Merge pull request #4 from tinabe/nanoseg-demo

Update with edge peaks filtering.

Author: dnjohnstone

06 Nanocrystal segmentation in SPED data - Demonstration on partly overlapping MgO cubes.ipynb

@@ -83,7 +83,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "dp = pxm.load_hspy('SPED_data_of_MgO_nanoparticles_bin2,2,1,1.hdf5',\n",
+    "dp = pxm.load_hspy('SPED_MgO.hdf5',\n",
     "                  lazy=False,\n",
     "                  assign_to='electron_diffraction2d')"
    ]
@@ -96,10 +96,8 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
     "dp.plot(cmap='magma_r')"
    ]
@@ -138,7 +136,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Find the position of the direct beam in background subtracted data."
+    "Find the position of the direct beam in the background subtracted data."
    ]
   },
   {
@@ -192,6 +190,15 @@
     "dp_rb.set_scan_calibration(scale_real)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "dp_rb.save('dp_rb_final.hdf5')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -260,35 +267,32 @@
    ]
   },
   {
-   "cell_type": "code",
-   "execution_count": null,
+   "cell_type": "markdown",
    "metadata": {},
-   "outputs": [],
    "source": [
-    "dp_padded = np.zeros((dp.data.shape[0],dp.data.shape[1],\n",
-    "                     dp.data.shape[2]+12,dp.data.shape[2]+12))\n",
-    "dp_padded[:,:,6:dp.data.shape[2]+6,6:dp.data.shape[2]+6] = dp_rb.data\n",
-    "dp_padded = pxm.ElectronDiffraction2D(dp_padded)\n",
-    "dp_padded.set_diffraction_calibration(scale)\n",
-    "dp_padded.set_scan_calibration(scale_real)"
+    "Filter away the peaks at the edges of the patterns, since it is not possible to get a correct sub-pixel refinement of these peaks. "
    ]
   },
   {
-   "cell_type": "markdown",
-   "metadata": {},
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [],
    "source": [
-    "Padding is used so that peaks at the edges of the diffraction patterns are treated correctly."
+    "peaks_filtered = peaks.filter_vectors_detector_edge(exclude_width=74)"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
    "metadata": {
-    "scrolled": false
+    "scrolled": true
    },
    "outputs": [],
    "source": [
-    "refine_gen = SubpixelrefinementGenerator(dp_padded, peaks)\n",
+    "refine_gen = SubpixelrefinementGenerator(dp_rb, peaks_filtered)\n",
     "peaks_refined = DiffractionVectors(\n",
     "    refine_gen.center_of_mass_method(square_size=4))\n",
     "peaks_refined.axes_manager.set_signal_dimension(0)"
@@ -392,7 +396,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "Gs = unique_peaks.filter_vector_magnitudes(\n",
+    "Gs = unique_peaks.filter_vectors_magnitudes(\n",
     "    min_magnitude=10*scale, max_magnitude=np.inf)\n",
     "print(np.shape(Gs)[0], ' unique vectors.')"
    ]
@@ -527,7 +531,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "i = 26\n",
+    "i = 25\n",
     "sep_i = separate_watershed(\n",
     "    VDFs.inav[i].data, min_distance=min_distance, min_size=min_size,\n",
     "    max_size=max_size, max_number_of_grains=max_number_of_grains,\n",