From ce503d94e139229a565689ba9601ee06cabdec19 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Wed, 11 Dec 2024 12:50:39 +0100
Subject: [PATCH 01/12] remove valid days and daytime assessment

---
 src/paradigma/config.py                       |  3 --
 src/paradigma/tremor/tremor_analysis.py       | 33 +++++--------------
 .../tremor/weekly_tremor.json                 |  4 +--
 3 files changed, 9 insertions(+), 31 deletions(-)

diff --git a/src/paradigma/config.py b/src/paradigma/config.py
index 3317e59..b5c50e5 100644
--- a/src/paradigma/config.py
+++ b/src/paradigma/config.py
@@ -361,9 +361,6 @@ class TremorQuantificationConfig(TremorBaseConfig):
     def __init__(self) -> None:
         super().__init__()
 
-        self.valid_day_threshold_hr: float = 0 # change to 10 later!
-        self.daytime_hours_lower_bound: float = 8
-        self.daytime_hours_upper_bound: float = 22
         self.percentile_tremor_power: float = 0.9
 
         self.set_filenames('tremor')
diff --git a/src/paradigma/tremor/tremor_analysis.py b/src/paradigma/tremor/tremor_analysis.py
index d74502a..2b89627 100644
--- a/src/paradigma/tremor/tremor_analysis.py
+++ b/src/paradigma/tremor/tremor_analysis.py
@@ -127,29 +127,14 @@ def aggregate_tremor_power(tremor_power: pd.Series, config: TremorQuantification
     return tremor_power_median, tremor_power_90th_perc, tremor_power_mode
 
 
-def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig, utc_start_time: str):
-
-    # Create time array in local time zone
-    utc_start_time = datetime.strptime(utc_start_time, "%Y-%m-%dT%H:%M:%SZ").replace(tzinfo=pytz.UTC) # convert to datetime
-    local_start_time = utc_start_time.astimezone(pytz.timezone("Europe/Amsterdam"))
-    time = [local_start_time + timedelta(seconds=x) for x in df.time]
-
-    # determine valid days
-    daytime_hours = range(config.daytime_hours_lower_bound,config.daytime_hours_upper_bound)
-    nr_windows_per_day = Counter([dt.date() for dt in time if dt.hour in daytime_hours])
-    valid_days = [day for day, count in nr_windows_per_day.items() 
-                  if count * config.window_length_s / 3600 >= config.valid_day_threshold_hr]
-    nr_valid_days = len(valid_days)
-
-    # remove windows during non-valid days, non-daytime hours and non-tremor arm movement
-    df_filtered = df.loc[[dt.date() in valid_days for dt in time]]
-    df_filtered = df_filtered.loc[[dt.hour in daytime_hours for dt in time]]
-    nr_windows_daytime = df_filtered.shape[0] # number of windows during daytime on valid days
-    df_filtered = df_filtered.loc[df_filtered.low_freq_power <= config.movement_threshold]
-    nr_windows_daytime_rest = df_filtered.shape[0] # number of windows during daytime on valid days without non-tremor arm movement
+def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig):
+
+    # remove windows with detected non-tremor movements
+    df_filtered = df.loc[df.low_freq_power <= config.movement_threshold]
+    nr_windows_rest = df_filtered.shape[0] # number of windows without non-tremor arm movement
 
     # calculate weekly tremor time
-    tremor_time= np.sum(df_filtered['pred_tremor_checked']) / df_filtered.shape[0] * 100
+    tremor_time= np.sum(df_filtered['pred_tremor_checked']) / nr_windows_rest * 100 # as percentage of total measured time without non-tremor arm movement
 
     # calculate weekly tremor power measures
     tremor_power = df_filtered.loc[df_filtered['pred_tremor_checked'] == 1, 'tremor_power']
@@ -158,9 +143,7 @@ def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig, utc_st
     # store aggregates in json format
     d_aggregates = {
         'metadata': {
-            'nr_valid_days': nr_valid_days,
-            'nr_windows_daytime': nr_windows_daytime,
-            'nr_windows_daytime_rest': nr_windows_daytime_rest
+            'nr_windows_rest': nr_windows_rest
         },
         'weekly_tremor_measures': {
             'tremor_time': tremor_time,
@@ -191,7 +174,7 @@ def quantify_tremor_io(path_to_feature_input: Union[str, Path], path_to_predicti
     df = pd.concat([df_predictions, df_features], axis=1)
 
