PAW_precipitate_detection.ipynb

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     "hide-input"
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     "text": [
      "Connected as root\n",
      "User ID: 0\n",
      "User Full Name: root root\n",
      "Your Groups:\n",
      "   Name: system  ID: 0\n",
      "   Name: public  ID: 3\n",
      "   Name: matolab  ID: 53\n",
      "Current group:  system\n"
     ]
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   ],
   "source": [
    "\n",
    "from getpass import getpass\n",
    "from scipy import ndimage\n",
    "from skimage.segmentation import clear_border\n",
    "from skimage.color import label2rgb\n",
    "import matplotlib.pyplot as plt\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from datetime import datetime\n",
    "import cv2\n",
    "\n",
    "from omero_tools import OmeroConnect\n",
    "from matolab_tools import annotate_csv_uri, csvw_to_rdf, get_joined_rdf, create_mapping\n",
    "# need credentials\n",
    "username = input(\"Username: \")\n",
    "password = getpass(\"OMERO Password: \")\n",
    "\n",
    "HOST = 'wss://wss.omero.matolab.org'\n",
    "omero_conn=OmeroConnect(HOST,username,password)\n",
    "\n",
    "def run_detection(\n",
    "        image,\n",
    "        threshold_method: str = \"Otsu\",\n",
    "        size_thresh: float = 80,\n",
    "        dilate_kernel_size: int = 3,\n",
    "        median_filter_radius: int = 4,\n",
    "        plot=False\n",
    "):\n",
    "\n",
    "    name = image.name\n",
    "    print(\"Image Name: \"+name)\n",
    "\n",
    "    gray = omero_conn.get_grayscale(image.id)\n",
    "\n",
    "    print(\"Grayscale image shape:\", gray.shape)\n",
    "    print(\"Grayscale image data type:\", gray.dtype)\n",
    "\n",
    "    # Apply median filter using OpenCV\n",
    "\n",
    "    #selem = cv2.getStructuringElement(cv2.MORPH_ELLIPSE, (2*median_filter_radius + 1, 2*median_filter_radius+1))\n",
    "    filtered = cv2.medianBlur(gray, 2 * median_filter_radius + 1)\n",
    "\n",
    "    # Display the original and filtered images side by side\n",
    "    if plot:\n",
    "        fig, (ax0, ax1) = plt.subplots(1, 2, figsize=(10, 5))\n",
    "        ax0.imshow(gray, cmap='gray')\n",
    "        ax0.set_title('Step1: Load Original Image')\n",
    "        ax0.axis('off')\n",
    "        ax1.imshow(filtered, cmap='gray')\n",
    "        ax1.set_title('Step2: Median Blur Filter')\n",
    "        ax1.axis('off')\n",
    "\n",
    "    # Apply Otsu's thresholding using OpenCV\n",
    "    if threshold_method == \"Otsu\":\n",
    "        ret, thresh = cv2.threshold(\n",
    "            filtered, 0, 255, cv2.THRESH_BINARY+cv2.THRESH_OTSU)\n",
    "        print('Threshold value is {}'.format(ret))\n",
    "    else:\n",
    "        print(\"only Otsu thresholding supported, skippping thresholding\")\n",
    "        thresh = gray\n",
    "\n",
    "    # Dilate the thresholded image using a 3x3 kernel\n",
    "    kernel = np.ones((dilate_kernel_size, dilate_kernel_size), np.uint8)\n",
    "    dilated = cv2.dilate(thresh, kernel)\n",
    "\n",
    "    if plot:\n",
    "        fig, (ax0, ax1) = plt.subplots(1, 2, figsize=(10, 5))\n",
    "        ax0.imshow(thresh, cmap='gray')\n",
    "        ax0.set_title('Step3: Otsu Threshold')\n",
    "        ax0.axis('off')\n",
    "        ax1.imshow(dilated, cmap='gray')\n",
    "        ax1.set_title('Step4: Dilated Image')\n",
    "        ax1.axis('off')\n",
    "\n",
    "    # Remove small objects using OpenCV's morphologyEx function\n",
    "    morphed = cv2.morphologyEx(dilated, cv2.MORPH_OPEN, kernel, iterations=1)\n",
    "    contours, hierarchy = cv2.findContours(\n",
    "        morphed, cv2.RETR_EXTERNAL, cv2.CHAIN_APPROX_SIMPLE)\n",
    "    for cnt in contours:\n",
    "        area = cv2.contourArea(cnt)\n",
    "        if area < size_thresh:\n",
    "            cv2.drawContours(morphed, [cnt], 0, 0, -1)\n",
    "\n",
    "    # delete all previously defined shapes\n",
    "    omero_conn.delete_rois(image.id)\n",
    "\n",
    "    # upload shapes to omero\n",
    "    omero_conn.create_omero_roi_polygons(image.id, contours)\n",
    "\n",
    "    # Apply clear border to the dilated image\n",
    "    mask = morphed == 255\n",
    "    mask = clear_border(mask)\n",
    "\n",
    "    # Label the mask and count the number of precipitates detected\n",
    "    s = [[1, 1, 1], [1, 1, 1], [1, 1, 1]]\n",
    "    labeled_mask, num_labels = ndimage.label(mask, structure=s)\n",
    "    img2 = label2rgb(labeled_mask, bg_label=0)\n",
    "\n",
    "    # Display the labeled mask\n",
    "    if plot:\n",
    "        fig, ax = plt.subplots(figsize=(6, 6))\n",
    "        ax.imshow(img2)\n",
    "        ax.set_title('Step5: Contour Finding')\n",
    "        ax.axis('off')\n",
    "        plt.show()\n",
    "        print(f\"Number of precipitates detected: {num_labels}\")\n",
    "\n",
