{"id":1285,"date":"2012-10-08T13:26:31","date_gmt":"2012-10-08T17:26:31","guid":{"rendered":"http:\/\/lukemiller.org\/?p=1285"},"modified":"2012-10-08T13:26:31","modified_gmt":"2012-10-08T17:26:31","slug":"another-r-ibutton-script","status":"publish","type":"post","link":"https:\/\/lukemiller.org\/index.php\/2012\/10\/another-r-ibutton-script\/","title":{"rendered":"Another R + iButton script"},"content":{"rendered":"

\"\"<\/a>Previously I’ve detailed R scripts that automate the launching<\/a> and downloading<\/a> Maxim iButton thermochron data loggers. I’m typically doing the launching and downloading at separate times in my workflow, since I have duplicate iButtons to swap out, so separate scripts work for me. Ryan Knowles recently contributed a combined version of these scripts that downloads and immediately re-launches each iButton. This is useful if you want to retrieve iButtons and then stick the same units back out in the field as soon as possible. As usual, this script saves the raw downloaded data from each iButton in one directory, and saves a collated csv file that contains the time and temperature information for the iButtons.<\/p>\n

If you haven’t read the previous posts that detail the additional software you’ll need, go back and check it out<\/a>. The code below will make a little more sense once you do that.<\/p>\n

The new script, ibutton_download_launch_combined.R, is available at the GitHub repository<\/a>. The code is also shown below.<\/p>\n

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# Filename: ibutton_download_launch_combined.R<\/span>\r\n# <\/span>\r\n# Author: Luke Miller Jul 11, 2012 (as modified by Ryan Knowles Oct 04, 2012)<\/span>\r\n###############################################################################<\/span>\r\n# This script will allow the user to download iButtons, giving a unique name <\/span>\r\n# to each file. It will parse the raw data file and extract the useful bits<\/span>\r\n# (to me at least): date\/time, temperature (Celsius), user's ID for this <\/span>\r\n# iButton, and the serial number for this iButton, and place all of these in a<\/span>\r\n# comma-separated-value file that can be easily opened in Excel or R. Each <\/span>\r\n# downloaded iButton data file has the current date and time included in the <\/span>\r\n# filename to avoid overwriting older data files. Raw data files are stored in a <\/span>\r\n# directory with today's date on it, while the parsed csv files go in a 2nd <\/span>\r\n# directory.<\/span>\r\n\r\n# The thermodl.exe file was originally downloaded as part of the Maxim iButton <\/span>\r\n# 1-Wire Public Domain Kit. <\/span>\r\n# There are several versions of the Kit available, including<\/span>\r\n# versions with pre-compiled binaries (executables) for Windows\/Linux\/OSX.<\/span>\r\n# http:\/\/www.maxim-ic.com\/products\/ibutton\/software\/1wire\/wirekit.cfm<\/span>\r\n# On my Windows 7 x64 computer using the DS9490B USB ibutton adapter, I used the<\/span>\r\n# precompiled binary build for Win64 USB (DS9490 + WinUSB) Preliminary Version <\/span>\r\n# 3.11 Beta 2,<\/span>\r\n# filename: winusb64vc311Beta2_r2.zip, downloaded 2012-03-15<\/span>\r\n# Unzip this file and find the .exe files thermoms.exe and thermodl.exe in the<\/span>\r\n# builds\\winusb64vc\\release folder. Copy these to your R working directory.