Merge pull request #349 from hakonanes/fix-346

Fix scaling of region of interest coordinates in virtual backscatter electron imaging generator

MANIFEST.in

@@ -1,13 +1,13 @@
+include kikuchipy/hyperspy_extension.yaml
 include LICENSE
 include MANIFEST.in
 include pyproject.toml
 include setup.cfg
 include README.rst
+include RELEASE.rst
 include readthedocs.yml
 include setup.py
-include kikuchipy/hyperspy_extension.yaml
 
-recursive-include doc Makefile make.bat
-recursive-include doc *.rst *.py *.ipynb
-recursive-include doc/_static *.png *.jpg *.svg *.gif *.sh
+recursive-include doc Makefile make.bat *.rst *.py *.ipynb
+recursive-include doc/_static *.png *.jpg *.svg *.gif
 recursive-include kikuchipy/data *

doc/changelog.rst

@@ -32,6 +32,12 @@ Added
 - Reading of NORDIF calibration patterns specified in a setting file into an
   EBSD signal. (`#317 <https://github.com/pyxem/kikuchipy/pull/317>`_)
 
+Fixed
+-----
+- Scaling of region of interest coordinates used in virtual backscatter electron
+  imaging to physical coordinates
+  (`#349 <https://github.com/pyxem/kikuchipy/pull/349>`_)
+
 0.3.3 (2021-04-18)
 ==================
 

doc/virtual_backscatter_electron_imaging.ipynb

@@ -53,14 +53,22 @@
     "s"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "We create a rectangular ROI by specifying the upper left and lower right\n",
+    "coordinates of the rectangle in units of the detector pixel size (scale of `dx`\n",
+    "and `dy` in the signal axes manager)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
-    "roi = hs.roi.RectangularROI(left=0, top=0, right=10, bottom=10)\n",
-    "roi"
+    "s.axes_manager"
    ]
   },
   {
@@ -69,6 +77,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "roi = hs.roi.RectangularROI(left=0, top=0, right=10, bottom=10)\n",
     "s.plot_virtual_bse_intensity(roi)"
    ]
   },
@@ -400,7 +409,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.6"
+   "version": "3.8.8"
   }
  },
  "nbformat": 4,

kikuchipy/data/bruker/create_bruker_h5ebsd_file.py

@@ -193,8 +193,12 @@
 # Header
 ebsd_header = ebsd.create_group("Header")
 ebsd_header.create_dataset("CameraTilt", dtype=float, data=0)
-ebsd_header.create_dataset("DetectorFullHeightMicrons", dtype=np.int32, data=sy)
-ebsd_header.create_dataset("DetectorFullWidthMicrons", dtype=np.int32, data=sx)
+ebsd_header.create_dataset(
+    "DetectorFullHeightMicrons", dtype=np.int32, data=23700
+)
+ebsd_header.create_dataset(
+    "DetectorFullWidthMicrons", dtype=np.int32, data=31600
+)
 grid_type = ebsd_header.create_dataset("Grid Type", shape=(1,), dtype="|S9")
 grid_type[()] = b"isometric"
 ebsd_header.create_dataset("KV", dtype=float, data=20)

kikuchipy/generators/virtual_bse_generator.py

@@ -217,8 +217,8 @@ def get_images_from_grid(
             images[row, col] = self.signal.get_virtual_bse_intensity(roi).data
 
         vbse_images = VirtualBSEImage(images)
-        # TODO: Transfer signal's detector axes to new navigation axes with
-        #  proper binning
+        # TODO: Transfer signal's detector axes to new navigation axes
+        #  with proper binning
         vbse_images.axes_manager = _transfer_navigation_axes_to_signal_axes(
             new_axes=vbse_images.axes_manager, old_axes=self.signal.axes_manager
         )
@@ -243,15 +243,16 @@ def roi_from_grid(self, index: Union[Tuple, List[Tuple]]) -> RectangularROI:
         """
         rows = self.grid_rows
         cols = self.grid_cols
+        dc, dr = [i.scale for i in self.signal.axes_manager.signal_axes]
 
         if isinstance(index, tuple):
             index = (index,)
         index = np.array(index)
 
