Merge pull request #1851 from Philoul/Autotune/UnitTests
Add Unit test for AutotunePrep
This commit is contained in:
Milos Kozak
GitHub
commit
5ea5e80393
6 changed files with 546 additions and 12 deletions
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@ -29,7 +29,7 @@ import kotlin.math.ceil
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import kotlin.math.roundToInt
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@Singleton
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class AutotuneIob @Inject constructor(
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open class AutotuneIob @Inject constructor(
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private val aapsLogger: AAPSLogger,
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private val repository: AppRepository,
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private val profileFunction: ProfileFunction,
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@ -41,10 +41,10 @@ class AutotuneIob @Inject constructor(
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private val nsTreatments = ArrayList<NsTreatment>()
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private var dia: Double = Constants.defaultDIA
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var boluses: MutableList<Bolus> = ArrayList()
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var boluses: ArrayList<Bolus> = ArrayList()
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var meals = ArrayList<Carbs>()
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lateinit var glucose: List<GlucoseValue> // newest at index 0
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private lateinit var tempBasals: MutableList<TemporaryBasal>
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private lateinit var tempBasals: ArrayList<TemporaryBasal>
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var startBG: Long = 0
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var endBG: Long = 0
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private fun range(): Long = (60 * 60 * 1000L * dia + T.hours(2).msecs()).toLong()
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@ -225,7 +225,7 @@ class AutotuneIob @Inject constructor(
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}
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}
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fun getIOB(time: Long, localInsulin: LocalInsulin): IobTotal {
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open fun getIOB(time: Long, localInsulin: LocalInsulin): IobTotal {
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val bolusIob = getCalculationToTimeTreatments(time, localInsulin).round()
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return bolusIob
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}
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@ -302,7 +302,7 @@ class AutotunePrep @Inject constructor(
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// Then, calculate carb absorption for that 5m interval using the deviation.
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if (mealCOB > 0) {
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val ci = Math.max(deviation, sp.getDouble("openapsama_min_5m_carbimpact", 3.0))
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val ci = Math.max(deviation, sp.getDouble(R.string.key_openapsama_min_5m_carbimpact, 3.0))
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val absorbed = ci * tunedprofile.ic / sens
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// Store the COB, and use it as the starting point for the next data point.
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mealCOB = Math.max(0.0, mealCOB - absorbed)
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@ -30,9 +30,6 @@ class AutotuneCoreTest : TestBaseWithProfile() {
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@Mock lateinit var injector: HasAndroidInjector
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@Mock lateinit var activePlugin: ActivePlugin
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lateinit var autotuneCore: AutotuneCore
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lateinit var prep: PreppedGlucose
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lateinit var prepjson: String
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lateinit var inputProfile: ATProfile
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var min5mCarbImpact = 0.0
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var autotuneMin = 0.0
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var autotuneMax = 0.0
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@ -41,14 +38,15 @@ class AutotuneCoreTest : TestBaseWithProfile() {
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fun initData() {
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autotuneCore = AutotuneCore(sp,autotuneFS)
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TimeZone.setDefault(TimeZone.getTimeZone("GMT+2"))
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prepjson = File("src/test/res/autotune/test1/autotune.2022-05-21.json").readText()
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val inputProfileJson = File("src/test/res/autotune/test1/profile.pump.json").readText()
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inputProfile = atProfileFromOapsJson(JSONObject(inputProfileJson), dateUtil)!!
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prep = PreppedGlucose(JSONObject(prepjson), dateUtil)
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}
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@Test
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fun autotuneCoreTest() { // Test if load from file of OpenAPS categorisation is Ok
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val prepjson = File("src/test/res/autotune/test1/autotune.2022-05-21.json").readText()
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val inputProfileJson = File("src/test/res/autotune/test1/profile.pump.json").readText()
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val inputProfile = atProfileFromOapsJson(JSONObject(inputProfileJson), dateUtil)!!
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val prep = PreppedGlucose(JSONObject(prepjson), dateUtil)
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`when`(sp.getDouble(R.string.key_openapsama_autosens_max, 1.2)).thenReturn(autotuneMax)
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`when`(sp.getDouble(R.string.key_openapsama_autosens_min, 0.7)).thenReturn(autotuneMin)
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`when`(sp.getDouble(R.string.key_openapsama_min_5m_carbimpact, 3.0)).thenReturn(min5mCarbImpact)
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@ -0,0 +1,250 @@
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package info.nightscout.androidaps.plugins.general.autotune
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import dagger.android.HasAndroidInjector
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import info.nightscout.androidaps.R
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import info.nightscout.androidaps.TestBaseWithProfile
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import info.nightscout.androidaps.data.IobTotal
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import info.nightscout.androidaps.data.LocalInsulin
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import info.nightscout.androidaps.data.ProfileSealed
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import info.nightscout.androidaps.data.PureProfile
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import info.nightscout.androidaps.database.AppRepository
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import info.nightscout.androidaps.database.data.Block
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import info.nightscout.androidaps.database.data.TargetBlock
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import info.nightscout.androidaps.database.entities.Bolus
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import info.nightscout.androidaps.database.entities.Carbs
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import info.nightscout.androidaps.database.entities.GlucoseValue
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import info.nightscout.androidaps.interfaces.*
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import info.nightscout.androidaps.plugins.general.autotune.data.*
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import info.nightscout.androidaps.utils.DateUtil
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import info.nightscout.androidaps.utils.JsonHelper
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import info.nightscout.androidaps.utils.T
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import info.nightscout.shared.logging.AAPSLogger
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import info.nightscout.shared.sharedPreferences.SP
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import org.json.JSONArray
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import org.json.JSONObject
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import org.junit.Assert
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import org.junit.Before
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import org.junit.Test
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import org.mockito.Mock
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import org.mockito.Mockito.`when`
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import java.io.File
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import java.util.*
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import kotlin.collections.ArrayList
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class AutotunePrepTest : TestBaseWithProfile() {
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@Mock lateinit var sp: SP
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@Mock lateinit var autotuneFS: AutotuneFS
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@Mock lateinit var injector: HasAndroidInjector
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@Mock lateinit var activePlugin: ActivePlugin
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@Mock lateinit var repository: AppRepository
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lateinit var autotunePrep: AutotunePrep
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lateinit var autotuneIob: TestAutotuneIob
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lateinit var inputProfile: ATProfile
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var min5mCarbImpact = 0.0
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var autotuneMin = 0.0
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var autotuneMax = 0.0
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var startDayTime = 0L
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@Before
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fun initData() {
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TimeZone.setDefault(TimeZone.getTimeZone("GMT+2"))
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val inputProfileJson = File("src/test/res/autotune/test1/profile.pump.json").readText()
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inputProfile = atProfileFromOapsJson(JSONObject(inputProfileJson), dateUtil)!!
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val inputIobJson = File("src/test/res/autotune/test1/oaps-iobCalc.2022-05-21.json").readText() //json files build with iob/activity calculated by OAPS
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val iobOapsCalcul = buildIobOaps(JSONArray(inputIobJson))
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autotuneIob = TestAutotuneIob(aapsLogger, repository, profileFunction, sp, dateUtil, activePlugin, autotuneFS, iobOapsCalcul)
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autotunePrep = AutotunePrep(sp, dateUtil, autotuneFS, autotuneIob)
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}
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@Test
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fun autotunePrepTest() { // Test if load from file of OpenAPS categorisation is Ok
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val prepjson = File("src/test/res/autotune/test1/autotune.2022-05-21.json").readText()
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val oapsPreppedGlucose = PreppedGlucose(JSONObject(prepjson), dateUtil) //prep data calculated by OpenAPS autotune
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val oapsEntriesJson = File("src/test/res/autotune/test1/aaps-entries.2022-05-21.json").readText()
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autotuneIob.glucose = buildGlucose(JSONArray(oapsEntriesJson))
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val oapsTreatmentsJson = File("src/test/res/autotune/test1/aaps-treatments.2022-05-21.json").readText()
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autotuneIob.meals = buildMeals(JSONArray(oapsTreatmentsJson)) //Only meals is used in unit test, Insulin only used for iob calculation
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autotuneIob.boluses = buildBoluses(oapsPreppedGlucose) //Values from oapsPrepData because linked to iob calculation method for TBR
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`when`(sp.getDouble(R.string.key_openapsama_min_5m_carbimpact, 3.0)).thenReturn(min5mCarbImpact)
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val aapsPreppedGlucose = autotunePrep.categorizeBGDatums(inputProfile, inputProfile.localInsulin, false)
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try {
