update pyslide package setup

Author: PingjunChen

pyslide/__init__.py

@@ -2,9 +2,8 @@
 
 import os, sys
 
-__all__ = ["PKG_DIR", "DATA_DIR", "__version__"]
+__all__ = ["PKG_DIR", "__version__"]
 
 PKG_DIR = os.path.abspath(os.path.dirname(__file__))
-DATA_DIR = os.path.join(os.path.dirname(PKG_DIR), 'data')
 
-__version__ = '0.2.0'
+__version__ = '0.3.0'

pyslide/patch/_sample.py

@@ -1,7 +1,8 @@
 # -*- coding: utf-8 -*-
 
 import os, sys
-import math, itertools
+import numpy as np
+import itertools
 
 __all__ = ['wsi_patch_splitting',]
 
@@ -20,10 +21,10 @@ def split_patch_overlay(ttl_len, sub_len):
             p_sets.append(0)
             return p_sets
 
-        p_num = int(math.ceil(ttl_len * 1.0 / sub_len))
+        p_num = int(np.ceil(ttl_len * 1.0 / sub_len))
         overlap_len = (p_num * sub_len - ttl_len) * 1.0 / (p_num - 1)
         extend_len = sub_len - overlap_len
-        for ind in range(p_num):
+        for ind in np.arange(p_num):
             p_sets.append(int(round(extend_len * ind)))
         return p_sets
 
@@ -36,8 +37,8 @@ def split_patch_no_overlay(ttl_len, sub_len):
             p_sets.append(0)
             return p_sets
 
-        p_num = int(math.floor(ttl_len * 1.0 / sub_len))
-        p_sets = [ele*sub_len for ele in range(p_num)]
+        p_num = int(np.floor(ttl_len * 1.0 / sub_len))
+        p_sets = [ele*sub_len for ele in np.arange(p_num)]
         return p_sets
 
     if overlay == True:
@@ -53,4 +54,5 @@ def split_patch_no_overlay(ttl_len, sub_len):
     else:
         raise Exception("Cannot splitting")
 
+
     return coors_arr

pyslide/patch/setup.py

@@ -2,7 +2,6 @@
 
 import os, sys
 
-BASE_PATH = os.path.abspath(os.path.dirname(__file__))
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
@@ -11,12 +10,13 @@ def configuration(parent_package='', top_path=None):
 
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(maintainer='Pingjun Chen',
           maintainer_email='chenpingjun@gmx.com',
           description='Patch utility in whole slide image analysis',
           url='https://github.com/PingjunChen/pyslide',
-          license='Apache',
+          license='MIT',
           **(configuration(top_path='').todict())
           )

pyslide/pyramid/_pyramid.py

@@ -8,11 +8,12 @@
             "load_wsi_head",
             ]
 
+
 def create_pyramidal_img(img_path, save_dir):
     """ Convert normal image to pyramidal image.
 
     Parameters
-    ----------
+    -------
     img_path: str
         Whole slide image path (absolute path is needed)
     save_dir: str
@@ -35,6 +36,7 @@ def create_pyramidal_img(img_path, save_dir):
     >>> save_dir = os.path.join(PRJ_PATH, "test/data/Slides")
     >>> status = pyramid.create_pyramidal_img(img_path, save_dir)
     >>> assert status == 0
+
     """
 
     convert_cmd = "convert " + img_path
@@ -45,8 +47,20 @@ def create_pyramidal_img(img_path, save_dir):
 
     return status
 
+
 def load_wsi_head(wsi_img_path):
     """ Load the header meta data of whole slide pyramidal image.
+
+    Parameters
+    -------
+    wsi_img_path: str
+        The path to whole slide image
+
+    Returns
+    -------
+    wsi_header: slide class
+        Meta information of whole slide image
+
     """
 
     wsi_header = openslide.OpenSlide(wsi_img_path)

pyslide/pyramid/setup.py

@@ -1,8 +1,6 @@
 # -*- coding: utf-8 -*-
 
-import os, sys, pdb
-
-BASE_PATH = os.path.abspath(os.path.dirname(__file__))
+import os, sys
 
 
 def configuration(parent_package='', top_path=None):
@@ -12,12 +10,13 @@ def configuration(parent_package='', top_path=None):
 
     return config
 
+
 if __name__ == '__main__':
     from numpy.distutils.core import setup
     setup(maintainer='Pingjun Chen',
           maintainer_email='chenpingjun@gmx.com',
           description='File format utilities of whole slide image',
           url='https://github.com/PingjunChen/pyslide',
-          license='Apache',
+          license='MIT',
           **(configuration(top_path='').todict())
           )

pyslide/setup.py

@@ -1,10 +1,11 @@
 # -*- coding: utf-8 -*-
 
-import os, sys, pdb
+import os, sys
+
 
 def configuration(parent_package='', top_path=None):
     from numpy.distutils.misc_util import Configuration
-    
+
     config = Configuration('pyslide', parent_package, top_path)
     config.add_subpackage('patch')
     config.add_subpackage('pyramid')

requirements.txt

@@ -1,3 +1,7 @@
-numpy==1.12.1
+numpy==1.15.4
 tissueloc==1.5.0
 pycontour==1.1.0
+Pillow==5.3.0
+openslide-python==1.1.1
+scikit-image==0.14.1
+opencv-python==3.4.4.19

setup.py

@@ -8,7 +8,7 @@
 VERSION = pyslide.__version__
 DESCRIPTION = "Whole slide image analysis toolbox."
 HOMEPAGE = "https://github.com/PingjunChen/pyslide"
-LICENSE = "Apache"
+LICENSE = "MIT"
 AUTHOR_NAME = "Pingjun Chen"
 AUTHOR_EMAIL = "chenpingjun@gmx.com"