Create_manually_curaited_cell_classifcation_files.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "import xml.etree.ElementTree as ET\n",
    "import pandas as pd\n",
    "import numpy as np"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Read in CSV file from google sheets, that you manually added (2 or 1) for (cell , non-cell) respectivally. in a column titled Manual"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "total non-cells: 274percent: 56.84647302904564\n",
      "total cells: 208percent: 43.15352697095436\n",
      "--------- NOT CELLS --------------\n",
      "    Image_Filename  Type  MarkerZ  MarkerY  MarkerX  Manual rfp_cell notes\n",
      "0  placeholder.tif     2       13     5123     2880     1.0      NaN   NaN\n",
      "1  placeholder.tif     2       16     5127     2914     1.0      NaN   NaN\n",
      "2  placeholder.tif     2       17     5152     2609     1.0      NaN   NaN\n",
      "3  placeholder.tif     2       17     6612     3396     1.0      NaN   NaN\n",
      "4  placeholder.tif     2       20     6801     2712     1.0      NaN   NaN\n",
      "---------- CELLS -----------------\n",
      "     Image_Filename  Type  MarkerZ  MarkerY  MarkerX  Manual rfp_cell notes\n",
      "11  placeholder.tif     2       29     4938     4367     2.0        0   NaN\n",
      "29  placeholder.tif     2       40     5097     5026     2.0        0   NaN\n",
      "41  placeholder.tif     2       43     5067     4831     2.0        1   NaN\n",
      "68  placeholder.tif     2       54     5307     4615     2.0        1   NaN\n",
      "81  placeholder.tif     2       58     5599     4702     2.0        1     y\n"
     ]
    }
   ],
   "source": [
    "# Read the CSV file\n",
    "csv_file = '/Users/grant/Desktop/G21/G21_gfp_cellClassificaion_450_cells.csv'\n",
    "df = pd.read_csv(csv_file)\n",
    "\n",
    "\n",
    "# Convert the Manual column to numeric values\n",
    "df['Manual'] = pd.to_numeric(df['Manual'], errors='coerce')\n",
    "\n",
    "# Filter rows based on the Manual column value\n",
    "manual_1_df = df[df['Manual'] == 1]\n",
    "manual_2_df = df[df['Manual'] == 2]\n",
    "\n",
    "# find length of data frams\n",
    "num_rows_1  = manual_1_df.shape[0]\n",
    "num_rows_2  = manual_2_df.shape[0]\n",
    "total_cells = num_rows_1 + num_rows_2\n",
    "print('total non-cells: ' +  str(num_rows_1) + \"percent: \" + str((num_rows_1 /total_cells)*100))\n",
    "print('total cells: ' +  str(num_rows_2)+  \"percent: \" + str((num_rows_2 /total_cells)*100))\n",
    "\n",
    "# Print the filtered data frames\n",
    "print(\"--------- NOT CELLS --------------\")\n",
    "print(manual_1_df.head())\n",
    "\n",
    "print(\"---------- CELLS -----------------\")\n",
    "print(manual_2_df.head())"
   ]
  },
  {
   "attachments": {},
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### drop the extra columns from the data frames, to match the layout of the cell_classification.xml files from cellfinder"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "------------ non-cells -------------\n",
      "       Image_Filename  Type  MarkerX  MarkerY  MarkerZ\n",
      "0     placeholder.tif     1     2880     5123       13\n",
      "1     placeholder.tif     1     2914     5127       16\n",
      "2     placeholder.tif     1     2609     5152       17\n",
      "3     placeholder.tif     1     3396     6612       17\n",
      "4     placeholder.tif     1     2712     6801       20\n",
      "...               ...   ...      ...      ...      ...\n",
      "5073  placeholder.tif     1     3646      923     1623\n",
      "5074  placeholder.tif     1     3568      818     1623\n",
      "5075  placeholder.tif     1     3585     1046     1625\n",
      "5076  placeholder.tif     1     3568      822     1625\n",
      "5077  placeholder.tif     1     5036     1966     1626\n",
      "\n",
      "[274 rows x 5 columns]\n",
