From 608c584b1177802527df63ac69abdd43df7191e3 Mon Sep 17 00:00:00 2001
From: Heath Patterson <nheathpatterson@gmail.com>
Date: Fri, 17 Sep 2021 14:15:35 -0500
Subject: [PATCH 1/3] check if graph contains array like data before writing.

---
 wsireg/wsireg2d.py | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/wsireg/wsireg2d.py b/wsireg/wsireg2d.py
index 0b4a23c..37b72c7 100644
--- a/wsireg/wsireg2d.py
+++ b/wsireg/wsireg2d.py
@@ -21,7 +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 +568,16 @@ 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"

From f004dde4e23067e07752534778f1dc7e59934fa8 Mon Sep 17 00:00:00 2001
From: Heath Patterson <nheathpatterson@gmail.com>
Date: Fri, 17 Sep 2021 14:15:45 -0500
Subject: [PATCH 2/3] add attachment modality test

---
 tests/test_wsireg.py | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/tests/test_wsireg.py b/tests/test_wsireg.py
index 15d312c..af4fdfc 100644
--- a/tests/test_wsireg.py
+++ b/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())

From deec37eaded5342bb0be3f829e6a4c036c6d7421 Mon Sep 17 00:00:00 2001
From: Heath Patterson <nheathpatterson@gmail.com>
Date: Fri, 17 Sep 2021 14:16:14 -0500
Subject: [PATCH 3/3] formatting

---
 wsireg/wsireg2d.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/wsireg/wsireg2d.py b/wsireg/wsireg2d.py
index 37b72c7..0bdb0ce 100644
--- a/wsireg/wsireg2d.py
+++ b/wsireg/wsireg2d.py
@@ -25,6 +25,7 @@
     ARRAYLIKE_CLASSES,
 )
 
+
 class WsiReg2D(object):
     """
     Class to define a 2D registration graph and execute the registrations and transformations of the graph
@@ -569,7 +570,7 @@ 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():
+        for mod, data in modalities_out.items():
             if isinstance(data["image_filepath"], ARRAYLIKE_CLASSES):
                 data["image_filepath"] = "ArrayLike"