Create_db_files.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import os\n",
    "import pandas as pd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First build the method to handle the ID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "ID_LENGTH = 15\n",
    "\n",
    "def ID_build(ID_keyword, ID_sequence):\n",
    "    FILL_LENGTH = ID_LENGTH - len(ID_keyword)\n",
    "    ID = ID_keyword+str(ID_sequence).zfill(FILL_LENGTH)\n",
    "    return ID"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Testing the function. As shown below, the ID as expected lenth of 15."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SLIDE0000000032 15\n"
     ]
    }
   ],
   "source": [
    "Sample_id = ID_build('SLIDE',32)\n",
    "print(Sample_id,str(len(Sample_id)))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Read all the datasets prepared"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_data = pd.read_csv('../export_data/grid_data_base.csv')\n",
    "slide_data = pd.read_csv('../export_data/slide_data_raw.csv')\n",
    "specimen_data = pd.read_csv('../export_data/specimen_data.csv')\n",
    "annotation_genus = pd.read_csv('../export_data/grid_annotation_genus.csv')\n",
    "annotation_pseudo = pd.read_csv('../export_data/grid_annotation_pseudo.csv')\n",
    "annotation_species = pd.read_csv('../export_data/grid_annotation_species.csv')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "First handle the slide data. Two tables are expected to be created: Slide ID hub and slide_data. They are linked through the slide ID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Magnification</th>\n",
       "      <th>Height</th>\n",
       "      <th>Width</th>\n",
       "      <th>Path</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td>NaN</td>\n",
       "      <td>50X</td>\n",
       "      <td>4885</td>\n",
       "      <td>11714</td>\n",
       "      <td>\\raw_images\\F403_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>50X</td>\n",
       "      <td>9334</td>\n",
       "      <td>21409</td>\n",
       "      <td>\\raw_images\\HK14DB1C_0_1_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>50X</td>\n",
       "      <td>9326</td>\n",
       "      <td>21391</td>\n",
       "      <td>\\raw_images\\HK14DB1C_104_105_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(1)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9185</td>\n",
       "      <td>21471</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(1)_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(2)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9404</td>\n",
       "      <td>21290</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(2)_50X.tif</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core    Sub_core Magnification  Height  Width  \\\n",
       "0      F403         NaN           50X    4885  11714   \n",
       "1  HK14DB1C         0_1           50X    9334  21409   \n",
       "2  HK14DB1C     104_105           50X    9326  21391   \n",
       "3  HK14DB1C  112_113(1)           50X    9185  21471   \n",
       "4  HK14DB1C  112_113(2)           50X    9404  21290   \n",
       "\n",
       "                                      Path  \n",
       "0                 \\raw_images\\F403_50X.tif  \n",
       "1         \\raw_images\\HK14DB1C_0_1_50X.tif  \n",
       "2     \\raw_images\\HK14DB1C_104_105_50X.tif  \n",
       "3  \\raw_images\\HK14DB1C_112_113(1)_50X.tif  \n",
       "4  \\raw_images\\HK14DB1C_112_113(2)_50X.tif  "
      ]
     },
     "execution_count": 6,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "slide_data = pd.read_csv('slide_data_raw.csv')\n",
    "slide_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Considering the NaN value, we should replace the string fields with empty string and numerical fields with 0."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Magnification</th>\n",
       "      <th>Height</th>\n",
       "      <th>Width</th>\n",
       "      <th>Path</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>50X</td>\n",
       "      <td>4885</td>\n",
       "      <td>11714</td>\n",
       "      <td>\\raw_images\\F403_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>50X</td>\n",
       "      <td>9334</td>\n",
       "      <td>21409</td>\n",
       "      <td>\\raw_images\\HK14DB1C_0_1_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>50X</td>\n",
       "      <td>9326</td>\n",
       "      <td>21391</td>\n",
       "      <td>\\raw_images\\HK14DB1C_104_105_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(1)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9185</td>\n",
       "      <td>21471</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(1)_50X.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(2)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9404</td>\n",
       "      <td>21290</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(2)_50X.tif</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core    Sub_core Magnification  Height  Width  \\\n",
       "0      F403                       50X    4885  11714   \n",
       "1  HK14DB1C         0_1           50X    9334  21409   \n",
       "2  HK14DB1C     104_105           50X    9326  21391   \n",
       "3  HK14DB1C  112_113(1)           50X    9185  21471   \n",
       "4  HK14DB1C  112_113(2)           50X    9404  21290   \n",
       "\n",
       "                                      Path  \n",
       "0                 \\raw_images\\F403_50X.tif  \n",
       "1         \\raw_images\\HK14DB1C_0_1_50X.tif  \n",
       "2     \\raw_images\\HK14DB1C_104_105_50X.tif  \n",
       "3  \\raw_images\\HK14DB1C_112_113(1)_50X.tif  \n",
       "4  \\raw_images\\HK14DB1C_112_113(2)_50X.tif  "
      ]
     },
     "execution_count": 7,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "slide_data = slide_data.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))\n",
    "slide_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "According to the case listed above, transform all table with the transformation to avoid the future problems."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_data = grid_data.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))\n",
    "specimen_data = specimen_data.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))\n",
    "annotation_genus = annotation_genus.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))\n",
    "annotation_pseudo = annotation_pseudo.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))\n",
    "annotation_species = annotation_species.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "As observed above, the Core, Sub_core and Magnification field will be used to create the ID."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [],
   "source": [
    "slide_data['num_id'] = slide_data.groupby(['Path']).ngroup()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "The numeric ID is increasing form 0. Therefore all the IDs could be generated by using the num_id."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "slide_data['slide_id'] = slide_data.apply(lambda x: ID_build('SLIDE',x['num_id']), axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "</style>\n",
       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
       "      <th></th>\n",
       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Magnification</th>\n",
       "      <th>Height</th>\n",
       "      <th>Width</th>\n",
       "      <th>Path</th>\n",
       "      <th>num_id</th>\n",
       "      <th>slide_id</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>50X</td>\n",
       "      <td>4885</td>\n",
       "      <td>11714</td>\n",
       "      <td>\\raw_images\\F403_50X.tif</td>\n",
       "      <td>0</td>\n",
       "      <td>SLIDE0000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>50X</td>\n",
       "      <td>9334</td>\n",
       "      <td>21409</td>\n",
       "      <td>\\raw_images\\HK14DB1C_0_1_50X.tif</td>\n",
