YAML for windef settings

openpiv/examples/notebooks/default_settings.yaml

@@ -0,0 +1,47 @@
+MinMax_U_disp: &id001 !!python/tuple
+- -30
+- 30
+MinMax_V_disp: *id001
+ROI: full
+correlation_method: circular
+deformation_method: symmetric
+do_sig2noise_validation: false
+dt: 1
+dynamic_masking_filter_size: 7
+dynamic_masking_method: None
+dynamic_masking_threshold: 0.005
+extract_sig2noise: false
+filepath_images: .
+filter_kernel_size: 2
+filter_method: localmean
+frame_pattern_a: exp1_001_a.bmp
+frame_pattern_b: exp1_001_b.bmp
+interpolation_order: 3
+iterations: 3
+max_filter_iteration: 4
+median_size: 1
+median_threshold: 3
+normalized_correlation: false
+overlap: !!python/tuple
+- 32
+- 16
+- 8
+replace_vectors: true
+save_folder_suffix: Test_4
+save_path: ./res
+save_plot: true
+scale_plot: 100
+scaling_factor: 1
+show_plot: true
+sig2noise_mask: 2
+sig2noise_method: peak2peak
+sig2noise_threshold: 1.05
+smoothn: true
+smoothn_p: 0.5
+std_threshold: 10
+subpixel_method: gaussian
+validation_first_pass: true
+windowsizes: !!python/tuple
+- 64
+- 32
+- 16

