spacetx · ttung · Apr 5, 2019 · Apr 5, 2019
diff --git a/docs/source/api/image/apply_transform/index.rst b/docs/source/api/image/apply_transform/index.rst
@@ -16,5 +16,5 @@ ApplyTransform can be imported using ``starfish.image.ApplyTransform``, the subc
 Warp
 -----
 
-.. autoclass:: starfish.image._apply_transform.warp.Warp
-   :members:
+.. autoclass:: starfish.image._registration._apply_transform.warp.Warp
+   :members:
diff --git a/docs/source/api/image/learn_transform/index.rst b/docs/source/api/image/learn_transform/index.rst
@@ -16,5 +16,5 @@ LearnTransform can be imported using ``starfish.image.LearnTransform``, the subc
 Translation
 ------------
 
-.. autoclass:: starfish.image._learn_transform.translation.Translation
-   :members:
+.. autoclass:: starfish.image._registration._learn_transform.translation.Translation
+   :members:
diff --git a/starfish/image/__init__.py b/starfish/image/__init__.py
@@ -1,4 +1,4 @@
-from ._apply_transform import ApplyTransform
 from ._filter import Filter
-from ._learn_transform import LearnTransform
+from ._registration._apply_transform import ApplyTransform
+from ._registration._learn_transform import LearnTransform
 from ._segmentation import Segmentation
diff --git a/starfish/spots/test/__init__.py → starfish/image/_registration/__init__.py b/starfish/spots/test/__init__.py → starfish/image/_registration/__init__.py
diff --git a/starfish/image/_apply_transform/__init__.py → ...registration/_apply_transform/__init__.py b/starfish/image/_apply_transform/__init__.py → ...registration/_apply_transform/__init__.py
diff --git a/starfish/image/_apply_transform/_base.py → ...e/_registration/_apply_transform/_base.py b/starfish/image/_apply_transform/_base.py → ...e/_registration/_apply_transform/_base.py
@@ -1,7 +1,7 @@
 from abc import abstractmethod
 from typing import Type
 
-from starfish.image._learn_transform.transforms_list import TransformsList
+from starfish.image._registration.transforms_list import TransformsList
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline import PipelineComponent
 from starfish.pipeline.algorithmbase import AlgorithmBase

diff --git a/starfish/image/_registration/_apply_transform/test/__init__.py b/starfish/image/_registration/_apply_transform/test/__init__.py
diff --git a/starfish/image/_registration/_apply_transform/test/test_warp.py b/starfish/image/_registration/_apply_transform/test/test_warp.py
@@ -0,0 +1,44 @@
+import numpy as np
+
+from starfish import data
+from starfish.image._registration._apply_transform.warp import Warp
+from starfish.image._registration._learn_transform.translation import Translation
+from starfish.types import Axes
+
+
+expected_registered_values = np.array(
+    [[0.090654, 0.090593, 0.091554, 0.091661, 0.089967, 0.094072, 0.097398,
+      0.099046, 0.100969, 0.112108],
+     [0.09926, 0.096925, 0.096269, 0.097002, 0.095842, 0.097704, 0.09984,
+      0.101457, 0.105455, 0.106004],
+     [0.109834, 0.103609, 0.102693, 0.099931, 0.098222, 0.10074, 0.10251,
+      0.103838, 0.106874, 0.113451],
+     [0.12369, 0.112428, 0.111482, 0.10631, 0.106203, 0.104753, 0.106706,
+      0.105013, 0.10811, 0.11371],
+     [0.141802, 0.129946, 0.124285, 0.120928, 0.115908, 0.110735, 0.110735,
+      0.107454, 0.109468, 0.109255],
+     [0.147326, 0.14464, 0.141436, 0.132845, 0.124071, 0.121828, 0.118074,
+      0.112306, 0.109163, 0.109483],
+     [0.145296, 0.150362, 0.15082, 0.140337, 0.133806, 0.1299, 0.120592,
+      0.114046, 0.115496, 0.111666],
+     [0.131121, 0.145525, 0.150011, 0.146609, 0.137407, 0.129198, 0.127306,
+      0.118029, 0.116594, 0.111559],
+     [0.126482, 0.132372, 0.142596, 0.149538, 0.144701, 0.137469, 0.125353,
+      0.121996, 0.117342, 0.118273],
+     [0.122866, 0.126543, 0.133669, 0.145418, 0.150515, 0.140139, 0.129992,
+      0.124605, 0.120867, 0.121889]], dtype=np.float32)
+
+
+def test_calculate_translation_transforms_and_apply():
+    exp = data.ISS(use_test_data=True)
+    stack = exp.fov().get_image('primary')
+    reference_stack = exp.fov().get_image('dots')
+    translation = Translation(reference_stack=reference_stack, axes=Axes.ROUND)
+    # Calculate max_proj accrss
+    mp = stack.max_proj(Axes.CH, Axes.ZPLANE)
+    transform_list = translation.run(mp)
+    apply_transform = Warp()
+    warped_stack = apply_transform.run(stack=stack, transforms_list=transform_list)
+    assert np.allclose(
+        expected_registered_values,
+        warped_stack.xarray[2, 2, 0, 40:50, 40:50])
diff --git a/starfish/image/_apply_transform/warp.py → ...ge/_registration/_apply_transform/warp.py b/starfish/image/_apply_transform/warp.py → ...ge/_registration/_apply_transform/warp.py
@@ -8,8 +8,8 @@
 from tqdm import tqdm
 