    "    plt.show()"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "634f3b1f",
   "metadata": {},
   "source": [
    "## The Pipeline"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "dc57a6f7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "190C_1000h\n",
      "---- Loaded image ID: 126\n",
      "---- Loaded image ID: 127\n",
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      "---- Loaded image ID: 123\n",
      "---- Loaded image ID: 124\n",
      "---- Loaded image ID: 125\n",
      "Dataset ID: 13\n",
      "Dataset Name: 190C_1000h\n",
      "Image Name: 190C-1000h_Sample1_Stelle10 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 61.0\n",
      "deleted rois: []\n",
      "added 33 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle11 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 89.0\n",
      "deleted rois: []\n",
      "added 98 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle12 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 90.0\n",
      "deleted rois: []\n",
      "added 100 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle1 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 54.0\n",
      "deleted rois: []\n",
      "added 52 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle2 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 58.0\n",
      "deleted rois: []\n",
      "added 34 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle3 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 48.0\n",
      "deleted rois: []\n",
      "added 63 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle4 DF 30s 2.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 38.0\n",
      "deleted rois: []\n",
      "added 30 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle5 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 63.0\n",
      "deleted rois: []\n",
      "added 70 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle6 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 55.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle7 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 53.0\n",
      "deleted rois: []\n",
      "added 40 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle8 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 54.0\n",
      "deleted rois: []\n",
      "added 111 polygon shapes to image\n",
      "Image Name: 190C-1000h_Sample1_Stelle9 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 72.0\n",
      "deleted rois: []\n",
      "added 73 polygon shapes to image\n",
      "190C_25000h_S1\n",
      "---- Loaded image ID: 89\n",
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      "---- Loaded image ID: 86\n",
      "---- Loaded image ID: 87\n",
      "---- Loaded image ID: 88\n",
      "Dataset ID: 10\n",
      "Dataset Name: 190C_25000h_S1\n",
      "Image Name: 190C-25000h_Sample1_Stelle10.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 100.0\n",
      "deleted rois: []\n",
      "added 12 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle11.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 143.0\n",
      "deleted rois: []\n",
      "added 5 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle1.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 104.0\n",
      "deleted rois: []\n",
      "added 31 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle2.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 106.0\n",
      "deleted rois: []\n",
      "added 13 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle3.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 101.0\n",
      "deleted rois: []\n",
      "added 6 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle4.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 101.0\n",
      "deleted rois: []\n",
      "added 7 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle5.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 78.0\n",
      "deleted rois: []\n",
      "added 78 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle6.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 104.0\n",
      "deleted rois: []\n",
      "added 75 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle7.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 70.0\n",
      "deleted rois: []\n",
      "added 17 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle8.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 94.0\n",
      "deleted rois: []\n",
      "added 62 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample1_Stelle9.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 111.0\n",
      "deleted rois: []\n",
      "added 4 polygon shapes to image\n",
      "190C_25000h_S2\n",
      "---- Loaded image ID: 98\n",
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      "---- Loaded image ID: 104\n",
      "---- Loaded image ID: 95\n",
      "---- Loaded image ID: 96\n",
      "---- Loaded image ID: 97\n",
      "Dataset ID: 11\n",
      "Dataset Name: 190C_25000h_S2\n",
