adding key files

.coverage

@@ -0,0 +1,16 @@
+language: python
+python:
+  - "3.5"
+install:
+  - pip install -e . --use-mirrors
+before_script:
+  - pip install -r requirements.txt --use-mirrors
+  - git clone https://github.com/ccurtis7/diff_classifier.git
+  - cd ./diff_classifier/diff_classifier/tests/
+script:
+  - py.test test_features.py --doctest-modules --pep8 coveralls -v --cov coveralls --cov-report term-missing
+  - py.test test_imagej.py --doctest-modules --pep8 coveralls -v --cov coveralls --cov-report term-missing
+  - py.test test_msd.py --doctest-modules --pep8 coveralls -v --cov coveralls --cov-report term-missing
+  - py.test test_utils.py --doctest-modules --pep8 coveralls -v --cov coveralls --cov-report term-missing
+after_success:
+  - coveralls

.coveragerc

@@ -0,0 +1,7 @@
+[run]
+branch = True
+source = diff_classifier/*
+include = diff_classifier/*
+omit = */setup.py
+[report]
+include = diff_classifier/*

.gitignore

@@ -0,0 +1,14 @@
+diff_classifier/__pycache__
+*.csv
+*.tif
+diff_classifier/notebooks/.ipynb_checkpoints/*
+*.cache
+diff_classifier/tests/__pycache__
+*-checkpoint.ipynb
+*.pyc
+*.egg-info
+notebooks/cloudknot_docker*
+*.swp
+*.png
+*.travis.yml
+*.DS_store

CONTRIBUTING.md

@@ -0,0 +1,62 @@
+# Contributing
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+## Types of Contributions
+
+### Report Bugs
+
+Report bugs at https://github.com/ccurtis7/diff_classifier/issues.
+
+If you are reporting a bug, please include:
+
+- Your operating system name and version.
+- Any details about your local setup that might be helpful in troubleshooting.
+- Detailed steps to reproduce the bug.
+
+### Work on "good first issues"
+
+Look through the GitHub issues for anything labelled "good first issue." These
+are issues that we think would be especially appropriate for those new to
+open-source software contribution.
+
+### Fix Bugs
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+### Implement Features
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+When submitting a new feature, please use a [Pull Request](https://scikit-learn.org/dev/developers/contributing.html#how-to-contribute) with a title and description
+of the proposed use case. Ideally, new features will include
+
+- Docstrings implemented with the [Numpy format](https://www.numpy.org/devdocs/docs/howto_document.html)
+- Unit tests (see examples [here](https://github.com/ccurtis7/diff_classifier/tree/master/diff_classifier/tests))
+
+### Write Documentation
+
+Diff_classifier could always use more documentation, whether as part of the
+official afq-insight docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+### Submit Feedback
+
+We appreciate any and all feedback in your own implementations of diff_classifier :)
+
+The best way to send feedback is to file an issue at
+https://github.com/ccurtis7/diff_classifier/issues.
+
+
+
+If you are proposing a feature:
+
+- Explain in detail how it would work.
+- Keep the scope as narrow as possible, to make it easier to implement.
+- Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2018 ccurtis7
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -0,0 +1,39 @@
+## diff_classifier
+[![status](http://joss.theoj.org/papers/003901de75c26c1dd3f060043249bc4f/status.svg)](http://joss.theoj.org/papers/003901de75c26c1dd3f060043249bc4f)
+[![Build Status](https://travis-ci.org/ccurtis7/diff_classifier.svg?branch=master)](https://travis-ci.org/ccurtis7/diff_classifier)
+[![Coverage Status](https://coveralls.io/repos/github/ccurtis7/diff_classifier/badge.svg)](https://coveralls.io/github/ccurtis7/diff_classifier)
+[![Scrutinizer Code Quality](https://img.shields.io/scrutinizer/g/ccurtis7/diff_classifier.svg)](https://scrutinizer-ci.com/g/ccurtis7/diff_classifier/?branch=master)
+[![Average time to resolve an issue](http://isitmaintained.com/badge/resolution/ccurtis7/diff_classifier.svg)](http://isitmaintained.com/project/ccurtis7/diff_classifier "Average time to resolve an issue")
+[![Percentage of issues still open](http://isitmaintained.com/badge/open/ccurtis7/diff_classifier.svg)](http://isitmaintained.com/project/ccurtis7/diff_classifier "Percentage of issues still open")
+[![GitHub license](
+https://img.shields.io/github/license/ccurtis7/diff_classifier.svg)](https://github.com/ccurtis7/diff_classifier/blob/master/LICENSE)
+[![DOI](https://zenodo.org/badge/116980257.svg)](https://zenodo.org/badge/latestdoi/116980257)
+
+
+diff_classifier is a python package for analyzing and visualizing 2D
+nanoparticle trajectory data from multi-particle tracking analysis.  The package
+utilizes the ImageJ package Trackmate for tracking analysis, and Cloudknot for
+parallelization on AWS.
+
+<p align="center"><img src="doc/source/_static/summary.png"
+alt="diff_classifier" height="300" title="diff_classifier"/></p>
+
+
+This is the diff_classifier development site.  You can view the source code and
+file new issues. If you are just getting started, you should look at the
+[diff_classifier documentation](https://Nance-Lab.github.io/diff_classifier/)
+
+## Contributing
+
+Contributions are welcome! Diff_classifier is open source, built on open source,
+and we love any input, suggestions, and problems.
+
+[Guidelines](CONTRIBUTING.md) for contributing are included for your convenience.
+
+## Credits
+
+This package was created with [shablona](https://github.com/uwescience/shablona).
+
+Guidelines for contributions were based off the
+[CONTRIBUTIONS](https://github.com/richford/cloudknot/blob/master/CONTRIBUTING.md)
+file developed by [Adam Richie-Halford](https://github.com/richford).