<\/span>\r\n# The drivers for the DS9490 USB iButton adapter must also be downloaded and <\/span>\r\n# installed: <\/span>\r\n# http:\/\/www.maxim-ic.com\/products\/ibutton\/software\/tmex\/<\/span>\r\n# I downloaded and installed the file \"install_1_wire_drivers_x64_v403.msi\"<\/span>\r\n# The Java OneWireViewer app can also be downloaded and used to verify that your<\/span>\r\n# drivers work and that you can communicate with iButtons successfully through <\/span>\r\n# the USB adapter. You can download this app here: <\/span>\r\n# http:\/\/www.maxim-ic.com\/products\/ibutton\/software\/1wire\/OneWireViewer.cfm<\/span>\r\n\r\n# NOTE: the Maxim program \"thermodl.exe\" must be present in the current R <\/span>\r\n# working directory. Uncomment the setwd() line below to change the R working <\/span>\r\n# directory. Enter your working directory location inside the quotes.<\/span>\r\nsetwd<\/span><\/a>(<\/span>'C:\/Users\/Ryan\/Dropbox\/R\/'<\/span>)<\/span> \r\n\r\ncur.date = Sys.Date<\/span><\/a>(<\/span>)<\/span> # Get current date<\/span>\r\n# Assemble a directory name to store raw downloaded data into<\/span>\r\ndir.name = \"C:\/Users\/Ryan\/Dropbox\/R\/temp\"<\/span>\r\n# Assemble a directory name to store the parsed csv output files in<\/span>\r\ndir.name2 = \"C:\/Users\/Ryan\/Dropbox\/Project\/Heat Stress\/Data\/ibutton\"<\/span>\r\n# Check to see if that folder already exists, if not then create it.<\/span>\r\nif<\/span> (<\/span>is.na<\/span><\/a>(<\/span>file.info<\/span><\/a>(<\/span>dir.name)<\/span>$<\/span>isdir)<\/span>)<\/span> {<\/span>\r\n\tdir.create<\/span><\/a>(<\/span>dir.name)<\/span>\t\r\n}<\/span>\r\n# Check to see if the other folder already exists, if not then create it.<\/span>\r\nif<\/span> (<\/span>is.na<\/span><\/a>(<\/span>file.info<\/span><\/a>(<\/span>dir.name2)<\/span>$<\/span>isdir)<\/span>)<\/span> {<\/span>\r\n\tdir.create<\/span><\/a>(<\/span>dir.name2)<\/span>\t\r\n}<\/span>\r\ncat<\/span><\/a>(<\/span>'Enter a desired mission start time YYYY-MM-DD HH:MM\\n<\/span>'<\/span>)<\/span>\r\ncat<\/span><\/a>(<\/span>'Enter 0 for immediate start. Delay must be less than 45.5 days.\\n<\/span>'<\/span>)<\/span>\r\ntime.delay = scan<\/span><\/a>(<\/span>file<\/span><\/a> = ''<\/span>,<\/span> what = character<\/span><\/a>(<\/span>)<\/span>,<\/span> n = 1<\/span>,<\/span> sep = ','<\/span>)<\/span>\r\n# The sep value in scan is necessary so that spaces are not interpreted as the<\/span>\r\n# default record delimiter.<\/span>\r\n\r\nif<\/span> (<\/span>time.delay ==<\/span> '0'<\/span>)<\/span> {<\/span>\r\n\tlaunch = TRUE<\/span>\r\n}<\/span> else<\/span> {<\/span>\r\n\t# Convert the date\/time into a POSIX time object<\/span>\r\n\ttime.delay = as.POSIXct<\/span><\/a>(<\/span>strptime(<\/span>time.delay,<\/span> format<\/span><\/a> = '%Y-%m-%d %H:%M'<\/span>)<\/span>)<\/span>\r\n\r\n\t# Check to make sure that the delay time is usable<\/span>\r\n\tif<\/span> (<\/span>is.na<\/span><\/a>(<\/span>time.delay)<\/span>)<\/span> {<\/span> # If time.delay can't be interpreted, fail <\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Time could not be interpreted\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Quitting now\\n<\/span>'<\/span>)<\/span>\r\n\t\tlaunch = FALSE<\/span>\r\n\t}<\/span>\r\n\t# If time.delay is a valid POSIX time, check that it is within limits<\/span>\r\n\tif<\/span> (<\/span>!<\/span>is.na<\/span><\/a>(<\/span>time.delay)<\/span>)<\/span> {<\/span>\r\n\t\tcurr.time = as.POSIXct<\/span><\/a>(<\/span>Sys.time<\/span><\/a>(<\/span>)<\/span>)<\/span> # get current time<\/span>\r\n\t\t# Check time difference between user's delay and current computer time<\/span>\r\n\t\tt.diff = as.numeric<\/span><\/a>(<\/span>time.delay)<\/span> -<\/span> as.numeric<\/span><\/a>(<\/span>curr.time)<\/span>\r\n\t\tt.diff = t.diff \/<\/span> 60<\/span> # convert to minutes<\/span>\r\n\r\n\t\tif<\/span> (<\/span>t.diff <<\/span> 0<\/span>)<\/span> {<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'Time delay is less than zero. Check your watch.