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aapsPreppedGlucose?.let { // compare all categorization calculated by aaps plugin (aapsPreppedGlucose) with categorization calculated by OpenAPS (oapsPreppedGlucose)
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for (i in aapsPreppedGlucose.crData.indices)
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Assert.assertTrue(oapsPreppedGlucose.crData[i].equals(aapsPreppedGlucose.crData[i]))
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for (i in aapsPreppedGlucose.csfGlucoseData.indices)
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Assert.assertTrue(oapsPreppedGlucose.csfGlucoseData[i].equals(aapsPreppedGlucose.csfGlucoseData[i]))
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for (i in aapsPreppedGlucose.isfGlucoseData.indices)
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Assert.assertTrue(oapsPreppedGlucose.isfGlucoseData[i].equals(aapsPreppedGlucose.isfGlucoseData[i]))
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for (i in aapsPreppedGlucose.basalGlucoseData.indices)
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Assert.assertTrue(oapsPreppedGlucose.basalGlucoseData[i].equals(aapsPreppedGlucose.basalGlucoseData[i]))
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}
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?: Assert.fail()
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} catch (e: Exception) {
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Assert.fail()
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}
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}
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/**
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* OpenAPS profile for Autotune only have one ISF value and one IC value
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*/
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fun atProfileFromOapsJson(jsonObject: JSONObject, dateUtil: DateUtil, defaultUnits: String? = null): ATProfile? {
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try {
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min5mCarbImpact = JsonHelper.safeGetDoubleAllowNull(jsonObject, "min_5m_carbimpact") ?: return null
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autotuneMin = JsonHelper.safeGetDoubleAllowNull(jsonObject, "autosens_min") ?: return null
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autotuneMax = JsonHelper.safeGetDoubleAllowNull(jsonObject, "autosens_max") ?: return null
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val txtUnits = JsonHelper.safeGetStringAllowNull(jsonObject, "units", defaultUnits) ?: return null
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val units = GlucoseUnit.fromText(txtUnits)
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val dia = JsonHelper.safeGetDoubleAllowNull(jsonObject, "dia") ?: return null
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val peak = JsonHelper.safeGetIntAllowNull(jsonObject, "insulinPeakTime") ?: return null
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val localInsulin = LocalInsulin("insulin", peak, dia)
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val timezone = TimeZone.getTimeZone(JsonHelper.safeGetString(jsonObject, "timezone", "UTC"))
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val isfJson = jsonObject.getJSONObject("isfProfile")
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val isfBlocks = ArrayList<Block>(1).also {
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val isfJsonArray = isfJson.getJSONArray("sensitivities")
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val value = isfJsonArray.getJSONObject(0).getDouble("sensitivity")
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it.add(0,Block((T.hours(24).secs()) * 1000L, value))
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}
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val icBlocks = ArrayList<Block>(1).also {
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val value = jsonObject.getDouble("carb_ratio")
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it.add(0,Block((T.hours(24).secs()) * 1000L, value))
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}
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val basalBlocks = blockFromJsonArray(jsonObject.getJSONArray("basalprofile"), dateUtil)
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?: return null
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val targetBlocks = ArrayList<TargetBlock>(1).also {
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it.add(0, TargetBlock((T.hours(24).secs()) * 1000L, 100.0, 100.0))
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}
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val pure = PureProfile(
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jsonObject = jsonObject,
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basalBlocks = basalBlocks,
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isfBlocks = isfBlocks,
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icBlocks = icBlocks,
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targetBlocks = targetBlocks,
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glucoseUnit = units,
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timeZone = timezone,
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dia = dia
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)
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return ATProfile(ProfileSealed.Pure(pure), localInsulin, profileInjector).also { it.dateUtil = dateUtil}
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} catch (ignored: Exception) {
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return null
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}
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}
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fun blockFromJsonArray(jsonArray: JSONArray?, dateUtil: DateUtil): List<Block>? {
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val size = jsonArray?.length() ?: return null
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val ret = ArrayList<Block>(size)
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try {
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for (index in 0 until jsonArray.length() - 1) {
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val o = jsonArray.getJSONObject(index)
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val tas = o.getInt("minutes") * 60
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val next = jsonArray.getJSONObject(index + 1)
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val nextTas = next.getInt("minutes") * 60
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val value = o.getDouble("rate")
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if (tas % 3600 != 0) return null
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if (nextTas % 3600 != 0) return null
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ret.add(index, Block((nextTas - tas) * 1000L, value))
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}
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val last: JSONObject = jsonArray.getJSONObject(jsonArray.length() - 1)
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val lastTas = last.getInt("minutes") * 60
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val value = last.getDouble("rate")
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ret.add(jsonArray.length() - 1, Block((T.hours(24).secs() - lastTas) * 1000L, value))
