resolve conflict in README

.circleci/config.yml

@@ -0,0 +1,20 @@
+version: 2
+jobs:
+    build:
+        docker:
+            - image: circleci/python:3.6
+        steps:
+            - checkout
+            - run: sudo apt-get install openslide-tools
+            - run:
+                command: |
+                    python3 -m venv venv
+                    . venv/bin/activate
+                    pip install --upgrade pip
+                    pip install -r requirements.txt
+                    pip install -U pytest
+            - run:
+                command: |
+                    . venv/bin/activate
+                    cd test
+                    pytest .

AUTHORS.md

@@ -1,7 +1,7 @@
-#### Main author:
+#### Main author
 
-- [Pingjun Chen](https://github.com/PingjunChen)
+    - [Pingjun Chen](https://github.com/PingjunChen)
 
-#### Contributors (alphabetical last name):
+#### Contributors (alphabetical last name)
 
-- Lin Yang
+    - Lin Yang

README.md

@@ -1,16 +1,16 @@
 tissueloc: Whole slide digital pathology image tissue localization
-========
+=============
+[![Codacy Badge](https://api.codacy.com/project/badge/Grade/2f1d165f709e43c4bc6d1d3a6563418e)](https://app.codacy.com/app/PingjunChen/tissueloc?utm_source=github.com&utm_medium=referral&utm_content=PingjunChen/tissueloc&utm_campaign=Badge_Grade_Dashboard)
 [![Build Status](https://travis-ci.org/PingjunChen/tissueloc.svg?branch=master)](https://travis-ci.org/PingjunChen/tissueloc)
 [![Documentation Status](https://readthedocs.org/projects/tissueloc/badge/?version=latest)](https://tissueloc.readthedocs.io/en/latest/?badge=latest)
 [![PyPI version](https://badge.fury.io/py/tissueloc.svg)](https://badge.fury.io/py/tissueloc)
 [![DOI](http://joss.theoj.org/papers/10.21105/joss.01148/status.svg)](https://doi.org/10.21105/joss.01148)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2529982.svg)](https://doi.org/10.5281/zenodo.2529982)
+[![Donate](https://img.shields.io/badge/Donate-PayPal-green.svg)](https://www.paypal.me/PingjunChen)
 ![](https://img.shields.io/github/stars/PingjunChen/tissueloc.svg)
+<img src="./docs/media/tissuelocDemo.png" width="800" height="320" alt="Banner">
 
-
-<img src="tissuelocDemo.png" width="800" height="320" alt="Banner">
-
-## Installation
+Installation
+-------------
 1. Install [OpenSlide](https://openslide.org/download/).
 ```
 $ sudo apt-get install openslide-tools
@@ -26,7 +26,8 @@ $ pip install openslide-python
 $ pip install tissueloc==2.0.0
 ```
 
-## Usage example
+Usage example
+-------------
 #### Interface
 ```
 def locate_tissue_cnts(slide_path,
@@ -69,25 +70,27 @@ cnts, d_factor = locate_tissue_cnts(slide_path,
                                     min_tissue_size=10000)
 ```
 
-
-
-## Documentation
+Documentation
+-------------
 Hosted in [https://tissueloc.readthedocs.io](https://tissueloc.readthedocs.io), powered by [readthedocs](https://readthedocs.org) and [Sphinx](http://www.sphinx-doc.org).
 
-
-## Contributing
+Contributing
+-------------
 ``tissueloc`` is an  open source project and anyone is welcome to contribute. An easy way to get started is by suggesting a new enhancement on the [Issues](https://github.com/PingjunChen/tissueloc/issues). If you have found a bug, then either report this through [Issues](https://github.com/PingjunChen/tissueloc/issues), or even better, make a fork of the repository, fix the bug and then create a [Pull Requests](https://github.com/PingjunChen/tissueloc/pulls) to get the fix into the master branch.
 
 We would like to test this package on more diversified digital slides. Slides (low level images would be better) and their corresponding results are also very welcome as [Pull Requests](https://github.com/PingjunChen/tissueloc/pulls).
 
-## License
+License
+-------------
 [tissueloc](https://github.com/PingjunChen/tissueloc) is free software made available under the MIT License. For details see the [LICENSE](LICENSE) file.
 