\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'Quitting now\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tlaunch = FALSE<\/span>\r\n\t\t}<\/span> else<\/span> if<\/span> (<\/span>t.diff ><\/span> 65535<\/span>)<\/span> {<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'Time delay is longer than 45.5 days. You are bad at math.\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'Quitting now\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tlaunch = FALSE<\/span>\r\n\t\t}<\/span> else<\/span> if<\/span> (<\/span>t.diff ><\/span> 0<\/span> &<\/span> t.diff <<\/span> 1<\/span>)<\/span> {<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'Time delay is being set to 0 for immediate launch.\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tlaunch = TRUE<\/span>\r\n\t\t}<\/span> else<\/span> {<\/span> \r\n\t\t\t# time.delay is a readable time, and t.diff is between 0 and 65535<\/span>\r\n\t\t\tlaunch = TRUE<\/span>\r\n\t\t}<\/span>\r\n\t}<\/span> # end of !is.na(time.delay) if-statement<\/span>\r\n}<\/span> # end of time.delay if-statement<\/span>\r\n\r\ncat<\/span><\/a>(<\/span>'Enter the desired sampling frequency in minutes (1 to 255):\\n<\/span>'<\/span>)<\/span>\r\nfreq = scan<\/span><\/a>(<\/span>file<\/span><\/a> = ''<\/span>,<\/span> what = numeric<\/span><\/a>(<\/span>)<\/span>,<\/span> n = 1<\/span>)<\/span>\r\nfreq = as.character<\/span><\/a>(<\/span>freq)<\/span> # convert to character<\/span>\r\n\r\n#######################################<\/span>\r\n# This main while loop will repeat continuously to download data and launch<\/span>\r\n# multiple iButtons. The same parameters will be used to launch every iButton,<\/span>\r\n# except that the start delay (if >0) will automatically adjust as time<\/span>\r\n# elapses so that each iButton will start at the same absolute time.<\/span>\r\n# Data is downloaded in a separate sequence from the launch so the launch may<\/span>\r\n# fail even if the download is successful. The opposite situation is prevented<\/span>\r\n# since launching a new iButton will delete the previous data before it can<\/span>\r\n# be downloaded successfully.<\/span>\r\nCounter = 0<\/span>\r\nloop = TRUE<\/span>\r\nwhile<\/span>(<\/span>loop)<\/span> {<\/span>\r\n\tCounter = Counter +<\/span> 1<\/span>\r\n\t# Get current time to insert in filename so we don't overwrite old data<\/span>\r\n\tcurrTime = strftime<\/span><\/a>(<\/span>Sys.time<\/span><\/a>(<\/span>)<\/span>,<\/span> format<\/span><\/a> = \"%Y%m%d_%H%M%S\"<\/span>)<\/span>\r\n\t# Assemble filename<\/span>\r\n\tfname = paste<\/span><\/a>(<\/span>dir.name,<\/span>'\\\\<\/span>'<\/span>,<\/span>currTime,<\/span>'.dat'<\/span>,<\/span> sep = ''<\/span>)<\/span>\r\n\t# Call the thermodl.exe program provided by Maxim. This must be in the <\/span>\r\n\t# current R working directory. Start by assembling a command to be issued<\/span>\r\n\tsys.com = paste<\/span><\/a>(<\/span>'thermodl.exe ds2490-0 '<\/span>,<\/span> fname,<\/span> sep = ''<\/span>)<\/span>\r\n\t# Now issue the command to the system using the system() function<\/span>\r\n\ttemp = system<\/span><\/a>(<\/span>sys.com,<\/span> wait = TRUE<\/span>,<\/span> intern = TRUE<\/span>)<\/span>\r\n\t# The raw downloaded data should now be in the \"raw_downloads\" directory <\/span>\r\n\t# created at the start of the script.