Added support for other file formats to APPLYXFM

slider/slide_reg.py

@@ -175,7 +175,8 @@ def _load_image(p):
         timg = _load_jpg2k(p.file, p.resolution, p.resolution_level, p.dtype)
 
         # add mask
-        tirl.scripts.mnd.image.set_mask(timg, scope=globals(), **p.mask)
+        if 'mask' in p.keys():
+            tirl.scripts.mnd.image.set_mask(timg, scope=globals(), **p.mask)
 
         # Export
         tirl.scripts.mnd.inout.export(timg, p.export, default=None)
@@ -1273,8 +1274,7 @@ def apply_slide_xfm(
     fixed_reg,
     out,
     rlevel=0,
-    inverse=False,
-):
+    inverse=False):
 
     moving_reg = tirl.load(moving_reg)
     fixed_reg = tirl.load(fixed_reg)
@@ -1297,8 +1297,30 @@ def apply_slide_xfm(
 
     # load native resolution images
 
-    moving_native = _load_jpg2k(moving, moving_res, rlevel)
-    fixed_native = _load_jpg2k(fixed, fixed_res, rlevel)
+    moving_native = _load_image(AttrMap(
+        {
+            'file': moving,
+            'resolution': moving_res, 
+            'resolution_level': rlevel,
+            'dtype': 'uint8',
+            'export': False,
+            'snapshot': 'moving_native.png',
+        }
+    ))
+
+    fixed_native = _load_image(AttrMap(
+        {
+            'file': fixed,
+            'resolution': fixed_res, 
+            'resolution_level': rlevel,
+            'dtype': 'uint8',
+            'export': False,
+            'snapshot': 'fixed_native.png',
+        }
+    ))
+
+    # moving_native = _load_jpg2k(moving, moving_res, rlevel)
+    # fixed_native = _load_jpg2k(fixed, fixed_res, rlevel)
 
     # fixed pixel coordinates in native res
 
@@ -1316,9 +1338,15 @@ def apply_slide_xfm(
     )
 
     # TODO: additional ouput types (beyond jp2) should be supported
-    import glymur
 
-    glymur.Jp2k(out, data=np.round(moving_value_reshaped).astype(moving_native.dtype))
+    ext = op.splitext(out)[-1]
+
+    if ext == '.jp2':
+        import glymur
+        glymur.Jp2k(out, data=np.round(moving_value_reshaped).astype(moving_native.dtype))
+    else:
+        import skimage.io
+        skimage.io.imsave(out, np.round(moving_value_reshaped).astype(moving_native.dtype))
 
     # import imageio
     # imageio.imsave('test_moving.png', np.round(moving_value_reshaped).astype(moving_native.dtype))