Merge 0.6.0-dev to dev for eventual 0.6.0 release

bin/oref0-autotune-prep.js

@@ -22,7 +22,7 @@
 
 var generate = require('oref0/lib/autotune-prep');
 function usage ( ) {
-        console.error('usage: ', process.argv.slice(0, 2), '<pumphistory.json> <profile.json> <glucose.json> [carbhistory.json] [autotune/glucose.json]');
+        console.error('usage: ', process.argv.slice(0, 2), '<pumphistory.json> <profile.json> <glucose.json> [pumpprofile.json] [carbhistory.json] [autotune/glucose.json]');
 }
 
 if (!module.parent) {
@@ -33,8 +33,9 @@ if (!module.parent) {
     }
     var profile_input = process.argv.slice(3, 4).pop();
     var glucose_input = process.argv.slice(4, 5).pop();
-    var carb_input = process.argv.slice(5, 6).pop()
-    var prepped_glucose_input = process.argv.slice(6, 7).pop()
+    var pumpprofile_input = process.argv.slice(5, 6).pop()
+    var carb_input = process.argv.slice(6, 7).pop()
+    var prepped_glucose_input = process.argv.slice(7, 8).pop()
 
     if ( !pumphistory_input || !profile_input || !glucose_input ) {
         usage( );
@@ -51,10 +52,23 @@ if (!module.parent) {
         return console.error("Could not parse input data: ", e);
     }
 
+    var pumpprofile_data = { };
+    if (typeof pumpprofile_input != 'undefined') {
+        try {
+            pumpprofile_data = JSON.parse(fs.readFileSync(pumpprofile_input, 'utf8'));
+        } catch (e) {
+            console.error("Warning: could not parse "+pumpprofile_input);
+        }
+    }
+
     // disallow impossibly low carbRatios due to bad decoding
     if ( typeof(profile_data.carb_ratio) == 'undefined' || profile_data.carb_ratio < 2 ) {
-        console.log('{ "carbs": 0, "mealCOB": 0, "reason": "carb_ratio ' + profile_data.carb_ratio + ' out of bounds" }');
-        return console.error("Error: carb_ratio " + profile_data.carb_ratio + " out of bounds");
+        if ( typeof(pumpprofile_data.carb_ratio) == 'undefined' || pumpprofile_data.carb_ratio < 2 ) {
+            console.log('{ "carbs": 0, "mealCOB": 0, "reason": "carb_ratios ' + profile_data.carb_ratio + ' and ' + pumpprofile_data.carb_ratio + ' out of bounds" }');
+            return console.error("Error: carb_ratios " + profile_data.carb_ratio + ' and ' + pumpprofile_data.carb_ratio + " out of bounds");
+        } else {
+            profile_data.carb_ratio = pumpprofile_data.carb_ratio;
+        }
     }
 
     try {

bin/oref0-autotune-recommends-report.sh

@@ -64,7 +64,7 @@ csf_new=$(cat $directory/autotune/profile.json | jq '.csf')
 carb_ratio_new=$(cat $directory/autotune/profile.json | jq '.carb_ratio')
 
 # Print Header Info
-printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}s\n" "Parameter" "Current" "Autotune" >> $report_file
+printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}s\n" "Parameter" "Pump" "Autotune" >> $report_file
 printf "%s\n" "-------------------------------------" >> $report_file
 
 # Print ISF, CSF and Carb Ratio Recommendations
@@ -74,10 +74,10 @@ if [ $csf_current != null ]; then
 else
   printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}.3f\n" "CSF [mg/dL/g]" "n/a" $csf_new >> $report_file
 fi
-printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "Carb Ratio [g]" $carb_ratio_current $carb_ratio_new >> $report_file
+printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "Carb Ratio[g/U]" $carb_ratio_current $carb_ratio_new >> $report_file
 
 # Print Basal Profile Recommendations
-printf "%-${parameter_width}s| %-${data_width}s|\n" "Basal Profile  [unit/hour]" "-" >> $report_file
+printf "%-${parameter_width}s| %-${data_width}s|\n" "Basals [U/hr]" "-" >> $report_file
 
