Merge pull request #3 from thennen/fix-module-file-structure

Fix module file structure

Author: jhellerstedt

.gitignore

@@ -0,0 +1 @@
+.DS_Store

README.md

@@ -2,34 +2,44 @@
 
 This project is a set of functions to automate the counting and categorization of molecules, specifically tailored for data generated from low temperature scanning probe microscopes.
 
-We wrote about our approach to this problem here: <CITE ARTICLE>
+We wrote about our approach to this problem at [this ArXiv article to be posted](arxiv.org/abs/).
 
 The functionality of this code was used to generate Fig. 3 of [this publication.](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334)
 
 ## Getting Started
 
 This is a glorified script that makes use of existing python libraries.  Written in python 3+, if unsure, start by installing [Anaconda](https://www.anaconda.com/download).
 
-### Prerequisites
+### Dependencies
 
 * [Python 3+](https://www.anaconda.com/download)
 * [SciPy](https://www.scipy.org/)
 * [NumPy](http://www.numpy.org/)
 * [Matplotlib](https://matplotlib.org/)
+* [matplotlib-scalebar](https://pypi.org/project/matplotlib-scalebar/)
 * [Scikit-image](https://scikit-image.org/)
 * [Scikit-learn](https://scikit-learn.org/stable/)
-* [Nanonispy](http://ysebastien.me/nanonispy-my-first-python-package.html)
+* [Nanonispy](https://github.com/underchemist/nanonispy)
 * [Mahotas](https://mahotas.readthedocs.io/en/latest/)
 
 ### Installing
 
-Clone this repository.
+Clone this repository, navigate to said directory, and run:
+
+```
+pip install .
+```
 
 ### Examples
 
-`Helicene_example`, `APT_example` and `APT_2_example` are three example scripts that generate the figures in <CITE ARTICLE>.
+`Helicene_example`, `APT_example` and `APT_2_example` are three example scripts that generate the figures in [the ArXiv article to be posted](arxiv.org/abs/).
+
+Steps to reproduce:
+
+1. Download the data files from this [figshare repo](https://doi.org/10.6084/m9.figshare.19217556) into the examples folder.
+2. Run the individual script files in the examples folder to generate each figure.
+
 
-The data files they analyze can be downloaded [here](some data dump URL).
 
 ## Versioning
 
@@ -46,6 +56,6 @@ This project is licensed under the MIT License.
 
 ## Acknowledgements
 
-This project was inspired by the need to analyze the data that eventually resulted in [this publication.](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).
+This project was inspired by the need to analyze the data that eventually resulted in [this publication](https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201812334).
 We also made use of the data available from [this work.](https://www.nature.com/articles/nchem.2662)
 This happened at the [Nanosurf lab.](https://nanosurf.fzu.cz/)

counting_molecules/.gitignore

@@ -0,0 +1 @@
+__pycache__/

counting_molecules/__init__.py

@@ -0,0 +1 @@
+from .counting_molecules import *

counting_molecules.py renamed to counting_molecules/counting_molecules.py

@@ -29,7 +29,7 @@
 from skimage.filters import gaussian, threshold_otsu, threshold_local
 from skimage.measure import find_contours
 
-import pairwise_chirality
+from . import pairwise_chirality
 
 ### read sxm file, requires nanonispy
 
@@ -467,15 +467,8 @@ def manual_resorting(pickle_file=None, filename=None, im=None, contours=None, pa
 
     extent = (0, im.shape[1]*rescale[1], im.shape[0]*rescale[0], 0)
     ax.imshow(im, cmap='gray', extent=extent) #, vmin=np.amin(im)*.1)
-    
-    ax.axis('off')
-
-    font_properties = dict()
-    font_properties['size'] = 12
-    scalebar = ScaleBar(dx=1, units='m', length_fraction=.5,
-    font_properties=font_properties, frameon=False, location=4, color='w')
-    
-    ax.add_artist(scalebar)
+    ax.set_xlabel('x (m)')
+    ax.set_ylabel('y (m)')
 
     cmap = matplotlib.cm.get_cmap('viridis')
     cmap2 = matplotlib.cm.get_cmap('plasma_r')
@@ -646,8 +639,8 @@ def default_sort(filename, sort_by_chirality=False):
     """ Saves png images of sorted molecule histogram using default sorting parameters. """
     im, rescale = read_data(filename)
     im = filter_image(im)
-    contours, otsu_output, templates, contour_lengths, max_pixels, zernike_moments = get_contours(im, rescale=rescale, minimum_separation=0)
-    sorted_labels = sort_contours(zernike_moments, damping=.3, method='Birch')
+    contours_dict = get_contours(im, rescale=rescale, minimum_separation=0)
+    sorted_labels = sort_contours(contours_dict['zernike_moments'], damping=.3, method='Birch')
     if sort_by_chirality == True:
-        sorted_labels = sort_chirality(templates, sorted_labels)
-    plot_contours_histogram(im, contours, rescale, sorted_labels, saveplot=True, filename=filename)
+        sorted_labels = sort_chirality(contours_dict['templates'], sorted_labels)
+    plot_contours_histogram(im, contours_dict['contours'], contours_dict['rescale'], sorted_labels, saveplot=True, filename=filename)

pairwise_chirality.py renamed to counting_molecules/pairwise_chirality.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python
+
+from setuptools import setup, find_packages
+
+with open("README.md", "r", encoding="utf-8") as fh:
+    long_description = fh.read()
+
+version = '0'
+
+setup(
+    name='counting_molecules',
+    version=version,
+    author='Jack Hellerstedt and Tyler Hennen',
+    author_email='[email protected]',
+    description='Library to count molecules in STM images',
+    long_description=long_description,
+    url='https://github.com/thennen/counting-molecules',
+    project_urls = {
+        "Bug Tracker": "https://github.com/thennen/counting-molecules/issues"
+    },
+    license='MIT',
+    packages=find_packages(),
+    install_requires=['numpy', 'matplotlib', 'matplotlib_scalebar', 'nanonispy', 'mahotas', 'scipy', 'scikit-image', 'sklearn'],
+)