Version 1.5.1

pyproject.toml

@@ -4,9 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "py4D_browser"
-version = "1.5.0"
+version = "1.5.1"
 authors = [
-  { name="Steven Zeltmann", email="steven.zeltmann@lbl.gov" },
+  { name="Steven Zeltmann", email="steven.zeltmann@berkeley.edu" },
 ]
 description = "A 4D-STEM data browser built on py4DSTEM."
 readme = "README.md"

src/py4D_browser/main_window.py

@@ -51,7 +51,6 @@ class DataViewer(QMainWindow):
         show_keyboard_map,
         reshape_data,
         set_datacube,
-        update_scalebars,
         copy_vimg_to_clipboard,
         copy_diff_to_clipboard,
         copy_result_to_clipboard,

src/py4D_browser/menu_actions.py

@@ -39,12 +39,6 @@ def load_data_arina(self: "DataViewer"):
         self.statusBar().showMessage(f"Arina data was loaded as 3D, please reshape...")
 
     self.datacube = dataset
-    self.diffraction_scale_bar.pixel_size = self.datacube.calibration.get_Q_pixel_size()
-    self.diffraction_scale_bar.units = self.datacube.calibration.get_Q_pixel_units()
-
-    self.real_space_scale_bar.pixel_size = self.datacube.calibration.get_R_pixel_size()
-    self.real_space_scale_bar.units = self.datacube.calibration.get_R_pixel_units()
-
     self.update_diffraction_space_view(reset=True)
     self.update_real_space_view(reset=True)
 
@@ -68,6 +62,13 @@ def load_file(self: "DataViewer", filepath, mmap=False, binning=1):
             if len(parent) > 1 and "emd_group_type" in file[parent].attrs:
                 print("This appears to be an emdfile... reading natively")
                 self.datacube = py4DSTEM.DataCube.from_h5(datacubes[0].file[parent])
+                try:
+                    calibration = py4DSTEM.Calibration.from_h5(
+                        datacubes[0].file["/datacube_root/metadatabundle/calibration"]
+                    )
+                    self.datacube.calibration = calibration
+                except Exception as e:
+                    self.statusBar().showMessage(str(e))
             else:
                 self.datacube = py4DSTEM.DataCube(
                     datacubes[0] if mmap else datacubes[0][()]
@@ -101,8 +102,6 @@ def load_file(self: "DataViewer", filepath, mmap=False, binning=1):
             binfactor=binning,
         )
 
-    self.update_scalebars()
-
     self.update_diffraction_space_view(reset=True)
     self.update_real_space_view(reset=True)
 
@@ -113,44 +112,13 @@ def load_file(self: "DataViewer", filepath, mmap=False, binning=1):
 def set_datacube(self: "DataViewer", datacube, window_title):
     self.datacube = datacube
 
-    self.update_scalebars()
-
     self.update_diffraction_space_view(reset=True)
     self.update_real_space_view(reset=True)
 
     self.setWindowTitle(window_title)
     self.signal_datacube_changed.emit()
 
 
-def update_scalebars(self: "DataViewer"):
-
-    realspace_translation = {
-        "A": "Å",
-    }
-    reciprocal_translation = {
-        "A^-1": "Å⁻¹",
-    }
-
-    self.diffraction_scale_bar.pixel_size = self.datacube.calibration.get_Q_pixel_size()
-    q_units = self.datacube.calibration.get_Q_pixel_units()
-    self.diffraction_scale_bar.units = (
-        reciprocal_translation[q_units]
-        if q_units in reciprocal_translation.keys()
-        else q_units
-    )
-
-    self.real_space_scale_bar.pixel_size = self.datacube.calibration.get_R_pixel_size()
-    r_units = self.datacube.calibration.get_R_pixel_units()
-    self.real_space_scale_bar.units = (
-        realspace_translation[r_units]
-        if r_units in realspace_translation.keys()
-        else r_units
-    )
-
-    self.diffraction_scale_bar.updateBar()
-    self.real_space_scale_bar.updateBar()
-
-
 def reshape_data(self: "DataViewer"):
     new_shape = ResizeDialog.get_new_size(self.datacube.shape[:2], parent=self)
     self.datacube.data = self.datacube.data.reshape(

src/py4D_browser/update_views.py

@@ -7,6 +7,7 @@
 from PyQt5 import QtCore
 from PyQt5.QtGui import QCursor
 import os
+from py4D_browser.utils import format_unit
 
 
 from py4D_browser.utils import (
@@ -21,6 +22,7 @@
     CircleGeometry,
     AnnulusGeometry,
     PointGeometry,
+    strtobool,
 )
 
 from typing import TYPE_CHECKING
@@ -248,7 +250,12 @@ def update_real_space_view(self: "DataViewer", reset=False):
 