      "------------ cells -------------\n",
      "       Image_Filename  Type  MarkerX  MarkerY  MarkerZ\n",
      "11    placeholder.tif     2     4367     4938       29\n",
      "29    placeholder.tif     2     5026     5097       40\n",
      "41    placeholder.tif     2     4831     5067       43\n",
      "68    placeholder.tif     2     4615     5307       54\n",
      "81    placeholder.tif     2     4702     5599       58\n",
      "...               ...   ...      ...      ...      ...\n",
      "4368  placeholder.tif     2     4698     1374     1227\n",
      "4369  placeholder.tif     2     1487     6205     1227\n",
      "5028  placeholder.tif     2     4829      879     1602\n",
      "5031  placeholder.tif     2     4472      547     1603\n",
      "5050  placeholder.tif     2     4389      741     1614\n",
      "\n",
      "[208 rows x 5 columns]\n"
     ]
    }
   ],
   "source": [
    "# -------- non-Cells df -------------\n",
    "# Drop the unnecessary columns\n",
    "manual_1_df = manual_1_df.drop(columns=['Manual', 'rfp_cell', 'notes'])\n",
    "\n",
    "# Update the 'Type' column to have values 1 and 2\n",
    "# You will need to adjust the condition as needed depending on how you want to distinguish between Type 1 and 2\n",
    "# manual_1_df['Type'] = np.where(manual_1_df['MarkerZ'] <= 12, 1, 2)\n",
    "\n",
    "# Reorder the columns\n",
    "manual_1_df = manual_1_df[['Image_Filename', 'Type', 'MarkerX', 'MarkerY', 'MarkerZ']]\n",
    "manual_1_df['Type'] = 1\n",
    "\n",
    "# -------- Cells df -------------\n",
    "# Drop the unnecessary columns\n",
    "manual_2_df = manual_2_df.drop(columns=['Manual', 'rfp_cell', 'notes'])\n",
    "\n",
    "# Reorder the columns\n",
    "manual_2_df = manual_2_df[['Image_Filename', 'Type', 'MarkerX', 'MarkerY', 'MarkerZ']]\n",
    "\n",
    "print('------------ non-cells -------------')\n",
    "print(manual_1_df)\n",
    "\n",
    "print('------------ cells -------------')\n",
    "print(manual_2_df)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Combine the two manually curiated data frames"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "       Image_Filename  Type  MarkerX  MarkerY  MarkerZ\n",
      "0     placeholder.tif     1     2880     5123       13\n",
      "1     placeholder.tif     1     2914     5127       16\n",
      "2     placeholder.tif     1     2609     5152       17\n",
      "3     placeholder.tif     1     3396     6612       17\n",
      "4     placeholder.tif     1     2712     6801       20\n",
      "...               ...   ...      ...      ...      ...\n",
      "4356  placeholder.tif     2     4554     1281     1222\n",
      "4361  placeholder.tif     2     4788     1124     1223\n",
      "4362  placeholder.tif     2      941     5629     1224\n",
      "4365  placeholder.tif     2     2787     2037     1226\n",
      "4367  placeholder.tif     2     4608     1422     1227\n",
      "\n",
      "[477 rows x 5 columns]\n",
      "482\n"
     ]
    }
   ],
   "source": [
    "combined_df = pd.concat([manual_1_df , manual_2_df ])\n",
    "\n",
    "# Display the first few rows of the combined DataFrame\n",
    "print(combined_df.head(-5))\n",
    "\n",
    "print(len(combined_df))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Save out the CSV file and XML file of this new data frame"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Assuming you have a DataFrame named 'df'\n",
    "# Save DataFrame as a CSV file\n",
    "combined_df.to_csv(\"/Users/grant/Desktop/G21/combined_cell_cordinates_output.csv\", index=False)\n",
    "\n",
    "# Create an XML file from the DataFrame\n",
    "root = ET.Element(\"root\")\n",
    "\n",
    "for _, row in combined_df.iterrows():\n",
    "    record = ET.SubElement(root, \"record\")\n",
    "    for col in combined_df.columns:\n",
    "        col_element = ET.SubElement(record, col)\n",
