Merge pull request #176 from OpenPIV/windef_with_mask

Windef with mask

Author: alexlib

openpiv/docs/src/developers.rst

@@ -43,3 +43,19 @@ Things OpenPIV currently needs, (in order of importance)
 * Cython wrappers for C/C++ codes.
 * A good graphical user interface (in progress)
 
+
+How to test all the notebooks
+-----------------------------
+
+    conda install ipykernel
+    python -m ipykernel install --user --name openpiv --display-name="openpiv"
+    jupyter nbconvert --to html --ExecutePreprocessor.kernel_name=openpiv --execute *.ipynb
+
+Then open the `openpiv/examples/notebooks` and check the HTML files. If one of those will fail, the error message will be in the command shell
+
+If you need to install cv2
+--------------------------
+
+    conda install -c conda-forge opencv
+
+

openpiv/examples/notebooks/PIV_3D_example.ipynb

@@ -28,21 +28,21 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "CPython 3.8.5\n",
+      "CPython 3.8.3\n",
       "IPython 7.19.0\n",
       "\n",
       "numpy 1.19.4\n",
-      "openpiv 0.23.1a0\n",
+      "openpiv 0.23.2rc1\n",
       "\n",
-      "compiler   : GCC 7.3.0\n",
+      "compiler   : GCC 7.5.0\n",
       "system     : Linux\n",
-      "release    : 5.4.0-54-generic\n",
+      "release    : 5.4.0-56-generic\n",
       "machine    : x86_64\n",
       "processor  : x86_64\n",
       "CPU cores  : 8\n",
       "interpreter: 64bit\n",
-      "Git hash   : 6edda3f747a61489b040b4d59a7a6d0442e8e341\n",
-      "Git branch : sig2noise_validation\n"
+      "Git hash   : b750f179dc14baecdad6dbf0bb96622bcc199fd4\n",
+      "Git branch : windef_with_mask\n"
      ]
     }
    ],
@@ -304,7 +304,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

openpiv/examples/notebooks/all_test_cases_sample.ipynb

@@ -71,7 +71,7 @@
     "'Processing Parameters'\n",
     "settings.correlation_method='circular'  # 'circular' or 'linear'\n",
     "settings.normalized_correlation = True\n",
-    "settings.iterations = 3  # select the number of PIV passes\n",
+    "settings.num_iterations = 3  # select the number of PIV passes\n",
     "# add the interrogation window size for each pass. \n",
     "# For the moment, it should be a power of 2 \n",
     "\n",
@@ -366,7 +366,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.5"
+   "version": "3.8.3"
   }
  },
  "nbformat": 4,

openpiv/examples/notebooks/case_B_windef_small_window.ipynb

@@ -105,7 +105,7 @@
     "settings.deformation_method = 'symmetric' # or 'second image'\n",
     "\n",
     "\n",
-    "settings.iterations = 4  # select the number of PIV passes\n",
+    "settings.num_iterations = 4  # select the number of PIV passes\n",
     "\n",
     "# add the interrogation window size for each pass. \n",
     "# For the moment, it should be a power of 2 \n",
@@ -415,7 +415,7 @@
     "    frame_b,\n",
     "    settings.windowsizes[0],\n",
     "    settings.overlap[0],\n",
-    "    settings.iterations,\n",
+    "    settings.num_iterations,\n",
     "    correlation_method=settings.correlation_method,\n",
     "    subpixel_method=settings.subpixel_method,\n",
     "    do_sig2noise=settings.extract_sig2noise,\n",
@@ -989,7 +989,7 @@
    "outputs": [],
    "source": [
     "# \"filter to replace the values that where marked by the validation\"\n",
-    "# if settings.iterations > 1:\n",
+    "# if settings.num_iterations > 1:\n",
     "\n",
     "\n",
     "u, v = filters.replace_outliers(\n",
@@ -1272,13 +1272,13 @@
     }
    ],
    "source": [
-    "for i in range(1, settings.iterations): ## all other passes\n",
+    "for i in range(1, settings.num_iterations): ## all other passes\n",
     "    x, y, u, v, sig2noise_ratio = windef.multipass_img_deform(\n",
     "        frame_a,\n",
     "        frame_b,\n",
     "        settings.windowsizes[i],\n",
     "        settings.overlap[i],\n",
-    "        settings.iterations,\n",
+    "        settings.num_iterations,\n",
     "        i,\n",
     "        x,\n",
     "        y,\n",
@@ -1304,8 +1304,8 @@
     "    \n",
     "    if (\n",
     "        settings.extract_sig2noise is True\n",
-    "        and i == settings.iterations\n",
-    "        and settings.iterations != 1\n",
+    "        and i == settings.num_iterations\n",
+    "        and settings.num_iterations != 1\n",
     "        and settings.do_sig2noise_validation is True\n",
     "    ):\n",
     "        u, v, mask_s2n = validation.sig2noise_val(\n",
@@ -1340,7 +1340,7 @@
     "            kernel_size=settings.filter_kernel_size,\n",
     "        )\n",
     "        \n",
-    "    if (i != settings.iterations) and (settings.smoothn is True):\n",
+    "    if (i != settings.num_iterations) and (settings.smoothn is True):\n",
     "        u, _, _, _ = smoothn.smoothn(\n",
     "                     u, s=settings.smoothn_p )\n",
     "        v, _, _, _ = smoothn.smoothn(\n",

openpiv/examples/notebooks/vonKarman_pivlab_with_openpiv.ipynb

@@ -69,7 +69,7 @@
     "settings.correlation_method='circular'  # 'circular' or 'linear'\n",
     "settings.normalized_correlation=False\n",
     "\n",
-    "settings.iterations = 2  # select the number of PIV passes\n",
+    "settings.num_iterations = 2  # select the number of PIV passes\n",
     "# add the interroagtion window size for each pass. \n",
     "# For the moment, it should be a power of 2 \n",
     "settings.windowsizes = (64, 32, 16) # if longer than n iteration the rest is ignored\n",

openpiv/examples/notebooks/window_deformation_comparison.ipynb

@@ -131,7 +131,7 @@ def global_std(u, v, std_threshold=3):
     return u, v, mask
 
 
-def sig2noise_val(u, v, sig2noise, w=None, threshold=1.05):
+def sig2noise_val(u, v, s2n, w=None, threshold=1.05):
     """Eliminate spurious vectors from cross-correlation signal to noise ratio.
 
     Replace spurious vectors with zero if signal to noise ratio
@@ -145,7 +145,7 @@ def sig2noise_val(u, v, sig2noise, w=None, threshold=1.05):
     v : 2d or 3d np.ndarray
         a two or three dimensional array containing the v velocity component.
 
-    sig2noise : 2d np.ndarray
+    s2n : 2d np.ndarray
         a two or three dimensional array containing the value  of the signal to
         noise ratio from cross-correlation function.
     w : 2d or 3d np.ndarray
@@ -180,7 +180,7 @@ def sig2noise_val(u, v, sig2noise, w=None, threshold=1.05):
 
     """
 
-    ind = sig2noise < threshold
+    ind = s2n < threshold
 
     u[ind] = np.nan
     v[ind] = np.nan