Changed name to hsmm4acc

wadpac · Aug 7, 2017 · 5685497 · 5685497
1 parent f25f270
commit 5685497
Show file tree

Hide file tree

Showing 12 changed files with 13 additions and 35 deletions.
diff --git a/NOTICE b/NOTICE
diff --git a/README.md b/README.md
@@ -1,5 +1,6 @@
-# UK Movement Sensing
-This repository is for the project by NLeSC in collaboration with UCL, of analyzing movement sensor data of adolescents. It contains code for processing accelerometer data using Hidden Semi Markov models (using the [pyhsmm](https://github.com/mattjj/pyhsmm) package). This software is build for the [Millenium Cohort study](http://www.cls.ioe.ac.uk/page.aspx?sitesectionid=851).
+# HSMMs for accelerometer data
+This repository is for the project by NLeSC in collaboration with UCL, of analyzing movement sensor data of adolescents. It contains code for processing accelerometer data using Hidden Semi Markov models (using the [pyhsmm](https://github.com/mattjj/pyhsmm) package).
+This software is meant for accelerometer data processed with the [R-package GGIR](https://github.com/wadpac/GGIR).
 
 ## Installation
 Prerequisites:
@@ -44,20 +45,4 @@ To run tests:
 
 `nosetests test/`
 
-In order to run the 3-d visualizations (in [this notebook](https://github.com/NLeSC/UKMovementSensing/blob/master/notebooks/workflow/3_Visualization.ipynb) ) you need to install [mayavi](http://docs.enthought.com/mayavi/mayavi/installation.html).
 
-## Running the workflow
-For processing data of the Millenium Cohort studies, we created a flow of [Jupyter notebooks](http://jupyter.org) that can be found in the [notebooks/workflow directory](https://github.com/NLeSC/UKMovementSensing/tree/master/notebooks/workflow). 
-Input for this workflow is:
-* accelerometer data that is processed completely with the R-package GGIR into 5-second aggregated data
-* A file for diary annotations, and wearcode file for joining the datasets
-Edit the `config.py` file to specify the directories for input and output. Also specific settings for the HSMM can be set in this file.
-
-The workflow consists of the following steps:
-* **0.Prepare data** Joins the accelerometer with the diary data and performs some basic checks. 
-* **1.HSMM** Fits an HSMM model on the data and saves the data with the corresponding states for each time window
-* **1b.HSMM batches** If the dataset is very large, this notebook can be used to process the data in batches
-* **2.Analyze results** Makes comparison with diary and gives some statistics, to aid interpretation of the states
-* **3.Visualize Model** Creates a 3d visualization of the states
-
-The output from step 1 (the data with corresponding states) can be used for further processing, such as aggregating per individual.
diff --git a/doc/source/conf.py b/doc/source/conf.py
@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 #
-# UKMovementSensing documentation build configuration file, created by
+# hsmm4acc documentation build configuration file, created by
 # sphinx-quickstart on Tue Mar 29 15:46:32 2016.
 #
 # This file is execfile()d with the current directory set to its
@@ -48,7 +48,7 @@
 master_doc = 'index'
 
 # General information about the project.
-project = u'UKMovementSensing'
+project = u'hsmm4acc'
 copyright = u'2016, Netherlands eScience Center'
 author = u'Dafne van Kuppevelt'
 

diff --git a/doc/source/index.rst b/doc/source/index.rst
@@ -1,9 +1,9 @@
-.. UKMovementSensing documentation master file, created by
+.. hsmm4acc documentation master file, created by
    sphinx-quickstart on Tue Mar 29 15:46:32 2016.
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-The kernel_tuner documentation
+The hsmm4acc documentation
 ==============================
 
 Contents:

diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,4 @@
-name: ucl
+name: hsmm
 channels:
 - defaults
 dependencies:
@@ -52,5 +52,4 @@ dependencies:
   - future==0.16.0
   - pybasicbayes==0.2.2
   - pyhsmm==0.1.6
-prefix: /data/anaconda/anaconda3/envs/ucl
 
diff --git a/UKMovementSensing/__init__.py → hsmm4acc/__init__.py b/UKMovementSensing/__init__.py → hsmm4acc/__init__.py
diff --git a/UKMovementSensing/gamma.py → hsmm4acc/gamma.py b/UKMovementSensing/gamma.py → hsmm4acc/gamma.py
diff --git a/UKMovementSensing/hsmm.py → hsmm4acc/hsmm.py b/UKMovementSensing/hsmm.py → hsmm4acc/hsmm.py
diff --git a/UKMovementSensing/prepacc.py → hsmm4acc/prepacc.py b/UKMovementSensing/prepacc.py → hsmm4acc/prepacc.py
diff --git a/setup.py b/setup.py
@@ -8,13 +8,13 @@ def read(fname):
     required = f.read().splitlines()
 
 setup(
-    name = "UKMovementSensing",
+    name = "hsmm4acc",
     version = "0.0.1",
     description = ("Behaviour detection in wearable movement sensor data"),
     license = "Apache 2.0",
     keywords = "Python",
-    url = "https://github.com/NLeSC/UKMovementSensing",
-    packages=['UKMovementSensing'],
+    url = "https://github.com/wadpac/hsmm4acc",
+    packages=['hsmm4acc'],
     install_requires=required,
     long_description=read('README.md'),
     classifiers=[

diff --git a/test/context.py b/test/context.py
@@ -2,4 +2,4 @@
 import sys
 sys.path.insert(0, os.path.abspath('..'))
 
-import UKMovementSensing
+import hsmm4acc
diff --git a/test/test_hsmm.py b/test/test_hsmm.py
@@ -1,4 +1,4 @@
-import UKMovementSensing.hsmm as hsmm
+import hsmm4acc.hsmm as hsmm
 import numpy as np