diff_classifier/aws.py

@@ -0,0 +1,85 @@
+"""IO functions for downloading and uploading files from AWS S3 buckets.
+
+The diff_classifier module was built to be used with conjunction with AWS
+services. With the exception of Cloudknot parallelization capabilities, most
+functions can be used separate from AWS. These functions faciliate interaction
+with files stores in S3 buckets. Users must have appropriate credentials to
+access desired S3 buckets.
+
+"""
+import os
+import os.path as op
+
+import boto3
+
+
+# import diff_classifier.imagej as ij
+
+
+def download_s3(remote_fname, local_fname, bucket_name="ccurtis.data"):
+    """Download a file from S3 to local file-system
+
+    Parameters
+    ----------
+    remote_fname: string
+        Name of remote file in S3 bucket.
+    local_fname: string
+        Desired name to be stored on local computer.
+    bucket_name: string
+        Bucket name on S3.
+
+    """
+    if not os.path.exists(local_fname):
+        sthree = boto3.resource('s3')
+        buckt = sthree.Bucket(bucket_name)
+        buckt.download_file(remote_fname, local_fname)
+
+
+def upload_s3(local_fname, remote_fname, bucket_name="ccurtis.data"):
+    """
+    Upload a file from local file-system to S3.
+
+    Parameters
+    ----------
+    local_fname: string
+        Name of local file stored on computer.
+    remote_fname: string
+        Desired name to be stored in S3 bucket.
+    bucket_name: string
+        Bucket name on S3.
+
+    """
+
+    sthree = boto3.resource('s3')
+    buckt = sthree.Bucket(bucket_name)
+    buckt.upload_file(local_fname, remote_fname)
+
+
+# def partition_and_store(remote_fname, local_dir, bucket_name="ccurtis7.pup"):
+#     """
+#     Download image from S3, partition, and upload partitions to S3.
+
+#     Parameters
+#     ----------
+#     remote_fname: string
+#         Target filename in S3 bucket.
+#     local_dir: string
+#         Local directory to store downloaded file.
+#     bucket_name: string
+#         Bucket name on S3.
+
+#     Returns
+#     -------
+#     remote_names: list of strings.
+#         Names of partitioned images in S3.
+#     """
+#     remote_dir, remote_file = op.split(remote_fname)
+#     download_s3(remote_fname, op.join(local_dir, remote_file))
+#     names = ij.partition_im(op.join(local_dir, remote_file))
+
+#     remote_names = []
+#     for file in names:
+#         local_file = op.split(file)[1]
+#         upload_s3(op.join(local_dir, local_file), op.join(remote_dir, local_file))
+#         remote_names.append(op.join(remote_dir, local_file))
+#     return remote_names

diff_classifier/due.py

@@ -0,0 +1,74 @@
+# emacs: at the end of the file
+# ex: set sts=4 ts=4 sw=4 et:
+# ## ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### #
+"""
+
+Stub file for a guaranteed safe import of duecredit constructs:  if duecredit
+is not available.
+
+To use it, place it into your project codebase to be imported, e.g. copy as
+
+    cp stub.py /path/tomodule/module/due.py
+
+Note that it might be better to avoid naming it duecredit.py to avoid shadowing
+installed duecredit.
+
+Then use in your code as
+
+    from .due import due, Doi, BibTeX
+
+See  https://github.com/duecredit/duecredit/blob/master/README.md for examples.
+
+Origin:     Originally a part of the duecredit
+Copyright:  2015-2016  DueCredit developers
+License:    BSD-2
+"""
+from __future__ import absolute_import, division, print_function
+
+__version__ = '0.0.5'
+
+
+class InactiveDueCreditCollector(object):
+    """Just a stub at the Collector which would not do anything"""
+    def _donothing(self, *args, **kwargs):
+        """Perform no good and no bad"""
+        pass
+
+    def dcite(self, *args, **kwargs):
+        """If I could cite I would"""
+        def nondecorating_decorator(func):
+            return func
+        return nondecorating_decorator
+
+    cite = load = add = _donothing
+
+    def __repr__(self):
+        return self.__class__.__name__ + '()'
+
+
+def _donothing_func(*args, **kwargs):
+    """Perform no good and no bad"""
+    pass
+
+
+try:
+    from duecredit import due, BibTeX, Doi, Url
+    if 'due' in locals() and not hasattr(due, 'cite'):
+        raise RuntimeError(
+            "Imported due lacks .cite. DueCredit is now disabled")
+except Exception as e:
+    if type(e).__name__ != 'ImportError':
+        import logging
+        logging.getLogger("duecredit").error(
+            "Failed to import duecredit due to %s" % str(e))
+    # Initiate due stub
+    due = InactiveDueCreditCollector()
+    BibTeX = Doi = Url = _donothing_func
+
+# Emacs mode definitions
+# Local Variables:
+# mode: python
+# py-indent-offset: 4
+# tab-width: 4
+# indent-tabs-mode: nil
+# End: