Merge pull request #24 from NHPatterson/fix-config-write

Fix config write

tests/test_wsireg.py

@@ -410,3 +410,38 @@ def test_wsireg_run_reg_wmerge_and_indiv(data_out_dir, disk_im_gry):
     assert Path(im_fps[2]).exists() is True
     assert Path(im_fps[3]).exists() is True
     assert merged_im.im_dims == (2, 2048, 2048)
+
+
+def test_wsireg_run_reg_wattachment(data_out_dir, disk_im_gry):
+    wsi_reg = WsiReg2D("test_proj-attach", str(data_out_dir))
+    im1 = np.random.randint(0, 255, (2048, 2048), dtype=np.uint16)
+    im2 = np.random.randint(0, 255, (2048, 2048), dtype=np.uint16)
+
+    wsi_reg.add_modality(
+        "mod1",
+        im1,
+        0.65,
+        channel_names=["test"],
+        channel_colors=["red"],
+    )
+
+    wsi_reg.add_modality(
+        "mod2",
+        im2,
+        0.65,
+        channel_names=["test"],
+        channel_colors=["red"],
+    )
+    wsi_reg.add_attachment_images("mod2", "attached", im2, image_res=0.65)
+
+    wsi_reg.add_reg_path(
+        "mod2", "mod1", reg_params=["rigid_test", "affine_test"]
+    )
+
+    wsi_reg.register_images()
+    im_fps = wsi_reg.transform_images(transform_non_reg=False)
+
+    regim = reg_image_loader(im_fps[0], 0.65)
+    attachim = reg_image_loader(im_fps[1], 0.65)
+
+    assert np.array_equal(regim.image.compute(), attachim.image.compute())

wsireg/wsireg2d.py

@@ -21,6 +21,9 @@
 from wsireg.utils.tform_utils import (
     prepare_wsireg_transform_data,
 )
+from wsireg.utils.im_utils import (
+    ARRAYLIKE_CLASSES,
+)
 
 
 class WsiReg2D(object):
@@ -566,11 +569,16 @@ def save_config(self, registered=False):
 
         [rge.pop("reg_transforms", None) for rge in reg_graph_edges]
 
+        modalities_out = deepcopy(self.modalities)
+        for mod, data in modalities_out.items():
+            if isinstance(data["image_filepath"], ARRAYLIKE_CLASSES):
+                data["image_filepath"] = "ArrayLike"
+
         config = {
             "project_name": self.project_name,
             "output_dir": str(self.output_dir),
             "cache_images": self.cache_images,
-            "modalities": self.modalities,
+            "modalities": modalities_out,
             "reg_paths": reg_paths,
             "reg_graph_edges": reg_graph_edges
             if status == "registered"