       "      <td>1</td>\n",
       "      <td>SLIDE0000000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>50X</td>\n",
       "      <td>9326</td>\n",
       "      <td>21391</td>\n",
       "      <td>\\raw_images\\HK14DB1C_104_105_50X.tif</td>\n",
       "      <td>2</td>\n",
       "      <td>SLIDE0000000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(1)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9185</td>\n",
       "      <td>21471</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(1)_50X.tif</td>\n",
       "      <td>3</td>\n",
       "      <td>SLIDE0000000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>112_113(2)</td>\n",
       "      <td>50X</td>\n",
       "      <td>9404</td>\n",
       "      <td>21290</td>\n",
       "      <td>\\raw_images\\HK14DB1C_112_113(2)_50X.tif</td>\n",
       "      <td>4</td>\n",
       "      <td>SLIDE0000000004</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core    Sub_core Magnification  Height  Width  \\\n",
       "0      F403                       50X    4885  11714   \n",
       "1  HK14DB1C         0_1           50X    9334  21409   \n",
       "2  HK14DB1C     104_105           50X    9326  21391   \n",
       "3  HK14DB1C  112_113(1)           50X    9185  21471   \n",
       "4  HK14DB1C  112_113(2)           50X    9404  21290   \n",
       "\n",
       "                                      Path  num_id         slide_id  \n",
       "0                 \\raw_images\\F403_50X.tif       0  SLIDE0000000000  \n",
       "1         \\raw_images\\HK14DB1C_0_1_50X.tif       1  SLIDE0000000001  \n",
       "2     \\raw_images\\HK14DB1C_104_105_50X.tif       2  SLIDE0000000002  \n",
       "3  \\raw_images\\HK14DB1C_112_113(1)_50X.tif       3  SLIDE0000000003  \n",
       "4  \\raw_images\\HK14DB1C_112_113(2)_50X.tif       4  SLIDE0000000004  "
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "slide_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Export the target data to csv form"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "slide_id_hub_cols = ['slide_id','Core','Sub_core', 'Magnification']\n",
    "slide_data_cols = ['slide_id','Height','Width','Path']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "metadata": {},
   "outputs": [],
   "source": [
    "slide_data.to_csv('slide_id_hub.csv', columns = slide_id_hub_cols, index=None)\n",
    "slide_data.to_csv('slide_data.csv', columns = slide_data_cols, index=None)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Next handle grid related tables. First crated the id for the grids. Follows the sequence of the slide."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th></th>\n",
       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Magnification</th>\n",
       "      <th>Height</th>\n",
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       "      <th>Grid Path</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>1</td>\n",
       "      <td>50X</td>\n",
       "      <td>910</td>\n",
       "      <td>895</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_1.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>10</td>\n",
       "      <td>50X</td>\n",
       "      <td>895</td>\n",
       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_10.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>11</td>\n",
       "      <td>50X</td>\n",
       "      <td>905</td>\n",
       "      <td>904</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_11.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>50X</td>\n",
       "      <td>900</td>\n",
       "      <td>910</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_12.tif</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>50X</td>\n",
       "      <td>890</td>\n",
       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_13.tif</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Core Sub_core  Grid number Magnification  Height  Width  \\\n",
       "0  F403                     1           50X     910    895   \n",
       "1  F403                    10           50X     895    905   \n",
       "2  F403                    11           50X     905    904   \n",
       "3  F403                    12           50X     900    910   \n",
       "4  F403                    13           50X     890    905   \n",
       "\n",
       "                                    Grid Path  \n",
       "0   \\Grid_images\\F403_50X\\F403_50X_grid_1.tif  \n",
       "1  \\Grid_images\\F403_50X\\F403_50X_grid_10.tif  \n",
       "2  \\Grid_images\\F403_50X\\F403_50X_grid_11.tif  \n",
       "3  \\Grid_images\\F403_50X\\F403_50X_grid_12.tif  \n",
       "4  \\Grid_images\\F403_50X\\F403_50X_grid_13.tif  "
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grid_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [],
   "source": [
    "def build_id_from_column(unique_col_name, id_col_name, id_target, df):\n",
    "    df['num_id'] = df.groupby([unique_col_name]).ngroup()\n",
    "    df[id_col_name] = df.apply(lambda x: ID_build(id_target,x['num_id']), axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [],
   "source": [
    "build_id_from_column('Grid Path', 'grid_id','GRID',grid_data)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Magnification</th>\n",
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       "      <th>Width</th>\n",
       "      <th>Grid Path</th>\n",
       "      <th>num_id</th>\n",
       "      <th>grid_id</th>\n",
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       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
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       "      <td>50X</td>\n",
       "      <td>910</td>\n",
       "      <td>895</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_1.tif</td>\n",
       "      <td>0</td>\n",
       "      <td>GRID00000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>10</td>\n",
       "      <td>50X</td>\n",
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       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_10.tif</td>\n",
       "      <td>1</td>\n",
       "      <td>GRID00000000001</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>11</td>\n",
       "      <td>50X</td>\n",
       "      <td>905</td>\n",
       "      <td>904</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_11.tif</td>\n",
       "      <td>2</td>\n",
       "      <td>GRID00000000002</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>50X</td>\n",
       "      <td>900</td>\n",
       "      <td>910</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_12.tif</td>\n",
       "      <td>3</td>\n",
       "      <td>GRID00000000003</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>50X</td>\n",
       "      <td>890</td>\n",
       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_13.tif</td>\n",
       "      <td>4</td>\n",
       "      <td>GRID00000000004</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Core Sub_core  Grid number Magnification  Height  Width  \\\n",
       "0  F403                     1           50X     910    895   \n",
       "1  F403                    10           50X     895    905   \n",
       "2  F403                    11           50X     905    904   \n",
       "3  F403                    12           50X     900    910   \n",
       "4  F403                    13           50X     890    905   \n",
       "\n",
       "                                    Grid Path  num_id          grid_id  \n",
       "0   \\Grid_images\\F403_50X\\F403_50X_grid_1.tif       0  GRID00000000000  \n",
       "1  \\Grid_images\\F403_50X\\F403_50X_grid_10.tif       1  GRID00000000001  \n",
       "2  \\Grid_images\\F403_50X\\F403_50X_grid_11.tif       2  GRID00000000002  \n",
       "3  \\Grid_images\\F403_50X\\F403_50X_grid_12.tif       3  GRID00000000003  \n",
       "4  \\Grid_images\\F403_50X\\F403_50X_grid_13.tif       4  GRID00000000004  "
      ]
     },