    "        col_element.text = str(row[col])\n",
    "\n",
    "# Save the XML data to a file\n",
    "tree = ET.ElementTree(root)\n",
    "tree.write(\"/Users/grant/Desktop/G21/manual_cell_classification.xml\", encoding=\"utf-8\", xml_declaration=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      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MarkerX><MarkerY>1916</MarkerY><MarkerZ>1216</MarkerZ></Marker><Marker><MarkerX>1043</MarkerX><MarkerY>5241</MarkerY><MarkerZ>1221</MarkerZ></Marker><Marker><MarkerX>6507</MarkerX><MarkerY>4780</MarkerY><MarkerZ>1221</MarkerZ></Marker><Marker><MarkerX>4554</MarkerX><MarkerY>1281</MarkerY><MarkerZ>1222</MarkerZ></Marker><Marker><MarkerX>4788</MarkerX><MarkerY>1124</MarkerY><MarkerZ>1223</MarkerZ></Marker><Marker><MarkerX>941</MarkerX><MarkerY>5629</MarkerY><MarkerZ>1224</MarkerZ></Marker><Marker><MarkerX>2787</MarkerX><MarkerY>2037</MarkerY><MarkerZ>1226</MarkerZ></Marker><Marker><MarkerX>4608</MarkerX><MarkerY>1422</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>4698</MarkerX><MarkerY>1374</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>1487</MarkerX><MarkerY>6205</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>4829</MarkerX><MarkerY>879</MarkerY><MarkerZ>1602</MarkerZ></Marker><Marker><MarkerX>4472</MarkerX><MarkerY>547</MarkerY><MarkerZ>1603</MarkerZ></Marker><Marker><MarkerX>4389</MarkerX><MarkerY>741</MarkerY><MarkerZ>1614</MarkerZ></Marker></Marker_Type></Marker_Data></CellCounter_Marker_File>\n"
     ]
    }
   ],
   "source": [
    "input_file = '/Users/grant/Desktop/G21/manual_cell_classification.xml'\n",
    "\n",
    "\n",
    "with open(input_file, 'r', encoding='utf-8') as file:\n",
    "    input_xml = file.read()\n",
    "\n",
    "# Parse the input XML\n",
    "root = ET.fromstring(input_xml)\n",
    "\n",
    "# Create the output XML structure\n",
    "output_root = ET.Element(\"CellCounter_Marker_File\")\n",
    "image_properties = ET.SubElement(output_root, \"Image_Properties\")\n",
    "filename = ET.SubElement(image_properties, \"Image_Filename\")\n",
    "marker_data = ET.SubElement(output_root, \"Marker_Data\")\n",
    "current_type = ET.SubElement(marker_data, \"Current_Type\")\n",
    "marker_type = ET.SubElement(marker_data, \"Marker_Type\")\n",
    "type_elem = ET.SubElement(marker_type, \"Type\")\n",
    "\n",
    "# Set the filename and type from the input XML\n",
    "filename.text = root.find(\"record/Image_Filename\").text\n",
    "type_elem.text = root.find(\"record/Type\").text\n",
    "current_type.text = root.find(\"record/Type\").text\n",
    "\n",
    "# Iterate through the input XML records and add the markers to the output XML\n",
    "for record in root.findall(\"record\"):\n",
    "    marker = ET.SubElement(marker_type, \"Marker\")\n",
    "    marker_x = ET.SubElement(marker, \"MarkerX\")\n",
    "    marker_y = ET.SubElement(marker, \"MarkerY\")\n",
    "    marker_z = ET.SubElement(marker, \"MarkerZ\")\n",
    "\n",
    "    marker_x.text = record.find(\"MarkerX\").text\n",
    "    marker_y.text = record.find(\"MarkerY\").text\n",
    "    marker_z.text = record.find(\"MarkerZ\").text\n",
    "\n",
    "# Convert the output XML tree to a string\n",
    "output_xml = ET.tostring(output_root, encoding=\"UTF-8\", method=\"xml\").decode(\"UTF-8\")\n",
    "\n",
    "print(output_xml)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Output XML saved to /Users/grant/Desktop/G21/cell_classification.xml\n"
     ]
    }
   ],
   "source": [
    "output_filename = \"/Users/grant/Desktop/G21/cell_classification.xml\"\n",
    "\n",
    "with open(output_filename, \"w\", encoding=\"utf-8\") as output_file:\n",
    "    output_file.write(output_xml)\n",
    "\n",
