deepliif 1.1.12__tar.gz → 1.1.13__tar.gz

{deepliif-1.1.12/deepliif.egg-info → deepliif-1.1.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.1.12
+Version: 1.1.13
 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=v1.1.12&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.1.13&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-1.1.12 → deepliif-1.1.13}/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=v1.1.12&color=darkgreen)
+![Version](https://img.shields.io/static/v1?label=latest&message=v1.1.13&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-1.1.12/deepliif/models/__init__.py → deepliif-1.1.13/deepliif/models/__init__ - different weighted.py

@@ -273,6 +273,27 @@ def run_dask(img, model_path, eager_mode=False, opt=None, seg_only=False):
             'G54': 0.00, # Lap2
             'G55': 0.25, # Marker
         }
+        weights1 = {
+            'G51': 0.5, # IHC
+            'G52': 0.0, # Hema
+            'G53': 0.0, # DAPI
+            'G54': 0.0, # Lap2
+            'G55': 0.5, # Marker
+        }
+        weights2 = {
+            'G51': 0.34, # IHC
+            'G52': 0.00, # Hema
+            'G53': 0.33, # DAPI
+            'G54': 0.00, # Lap2
+            'G55': 0.33, # Marker
+        }
+        weights3 = {
+            'G51': 0.34, # IHC
+            'G52': 0.33, # Hema
+            'G53': 0.00, # DAPI
+            'G54': 0.00, # Lap2
+            'G55': 0.33, # Marker
+        }
 
         seg_map = {'G1': 'G52', 'G2': 'G53', 'G3': 'G54', 'G4': 'G55'}
         if seg_only:
@@ -289,6 +310,9 @@ def run_dask(img, model_path, eager_mode=False, opt=None, seg_only=False):
         segs = compute(lazy_segs)[0]
     
         seg = torch.stack([torch.mul(segs[k], weights[k]) for k in segs.keys()]).sum(dim=0)
+        seg1 = torch.stack([torch.mul(segs[k], weights1[k]) for k in segs.keys()]).sum(dim=0)
+        seg2 = torch.stack([torch.mul(segs[k], weights2[k]) for k in segs.keys()]).sum(dim=0)
+        seg3 = torch.stack([torch.mul(segs[k], weights3[k]) for k in segs.keys()]).sum(dim=0)
     
         if seg_only:
             res = {'G4': tensor_to_pil(gens['G4'])} if 'G4' in gens else {}
@@ -296,6 +320,9 @@ def run_dask(img, model_path, eager_mode=False, opt=None, seg_only=False):
             res = {k: tensor_to_pil(v) for k, v in gens.items()}
             res.update({k: tensor_to_pil(v) for k, v in segs.items()})
         res['G5'] = tensor_to_pil(seg)
+        res['G5a'] = tensor_to_pil(seg1)
+        res['G5b'] = tensor_to_pil(seg2)
+        res['G5c'] = tensor_to_pil(seg3)
     
         return res
     elif opt.model in ['DeepLIIFExt','SDG','CycleGAN']:
@@ -348,6 +375,9 @@ def run_wrapper(tile, run_fn, model_path, eager_mode=False, opt=None, seg_only=F
                     'G3': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
                     'G4': Image.new(mode='RGB', size=(512, 512), color=(10, 10, 10)),
                     'G5': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
+                    'G5a': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
+                    'G5b': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
+                    'G5c': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
                     'G51': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
                     'G52': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
                     'G53': Image.new(mode='RGB', size=(512, 512), color=(0, 0, 0)),
@@ -409,6 +439,9 @@ def inference(img, tile_size, overlap_size, model_path, use_torchserve=False,
                 'Lap2': results['G3'],
                 'Marker': results['G4'],
                 'Seg': results['G5'],
+                'Seg1': results['G5a'],
+                'Seg2': results['G5b'],
+                'Seg3': results['G5c'],
             }
         
         if return_seg_intermediate and not seg_only: