Moved Python code.

Author: danielgjackson

.gitignore

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+__pycache__
+_local

.vscode/settings.json

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+{
+    "cSpell.words": [
+        "AAAGGGLLLLLLLLLL",
+        "Acti",
+        "Activ",
+        "Arvidsson",
+        "Borazio",
+        "Brønd",
+        "DWORD",
+        "Dowd",
+        "ENMO",
+        "Esliger",
+        "Eston",
+        "GENEA",
+        "Hees",
+        "Kearney",
+        "Kozarski",
+        "Kyung",
+        "Kücükyildiz",
+        "Laerhoven",
+        "MMDDDD",
+        "PAEE",
+        "Rennie",
+        "Renstr",
+        "Renström",
+        "Schaefer",
+        "Scholl",
+        "Verisense",
+        "YYYYYYMM",
+        "astype",
+        "csvm",
+        "cwtv",
+        "dtype",
+        "eezzzzzz",
+        "hhhhmmmm",
+        "iloc",
+        "isdigit",
+        "kyildiz",
+        "ldjson",
+        "loadtxt",
+        "mmssssss",
+        "nditer",
+        "numpy",
+        "omconvert",
+        "resampling",
+        "struct",
+        "tscsv",
+        "yyyyyyxx",
+        "zzzzyyyy"
+    ]
+}

LICENSE

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+Copyright (c) 2009-2021, Newcastle University, UK.
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without 
+modification, are permitted provided that the following conditions are met: 
+1. Redistributions of source code must retain the above copyright notice, 
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, 
+   this list of conditions and the following disclaimer in the documentation 
+   and/or other materials provided with the distribution.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" 
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE 
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE 
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE 
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR 
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF 
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS 
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN 
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE 
+POSSIBILITY OF SUCH DAMAGE. 

README.md

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+# Open Movement Python Code
+
+<!--
+```
+python -m pip install -e "git+https://github.com/digitalinteraction/openmovement-python.git#egg=openmovement"
+```
+-->
+
+
+
+## omconvert wrapper
+
+This is a Python wrapper for the `omconvert` binary, and Python implementations of some of the `omconvert` algorithms.  The `omconvert` program will process `.cwa` and `.omx` binary files and produce calculated outputs, such as SVM and WTV (wear-time validation).  It can also be used to output raw accelerometer `.csv` files (these will be very large), and they can be run through the Python versions of the analysis algorithms (slowly).
+
+* [omconvert.py](openmovement/omconvert.py) - the Python wrapper containing the `OmConvert` class.
+
+* [run_omconvert.py](openmovement/run_omconvert.py) - example code using the `OmConvert` class.
+
+The example code exports the SVM and WTV files.
+
+*IMPORTANT:* You will need the `omconvert` binary either in your `PATH`, in the current working directory, or in the same directory as the `omconvert.py` file (or, on Windows, if you have *OmGui* installed in the default location).  On Windows you can use the `bin/build-omconvert.bat` script, or on macOS/Linux you can use the `bin/build-omconvert.sh` script, or see [omconvert](https://github.com/digitalinteraction/omconvert#open-movement-file-converter) for further instructions.
+
+
+## Iterable time series CSV loader
+
+Note: This is quite slow for large amounts of data, and a `numpy`/`np.loadtxt()`, or `pandas`/`pd.readcsv()` would be faster if it was OK to load all of the data to memory.
+
+* [timeseries_csv.py](openmovement/timeseries_csv.py) - An iterable CSV file reader.  The first row can contain column headers.  The first column must contain a timestamp.  If the timestamp is numeric, the 'time_zero' option may be added.  If the timestamp is an ISO-ish date/time, it is parsed as a time in seconds since the 1970 epoch date.  In either case, no timezone information is known, so treat as a UTC time to correctly recover date/time of day.  All other values must be numeric (a global scaling factor may be applied to these).
+
+For files using a zero-based numeric timestamp, a helper `csv_time_from_filename()` has been provided to set the `"time_zero"` option in cases where the filename starts with the timestamp for the `0` time.
+
+For files using raw data units, a helper `csv_scale_from_filename()` has been provided to set the `"global_scale"` option in cases where the base of the filename ends with a suffix that indicates the data type, from which the scaling may be derived.
+
+
+## Python implementations of some omconvert algorithms
+
+Note: These iteration-based versions are quite slow for large amounts of data, and would probably benefit from a `numpy` version that operates from already-loaded data.
+
+### SVM
+
+* [calc_svm.py](openmovement/calc_svm.py) - Calculates (as an iterator) the mean *abs(SVM-1)* value for an epoch (default 60 seconds) given an iterator yielding `[time_seconds, x, y, z]`.
+
+* [run_svm.py](openmovement/run_svm.py) - Example showing how to run the SVM calculation from a source `.csv` file to an output `.csvm.csv` file.
+
+### WTV
+
+* [calc_wtv.py](openmovement/calc_svm.py) - Calculates (as an iterator) the WTV (wear-time validation) value (30 minute epochs) given an iterator yielding `[time_seconds, x, y, z]`.
+
+* [run_wtv.py](openmovement/run_wtv.py) - Example showing how to run the WTV calculation from a source `.csv` file to an output `.cwtv.csv` file.
+

