From e9bd67ca7a98ed69ecd61014a4c932e3a9c8a7bc Mon Sep 17 00:00:00 2001
From: Andreas M Arnold <andreas.arnold@nih.gov>
Date: Thu, 16 Nov 2023 23:05:09 -0500
Subject: [PATCH] Add ability to load transformations from a file (#84)

Partially addresses #17.

---------

Co-authored-by: Juan Nunez-Iglesias <jni@fastmail.com>
---
 src/affinder/__init__.py             |  1 +
 src/affinder/_tests/test_affinder.py | 18 +++++++++++++++++-
 src/affinder/load_tf.py              | 20 ++++++++++++++++++++
 src/affinder/napari.yaml             |  7 ++++++-
 4 files changed, 44 insertions(+), 2 deletions(-)
 create mode 100644 src/affinder/load_tf.py

diff --git a/src/affinder/__init__.py b/src/affinder/__init__.py
index ffaba85..f14c759 100644
--- a/src/affinder/__init__.py
+++ b/src/affinder/__init__.py
@@ -5,4 +5,5 @@
 
 from .affinder import start_affinder
 from .copy_tf import copy_affine
+from .load_tf import load_affine
 from .apply_tf import apply_affine
diff --git a/src/affinder/_tests/test_affinder.py b/src/affinder/_tests/test_affinder.py
index 1258086..ef5f0c7 100644
--- a/src/affinder/_tests/test_affinder.py
+++ b/src/affinder/_tests/test_affinder.py
@@ -1,4 +1,4 @@
-from affinder import start_affinder, copy_affine, apply_affine
+from affinder import start_affinder, copy_affine, apply_affine, load_affine
 from affinder.affinder import AffineTransformChoices
 from skimage import data, transform
 import numpy as np
@@ -137,3 +137,19 @@ def test_apply_affine_nonimage():
     widget = apply_affine()
     with pytest.raises(NotImplementedError):
         widget(ref_layer, mov_layer)
+
+
+def test_load_affine(tmp_path):
+    affile = tmp_path / 'test_affine.txt'
+    affine = np.array([[2, 0, 5], [0, 2, 5], [0, 0, 1]])
+    np.savetxt(affile, affine, delimiter=',')
+
+    layer = napari.layers.Image(np.random.random((5, 5)))
+
+    widget = load_affine()
+    widget(layer, affile)
+
+    np.testing.assert_allclose(
+        layer.affine, affine
+    )
+
diff --git a/src/affinder/load_tf.py b/src/affinder/load_tf.py
new file mode 100644
index 0000000..d85c488
--- /dev/null
+++ b/src/affinder/load_tf.py
@@ -0,0 +1,20 @@
+from pathlib import Path
+
+import numpy as np
+from magicgui import magic_factory
+
+
+@magic_factory(call_button='Load', affine={'mode': 'r'})
+def load_affine(layer: 'napari.layers.Layer', affine: Path):
+    """Load affine matrix from a file.
+
+    Parameters
+    ----------
+    layer : napari.layers.Layer
+        Layer to load affine to.
+    affine : string or path
+        Path to the file containing affine matrix. Must be
+        comma-delimited txt.
+    """
+    affine = np.loadtxt(affine, delimiter=',')
+    layer.affine = affine
diff --git a/src/affinder/napari.yaml b/src/affinder/napari.yaml
index 91b50f6..16084a2 100644
--- a/src/affinder/napari.yaml
+++ b/src/affinder/napari.yaml
@@ -13,10 +13,15 @@ contributions:
   - id: affinder.apply_affine
     python_name: affinder:apply_affine
     title: Apply affine...
+  - id: affinder.load_affine
+    python_name: affinder:load_affine
+    title: Load affine...
   widgets:
   - command: affinder.start_affinder
     display_name: Start affinder
   - command: affinder.copy_affine
     display_name: Copy affine
   - command: affinder.apply_affine
-    display_name: Apply affine
\ No newline at end of file
+    display_name: Apply affine
+  - command: affinder.load_affine
+    display_name: Load affine
\ No newline at end of file