Merge pull request #28 from sezelt/config

Visual updates and bugfixes

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "py4D_browser"
-version = "1.2.0"
+version = "1.2.1"
 authors = [
   { name="Steven Zeltmann", email="[email protected]" },
 ]

src/py4D_browser/main_window.py

@@ -397,6 +397,18 @@ def setup_menus(self):
         detector_mode_group.addAction(detector_CoM)
         self.detector_menu.addAction(detector_CoM)
 
+        detector_CoMx = QAction("CoM &X", self)
+        detector_CoMx.setCheckable(True)
+        detector_CoMx.triggered.connect(partial(self.update_real_space_view, True))
+        detector_mode_group.addAction(detector_CoMx)
+        self.detector_menu.addAction(detector_CoMx)
+
+        detector_CoMy = QAction("CoM &Y", self)
+        detector_CoMy.setCheckable(True)
+        detector_CoMy.triggered.connect(partial(self.update_real_space_view, True))
+        detector_mode_group.addAction(detector_CoMy)
+        self.detector_menu.addAction(detector_CoMy)
+
         detector_iCoM = QAction("i&CoM", self)
         detector_iCoM.setCheckable(True)
         detector_iCoM.triggered.connect(partial(self.update_real_space_view, True))
@@ -552,12 +564,7 @@ def setup_views(self):
         self.diffraction_space_widget.setMouseTracking(True)
 
         # Create virtual detector ROI selector
-        self.virtual_detector_point = pg_point_roi(
-            self.diffraction_space_widget.getView()
-        )
-        self.virtual_detector_point.sigRegionChanged.connect(
-            partial(self.update_real_space_view, False)
-        )
+        self.update_diffraction_detector()
 
         # Scalebar
         self.diffraction_scale_bar = ScaleBar(pixel_size=1, units="px", width=10)
@@ -574,10 +581,7 @@ def setup_views(self):
         self.real_space_widget.setImage(np.zeros((512, 512)))
 
         # Add point selector connected to displayed diffraction pattern
-        self.real_space_point_selector = pg_point_roi(self.real_space_widget.getView())
-        self.real_space_point_selector.sigRegionChanged.connect(
-            partial(self.update_diffraction_space_view, False)
-        )
+        self.update_realspace_detector()
 
         # Scalebar, None by default
         self.real_space_scale_bar = ScaleBar(pixel_size=1, units="px", width=10)

src/py4D_browser/menu_actions.py

@@ -196,7 +196,7 @@ def export_datacube(self, save_format: str):
         py4DSTEM.save(filename, self.datacube, mode="o")
 
     elif save_format == "Plain HDF5":
-        with h5py.File(filename, "o") as f:
+        with h5py.File(filename, "w") as f:
             f["array"] = self.datacube.data
 
 

src/py4D_browser/update_views.py

@@ -29,6 +29,8 @@ def update_real_space_view(self, reset=False):
         "Integrating",
         "Maximum",
         "CoM",
+        "CoM X",
+        "CoM Y",
         "iCoM",
     ], detector_mode
 
@@ -50,7 +52,8 @@ def update_real_space_view(self, reset=False):
     if detector_shape == "Rectangular":
         # Get slices corresponding to ROI
         slices, transforms = self.virtual_detector_roi.getArraySlice(
-            self.datacube.data[0, 0, :, :], self.diffraction_space_widget.getImageItem()
+            self.datacube.data[0, 0, :, :].T,
+            self.diffraction_space_widget.getImageItem(),
         )
         slice_y, slice_x = slices
 
@@ -156,6 +159,10 @@ def update_real_space_view(self, reset=False):
 
             if detector_mode == "CoM":
                 vimg = CoMx + 1.0j * CoMy
+            elif detector_mode == "CoM X":
+                vimg = CoMx
+            elif detector_mode == "CoM Y":
+                vimg = CoMy
             elif detector_mode == "iCoM":
                 dpc = py4DSTEM.process.phase.DPC(verbose=False)
                 dpc.preprocess(
@@ -313,7 +320,7 @@ def update_diffraction_space_view(self, reset=False):
     elif detector_shape == "Rectangular":
         # Get slices corresponding to ROI
         slices, _ = self.real_space_rect_selector.getArraySlice(
-            np.zeros((self.datacube.Rshape)), self.real_space_widget.getImageItem()
+            np.zeros((self.datacube.Rshape)).T, self.real_space_widget.getImageItem()
         )
         slice_y, slice_x = slices
 
