deepliif 1.2.1__tar.gz → 1.2.2__tar.gz

{deepliif-1.2.1/deepliif.egg-info → deepliif-1.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.2.1
+Version: 1.2.2
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -53,7 +53,7 @@ segmentation.*
 
 © This code is made available for non-commercial academic purposes.
 
-![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.1&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.2&color=darkgreen)
 [![Total Downloads](https://static.pepy.tech/personalized-badge/deepliif?period=total&units=international_system&left_color=grey&right_color=blue&left_text=total%20downloads)](https://pepy.tech/project/deepliif?&left_text=totalusers)
 
 ![overview_image](./images/overview.png)*Overview of DeepLIIF pipeline and sample input IHCs (different 

{deepliif-1.2.1 → deepliif-1.2.2}/README.md

@@ -42,7 +42,7 @@ segmentation.*
 
 © This code is made available for non-commercial academic purposes.
 
-![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.1&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.2&color=darkgreen)
 [![Total Downloads](https://static.pepy.tech/personalized-badge/deepliif?period=total&units=international_system&left_color=grey&right_color=blue&left_text=total%20downloads)](https://pepy.tech/project/deepliif?&left_text=totalusers)
 
 ![overview_image](./images/overview.png)*Overview of DeepLIIF pipeline and sample input IHCs (different 

{deepliif-1.2.1 → deepliif-1.2.2}/deepliif/postprocessing.py

@@ -938,16 +938,11 @@ def create_cell_classification(mask, cellsinfo,
                     idx = (seed[0] + n[0], seed[1] + n[1])
                     if in_bounds(mask, idx) and mask[idx] == LABEL_CELL:
                         seeds.append(idx)
-                        is_boundary = False
                         for n in border_neighbors:
                             idx2 = (idx[0] + n[0], idx[1] + n[1])
                             if in_bounds(mask, idx2) and mask[idx2] == LABEL_BACKGROUND:
-                                is_boundary = True
-                                break
-                        if is_boundary:
-                            mask[idx] = label_border
-                        else:
-                            mask[idx] = label
+                                mask[idx2] = label_border
+                        mask[idx] = label
 
     num_total = num_pos + num_neg
     return {
@@ -976,7 +971,7 @@ def enlarge_cell_boundaries(mask):
                 value = LABEL_BORDER_POS2 if mask[y, x] == LABEL_BORDER_POS else LABEL_BORDER_NEG2
                 for n in neighbors:
                     idx = (y + n[0], x + n[1])
-                    if in_bounds(mask, idx) and mask[idx] != LABEL_BORDER_POS and mask[idx] != LABEL_BORDER_NEG:
+                    if in_bounds(mask, idx) and mask[idx] == LABEL_BACKGROUND:
                         mask[idx] = value
 
     for y in range(mask.shape[0]):
@@ -1048,6 +1043,36 @@ def fill_cells(mask):
                 else:
                     mask[y, x] = LABEL_NEGATIVE
 
+    for y in range(mask.shape[0]):
+        for x in range(mask.shape[1]):
+            if mask[y, x] == LABEL_BORDER_POS:
+                mask[y, x] = LABEL_POSITIVE
+            elif mask[y, x] == LABEL_BORDER_NEG:
+                mask[y, x] = LABEL_NEGATIVE
+
+
+@jit(nopython=True)
+def create_outer_boundary(mask):
+    """
+    For a mask with positive and negative cell labels,
+    set pixels neighboring the cells in-place to border labels.
+
+    Parameters
+    ----------
+    mask : ndarray
+        2D uint8 label map.
+    """
+
+    border_neighbors = [(0, -1), (-1, 0), (1, 0), (0, 1)]
+
+    for y in range(mask.shape[0]):
+        for x in range(mask.shape[1]):
+            if mask[y, x] == LABEL_POSITIVE or mask[y, x] == LABEL_NEGATIVE:
+                for n in border_neighbors:
+                    idx2 = (y + n[0], x + n[1])
+                    if in_bounds(mask, idx2) and mask[idx2] == LABEL_BACKGROUND:
+                        mask[idx2] = LABEL_BORDER_POS if mask[y, x] == LABEL_POSITIVE else LABEL_BORDER_NEG
+
 