     "execution_count": 17,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grid_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 18,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_data['status_code'] = 99"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 19,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>Grid number</th>\n",
       "      <th>Magnification</th>\n",
       "      <th>Height</th>\n",
       "      <th>Width</th>\n",
       "      <th>Grid Path</th>\n",
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       "      <th>0</th>\n",
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       "      <td>0</td>\n",
       "      <td>GRID00000000000</td>\n",
       "      <td>99</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>F403</td>\n",
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       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_10.tif</td>\n",
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       "      <td>99</td>\n",
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       "      <th>2</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>11</td>\n",
       "      <td>50X</td>\n",
       "      <td>905</td>\n",
       "      <td>904</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_11.tif</td>\n",
       "      <td>2</td>\n",
       "      <td>GRID00000000002</td>\n",
       "      <td>99</td>\n",
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       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>50X</td>\n",
       "      <td>900</td>\n",
       "      <td>910</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_12.tif</td>\n",
       "      <td>3</td>\n",
       "      <td>GRID00000000003</td>\n",
       "      <td>99</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>50X</td>\n",
       "      <td>890</td>\n",
       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_13.tif</td>\n",
       "      <td>4</td>\n",
       "      <td>GRID00000000004</td>\n",
       "      <td>99</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Core Sub_core  Grid number Magnification  Height  Width  \\\n",
       "0  F403                     1           50X     910    895   \n",
       "1  F403                    10           50X     895    905   \n",
       "2  F403                    11           50X     905    904   \n",
       "3  F403                    12           50X     900    910   \n",
       "4  F403                    13           50X     890    905   \n",
       "\n",
       "                                    Grid Path  num_id          grid_id  \\\n",
       "0   \\Grid_images\\F403_50X\\F403_50X_grid_1.tif       0  GRID00000000000   \n",
       "1  \\Grid_images\\F403_50X\\F403_50X_grid_10.tif       1  GRID00000000001   \n",
       "2  \\Grid_images\\F403_50X\\F403_50X_grid_11.tif       2  GRID00000000002   \n",
       "3  \\Grid_images\\F403_50X\\F403_50X_grid_12.tif       3  GRID00000000003   \n",
       "4  \\Grid_images\\F403_50X\\F403_50X_grid_13.tif       4  GRID00000000004   \n",
       "\n",
       "   status_code  \n",
       "0           99  \n",
       "1           99  \n",
       "2           99  \n",
       "3           99  \n",
       "4           99  "
      ]
     },
     "execution_count": 19,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grid_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Creating slide ID column for the grid_data table."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 20,
   "metadata": {},
   "outputs": [],
   "source": [
    "slide_ID_match = slide_data[slide_id_hub_cols].copy()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 21,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>grid_id</th>\n",
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       "      <td>99</td>\n",
       "      <td>SLIDE0000000000</td>\n",
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       "      <td>50X</td>\n",
       "      <td>905</td>\n",
       "      <td>904</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_11.tif</td>\n",
       "      <td>2</td>\n",
       "      <td>GRID00000000002</td>\n",
       "      <td>99</td>\n",
       "      <td>SLIDE0000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>12</td>\n",
       "      <td>50X</td>\n",
       "      <td>900</td>\n",
       "      <td>910</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_12.tif</td>\n",
       "      <td>3</td>\n",
       "      <td>GRID00000000003</td>\n",
       "      <td>99</td>\n",
       "      <td>SLIDE0000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>13</td>\n",
       "      <td>50X</td>\n",
       "      <td>890</td>\n",
       "      <td>905</td>\n",
       "      <td>\\Grid_images\\F403_50X\\F403_50X_grid_13.tif</td>\n",
       "      <td>4</td>\n",
       "      <td>GRID00000000004</td>\n",
       "      <td>99</td>\n",
       "      <td>SLIDE0000000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "   Core Sub_core  Grid number Magnification  Height  Width  \\\n",
       "0  F403                     1           50X     910    895   \n",
       "1  F403                    10           50X     895    905   \n",
       "2  F403                    11           50X     905    904   \n",
       "3  F403                    12           50X     900    910   \n",
       "4  F403                    13           50X     890    905   \n",
       "\n",
       "                                    Grid Path  num_id          grid_id  \\\n",
       "0   \\Grid_images\\F403_50X\\F403_50X_grid_1.tif       0  GRID00000000000   \n",
       "1  \\Grid_images\\F403_50X\\F403_50X_grid_10.tif       1  GRID00000000001   \n",
       "2  \\Grid_images\\F403_50X\\F403_50X_grid_11.tif       2  GRID00000000002   \n",
       "3  \\Grid_images\\F403_50X\\F403_50X_grid_12.tif       3  GRID00000000003   \n",
       "4  \\Grid_images\\F403_50X\\F403_50X_grid_13.tif       4  GRID00000000004   \n",
       "\n",
       "   status_code         slide_id  \n",
       "0           99  SLIDE0000000000  \n",
       "1           99  SLIDE0000000000  \n",
       "2           99  SLIDE0000000000  \n",
       "3           99  SLIDE0000000000  \n",
       "4           99  SLIDE0000000000  "
      ]
     },
     "execution_count": 21,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grid_data = grid_data.merge(slide_ID_match, how='left')\n",
    "grid_data.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 22,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_data_cols = ['grid_id','slide_id','Grid number','Height','Width','status_code','Grid Path']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 23,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_data.to_csv('grid_data.csv',columns = grid_data_cols, index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Ceating the annotation tables. First bind the dataframes"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 24,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_annotation = pd.concat([annotation_pseudo,annotation_genus, annotation_species], ignore_index=True)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 25,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
       "<div>\n",
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       "<table border=\"1\" class=\"dataframe\">\n",
       "  <thead>\n",
       "    <tr style=\"text-align: right;\">\n",
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       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Annotation type</th>\n",
       "      <th>Ostracod count</th>\n",
       "      <th>Annotation path</th>\n",
       "    </tr>\n",
       "  </thead>\n",
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>1</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>8</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>2</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>5</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>3</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>4</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>6</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>1</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core Sub_core  Grid number Annotation type  Ostracod count  \\\n",
