{ "cells": [ { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "# CytoTRACE runtime comparison" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Library imports" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Global seed set to 0\n" ] } ], "source": [ "import os\n", "import sys\n", "\n", "import numpy as np\n", "import pandas as pd\n", "\n", "import matplotlib.pyplot as plt\n", "import seaborn as sns\n", "\n", "from cr2 import running_in_notebook\n", "\n", "sys.path.extend([\"../../../\", \".\"])\n", "from paths import DATA_DIR, FIG_DIR # isort: skip # noqa: E402" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## General settings" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "SAVE_FIGURES = True\n", "if SAVE_FIGURES:\n", " os.makedirs(FIG_DIR / \"cytotrace_kernel\" / \"benchmarks\", exist_ok=True)" ] }, { "attachments": {}, "cell_type": "markdown", "metadata": {}, "source": [ "## Data loading" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "data = []\n", "for fname in os.listdir(DATA_DIR / \"cytotrace_benchmark\" / \"out\"):\n", " algo, subset, split = fname.split(\".\")[0].split(\"_\")\n", " if algo == \"cr\":\n", " df = pd.read_csv(DATA_DIR / \"cytotrace_benchmark\" / \"out\" / fname, index_col=\"sample\")\n", " time_s = df[\"ct_time\"].iloc[0]\n", " time_p = df[\"preprocess_time\"].iloc[0]\n", " else:\n", " df = pd.read_csv(DATA_DIR / \"cytotrace_benchmark\" / \"out\" / fname, index_col=0)\n", " time_s = df.loc[\"time\"][0]\n", " time_p = 0\n", " data.append((algo, subset, split, time_s, time_p))" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | algorithm | \n", "subset | \n", "split | \n", "time | \n", "
---|---|---|---|---|
0 | \n", "CytoTRACE (CellRank) | \n", "30 | \n", "2 | \n", "1.546217 | \n", "
1 | \n", "CytoTRACE (CellRank) | \n", "20 | \n", "2 | \n", "1.139597 | \n", "
2 | \n", "CytoTRACE (CellRank) | \n", "20 | \n", "7 | \n", "1.095124 | \n", "
3 | \n", "CytoTRACE (original) | \n", "10 | \n", "3 | \n", "52.885000 | \n", "
4 | \n", "CytoTRACE (CellRank) | \n", "1100 | \n", "3 | \n", "61.587730 | \n", "