         # Debug mode for displaying the mask
         if "MASK_DEBUG" in os.environ:
-            self.set_diffraction_image(mask.astype(np.float32), reset=reset)
+            self.set_diffraction_image(
+                mask.astype(np.float32),
+                reset=reset,
+                pixel_size=self.datacube.calibration.get_Q_pixel_size(),
+                pixel_units=format_unit(self.datacube.calibration.get_Q_pixel_units()),
+            )
             return
 
         mask = mask.astype(np.float32)
@@ -309,12 +316,25 @@ def update_real_space_view(self: "DataViewer", reset=False):
         else:
             raise ValueError("Oopsie")
 
-    self.set_virtual_image(vimg, reset=reset)
+    self.set_virtual_image(
+        vimg,
+        reset=reset,
+        pixel_size=self.datacube.calibration.get_R_pixel_size(),
+        pixel_units=format_unit(self.datacube.calibration.get_R_pixel_units()),
+    )
 
 
-def set_virtual_image(self: "DataViewer", vimg, reset=False):
+def set_virtual_image(
+    self: "DataViewer", vimg, reset=False, pixel_size=None, pixel_units=None
+):
     self.unscaled_realspace_image = vimg
     self._render_virtual_image(reset=reset)
+    if pixel_size is not None:
+        self.real_space_scale_bar.pixel_size = pixel_size
+    if pixel_units is not None:
+        self.real_space_scale_bar.units = pixel_units
+    if pixel_size is not None or pixel_units is not None:
+        self.real_space_scale_bar.updateBar()
     self.signal_virtual_image_data_changed.emit()
 
 
@@ -404,12 +424,25 @@ def update_diffraction_space_view(self: "DataViewer", reset=False):
         case _:
             raise ValueError("Unsupported detector shape...")
 
-    self.set_diffraction_image(DP, reset=reset)
+    self.set_diffraction_image(
+        DP,
+        reset=reset,
+        pixel_size=self.datacube.calibration.get_Q_pixel_size(),
+        pixel_units=format_unit(self.datacube.calibration.get_Q_pixel_units()),
+    )
 
 
-def set_diffraction_image(self: "DataViewer", DP, reset=False):
+def set_diffraction_image(
+    self: "DataViewer", DP, reset=False, pixel_size=None, pixel_units=None
+):
     self.unscaled_diffraction_image = DP
     self._render_diffraction_image(reset=reset)
+    if pixel_size is not None:
+        self.diffraction_scale_bar.pixel_size = pixel_size
+    if pixel_units is not None:
+        self.diffraction_scale_bar.units = pixel_units
+    if pixel_size is not None or pixel_units is not None:
+        self.diffraction_scale_bar.updateBar()
     self.signal_diffraction_data_changed.emit()
 
 
@@ -487,7 +520,9 @@ def update_fft_view(self: "DataViewer", mode: Optional[str] = None):
             pixel_size=(
                 1.0 / self.datacube.calibration.get_R_pixel_size() / self.datacube.R_Ny
             ),
-            pixel_units=f"{self.datacube.calibration.get_R_pixel_units()}⁻¹",
+            pixel_units=format_unit(
+                f"{self.datacube.calibration.get_R_pixel_units()}⁻¹"
+            ),
         )
         self.fft_widget.getImageItem().setRect(0, 0, fft.shape[1], fft.shape[1])
         if mode_switch:
@@ -509,7 +544,9 @@ def update_fft_view(self: "DataViewer", mode: Optional[str] = None):
             pixel_size=(
                 1.0 / self.datacube.calibration.get_R_pixel_size() / self.datacube.R_Ny
             ),
-            pixel_units=f"{self.datacube.calibration.get_R_pixel_units()}⁻¹",
+            pixel_units=format_unit(
+                f"{self.datacube.calibration.get_R_pixel_units()}⁻¹"
+            ),
         )
         self.fft_widget.getImageItem().setRect(0, 0, fft.shape[1], fft.shape[1])
         if mode_switch:
@@ -527,7 +564,9 @@ def update_fft_view(self: "DataViewer", mode: Optional[str] = None):
             pixel_size=(
                 1.0 / self.datacube.calibration.get_Q_pixel_size() / self.datacube.Q_Ny
             ),
-            pixel_units=f"{self.datacube.calibration.get_Q_pixel_units()}⁻¹",
+            pixel_units=format_unit(
+                f"{self.datacube.calibration.get_Q_pixel_units()}⁻¹"
+            ),
         )
     else:
         raise RuntimeError(
@@ -609,11 +648,11 @@ def update_realspace_detector(self: "DataViewer"):
     hover_pen = {"color": "c", "width": 6}
     hover_handle = {"color": "c", "width": 9}
 