       "0      F403                     1          pseudo               8   \n",
       "1      F403                     2          pseudo               5   \n",
       "2      F403                     3          pseudo               2   \n",
       "3      F403                     4          pseudo               6   \n",
       "4  HK14DB1C      0_1            1          pseudo               2   \n",
       "\n",
       "                                     Annotation path  \n",
       "0  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  \n",
       "1  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  \n",
       "2  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  \n",
       "3  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  \n",
       "4  \\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...  "
      ]
     },
     "execution_count": 25,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_annotation = all_annotation.rename(columns = {\"Grid No.\":\"Grid number\"})\n",
    "all_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 26,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Annotation type</th>\n",
       "      <th>Ostracod count</th>\n",
       "      <th>Annotation path</th>\n",
       "      <th>grid_id</th>\n",
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       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
       "      <td>F403</td>\n",
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       "      <td>8</td>\n",
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       "      <td>GRID00000000000</td>\n",
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       "      <th>1</th>\n",
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       "      <td>5</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000011</td>\n",
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       "      <td></td>\n",
       "      <td>3</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000022</td>\n",
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       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>4</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>6</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000033</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>1</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...</td>\n",
       "      <td>GRID00000000060</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core Sub_core  Grid number Annotation type  Ostracod count  \\\n",
       "0      F403                     1          pseudo               8   \n",
       "1      F403                     2          pseudo               5   \n",
       "2      F403                     3          pseudo               2   \n",
       "3      F403                     4          pseudo               6   \n",
       "4  HK14DB1C      0_1            1          pseudo               2   \n",
       "\n",
       "                                     Annotation path          grid_id  \n",
       "0  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000000  \n",
       "1  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000011  \n",
       "2  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000022  \n",
       "3  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000033  \n",
       "4  \\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...  GRID00000000060  "
      ]
     },
     "execution_count": 26,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "grid_ID_match = grid_data[['grid_id','Core','Sub_core','Grid number']].copy()\n",
    "all_annotation = all_annotation.merge(grid_ID_match, how='left')\n",
    "all_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 27,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>Core</th>\n",
       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Annotation type</th>\n",
       "      <th>Ostracod count</th>\n",
       "      <th>Annotation path</th>\n",
       "      <th>grid_id</th>\n",
       "      <th>num_id</th>\n",
       "      <th>Annotation_id</th>\n",
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       "  <tbody>\n",
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       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000000</td>\n",
       "      <td>17400</td>\n",
       "      <td>ANNO00000017400</td>\n",
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       "    <tr>\n",
       "      <th>1</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>2</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>5</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000011</td>\n",
       "      <td>17401</td>\n",
       "      <td>ANNO00000017401</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>3</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000022</td>\n",
       "      <td>17402</td>\n",
       "      <td>ANNO00000017402</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>F403</td>\n",
       "      <td></td>\n",
       "      <td>4</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>6</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...</td>\n",
       "      <td>GRID00000000033</td>\n",
       "      <td>17403</td>\n",
       "      <td>ANNO00000017403</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB1C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>1</td>\n",
       "      <td>pseudo</td>\n",
       "      <td>2</td>\n",
       "      <td>\\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...</td>\n",
       "      <td>GRID00000000060</td>\n",
       "      <td>17404</td>\n",
       "      <td>ANNO00000017404</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core Sub_core  Grid number Annotation type  Ostracod count  \\\n",
       "0      F403                     1          pseudo               8   \n",
       "1      F403                     2          pseudo               5   \n",
       "2      F403                     3          pseudo               2   \n",
       "3      F403                     4          pseudo               6   \n",
       "4  HK14DB1C      0_1            1          pseudo               2   \n",
       "\n",
       "                                     Annotation path          grid_id  num_id  \\\n",
       "0  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000000   17400   \n",
       "1  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000011   17401   \n",
       "2  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000022   17402   \n",
       "3  \\pseudo_annotation\\pascal_voc\\F403_50X\\F403_50...  GRID00000000033   17403   \n",
       "4  \\pseudo_annotation\\pascal_voc\\HK14DB1C_0_1_50X...  GRID00000000060   17404   \n",
       "\n",
       "     Annotation_id  \n",
       "0  ANNO00000017400  \n",
       "1  ANNO00000017401  \n",
       "2  ANNO00000017402  \n",
       "3  ANNO00000017403  \n",
       "4  ANNO00000017404  "
      ]
     },
     "execution_count": 27,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "build_id_from_column('Annotation path','Annotation_id','ANNO',all_annotation)\n",
    "all_annotation.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 44,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_annotations_cols = ['Annotation_id', 'grid_id', 'Annotation type', 'Annotation path']\n",
    "annotation_data_cols = ['Annotation_id', 'Ostracod count']\n",
    "all_annotation.to_csv('grid_annotations.csv',columns = grid_annotations_cols,index=False)\n",
    "all_annotation.to_csv('annotation_data.csv',columns=annotation_data_cols,index=False)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create the data table for genus and species. First binding the slide id and grid id into the dataset"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [],