bin/.gitattributes

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+build-omconvert.sh text=auto eol=lf

bin/.gitignore

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+/omconvert.build
+/omconvert
+/omconvert.exe

bin/build-omconvert.bat

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+@echo off
+cd /d "%~dp0"
+if not exist "..\..\..\src\omconvert\build.cmd" goto download_build
+call "..\..\..\src\omconvert\build.cmd"
+copy /y "..\..\..\src\omconvert\omconvert.exe" .
+goto end
+
+:download_build
+powershell -Command "& {Invoke-WebRequest https://github.com/digitalinteraction/omconvert/archive/master.zip -o omconvert.build.zip ; Expand-Archive omconvert.build.zip ; del omconvert.build.zip ; omconvert.build/omconvert-master/src/omconvert/build.cmd ; copy omconvert.build/omconvert-master/src/omconvert/omconvert.exe . }"
+goto end
+
+:end

bin/build-omconvert.sh

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+#!/bin/bash
+set -e
+cd $(cd -P -- "$(dirname -- "$0")" && pwd -P)
+BUILD_DIR=../../../src/omconvert
+if [ ! -f "$BUILD_DIR/Makefile" ]; then
+	mkdir -p omconvert.build
+	curl -L https://github.com/digitalinteraction/omconvert/archive/master.zip -o omconvert.build/master.zip
+	unzip -o omconvert.build/master.zip -d omconvert.build
+	BUILD_DIR=omconvert.build/omconvert-master/src/omconvert
+fi
+make -C "$BUILD_DIR"
+cp "$BUILD_DIR/omconvert" .

openmovement/__init__.py

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+from math import sqrt
+
+class CalcSvm:
+    """
+    An iterator to calculate the SVM value for a given iterator yielding [time_seconds, x, y, z].
+    options['epoch_size'] # seconds per epoch
+    options['alignment']  # offset to align epoch; None=align to start of data; 0=align to wall-clock time
+    """
+
+    def __init__(self, input, options):
+        self.input = input
+        self.options = options
+
+        # Epoch size (default 1 minute)
+        self.epoch_size = self.options.get('epoch_size', 60)
+
+        # Epoch alignment offset, e.g. 0=Align epochs since start; None=Align from start of data
+        self.alignment = self.options.get('alignment', None)
+
+        self.current_epoch_id = None
+        self.current_epoch_time = None
+        self.ended = False
+
+        # Status
+        self.count = 0
+        self.sum = 0
+
+
+    # Iterate on self
+    def __iter__(self):
+        return self
+    
+    def __next__(self):
+        while True:
+            time = None
+            if not self.ended:
+                try:
+                    [time, x, y, z, *_] = next(self.input)
+                except StopIteration:
+                    self.ended = True
+
+            # If epoch alignment is None, align to start of data stream
+            if self.alignment is None and time is not None:
+                self.alignment = -time
+
+            # Determine which epoch we are in
+            next_epoch_id = None
+            next_epoch_time = None
+            if time is not None:
+                next_epoch_id = (time + self.alignment) // self.epoch_size
+                next_epoch_time = (next_epoch_id * self.epoch_size) - self.alignment
+
+            # If the epoch has changed, emit the previous result
+            result = None
+            if next_epoch_id != self.current_epoch_id:
+                if self.count > 0:
+                    # Return mean SVM
+                    value = self.sum / self.count
+                    result = (self.current_epoch_time, value)
+                self.sum = 0
+                self.count = 0
+                self.current_epoch_id = next_epoch_id
+                self.current_epoch_time = next_epoch_time
+
+            # Calculate SVM and add to current epoch
+            if time is not None:
+                en = sqrt((x * x) + (y * y) + (z * z))
+                enmo = en - 1
+                svm = abs(enmo)
+                self.sum += svm
+                self.count += 1
+
+            # Return result
+            if result is not None:
+                return result
+            
+            if time is None:
+                raise StopIteration
+