      "Image Name: 190C-25000h_Sample2_Stelle10 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 106.0\n",
      "deleted rois: []\n",
      "added 15 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle1 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 112.0\n",
      "deleted rois: []\n",
      "added 7 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle2 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 118.0\n",
      "deleted rois: []\n",
      "added 21 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle3 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 114.0\n",
      "deleted rois: []\n",
      "added 21 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle4 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 97.0\n",
      "deleted rois: []\n",
      "added 3 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle5 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 81.0\n",
      "deleted rois: []\n",
      "added 10 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle6 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 106.0\n",
      "deleted rois: []\n",
      "added 49 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle7 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 98.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle8 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 163.0\n",
      "deleted rois: []\n",
      "added 9 polygon shapes to image\n",
      "Image Name: 190C-25000h_Sample2_Stelle9 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 150.0\n",
      "deleted rois: []\n",
      "added 5 polygon shapes to image\n",
      "190C_2500h_S1\n",
      "---- Loaded image ID: 70\n",
      "---- Loaded image ID: 71\n",
      "---- Loaded image ID: 67\n",
      "---- Loaded image ID: 68\n",
      "---- Loaded image ID: 69\n",
      "Dataset ID: 8\n",
      "Dataset Name: 190C_2500h_S1\n",
      "Image Name: 190C-2500h_Sample1_Stelle1 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 155.0\n",
      "deleted rois: []\n",
      "added 20 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample1_Stelle2 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 144.0\n",
      "deleted rois: []\n",
      "added 20 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample1_Stelle3 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 71.0\n",
      "deleted rois: []\n",
      "added 18 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample1_Stelle4 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 124.0\n",
      "deleted rois: []\n",
      "added 15 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample1_Stelle5 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 162.0\n",
      "deleted rois: []\n",
      "added 13 polygon shapes to image\n",
      "190C_2500h_S2\n",
      "---- Loaded image ID: 77\n",
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      "---- Loaded image ID: 75\n",
      "---- Loaded image ID: 76\n",
      "Dataset ID: 9\n",
      "Dataset Name: 190C_2500h_S2\n",
      "Image Name: 190C-2500h_Sample2_Stelle10 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 50.0\n",
      "deleted rois: []\n",
      "added 74 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle11 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 43.0\n",
      "deleted rois: []\n",
      "added 145 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle12 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 41.0\n",
      "deleted rois: []\n",
      "added 32 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle1 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 36.0\n",
      "deleted rois: []\n",
      "added 25 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle2 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (1024, 1024)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 12.0\n",
      "deleted rois: []\n",
      "added 23 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle3 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 45.0\n",
      "deleted rois: []\n",
      "added 44 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle4 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 41.0\n",
      "deleted rois: []\n",
      "added 44 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle5 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 58.0\n",
      "deleted rois: []\n",
      "added 29 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle6 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 46.0\n",
      "deleted rois: []\n",
      "added 36 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle7 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 35.0\n",
      "deleted rois: []\n",
      "added 40 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle8 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 63.0\n",
      "deleted rois: []\n",
      "added 59 polygon shapes to image\n",
      "Image Name: 190C-2500h_Sample2_Stelle9 DF 30s Spot 3 alpha 1 deltaE 15eV.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 57.0\n",