   "source": [
    "specimen_data = pd.read_csv('specimen_data.csv')\n",
    "specimen_data = specimen_data.transform(lambda x: x.fillna('') if x.dtype == 'object' else x.fillna(0))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 31,
   "metadata": {},
   "outputs": [],
   "source": [
    "grid_slide_id_match = grid_data[['grid_id','slide_id','Core','Sub_core','Grid number']]"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 32,
   "metadata": {},
   "outputs": [],
   "source": [
    "specimen_data = specimen_data.rename(columns = {\"Grid No.\": \"Grid number\"})\n",
    "specimen_data = specimen_data.merge(grid_slide_id_match, how = 'left')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 33,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/html": [
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       "      <th>Sub_core</th>\n",
       "      <th>Grid number</th>\n",
       "      <th>Height</th>\n",
       "      <th>Width</th>\n",
       "      <th>Genus</th>\n",
       "      <th>Species</th>\n",
       "      <th>Specimen Path</th>\n",
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       "      <th>slide_id</th>\n",
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       "      <td>117</td>\n",
       "      <td>215</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001095</td>\n",
       "      <td>SLIDE0000000018</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
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       "      <td>144</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001503</td>\n",
       "      <td>SLIDE0000000024</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>2</th>\n",
       "      <td>HK14DB2C</td>\n",
       "      <td>0_1</td>\n",
       "      <td>8</td>\n",
       "      <td>260</td>\n",
       "      <td>220</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001558</td>\n",
       "      <td>SLIDE0000000024</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HK14DB2C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>10</td>\n",
       "      <td>201</td>\n",
       "      <td>277</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001561</td>\n",
       "      <td>SLIDE0000000025</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB2C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>10</td>\n",
       "      <td>169</td>\n",
       "      <td>285</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001561</td>\n",
       "      <td>SLIDE0000000025</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core Sub_core  Grid number  Height  Width         Genus  \\\n",
       "0  HK14DB1C    72_73           23     117    215  aglaiocypris   \n",
       "1  HK14DB2C      0_1           12     254    144  aglaiocypris   \n",
       "2  HK14DB2C      0_1            8     260    220  aglaiocypris   \n",
       "3  HK14DB2C  104_105           10     201    277  aglaiocypris   \n",
       "4  HK14DB2C  104_105           10     169    285  aglaiocypris   \n",
       "\n",
       "                     Species  \\\n",
       "0  aglaiocypris unidentified   \n",
       "1  aglaiocypris unidentified   \n",
       "2  aglaiocypris unidentified   \n",
       "3  aglaiocypris unidentified   \n",
       "4  aglaiocypris unidentified   \n",
       "\n",
       "                                       Specimen Path          grid_id  \\\n",
       "0  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001095   \n",
       "1  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001503   \n",
       "2  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001558   \n",
       "3  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001561   \n",
       "4  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001561   \n",
       "\n",
       "          slide_id  \n",
       "0  SLIDE0000000018  \n",
       "1  SLIDE0000000024  \n",
       "2  SLIDE0000000024  \n",
       "3  SLIDE0000000025  \n",
       "4  SLIDE0000000025  "
      ]
     },
     "execution_count": 33,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "specimen_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Build ID from the specimen path for specimen ID, species for species ID and genus for genus ID"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 34,
   "metadata": {},
   "outputs": [
    {
     "data": {
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       "      <td>HK14DB1C</td>\n",
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       "      <td>144</td>\n",
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       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001503</td>\n",
       "      <td>SLIDE0000000024</td>\n",
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       "    <tr>\n",
       "      <th>2</th>\n",
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       "      <td>0_1</td>\n",
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       "      <td>260</td>\n",
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       "      <td>aglaiocypris unidentified</td>\n",
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       "      <td>GRID00000001558</td>\n",
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       "      <td>SPCM00000000002</td>\n",
       "      <td>GENU00000000000</td>\n",
       "      <td>SPEC00000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>3</th>\n",
       "      <td>HK14DB2C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>10</td>\n",
       "      <td>201</td>\n",
       "      <td>277</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001561</td>\n",
       "      <td>SLIDE0000000025</td>\n",
       "      <td>0</td>\n",
       "      <td>SPCM00000000003</td>\n",
       "      <td>GENU00000000000</td>\n",
       "      <td>SPEC00000000000</td>\n",
       "    </tr>\n",
       "    <tr>\n",
       "      <th>4</th>\n",
       "      <td>HK14DB2C</td>\n",
       "      <td>104_105</td>\n",
       "      <td>10</td>\n",
       "      <td>169</td>\n",
       "      <td>285</td>\n",
       "      <td>aglaiocypris</td>\n",
       "      <td>aglaiocypris unidentified</td>\n",
       "      <td>\\class_images\\aglaiocypris unidentified\\HK14DB...</td>\n",
       "      <td>GRID00000001561</td>\n",
       "      <td>SLIDE0000000025</td>\n",
       "      <td>0</td>\n",
       "      <td>SPCM00000000004</td>\n",
       "      <td>GENU00000000000</td>\n",
       "      <td>SPEC00000000000</td>\n",
       "    </tr>\n",
       "  </tbody>\n",
       "</table>\n",
       "</div>"
      ],
      "text/plain": [
       "       Core Sub_core  Grid number  Height  Width         Genus  \\\n",
       "0  HK14DB1C    72_73           23     117    215  aglaiocypris   \n",
       "1  HK14DB2C      0_1           12     254    144  aglaiocypris   \n",
       "2  HK14DB2C      0_1            8     260    220  aglaiocypris   \n",
       "3  HK14DB2C  104_105           10     201    277  aglaiocypris   \n",
       "4  HK14DB2C  104_105           10     169    285  aglaiocypris   \n",
       "\n",
       "                     Species  \\\n",
       "0  aglaiocypris unidentified   \n",
       "1  aglaiocypris unidentified   \n",
       "2  aglaiocypris unidentified   \n",
       "3  aglaiocypris unidentified   \n",
       "4  aglaiocypris unidentified   \n",
       "\n",
       "                                       Specimen Path          grid_id  \\\n",
       "0  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001095   \n",
       "1  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001503   \n",
       "2  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001558   \n",
       "3  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001561   \n",
       "4  \\class_images\\aglaiocypris unidentified\\HK14DB...  GRID00000001561   \n",
       "\n",
       "          slide_id  num_id      specimen_id         genus_id       species_id  \n",