<\/span>\r\n\t# Output the status updates from thermodl.exe <\/span>\r\n\tcat<\/span><\/a>(<\/span>temp[<\/span>7<\/span>]<\/span>,<\/span> '\\n<\/span>'<\/span>)<\/span>\r\n\tcat<\/span><\/a>(<\/span>temp[<\/span>9<\/span>]<\/span>,<\/span>'\\n<\/span>'<\/span>)<\/span>\r\n\tcat<\/span><\/a>(<\/span>temp[<\/span>18<\/span>]<\/span>,<\/span> '\\n<\/span>'<\/span>)<\/span>\r\n\tcat<\/span><\/a>(<\/span>temp[<\/span>20<\/span>]<\/span>,<\/span> '\\n<\/span>'<\/span>)<\/span>\r\n\t# Open the data file created by thermodl.exe<\/span>\r\n\tx <-<\/span> readLines<\/span><\/a>(<\/span>fname)<\/span> # read data into a character vector<\/span>\r\n\t# Extract serial number from line 4 of file<\/span>\r\n\tserialnum <-<\/span> substr<\/span><\/a>(<\/span>x[<\/span>4<\/span>]<\/span>,<\/span> 37<\/span>,<\/span> 39<\/span>)<\/span>\r\n\r\n\t# Parse the iButton data file to extract the relevant temp\/time data<\/span>\r\n\tlog.start <-<\/span> grep<\/span><\/a>(<\/span>'Log Data'<\/span>,<\/span> x)<\/span> # Find what line the log data starts below<\/span>\r\n\tlog.start <-<\/span> log.start +<\/span> 3<\/span> # change value to first line of log data<\/span>\r\n\tlog.end <-<\/span> grep<\/span><\/a>(<\/span>'Debug Dump'<\/span>,<\/span> x)<\/span> # Find where the log data ends (roughly)<\/span>\r\n\tlog.end <-<\/span> log.end -<\/span> 2<\/span> # change value to last line of log data<\/span>\r\n\t# Check if there were any logged temperature data<\/span>\r\n\tif<\/span> (<\/span>!<\/span>(<\/span>log.end -<\/span> log.start <<\/span> 0<\/span>)<\/span>)<\/span> {<\/span>\r\n\t\ttemps <-<\/span> x[<\/span>log.start:<\/span>log.end]<\/span> # extract log data, still as characters<\/span>\r\n\r\n\t\t# Convert time stamps to POSIX object<\/span>\r\n\t\ttimes <-<\/span> as.POSIXct<\/span><\/a>(<\/span>strptime(<\/span>substr<\/span><\/a>(<\/span>temps,<\/span>1<\/span>,<\/span>17<\/span>)<\/span>,<\/span> \r\n\t\t\t\t\t\tformat<\/span><\/a> = '%m\/%d\/%Y %H:%M'<\/span>)<\/span>)<\/span>\r\n\t\ttemp.data <-<\/span> data.frame<\/span><\/a>(<\/span>Time<\/span><\/a> = times)<\/span> # stick into a new data frame<\/span>\r\n\t\t# convert temps to numeric and insert into temp.data<\/span>\r\n\t\ttemp.data$<\/span>TempC <-<\/span> as.numeric<\/span><\/a>(<\/span>substr<\/span><\/a>(<\/span>temps,<\/span>20<\/span>,<\/span>26<\/span>)<\/span>)<\/span>\r\n\t\t# Insert column with iButton's unique serial number<\/span>\r\n\t\ttemp.data$<\/span>Serial.number <-<\/span> serialnum\r\n\t\t# Output temperature data to console<\/span>\r\n\r\n\t\tif<\/span> (<\/span>Counter ==<\/span> 1<\/span>)<\/span> {<\/span> # Copy times and temps for first ibutton<\/span>\r\n\t\t\t# The times and number of readings of the first ibutton<\/span>\r\n\t\t\t# will dictate how much is read from each subsequent button.<\/span>\r\n\t\t\t# For example, if the first ibutton has 100 readings and the<\/span>\r\n\t\t\t# second has 120 readings, only the first 100 readings of the<\/span>\r\n\t\t\t# second ibutton will be saved in the combined csv file.<\/span>\r\n\t\t\t# The remaining data will still be available in the .dat file.<\/span>\r\n\t\t\tcombdatah <-<\/span> as.data.frame<\/span><\/a>(<\/span>temp.data$<\/span>Time)<\/span>\r\n\t\t\tnames<\/span><\/a>(<\/span>combdatah)<\/span>[<\/span>1<\/span>]<\/span> <-<\/span> \"Time\"<\/span>\r\n\t\t\ttemprow <-<\/span> nrow<\/span><\/a>(<\/span>combdatah)<\/span>\r\n\t\t}<\/span> # End of first button IF<\/span>\r\n\t\t# Only copy temps for all subsequent ibuttons (add *'s to ibuttons with<\/span>\r\n\t\t# times that don't line up with the first ibutton)<\/span>\r\n\t\tColcounter <-<\/span> Counter +<\/span> 1<\/span>\r\n\t\tCheckdiff = temp.data[<\/span>1<\/span>,<\/span>1<\/span>]<\/span> # Extract time<\/span>\r\n\t\tif<\/span>(<\/span>Checkdiff !<\/span>= combdatah[<\/span>1<\/span>,<\/span>1<\/span>]<\/span>)<\/span> {<\/span>\r\n\t\t\tserialnum<-<\/span>paste<\/span><\/a>(<\/span>serialnum,<\/span>\"*\"<\/span>,<\/span>sep=\"\"<\/span>)<\/span> # Add * to serialnum<\/span>\r\n\t\t}<\/span> \r\n\t\t# Add temperature data to combined data frame<\/span>\r\n\t\tcombdatah[<\/span>Colcounter]<\/span> <-<\/span> temp.data$<\/span>TempC[<\/span>1<\/span>:<\/span>temprow]<\/span>\r\n\t\t# Rename new temp data with serial num.