 from starfish.config import StarfishConfig
-from starfish.image._apply_transform._base import ApplyTransformBase
-from starfish.image._learn_transform.transforms_list import TransformsList
+from starfish.image._registration._apply_transform._base import ApplyTransformBase
+from starfish.image._registration.transforms_list import TransformsList
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Axes
 from starfish.util import click

diff --git a/starfish/image/_learn_transform/__init__.py → ...registration/_learn_transform/__init__.py b/starfish/image/_learn_transform/__init__.py → ...registration/_learn_transform/__init__.py
diff --git a/starfish/image/_learn_transform/_base.py → ...e/_registration/_learn_transform/_base.py b/starfish/image/_learn_transform/_base.py → ...e/_registration/_learn_transform/_base.py
@@ -2,7 +2,7 @@
 from typing import Type
 
 
-from starfish.image._learn_transform.transforms_list import TransformsList
+from starfish.image._registration.transforms_list import TransformsList
 from starfish.imagestack.imagestack import ImageStack
 from starfish.pipeline.algorithmbase import AlgorithmBase
 from starfish.pipeline.pipelinecomponent import PipelineComponent

diff --git a/starfish/image/_registration/_learn_transform/test/__init__.py b/starfish/image/_registration/_learn_transform/test/__init__.py
diff --git a/starfish/image/_registration/_learn_transform/test/test_translation.py b/starfish/image/_registration/_learn_transform/test/test_translation.py
@@ -0,0 +1,35 @@
+import numpy as np
+
+from starfish import data
+from starfish.image._registration._learn_transform.translation import Translation
+from starfish.types import Axes
+
+
+ISS_SHIFTS = [[-23, 6], [-22, 2], [-22, -3], [-15, -4]]
+
+
+def test_learn_transforms_throws_error():
+    exp = data.ISS(use_test_data=True)
+    stack = exp.fov().get_image('primary')
+    reference_stack = exp.fov().get_image('dots')
+    translation = Translation(reference_stack=reference_stack, axes=Axes.ROUND)
+    try:
+        translation.run(stack)
+    except ValueError as e:
+        # Assert value error is thrown when the stack is not max projected across all other axes.
        assert e.args[0] == "Only axes: r can have a length > 1, please use the MaxProj filter."
+
+
+def test_learn_transforms_translation():
+    exp = data.ISS(use_test_data=True)
+    stack = exp.fov().get_image('primary')
+    reference_stack = exp.fov().get_image('dots')
+    translation = Translation(reference_stack=reference_stack, axes=Axes.ROUND)
+    # Calculate max_proj accrss CH/Z
+    stack = stack.max_proj(Axes.CH, Axes.ZPLANE)
+    transform_list = translation.run(stack)
+    # assert there's a transofrmation object for each round
+    assert len(transform_list.transforms) == stack.num_rounds
+    for (_, _, transform), shift in zip(transform_list.transforms, ISS_SHIFTS):
+        # assert that each TransformationObject has the correct translation shift
+        assert np.array_equal(transform.translation, shift)
diff --git a/...ish/image/_learn_transform/translation.py → ...istration/_learn_transform/translation.py b/...ish/image/_learn_transform/translation.py → ...istration/_learn_transform/translation.py
@@ -2,7 +2,7 @@
 from skimage.feature import register_translation
 from skimage.transform._geometric import SimilarityTransform
 
-from starfish.image._learn_transform.transforms_list import TransformsList
+from starfish.image._registration.transforms_list import TransformsList
 from starfish.imagestack.imagestack import ImageStack
 from starfish.types import Axes, TransformType
 from starfish.util import click

diff --git a/starfish/image/_registration/test/__init__.py b/starfish/image/_registration/test/__init__.py
diff --git a/starfish/image/_registration/test/test_transforms_list.py b/starfish/image/_registration/test/test_transforms_list.py
@@ -0,0 +1,29 @@
+import tempfile
+
+import numpy as np
+
+from starfish import data
+from starfish.image._registration._learn_transform.translation import Translation
+from starfish.image._registration.transforms_list import TransformsList
+from starfish.types import Axes, TransformType
+
+
+ISS_SHIFTS = [[-23, 6], [-22, 2], [-22, -3], [-15, -4]]
+
+
+def test_export_import_transforms_object():
+    exp = data.ISS(use_test_data=True)
+    stack = exp.fov().get_image('primary')
+    reference_stack = exp.fov().get_image('dots')
+    translation = Translation(reference_stack=reference_stack, axes=Axes.ROUND)
+    # Calculate max_proj accrss CH/Z
+    stack = stack.max_proj(Axes.CH, Axes.ZPLANE)
+    tr
945B
ansform_list = translation.run(stack)
+    _, filename = tempfile.mkstemp()
+    # save to tempfile and import
+    transform_list.to_json(filename)
+    imported = TransformsList.from_json(filename)
+    for (_, transform_type, transform), shift in zip(imported.transforms, ISS_SHIFTS):
+        # assert that each TransformationObject has the correct translation shift
+        assert transform_type == TransformType.SIMILARITY
+        assert np.array_equal(transform.translation, shift)
diff --git a/...image/_learn_transform/transforms_list.py → ...sh/image/_registration/transforms_list.py b/...image/_learn_transform/transforms_list.py → ...sh/image/_registration/transforms_list.py
diff --git a/starfish/test/image/registration/test_registration.py b/starfish/test/image/registration/test_registration.py