      "deleted rois: []\n",
      "added 84 polygon shapes to image\n",
      "190C_250h\n",
      "---- Loaded image ID: 109\n",
      "---- Loaded image ID: 110\n",
      "---- Loaded image ID: 111\n",
      "---- Loaded image ID: 112\n",
      "---- Loaded image ID: 113\n",
      "---- Loaded image ID: 114\n",
      "---- Loaded image ID: 115\n",
      "---- Loaded image ID: 105\n",
      "---- Loaded image ID: 106\n",
      "---- Loaded image ID: 107\n",
      "---- Loaded image ID: 108\n",
      "Dataset ID: 12\n",
      "Dataset Name: 190C_250h\n",
      "Image Name: 190C-250h_Sample1_Stelle10 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 90.0\n",
      "deleted rois: []\n",
      "added 69 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle11 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 55.0\n",
      "deleted rois: []\n",
      "added 122 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle1 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 82.0\n",
      "deleted rois: []\n",
      "added 147 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle2 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 67.0\n",
      "deleted rois: []\n",
      "added 56 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle3 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 101.0\n",
      "deleted rois: []\n",
      "added 65 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle4 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 123.0\n",
      "deleted rois: []\n",
      "added 105 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle5 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 51.0\n",
      "deleted rois: []\n",
      "added 117 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle6 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 142.0\n",
      "deleted rois: []\n",
      "added 84 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle7 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 66.0\n",
      "deleted rois: []\n",
      "added 67 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle8 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 114.0\n",
      "deleted rois: []\n",
      "added 37 polygon shapes to image\n",
      "Image Name: 190C-250h_Sample1_Stelle9 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 84.0\n",
      "deleted rois: []\n",
      "added 49 polygon shapes to image\n",
      "190C_5000h_S1\n",
      "---- Loaded image ID: 49\n",
      "---- Loaded image ID: 50\n",
      "---- Loaded image ID: 51\n",
      "---- Loaded image ID: 52\n",
      "---- Loaded image ID: 53\n",
      "---- Loaded image ID: 54\n",
      "---- Loaded image ID: 44\n",
      "---- Loaded image ID: 45\n",
      "---- Loaded image ID: 46\n",
      "---- Loaded image ID: 47\n",
      "---- Loaded image ID: 48\n",
      "Dataset ID: 6\n",
      "Dataset Name: 190C_5000h_S1\n",
      "Image Name: 190C-5000h_Sample1_Stelle10 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 99.0\n",
      "deleted rois: []\n",
      "added 6 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle11 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 99.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle1 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 96.0\n",
      "deleted rois: []\n",
      "added 8 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle2 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 105.0\n",
      "deleted rois: []\n",
      "added 3 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle3 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 99.0\n",
      "deleted rois: []\n",
      "added 8 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle4 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 92.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle5 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 84.0\n",
      "deleted rois: []\n",
      "added 10 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle6 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 86.0\n",
      "deleted rois: []\n",
      "added 7 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle7 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 141.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle8 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 77.0\n",
      "deleted rois: []\n",
      "added 9 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample1_Stelle9 DF 20s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 72.0\n",
      "deleted rois: []\n",
      "added 10 polygon shapes to image\n",
      "190C_5000h_S2\n",
      "---- Loaded image ID: 57\n",
      "---- Loaded image ID: 58\n",
      "---- Loaded image ID: 59\n",
      "---- Loaded image ID: 60\n",
      "---- Loaded image ID: 61\n",
      "---- Loaded image ID: 62\n",
      "---- Loaded image ID: 63\n",
      "---- Loaded image ID: 64\n",
      "---- Loaded image ID: 65\n",
      "---- Loaded image ID: 66\n",
      "---- Loaded image ID: 55\n",