 def calculate_large_noise_thresh(large_noise_thresh, resolution):
     if large_noise_thresh != 'default':
@@ -1184,6 +1209,7 @@ def compute_final_results(orig, seg, marker, resolution,
 
     counts = create_cell_classification(mask, cellsinfo, size_thresh, marker_thresh, size_thresh_upper)
     enlarge_cell_boundaries(mask)
+    enlarge_cell_boundaries(mask)
     overlay, refined = create_final_images(np.array(orig), mask)
 
     scoring = {
@@ -1260,6 +1286,8 @@ def cells_to_final_results(data, orig,
     mark_background(mask)
     fill_cells(mask)
 
+    create_outer_boundary(mask)
+    enlarge_cell_boundaries(mask)
     enlarge_cell_boundaries(mask)
     overlay, refined = create_final_images(np.array(orig), mask)
 

{deepliif-1.2.1 → deepliif-1.2.2}/deepliif/util/__init__.py

@@ -489,9 +489,8 @@ class WSIReader:
                     self._file.close()
 
         self._bfreader = None
-        if self._tif is None:
-            self._rescale = (self._pixel_type != 'uint8')
-            self._bfreader = bioformats.ImageReader(path)
+        self._rescale = (self._pixel_type != 'uint8')
+        self._bfreader = bioformats.ImageReader(path)
 
         if self._tif is None and self._bfreader is None:
             raise Exception('Cannot read WSI file.')
@@ -520,7 +519,10 @@ class WSIReader:
     def read(self, xywh):
         if self._tif is not None:
             x, y, w, h = xywh
-            return self._zarr[y:y+h, x:x+w]
+            try:
+                return self._zarr[y:y+h, x:x+w]
+            except Exception as e:
+                pass
 
         px = self._bfreader.read(XYWH=xywh, rescale=self._rescale)
         if self._rescale:

{deepliif-1.2.1 → deepliif-1.2.2/deepliif.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.2.1
+Version: 1.2.2
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -53,7 +53,7 @@ segmentation.*
 
 © This code is made available for non-commercial academic purposes.
 
-![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.1&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.2&color=darkgreen)
 [![Total Downloads](https://static.pepy.tech/personalized-badge/deepliif?period=total&units=international_system&left_color=grey&right_color=blue&left_text=total%20downloads)](https://pepy.tech/project/deepliif?&left_text=totalusers)
 
 ![overview_image](./images/overview.png)*Overview of DeepLIIF pipeline and sample input IHCs (different 

{deepliif-1.2.1 → deepliif-1.2.2}/deepliif.egg-info/requires.txt

@@ -1,5 +1,5 @@
 opencv-python==4.8.1.78
-torch==1.13.1
+torch==2.8.0
 torchvision==0.14.1
 scikit-image==0.18.3
 dominate==2.6.0

{deepliif-1.2.1 → deepliif-1.2.2}/setup.cfg

@@ -3,7 +3,7 @@ name = deepliif
 description_file = README.md
 author = Parmida93
 author_email = ghahremani.parmida@gmail.com
-version = 1.2.1
+version = 1.2.2
 url = https://github.com/nadeemlab/DeepLIIF
 
 [egg_info]

{deepliif-1.2.1 → deepliif-1.2.2}/setup.py

@@ -6,7 +6,7 @@ README = (HERE / "README.md").read_text()
 
 setup(
     name='deepliif',
-    version='1.2.1',
+    version='1.2.2',
     packages=['deepliif', 'deepliif.data', 'deepliif.models', 'deepliif.util', 'deepliif.options'],
 
     description='DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification',
@@ -21,7 +21,7 @@ setup(
     py_modules=['cli'],
     install_requires=[
         "opencv-python==4.8.1.78",
-        "torch==1.13.1",
+        "torch==2.8.0",
         "torchvision==0.14.1",
         "scikit-image==0.18.3",
         "dominate==2.6.0",