AllenInstitute · fcollman · Jun 23, 2018 · Jun 15, 2018 · Jun 15, 2018 · Jun 15, 2018
diff --git a/renderapi/transform.py b/renderapi/transform.py
@@ -11,7 +11,7 @@
 import numpy as np
 
 from .errors import ConversionError, EstimationError, RenderError
-from .utils import NullHandler
+from .utils import NullHandler, encodeBase64, decodeBase64
 
 logger = logging.getLogger(__name__)
 logger.addHandler(NullHandler())
@@ -1626,6 +1626,85 @@ def dataString(self):
             shapestring, betastring, meanstring, varstring, dimstring)
 
 
+class ThinPlateSplineTransform(Transform):
+    """
+    render-python class that can hold a dataString for
+    mpicbg.trakem2.transform.ThinPlateSplineTransform class.
+    Parameters
+    ----------
+    dataString: str or None
+        data string of transformation
+    labels : list of str
+        list of labels to give this transform
+    json: dict or None
+        json compatible dictionary representation of the transformation
+    Returns
+    -------
+    :class:`ThinPlateSplineTransform`
+        a transform instance
+    """
+
+    className = 'mpicbg.trakem2.transform.ThinPlateSplineTransform'
+
+    def __init__(self, dataString=None, json=None, transformId=None,
+                 labels=None):
+        if json is not None:
+            self.from_dict(json)
+        else:
+            if dataString is not None:
+                self._process_dataString(dataString)
+            self.labels = labels
+            self.transformId = transformId
+            self.className = (
+                'mpicbg.trakem2.transform.ThinPlateSplineTransform')
+
+    def _process_dataString(self, dataString):
+        fields = dataString.split(" ")
+
+        self.ndims = int(fields[1])
+        self.nLm = int(fields[2])
+
+        if fields[3] != "null":
+            try:
+                values = decodeBase64(fields[3])
+                self.aMtx = values[0:self.ndims*self.ndims].reshape(
+                                             self.ndims, self.ndims)
+                self.bVec = values[self.ndims*self.ndims:]
+            except ValueError:
+                raise RenderError(
+                    "inconsistent sizes and array lengths, \
+                     in ThinPlateSplineTransform dataString")
+        else:
+            self.aMtx = None
+            self.bVec = None
+
+        try:
+            values = decodeBase64(fields[4])
+            self.srcPts = values[0:self.ndims*self.nLm].reshape(
+                                           self.ndims, self.nLm)
+            self.dMtxDat = values[self.ndims*self.nLm:].reshape(
+                                           self.ndims, self.nLm)
+        except ValueError:
+            raise RenderError(
+                "inconsistent sizes and array lengths, \
+                 in ThinPlateSplineTransform dataString")
+
+    @property
+    def dataString(self):
+        header = 'ThinPlateSplineR2LogR {} {}'.format(self.ndims, self.nLm)
+
+        if self.aMtx is not None:
+            blk1 = np.concatenate((self.aMtx.flatten(), self.bVec))
+            b64_1 = encodeBase64(blk1)
+        else:
+            b64_1 = "null"
+
+        blk2 = np.concatenate((self.srcPts.flatten(), self.dMtxDat.flatten()))
+        b64_2 = encodeBase64(blk2)
+
+        return '{} {} {}'.format(header, b64_1, b64_2)
+
+
 class NonLinearTransform(NonLinearCoordinateTransform):
     className = 'mpicbg.trakem2.transform.nonLinearTransform'
 

diff --git a/renderapi/utils.py b/renderapi/utils.py
@@ -7,6 +7,8 @@
 import inspect
 import copy
 import json
+import base64
+import zlib
 