       "0  SLIDE0000000018       0  SPCM00000000000  GENU00000000000  SPEC00000000000  \n",
       "1  SLIDE0000000024       0  SPCM00000000001  GENU00000000000  SPEC00000000000  \n",
       "2  SLIDE0000000024       0  SPCM00000000002  GENU00000000000  SPEC00000000000  \n",
       "3  SLIDE0000000025       0  SPCM00000000003  GENU00000000000  SPEC00000000000  \n",
       "4  SLIDE0000000025       0  SPCM00000000004  GENU00000000000  SPEC00000000000  "
      ]
     },
     "execution_count": 34,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "build_id_from_column('Specimen Path','specimen_id','SPCM',specimen_data)\n",
    "build_id_from_column('Genus','genus_id','GENU',specimen_data)\n",
    "build_id_from_column('Species','species_id','SPEC',specimen_data)\n",
    "specimen_data.head()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Generate output for the database"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 35,
   "metadata": {},
   "outputs": [],
   "source": [
    "specimens_cols = ['specimen_id','grid_id','slide_id','genus_id', 'species_id', 'Height', 'Width', 'Specimen Path']"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 36,
   "metadata": {},
   "outputs": [],
   "source": [
    "specimen_data.to_csv('specimen_data_to_DB.csv', columns = specimens_cols, index = None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 37,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_genus = specimen_data[['Genus','genus_id']].value_counts()\n",
    "all_species = specimen_data[['Species', 'species_id']].value_counts()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 38,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Species                      species_id     \n",
       "sinocytheridea impressa      SPEC00000000175    22283\n",
       "neomonoceratina delicata     SPEC00000000125     9416\n",
       "propontocypris unidentified  SPEC00000000161     4888\n",
       "bicornucythere bisanensis    SPEC00000000019     3035\n",
       "keijella kloempritensis      SPEC00000000089     2870\n",
       "                                                ...  \n",
       "semicytherura cfundata       SPEC00000000168        1\n",
       "parakrithe japonica          SPEC00000000146        1\n",
       "pistocythereis unidentified  SPEC00000000157        1\n",
       "bythoceratina cfrobusta      SPEC00000000026        1\n",
       "hemicytheridea cancellata    SPEC00000000072        1\n",
       "Length: 197, dtype: int64"
      ]
     },
     "execution_count": 38,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_species"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 39,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_species_data = all_species.rename_axis(['Species', 'species_id']).reset_index(name='counts')\n",
    "all_genus_data = all_genus.rename_axis(['Genus', 'genus_id']).reset_index(name='counts')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 40,
   "metadata": {},
   "outputs": [],
   "source": [
    "all_species_data.to_csv('species.csv', columns = ['species_id', 'Species'], index=None)\n",
    "all_genus_data.to_csv('genus.csv', columns = ['genus_id', 'Genus'], index=None)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 41,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "'SPEC00000000196'"
      ]
     },
     "execution_count": 41,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "all_species_data['species_id'].max()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Record the maximun id for future use."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 42,
   "metadata": {},
   "outputs": [],
   "source": [
    "def decode_max_id(max_id):\n",
    "    return int(max_id[5:])"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 43,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "SLIDE0000000325 GRID00000019276 ANNO00000046630 SPCM00000069114 SPEC00000000196 GENU00000000078\n"
     ]
    }
   ],
   "source": [
    "all_ids = ['slide_id','grid_id','genus_id','species_id','specimen_id','annotation_id']\n",
    "slide_id_max = slide_data['slide_id'].max()\n",
    "grid_id_max = grid_data['grid_id'].max()\n",
    "annotation_id_max = all_annotation['Annotation_id'].max()\n",
    "specimen_id_max = specimen_data['specimen_id'].max()\n",
    "species_id_max = all_species_data['species_id'].max()\n",
    "genus_id_max = all_genus_data['genus_id'].max()\n",
    "print(slide_id_max, grid_id_max, annotation_id_max, specimen_id_max, species_id_max, genus_id_max)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Create the initial data by hand"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Experiments"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {},
   "outputs": [],
   "source": [
    "target_cols = slide_id_hub_cols\n",
    "target_cols.remove('slide_id')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Core        Sub_core  Magnification\n",
       "HK14DB1C    0_1       50X              1\n",
       "subSurface  ES4       50X              1\n",
       "            MS16      50X              1\n",
       "            MS15      50X              1\n",
       "            MS14      50X              1\n",
       "                                      ..\n",
       "HK14TLH2C   4_5       50X              1\n",
       "            48_49     50X              1\n",
       "            32_33     50X              1\n",
       "            16_17     50X              1\n",
       "surface     _NS5      50X              1\n",
       "Length: 318, dtype: int64"
      ]
     },
     "execution_count": 14,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "vc = slide_data[target_cols].value_counts()\n",
    "vc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "pandas.core.series.Series"
      ]
     },
     "execution_count": 15,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "type(vc)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "('HK14DB1C', '0_1', '50X')\n",
      "1\n",
      "('subSurface', 'ES4', '50X')\n",
      "1\n",
      "('subSurface', 'MS16', '50X')\n",
      "1\n",
      "('subSurface', 'MS15', '50X')\n",
      "1\n",
      "('subSurface', 'MS14', '50X')\n",
      "1\n",
      "('subSurface', 'MS13', '50X')\n",
      "1\n",
      "('subSurface', 'MS1', '50X')\n",
      "1\n",
      "('subSurface', 'JS2', '50X')\n",
      "1\n",
      "('subSurface', 'ES5', '50X')\n",
      "1\n",
      "('subSurface', 'ES3', '50X')\n",
      "1\n",
      "('subSurface', 'MS2', '50X')\n",
      "1\n",
      "('subSurface', 'ES2', '50X')\n",
      "1\n",
      "('subSurface', 'ES1', '50X')\n",
      "1\n",
      "('subSurface', 'DS7', '50X')\n",
      "1\n",
      "('subSurface', 'DS4', '50X')\n",
      "1\n",
      "('subSurface', 'DS3', '50X')\n",
      "1\n",
      "('subSurface', 'DS2', '50X')\n",
      "1\n",
      "('subSurface', 'DS1', '50X')\n",
      "1\n",
      "('subSurface', 'MS17', '50X')\n",
      "1\n",
      "('subSurface', 'MS3', '50X')\n",
      "1\n",
      "('rawSample', 'B5b', '50X')\n",
      "1\n",
      "('subSurface', 'NS6', '50X')\n",
      "1\n",
      "('subSurface', 'SS2', '50X')\n",
      "1\n",
      "('subSurface', 'SS1', '50X')\n",
      "1\n",
      "('subSurface', 'PS6', '50X')\n",
      "1\n",
      "('subSurface', 'PS5', '50X')\n",
      "1\n",
      "('subSurface', 'PS4', '50X')\n",
      "1\n",
      "('subSurface', 'PS3', '50X')\n",
      "1\n",
      "('subSurface', 'PS2', '50X')\n",
      "1\n",
      "('subSurface', 'NS5', '50X')\n",
      "1\n",
      "('subSurface', 'MS4', '50X')\n",
      "1\n",
      "('subSurface', 'NS4', '50X')\n",
      "1\n",
      "('subSurface', 'NS3', '50X')\n",
      "1\n",
      "('subSurface', 'NS2', '50X')\n",
      "1\n",
      "('subSurface', 'MS8', '50X')\n",
      "1\n",
      "('subSurface', 'MS7', '50X')\n",
      "1\n",
      "('subSurface', 'MS6', '50X')\n",
      "1\n",
      "('subSurface', 'MS5', '50X')\n",
      "1\n",