<\/span>\r\n\t\tnames<\/span><\/a>(<\/span>combdatah)<\/span>[<\/span>Colcounter]<\/span> <-<\/span> serialnum \r\n\r\n\t\tcat<\/span><\/a>(<\/span>'Temperature data downloaded \\n<\/span>'<\/span>)<\/span>\r\n\t}<\/span> else<\/span> {<\/span> # Continue logged data check IF<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'\\n<\/span>\\n<\/span>*****No temperature data*****\\a<\/span>\\n<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Would you still like to launch this iButton?\\n<\/span>'<\/span>)<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Doing so will erase any data that has not been downloaded.\\n<\/span>'<\/span>)<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Enter y to continue.\\n<\/span>'<\/span>)<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Leave blank to skip launch and (re)download ibutton.\\n<\/span>'<\/span>)<\/span>\r\n\t\t# Ask user to continue<\/span>\r\n\t\tcont.launch = scan<\/span><\/a>(<\/span>file<\/span><\/a> = ''<\/span>,<\/span> what = character<\/span><\/a>(<\/span>)<\/span>,<\/span> n = 1<\/span>)<\/span> \r\n\t\tif<\/span> (<\/span>length<\/span><\/a>(<\/span>cont.launch)<\/span> ><\/span> 0<\/span>)<\/span> {<\/span> # Allows user to not type anything<\/span>\r\n\t\t\tif<\/span> (<\/span>cont.launch ==<\/span> 'y'<\/span>)<\/span> launch = TRUE<\/span>\r\n\t\t}<\/span> else<\/span> {<\/span>launch = FALSE<\/span>}<\/span>\r\n\t\t# Cancel launch if entry is anything but 'y'<\/span>\r\n\t}<\/span> # End of logged data check IF<\/span>\r\n\r\n\t############################################################################<\/span>\r\n\t## Start the launch loop. <\/span>\r\n\r\n\tif<\/span> (<\/span>launch)<\/span> {<\/span> # only do this part if launch == TRUE<\/span>\r\n\t\tif<\/span> (<\/span>time.delay !<\/span>= '0'<\/span>)<\/span> {<\/span>\r\n\t\t\tcurr.time = as.POSIXct<\/span><\/a>(<\/span>Sys.time<\/span><\/a>(<\/span>)<\/span>)<\/span> # Get current time<\/span>\r\n\t\t\t# Calculate difference between current time and time.delay value<\/span>\r\n\t\t\ttime.diff = as.numeric<\/span><\/a>(<\/span>time.delay)<\/span> -<\/span> as.numeric<\/span><\/a>(<\/span>curr.time)<\/span>\r\n\t\t\ttime.diff = time.diff \/<\/span> 60<\/span> # convert from seconds to minutes<\/span>\r\n\t\t\ttime.diff = floor<\/span><\/a>(<\/span>time.diff)<\/span> # round down to nearest minute<\/span>\r\n\t\t\t# iButtons only read out to the nearest minute. Rounding down to the<\/span>\r\n\t\t\t# nearest minute should produce the proper delay to start at the <\/span>\r\n\t\t\t# desired time. <\/span>\r\n\r\n\t\t\t# If too much time elapses during this script, the time difference <\/span>\r\n\t\t\t# could eventually shrink to zero or less than zero. In that case, <\/span>\r\n\t\t\t# warn the user and set the iButton for immediate launch. <\/span>\r\n\t\t\tif<\/span> (<\/span>time.diff <<\/span> 1<\/span>)<\/span> {<\/span>\r\n\t\t\t\ttime.diff = 0<\/span> # set for immediate launch.<\/span>\r\n\t\t\t\tcat<\/span><\/a>(<\/span>'*********************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\tcat<\/span><\/a>(<\/span>'Delay has shrunk to zero. Setting for immediate launch.'<\/span>)<\/span>\r\n\t\t\t\tcat<\/span><\/a>(<\/span>'*********************************\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t}<\/span> # End time.diff < 1 IF<\/span>\r\n\t\t\ttime.diff = as.character<\/span><\/a>(<\/span>time.diff)<\/span> # convert to character <\/span>\r\n\t\t}<\/span> else<\/span> {<\/span> # time.delay was originally set to 0, so keep that.