-    if self.datacube is None:
+    if self.unscaled_realspace_image is None:
         x0, y0 = 0, 0
         xr, yr = 4, 4
     else:
-        x, y = self.datacube.data.shape[2:]
+        x, y = self.unscaled_realspace_image.shape[:2]
         y0, x0 = x // 2, y // 2
         xr, yr = (np.minimum(x, y) / 10,) * 2
 
@@ -669,11 +708,11 @@ def update_diffraction_detector(self: "DataViewer"):
     hover_pen = {"color": "c", "width": 6}
     hover_handle = {"color": "c", "width": 9}
 
-    if self.datacube is None:
+    if self.unscaled_diffraction_image is None:
         x0, y0 = 0, 0
         xr, yr = 4, 4
     else:
-        x, y = self.datacube.data.shape[2:]
+        x, y = self.unscaled_diffraction_image.shape[:2]
         y0, x0 = x // 2, y // 2
         xr, yr = (np.minimum(x, y) / 10,) * 2
 
@@ -880,11 +919,19 @@ def update_tooltip(self: "DataViewer"):
                 x = int(np.clip(np.floor(pos_in_data.y()), 0, data.shape[0] - 1))
 
                 if np.isrealobj(data):
-                    if QtCore.Qt.ControlModifier == modifier_keys and data.dtype in (
-                        np.uint32,
-                        np.float32,
+                    if (
+                        QtCore.Qt.ControlModifier == modifier_keys
+                        and strtobool(
+                            self.settings.value("gui/concatenation_tooltip", "0")
+                        )
+                        and data.itemsize == 4
                     ):
-                        display_text = f"[{x},{y}]: {data.view(np.uint32)[x,y]:#08X}"
+                        val = data.view(np.uint32)[x, y]
+                        analog = val & 0x3FFF
+                        digital = (val & 0x3FFFC000) >> 14
+                        gain = (val & 0x80000000) >> 31
+                        reserved = (val & 0x40000000) >> 30
+                        display_text = f"[{x},{y}]: {data.view(np.uint32)[x,y]:#041_b} (R{reserved} G{gain} D{digital} A{analog})"
                     else:
                         display_text = f"[{x},{y}]: {data[x,y]:.5g}"
                 else:

src/py4D_browser/utils.py

@@ -243,16 +243,34 @@ def complex_to_Lab(
     return rgb
 
 
-def strtobool(val):
+def strtobool(val: str) -> bool:
     """Convert a string representation of truth to true (1) or false (0).
     True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
     are 'n', 'no', 'f', 'false', 'off', and '0'.  Raises ValueError if
     'val' is anything else.
     """
     val = val.lower()
     if val in ("y", "yes", "t", "true", "on", "1"):
-        return 1
+        return True
     elif val in ("n", "no", "f", "false", "off", "0"):
-        return 0
+        return False
     else:
         raise ValueError("invalid truth value %r" % (val,))
+
+
+def format_unit(raw_unit):
+    """Translate py4DSTEM ASCII unit strings to Unicode for display on scale bars.
+
+    py4DSTEM calibration objects return ASCII unit strings like 'A' and 'A^-1'.
+    This function translates them to their Unicode equivalents for nicer display.
+    """
+    if raw_unit == "A":
+        return "Å"
+    if raw_unit == "A^-1":
+        return "Å⁻¹"
+    if raw_unit == "px^-1":
+        return "px⁻¹"
+    # generic fallback: replace "^-1" with the Unicode superscript
+    if raw_unit.endswith("^-1"):
+        return raw_unit[:-3] + "⁻¹"
+    return raw_unit