      "('slide1', '1_60', '50X')\n",
      "1\n",
      "('rawSample', 'B5a', '50X')\n",
      "1\n",
      "('subSurface', 'SS4', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_71', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_85', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_83', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_81', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_79', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_77', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_75', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_73', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_7', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_89', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_69', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_67', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_65', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_64(2)', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_64(1)', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_63', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_62', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_87', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_9', '50X')\n",
      "1\n",
      "('rawSample', 'B4b', '50X')\n",
      "1\n",
      "('STZK04', '726_1007g', '50X')\n",
      "1\n",
      "('rawSample', 'B4a', '50X')\n",
      "1\n",
      "('rawSample', 'B3b', '50X')\n",
      "1\n",
      "('rawSample', 'B3a', '50X')\n",
      "1\n",
      "('rawSample', 'B2b', '50X')\n",
      "1\n",
      "('rawSample', 'B2a', '50X')\n",
      "1\n",
      "('rawSample', 'B1b', '50X')\n",
      "1\n",
      "('rawSample', 'B1a', '50X')\n",
      "1\n",
      "('STZK04', '726', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_91', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_99', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_97', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_96', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_95', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_94', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_93', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_92', '50X')\n",
      "1\n",
      "('subSurface', 'SS3', '50X')\n",
      "1\n",
      "('subSurface', 'SS5', '50X')\n",
      "1\n",
      "('HK14DB1C', '104_105', '50X')\n",
      "1\n",
      "('surface', 'PS6', '50X')\n",
      "1\n",
      "('surface', 'SS7', '50X')\n",
      "1\n",
      "('surface', 'SS6', '50X')\n",
      "1\n",
      "('surface', 'SS5', '50X')\n",
      "1\n",
      "('surface', 'SS4', '50X')\n",
      "1\n",
      "('surface', 'SS3', '50X')\n",
      "1\n",
      "('surface', 'SS2', '50X')\n",
      "1\n",
      "('surface', 'SS1', '50X')\n",
      "1\n",
      "('surface', 'PS5', '50X')\n",
      "1\n",
      "('surface', 'TS2', '50X')\n",
      "1\n",
      "('surface', 'PS4', '50X')\n",
      "1\n",
      "('surface', 'PS3', '50X')\n",
      "1\n",
      "('surface', 'PS2', '50X')\n",
      "1\n",
      "('surface', 'NS6', '50X')\n",
      "1\n",
      "('surface', 'NS5', '50X')\n",
      "1\n",
      "('surface', 'NS4', '50X')\n",
      "1\n",
      "('surface', 'NS3', '50X')\n",
      "1\n",
      "('surface', 'SS8', '50X')\n",
      "1\n",
      "('surface', 'TS3', '50X')\n",
      "1\n",
      "('surface', 'MS8', '50X')\n",
      "1\n",
      "('surface', 'VS19', '50X')\n",
      "1\n",
      "('surface', '_NS4', '50X')\n",
      "1\n",
      "('surface', 'WS2', '50X')\n",
      "1\n",
      "('surface', 'VS9', '50X')\n",
      "1\n",
      "('surface', 'VS6', '50X')\n",
      "1\n",
      "('surface', 'VS5', '50X')\n",
      "1\n",
      "('surface', 'VS4', '50X')\n",
      "1\n",
      "('surface', 'VS21', '50X')\n",
      "1\n",
      "('surface', 'VS17', '50X')\n",
      "1\n",
      "('surface', 'TS4', '50X')\n",
      "1\n",
      "('surface', 'VS14', '50X')\n",
      "1\n",
      "('surface', 'VS13', '50X')\n",
      "1\n",
      "('surface', 'VS12', '50X')\n",
      "1\n",
      "('surface', 'VS10', '50X')\n",
      "1\n",
      "('surface', 'VS1', '50X')\n",
      "1\n",
      "('surface', 'TS7', '50X')\n",
      "1\n",
      "('surface', 'TS5', '50X')\n",
      "1\n",
      "('surface', 'NS2', '50X')\n",
      "1\n",
      "('surface', 'MS7', '50X')\n",
      "1\n",
      "('subSurface', 'SS6', '50X')\n",
      "1\n",
      "('subSurface', 'VS10', '50X')\n",
      "1\n",
      "('subSurface', 'WS2', '50X')\n",
      "1\n",
      "('subSurface', 'VS9', '50X')\n",
      "1\n",
      "('subSurface', 'VS6', '50X')\n",
      "1\n",
      "('subSurface', 'VS5', '50X')\n",
      "1\n",
      "('subSurface', 'VS21', '50X')\n",
      "1\n",
      "('subSurface', 'VS19', '50X')\n",
      "1\n",
      "('subSurface', 'VS13', '50X')\n",
      "1\n",
      "('subSurface', 'VS1', '50X')\n",
      "1\n",
      "('surface', 'DS3', '50X')\n",
      "1\n",
      "('subSurface', 'TS7', '50X')\n",
      "1\n",
      "('subSurface', 'TS5', '50X')\n",
      "1\n",
      "('subSurface', 'TS4', '50X')\n",
      "1\n",
      "('subSurface', 'TS3', '50X')\n",
      "1\n",
      "('subSurface', 'TS2', '50X')\n",
      "1\n",
      "('subSurface', 'SS8', '50X')\n",
      "1\n",
      "('subSurface', 'SS7', '50X')\n",
      "1\n",
      "('surface', 'DS2', '50X')\n",
      "1\n",
      "('surface', 'DS4', '50X')\n",
      "1\n",
      "('surface', 'MS6', '50X')\n",
      "1\n",
      "('surface', 'MS14', '50X')\n",
      "1\n",
      "('surface', 'MS5', '50X')\n",
      "1\n",
      "('surface', 'MS4', '50X')\n",
      "1\n",
      "('surface', 'MS3', '50X')\n",
      "1\n",
      "('surface', 'MS2', '50X')\n",
      "1\n",
      "('surface', 'MS17', '50X')\n",
      "1\n",
      "('surface', 'MS16', '50X')\n",
      "1\n",
      "('surface', 'MS15', '50X')\n",
      "1\n",
      "('surface', 'MS13', '50X')\n",
      "1\n",
      "('surface', 'DS7', '50X')\n",
      "1\n",
      "('surface', 'MS1', '50X')\n",
      "1\n",
      "('surface', 'JS2', '50X')\n",
      "1\n",
      "('surface', 'ES5', '50X')\n",
      "1\n",
      "('surface', 'ES4', '50X')\n",
      "1\n",
      "('surface', 'ES3', '50X')\n",
      "1\n",
      "('surface', 'ES2', '50X')\n",
      "1\n",
      "('surface', 'ES1', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_61(2)', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_61(1)', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_60', '50X')\n",
      "1\n",
      "('HK14DB2C', '76_77', '50X')\n",
      "1\n",
      "('HK14PCR1C', '0_1', '50X')\n",
      "1\n",
      "('HK14DB2C', '96_97', '50X')\n",
      "1\n",
      "('HK14DB2C', '92_93', '50X')\n",
      "1\n",
      "('HK14DB2C', '8_9', '50X')\n",
      "1\n",
      "('HK14DB2C', '88_89', '50X')\n",
      "1\n",
      "('HK14DB2C', '84_85', '50X')\n",
      "1\n",
      "('HK14DB2C', '80_81', '50X')\n",
      "1\n",
      "('HK14DB2C', '72_73', '50X')\n",
      "1\n",
      "('HK14PCR1C', '17_18', '50X')\n",
      "1\n",
      "('HK14DB2C', '68_69', '50X')\n",
      "1\n",
      "('HK14DB2C', '64_65', '50X')\n",
      "1\n",
      "('HK14DB2C', '60_61', '50X 2')\n",
      "1\n",
      "('HK14DB2C', '60_61', '50X')\n",
      "1\n",
      "('HK14DB2C', '56_57', '50X 2')\n",
      "1\n",
      "('HK14DB2C', '56_57', '50X')\n",
      "1\n",
      "('HK14DB2C', '52_53', '50X')\n",
      "1\n",
      "('HK14PCR1C', '13_14', '50X')\n",
      "1\n",
      "('HK14PCR1C', '22_23', '50X')\n",
      "1\n",
      "('HK14DB2C', '48_49', '50X')\n",
      "1\n",
      "('HK14TLH1C', '100_101', '50X')\n",
      "1\n",
      "('HK14TLH1C', '136_137', '50X')\n",
      "1\n",
      "('HK14TLH1C', '132_133', '50X')\n",
      "1\n",
      "('HK14TLH1C', '128_129', '50X')\n",
      "1\n",
      "('HK14TLH1C', '124_125', '40X')\n",
      "1\n",
      "('HK14TLH1C', '120_121', '50X')\n",
      "1\n",
      "('HK14TLH1C', '112_113', '50X')\n",
      "1\n",
      "('HK14TLH1C', '104_105', '50X')\n",
