{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# PhenoCam \"roistats\" Files\n", "\n", "Here's a python notebook demonstrating how to read in and plot an \"roistats\" file (formerly referred to as the \"all image\" file) using python. In this case I'm using the all image file from the alligatorriver site. The all image files are in CSV format and can be read directly from the site using a URL. First try reading directly from a file." ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "alligatorriver_DB_0001_roistats.csv\n" ] } ], "source": [ "%matplotlib inline\n", "\n", "import os, sys\n", "import numpy as np\n", "import matplotlib\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import requests\n", "import StringIO\n", "\n", "# set matplotlib style\n", "matplotlib.style.use('ggplot')\n", "\n", "sitename = 'alligatorriver'\n", "roiname = 'DB_0001'\n", "infile = \"{}_{}_roistats.csv\".format(sitename, roiname)\n", "print infile" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "While the data can be read directly from a URL we'll start by doing the simple thing of reading the CSV file directly from our local disk." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | date_local_std_time | \n", "doy | \n", "filename | \n", "solar_elev | \n", "exposure | \n", "mask_index | \n", "gcc | \n", "rcc | \n", "r_mean | \n", "r_std | \n", "... | \n", "b_5_qtl | \n", "b_10_qtl | \n", "b_25_qtl | \n", "b_50_qtl | \n", "b_75_qtl | \n", "b_90_qtl | \n", "b_95_qtl | \n", "r_g_correl | \n", "g_b_correl | \n", "b_r_correl | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "2012-05-03 11:31:16 | \n", "124 | \n", "alligatorriver_2012_05_03_113116.jpg | \n", "69.10992 | \n", "NaN | \n", "1 | \n", "0.41439 | \n", "0.38247 | \n", "106.48861 | \n", "42.40910 | \n", "... | \n", "0 | \n", "8 | \n", "29 | \n", "53 | \n", "79 | \n", "106 | \n", "124 | \n", "0.98528 | \n", "0.91897 | \n", "0.93210 | \n", "
1 | \n", "2012-05-03 12:01:10 | \n", "124 | \n", "alligatorriver_2012_05_03_120110.jpg | \n", "70.15241 | \n", "NaN | \n", "1 | \n", "0.41724 | \n", "0.38322 | \n", "106.30031 | \n", "43.31611 | \n", "... | \n", "0 | \n", "6 | \n", "28 | \n", "52 | \n", "77 | \n", "105 | \n", "124 | \n", "0.98469 | \n", "0.91892 | \n", "0.93140 | \n", "
2 | \n", "2012-05-06 07:31:09 | \n", "127 | \n", "alligatorriver_2012_05_06_073109.jpg | \n", "27.97539 | \n", "NaN | \n", "1 | \n", "0.42063 | \n", "0.36155 | \n", "95.32416 | \n", "27.79097 | \n", "... | \n", "18 | \n", "27 | \n", "41 | \n", "56 | \n", "72 | \n", "89 | \n", "100 | \n", "0.98217 | \n", "0.90238 | \n", "0.93948 | \n", "
3 | \n", "2012-05-06 08:01:09 | \n", "127 | \n", "alligatorriver_2012_05_06_080109.jpg | \n", "34.05378 | \n", "NaN | \n", "1 | \n", "0.42346 | \n", "0.37997 | \n", "99.63057 | \n", "29.50702 | \n", "... | \n", "10 | \n", "19 | \n", "34 | \n", "50 | \n", "67 | \n", "85 | \n", "98 | \n", "0.98120 | \n", "0.90373 | \n", "0.93859 | \n", "
4 | \n", "2012-05-06 08:31:09 | \n", "127 | \n", "alligatorriver_2012_05_06_083109.jpg | \n", "40.10441 | \n", "NaN | \n", "1 | \n", "0.42246 | \n", "0.37324 | \n", "94.99911 | \n", "30.65976 | \n", "... | \n", "8 | \n", "18 | \n", "33 | \n", "50 | \n", "68 | \n", "88 | \n", "101 | \n", "0.98070 | \n", "0.90047 | \n", "0.93602 | \n", "
5 rows × 38 columns
\n", "\n", " | date_local_std_time | \n", "doy | \n", "filename | \n", "solar_elev | \n", "exposure | \n", "mask_index | \n", "gcc | \n", "rcc | \n", "r_mean | \n", "r_std | \n", "... | \n", "b_5_qtl | \n", "b_10_qtl | \n", "b_25_qtl | \n", "b_50_qtl | \n", "b_75_qtl | \n", "b_90_qtl | \n", "b_95_qtl | \n", "r_g_correl | \n", "g_b_correl | \n", "b_r_correl | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "2012-05-03 11:31:16 | \n", "124 | \n", "alligatorriver_2012_05_03_113116.jpg | \n", "69.10992 | \n", "NaN | \n", "1 | \n", "0.41439 | \n", "0.38247 | \n", "106.48861 | \n", "42.40910 | \n", "... | \n", "0.0 | \n", "8.0 | \n", "29.0 | \n", "53.0 | \n", "79.0 | \n", "106.0 | \n", "124.0 | \n", "0.98528 | \n", "0.91897 | \n", "0.93210 | \n", "
1 | \n", "2012-05-03 12:01:10 | \n", "124 | \n", "alligatorriver_2012_05_03_120110.jpg | \n", "70.15241 | \n", "NaN | \n", "1 | \n", "0.41724 | \n", "0.38322 | \n", "106.30031 | \n", "43.31611 | \n", "... | \n", "0.0 | \n", "6.0 | \n", "28.0 | \n", "52.0 | \n", "77.0 | \n", "105.0 | \n", "124.0 | \n", "0.98469 | \n", "0.91892 | \n", "0.93140 | \n", "
2 | \n", "2012-05-06 07:31:09 | \n", "127 | \n", "alligatorriver_2012_05_06_073109.jpg | \n", "27.97539 | \n", "NaN | \n", "1 | \n", "0.42063 | \n", "0.36155 | \n", "95.32416 | \n", "27.79097 | \n", "... | \n", "18.0 | \n", "27.0 | \n", "41.0 | \n", "56.0 | \n", "72.0 | \n", "89.0 | \n", "100.0 | \n", "0.98217 | \n", "0.90238 | \n", "0.93948 | \n", "
3 rows × 38 columns
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