      "---- Loaded image ID: 56\n",
      "Dataset ID: 7\n",
      "Dataset Name: 190C_5000h_S2\n",
      "Image Name: 190C-5000h_Sample2_Stelle10.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 43.0\n",
      "deleted rois: []\n",
      "added 148 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle11.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 77.0\n",
      "deleted rois: []\n",
      "added 172 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle12.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 69.0\n",
      "deleted rois: []\n",
      "added 3 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle1.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 71.0\n",
      "deleted rois: []\n",
      "added 178 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle2.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 49.0\n",
      "deleted rois: []\n",
      "added 21 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle3.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 37.0\n",
      "deleted rois: []\n",
      "added 138 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle4.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 28.0\n",
      "deleted rois: []\n",
      "added 197 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle5.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 45.0\n",
      "deleted rois: []\n",
      "added 82 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle6.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 23.0\n",
      "deleted rois: []\n",
      "added 112 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle7.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 27.0\n",
      "deleted rois: []\n",
      "added 50 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle8.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 30.0\n",
      "deleted rois: []\n",
      "added 66 polygon shapes to image\n",
      "Image Name: 190C-5000h_Sample2_Stelle9.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 61.0\n",
      "deleted rois: []\n",
      "added 121 polygon shapes to image\n",
      "190C_8760h_s2\n",
      "---- Loaded image ID: 30\n",
      "---- Loaded image ID: 31\n",
      "---- Loaded image ID: 32\n",
      "---- Loaded image ID: 25\n",
      "---- Loaded image ID: 26\n",
      "---- Loaded image ID: 27\n",
      "---- Loaded image ID: 28\n",
      "---- Loaded image ID: 29\n",
      "Dataset ID: 4\n",
      "Dataset Name: 190C_8760h_s2\n",
      "Image Name: 190C-8760h_Sample2_Stelle1 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 58.0\n",
      "deleted rois: []\n",
      "added 43 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle2 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 112.0\n",
      "deleted rois: []\n",
      "added 25 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle3 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 73.0\n",
      "deleted rois: []\n",
      "added 25 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle4 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 77.0\n",
      "deleted rois: []\n",
      "added 47 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle5 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 57.0\n",
      "deleted rois: []\n",
      "added 40 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle6 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 58.0\n",
      "deleted rois: []\n",
      "added 29 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle7 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 87.0\n",
      "deleted rois: []\n",
      "added 25 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample2_Stelle8 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 66.0\n",
      "deleted rois: []\n",
      "added 31 polygon shapes to image\n",
      "190C_8760_s1\n",
      "---- Loaded image ID: 40\n",
      "---- Loaded image ID: 41\n",
      "---- Loaded image ID: 42\n",
      "---- Loaded image ID: 43\n",
      "---- Loaded image ID: 33\n",
      "---- Loaded image ID: 34\n",
      "---- Loaded image ID: 35\n",
      "---- Loaded image ID: 36\n",
      "---- Loaded image ID: 37\n",
      "---- Loaded image ID: 38\n",
      "---- Loaded image ID: 39\n",
      "Dataset ID: 5\n",
      "Dataset Name: 190C_8760_s1\n",
      "Image Name: 190C-8760h_Region2_Sample1_Stelle1 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 41.0\n",
      "deleted rois: []\n",
      "added 44 polygon shapes to image\n",
      "Image Name: 190C-8760h_Region2_Sample1_Stelle2 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 35.0\n",
      "deleted rois: []\n",
      "added 81 polygon shapes to image\n",
      "Image Name: 190C-8760h_Region2_Sample1_Stelle3 DF 100 60 kx 60s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 61.0\n",
      "deleted rois: []\n",
      "added 29 polygon shapes to image\n",
      "Image Name: 190C-8760h_Region2_Sample1_Stelle4 DF 100 60 kx 60s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 56.0\n",
