merge from develop

Jupyter/checkup.ipynb

@@ -48,10 +48,11 @@
  ],
  "metadata": {
   "interpreter": {
-   "hash": "d4f50e87ad7f9cd136d9d3dcf547b8236ee2585f92d0ab7c53dfb80e44e3fae9"
+   "hash": "bfd9857ee3bb42c16b52c1ffe04453343fea53c05fc5f9f2d5ac6a881cdaa36c"
   },
   "kernelspec": {
-   "display_name": "Python 3.9.5 64-bit ('.venv')",
+   "display_name": "Python 3.9.10 ('.venv': venv)",
+   "language": "python",
    "name": "python3"
   },
   "language_info": {

Jupyter/daily_trends.ipynb

@@ -0,0 +1,214 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "b8aada92",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%matplotlib inline\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matplotlib.dates as dates\n",
+    "import math\n",
+    "\n",
+    "import numpy as np\n",
+    "import datetime\n",
+    "from IPython.display import display, Markdown\n",
+    "import snakemd\n",
+    "import pandas as pd\n",
+    "\n",
+    "from garmindb import ConfigManager, Graph\n",
+    "from garmindb.garmindb import GarminSummaryDb, DaysSummary, MonitoringDb, MonitoringHeartRate, Sleep, GarminDb\n",
+    "from garmindb.summarydb import DaysSummary, WeeksSummary, MonthsSummary, SummaryDb\n",
+    "\n",
+    "from jupyter_funcs import format_number"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2d38e0f7-2ee5-40df-9373-b6485798d541",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def minsFromTime(t):\n",
+    "    return float(t.hour * 3600 + t.minute * 60 + t.second) / 60.0"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "7353aa53-92a0-44d9-b476-e050295c4748",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# start date\n",
+    "start_ts = datetime.datetime.combine(datetime.date(year=2022, month=5, day=1), datetime.datetime.min.time())\n",
+    "# end date (today)\n",
+    "end_ts = datetime.datetime.combine(datetime.date.today(), datetime.datetime.max.time())\n",
+    "\n",
+    "db_params = ConfigManager.get_db_params()\n",
+    "garmin_db = GarminDb(db_params)\n",
+    "sum_db = SummaryDb(db_params, False)\n",
+    "data = DaysSummary.get_for_period(sum_db, start_ts, end_ts, DaysSummary)\n",
+    "sleep = Sleep.get_for_period(garmin_db, start_ts, end_ts)\n",
+    "\n",
+    "time = [entry.day for entry in data]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "e41203c2-d435-4045-9c84-3559b4d3b367",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "stress_avg = [entry.stress_avg for entry in data]\n",
+    "bb_max = [entry.bb_max for entry in data]\n",
+    "bb_min = [entry.bb_min for entry in data]\n",
+    "rem_sleep_max = [minsFromTime(entry.rem_sleep_avg) for entry in data]\n",
+    "sleep_avg = [minsFromTime(entry.sleep_avg) / 60 for entry in data]\n",
+    "deep_sleep = [minsFromTime(sleep_event.deep_sleep) for sleep_event in sleep]\n",
+    "dm_df = pd.DataFrame([time, stress_avg, bb_max, bb_min, rem_sleep_max,deep_sleep, sleep_avg]).T\n",
+    "dm_df.columns = [\"Date\", \"stress_avg\", \"bb_max\", \"bb_min\", \"rem_sleep_max\", \"deep_sleep\", \"sleep_avg\"]\n",
+    "# remove the last record 'cause it's noisy sometimes\n",
+    "dm_df.drop(dm_df.tail(1).index,inplace=True) \n",
+    "dm_df\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ed0fe315",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "\n",
+    "columns = { \"stress_avg\" : \n",
+    "                   {\n",
+    "                       \"label\": \"Stress average\",\n",
+    "                       \"trend_marker\": \"--\",\n",
+    "                       \"color\": \"red\"\n",
+    "\n",
+    "                   }, \n",
