py4D-browser-transform 0.1.0__tar.gz → 0.1.1__tar.gz

{py4d_browser_transform-0.1.0/src/py4D_browser_transform.egg-info → py4d_browser_transform-0.1.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py4D-browser-transform
-Version: 0.1.0
+Version: 0.1.1
 Summary: py4D-browser plugin that adds utility functions which transform the datacube
 Author-email: Chia-Hao Lee <chia-hao.lee@cornell.edu>
 Project-URL: Homepage, https://github.com/chiahao3/py4D-browser-transform

{py4d_browser_transform-0.1.0 → py4d_browser_transform-0.1.1/src/py4D_browser_transform.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py4D-browser-transform
-Version: 0.1.0
+Version: 0.1.1
 Summary: py4D-browser plugin that adds utility functions which transform the datacube
 Author-email: Chia-Hao Lee <chia-hao.lee@cornell.edu>
 Project-URL: Homepage, https://github.com/chiahao3/py4D-browser-transform

{py4d_browser_transform-0.1.0 → py4d_browser_transform-0.1.1}/src/py4d_browser_plugin/transform/__init__.py

@@ -1,2 +1,2 @@
 from .transform import TransformPlugin
-__version__ = '0.1.0' # 2026.05.23
+__version__ = '0.1.1' # 2026.07.21

{py4d_browser_transform-0.1.0 → py4d_browser_transform-0.1.1}/src/py4d_browser_plugin/transform/checkpoints.py

@@ -22,10 +22,23 @@ class DatacubeCheckpoint:
 
 def copy_datacube(datacube):
     if hasattr(datacube, "copy"):
-        return datacube.copy()
-    copied = type(datacube)(datacube.data.copy())
-    if hasattr(datacube, "calibration"):
-        copied.calibration = datacube.calibration.copy()
+        copied = datacube.copy()
+    else:
+        copied = type(datacube)(datacube.data.copy())
+        if hasattr(datacube, "calibration"):
+            copied.calibration = datacube.calibration.copy()
+
+    # py4DSTEM's DataCube.copy() rebuilds a fresh Root, and constructing a
+    # DataCube with an explicit calibration object names that root
+    # "py4DSTEM_root" instead of preserving the original's name. That
+    # silently breaks py4D-browser's calibration reload for any file whose
+    # root name it hardcodes (e.g. "datacube_root"), so keep the original
+    # root's name on the copy.
+    original_root = getattr(datacube, "root", None)
+    copied_root = getattr(copied, "root", None)
+    if original_root is not None and copied_root is not None:
+        copied_root.name = original_root.name
+
     return copied
 
 

{py4d_browser_transform-0.1.0 → py4d_browser_transform-0.1.1}/src/py4d_browser_plugin/transform/datacube_ops.py

@@ -71,20 +71,24 @@ def _update_transform_calibration(datacube, starts, spacing_factors):
         )
 
     q_factors = (spacing_factors[2], spacing_factors[3])
-    old_q_pixel_size = calibration.get_Q_pixel_size()
     if q_factors[0] == q_factors[1] and q_factors[0] != 1:
+        old_q_pixel_size = calibration.get_Q_pixel_size()
         _set_calibration_value(
             calibration, "set_Q_pixel_size", old_q_pixel_size * q_factors[0]
         )
 
+    # The origin (qx0, qy0) is stored in *pixel* coordinates of the Q axes,
+    # not physical units, so it must be re-expressed in the transformed
+    # array's own pixel grid: shift by the crop start, then rescale by
+    # however many old pixels now make up one new pixel (step * bin).
     origin = calibration.get_origin() if hasattr(calibration, "get_origin") else None
-    if origin is not None and old_q_pixel_size is not None:
+    if origin is not None:
         qx0, qy0 = origin
         if qx0 is not None and qy0 is not None:
             calibration.set_origin(
                 (
-                    qx0 - starts[2] * old_q_pixel_size,
-                    qy0 - starts[3] * old_q_pixel_size,
+                    (qx0 - starts[2]) / spacing_factors[2],
+                    (qy0 - starts[3]) / spacing_factors[3],
                 )
             )
 

{py4d_browser_transform-0.1.0 → py4d_browser_transform-0.1.1}/tests/test_transform_datacube_updates.py

@@ -319,10 +319,31 @@ def test_apply_datacube_operations_adjusts_q_origin_for_slices(monkeypatch):
         ],
     )
 
-    assert transformed.calibration.get_origin() == (9.0, 18.0)
+    assert transformed.calibration.get_origin() == (8.0, 16.0)
     assert datacube.calibration.get_origin() == (10.0, 20.0)
 
 
+def test_apply_datacube_operations_adjusts_q_origin_for_binning(monkeypatch):
+    module = _load_datacube_ops_module(monkeypatch)
+    data = np.arange(2 * 2 * 8 * 8).reshape(2, 2, 8, 8)
+    datacube = _Datacube(data.copy(), _Calibration(q_pixel_size=0.5, origin=(6.0, 8.0)))
+
+    transformed = module.apply_datacube_operations(
+        datacube,
+        [
+            {"slice": ":", "bin": 1},
+            {"slice": ":", "bin": 1},
+            {"slice": "2:", "bin": 2},
+            {"slice": "0:", "bin": 2},
+        ],
+    )
+
+    # New origin = (old_origin - crop_start) / (step * bin), in the
+    # transformed array's own pixel grid.
+    assert transformed.calibration.get_origin() == (2.0, 4.0)
+    assert datacube.calibration.get_origin() == (6.0, 8.0)
+
+
 def test_apply_datacube_operations_preserves_pixel_size_for_asymmetric_spacing(monkeypatch):
     module = _load_datacube_ops_module(monkeypatch)
     data = np.arange(4 * 4 * 6 * 6).reshape(4, 4, 6, 6)
@@ -342,6 +363,38 @@ def test_apply_datacube_operations_preserves_pixel_size_for_asymmetric_spacing(m
     assert transformed.calibration.get_Q_pixel_size() == 3
 
 
+class _Root:
+    def __init__(self, name):
+        self.name = name
+
+
+class _DatacubeWithRoot(_Datacube):
+    def __init__(self, data, calibration=None, root_name="datacube_root"):
+        super().__init__(data, calibration)
+        self.root = _Root(root_name)
+
+    def copy(self):
+        # Mimic py4DSTEM's DataCube.copy(): rebuilding via the constructor
+        # gives the new object a differently-named root.
+        copied = _DatacubeWithRoot(
+            self.data.copy(), self.calibration.copy(), root_name="py4DSTEM_root"
+        )
+        return copied
+
+
+def test_copy_datacube_preserves_original_root_name(monkeypatch):
+    _install_pyqt_stubs(monkeypatch)
+    module = importlib.import_module("py4d_browser_plugin.transform.checkpoints")
+
+    datacube = _DatacubeWithRoot(np.arange(2 * 2 * 2 * 2).reshape(2, 2, 2, 2))
+    assert datacube.root.name == "datacube_root"
+
+    copied = module.copy_datacube(datacube)
+
+    assert copied.root.name == "datacube_root"
+    assert datacube.root.name == "datacube_root"
+
+
 def test_apply_datacube_operations_invalid_input_does_not_mutate(monkeypatch):
     module = _load_datacube_ops_module(monkeypatch)
     data = np.arange(2 * 3 * 4 * 5).reshape(2, 3, 4, 5)