      "deleted rois: []\n",
      "added 21 polygon shapes to image\n",
      "Image Name: 190C-8760h_Region2_Sample1_Stelle5 DF 100 60 kx 60s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 71.0\n",
      "deleted rois: []\n",
      "added 14 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle1 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 60.0\n",
      "deleted rois: []\n",
      "added 17 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle2 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 57.0\n",
      "deleted rois: []\n",
      "added 24 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle3 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 56.0\n",
      "deleted rois: []\n",
      "added 16 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle4 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 40.0\n",
      "deleted rois: []\n",
      "added 62 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle5 DF 100 60 kx 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 49.0\n",
      "deleted rois: []\n",
      "added 40 polygon shapes to image\n",
      "Image Name: 190C-8760h_Sample1_Stelle6 DF 100 60 kx 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 61.0\n",
      "deleted rois: []\n",
      "added 24 polygon shapes to image\n",
      "T61\n",
      "---- Loaded image ID: 21\n",
      "---- Loaded image ID: 22\n",
      "---- Loaded image ID: 23\n",
      "---- Loaded image ID: 24\n",
      "---- Loaded image ID: 13\n",
      "---- Loaded image ID: 14\n",
      "---- Loaded image ID: 15\n",
      "---- Loaded image ID: 16\n",
      "---- Loaded image ID: 17\n",
      "---- Loaded image ID: 18\n",
      "---- Loaded image ID: 19\n",
      "---- Loaded image ID: 20\n",
      "Dataset ID: 3\n",
      "Dataset Name: T61\n",
      "Image Name: T61_Sample1_Stelle1 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 66.0\n",
      "deleted rois: []\n",
      "added 78 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle2 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 70.0\n",
      "deleted rois: []\n",
      "added 51 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle3 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 48.0\n",
      "deleted rois: []\n",
      "added 108 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle4 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 51.0\n",
      "deleted rois: []\n",
      "added 1 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle5 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 50.0\n",
      "deleted rois: []\n",
      "added 174 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle6 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 46.0\n",
      "deleted rois: []\n",
      "added 152 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle7 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 42.0\n",
      "deleted rois: []\n",
      "added 136 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle8 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 56.0\n",
      "deleted rois: []\n",
      "added 105 polygon shapes to image\n",
      "Image Name: T61_Sample1_Stelle9 DF 30s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 49.0\n",
      "deleted rois: []\n",
      "added 84 polygon shapes to image\n",
      "Image Name: T61_Sample2_ZA 100 DF 60 kx Stelle 1 10s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 106.0\n",
      "deleted rois: []\n",
      "added 242 polygon shapes to image\n",
      "Image Name: T61_Sample2_ZA 100 DF 60 kx Stelle 2 15s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 110.0\n",
      "deleted rois: []\n",
      "added 227 polygon shapes to image\n",
      "Image Name: T61_Sample2_ZA 100 DF 60 kx Stelle 3 15s.dm3\n",
      "Grayscale image shape: (2048, 2048)\n",
      "Grayscale image data type: uint8\n",
      "Threshold value is 38.0\n",
      "deleted rois: []\n",
      "added 134 polygon shapes to image\n"
     ]
    }
   ],
   "source": [
    "#load all images from selected datasets, run detection algorithm and upload found contours as polygons in a omero roi\n",
    "#results are saved as detection_runs.csv\n",
    "meta_extractor_api = \"https://metadata.omero.matolab.org/api/\"\n",
    "df_tem_project_id=2\n",
    "datasets=omero_conn.get_datasets(df_tem_project_id)\n",
    "data=list()\n",
    "for dataset in datasets:\n",
    "    print(dataset.name)\n",
    "    images = omero_conn.get_images(dataset.id)\n",
    "    for image in images:\n",
    "        startTime = datetime.now().isoformat()\n",
    "        info = image.name.split(\".\",1)[0].split('_')\n",
    "        state=info[0].split(\"-\")\n",
    "        if len(state)>1:\n",
    "            anneal_temp, anneal_time = info[0].split(\"-\")\n",
    "            anneal_temp = float(anneal_temp.rsplit('C',1)[0])\n",
    "            anneal_time = float(anneal_time.rsplit('h',1)[0])\n",
    "        else:\n",
    "            anneal_temp, anneal_time = 23.0, 0.0\n",
