Added import/export functionality to patch stacks

model_server/base/accessors.py

@@ -292,6 +292,22 @@ class PatchStack(InMemoryDataAccessor):
     def count(self):
         return self.shape_dict['P']
 
+    def export_pyxcz(self, fpath: Path):
+        tzcyx = np.moveaxis(
+            self.pyxcz,  # yxcz
+            [0, 4, 3, 1, 2],
+            [0, 1, 2, 3, 4]
+        )
+
+        if self.is_mask():
+            if self.dtype == 'bool':
+                data = (tzcyx * 255).astype('uint8')
+            else:
+                data = tzcyx.astype('uint8')
+            tifffile.imwrite(fpath, data, imagej=True)
+        else:
+            tifffile.imwrite(fpath, tzcyx, imagej=True)
+
     @property
     def shape_dict(self):
         return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
@@ -321,16 +337,32 @@ class PatchStack(InMemoryDataAccessor):
         return dict(zip(('P', 'Y', 'X', 'C', 'Z'), self.data.shape))
 
 
-def make_patch_stack_from_file(fpath):  # interpret z-dimension as patch position
+def make_patch_stack_from_file(fpath):  # interpret t-dimension as patch position
     if not Path(fpath).exists():
         raise FileNotFoundError(f'Could not find {fpath}')
 
-    pyxc = np.moveaxis(
-        generate_file_accessor(fpath).data,  # yxcz
-        [0, 1, 2, 3],
-        [1, 2, 3, 0]
+    try:
+        tf = tifffile.TiffFile(fpath)
+    except Exception:
+        raise FileAccessorError(f'Unable to access data in {fpath}')
+
+    if len(tf.series) != 1:
+        raise DataShapeError(f'Expect only one series in {fpath}')
+
+    se = tf.series[0]
+
+    axs = [a for a in se.axes if a in [*'TZCYX']]
+    sd = dict(zip(axs, se.shape))
+    for a in [*'TZC']:
+        if a not in axs:
+            sd[a] = 1
+    tzcyx = se.asarray().reshape([sd[k] for k in [*'TZCYX']])
+
+    pyxcz = np.moveaxis(
+        tzcyx,
+        [0, 3, 4, 2, 1],
+        [0, 1, 2, 3, 4],
     )
-    pyxcz = np.expand_dims(pyxc, axis=3)
     return PatchStack(pyxcz)
 
 

tests/test_accessors.py

@@ -198,4 +198,11 @@ class TestPatchStackAccessor(unittest.TestCase):
         self.assertEqual(acc.count, n)
         self.assertEqual(acc.pczyx.shape, (n, nc, nz, h, w))
         self.assertEqual(acc.hw, (h, w))
-        return acc
\ No newline at end of file
+        return acc
+
+    def test_export_pczyx_patch_hyperstack(self):
+        acc = self.test_pczyx()
+        fp = output_path / 'patch_hyperstack.tif'
+        acc.export_pyxcz(fp)
+        acc2 = make_patch_stack_from_file(fp)
+        self.assertEqual(acc.shape, acc2.shape)
\ No newline at end of file