Updated simulation codes

zengjiexia · Jul 16, 2023 · 3dd5941 · 3dd5941
1 parent 5467fff
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diff --git a/simulation/generate_DL.py → simulation/ACT_DL_simulation.py b/simulation/generate_DL.py → simulation/ACT_DL_simulation.py
diff --git a/simulation/ACT_SR_simulation_final.ipynb b/simulation/ACT_SR_simulation_final.ipynb
@@ -0,0 +1,149 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "a0bc1bd5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "\n",
+    "import numpy as np\n",
+    "import pandas as pd\n",
+    "from PIL import Image, ImageDraw\n",
+    "from scipy import ndimage\n",
+    "import tifffile as tiff\n",
+    "import matplotlib.pyplot as plt\n",
+    "from tqdm import tqdm\n",
+    "%matplotlib inline"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "6e0364c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import toolbox"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "e300fdbf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "obj = toolbox.SR_image(4096, 8, 12.65)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "e1ed57e0-2313-465e-8568-68e52675aac5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "data_path = r\"D:\\Work\\ACT_simulation\\Simulated_imgs_straight_2\"\n",
+    "filenames = [\"X0Y0R0W0\",\"X0Y0R0W1\",\"X0Y0R0W2\",\"X0Y0R1W0\",\"X0Y0R1W1\",\"X0Y0R1W2\",\"X0Y0R2W0\",\"X0Y0R2W1\",\"X0Y0R2W2\" ]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "1c907763-61fb-4a95-a2a4-d8120ffe6013",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|████████████████████████████████████████████████████████████████████████████████████| 9/9 [11:04<00:00, 73.87s/it]\n"
+     ]
+    }
+   ],
+   "source": [
+    "obj.set_particle_details(shape='straight', number=50, size='auto')\n",
+    "obj.set_intensity(mean=4000, sigma=0.2)\n",
+    "obj.set_noise(mean=1000, sigma=0.2)\n",
+    "obj.set_frame(number_of_frame=500)\n",
+    "obj.set_drift(apply_drift=1, max_drift_per_frame=3)\n",
+    "obj.generate_particle_list()\n",
+    "for i in tqdm(filenames):\n",
+    "    obj.generate_particle_positions()\n",
+    "    obj.set_path_name(data_path, i)\n",
+    "    obj.draw_groundtruth()\n",
+    "    obj.generate_blinks()\n",
+    "    obj.generate_base_image()\n",
+    "    obj.add_fiducials(number_of_fiducial=3, fiducial_brightness_rate=8)\n",
+    "    obj.create_SR_stack()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "654e8e9e-cef1-48e0-8ace-dc92b7b2fd42",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "100%|████████████████████████████████████████████████████████████████████████████████████| 9/9 [11:50<00:00, 78.99s/it]\n"
+     ]
+    }
+   ],
+   "source": [
+    "data_path = r\"D:\\Work\\ACT_simulation\\Simulated_imgs_dot\"\n",
+    "filenames = [\"X0Y0R0W0\",\"X0Y0R0W1\",\"X0Y0R0W2\",\"X0Y0R1W0\",\"X0Y0R1W1\",\"X0Y0R1W2\",\"X0Y0R2W0\",\"X0Y0R2W1\",\"X0Y0R2W2\" ]\n",
+    "obj.set_particle_details(shape='dot', number=100, size=100)\n",
+    "obj.set_intensity(mean=4000, sigma=0.2)\n",
+    "obj.set_noise(mean=1000, sigma=0.2)\n",
+    "obj.set_frame(number_of_frame=500)\n",
+    "obj.set_drift(apply_drift=1, max_drift_per_frame=3)\n",
+    "obj.generate_particle_list()\n",
+    "for i in tqdm(filenames):\n",
+    "    obj.generate_particle_positions()\n",
+    "    obj.set_path_name(data_path, i)\n",
+    "    obj.draw_groundtruth()\n",
+    "    obj.generate_blinks()\n",
+    "    obj.generate_base_image()\n",
+    "    obj.add_fiducials(number_of_fiducial=3, fiducial_brightness_rate=8)\n",
+    "    obj.create_SR_stack()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "1e8242c5-a71e-4200-adf1-4c73577bed53",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python (py3venv)",
+   "language": "python",
+   "name": "py3venv"
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+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
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+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.16"
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+  "toc-autonumbering": true,
+  "toc-showmarkdowntxt": true
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+ "nbformat_minor": 5
+}