     # Compute weekly aggregated tremor measures
-    d_aggregates = quantify_tremor(df, config, utc_start_time = metadata_time.start_iso8601)
+    d_aggregates = quantify_tremor(df, config)
 
     # Save output
     with open(os.path.join(output_path,"weekly_tremor.json"), 'w') as json_file:
diff --git a/tests/data/5.quantification/tremor/weekly_tremor.json b/tests/data/5.quantification/tremor/weekly_tremor.json
index 73e1cc2..ca7b277 100644
--- a/tests/data/5.quantification/tremor/weekly_tremor.json
+++ b/tests/data/5.quantification/tremor/weekly_tremor.json
@@ -1,8 +1,6 @@
 {
     "metadata": {
-        "nr_valid_days": 1,
-        "nr_windows_daytime": 182,
-        "nr_windows_daytime_rest": 89
+        "nr_windows_rest": 89
     },
     "weekly_tremor_measures": {
         "tremor_time": 16.853932584269664,

From dec77e701811b71577793550ac0b8bf7e29c3b1a Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Fri, 13 Dec 2024 14:14:34 +0100
Subject: [PATCH 02/12] add notebook without io wrappers

---
 docs/notebooks/tremor/tremor_analysis.ipynb  |   8 +-
 docs/notebooks/tremor/tremor_analysis2.ipynb | 165 +++++++++++++++++++
 src/paradigma/tremor/tremor_analysis.py      |   2 -
 3 files changed, 169 insertions(+), 6 deletions(-)
 create mode 100644 docs/notebooks/tremor/tremor_analysis2.ipynb

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index bf60e65..836fc18 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/docs/notebooks/tremor/tremor_analysis2.ipynb b/docs/notebooks/tremor/tremor_analysis2.ipynb
new file mode 100644
index 0000000..e7266d8
--- /dev/null
+++ b/docs/notebooks/tremor/tremor_analysis2.ipynb
@@ -0,0 +1,165 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Tremor analysis"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import pandas as pd\n",
+    "from paradigma.config import IMUConfig, TremorFeatureExtractionConfig, TremorDetectionConfig, TremorQuantificationConfig\n",
+    "from paradigma.imu_preprocessing import preprocess_imu_data\n",
+    "from paradigma.tremor.tremor_analysis import extract_tremor_features, detect_tremor, quantify_tremor"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df_tremor_week = pd.DataFrame(columns=['low_freq_power','tremor_power','pred_tremor_checked'])"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Load data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 39,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import tsdf\n",
+    "from paradigma.util import read_metadata\n",
+    "\n",
+    "input_path =  'C:\\\\Users\\\\z835211\\\\Documents\\\\Data\\\\Raw IMU data\\\\WatchData.IMU.Week2\\\\POMU0000775B2E171842'\n",
+    "segment = 'WatchData.IMU.Week2.raw_segment0010'\n",
+    "\n",
+    "# Load data\n",
+    "metadata_time, metadata_values = read_metadata(str(input_path), str(segment+'_meta.json'),\n",
+    "                                                    str(segment+'_time.bin'), str(segment+'_samples.bin'))\n",
+    "df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)\n",
+    "\n",
+    "# Rename columns\n",
+    "df = df.rename(columns={f'rotation_{a}': f'gyroscope_{a}' for a in ['x', 'y', 'z']})\n",
+    "df = df.rename(columns={f'acceleration_{a}': f'accelerometer_{a}' for a in ['x', 'y', 'z']})\n",
+    "\n",
+    "config = IMUConfig()\n",
+    "\n",
+    "# Apply scale factors \n",
+    "df[list(config.d_channels_imu.keys())] *= metadata_values.scale_factors\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Preprocess gyroscope data"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 40,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "config = IMUConfig()\n",
+    "df_preprocessed = preprocess_imu_data(df, config, sensor='gyroscope')"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Extract features"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "config = TremorFeatureExtractionConfig()\n",
+    "df_features = extract_tremor_features(df_preprocessed, config)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Detect tremor"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "config = TremorDetectionConfig()\n",
+    "path_to_classifier_input =  '../../../tests/data/0.classification/tremor'\n",
+    "df_tremor_predictions = detect_tremor(df_features, config, path_to_classifier_input)\n",
+    "\n",
+    "df_tremor_week = pd.concat([df_tremor_week, df_tremor_predictions[['low_freq_power','tremor_power','pred_tremor_checked']]],ignore_index=True)\n"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Quantify tremor"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "config = TremorQuantificationConfig()\n",
+    "d_aggregates = quantify_tremor(df_tremor_week, config)\n",
+    "\n",
+    "import json\n",
+    "import os \n",
+    "\n",
+    "# Save output\n",
+    "with open(os.path.join(input_path,\"weekly_tremor.json\"), 'w') as json_file:\n",
+    "    json.dump(d_aggregates, json_file, indent=4)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "paradigma-cfWEGyqZ-py3.11",
+   "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": "3.11.8"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}
diff --git a/src/paradigma/tremor/tremor_analysis.py b/src/paradigma/tremor/tremor_analysis.py
index 2b89627..736a762 100644
--- a/src/paradigma/tremor/tremor_analysis.py
+++ b/src/paradigma/tremor/tremor_analysis.py
@@ -7,8 +7,6 @@
 from pathlib import Path
 from typing import Union
 from sklearn.linear_model import LogisticRegression
-from datetime import datetime, timedelta
-from collections import Counter
 from scipy.stats import gaussian_kde
 
