From c0ff9b3f67e7d63e0784edf0742403abf7e99525 Mon Sep 17 00:00:00 2001
From: Viktor van der Valk <33719474+ViktorvdValk@users.noreply.github.com>
Date: Mon, 31 May 2021 16:22:06 +0200
Subject: [PATCH] World coordinates support (#3)

* ENH: World coordinates support

* ENH: Update test for world coordinates version

* ENH: Version bump to 0.0.3
---
 checkerboard/__init__.py                |  2 +-
 checkerboard/_tests/test_dock_widget.py | 10 ++++++---
 checkerboard/checkerboard.py            | 28 +++++++++++++++----------
 requirements.txt                        |  2 ++
 4 files changed, 27 insertions(+), 15 deletions(-)

diff --git a/checkerboard/__init__.py b/checkerboard/__init__.py
index da1f85d..0d85720 100644
--- a/checkerboard/__init__.py
+++ b/checkerboard/__init__.py
@@ -3,7 +3,7 @@
 __author__ = "Viktor van der Valk"
 __email__ = "v.o.van_der_valk@lumc.nl"
 
-__version__ = "0.0.2"
+__version__ = "0.0.3"
 
 
 def get_module_version():
diff --git a/checkerboard/_tests/test_dock_widget.py b/checkerboard/_tests/test_dock_widget.py
index 2cd95f3..3e11cf4 100644
--- a/checkerboard/_tests/test_dock_widget.py
+++ b/checkerboard/_tests/test_dock_widget.py
@@ -3,6 +3,9 @@
 import itk
 import pytest
 import numpy as np
+from itk_napari_conversion import image_layer_from_image
+from itk_napari_conversion import image_from_image_layer
+import napari
 
 # this is your plugin name declared in your napari.plugins entry point
 MY_PLUGIN_NAME = "napari-checkerboard"
@@ -15,12 +18,13 @@ def image_generator(x1, x2, y1, y2, data_dir='none'):
     image = np.zeros([100, 100], np.float32)
     image[y1:y2, x1:x2] = 1
     image = itk.image_view_from_array(image)
+    image = image_layer_from_image(image)
     return image
 
 
 def checkerboard_filter(*args, **kwargs):
-    filter = checkerboard.checkerboard()
-    return filter(*args, **kwargs)
+    cb_filter = checkerboard.checkerboard()
+    return cb_filter(*args, **kwargs)
 
 
 # @pytest.mark.parametrize("widget_name", MY_WIDGET_NAMES)
@@ -41,4 +45,4 @@ def test_checkerboard():
     image1 = image_generator(25, 75, 25, 75)
     image2 = image_generator(1, 51, 10, 60)
     result_image = checkerboard_filter(image1, image2, pattern=4)
-    assert type(result_image[0]) == np.ndarray
+    assert isinstance(result_image, napari.layers.Image)
diff --git a/checkerboard/checkerboard.py b/checkerboard/checkerboard.py
index c5881fe..f372a5b 100644
--- a/checkerboard/checkerboard.py
+++ b/checkerboard/checkerboard.py
@@ -3,6 +3,9 @@
 import numpy as np
 import itk
 import checkerboard.utils as utils
+from itk_napari_conversion import image_from_image_layer
+from itk_napari_conversion import image_layer_from_image
+
 
 def on_init(widget):
     """
@@ -15,9 +18,9 @@ def on_init(widget):
                call_button="create checkerboard",
                pattern={"max": 20, "step": 1,
                         "tooltip": "Select the gridsize of the checkerboard"})
-def checkerboard(image1: "napari.types.ImageData",
-                 image2: "napari.types.ImageData",
-                 pattern: int = 3) -> 'napari.types.LayerDataTuple':
+def checkerboard(image1: "napari.layers.Image",
+                 image2: "napari.layers.Image",
+                 pattern: int = 3) -> 'napari.layers.Image':
     """
     Takes user input images and returns a checkerboard blend of the images.
     """
@@ -25,13 +28,11 @@ def checkerboard(image1: "napari.types.ImageData",
         print("No images selected for registration.")
         return error("No images selected for registration.")
 
-    image1 = np.asarray(image1).astype(np.float32)
-    image2 = np.asarray(image2).astype(np.float32)
-
-    itk_image1 = itk.GetImageFromArray(image1)
-    itk_image2 = itk.GetImageFromArray(image2)
-    input1 = itk_image1
-    input2 = itk_image2
+    # Convert image layer to itk_image
+    itk_image1 = image_from_image_layer(image1)
+    itk_image2 = image_from_image_layer(image2)
+    itk_image1 = itk_image1.astype(itk.F)
+    itk_image2 = itk_image2.astype(itk.F)
 
     region_image1 = itk_image1.GetLargestPossibleRegion()
     region_image2 = itk_image2.GetLargestPossibleRegion()
@@ -70,6 +71,9 @@ def checkerboard(image1: "napari.types.ImageData",
             resampler.SetReferenceImage(itk_image2)
             resampler.Update()
             input1 = resampler.GetOutput()
+    else:
+        input1 = itk_image1
+        input2 = itk_image2
 
     checkerboard_filter = itk.CheckerBoardImageFilter.New(input1, input2)
 
@@ -79,7 +83,9 @@ def checkerboard(image1: "napari.types.ImageData",
     checkerboard_filter.Update()
     checkerboard = checkerboard_filter.GetOutput()
 
-    return np.asarray(checkerboard).astype(np.float32), {'name': 'checkerboard'}
+    layer = image_layer_from_image(checkerboard)
+    layer.name = "checkerboard " + image1.name + " " + image2.name
+    return layer
 
 
 @napari_hook_implementation
diff --git a/requirements.txt b/requirements.txt
index 29fc18f..608f02d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -3,3 +3,5 @@ numpy>=1.19.0
 napari>=0.4.6
 magicgui>=0.2.6
 itk-elastix>=0.11.1
+itk_napari_conversion>=0.3.1
+napari-itk-io>=0.1.0