-        min_col = cols[min(index[:, 1])]
-        max_col = cols[max(index[:, 1])] + cols[1]
-        min_row = rows[min(index[:, 0])]
-        max_row = rows[max(index[:, 0])] + rows[1]
+        min_col = cols[min(index[:, 1])] * dc
+        max_col = (cols[max(index[:, 1])] + cols[1]) * dc
+        min_row = rows[min(index[:, 0])] * dr
+        max_row = (rows[max(index[:, 0])] + rows[1]) * dr
 
         return RectangularROI(
             left=min_col, top=min_row, right=max_col, bottom=max_row,
@@ -289,9 +290,9 @@ def plot_grid(
         pattern : kikuchipy.signals.EBSD
             A single pattern with the markers added.
         """
-        # Get detector scales
+        # Get detector scales (column, row)
         axes_manager = self.signal.axes_manager
-        dx, dy = [i.scale for i in axes_manager.signal_axes]
+        dc, dr = [i.scale for i in axes_manager.signal_axes]
 
         rows = self.grid_rows
         cols = self.grid_cols
@@ -303,17 +304,17 @@ def plot_grid(
             for row, col in np.ndindex(self.grid_shape):
                 markers.append(
                     Text(
-                        x=cols[col],
-                        y=rows[row] + (0.1 * rows[1]),
+                        x=cols[col] * dc,
+                        y=(rows[row] + (0.1 * rows[1])) * dr,
                         text=f"{row,col}",
                         color=color,
                     )
                 )
 
         # Set lines
         kwargs.setdefault("color", "w")
-        markers += [HorizontalLine((i - 0.5) * dy, **kwargs) for i in rows]
-        markers += [VerticalLine((j - 0.5) * dx, **kwargs) for j in cols]
+        markers += [HorizontalLine((i - 0.5) * dr, **kwargs) for i in rows]
+        markers += [VerticalLine((j - 0.5) * dc, **kwargs) for j in cols]
 
         # Color RGB tiles
         if rgb_channels is not None:
@@ -325,10 +326,10 @@ def plot_grid(
                     roi = self.roi_from_grid((row, col))
                     markers += [
                         Rectangle(
-                            x1=(roi.left - 0.5) * dx,
-                            y1=(roi.top - 0.5) * dx,
-                            x2=(roi.right - 0.5) * dy,
-                            y2=(roi.bottom - 0.5) * dy,
+                            x1=(roi.left - 0.5) * dc,
+                            y1=(roi.top - 0.5) * dc,
+                            x2=(roi.right - 0.5) * dr,
+                            y2=(roi.bottom - 0.5) * dr,
                             **kwargs,
                         )
                     ]

kikuchipy/indexing/tests/__init__.py

@@ -0,0 +1,17 @@
+# -*- coding: utf-8 -*-
+# Copyright 2019-2021 The kikuchipy developers
+#
+# This file is part of kikuchipy.
+#
+# kikuchipy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# kikuchipy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.

kikuchipy/io/plugins/h5ebsd.py

@@ -749,21 +749,21 @@ def brukerheader2dicts(
     # Get region of interest (ROI, only rectangular shape supported)
     try:
         sd = hdf5group2dict(group=scan_group["EBSD/SEM"])
-        iy = sd["IY"][()]
-        ix = sd["IX"][()]
+        ir = sd["IY"][()]
+        ic = sd["IX"][()]
         roi = True
     except KeyError:
         roi = False
-        ny = hd["NROWS"]
-        nx = hd["NCOLS"]
+        nr = hd["NROWS"]
+        nc = hd["NCOLS"]
     if roi:
-        ny_roi, nx_roi, is_rectangular = _bruker_roi_is_rectangular(iy, ix)
+        nr_roi, nc_roi, is_rectangular = _bruker_roi_is_rectangular(ir, ic)
         if is_rectangular:
-            ny = ny_roi
-            nx = nx_roi
+            nr = nr_roi
+            nc = nc_roi
             # Get indices of patterns in the 2D map
-            idx = np.array([iy - np.min(iy), ix - np.min(ix)])
-            scan_size["indices"] = np.ravel_multi_index(idx, (ny, nx)).argsort()
+            idx = np.array([ir - np.min(ir), ic - np.min(ic)])
+            scan_size["indices"] = np.ravel_multi_index(idx, (nr, nc)).argsort()
         else:
             raise ValueError(
                 "Only a rectangular region of interest is supported"
@@ -772,8 +772,8 @@ def brukerheader2dicts(
     # Populate scan size dictionary
     scan_size.set_item("sx", hd["PatternWidth"])
     scan_size.set_item("sy", hd["PatternHeight"])
-    scan_size.set_item("nx", nx)
-    scan_size.set_item("ny", ny)
+    scan_size.set_item("nx", nc)
+    scan_size.set_item("ny", nr)
     scan_size.set_item("step_x", hd["XSTEP"])
     scan_size.set_item("step_y", hd["YSTEP"])
     scan_size.set_item(
@@ -783,18 +783,27 @@ def brukerheader2dicts(
     return md, omd, scan_size
 