@@ -401,12 +408,18 @@ def update_realspace_detector(self):
     )
     assert detector_shape in ["Point", "Rectangular"], detector_shape
 
-    if self.datacube is None:
-        return
+    main_pen = {"color": "g", "width": 6}
+    handle_pen = {"color": "r", "width": 9}
+    hover_pen = {"color": "c", "width": 6}
+    hover_handle = {"color": "c", "width": 9}
 
-    x, y = self.datacube.data.shape[:2]
-    x0, y0 = x // 2, y // 2
-    xr, yr = x / 10, y / 10
+    if self.datacube is None:
+        x0, y0 = 0, 0
+        xr, yr = 4, 4
+    else:
+        x, y = self.datacube.data.shape[2:]
+        y0, x0 = x // 2, y // 2
+        xr, yr = (np.minimum(x, y) / 10,) * 2
 
     # Remove existing detector
     if hasattr(self, "real_space_point_selector"):
@@ -416,19 +429,27 @@ def update_realspace_detector(self):
         self.real_space_widget.view.scene().removeItem(self.real_space_rect_selector)
         self.real_space_rect_selector = None
 
-    # Rectangular detector
+    # Point detector
     if detector_shape == "Point":
         self.real_space_point_selector = pg_point_roi(
             self.real_space_widget.getView(),
             center=(x0 - 0.5, y0 - 0.5),
+            pen=main_pen,
+            hoverPen=hover_pen,
         )
         self.real_space_point_selector.sigRegionChanged.connect(
             partial(self.update_diffraction_space_view, False)
         )
 
+    # Rectangular detector
     elif detector_shape == "Rectangular":
         self.real_space_rect_selector = pg.RectROI(
-            [int(x0 - xr / 2), int(y0 - yr / 2)], [int(xr), int(yr)], pen=(3, 9)
+            [int(x0 - xr / 2), int(y0 - yr / 2)],
+            [int(xr), int(yr)],
+            pen=main_pen,
+            handlePen=handle_pen,
+            hoverPen=hover_pen,
+            handleHoverPen=hover_handle,
         )
         self.real_space_widget.getView().addItem(self.real_space_rect_selector)
         self.real_space_rect_selector.sigRegionChangeFinished.connect(
@@ -447,12 +468,18 @@ def update_diffraction_detector(self):
     detector_shape = self.detector_shape_group.checkedAction().text().strip("&")
     assert detector_shape in ["Point", "Rectangular", "Circle", "Annulus"]
 
-    if self.datacube is None:
-        return
+    main_pen = {"color": "g", "width": 6}
+    handle_pen = {"color": "r", "width": 9}
+    hover_pen = {"color": "c", "width": 6}
+    hover_handle = {"color": "c", "width": 9}
 
-    x, y = self.datacube.data.shape[2:]
-    x0, y0 = x // 2, y // 2
-    xr, yr = x / 10, y / 10
+    if self.datacube is None:
+        x0, y0 = 0, 0
+        xr, yr = 4, 4
+    else:
+        x, y = self.datacube.data.shape[2:]
+        y0, x0 = x // 2, y // 2
+        xr, yr = (np.minimum(x, y) / 10,) * 2
 