openpiv/examples/notebooks/windef_settings_yaml.ipynb

@@ -0,0 +1,255 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# test of YAML idea"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from openpiv import windef"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "settings = windef.Settings()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "filepath_images: . \n",
+      ", save_path: ./res \n",
+      ", save_folder_suffix: Test_4 \n",
+      ", frame_pattern_a: exp1_001_a.bmp \n",
+      ", frame_pattern_b: exp1_001_b.bmp \n",
+      ", ROI: full \n",
+      ", dynamic_masking_method: None \n",
+      ", dynamic_masking_threshold: 0.005 \n",
+      ", dynamic_masking_filter_size: 7 \n",
+      ", correlation_method: circular \n",
+      ", normalized_correlation: False \n",
+      ", windowsizes: (64, 32, 16) \n",
+      ", overlap: (32, 16, 8) \n",
+      ", iterations: 3 \n",
+      ", subpixel_method: gaussian \n",
+      ", deformation_method: symmetric \n",
+      ", interpolation_order: 3 \n",
+      ", scaling_factor: 1 \n",
+      ", dt: 1 \n",
+      ", extract_sig2noise: False \n",
+      ", sig2noise_method: peak2peak \n",
+      ", sig2noise_mask: 2 \n",
+      ", validation_first_pass: True \n",
+      ", MinMax_U_disp: (-30, 30) \n",
+      ", MinMax_V_disp: (-30, 30) \n",
+      ", std_threshold: 10 \n",
+      ", median_threshold: 3 \n",
+      ", median_size: 1 \n",
+      ", do_sig2noise_validation: False \n",
+      ", sig2noise_threshold: 1.05 \n",
+      ", replace_vectors: True \n",
+      ", smoothn: True \n",
+      ", smoothn_p: 0.5 \n",
+      ", filter_method: localmean \n",
+      ", max_filter_iteration: 4 \n",
+      ", filter_kernel_size: 2 \n",
+      ", save_plot: True \n",
+      ", show_plot: True \n",
+      ", scale_plot: 100 \n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "attrs = vars(settings)\n",
+    "print(', '.join(\"%s: %s \\n\" % item for item in attrs.items()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import yaml"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with open(r'default_settings.yaml', 'w') as file:\n",
+    "    documents = yaml.dump(attrs, file)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'MinMax_U_disp': (-30, 30), 'MinMax_V_disp': (-30, 30), 'ROI': 'full', 'correlation_method': 'circular', 'deformation_method': 'symmetric', 'do_sig2noise_validation': False, 'dt': 1, 'dynamic_masking_filter_size': 7, 'dynamic_masking_method': 'None', 'dynamic_masking_threshold': 0.005, 'extract_sig2noise': False, 'filepath_images': '.', 'filter_kernel_size': 2, 'filter_method': 'localmean', 'frame_pattern_a': 'exp1_001_a.bmp', 'frame_pattern_b': 'exp1_001_b.bmp', 'interpolation_order': 3, 'iterations': 3, 'max_filter_iteration': 4, 'median_size': 1, 'median_threshold': 3, 'normalized_correlation': False, 'overlap': (32, 16, 8), 'replace_vectors': True, 'save_folder_suffix': 'Test_4', 'save_path': './res', 'save_plot': True, 'scale_plot': 100, 'scaling_factor': 1, 'show_plot': True, 'sig2noise_mask': 2, 'sig2noise_method': 'peak2peak', 'sig2noise_threshold': 1.05, 'smoothn': True, 'smoothn_p': 0.5, 'std_threshold': 10, 'subpixel_method': 'gaussian', 'validation_first_pass': True, 'windowsizes': (64, 32, 16)}\n"
+     ]
+    }
+   ],
+   "source": [
+    "with open(r'default_settings.yaml') as file:\n",
+    "    # The FullLoader parameter handles the conversion from YAML\n",
+    "    # scalar values to Python the dictionary format\n",
+    "    settings1 = yaml.load(file, Loader=yaml.FullLoader)\n",
+    "\n",
+    "    print(settings1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "settings2 = windef.Settings()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for key in settings1:\n",
+    "    setattr(settings2, key, settings1[key])\n",
+    "# setattr(self, key, dictionary[key])"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 24,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 24,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "import pickle\n",
+    "pickle.dumps(settings) == pickle.dumps(settings2)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 25,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "filepath_images: . \n",
+      ", save_path: ./res \n",
+      ", save_folder_suffix: Test_4 \n",
+      ", frame_pattern_a: exp1_001_a.bmp \n",
+      ", frame_pattern_b: exp1_001_b.bmp \n",
+      ", ROI: full \n",
+      ", dynamic_masking_method: None \n",
+      ", dynamic_masking_threshold: 0.005 \n",
+      ", dynamic_masking_filter_size: 7 \n",
+      ", correlation_method: circular \n",
+      ", normalized_correlation: False \n",
+      ", windowsizes: (64, 32, 16) \n",
+      ", overlap: (32, 16, 8) \n",
+      ", iterations: 3 \n",
+      ", subpixel_method: gaussian \n",
+      ", deformation_method: symmetric \n",
+      ", interpolation_order: 3 \n",
+      ", scaling_factor: 1 \n",
+      ", dt: 1 \n",
+      ", extract_sig2noise: False \n",
+      ", sig2noise_method: peak2peak \n",
+      ", sig2noise_mask: 2 \n",
+      ", validation_first_pass: True \n",
+      ", MinMax_U_disp: (-30, 30) \n",
+      ", MinMax_V_disp: (-30, 30) \n",
+      ", std_threshold: 10 \n",
+      ", median_threshold: 3 \n",
+      ", median_size: 1 \n",
+      ", do_sig2noise_validation: False \n",
+      ", sig2noise_threshold: 1.05 \n",
+      ", replace_vectors: True \n",
+      ", smoothn: True \n",
+      ", smoothn_p: 0.5 \n",
+      ", filter_method: localmean \n",
+      ", max_filter_iteration: 4 \n",
+      ", filter_kernel_size: 2 \n",
+      ", save_plot: True \n",
+      ", show_plot: True \n",
+      ", scale_plot: 100 \n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "attrs2 = vars(settings2)\n",
+    "print(', '.join(\"%s: %s \\n\" % item for item in attrs2.items()))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python [conda env:openpiv] *",
+   "language": "python",
+   "name": "conda-env-openpiv-py"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}