<\/span>\r\n\t\t\ttime.diff ==<\/span> '0'<\/span>\r\n\t\t}<\/span> # End time delay != 0 IF<\/span>\r\n\t\tcat<\/span><\/a>(<\/span>'Calculated delay: '<\/span>,<\/span> time.diff,<\/span> ' minutes\\n<\/span>'<\/span>)<\/span>\r\n\t\t# The thermoms.exe program expects a series of inputs in order to establish the<\/span>\r\n\t\t# mission parameters. Rgui doesn't work all that well with interactive command <\/span>\r\n\t\t# line programs (Rterm is just fine, but our goal is to not have to interact), <\/span>\r\n\t\t# so instead we'll create a character vector of answers to thermoms.exe's <\/span>\r\n\t\t# queries and supply those via the input option of the system() function. <\/span>\r\n\t\t# The parameters are as follows:<\/span>\r\n\t\t# Erase current mission (0) yes, (1) no. Answer: 0<\/span>\r\n\t\t# Enter start delay in minutes (0 to 65535). Answer: whatever you choose<\/span>\r\n\t\t# Enter sample rate in minutes (1 to 255). Answer: whatever you choose<\/span>\r\n\t\t# Enable roll-over (0) yes, (1) no. Answer: 1<\/span>\r\n\t\t# Enter high temperature threshold in Celsius (-40 to 70). Answer: 70<\/span>\r\n\t\t# Enter low temperature threshold in Celsius (-40 to 70). Answer: -40<\/span>\r\n\r\n\t\tmission.params = c<\/span><\/a>(<\/span>'0'<\/span>,<\/span> # erase current mission <\/span>\r\n\t\t\t\ttime.diff,<\/span> # start delay in minutes (0 to 65535)<\/span>\r\n\t\t\t\tfreq,<\/span> # sample rate in minutes (1 to 255)<\/span>\r\n\t\t\t\t'1'<\/span>,<\/span> # enable roll-over? 1 = no roll over<\/span>\r\n\t\t\t\t'70'<\/span>,<\/span> # high temperature threshold<\/span>\r\n\t\t\t\t'-40'<\/span>)<\/span> # low temperature threshold<\/span>\r\n\r\n\t\t# Launch thermoms.exe<\/span>\r\n\t\t# The 1st argument supplied to thermoms needs to be the location of the iButton <\/span>\r\n\t\t# in the system. If using a DS9490B USB reader on Windows, you will probably get <\/span>\r\n\t\t# away with using ds2490-0. The DS9490 USB reader uses a ds2490 chip internally, <\/span>\r\n\t\t# so you need to tell thermoms.exe to look for a ds2490. <\/span>\r\n\t\tout = system<\/span><\/a>(<\/span>'thermoms.exe ds2490-0'<\/span>,<\/span> intern = TRUE<\/span>,<\/span> wait = TRUE<\/span>,<\/span> \r\n\t\t\t\tinput = mission.params)<\/span>\r\n\r\n\t\t# Check the output from the mission launch to ensure that the correct parameters<\/span>\r\n\t\t# were registered. Occasionally the time delay will not be properly registered <\/span>\r\n\t\t# on the first launch, so the loops below will immediately relaunch the mission<\/span>\r\n\t\t# to get the time delay to register properly.<\/span>\r\n\r\n\t\t# If no iButton is plugged in, this should be the failure message<\/span>\r\n\t\tif<\/span> (<\/span>out[<\/span>7<\/span>]<\/span> ==<\/span> 'Thermochron not present on 1-Wire'<\/span>)<\/span> {<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'******************************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>out[<\/span>7<\/span>]<\/span>,<\/span>'\\n<\/span>'<\/span>)<\/span>\r\n\t\t\tcat<\/span><\/a>(<\/span>'******************************************\\n<\/span>\\a<\/span>'<\/span>)<\/span>\r\n\t\t}<\/span> else<\/span> {<\/span> # if out[7] is blank, a mission was probably uploaded<\/span>\r\n\t\t\tfor<\/span> (<\/span>i in<\/span> 73<\/span>:<\/span>90<\/span>)<\/span> {<\/span> # Display read-back from mission upload<\/span>\r\n\t\t\t\tcat<\/span><\/a>(<\/span>out[<\/span>i]<\/span>,<\/span>'\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t}<\/span>\r\n\r\n\t\t\t# Make sure the delay was actually entered correctly if it's >0<\/span>\r\n\t\t\t# This while loop will run a maximum of 3 times. Each time through <\/span>\r\n\t\t\t# it