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} catch (e: Exception) {
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return null
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}
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return ret
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}
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fun buildBoluses(preppedGlucose: PreppedGlucose): ArrayList<Bolus> { //if categorization is correct then I return for dose function the crInsulin calculated in Oaps
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val boluses: ArrayList<Bolus> = ArrayList()
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try {
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for (i in preppedGlucose.crData.indices) {
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boluses.add(
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Bolus(
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timestamp = preppedGlucose.crData[i].crEndTime,
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amount = preppedGlucose.crData[i].crInsulin,
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type = Bolus.Type.NORMAL
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)
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)
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}
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} catch (e: Exception) { }
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return boluses
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}
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fun buildMeals(jsonArray: JSONArray): ArrayList<Carbs> {
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val list: ArrayList<Carbs> = ArrayList()
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try {
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for (index in 0 until jsonArray.length()) {
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val json = jsonArray.getJSONObject(index)
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val value = JsonHelper.safeGetDouble(json, "carbs", 0.0)
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val timestamp = JsonHelper.safeGetLong(json, "date")
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if (value > 0.0 && timestamp > startDayTime) {
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list.add(Carbs(timestamp=timestamp, amount = value, duration = 0))
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}
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}
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} catch (e: Exception) { }
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return list
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}
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fun buildGlucose(jsonArray: JSONArray): List<GlucoseValue> {
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val list: ArrayList<GlucoseValue> = ArrayList()
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try {
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for (index in 0 until jsonArray.length()) {
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val json = jsonArray.getJSONObject(index)
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val value = JsonHelper.safeGetDouble(json, "sgv")
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val timestamp = JsonHelper.safeGetLong(json, "date")
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list.add(GlucoseValue(raw = value, noise = 0.0, value = value, timestamp = timestamp, sourceSensor = GlucoseValue.SourceSensor.UNKNOWN, trendArrow = GlucoseValue.TrendArrow.FLAT))
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}
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} catch (e: Exception) { }
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if (list.size > 0)
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startDayTime = list[list.size-1].timestamp
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return list
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}
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fun buildIobOaps(jsonArray: JSONArray): ArrayList<IobTotal> { //if categorization is correct then I return for dose function the crInsulin calculated in Oaps
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val list: ArrayList<IobTotal> = ArrayList()
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for (index in 0 until jsonArray.length()) {
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val json = jsonArray.getJSONObject(index)
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val time = JsonHelper.safeGetLong(json,"date")
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val iob = JsonHelper.safeGetDouble(json, "iob")
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val activity = JsonHelper.safeGetDouble(json, "activity")
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val iobTotal = IobTotal(time)
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iobTotal.iob = iob
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iobTotal.activity = activity
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list.add(iobTotal)
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}
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return list
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}
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class TestAutotuneIob(
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val aapsLogger: AAPSLogger,
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repository: AppRepository,
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val profileFunction: ProfileFunction,
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val sp: SP,
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val dateUtil: DateUtil,
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val activePlugin: ActivePlugin,
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autotuneFS: AutotuneFS,
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val iobOapsCalcul: ArrayList<IobTotal>
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) : AutotuneIob(
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aapsLogger,
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repository,
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profileFunction,
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sp,
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dateUtil,
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activePlugin,
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autotuneFS
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) {
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override fun getIOB(time: Long, localInsulin: LocalInsulin): IobTotal {
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var bolusIob = IobTotal(time)
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iobOapsCalcul.forEach {
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if (it.time == time)
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return it
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}
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return bolusIob
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}
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}
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}
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BIN
app/src/test/res/autotune/test1/Convert_Log2JSON.xlsx
Normal file
BIN
app/src/test/res/autotune/test1/Convert_Log2JSON.xlsx
Normal file
Binary file not shown.