 from paradigma.constants import DataColumns

From 7592f21c34cfa42315a8ccf93f617efaa8b11538 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Tue, 17 Dec 2024 09:22:31 +0100
Subject: [PATCH 03/12] clear output notebook

---
 docs/notebooks/tremor/tremor_analysis2.ipynb | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/docs/notebooks/tremor/tremor_analysis2.ipynb b/docs/notebooks/tremor/tremor_analysis2.ipynb
index e7266d8..74488eb 100644
--- a/docs/notebooks/tremor/tremor_analysis2.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis2.ipynb
@@ -37,7 +37,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -71,7 +71,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 40,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,12 +88,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 41,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
     "config = TremorFeatureExtractionConfig()\n",
-    "df_features = extract_tremor_features(df_preprocessed, config)"
+    "df_features = extract_tremor_features(df_preprocessed, config)\n",
+    "print(df_features)"
    ]
   },
   {

From ea380d3fcfc0bb61c4e83d0c91ae34c4e48a9d9f Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Tue, 17 Dec 2024 09:28:09 +0100
Subject: [PATCH 04/12] add code for clear output

---
 docs/notebooks/tremor/tremor_analysis.ipynb | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index 836fc18..e67c3d1 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -51,6 +51,15 @@
     "preprocess_imu_data_io(path_to_sensor_data, path_to_preprocessed_data, config, sensor='gyroscope')"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print('hello')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},

From f2f4fca6a0a9b33594673505a506733812439fcf Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Tue, 17 Dec 2024 09:28:50 +0100
Subject: [PATCH 05/12] remove code

---
 docs/notebooks/tremor/tremor_analysis.ipynb | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index e67c3d1..836fc18 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -51,15 +51,6 @@
     "preprocess_imu_data_io(path_to_sensor_data, path_to_preprocessed_data, config, sensor='gyroscope')"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print('hello')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

From c780eed9e2e7c3a118da3b2abf29265193c7ae68 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Tue, 17 Dec 2024 09:32:51 +0100
Subject: [PATCH 06/12] add some documentation

---
 docs/notebooks/tremor/tremor_analysis.ipynb  |  9 +++++++++
 docs/notebooks/tremor/tremor_analysis2.ipynb | 11 ++++++++++-
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index 836fc18..d1b3842 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -68,6 +68,15 @@
     "extract_tremor_features_io(path_to_preprocessed_data, path_to_extracted_features, config)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print('hello')"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/docs/notebooks/tremor/tremor_analysis2.ipynb b/docs/notebooks/tremor/tremor_analysis2.ipynb
index 74488eb..9f23f68 100644
--- a/docs/notebooks/tremor/tremor_analysis2.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis2.ipynb
@@ -25,7 +25,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "df_tremor_week = pd.DataFrame(columns=['low_freq_power','tremor_power','pred_tremor_checked'])"
+    "df_tremor_week = pd.DataFrame(columns=['low_freq_power','tremor_power','pred_tremor_checked']) # create dataframe for concatenation of segments after the tremor detection step"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "print('hello')"
    ]
   },
   {

From 14ccae6ba44d804283c34d56efb3ff0e1d7f10e1 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Tue, 17 Dec 2024 09:34:00 +0100
Subject: [PATCH 07/12] remove code