    "print(f\"Output XML saved to {output_filename}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 45,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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kerX>2652</MarkerX><MarkerY>1916</MarkerY><MarkerZ>1216</MarkerZ></Marker><Marker><MarkerX>1043</MarkerX><MarkerY>5241</MarkerY><MarkerZ>1221</MarkerZ></Marker><Marker><MarkerX>6507</MarkerX><MarkerY>4780</MarkerY><MarkerZ>1221</MarkerZ></Marker><Marker><MarkerX>4554</MarkerX><MarkerY>1281</MarkerY><MarkerZ>1222</MarkerZ></Marker><Marker><MarkerX>4788</MarkerX><MarkerY>1124</MarkerY><MarkerZ>1223</MarkerZ></Marker><Marker><MarkerX>941</MarkerX><MarkerY>5629</MarkerY><MarkerZ>1224</MarkerZ></Marker><Marker><MarkerX>2787</MarkerX><MarkerY>2037</MarkerY><MarkerZ>1226</MarkerZ></Marker><Marker><MarkerX>4608</MarkerX><MarkerY>1422</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>4698</MarkerX><MarkerY>1374</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>1487</MarkerX><MarkerY>6205</MarkerY><MarkerZ>1227</MarkerZ></Marker><Marker><MarkerX>4829</MarkerX><MarkerY>879</MarkerY><MarkerZ>1602</MarkerZ></Marker><Marker><MarkerX>4472</MarkerX><MarkerY>547</MarkerY><MarkerZ>1603</MarkerZ></Marker><Marker><MarkerX>4389</MarkerX><MarkerY>741</MarkerY><MarkerZ>1614</MarkerZ></Marker></Marker_Type></Marker_Data></CellCounter_Marker_File>\n"
     ]
    }
   ],
   "source": [
    "import xml.etree.ElementTree as ET\n",
    "\n",
    "input_file = '/Users/grant/Desktop/G21/manual_cell_classification.xml'\n",
    "\n",
    "with open(input_file, 'r', encoding='utf-8') as file:\n",
    "    input_xml = file.read()\n",
    "\n",
    "root = ET.fromstring(input_xml)\n",
    "\n",
    "output_root = ET.Element(\"CellCounter_Marker_File\")\n",
    "image_properties = ET.SubElement(output_root, \"Image_Properties\")\n",
    "filename = ET.SubElement(image_properties, \"Image_Filename\")\n",
    "marker_data = ET.SubElement(output_root, \"Marker_Data\")\n",
    "\n",
    "filename.text = root.find(\"record/Image_Filename\").text\n",
    "\n",
    "# Group markers by type\n",
    "markers_by_type = {}\n",
    "\n",
    "for record in root.findall(\"record\"):\n",
    "    marker_type = record.find(\"Type\").text\n",
    "    marker_x = record.find(\"MarkerX\").text\n",
    "    marker_y = record.find(\"MarkerY\").text\n",
    "    marker_z = record.find(\"MarkerZ\").text\n",
    "\n",
    "    if marker_type not in markers_by_type:\n",
    "        markers_by_type[marker_type] = []\n",
    "\n",
    "    markers_by_type[marker_type].append((marker_x, marker_y, marker_z))\n",
    "\n",
    "# Add Marker_Type elements for each distinct type\n",
    "for marker_type, markers in markers_by_type.items():\n",
    "    type_element = ET.SubElement(marker_data, \"Marker_Type\")\n",
    "    type_elem = ET.SubElement(type_element, \"Type\")\n",
    "    type_elem.text = marker_type\n",
    "\n",
    "    for marker_coords in markers:\n",
    "        marker = ET.SubElement(type_element, \"Marker\")\n",
    "        marker_x = ET.SubElement(marker, \"MarkerX\")\n",
    "        marker_y = ET.SubElement(marker, \"MarkerY\")\n",
    "        marker_z = ET.SubElement(marker, \"MarkerZ\")\n",
    "\n",
    "        marker_x.text, marker_y.text, marker_z.text = marker_coords\n",
    "\n",
    "# Convert the output XML tree to a string\n",
    "output_xml = ET.tostring(output_root, encoding=\"UTF-8\", method=\"xml\").decode(\"UTF-8\")\n",
    "\n",
    "print(output_xml)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 46,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Output XML saved to /Users/grant/Desktop/G21/cell_classification.xml\n"
     ]
    }
   ],
   "source": [
    "output_filename = \"/Users/grant/Desktop/G21/cell_classification.xml\"\n",
    "\n",
    "with open(output_filename, \"w\", encoding=\"utf-8\") as output_file:\n",
    "    output_file.write(output_xml)\n",
    "\n",
    "print(f\"Output XML saved to {output_filename}\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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