286
app/src/test/res/autotune/test1/oaps-iobCalc.2022-05-21.json
Normal file
286
app/src/test/res/autotune/test1/oaps-iobCalc.2022-05-21.json
Normal file
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@ -0,0 +1,286 @@
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[
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{ "iob": 5.249, "activity": 0.0391, "date": 1653099848000},
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{ "iob": 5.292, "activity": 0.0438, "date": 1653100148000},
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{ "iob": 4.964, "activity": 0.047, "date": 1653100449000},
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{ "iob": 4.674, "activity": 0.0489, "date": 1653100748000},
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{ "iob": 4.377, "activity": 0.0498, "date": 1653101048000},
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{ "iob": 4.077, "activity": 0.0498, "date": 1653101348000},
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{ "iob": 3.73, "activity": 0.0491, "date": 1653101648000},
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{ "iob": 3.389, "activity": 0.0476, "date": 1653101948000},
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{ "iob": 3.055, "activity": 0.0457, "date": 1653102249000},
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{ "iob": 2.782, "activity": 0.0436, "date": 1653102548000},
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{ "iob": 2.47, "activity": 0.0411, "date": 1653102848000},
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{ "iob": 2.22, "activity": 0.0386, "date": 1653103149000},
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{ "iob": 1.935, "activity": 0.0358, "date": 1653103448000},
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{ "iob": 1.711, "activity": 0.0332, "date": 1653103748000},
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{ "iob": 1.452, "activity": 0.0304, "date": 1653104049000},
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{ "iob": 1.927, "activity": 0.028, "date": 1653104349000},
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{ "iob": 1.84, "activity": 0.027, "date": 1653104648000},
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{ "iob": 1.658, "activity": 0.0258, "date": 1653104949000},
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{ "iob": 1.482, "activity": 0.0245, "date": 1653105248000},
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{ "iob": 1.264, "activity": 0.0229, "date": 1653105549000},
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{ "iob": 1.104, "activity": 0.0212, "date": 1653105848000},
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{ "iob": 0.952, "activity": 0.0194, "date": 1653106149000},
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{ "iob": 1.619, "activity": 0.0181, "date": 1653106449000},
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{ "iob": 1.678, "activity": 0.0184, "date": 1653106749000},
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{ "iob": 1.775, "activity": 0.0187, "date": 1653107048000},
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{ "iob": 1.581, "activity": 0.019, "date": 1653107348000},
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{ "iob": 1.437, "activity": 0.0188, "date": 1653107648000},
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{ "iob": 1.294, "activity": 0.0183, "date": 1653107948000},
|
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{ "iob": 0.581, "activity": 0.0061, "date": 1653176950000},
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{ "iob": 1.238, "activity": 0.0075, "date": 1653177250000},
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{ "iob": 1.147, "activity": 0.0088, "date": 1653177550000},
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{ "iob": 1.151, "activity": 0.0098, "date": 1653177850000},
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{ "iob": 1.05, "activity": 0.0104, "date": 1653178149000},
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{ "iob": 0.947, "activity": 0.0107, "date": 1653178449000},
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{ "iob": 0.844, "activity": 0.0106, "date": 1653178750000},
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{ "iob": 0.741, "activity": 0.0104, "date": 1653179050000},
|
||||
{ "iob": 0.59, "activity": 0.0099, "date": 1653179350000},
|
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{ "iob": 0.542, "activity": 0.0093, "date": 1653179649000},
|
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{ "iob": 0.497, "activity": 0.0087, "date": 1653179949000},
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{ "iob": 0.456, "activity": 0.0081, "date": 1653180250000},
|
||||
{ "iob": 0.516, "activity": 0.0077, "date": 1653180549000},
|
||||
{ "iob": 0.429, "activity": 0.0072, "date": 1653180849000},
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||||
{ "iob": 0.294, "activity": 0.0066, "date": 1653181150000},
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{ "iob": 0.163, "activity": 0.0058, "date": 1653181450000},
|
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{ "iob": 0.037, "activity": 0.0049, "date": 1653181750000},
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{ "iob": -0.085, "activity": 0.0039, "date": 1653182050000},
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{ "iob": -0.153, "activity": 0.0029, "date": 1653182349000},
|
||||
{ "iob": -0.265, "activity": 0.0018, "date": 1653182650000},
|
||||
{ "iob": -0.371, "activity": 0.0007, "date": 1653182949000},
|
||||
{ "iob": -0.471, "activity": -0.0005, "date": 1653183249000},
|
||||
{ "iob": -0.566, "activity": -0.0016, "date": 1653183550000},
|
||||
{ "iob": -0.606, "activity": -0.0026, "date": 1653183850000},
|
||||
{ "iob": -0.64, "activity": -0.0036, "date": 1653184150000},
|
||||
{ "iob": -0.67, "activity": -0.0044, "date": 1653184450000}
|
||||
]
|
||||
|
||||
Loading…
Reference in a new issue