clEsperanto · haesleinhuepf · Jan 10, 2021 · Jan 10, 2021 · Jan 10, 2021 · Jan 10, 2021
diff --git a/README.md b/README.md
@@ -113,6 +113,14 @@ imsave("result.tif", cle.pull(labeled))
 
 </td></tr><tr><td>
 
+<img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_affine_transforms.png" width="300"/>
+
+</td><td>
+
+[Rotation, scaling, translation, affine transforms](https://github.com/clEsperanto/pyclesperanto_prototype/tree/master/demo/transforms/affine_transforms.ipynb)
+
+</td></tr><tr><td>
+
 <img src="https://github.com/clEsperanto/pyclesperanto_prototype/raw/master/docs/images/screenshot_multiply_vectors_and_matrices.png" width="300"/>
 
 </td><td>

diff --git a/demo/basics/browse_operations.ipynb b/demo/basics/browse_operations.ipynb
@@ -468,7 +468,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

diff --git a/demo/basics/count_blobs.ipynb b/demo/basics/count_blobs.ipynb
diff --git a/demo/basics/crop_and_paste_images.ipynb b/demo/basics/crop_and_paste_images.ipynb
diff --git a/demo/basics/multiply_matrices.ipynb b/demo/basics/multiply_matrices.ipynb
diff --git a/demo/basics/multiply_vectors_and_matrices.ipynb b/demo/basics/multiply_vectors_and_matrices.ipynb
@@ -47,8 +47,8 @@
     "voxel_size = np.asarray([[0.2], [0.2], [0.5]])\n",
     "print(\"Array shape:\" + str(voxel_size.shape))\n",
     "\n",
-    "gpu_voxel_size = cle.push_zyx(voxel_size)\n",
-    "print(\"GPU array shape:\" + str(voxel_size.shape))\n"
+    "gpu_voxel_size = cle.push(voxel_size)\n",
+    "print(\"GPU array shape:\" + str(voxel_size.shape))"
    ]
   },
   {
@@ -75,7 +75,7 @@
     ")\n",
     "print(\"Array shape:\" + str(pointlist.shape))\n",
     "\n",
-    "gpu_pointlist = cle.push_zyx(pointlist)\n",
+    "gpu_pointlist = cle.push(pointlist)\n",
     "print(\"GPU array shape:\" + str(gpu_pointlist.shape))"
    ]
   },
@@ -137,14 +137,6 @@
       " [0.  1.2 0.2 0.4]\n",
       " [4.5 5.5 3.  1. ]]\n"
      ]
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "c:\\users\\rober\\miniconda3\\lib\\site-packages\\pyopencl\\__init__.py:252: CompilerWarning: Non-empty compiler output encountered. Set the environment variable PYOPENCL_COMPILER_OUTPUT=1 to see more.\n",
-      "  warn(\"Non-empty compiler output encountered. Set the \"\n"
-     ]
     }
    ],
    "source": [
@@ -205,7 +197,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

diff --git a/demo/basics/spots_pointlists_matrices_tables.ipynb b/demo/basics/spots_pointlists_matrices_tables.ipynb
diff --git a/demo/basics/voronoi_diagrams.ipynb b/demo/basics/voronoi_diagrams.ipynb
diff --git a/demo/napari_gui/napari_.py b/demo/napari_gui/napari_.py
@@ -11,7 +11,7 @@
     viewer.add_image(image, name='blobs')
 
     # push image to GPU
-    input = cle.push_zyx(image)
+    input = cle.push(image)
 
     # process the image
     sigma = 1
@@ -20,7 +20,7 @@
     labels = cle.connected_components_labeling_box(binary)
 
     # pull result back
-    output = cle.pull_zyx(labels)
+    output = cle.pull(labels)
 
     # add it to napari
     viewer.add_labels(output)

diff --git a/demo/napari_gui/napari_magicgui.py b/demo/napari_gui/napari_magicgui.py
@@ -9,15 +9,15 @@
 def process_image(input: Image, sigma: float = 5) -> Labels:
     if input:
         # push image to GPU
-        input = cle.push_zyx(input.data)
+        input = cle.push(input.data)
 
         # process the image
         blurred = cle.gaussian_blur(input, sigma_x=sigma, sigma_y=sigma)
         binary = cle.threshold_otsu(blurred)
         labels = cle.connected_components_labeling_box(binary)
 