will compare the output in out[73] to make sure the correct <\/span>\r\n\t\t\t# delay was returned from the iButton. If not, it will re-launch the<\/span>\r\n\t\t\t# mission up to two more times before sending a failure message<\/span>\r\n\t\t\tretry = 0<\/span>\r\n\t\t\twhile<\/span> (<\/span>retry <<\/span> 3<\/span>)<\/span> {<\/span>\r\n\t\t\t\tsetting = out[<\/span>79<\/span>]<\/span>\r\n\t\t\t\tnums = gregexpr<\/span><\/a>(<\/span>'[0-9]'<\/span>,<\/span> setting)<\/span> # Find numbers in the string<\/span>\r\n\t\t\t\tdigs = substr<\/span><\/a>(<\/span>setting,<\/span> nums[<\/span>[<\/span>1<\/span>]<\/span>]<\/span>[<\/span>1<\/span>]<\/span>,<\/span> \r\n\t\t\t\t\t\tnums[<\/span>[<\/span>1<\/span>]<\/span>]<\/span>[<\/span>length<\/span><\/a>(<\/span>nums[<\/span>[<\/span>1<\/span>]<\/span>]<\/span>)<\/span>]<\/span>)<\/span> # Extract delay value<\/span>\r\n\t\t\t\tif<\/span> (<\/span>digs !<\/span>= time.diff &<\/span> retry <<\/span> 2<\/span>)<\/span> {<\/span>\r\n\t\t\t\t\t# If delay value returned by iButton doesn't match the <\/span>\r\n\t\t\t\t\t# programmed delay, warn the user and re-launch the mission<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'*****************************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'****Launch did not work, re-launching****\\a<\/span>\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'*****************************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tout = system<\/span><\/a>(<\/span>'thermoms.exe ds2490-0'<\/span>,<\/span> intern = TRUE<\/span>,<\/span>\r\n\t\t\t\t\t\t\twait = TRUE<\/span>,<\/span> input = mission.params)<\/span>\r\n\t\t\t\t\tfor<\/span> (<\/span>i in<\/span> 73<\/span>:<\/span>90<\/span>)<\/span> {<\/span> # Display the newly returned values<\/span>\r\n\t\t\t\t\t\tcat<\/span><\/a>(<\/span>out[<\/span>i]<\/span>,<\/span>'\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\t}<\/span>\r\n\t\t\t\t\tretry = retry +<\/span> 1<\/span> # increment the loop counter<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'---------------------------\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t}<\/span> else<\/span> if<\/span> (<\/span>digs !<\/span>= time.diff &<\/span> retry ==<\/span> 2<\/span>)<\/span> {<\/span>\r\n\t\t\t\t\t# If the returned delay still doesn't match the programmed<\/span>\r\n\t\t\t\t\t# delay after two more iterations, send a failure message<\/span>\r\n\t\t\t\t\t# to the user and let them deal with this issue. <\/span>\r\n\t\t\t\t\t# A common failure mode is due to a dead battery, which will<\/span>\r\n\t\t\t\t\t# keep returning a clock time of 01\/01\/1970 00:00:00<\/span>\r\n\t\t\t\t\tretry = 3<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'****************************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'*****Uploaded failed, check iButton*****\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'****************************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tfor<\/span> (<\/span>i in<\/span> 73<\/span>:<\/span>90<\/span>)<\/span> {<\/span>\r\n\t\t\t\t\t\tcat<\/span><\/a>(<\/span>out[<\/span>i]<\/span>,<\/span>'\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\t}<\/span>\r\n\r\n\t\t\t\t\tanswer = out[<\/span>85<\/span>]<\/span> # Check the iButton's internal clock<\/span>\r\n\r\n\t\t\t\t\t# Find the location of the date in this line (if present)<\/span>\r\n\t\t\t\t\td1 = regexpr<\/span><\/a>(<\/span>'[0-9]{2}\/[0-9]{2}\/[0-9]{4}'<\/span>,<\/span> answer)<\/span>\r\n\r\n\t\t\t\t\t# Extract the date as a character string<\/span>\r\n\t\t\t\t\tbutton.date = substr<\/span><\/a>(<\/span>answer,<\/span> d1,<\/span> \r\n\t\t\t\t\t\t\td1 +<\/span> attr<\/span><\/a>(<\/span>d1,<\/span>'match.length'<\/span>)<\/span> -<\/span> 1<\/span>)<\/span>\r\n\r\n\t\t\t\t\t# If the iButton date returns 01\/01\/1970, the iButton <\/span>\r\n\t\t\t\t\t# battery is probably dead<\/span>\r\n\t\t\t\t\tif<\/span> (<\/span>button.date ==<\/span> '01\/01\/1970'<\/span>)<\/span> {<\/span>\r\n\t\t\t\t\t\tcat<\/span><\/a>(<\/span>'********************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\t\tcat<\/span><\/a>(<\/span>'The iButton battery may be dead.