     # Remove existing detector
     if hasattr(self, "virtual_detector_point"):
@@ -479,6 +506,8 @@ def update_diffraction_detector(self):
         self.virtual_detector_point = pg_point_roi(
             self.diffraction_space_widget.getView(),
             center=(x0 - 0.5, y0 - 0.5),
+            pen=main_pen,
+            hoverPen=hover_pen,
         )
         self.virtual_detector_point.sigRegionChanged.connect(
             partial(self.update_real_space_view, False)
@@ -487,7 +516,12 @@ def update_diffraction_detector(self):
     # Rectangular detector
     elif detector_shape == "Rectangular":
         self.virtual_detector_roi = pg.RectROI(
-            [int(x0 - xr / 2), int(y0 - yr / 2)], [int(xr), int(yr)], pen=(3, 9)
+            [int(x0 - xr / 2), int(y0 - yr / 2)],
+            [int(xr), int(yr)],
+            pen=main_pen,
+            handlePen=handle_pen,
+            hoverPen=hover_pen,
+            handleHoverPen=hover_handle,
         )
         self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi)
         self.virtual_detector_roi.sigRegionChangeFinished.connect(
@@ -497,7 +531,12 @@ def update_diffraction_detector(self):
     # Circular detector
     elif detector_shape == "Circle":
         self.virtual_detector_roi = pg.CircleROI(
-            [int(x0 - xr / 2), int(y0 - yr / 2)], [int(xr), int(yr)], pen=(3, 9)
+            [int(x0 - xr / 2), int(y0 - yr / 2)],
+            [int(xr), int(yr)],
+            pen=main_pen,
+            handlePen=handle_pen,
+            hoverPen=hover_pen,
+            handleHoverPen=hover_handle,
         )
         self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi)
         self.virtual_detector_roi.sigRegionChangeFinished.connect(
@@ -508,15 +547,23 @@ def update_diffraction_detector(self):
     elif detector_shape == "Annulus":
         # Make outer detector
         self.virtual_detector_roi_outer = pg.CircleROI(
-            [int(x0 - xr), int(y0 - yr)], [int(2 * xr), int(2 * yr)], pen=(3, 9)
+            [int(x0 - xr), int(y0 - yr)],
+            [int(2 * xr), int(2 * yr)],
+            pen=main_pen,
+            handlePen=handle_pen,
+            hoverPen=hover_pen,
+            handleHoverPen=hover_handle,
         )
         self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi_outer)
 
         # Make inner detector
         self.virtual_detector_roi_inner = pg.CircleROI(
             [int(x0 - xr / 2), int(y0 - yr / 2)],
             [int(xr), int(yr)],
-            pen=(4, 9),
+            pen=main_pen,
+            hoverPen=hover_pen,
+            handlePen=handle_pen,
+            handleHoverPen=hover_handle,
             movable=False,
         )
         self.diffraction_space_widget.getView().addItem(self.virtual_detector_roi_inner)
@@ -623,8 +670,8 @@ def update_tooltip(self):
             if scene.getView().rect().contains(pos_in_scene):
                 pos_in_data = scene.view.mapSceneToView(pos_in_scene)
 
-                y = int(np.clip(np.floor(pos_in_data.x()), 0, data.shape[0] - 1))
-                x = int(np.clip(np.floor(pos_in_data.y()), 0, data.shape[1] - 1))
+                y = int(np.clip(np.floor(pos_in_data.x()), 0, data.shape[1] - 1))
+                x = int(np.clip(np.floor(pos_in_data.y()), 0, data.shape[0] - 1))
 
                 if np.isrealobj(data):
                     display_text = f"[{x},{y}]: {data[x,y]:.5g}"

src/py4D_browser/utils.py

@@ -66,12 +66,12 @@ def on_click(self, *args):
                     self.status_bar.showMessage("Shift+click to keep on", 5_000)
 
 
-def pg_point_roi(view_box, center=(-0.5, -0.5)):
+def pg_point_roi(view_box, center=(-0.5, -0.5), pen=(0, 9), hoverPen=None):
     """
     Point selection.  Based in pyqtgraph, and returns a pyqtgraph CircleROI object.
     This object has a sigRegionChanged.connect() signal method to connect to other functions.
     """
-    circ_roi = pg.CircleROI(center, (2, 2), movable=True, pen=(0, 9))
+    circ_roi = pg.CircleROI(center, (2, 2), movable=True, pen=pen, hoverPen=hoverPen)
     h = circ_roi.addTranslateHandle((0.5, 0.5))
     h.pen = pg.mkPen("r")
     h.update()