         # pull result back
-        output = cle.pull_zyx(labels)
+        output = cle.pull(labels)
         return output
 
 # load data

diff --git a/demo/neighbors/mesh_between_centroids.ipynb b/demo/neighbors/mesh_between_centroids.ipynb
diff --git a/demo/neighbors/mesh_between_touching_neighbors.ipynb b/demo/neighbors/mesh_between_touching_neighbors.ipynb
diff --git a/demo/neighbors/mesh_nearest_neighbors.ipynb b/demo/neighbors/mesh_nearest_neighbors.ipynb
diff --git a/demo/neighbors/mesh_with_distances.ipynb b/demo/neighbors/mesh_with_distances.ipynb
diff --git a/demo/neighbors/neighborhood_definitions.ipynb b/demo/neighbors/neighborhood_definitions.ipynb
diff --git a/demo/neighbors/quantitative_neighbor_maps.ipynb b/demo/neighbors/quantitative_neighbor_maps.ipynb
diff --git a/demo/neighbors/shape_descriptors_based_on_neighborhood_graphs.ipynb b/demo/neighbors/shape_descriptors_based_on_neighborhood_graphs.ipynb
@@ -303,7 +303,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.6"
   }
  },
  "nbformat": 4,

diff --git a/demo/tissues/parametric_maps.ipynb b/demo/tissues/parametric_maps.ipynb
diff --git a/demo/tissues/tissue_neighborhood_quantification.ipynb b/demo/tissues/tissue_neighborhood_quantification.ipynb
diff --git a/demo/transforms/affine_transforms.ipynb b/demo/transforms/affine_transforms.ipynb
diff --git a/demo/tribolium_morphometry/tribolium.py b/demo/tribolium_morphometry/tribolium.py
@@ -36,7 +36,7 @@
 def workflow(input: Image, sigma=3, threshold : float = 30) -> Labels:
     if input:
         # push image to GPU memory and show it
-        gpu_input = cle.push_zyx(input.data)
+        gpu_input = cle.push(input.data)
 
         # Spot detection
         # After some noise removal/smoothing, we perform a local maximum detection
@@ -86,7 +86,7 @@ def workflow(input: Image, sigma=3, threshold : float = 30) -> Labels:
 
         gpu_labels = cle.mask(flip, flap)
 
-        output = cle.pull_zyx(gpu_labels)
+        output = cle.pull(gpu_labels)
         return output
 
 # Start up napari

diff --git a/demo/tribolium_morphometry/tribolium_morphometry.ipynb b/demo/tribolium_morphometry/tribolium_morphometry.ipynb
diff --git a/docs/images/screenshot_affine_transforms.png b/docs/images/screenshot_affine_transforms.png
diff --git a/docs/release_notes.md b/docs/release_notes.md
@@ -39,6 +39,11 @@ results of the GPU-accelerated statistics are dictionaries which contain the sam
 * `mode_of_proximal_neighbors_map` and alias `mode_of_distal_neighbors_map`
 * `standard_deviation_of_n_nearest_neighbors_map`
 * `standard_deviation_of_proximal_neighbors_map` and alias `standard_deviation_of_distal_neighbors_map`
+* `affine_transform` (yet without shearing)
+* `translate`
+* `rotate`
+* `scale`
+* `rigid_transform`
 
 ### Backwards compatibility breaking changes
 * `statistics_of_labelled_pixels` and `statistics_of_background_and_labelled_pixels` produce different output now. 
@@ -49,6 +54,9 @@ dictionaries,e.g. `stats['area']` instead of `[s.area for s in stats]`. If not p
 * `n_closest_points` ignores the background position and the distance to labels themselves per default now. 
   Consider passing `ignore_background=False` and `ignore_self=False` to go back to former functionality.
 
+### Deprecation warnings
+* `resample` has been deprecated. Use `scale` instead.
+
 ### Bug fixes
 * `imshow` in 3D caused an error
 * `push_regionprops_column` didn't actually push

diff --git a/pyclesperanto_prototype/__init__.py b/pyclesperanto_prototype/__init__.py
@@ -4,6 +4,7 @@
 from ._tier3 import *
 from ._tier4 import *
 from ._tier5 import *
+from ._tier8 import *
 from ._tier9 import *
 
 __version__ = "0.6.0"
diff --git a/pyclesperanto_prototype/_tier0/__init__.py b/pyclesperanto_prototype/_tier0/__init__.py
@@ -16,15 +16,16 @@
     create_2d_yx,
     create_2d_zx,
     create_2d_zy,
+    create_2d_yz,
     create_none,
 )
 from ._execute import execute
 from ._operations import operation
 from ._operations import operations
-from ._pull import pull
 from ._pull import pull_zyx
-from ._push import push
+from ._pull import pull
 from ._push import push_zyx
+from ._push import push
 from ._plugin_function import plugin_function
 from ._types import Image
 from ._cl_info import cl_info

diff --git a/pyclesperanto_prototype/_tier0/_create.py b/pyclesperanto_prototype/_tier0/_create.py
@@ -54,7 +54,7 @@ def create_from_pointlist(pointlist: OCLArray, *args):
     from .._tier1 import maximum_x_projection
     from .._tier0 import pull
 
