deepliif 1.2.0__py3-none-any.whl → 1.2.2__py3-none-any.whl

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]):
@@ -1048,22 +1043,52 @@ 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':
         return large_noise_thresh
     if resolution == '10x':
-        return 250
-    elif resolution == '20x':
         return 1000
-    else: # 40x
+    elif resolution == '20x':
         return 4000
+    else: # 40x
+        return 16000
 
 
 def compute_cell_results(seg, marker, resolution, version=3,
                          seg_thresh=DEFAULT_SEG_THRESH,
                          noise_thresh=DEFAULT_NOISE_THRESH,
-                         large_noise_thresh='default'):
+                         large_noise_thresh=None):
     """
     Perform postprocessing to compute individual cell results.
 
@@ -1134,7 +1159,7 @@ def compute_final_results(orig, seg, marker, resolution,
                           size_thresh_upper=None,
                           seg_thresh=DEFAULT_SEG_THRESH,
                           noise_thresh=DEFAULT_NOISE_THRESH,
-                          large_noise_thresh='default'):
+                          large_noise_thresh=None):
     """
     Perform postprocessing to compute final count and image results.
 
@@ -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/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-1.2.0.dist-info → deepliif-1.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: deepliif
-Version: 1.2.0
+Version: 1.2.2
 Summary: DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification
 Home-page: https://github.com/nadeemlab/DeepLIIF
 Author: Parmida93
@@ -9,7 +9,7 @@ Keywords: DeepLIIF,IHC,Segmentation,Classification
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Requires-Dist: opencv-python (==4.8.1.78)
-Requires-Dist: torch (==1.13.1)
+Requires-Dist: torch (==2.8.0)
 Requires-Dist: torchvision (==0.14.1)
 Requires-Dist: scikit-image (==0.18.3)
 Requires-Dist: dominate (==2.6.0)
@@ -66,7 +66,7 @@ segmentation.*
 
 © This code is made available for non-commercial academic purposes.
 
-![Version](https://img.shields.io/static/v1?label=latest&message=v1.2.0&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-1.2.0.dist-info → deepliif-1.2.2.dist-info}/RECORD

