+
+    npts = 1000
+    src = np.random.rand(npts, 2)
+    src[:, 0] = src[:, 0] * (mx[0] - mn[0]) + mn[0]
+    src[:, 1] = src[:, 1] * (mx[1] - mn[1]) + mn[1]
+    dst = tform.tform(src)
+
+    scaled_tform = tform.scale_coordinates(
+            factor, ngrid=ngrid, preserve_srcPts=preserve_srcPts)
+    dst_scaled = scaled_tform.tform(src * factor)
+
+    delta = np.linalg.norm(dst_scaled - dst * factor, axis=1)
+    scale = dst_scaled.ptp(axis=0).mean()
+    tol = 1e-4
+    if ngrid == 5:
+        tol = 1e-3
+    assert (delta.max() / scale) < tol
+
+    if preserve_srcPts:
+        dist = cdist(
+                tform.srcPts.transpose() * factor,
+                scaled_tform.srcPts.transpose(),
+                metric='euclidean')
+        # check that the original srcPts have a close neighbor still
+        # in the scaled srcPts
+        assert np.all(np.any(dist < 1e-3, axis=1))

test_requirements.txt

@@ -1,7 +1,7 @@
 coverage>=4.1
 mock>=2.0.0
 pep8>=1.7.0
-pytest>=3.0.5
+pytest>4.6,<5.0
 pytest-cov>=2.2.1
 pytest-pep8>=1.0.6
 pytest-xdist>=1.14