+    "            \"bb_max\": \n",
+    "                   {\n",
+    "                       \"label\": \"Body battery max\",\n",
+    "                       \"trend_marker\": \"--\",\n",
+    "                       \"color\": \"orange\"\n",
+    "                   },\n",
+    "           \n",
+    "            \"sleep_avg\": \n",
+    "                   {\n",
+    "                       \"label\": \"Sleep time (hrs)\",\n",
+    "                       \"trend_marker\": \"-.\",\n",
+    "                       \"color\": \"blue\"\n",
+    "                  },\n",
+    "            \"rem_sleep_max\": \n",
+    "                   {\n",
+    "                       \"label\": \"Rem Sleep time (mins)\",\n",
+    "                       \"trend_marker\": \"-\",\n",
+    "                       \"color\": \"purple\"\n",
+    "                   },\n",
+    "           \n",
+    "            \"deep_sleep\": \n",
+    "                   {\n",
+    "                       \"label\": \"Deep sleep (mins)\",\n",
+    "                       \"trend_marker\": \"-\",\n",
+    "                       \"color\": \"green\"\n",
+    "                   }\n",
+    "          }\n",
+    "\n",
+    "# these are the data columns to plot\n",
+    "show_cols = {\"deep_sleep\", \"stress_avg\", \"bb_max\"}\n",
+    "\n",
+    "fig, host = plt.subplots(figsize=(22,16))\n",
+    "\n",
+    "plots = []\n",
+    "fit_summary = []\n",
+    "step = 0\n",
+    "\n",
+    "for col in show_cols:\n",
+    "    label=columns[col][\"label\"]\n",
+    "   \n",
+    "    ax2 = host.twinx()\n",
+    "    ax2.set_ylabel(label)\n",
+    "    ax2.tick_params(axis='y', labelcolor=columns[col][\"color\"])\n",
+    "\n",
+    "    # data\n",
+    "    plot, = ax2.plot(dm_df.Date, dm_df[col], 'o', ms=3.0, color=columns[col][\"color\"], label=label)\n",
+    "    plots.append(plot)\n",
+    "    \n",
+    "    # trend\n",
+    "    fitlabel = 'Fit {}'.format(label)\n",
+    "    x_dates = dates.date2num(dm_df.Date)\n",
+    "    trend = np.polyfit(x_dates, dm_df[col].astype(float) , 1)\n",
+    "    fit = np.poly1d(trend)\n",
+    "    x_fit = np.linspace(x_dates.min(), x_dates.max())\n",
+    "    fit, = ax2.plot(dates.num2date(x_fit), fit(x_fit), linestyle=columns[col][\"trend_marker\"], color=columns[col][\"color\"],label=fitlabel)\n",
+    "    plots.append(fit)\n",
+    "    \n",
+    "    ax2.spines['right'].set_position(('outward', step))\n",
+    "    \n",
+    "    step = step + 60\n",
+    "\n",
+    "    fit_data = fit.get_ydata()\n",
+    "    \n",
+    "    fit_summary.append({\"\": fitlabel, \"min\": math.floor(fit_data.min()), \"max\":math.floor(fit_data.max())})\n",
+    "  \n",
+    " \n",
+    "    \n",
+    "    \n",
+    "host.legend(handles=plots, loc='best')\n",
+    "\n",
+    "col_label = \"\"\n",
+    "for col in show_cols:\n",
+    "    if len(col_label):\n",
+    "        col_label += \", \"\n",
+    "    col_label += f\"{col}\"\n",
+    "\n",
+    "title = f\"{col_label} from {start_ts.date()} to {end_ts.date()}\"\n",
+    "\n",
+    "plt.title(label=title, fontsize=25)\n",
+    "\n",
+    "plt.show()\n",
+    "pd.DataFrame(fit_summary)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cab36f4b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "interpreter": {
+   "hash": "bfd9857ee3bb42c16b52c1ffe04453343fea53c05fc5f9f2d5ac6a881cdaa36c"
+  },
+  "kernelspec": {
+   "display_name": "Python 3.9.10 ('.venv': venv)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.9.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

