major refactoring and import fix

.github/workflows/python-publish.yml

@@ -5,7 +5,7 @@ name: Upload Python Package
 
 on:
   release:
-    types: [created, edited, deleted]
+    types: [created]
 
 jobs:
   deploy:

.gitignore

@@ -4,5 +4,6 @@
 *dist*
 *PyPlaque.egg-info*
 *MANIFEST*
+*__pycache__*
 *__pycache__/*
 *ipynb_checkpoints*

PyPlaque/phenotypes/CrystalVioletPlaque.py

@@ -1,6 +1,7 @@
 import numpy as np
 from skimage.measure import label, regionprops, moments
-from plq_utils import check_numbers
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers
 
 
 class CrystalVioletPlaque(Plaque):

PyPlaque/phenotypes/FluorescencePlaque.py

@@ -1,6 +1,7 @@
 import numpy as np
 from skimage.measure import label, regionprops, moments
-from plq_utils import check_numbers
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers
 
 class FluorescencePlaque(Plaque):
     """

PyPlaque/phenotypes/Plaque.py

@@ -1,6 +1,6 @@
 import numpy as np
 from skimage.measure import label, regionprops, moments
-from plq_utils import check_numbers
+from PyPlaque.utils import check_numbers
 
 class Plaque:
     """

PyPlaque/phenotypes/__init__.py

@@ -0,0 +1,3 @@
+from PyPlaque.phenotypes.Plaque import *
+from PyPlaque.phenotypes.FluorescencePlaque import *
+from PyPlaque.phenotypes.CrystalVioletPlaque import *

PyPlaque/specimen/PlaquesImageGray.py

@@ -1,8 +1,9 @@
 import numpy as np
 from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops, moments
-from phenotypes import Plaque
-from plq_utils import check_numbers, fixed_threshold
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.specimen import PlaquesMask
+from PyPlaque.utils import check_numbers, fixed_threshold
 
 
 class PlaquesImageGray(PlaquesMask):

PyPlaque/specimen/PlaquesImageRGB.py

@@ -1,8 +1,9 @@
 import numpy as np
 from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops, moments
-from phenotypes import Plaque
-from plq_utils import check_numbers, fixed_threshold
+from PyPlaque.specimen import PlaquesMask
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers, fixed_threshold
 
 
 class PlaquesImageRGB(PlaquesMask):

PyPlaque/specimen/PlaquesMask.py

@@ -1,8 +1,8 @@
 import numpy as np
 from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops, moments
-from phenotypes import Plaque
-from plq_utils import check_numbers, fixed_threshold
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers, fixed_threshold
 
 
 class PlaquesMask:

PyPlaque/specimen/PlaquesWell.py

@@ -1,8 +1,8 @@
 import numpy as np
 from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops, moments
-from phenotypes import Plaque
-from plq_utils import check_numbers, fixed_threshold
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers, fixed_threshold
 
 
 class PlaquesWell:

PyPlaque/specimen/PlateImage.py

@@ -1,8 +1,8 @@
 import numpy as np
 from skimage.segmentation import clear_border
 from skimage.measure import label, regionprops, moments
-from phenotypes import Plaque
-from plq_utils import check_numbers, fixed_threshold
+from PyPlaque.phenotypes import Plaque
+from PyPlaque.utils import check_numbers, fixed_threshold
 
 
 class PlateImage:

PyPlaque/specimen/__init__.py

@@ -0,0 +1,5 @@
+from PyPlaque.specimen.PlaquesMask import *
+from PyPlaque.specimen.PlaquesImageGray import *
+from PyPlaque.specimen.PlaquesImageRGB import *
+from PyPlaque.specimen.PlaquesWell import *
+from PyPlaque.specimen.PlateImage import *

PyPlaque/utils/__init__.py

@@ -0,0 +1,2 @@
+from PyPlaque.utils.check_numbers import *
+from PyPlaque.utils.fixed_threshold import *

PyPlaque/utils/check_numbers.py

@@ -0,0 +1,5 @@
+def check_numbers(tup):
+    for idx,i in enumerate(tup):
+        if (not type(tup[idx]) is int) or (not type(tup[idx]) is float):
+            return False
+    return True

PyPlaque/utils/fixed_threshold.py

@@ -0,0 +1,7 @@
+from skimage.filters import gaussian
+
+def fixed_threshold(img, thr, s):
+        img = gaussian(img, sigma = s)
+        img[img > thr] = 1
+        img[img <= thr] = 0
+        return img