-    max_pos = pull(maximum_x_projection(pointlist)).astype(int)
+    max_pos = pull(maximum_x_projection(pointlist)).T.astype(int)
     max_pos = max_pos[0]
 
     if len(max_pos) == 3:  # 3D image requested
@@ -89,17 +89,42 @@ def create_square_matrix_from_two_labelmaps(labelmap1: OCLArray, labelmap2: OCLA
 def create_vector_from_square_matrix(square_matrix : OCLArray, *args):
     return create([1, square_matrix.shape[0]])
 
+
 def create_2d_xy(input):
-    return create([input.shape[2], input.shape[1]])
+    if len(input.shape) == 3:
+        return create([input.shape[2], input.shape[1]])
+    else:
+        return create([input.shape[1], input.shape[0]])
 
 def create_2d_yx(input):
-    return create([input.shape[1], input.shape[2]])
+    if len(input.shape) == 3:
+        return create([input.shape[1], input.shape[2]])
+    else:
+        return create([input.shape[0], 1])
 
 def create_2d_zy(input):
-    return create([input.shape[0], input.shape[1]])
+    if len(input.shape) == 3:
+        return create([input.shape[0], input.shape[1]])
+    else:
+        return create([1, input.shape[0]])
+
+def create_2d_yz(input):
+    if len(input.shape) == 3:
+        return create([input.shape[1], input.shape[0]])
+    else:
+        return create([input.shape[0], 1])
 
 def create_2d_zx(input):
-    return create([input.shape[0], input.shape[2]])
+    if len(input.shape) == 3:
+        return create([input.shape[0], input.shape[2]])
+    else:
+        return create([1, input.shape[1]])
+
+def create_2d_xz(input):
+    if len(input.shape) == 3:
+        return create([input.shape[2], input.shape[0]])
+    else:
+        return create([input.shape[1], 1])
 
 def create_none(*args):
     return None
diff --git a/pyclesperanto_prototype/_tier0/_pull.py b/pyclesperanto_prototype/_tier0/_pull.py
@@ -22,14 +22,12 @@ def pull(oclarray):
     ----------
     .. [1] https://clij.github.io/clij2-docs/reference_pull
     """
-    import warnings
-    warnings.warn(
-            "Deprecated: The behaviour of `pull()` will change in a future release. Switch to using push_zyx now to prvent issues in the future.",
-            DeprecationWarning
-        )
-
-    return oclarray.get().T
-
+    return oclarray.get()
 
 def pull_zyx(oclarray):
+    import warnings
+    warnings.warn(
+        "Deprecated: `pull_zyx()` is now deprecated as it does the same as `pull()`.",
+        DeprecationWarning
+    )
     return oclarray.get()
diff --git a/pyclesperanto_prototype/_tier0/_push.py b/pyclesperanto_prototype/_tier0/_push.py
@@ -26,20 +26,20 @@ def push(any_array):
     ----------
     .. [1] https://clij.github.io/clij2-docs/reference_push
     """
-    import warnings
-    warnings.warn(
-            "Deprecated: The behaviour of `push()` will change in a future release. Switch to using push_zyx now to prevent issues in the future.",
-            DeprecationWarning
-        )
-
     if isinstance(any_array, OCLArray):
         return any_array
 
-    transposed = any_array.astype(np.float32).T
+    transposed = any_array.astype(np.float32)
     return OCLArray.from_array(transposed)
 
 
 def push_zyx(any_array):
+    import warnings
+    warnings.warn(
+        "Deprecated: `push_zyx()` is now deprecated as it does the same as `push()`.",
+        DeprecationWarning
+    )
+
     if isinstance(any_array, OCLArray):
         return any_array
 

diff --git a/pyclesperanto_prototype/_tier1/_downsample_slice_by_slice_half_median.py b/pyclesperanto_prototype/_tier1/_downsample_slice_by_slice_half_median.py
@@ -1,6 +1,5 @@
 from .._tier1 import copy
 from .._tier0 import empty_image_like
-from .._tier0 import push_zyx
 from .._tier0 import push
 from .._tier0 import execute
 from .._tier0 import plugin_function

diff --git a/pyclesperanto_prototype/_tier1/_maximum_x_projection.py b/pyclesperanto_prototype/_tier1/_maximum_x_projection.py
@@ -1,9 +1,9 @@
 from .._tier0 import execute
 from .._tier0 import plugin_function
 from .._tier0 import Image
-from .._tier0 import create_2d_zy
+from .._tier0 import create_2d_yz
 