      "1\n",
      "('HK14PCR1C', '9_10', '50X')\n",
      "1\n",
      "('HK14PCR1C', '23_24', '50X')\n",
      "1\n",
      "('HK14PCR1C', '8_9', '50X')\n",
      "1\n",
      "('HK14PCR1C', '69_70', '50X')\n",
      "1\n",
      "('HK14PCR1C', '64_65', '50X')\n",
      "1\n",
      "('HK14PCR1C', '56_57', '50X')\n",
      "1\n",
      "('HK14PCR1C', '48_49', '50X')\n",
      "1\n",
      "('HK14PCR1C', '40_41', '50X')\n",
      "1\n",
      "('HK14PCR1C', '32_33', '50X')\n",
      "1\n",
      "('HK14DB2C', '4_5', '50X')\n",
      "1\n",
      "('HK14DB2C', '44_45', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_59', '50X')\n",
      "1\n",
      "('HK14DB1C', '16_17', '50X')\n",
      "1\n",
      "('HK14DB1C', '72_73', '50X')\n",
      "1\n",
      "('HK14DB1C', '64_65', '50X')\n",
      "1\n",
      "('HK14DB1C', '56_57', '50X')\n",
      "1\n",
      "('HK14DB1C', '48_49', '50X')\n",
      "1\n",
      "('HK14DB1C', '40_41', '50X')\n",
      "1\n",
      "('HK14DB1C', '32_33', '50X')\n",
      "1\n",
      "('HK14DB1C', '24_25', '50X')\n",
      "1\n",
      "('HK14DB1C', '159_160', '50X')\n",
      "1\n",
      "('HK14DB1C', '88_89(1)', '50X')\n",
      "1\n",
      "('HK14DB1C', '152_153', '50X')\n",
      "1\n",
      "('HK14DB1C', '144_145', '50X')\n",
      "1\n",
      "('HK14DB1C', '136_137', '50X')\n",
      "1\n",
      "('HK14DB1C', '128_129', '50X')\n",
      "1\n",
      "('HK14DB1C', '120_121', '50X')\n",
      "1\n",
      "('HK14DB1C', '112_113(2)', '50X')\n",
      "1\n",
      "('HK14DB1C', '112_113(1)', '50X')\n",
      "1\n",
      "('HK14DB1C', '80_81', '50X')\n",
      "1\n",
      "('HK14DB1C', '88_89(2)', '50X')\n",
      "1\n",
      "('HK14DB2C', '40_41', '50X')\n",
      "1\n",
      "('HK14DB2C', '164_165', '50X')\n",
      "1\n",
      "('HK14DB2C', '36_37', '80X')\n",
      "1\n",
      "('HK14DB2C', '32_33', '80X')\n",
      "1\n",
      "('HK14DB2C', '28_29', '50X')\n",
      "1\n",
      "('HK14DB2C', '24_25', '50X')\n",
      "1\n",
      "('HK14DB2C', '20_21', '50X')\n",
      "1\n",
      "('HK14DB2C', '16_17', '50X')\n",
      "1\n",
      "('HK14DB2C', '168_169', '50X')\n",
      "1\n",
      "('HK14DB2C', '160_161', '50X')\n",
      "1\n",
      "('HK14DB1C', '8_9', '50X')\n",
      "1\n",
      "('HK14DB2C', '156_157', '50X')\n",
      "1\n",
      "('HK14DB2C', '152_153', '50X')\n",
      "1\n",
      "('HK14DB2C', '148_149', '50X')\n",
      "1\n",
      "('HK14DB2C', '12_13', '50X')\n",
      "1\n",
      "('HK14DB2C', '104_105', '50X')\n",
      "1\n",
      "('HK14DB2C', '0_1', '50X')\n",
      "1\n",
      "('HK14DB1C', '96_97', '50X')\n",
      "1\n",
      "('HK14TLH1C', '136_137', '80X')\n",
      "1\n",
      "('HK14TLH1C', '144_145', '50X')\n",
      "1\n",
      "('HK14TLH1C', '151_152', '100X')\n",
      "1\n",
      "('HKUV12', 'FD_13', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_27', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_25', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_23', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_21', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_19', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_17', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_15', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_11', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_3', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_105', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_103', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_101', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_1', '50X')\n",
      "1\n",
      "('HKUV12', '84_86', '50X')\n",
      "1\n",
      "('HKUV12', '564_566', '50X')\n",
      "1\n",
      "('HKUV12', '534_536', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_29', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_31', '50X')\n",
      "1\n",
      "('HK14TLH1C', '16_17', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_48', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_57', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_55', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_53', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_51', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_50', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_5', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_49', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_47', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_33', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_46', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_45', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_43', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_41', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_39', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_37', '50X')\n",
      "1\n",
      "('HKUV12', 'FD_35', '50X')\n",
      "1\n",
      "('HKUV12', '465_467', '50X')\n",
      "1\n",
      "('HKUV12', '375_377', '50X')\n",
      "1\n",
      "('HKUV12', '325_327', '50X')\n",
      "1\n",
      "('HK14TLH1C', '64_65', '50X')\n",
      "1\n",
      "('HK14TLH2C', '0_1', '50X')\n",
      "1\n",
      "('HK14TLH1C', '96_97', '50X')\n",
      "1\n",
      "('HK14TLH1C', '92_93', '40X')\n",
      "1\n",
      "('HK14TLH1C', '8_9', '50X')\n",
      "1\n",
      "('HK14TLH1C', '88_89', '50X')\n",
      "1\n",
      "('HK14TLH1C', '80_81', '50X')\n",
      "1\n",
      "('HK14TLH1C', '72_73', '50X')\n",
      "1\n",
      "('HK14TLH1C', '59_60', '40X')\n",
      "1\n",
      "('HKUV12', '295_297', '50X')\n",
      "1\n",
      "('HK14TLH1C', '52_53', '40X')\n",
      "1\n",
      "('HK14TLH1C', '4_5', '50X')\n",
      "1\n",
      "('HK14TLH1C', '48_49', '50X')\n",
      "1\n",
      "('HK14TLH1C', '40_41', '50X')\n",
      "1\n",
      "('HK14TLH1C', '32_33', '50X')\n",
      "1\n",
      "('HK14TLH1C', '24_25', '50X')\n",
      "1\n",
      "('HK14TLH1C', '1_2', '50X')\n",
      "1\n",
      "('HK14TLH2C', '112_113', '50X')\n",
      "1\n",
      "('HK14TLH2C', '128_129', '50X')\n",
      "1\n",
      "('HK14TLH2C', '144_145', '50X')\n",
      "1\n",
      "('HK14TLH2C', '152_153', '50X')\n",
      "1\n",
      "('HKUV12', '266_268', '50X')\n",
      "1\n",
      "('HKUV12', '246_248', '50X')\n",
      "1\n",
      "('HKUV12', '216_218', '50X')\n",
      "1\n",
      "('HKUV12', '185_187', '50X')\n",
      "1\n",
      "('HKUV12', '1765_1767', '40X')\n",
      "1\n",
      "('HKUV12', '135_137', '50X')\n",
      "1\n",
      "('HKUV12', '104_106', '50X')\n",
      "1\n",
      "('HK14TLH2C', '96_97', '50X')\n",
      "1\n",
      "('HK14TLH2C', '8_9', '50X')\n",
      "1\n",
      "('HK14TLH2C', '80_81', '50X')\n",
      "1\n",
      "('HK14TLH2C', '64_65', '50X')\n",
      "1\n",
      "('HK14TLH2C', '4_5', '50X')\n",
      "1\n",
      "('HK14TLH2C', '48_49', '50X')\n",
      "1\n",
      "('HK14TLH2C', '32_33', '50X')\n",
      "1\n",
      "('HK14TLH2C', '16_17', '50X')\n",
      "1\n",
      "('surface', '_NS5', '50X')\n",
      "1\n"
     ]
    }
   ],
   "source": [
    "for val, cnt in vc.iteritems():\n",
    "    print(val)\n",
    "    print(cnt)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 30,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/plain": [
       "Int64Index([1], dtype='int64')"
      ]
     },
     "execution_count": 30,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "tp_search = ('HK14DB1C', '0_1', '50X')\n",
    "slide_data.index[(slide_data['Core']==tp_search[0]) & (slide_data['Sub_core']==tp_search[1]) & (slide_data['Magnification']==tp_search[2])]"
   ]
  }
 ],
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    "name": "ipython",
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   "file_extension": ".py",
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   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
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