 
-def _bruker_roi_is_rectangular(iy, ix):
-    iy_unique, iy_unique_counts = np.unique(iy, return_counts=True)
-    ix_unique, ix_unique_counts = np.unique(ix, return_counts=True)
+def _bruker_roi_is_rectangular(ir, ic):
+    ir_unique, ir_unique_counts = np.unique(ir, return_counts=True)
+    ic_unique, ic_unique_counts = np.unique(ic, return_counts=True)
     is_rectangular = (
-        np.all(np.diff(np.sort(iy_unique)) == 1)
-        and np.all(np.diff(np.sort(ix_unique)) == 1)
-        and np.unique(iy_unique_counts).size == 1
-        and np.unique(ix_unique_counts).size == 1
+        np.all(np.diff(np.sort(ir_unique)) == 1)
+        and np.all(np.diff(np.sort(ic_unique)) == 1)
+        and np.unique(ir_unique_counts).size == 1
+        and np.unique(ic_unique_counts).size == 1
     )
-    iy2 = np.max(iy) - np.min(iy) + 1
-    ix2 = np.max(ix) - np.min(ix) + 1
-    return iy2, ix2, is_rectangular
+    ir2 = np.max(ir) - np.min(ir) + 1
+    ic2 = np.max(ic) - np.min(ic) + 1
+    return ir2, ic2, is_rectangular
+
+
+# (n rows, n columns). Source: internet
+BRUKER_DETECTOR_MODEL_RESOLUTION = dict(
+    eflash_fs=(480, 640),
+    eflash_hd=(1200, 1600),
+    eflash_hr=(1200, 1600),
+    eflash_xs=(540, 720),
+)
 
 
 def file_writer(

kikuchipy/pattern/tests/__init__.py

@@ -0,0 +1,17 @@
+# -*- coding: utf-8 -*-
+# Copyright 2019-2021 The kikuchipy developers
+#
+# This file is part of kikuchipy.
+#
+# kikuchipy is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# kikuchipy is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with kikuchipy. If not, see <http://www.gnu.org/licenses/>.

kikuchipy/signals/ebsd.py

@@ -1430,7 +1430,7 @@ def plot_virtual_bse_intensity(
 
         # Create the interactive signal
         interactive(
-            f=sliced_signal.sum,
+            f=sliced_signal.nansum,
             axis=sliced_signal.axes_manager.signal_axes,
             event=roi.events.changed,
             recompute_out_event=None,
@@ -1442,7 +1442,7 @@ def plot_virtual_bse_intensity(
 
     @staticmethod
     def _get_sum_signal(signal, out_signal_axes: Optional[List] = None):
-        out = signal.sum(signal.axes_manager.signal_axes)
+        out = signal.nansum(signal.axes_manager.signal_axes)
         if out_signal_axes is None:
             out_signal_axes = list(
                 np.arange(min(signal.axes_manager.navigation_dimension, 2))

setup.cfg

@@ -1,3 +1,5 @@
+# Note that Black does not support setup.cfg
+
 [tool:pytest]
 addopts = -ra
 
@@ -11,4 +13,12 @@ relative_files = True
 [coverage:report]
 precision = 2
 
-# Note that Black does not support setup.cfg
+[manifix]
+known_excludes =
+    .*
+    .*/**
+    .git/**
+    **/*.pyc
+    doc/build*
+    htmlcov/**
+    *.code-workspace