 # Build time_list array of H:M in 30 minute increments to mirror pump basal schedule
 time_list=()

bin/oref0-autotune.sh

@@ -1,7 +1,7 @@
 #!/bin/bash
 
 # This script sets up an easy test environment for autotune, allowing the user to vary parameters 
-# like start/end date and number of runs.
+# like start/end date.
 # 
 # Required Inputs: 
 #   DIR, (--dir=<OpenAPS Directory>)
@@ -10,8 +10,6 @@
 # Optional Inputs:
 #   END_DATE, (--end-date=<YYYY-MM-DD>) 
 #     if no end date supplied, assume we want a months worth or until day before current day
-#   NUMBER_OF_RUNS (--runs=<integer, number of runs desired>)
-#     if no number of runs designated, then default to 5
 #   EXPORT_EXCEL (--xlsx=<filenameofexcel>)
 #     export to excel. Disabled by default
 #   TERMINAL_LOGGING (--log <true/false(true)>
@@ -39,7 +37,8 @@ DIR=""
 NIGHTSCOUT_HOST=""
 START_DATE=""
 END_DATE=""
-NUMBER_OF_RUNS=1  # Default to a single run if not otherwise specified
+START_DAYS_AGO=1  # Default to yesterday if not otherwise specified
+END_DAYS_AGO=1  # Default to yesterday if not otherwise specified
 EXPORT_EXCEL="" # Default is to not export to Microsoft Excel
 TERMINAL_LOGGING=true
 RECOMMENDS_REPORT=true
@@ -96,8 +95,12 @@ case $i in
     END_DATE=`date --date="$END_DATE" +%Y-%m-%d`
     shift # past argument=value
     ;;
-    -r=*|--runs=*)
-    NUMBER_OF_RUNS="${i#*=}"
+    -t=*|--start-days-ago=*)
+    START_DAYS_AGO="${i#*=}"
+    shift # past argument=value
+    ;;
+    -d=*|--end-days-ago=*)
+    END_DAYS_AGO="${i#*=}"
     shift # past argument=value
     ;;
     -x=*|--xlsx=*)
@@ -116,28 +119,31 @@ case $i in
 esac
 done
 
+# remove any trailing / from NIGHTSCOUT_HOST
+NIGHTSCOUT_HOST=$(echo $NIGHTSCOUT_HOST | sed 's/\/$//g')
+
 if [[ -z "$DIR" || -z "$NIGHTSCOUT_HOST" ]]; then
-    echo "Usage: oref0-autotune <--dir=myopenaps_directory> <--ns-host=https://mynightscout.azurewebsites.net> [--start-date=YYYY-MM-DD] [--end-date=YYYY-MM-DD] [--runs=number_of_runs] [--xlsx=autotune.xlsx] [--log=(true)|false]"
+    echo "Usage: oref0-autotune <--dir=myopenaps_directory> <--ns-host=https://mynightscout.azurewebsites.net> [--start-days-ago=number_of_days] [--end-days-ago=number_of_days] [--start-date=YYYY-MM-DD] [--end-date=YYYY-MM-DD] [--xlsx=autotune.xlsx] [--log=(true)|false]"
 exit 1
 fi
 if [[ -z "$START_DATE" ]]; then
     # Default start date of yesterday
-    START_DATE=`date --date="1 day ago" +%Y-%m-%d`
+    START_DATE=`date --date="$START_DAYS_AGO days ago" +%Y-%m-%d`
 fi
 if [[ -z "$END_DATE" ]]; then
     # Default end-date as this morning at midnight in order to not get partial day samples for now
     # (ISF/CSF adjustments are still single values across each day)
-    END_DATE=`date --date="1 day ago" +%Y-%m-%d`
+    END_DATE=`date --date="$END_DAYS_AGO days ago" +%Y-%m-%d`
 fi
 
 if [[ -z "$UNKNOWN_OPTION" ]] ; then # everything is ok
-  echo "Running oref0-autotune --dir=$DIR --ns-host=$NIGHTSCOUT_HOST --start-date=$START_DATE --runs=$NUMBER_OF_RUNS --end-date=$END_DATE"
+  echo "Running oref0-autotune --dir=$DIR --ns-host=$NIGHTSCOUT_HOST --start-date=$START_DATE --end-date=$END_DATE"
 else
   echo "Unknown options. Exiting"
   exit 1
 fi
 
-# Get profile for testing copied to home directory. "openaps" is my loop directory name.
+# Get profile for testing copied to home directory.
 cd $directory && mkdir -p autotune
 cp settings/pumpprofile.json autotune/profile.pump.json || die "Cannot copy settings/pumpprofile.json"
 # This allows manual users to be able to run autotune by simply creating a settings/pumpprofile.json file.
@@ -157,15 +163,6 @@ if [[ $TERMINAL_LOGGING = "true" ]]; then
   exec &> >(tee -a autotune.$(date +%Y-%m-%d-%H%M%S).log)
 fi
 
-# Pull Nightscout Data
-echo "Grabbing NIGHTSCOUT treatments.json for date range..."
-
-# Get Nightscout carb and insulin Treatments
-query="find%5Bcreated_at%5D%5B%24gte%5D=`date --date="$START_DATE -4 hours" -Iminutes`&find%5Bcreated_at%5D%5B%24lte%5D=`date --date="$END_DATE +1 days" -Iminutes`"
-echo Query: $NIGHTSCOUT_HOST/$query
-ns-get host $NIGHTSCOUT_HOST treatments.json $query > ns-treatments.json || die "Couldn't download ns-treatments.json"
-ls -la ns-treatments.json || die "No ns-treatments.json downloaded"
-
 # Build date list for autotune iteration
 date_list=()
 date=$START_DATE; 
@@ -179,76 +176,74 @@ do
   fi
 done
 
-echo "Grabbing NIGHTSCOUT entries/sgv.json for date range..."
+echo "Grabbing NIGHTSCOUT treatments.json and entries/sgv.json for date range..."
 
