A library for detecting and classifying local order in spatial data. Picolo stands for Point-Intensity Classification Of Local Order.
Pattern detection in images is a common task in many fields, including nanoscience. For instance, there is a need for robust methods that can classify individual membrane proteins as "disordered" or "crystalline," whether the data source is atomic force micrographs, electron micrographs, or molecular simulation trajectories. Picolo meets this need by providing Python tools for extracting features from local neighborhoods in (x,y) data sets (e.g., points picked from micrographs using other software), training and applying statistical classifiers on these features, and computing spatial correlation functions on the labeled data.
src contains 3 packages: picolo, config, and shapes.
The Trainer, Matcher, and Writer classes in the picolo package are the primary interfaces for building, applying, and analyzing the results of classifiers, respectively.
The config and shapes packages provide various helper classes that are used by picolo.
test contains automated tests that can be run with nosetests.
scripts contains sample scripts, which can be run using files in data.
cd picolo
python setup.py build
sudo python setup.py install
To make documentation with doxypy and LaTeX:
doxygen Doxyfile
cd docs/latex
make refman.pdf
Then open docs/html/index.html or docs/latex/refman.pdf.
To run tests with nose and coverage:
nosetests --cover-package=picolo --with-coverage
There are sample scripts in the scripts directory. Call any of the scripts with -h for instructions.
Picolo is written and maintained by Anna Schneider <annarschneider@gmail.com>, and was tested on AFM data collected by Bibiana Onoa.
picolo is released under the Apache License 2.0.
Copyright 2013 Anna Schneider
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.