Jupyter/monitoring.ipynb

@@ -110,10 +110,11 @@
  ],
  "metadata": {
   "interpreter": {
-   "hash": "d4f50e87ad7f9cd136d9d3dcf547b8236ee2585f92d0ab7c53dfb80e44e3fae9"
+   "hash": "bfd9857ee3bb42c16b52c1ffe04453343fea53c05fc5f9f2d5ac6a881cdaa36c"
   },
   "kernelspec": {
-   "display_name": "Python 3.9.5 64-bit ('.venv')",
+   "display_name": "Python 3.9.10 ('.venv': venv)",
+   "language": "python",
    "name": "python3"
   },
   "language_info": {

Jupyter/requirements.txt

@@ -1 +1,2 @@
-snakemd
+snakemd
+pandas

README.md

@@ -4,6 +4,10 @@
 
 [![Screen shot of an activity display](https://raw.githubusercontent.com/tcgoetz/GarminDB/master/Screenshots/Screen_Shot_activity_sm.jpg)](https://github.com/tcgoetz/GarminDB/wiki/Screenshots)
 
+---
+
+[![Screen shot of daily trend ](Screenshots/Screen_Shot_daily_trend.png)](https://github.com/tcgoetz/GarminDB/wiki/Screenshots)
+
 
 # GarminDB
 

garmindb/__init__.py

@@ -20,6 +20,7 @@
 from .statistics import Statistics
 from .tcx import Tcx
 from .monitoring_fit_file_processor import MonitoringFitFileProcessor
+from .sleep_fit_file_processor import SleepFitFileProcessor
 from .export_activities import ActivityExporter
 from .open_with_basecamp import OpenWithBaseCamp
 from .open_with_google_earth import OpenWithGoogleEarth
@@ -34,7 +35,7 @@
 from .plugin_manager import PluginManager
 from .version import format_version, log_version, python_version_check
 
-from .import_monitoring import GarminMonitoringFitData, GarminSummaryData, GarminProfile, GarminWeightData, GarminSleepData, GarminRhrData, GarminSettingsFitData, GarminHydrationData
+from .import_monitoring import GarminMonitoringFitData, GarminSleepFitData, GarminSummaryData, GarminProfile, GarminWeightData, GarminSleepData, GarminRhrData, GarminSettingsFitData, GarminHydrationData
 from .activities_fit_data import GarminActivitiesFitData
 from .garmin_tcx_data import GarminTcxData
 from .garmin_json_data import GarminJsonSummaryData, GarminJsonDetailsData

garmindb/fit_file_processor.py

@@ -21,7 +21,7 @@
 class FitFileProcessor():
     """Class that takes a parsed FIT file object and imports it into a database."""
 
-    def __init__(self, db_params, plugin_manager, debug=0):
+    def __init__(self, db_params, plugin_manager=None, debug=0):
         """
         Return a new FitFileProcessor instance.
 
@@ -204,15 +204,15 @@ def _write_attributes(self, timestamp, message_fields, attribute_names):
         for attribute_name in attribute_names:
             self._write_attribute(timestamp, message_fields, attribute_name)
 
-    def _write_measurement_ssytem_attributes(self, timestamp, message_fields):
+    def _write_measurement_sytem_attributes(self, timestamp, message_fields):
         for attribute_name in ['dist_setting', 'speed_setting', 'height_setting', 'temperature_setting']:
             self._write_attribute(timestamp, message_fields, attribute_name, 'measurement_system')
 
     def _write_device_settings_entry(self, fit_file, message_fields):
         root_logger.debug("device settings message: %r", message_fields)
         timestamp = fit_file.time_created_local
         self._write_attributes(timestamp, message_fields, ['active_time_zone', 'date_mode'])
-        self._write_measurement_ssytem_attributes(timestamp, message_fields)
+        self._write_measurement_sytem_attributes(timestamp, message_fields)
         self._write_attribute(timestamp, message_fields, 'active_time_zone', 'time_zone')
         self._write_attribute(timestamp, message_fields, 'date_mode', 'date_format')
 
@@ -223,11 +223,11 @@ def _write_user_profile_entry(self, fit_file, message_fields):
         root_logger.debug("user profile message: %r", message_fields)
         timestamp = fit_file.time_created_local
         attribute_names = [
-            'gender', 'height', 'weight', 'language', 'dist_setting', 'weight_setting', 'position_setting', 'elev_setting', 'sleep_time', 'wake_time',
+            'gender', 'height', 'weight', 'age', 'year_of_birth', 'language', 'dist_setting', 'weight_setting', 'position_setting', 'elev_setting', 'sleep_time', 'wake_time',
             'speed_setting'
         ]
         self._write_attributes(timestamp, message_fields, attribute_names)
-        self._write_measurement_ssytem_attributes(timestamp, message_fields)
+        self._write_measurement_sytem_attributes(timestamp, message_fields)
 
     def _write_activity_entry(self, fit_file, message_fields):
         root_logger.debug("activity message: %r", message_fields)

garmindb/garmindb/garmin_db.py

@@ -225,7 +225,7 @@ class Sleep(GarminDb.Base, idbutils.DbObject):
     __tablename__ = 'sleep'
 
     db = GarminDb
-    table_version = 1
+    table_version = 2
 
     day = Column(Date, primary_key=True)
     start = Column(DateTime)
@@ -235,6 +235,9 @@ class Sleep(GarminDb.Base, idbutils.DbObject):
     light_sleep = Column(Time, nullable=False, default=datetime.time.min)
     rem_sleep = Column(Time, nullable=False, default=datetime.time.min)
     awake = Column(Time, nullable=False, default=datetime.time.min)
+    avg_spo2 = Column(Float)
+    avg_rr = Column(Float)
+    avg_stress = Column(Float)
 
     @classmethod
     def get_stats(cls, session, start_ts, end_ts):
@@ -270,6 +273,30 @@ def get_wake_time(cls, db, day_date):
         if len(values) > 0:
             return values[0][0]
 
+    @classmethod
+    def get_level_time(cls, session, day_date, sleep_level):
+        """Return the time in a given sleep level for a given date."""
+        day_start_ts = datetime.datetime.combine(day_date, datetime.time.min)
+        day_stop_ts = datetime.datetime.combine(day_date, datetime.time.max)
+        result = cls._s_query(session, cls._time_from_secs(func.sum(cls._secs_from_time(cls.duration))), None, day_start_ts, day_stop_ts,
+                              cls._secs_from_time(cls.duration)).filter(cls.event == sleep_level).scalar()
+        return datetime.datetime.strptime(result, '%H:%M:%S').time() if result is not None else datetime.time.min
+
+    @classmethod
+    def get_day_stats(cls, session, day_date):
+        """Return a dictionary of aggregate statistics for the given time period."""
+        deep_sleep = cls.get_level_time(cls, session, day_date, 'deep_sleep')
+        light_sleep = cls.get_level_time(cls, session, day_date, 'light_sleep')
+        rem_sleep = cls.get_level_time(cls, session, day_date, 'rem_sleep')
+        awake = cls.get_level_time(cls, session, day_date, 'awake')
+        return {
+            'total_sleep': deep_sleep + light_sleep + rem_sleep,
+            'deep_sleep': deep_sleep,
+            'light_sleep': light_sleep,
+            'rem_sleep': rem_sleep,
+            'awake': awake
+        }
+
 
 class RestingHeartRate(GarminDb.Base, idbutils.DbObject):
     """Class representing a daily resting heart rate reading."""