\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\t\tcat<\/span><\/a>(<\/span>'********************************\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\t}<\/span>\r\n\r\n\t\t\t\t}<\/span> else<\/span> if<\/span> (<\/span>digs ==<\/span> time.diff)<\/span> {<\/span> # iButton mission launch worked<\/span>\r\n\t\t\t\t\tcat<\/span><\/a>(<\/span>'\\n<\/span>----------Success---------\\n<\/span>'<\/span>)<\/span>\r\n\t\t\t\t\tretry = 3<\/span>\r\n\t\t\t\t}<\/span>\r\n\t\t\t}<\/span> # End of retry while-loop<\/span>\r\n\t\t}<\/span> # End of if (out[7]... if-else statements<\/span>\r\n\t}<\/span> # End of launch IF <\/span>\r\n\tcat<\/span><\/a>(<\/span>'\\a<\/span>\\n<\/span>---------------------\\n<\/span>'<\/span>)<\/span>\r\n\tcat<\/span><\/a>(<\/span>'Swap in next iButton and hit enter. Enter q to quit.\\n<\/span>'<\/span>)<\/span>\r\n\tuser.input = scan<\/span><\/a>(<\/span>file<\/span><\/a> = ''<\/span>,<\/span> what = character<\/span><\/a>(<\/span>)<\/span>,<\/span> n = 1<\/span>)<\/span>\r\n\tif<\/span> (<\/span>length<\/span><\/a>(<\/span>user.input)<\/span> ><\/span> 0<\/span>)<\/span> {<\/span> # Allows user to not type anything<\/span>\r\n\t\tif<\/span> (<\/span>user.input ==<\/span> 'q'<\/span>)<\/span> loop = FALSE<\/span> # quit out of while loop<\/span>\r\n\t}<\/span> else<\/span> {<\/span>\r\n\t\tloop = TRUE<\/span> # return to start of while loop to download next iButton<\/span>\r\n\t}<\/span> # End of \"q\" IF<\/span>\r\n\r\n}<\/span> # End of main loop<\/span>\r\n\r\n# Write the contents of combdatah to a comma-separated-values file.<\/span>\r\nwrite.csv<\/span><\/a>(<\/span>combdatah,<\/span> \"horizontal.csv\"<\/span>,<\/span> row.names<\/span><\/a> = FALSE<\/span>)<\/span>\r\n\r\ncat<\/span><\/a>(<\/span>'Finished\\n<\/span>'<\/span>)<\/span><\/pre>\n<\/div>\n<\/div>\n
Created by Pretty R at inside-R.org<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
Previously I’ve detailed R scripts that automate the launching and downloading Maxim iButton thermochron data loggers. I’m typically doing the launching and downloading at separate times in my workflow, since I have duplicate iButtons to swap out, so separate scripts work for me. Ryan Knowles recently contributed a combined version of these scripts that downloads […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[218],"tags":[125,137,130],"class_list":["post-1285","post","type-post","status-publish","format-standard","hentry","category-r-project","tag-ibutton","tag-r-script","tag-thermochron"],"_links":{"self":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/1285","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/comments?post=1285"}],"version-history":[{"count":7,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/1285\/revisions"}],"predecessor-version":[{"id":1370,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/posts\/1285\/revisions\/1370"}],"wp:attachment":[{"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/media?parent=1285"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/categories?post=1285"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/lukemiller.org\/index.php\/wp-json\/wp\/v2\/tags?post=1285"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}