-@plugin_function(output_creator=create_2d_zy, categories=['projection'])
+@plugin_function(output_creator=create_2d_yz, categories=['projection'])
 def maximum_x_projection(source : Image, destination_max : Image = None):
     """Determines the maximum intensity projection of an image along X. 
 

diff --git a/pyclesperanto_prototype/_tier1/_resample.py b/pyclesperanto_prototype/_tier1/_resample.py
@@ -1,6 +1,5 @@
 from .._tier1 import copy
 from .._tier0 import empty_image_like
-from .._tier0 import push_zyx
 from .._tier0 import push
 from .._tier0 import execute
 from .._tier0 import plugin_function
@@ -30,6 +29,12 @@ def resample(source : Image, destination : Image = None, factor_x : float = 1, f
     ----------
     .. [1] https://clij.github.io/clij2-docs/reference_resample
     """
+    import warnings
+    warnings.warn(
+        "Deprecated: pyclesperanto_prototype.resample() is deprecated. Use scale() instead",
+        DeprecationWarning
+    )
+
     import numpy as np
 
     source_dimensions = source.shape
@@ -52,7 +57,7 @@ def resample(source : Image, destination : Image = None, factor_x : float = 1, f
     if destination is None:
         destination = create(destination_dimensions)
 
-    gpu_transform_matrix = push_zyx(transform_matrix)
+    gpu_transform_matrix = push(transform_matrix)
 
     kernel_suffix = ''
     if linear_interpolation:

diff --git a/pyclesperanto_prototype/_tier1/_write_values_to_positions.py b/pyclesperanto_prototype/_tier1/_write_values_to_positions.py
@@ -28,7 +28,7 @@ def write_values_to_positions(positions_and_values : Image, destination : Image
     """
 
     if destination is None:
-        max_pos = pull(maximum_x_projection(positions_and_values)).astype(int)
+        max_pos = pull(maximum_x_projection(positions_and_values)).T.astype(int)
         max_pos = max_pos[0]
 
         if len(max_pos) == 4: # 3D image requested

diff --git a/pyclesperanto_prototype/_tier3/_exclude_labels.py b/pyclesperanto_prototype/_tier3/_exclude_labels.py
@@ -1,7 +1,6 @@
 from pyclesperanto_prototype._tier0 import plugin_function
 from pyclesperanto_prototype._tier0 import Image
 from .._tier0 import push
-from .._tier0 import push_zyx
 from .._tier0 import pull
 from .._tier0 import create_none
 from .._tier0 import create_like
@@ -41,15 +40,15 @@ def exclude_labels(binary_flaglist : Image, label_map_input : Image, label_map_d
 
     flaglist_np = pull(binary_flaglist)
 
-    flaglist_np[0] = 0
+    flaglist_np[0][0] = 0
 
     count = 1
     for i in range(1, num_labels):
-        if (flaglist_np[i] == 0):
-            flaglist_np[i] = count
+        if (flaglist_np[0][i] == 0):
+            flaglist_np[0][i] = count
             count = count + 1
         else:
-            flaglist_np[i] = 0
+            flaglist_np[0][i] = 0
 
     label_index_map = push(flaglist_np)
 

diff --git a/pyclesperanto_prototype/_tier3/_exclude_labels_outside_size_range.py b/pyclesperanto_prototype/_tier3/_exclude_labels_outside_size_range.py
@@ -1,13 +1,8 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 from .. import smaller_constant, greater_constant, binary_or
-from .._tier0 import push
-from .._tier0 import push_zyx
-from .._tier0 import pull
 from .._tier0 import create_none
 from .._tier0 import create_like
-from .._tier1 import replace_intensities
-import numpy as np
 
 @plugin_function(output_creator=create_none, categories=['label processing', 'in assistant'])
 def exclude_labels_outside_size_range(input : Image, destination : Image = None, minimum_size : float = 0, maximum_size : float = 100):

diff --git a/pyclesperanto_prototype/_tier3/_exclude_labels_with_values_out_of_range.py b/pyclesperanto_prototype/_tier3/_exclude_labels_with_values_out_of_range.py
@@ -1,13 +1,8 @@
 from .._tier0 import plugin_function
 from .._tier0 import Image
 from .. import smaller_constant, greater_constant, binary_or
-from .._tier0 import push
-from .._tier0 import push_zyx
-from .._tier0 import pull
 from .._tier0 import create_none
 from .._tier0 import create_like
-from .._tier1 import replace_intensities
-import numpy as np
 
 @plugin_function(output_creator=create_none, categories=['label processing'])
 def exclude_labels_with_values_out_of_range(values_vector : Image, label_map_input : Image, label_map_destination : Image = None, minimum_value_range : float = 0, maximum_value_range : float = 100):