-## Contributors
+Contributors
+-------------
 See the [AUTHORS.md](AUTHORS.md) file for a complete list of contributors to the project.
 
-## Citing
-``tissueloc`` is published in the Journal of Open Source Software - if it's ever useful for your research please consider citing it:
+Citing
+-------------
+``tissueloc`` is published in the Journal of Open Source Software - please cite if it's useful for your research:
 ```
 @article{chen2019tissueloc,
   author    = {Pingjun Chen and Lin Yang},

setup.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import os, sys
 from setuptools import setup, find_packages
 import tissueloc
 

test/test_load_slide.py

@@ -1,13 +1,14 @@
 # -*- coding: utf-8 -*-
 
 import os, sys
-import numpy as np
-import pytest
+# import numpy as np
+# import pytest
 
 TEST_PATH = os.path.abspath(os.path.dirname(__file__))
 PRJ_PATH = os.path.dirname(TEST_PATH)
 sys.path.insert(0, PRJ_PATH)
-from tissueloc.load_slide import select_slide_level, load_slide_img
+# from tissueloc.load_slide import select_slide_level
+# from tissueloc.load_slide import load_slide_img
 
 
 # def test_select_slide_level():

test/test_locate_tissue.py

@@ -5,17 +5,16 @@
 import numpy as np
 import scipy.misc as misc
 import cv2
-import pytest
 
 TEST_PATH = os.path.abspath(os.path.dirname(__file__))
 PRJ_PATH = os.path.dirname(TEST_PATH)
 sys.path.insert(0, PRJ_PATH)
 
-
-from tissueloc.load_slide import select_slide_level, load_slide_img
+# from tissueloc.load_slide import select_slide_level
+from tissueloc.load_slide import load_slide_img
 from tissueloc.locate_tissue import rgb2gray, thresh_slide, fill_tissue_holes
 from tissueloc.locate_tissue import remove_small_tissue, find_tissue_cnts
-from tissueloc.locate_tissue import locate_tissue_cnts
+# from tissueloc.locate_tissue import locate_tissue_cnts
 
 
 
@@ -34,7 +33,7 @@ def test_gen_intermediate_files():
     misc.imsave(os.path.join(output_dir, "gray.png"), gray_img)
     # Step 4: Smooth and Binarize
     thresh_val = 0.8
-    bw_img = thresh_slide(gray_img, thresh_val=0.8, sigma=5)
+    bw_img = thresh_slide(gray_img, thresh_val=thresh_val, sigma=5)
     misc.imsave(os.path.join(output_dir, "bw.png"), (bw_img*255.0).astype(np.uint8))
     # Step 5: Fill tissue holes
     bw_fill = fill_tissue_holes(bw_img)

tissueloc/load_slide.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import os, sys
 import openslide
 from PIL import Image
 import numpy as np
@@ -35,7 +34,7 @@ def select_slide_level(slide_path, max_size=2048):
     level_dims = slide_head.level_dimensions
 
     d_factors = slide_head.level_downsamples
-    assert len(level_dims) > 1, "This slide doesnot have mutliple levels"
+    # assert len(level_dims) > 1, "This slide doesnot have mutliple levels"
     select_level = len(level_dims) - 1
     for ind in np.arange(len(level_dims)):
         cur_w, cur_h = level_dims[ind]
@@ -77,7 +76,7 @@ def load_slide_img(slide_path, level=0):
     img_size = slide_head.level_dimensions[level]
     slide_img = slide_head.read_region((0, 0), level, img_size)
     if isinstance(slide_img, Image.Image):
-        slide_img = im = np.asarray(slide_img)
+        slide_img = np.asarray(slide_img)
     if slide_img.shape[2] == 4:
         slide_img = slide_img[:, :, :-1]
     return slide_img

tissueloc/locate_tissue.py

@@ -1,6 +1,5 @@
 # -*- coding: utf-8 -*-
 
-import os, sys
 import numpy as np
 from scipy.ndimage import binary_fill_holes
 from skimage import filters, img_as_ubyte

tissueloc/setup.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-import os, sys
+import os
 
 BASE_PATH = os.path.abspath(os.path.dirname(__file__))
 PKG_NAME = os.path.basename(BASE_PATH)