---
 docs/notebooks/tremor/tremor_analysis.ipynb  | 9 ---------
 docs/notebooks/tremor/tremor_analysis2.ipynb | 9 ---------
 2 files changed, 18 deletions(-)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index d1b3842..836fc18 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -68,15 +68,6 @@
     "extract_tremor_features_io(path_to_preprocessed_data, path_to_extracted_features, config)"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print('hello')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},
diff --git a/docs/notebooks/tremor/tremor_analysis2.ipynb b/docs/notebooks/tremor/tremor_analysis2.ipynb
index 9f23f68..beeb867 100644
--- a/docs/notebooks/tremor/tremor_analysis2.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis2.ipynb
@@ -28,15 +28,6 @@
     "df_tremor_week = pd.DataFrame(columns=['low_freq_power','tremor_power','pred_tremor_checked']) # create dataframe for concatenation of segments after the tremor detection step"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "print('hello')"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

From 5b78ff3e0299a17206f67c1ac111db3ca5d2f4f8 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Wed, 18 Dec 2024 14:59:22 +0100
Subject: [PATCH 08/12] delete second notebook (only for testing)

---
 docs/notebooks/tremor/tremor_analysis2.ipynb | 166 -------------------
 1 file changed, 166 deletions(-)
 delete mode 100644 docs/notebooks/tremor/tremor_analysis2.ipynb

diff --git a/docs/notebooks/tremor/tremor_analysis2.ipynb b/docs/notebooks/tremor/tremor_analysis2.ipynb
deleted file mode 100644
index beeb867..0000000
--- a/docs/notebooks/tremor/tremor_analysis2.ipynb
+++ /dev/null
@@ -1,166 +0,0 @@
-{
- "cells": [
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "# Tremor analysis"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 1,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import pandas as pd\n",
-    "from paradigma.config import IMUConfig, TremorFeatureExtractionConfig, TremorDetectionConfig, TremorQuantificationConfig\n",
-    "from paradigma.imu_preprocessing import preprocess_imu_data\n",
-    "from paradigma.tremor.tremor_analysis import extract_tremor_features, detect_tremor, quantify_tremor"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "df_tremor_week = pd.DataFrame(columns=['low_freq_power','tremor_power','pred_tremor_checked']) # create dataframe for concatenation of segments after the tremor detection step"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Load data"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 2,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import tsdf\n",
-    "from paradigma.util import read_metadata\n",
-    "\n",
-    "input_path =  'C:\\\\Users\\\\z835211\\\\Documents\\\\Data\\\\Raw IMU data\\\\WatchData.IMU.Week2\\\\POMU0000775B2E171842'\n",
-    "segment = 'WatchData.IMU.Week2.raw_segment0010'\n",
-    "\n",
-    "# Load data\n",
-    "metadata_time, metadata_values = read_metadata(str(input_path), str(segment+'_meta.json'),\n",
-    "                                                    str(segment+'_time.bin'), str(segment+'_samples.bin'))\n",
-    "df = tsdf.load_dataframe_from_binaries([metadata_time, metadata_values], tsdf.constants.ConcatenationType.columns)\n",
-    "\n",
-    "# Rename columns\n",
-    "df = df.rename(columns={f'rotation_{a}': f'gyroscope_{a}' for a in ['x', 'y', 'z']})\n",
-    "df = df.rename(columns={f'acceleration_{a}': f'accelerometer_{a}' for a in ['x', 'y', 'z']})\n",
-    "\n",
-    "config = IMUConfig()\n",
-    "\n",
-    "# Apply scale factors \n",
-    "df[list(config.d_channels_imu.keys())] *= metadata_values.scale_factors\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Preprocess gyroscope data"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 3,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "config = IMUConfig()\n",
-    "df_preprocessed = preprocess_imu_data(df, config, sensor='gyroscope')"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Extract features"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "config = TremorFeatureExtractionConfig()\n",
-    "df_features = extract_tremor_features(df_preprocessed, config)\n",
-    "print(df_features)"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Detect tremor"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "config = TremorDetectionConfig()\n",
-    "path_to_classifier_input =  '../../../tests/data/0.classification/tremor'\n",
-    "df_tremor_predictions = detect_tremor(df_features, config, path_to_classifier_input)\n",
-    "\n",
-    "df_tremor_week = pd.concat([df_tremor_week, df_tremor_predictions[['low_freq_power','tremor_power','pred_tremor_checked']]],ignore_index=True)\n"
-   ]
-  },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Quantify tremor"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "config = TremorQuantificationConfig()\n",
-    "d_aggregates = quantify_tremor(df_tremor_week, config)\n",
-    "\n",
-    "import json\n",
-    "import os \n",
-    "\n",
-    "# Save output\n",
-    "with open(os.path.join(input_path,\"weekly_tremor.json\"), 'w') as json_file:\n",
-    "    json.dump(d_aggregates, json_file, indent=4)"
-   ]
-  }
- ],
- "metadata": {
-  "kernelspec": {
-   "display_name": "paradigma-cfWEGyqZ-py3.11",
-   "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": "3.11.8"
-  }
- },
- "nbformat": 4,
- "nbformat_minor": 2
-}