    "        specimen = info[1].split('Sample',1)[-1]\n",
    "        pos = info[2].split('Sample',1)[-1]\n",
    "        threshold_method=\"Otsu\"\n",
    "        size_thresh=50\n",
    "        dilate_kernel_size=3\n",
    "        median_filter_radius=4\n",
    "        info_dict={\n",
    "            \"SpecimenName\": dataset.name+'_'+specimen,\n",
    "            \"Aging Temp [°C]\": float(anneal_temp),\n",
    "            \"Aging Time [h]\": float(anneal_time),\n",
    "            \"Creep Stress [MPa]\": 0,\n",
    "            \"Dataset\": meta_extractor_api+\"dataset/\"+str(dataset.id),\n",
    "            \"Position_Id\": pos,\n",
    "            \"Image\": meta_extractor_api+\"image/\"+str(image.id),\n",
    "            \"ROIs\": meta_extractor_api+\"rois/\"+str(image.id),\n",
    "            \"DiskRadiusValue [px]\": median_filter_radius,\n",
    "            \"Threshold Method\": threshold_method,\n",
    "            \"Threshold Size\": size_thresh,\n",
    "            \"Dilation Kernel Size [px]\": dilate_kernel_size,\n",
    "            \"Date\": startTime\n",
    "        }\n",
    "        run_detection(image,threshold_method=threshold_method,size_thresh=size_thresh,dilate_kernel_size=dilate_kernel_size,median_filter_radius=median_filter_radius)\n",
    "        data.append(info_dict)\n",
    "        #break\n",
    "    #break\n",
    "df=pd.DataFrame(data)\n",
    "df.to_csv('detection_runs.csv')"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "id": "9b226c24",
   "metadata": {},
   "source": [
    "# Processing Metadata"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "9cfe3ee3",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "csvw annotation file created, suggested name: detection_runs-metadata.json\n",
      "wrote csvw meta data to detection_runs-metadata.json\n"
     ]
    }
   ],
   "source": [
    "# annotate detection_runs.csv\n",
    "response=annotate_csv_uri(\"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/detection_runs.csv\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "4db349af",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "writen serialized table to detection_runs.ttl\n"
     ]
    }
   ],
   "source": [
    "# serialize table to rdf, uses already commited files on main branch\n",
    "meta_url=\"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/detection_runs-metadata.json\"\n",
    "response=csvw_to_rdf(meta_url)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "2cb82cc8",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "writen mapping file to detection_runs-map.yaml\n"
     ]
    },
    {
     "data": {
      "text/plain": [
       "True"
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "# create a rule bases mapping between the data in detection_runs and the precipitate analysis knowledge graph \n",
    "meta_url=\"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/detection_runs-metadata.json\"\n",
    "method_url=\"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/PrecipitateAnalysisWorkflow.ttl\"\n",
    "d_classes= [\n",
    "    \"http://www.w3.org/ns/oa#Annotation\",''\n",
    "    \"http://www.w3.org/ns/csvw#Column\"\n",
    "]\n",
    "m_classes=[\"https://w3id.org/pmd/co/ValueObject\",]\n",
    "pred=\"https://w3id.org/pmd/co/isResourceOf\"\n",
    "use_template_rowwise=True\n",
    "map_dict={\n",
    "    \"diskRadius\": \"table-1-DiskradiusvaluePx\",\n",
    "    \"kernelSize\": \"table-1-DilationKernelSizePx\",\n",
    "    \"thresholdMethod\": \"table-1-ThresholdMethod\",\n",
    "    \"thresholdAreaSize\": \"table-1-ThresholdSize\",\n",
    "    \"specimenAgingTemperature\": \"table-1-AgingTempC\",\n",
    "    \"specimenCreepStress\": \"table-1-CreepStressMpa\",\n",
    "    \"investigationPosition\": \"table-1-Position_Id\",\n",
    "    \"specimenName\": \"table-1-Specimenname\",\n",
    "    \"specimenAgingTime\": \"table-1-AgingTimeH\",\n",
    "    \"darkfieldTransmissionElectronMicroscopeImage\": \"table-1-Image\",\n",
    "    \"precipitateRegion\": \"table-1-Rois\",\n",
    "    \"executionDate\": \"table-1-Date\",\n",
    "}\n",
    "create_mapping(meta_url=meta_url,method_url=method_url, use_template_rowwise=use_template_rowwise, data_super_classes=d_classes,predicate=pred,method_super_classes=m_classes,map_dict=map_dict)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "f46d6bdb",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "applied 11 mapping rules and skipped 0\n",
      "wrote joint graph to detection_runs-joined.ttl\n"
     ]
    }
   ],
   "source": [
    "# join all data and replicate template knowledge graph for every row in table\n",
    "mapping_url = \"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/detection_runs-map.yaml\"\n",
    "data_url = \"https://github.com/BAMresearch/DF-TEM-PAW/raw/main/detection_runs.ttl\"\n",
    "get_joined_rdf(map_url=mapping_url,data_url=data_url)"
   ]
  }
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