 # Get Nightscout BG (sgv.json) Entries
 for i in "${date_list[@]}"
 do 
-  query="find%5Bdate%5D%5B%24gte%5D=`(date -d $i +%s | tr -d '\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
-  echo Query: $NIGHTSCOUT_HOST $query
-  ns-get host $NIGHTSCOUT_HOST entries/sgv.json $query > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
-  ls -la ns-entries.$i.json || die "No ns-entries.$i.json downloaded"
-done
-
-echo "Running $NUMBER_OF_RUNS runs from $START_DATE to $END_DATE"
-sleep 2
-
-# Do iterative runs over date range, save autotune.json (prepped data) and input/output 
-# profile.json
-# Loop 1: Run 1 to Number of Runs specified by user or by default (1)
-for run_number in $(seq 1 $NUMBER_OF_RUNS)
-do
-  # Loop 2: Iterate through Date Range
-  for i in "${date_list[@]}"
-  do
-    cp profile.json profile.$run_number.$i.json
+    query="find%5Bdate%5D%5B%24gte%5D=`(date -d $i +%s | tr -d '\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
+    echo Query: $NIGHTSCOUT_HOST $query
+    ns-get host $NIGHTSCOUT_HOST entries/sgv.json $query > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
+    ls -la ns-entries.$i.json || die "No ns-entries.$i.json downloaded"
+
+    # Get Nightscout carb and insulin Treatments
+    # echo $i $START_DATE;
+    #query="find%5Bdate%5D%5B%24gte%5D=`(date -d $i +%s | tr -d'\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
+    query="find%5Bcreated_at%5D%5B%24gte%5D=`date --date="$i -5 hours" -Iminutes`&find%5Bcreated_at%5D%5B%24lte%5D=`date --date="$i +1 days" -Iminutes`"
+    echo Query: $NIGHTSCOUT_HOST/$query
+    ns-get host $NIGHTSCOUT_HOST treatments.json $query > ns-treatments.$i.json || die "Couldn't download ns-treatments.$i.json"
+    ls -la ns-treatments.$i.json || die "No ns-treatments.$i.json downloaded"
+
+
+    # Do iterative runs over date range, save autotune.json (prepped data) and input/output profile.json
+    cp profile.json profile.$i.json
     # Autotune Prep (required args, <pumphistory.json> <profile.json> <glucose.json>), output prepped glucose 
     # data or <autotune/glucose.json> below
-    echo "oref0-autotune-prep ns-treatments.json profile.json ns-entries.$i.json > autotune.$run_number.$i.json"
-    oref0-autotune-prep ns-treatments.json profile.json ns-entries.$i.json > autotune.$run_number.$i.json \
-        || die "Could not run oref0-autotune-prep ns-treatments.json profile.json ns-entries.$i.json"
+    echo "oref0-autotune-prep ns-treatments.$i.json profile.json ns-entries.$i.json profile.pump.json > autotune.$i.json"
+    oref0-autotune-prep ns-treatments.$i.json profile.json ns-entries.$i.json profile.pump.json > autotune.$i.json \
+        || die "Could not run oref0-autotune-prep ns-treatments.$i.json profile.json ns-entries.$i.json"
 
     # Autotune  (required args, <autotune/glucose.json> <autotune/autotune.json> <settings/profile.json>), 
     # output autotuned profile or what will be used as <autotune/autotune.json> in the next iteration
-    echo "oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json > newprofile.$run_number.$i.json"
-    if ! oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json > newprofile.$run_number.$i.json; then
+    echo "oref0-autotune-core autotune.$i.json profile.json profile.pump.json > newprofile.$i.json"
+    if ! oref0-autotune-core autotune.$i.json profile.json profile.pump.json > newprofile.$i.json; then
         if cat profile.json | jq --exit-status .carb_ratio==null; then
             echo "ERROR: profile.json contains null carb_ratio: using profile.pump.json"
             cp profile.pump.json profile.json
             exit
         else
-            die "Could not run oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json"
+            die "Could not run oref0-autotune-core autotune.$i.json profile.json profile.pump.json"
         fi
     else
         # Copy tuned profile produced by autotune to profile.json for use with next day of data
-        cp newprofile.$run_number.$i.json profile.json
+        cp newprofile.$i.json profile.json
     fi
 