From 9465193a0ff61e3f3144f6bd38d4591d5bf98098 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Mon, 23 Dec 2024 13:09:18 +0100
Subject: [PATCH 09/12] added suggestions

---
 docs/notebooks/tremor/tremor_analysis.ipynb | 10 +++++-----
 src/paradigma/tremor/tremor_analysis.py     |  5 ++++-
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index 836fc18..e678dd3 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -43,7 +43,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [],
    "source": [
diff --git a/src/paradigma/tremor/tremor_analysis.py b/src/paradigma/tremor/tremor_analysis.py
index 736a762..7fcbfca 100644
--- a/src/paradigma/tremor/tremor_analysis.py
+++ b/src/paradigma/tremor/tremor_analysis.py
@@ -127,7 +127,9 @@ def aggregate_tremor_power(tremor_power: pd.Series, config: TremorQuantification
 
 def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig):
 
-    # remove windows with detected non-tremor movements
+    nr_windows_total = df_filtered.shape[0] 
+
+    # remove windows with detected non-tremor movements to control for the amount of arm activities performed
     df_filtered = df.loc[df.low_freq_power <= config.movement_threshold]
     nr_windows_rest = df_filtered.shape[0] # number of windows without non-tremor arm movement
 
@@ -141,6 +143,7 @@ def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig):
     # store aggregates in json format
     d_aggregates = {
         'metadata': {
+            'nr_windows_total': nr_windows_total,
             'nr_windows_rest': nr_windows_rest
         },
         'weekly_tremor_measures': {

From edb7b904cc2e25f119358caf1beb543997b2efb4 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Mon, 23 Dec 2024 13:13:46 +0100
Subject: [PATCH 10/12] fix bug

---
 src/paradigma/tremor/tremor_analysis.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/paradigma/tremor/tremor_analysis.py b/src/paradigma/tremor/tremor_analysis.py
index 7fcbfca..c5886aa 100644
--- a/src/paradigma/tremor/tremor_analysis.py
+++ b/src/paradigma/tremor/tremor_analysis.py
@@ -127,7 +127,7 @@ def aggregate_tremor_power(tremor_power: pd.Series, config: TremorQuantification
 
 def quantify_tremor(df: pd.DataFrame, config: TremorQuantificationConfig):
 
-    nr_windows_total = df_filtered.shape[0] 
+    nr_windows_total = df.shape[0] 
 
     # remove windows with detected non-tremor movements to control for the amount of arm activities performed
     df_filtered = df.loc[df.low_freq_power <= config.movement_threshold]

From dadace19db8db26df80550d6f006632fdf3edf57 Mon Sep 17 00:00:00 2001
From: nienketimmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Mon, 23 Dec 2024 13:19:55 +0100
Subject: [PATCH 11/12] change test output

---
 tests/data/5.quantification/tremor/weekly_tremor.json | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/data/5.quantification/tremor/weekly_tremor.json b/tests/data/5.quantification/tremor/weekly_tremor.json
index ca7b277..6a70bb1 100644
--- a/tests/data/5.quantification/tremor/weekly_tremor.json
+++ b/tests/data/5.quantification/tremor/weekly_tremor.json
@@ -1,5 +1,6 @@
 {
     "metadata": {
+        "nr_windows_total": 182,
         "nr_windows_rest": 89
     },
     "weekly_tremor_measures": {

From 9df1e971ca2d4c65a1fd14fdb2fbacbff71ae681 Mon Sep 17 00:00:00 2001
From: Nienke Timmermans <65012819+nienketimmermans@users.noreply.github.com>
Date: Mon, 23 Dec 2024 13:21:32 +0100
Subject: [PATCH 12/12] Update tremor_analysis.ipynb

---
 docs/notebooks/tremor/tremor_analysis.ipynb | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/docs/notebooks/tremor/tremor_analysis.ipynb b/docs/notebooks/tremor/tremor_analysis.ipynb
index e678dd3..bf60e65 100644
--- a/docs/notebooks/tremor/tremor_analysis.ipynb
+++ b/docs/notebooks/tremor/tremor_analysis.ipynb
@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -21,7 +21,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -60,7 +60,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -94,7 +94,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": null,
    "metadata": {},
    "outputs": [],
    "source": [