 import numpy
 import requests
@@ -358,3 +360,44 @@ def fitargspec(f, oldargs, oldkwargs):
         logger.error('Cannot fit argspec for {}'.format(f))
         logger.error(e)
         return oldargs, oldkwargs
+
+
+def encodeBase64(src):
+    """encode an array or list of doubles
+    in Base64 binary-to-text encoding
+    same as in trakem2...ThinPlateSplineTransform.java
+
+    Parameters
+    ----------
+    src : 1D numpy array
+        floating point values to be encoded
+
+    Returns
+    -------
+    encoded: string
+    """
+    return base64.b64encode(
+            zlib.compress(
+                src.byteswap().tobytes())
+                            ).decode('utf-8')
+
+
+def decodeBase64(src):
+    """decode a string
+    encoded in base64 binary-to-text encoding
+    same as in trakem2...ThinPlateSplineTransform.java
+
+    Parameters
+    ----------
+    src : string
+        encoded string
+
+    Returns
+    -------
+    arr: length n numpy array of double-precision floats
+    """
+    if src[0] == '@':
+        b = base64.b64decode(src[1:])
+    else:
+        b = zlib.decompress(base64.b64decode(src))
+    return numpy.frombuffer(b).byteswap()
diff --git a/requirements.txt b/requirements.txt
@@ -3,4 +3,4 @@ numpy
 pillow
 sphinxcontrib-napoleon
 decorator
-six
+six
diff --git a/test/rendersettings.py b/test/rendersettings.py
@@ -33,6 +33,9 @@
 
 TEST_TILESPECS_FILE = os.path.join(TEST_FILES_DIR, 'tilespecs.json')
 
+TEST_THINPLATESPLINE_FILE = os.path.join(TEST_FILES_DIR,
+                                         'thin_plate_spline.json')
+
 INTERPOLATED_TRANSFORM_TILESPEC = os.path.join(
     TEST_FILES_DIR, 'tilespec_interpolated.json')
 

diff --git a/test/test_files/thin_plate_spline.json b/test/test_files/thin_plate_spline.json
diff --git a/test/test_transform.py b/test/test_transform.py
@@ -600,3 +600,40 @@ def test_similarity_init():
     assert(isinstance(tform, renderapi.transform.SimilarityModel))
     assert(np.abs(tform.M[0, 0]-2) < EPSILON)
     assert(tform.M[0, 2] == 10)
+
+
+def test_thinplatespline():
+    j = json.load(open(rendersettings.TEST_THINPLATESPLINE_FILE, 'r'))
+    t = renderapi.transform.ThinPlateSplineTransform(
+            dataString=j['dataString'])
+    assert (j['dataString'] == t.dataString)
+    t.aMtx = np.zeros(4)
+    t.bVec = np.zeros(2)
+    t2 = renderapi.transform.ThinPlateSplineTransform(
+            dataString=t.dataString)
+    assert (t == t2)
+    # test incorrect lengths
+    with pytest.raises(renderapi.errors.RenderError):
+        s = t2.dataString.split(' ')
+        s[1] = str(int(s[1])+1)
+        t3 = renderapi.transform.ThinPlateSplineTransform(
+                dataString=" ".join(s))
+    with pytest.raises(renderapi.errors.RenderError):
+        s = t2.dataString.split(' ')
+        s[2] = str(int(s[2])-4)
+        t3 = renderapi.transform.ThinPlateSplineTransform(
+                dataString=" ".join(s))
+
+
+def test_encode64():
+    # case for Stephan's '@' character
+    s = '@QAkh+fAbhm6/8AAAAAAAAA=='
+    x = renderapi.utils.decodeBase64(s)
+    assert(x.size == 2)
+    assert(x[0] == 3.14159)
+    assert(x[1] == -1.0)
+    # all other
+    x = np.array([1.0, 3.0, 3.14159, -4.0, 10.0])
+    s = renderapi.utils.encodeBase64(x)
+    y = renderapi.utils.decodeBase64(s)
+    assert(np.all(x == y))
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,4 +3,4 @@ numpy @@
     pillow
     sphinxcontrib-napoleon
     decorator
-    six
+    six