-  done # End Date Range Iteration
-done # End Number of Runs Loop
 
-if ! [[ -z "$EXPORT_EXCEL" ]]; then
-  echo Exporting to $EXPORT_EXCEL
-  oref0-autotune-export-to-xlsx --dir $DIR --output $EXPORT_EXCEL
-fi
+    if ! [[ -z "$EXPORT_EXCEL" ]]; then
+        echo Exporting to $EXPORT_EXCEL
+        oref0-autotune-export-to-xlsx --dir $DIR --output $EXPORT_EXCEL
+    fi
 
-# Create Summary Report of Autotune Recommendations and display in the terminal
-if [[ $RECOMMENDS_REPORT == "true" ]]; then
-  # Set the report file name, so we can let the user know where it is and cat
-  # it to the screen
-  report_file=$directory/autotune/autotune_recommendations.log
+    # Create Summary Report of Autotune Recommendations and display in the terminal
+    if [[ $RECOMMENDS_REPORT == "true" ]]; then
+        # Set the report file name, so we can let the user know where it is and cat
+        # it to the screen
+        report_file=$directory/autotune/autotune_recommendations.log
 
-  echo
-  echo "Autotune pump profile recommendations:"
-  echo "---------------------------------------------------------"
+        echo
+        echo "Autotune pump profile recommendations:"
+        echo "---------------------------------------------------------"
 
-  # Let the user know where the Autotune Recommendations are logged
-  echo "Recommendations Log File: $report_file"
-  echo
+        # Let the user know where the Autotune Recommendations are logged
+        echo "Recommendations Log File: $report_file"
+        echo
 
-  # Run the Autotune Recommends Report
-  oref0-autotune-recommends-report $directory
+        # Run the Autotune Recommends Report
+        oref0-autotune-recommends-report $directory
 
-  # Go ahead and echo autotune_recommendations.log to the terminal, minus blank lines
-  cat $report_file | egrep -v "\| *\| *$"
-fi
+        # Go ahead and echo autotune_recommendations.log to the terminal, minus blank lines
+        cat $report_file | egrep -v "\| *\| *$"
+    fi
+
+done # End Date Range Iteration

bin/oref0-detect-sensitivity.js

@@ -17,7 +17,7 @@
 
 var basal = require('oref0/lib/profile/basal');
 var get_iob = require('oref0/lib/iob');
-var detect = require('oref0/lib/determine-basal/cob-autosens');
+var detect = require('oref0/lib/determine-basal/autosens');
 
 if (!module.parent) {
     var detectsensitivity = init();
@@ -27,9 +27,10 @@ if (!module.parent) {
     var isf_input = process.argv.slice(4, 5).pop()
     var basalprofile_input = process.argv.slice(5, 6).pop()
     var profile_input = process.argv.slice(6, 7).pop();
+    var carb_input = process.argv.slice(7, 8).pop()
 
     if (!glucose_input || !pumphistory_input || !profile_input) {
-        console.error('usage: ', process.argv.slice(0, 2), '<glucose.json> <pumphistory.json> <insulin_sensitivities.json> <basal_profile.json> <profile.json>');
+        console.error('usage: ', process.argv.slice(0, 2), '<glucose.json> <pumphistory.json> <insulin_sensitivities.json> <basal_profile.json> <profile.json> [carbhistory.json]');
         process.exit(1);
     }
 
@@ -62,6 +63,15 @@ if (!module.parent) {
         }
         var basalprofile = require(cwd + '/' + basalprofile_input);
 
+        var carb_data = { };
+        if (typeof carb_input != 'undefined') {
+            try {
+                carb_data = JSON.parse(fs.readFileSync(carb_input, 'utf8'));
+            } catch (e) {
+                console.error("Warning: could not parse "+carb_input);
+            }
+        }
+
         var iob_inputs = {
             history: pumphistory_data
             , profile: profile
@@ -73,9 +83,10 @@ if (!module.parent) {
 
     var detection_inputs = {
         iob_inputs: iob_inputs
-    , glucose_data: glucose_data
-    , basalprofile: basalprofile
-    //, clock: clock_data
+        , carbs: carb_data
+        , glucose_data: glucose_data
+        , basalprofile: basalprofile
+        //, clock: clock_data
     };
     detect(detection_inputs);
     var sensAdj = {

bin/oref0-meal.js

@@ -99,7 +99,7 @@ if (!module.parent) {
     , glucose: glucose_data
     };
 
-    var dia_carbs = generate(inputs);
-    console.log(JSON.stringify(dia_carbs));
+    var recentCarbs = generate(inputs);
+    console.log(JSON.stringify(recentCarbs));
 }