@@ -1,8 +1,6 @@
 cli.py,sha256=luwzcSrRZMePfJ-h4Hgz2X7lYC70TUVxGfEo3LyPJgQ,58938
 deepliif/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-deepliif/postprocessing.py,sha256=QkeyTpR5zMvsv5mj59hRK7HXpIb2fZ_81ezfMSGAhTA,42610
-deepliif/postprocessing__OLD__DELETE.py,sha256=cM-cYVidY691Sjb1-B8a1jkLq5UR_hTCbuKzuF4765o,17589
-deepliif/train.py,sha256=-ZORL5vQrD0_Jq2Adgr3w8vJ7L1QcAgNTqMnBgtixgk,15757
+deepliif/postprocessing.py,sha256=Uu4axoOLgPgBgXxSVAgviuLi9cr4U_eE4KgFLbleMro,43512
 deepliif/data/__init__.py,sha256=IfqVFnFSPQJZnORdRq4sNkJiylr1TaKNmhvWP_aLHdg,5492
 deepliif/data/aligned_dataset.py,sha256=CkKXj94ANSi8RdhpRQjVETFYlRMER2XErIf-87BStTE,5175
 deepliif/data/base_dataset.py,sha256=bQlxfY7bGSE9WPj31ZHkCxv5CAEJovjakGDCcK-aYdc,5564
@@ -16,12 +14,6 @@ deepliif/models/DeepLIIFExt_model.py,sha256=HZaX9Z2ue0HQCFFN3guLkBcByCP70i8JvmPY
 deepliif/models/DeepLIIFKD_model.py,sha256=edq9fxrDspGivuFlAYZp9B0Opp3BRIosA9e1TI_gxpc,27152
 deepliif/models/DeepLIIF_model.py,sha256=6vmsXcBcoALrhJLa7XGhDmLamO_WCzTDYEyVUBE482o,23857
 deepliif/models/SDG_model.py,sha256=3opz7uEyhvVJ8fF4_Jw4ho1MBcc9OVye-ByZD_KF2j0,10142
-deepliif/models/__init__ - different weighted.py,sha256=Oe6ichU-Qia2mODGUtQTh1OBZZnv5N-93AzOfzQiHlw,32227
-deepliif/models/__init__ - multiprocessing (failure).py,sha256=bxM2hTvpdwzz3DG6Fbxu03C4MHsEE9lF_rd34TwiGOg,39835
-deepliif/models/__init__ - run_dask_multi dev.py,sha256=vt8X8qeiJr2aPhFi6muZEJLUSsr8XChfI45NSwL8Rfg,39449
-deepliif/models/__init__ - time gens.py,sha256=mRUtxNaGDZuhlQtKdA-OvGWTQwl7z2yMWc-9l0QrgaY,32922
-deepliif/models/__init__ - timings.py,sha256=S_wFImwxzGKx8STqbpcYCPOlbb_84WLMRDSnaWC8qFg,31750
-"deepliif/models/__init__ - weights, empty, zarr, tile count.py",sha256=JsU9ui0Kv8AzlP3_1LeiNrQLHg9X_3r8WwYy3W4JgfA,33315
 deepliif/models/__init__.py,sha256=FLMYnTyF4XvsSqN11df4a7dqFuB8-Nq4pQnTskL2DUE,34398
 deepliif/models/att_unet.py,sha256=tqaFMNbGQUjXObOG309P76c7sIPxEvFR38EyuyHY40o,7116
 deepliif/models/base_model.py,sha256=ZQBI-wVfDdu296HzB_YzQraE9oUwfyRlAolNlrMi-4g,16858
@@ -31,17 +23,16 @@ deepliif/options/base_options.py,sha256=m5UXY8MvjNcDisUWuiP228yoT27SsCh1bXS_Td6S
 deepliif/options/processing_options.py,sha256=OnNT-ytoTQzetFiMEKrWvrsrhZlupRK4smcnIk0MbqY,2947
 deepliif/options/test_options.py,sha256=4ZbQC5U-nTbUz8jvdDIbse5TK_mjw4D5yNjpVevWD5M,1114
 deepliif/options/train_options.py,sha256=5eA_oxpRj2-HiuMMvC5-HLapxNFG_JXOQ3K132JjpR8,3580
-deepliif/util/__init__.py,sha256=srhHheHPy2w2AirI22HWHkb3Qn58p--Jl1Fbl5YlGqc,31541
+deepliif/util/__init__.py,sha256=Vl_mUSCFLWZiX-eN9I-DBrbJlW29G8nPo8b5Je5pHnY,31582
 deepliif/util/checks.py,sha256=xQirKbZxZErsAXc27M5miQUUyxptoIEJSDaUKv1nY7c,1371
 deepliif/util/get_data.py,sha256=HaRoQYb2u0LUgLT7ES-w35AmJ4BrlBEJWU4Cok29pxI,3749
 deepliif/util/html.py,sha256=RNAONZ4opP-bViahgmpSbHwOc6jXKQRnWRAVIaeIvac,3309
 deepliif/util/image_pool.py,sha256=M89Hc7DblRWroNP71S9mAdRn7h3DrhPFPjqFxxZYSgw,2280
-deepliif/util/util - modified tensor_to_pil.py,sha256=fd2SeSuiWIuUIOx4FWhGGw8mP7zsfShlMM2l1tQAWQU,8438
 deepliif/util/util.py,sha256=WV2a1Rt-McmZm3BKW7TqC2oAKkvxWhZvjofGSfY6y7s,6810
 deepliif/util/visualizer.py,sha256=6E1sPbXdgLFB9mnPwtfEjm9O40viG4dfv5MyTpOQQpo,20210
-deepliif-1.2.0.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
-deepliif-1.2.0.dist-info/METADATA,sha256=aotU9YHFS0Y9Cxz57c81Bz_CmBEuMfw_vmXvgjRwoy0,35267
-deepliif-1.2.0.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-deepliif-1.2.0.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
-deepliif-1.2.0.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
-deepliif-1.2.0.dist-info/RECORD,,
+deepliif-1.2.2.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
+deepliif-1.2.2.dist-info/METADATA,sha256=qaQ--slj1E0Ypwo-uyrM4u2aWNnJxlyjpNgavWwQUYQ,35266
+deepliif-1.2.2.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+deepliif-1.2.2.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
+deepliif-1.2.2.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
+deepliif-1.2.2.dist-info/RECORD,,