deepliif 1.2.0__tar.gz → 1.2.2__tar.gz

{deepliif-1.2.0 → deepliif-1.2.2}/PKG-INFO

@@ -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
@@ -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=v1.2.0&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 → 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=v1.2.0&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 → 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]):
@@ -1048,22 +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-1.2.0 → 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-1.2.0 → deepliif-1.2.2}/deepliif.egg-info/PKG-INFO

@@ -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
@@ -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=v1.2.0&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-1.2.2/deepliif.egg-info/SOURCES.txt

@@ -0,0 +1,47 @@
+LICENSE.md
+README.md
+cli.py
+setup.cfg
+setup.py
+deepliif/__init__.py
+deepliif/postprocessing.py
+deepliif.egg-info/PKG-INFO
+deepliif.egg-info/SOURCES.txt
+deepliif.egg-info/dependency_links.txt
+deepliif.egg-info/entry_points.txt
+deepliif.egg-info/requires.txt
+deepliif.egg-info/top_level.txt
+deepliif/data/__init__.py
+deepliif/data/aligned_dataset.py
+deepliif/data/base_dataset.py
+deepliif/data/colorization_dataset.py
+deepliif/data/image_folder.py
+deepliif/data/single_dataset.py
+deepliif/data/template_dataset.py
+deepliif/data/unaligned_dataset.py
+deepliif/models/CycleGAN_model.py
+deepliif/models/DeepLIIFExt_model.py
+deepliif/models/DeepLIIFKD_model.py
+deepliif/models/DeepLIIF_model.py
+deepliif/models/SDG_model.py
+deepliif/models/__init__.py
+deepliif/models/att_unet.py
+deepliif/models/base_model.py
+deepliif/models/networks.py
+deepliif/options/__init__.py
+deepliif/options/base_options.py
+deepliif/options/processing_options.py
+deepliif/options/test_options.py
+deepliif/options/train_options.py
+deepliif/util/__init__.py
+deepliif/util/checks.py
+deepliif/util/get_data.py
+deepliif/util/html.py
+deepliif/util/image_pool.py
+deepliif/util/util.py
+deepliif/util/visualizer.py
+tests/test_args.py
+tests/test_cli_inference.py
+tests/test_cli_serialize.py
+tests/test_cli_train.py
+tests/test_cli_trainlaunch.py

{deepliif-1.2.0 → 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-1.2.0 → 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 = 1.2.0
+version = 1.2.2
 url = https://github.com/nadeemlab/DeepLIIF
 
 [egg_info]

{deepliif-1.2.0 → deepliif-1.2.2}/setup.py

@@ -6,7 +6,7 @@ README = (HERE / "README.md").read_text()
 
 setup(
     name='deepliif',
-    version='1.2.0',
+    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",

deepliif-1.2.0/.gitignore

@@ -1,147 +0,0 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-.idea/*
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-wheels/
-pip-wheel-metadata/
-share/python-wheels/
-*.egg-info/
-.installed.cfg
-*.egg
-MANIFEST
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
-*.log
-*.out
-local_settings.py
-db.sqlite3
-db.sqlite3-journal
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# Jupyter Notebook
-.ipynb_checkpoints
-
-# IPython
-profile_default/
-ipython_config.py
-
-# pyenv
-.python-version
-
-# pipenv
-#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
-#   However, in case of collaboration, if having platform-specific dependencies or dependencies
-#   having no cross-platform support, pipenv may install dependencies that don't work, or not
-#   install all needed dependencies.
-#Pipfile.lock
-
-# PEP 582; used by e.g. github.com/David-OConnor/pyflow
-__pypackages__/
-
-# Celery stuff
-celerybeat-schedule
-celerybeat.pid
-
-# SageMath parsed files
-*.sage.py
-
-# Environments
-.env
-.venv
-env/
-venv/
-ENV/
-env.bak/
-venv.bak/
-
-# Spyder project settings
-.spyderproject
-.spyproject
-
-# Rope project settings
-.ropeproject
-
-# mkdocs documentation
-/site
-
-# mypy
-.mypy_cache/
-.dmypy.json
-dmypy.json
-
-# Pyre type checker
-.pyre/
-
-
-# Checkpoints and results
-/checkpoints/
-/model-server/
-/results/*
-
-**/.ipynb_checkpoints/*
-**/.virtual_documents/*
-assets/.METADATA/job_run.*
-assets/job_run
-cover/
-.pybuilder/
-.pytype/
-cython_debug/

deepliif-1.2.0/Datasets/Sample_Dataset/val/Bladder1.json

@@ -1,10 +0,0 @@
-{
-  "num_total": 183,
-  "num_pos": 15,
-  "num_neg": 168,
-  "percent_pos": 8.2,
-  "prob_thresh": 150,
-  "size_thresh": 30,
-  "size_thresh_upper": null,
-  "marker_thresh": null
-}

deepliif-1.2.0/Datasets/Sample_Dataset/val/Lung1.json

@@ -1,10 +0,0 @@
-{
-  "num_total": 60,
-  "num_pos": 11,
-  "num_neg": 49,
-  "percent_pos": 18.3,
-  "prob_thresh": 150,
-  "size_thresh": 78,
-  "size_thresh_upper": null,
-  "marker_thresh": null
-}

deepliif-1.2.0/Datasets/Sample_Dataset/val/metrics.json

@@ -1,22 +0,0 @@
-{
-  "Lung1": {
-    "num_total": 60,
-    "num_pos": 11,
-    "num_neg": 49,
-    "percent_pos": 18.3,
-    "prob_thresh": 150,
-    "size_thresh": 78,
-    "size_thresh_upper": null,
-    "marker_thresh": null
-  },
-  "Bladder1": {
-    "num_total": 183,
-    "num_pos": 15,
-    "num_neg": 168,
-    "percent_pos": 8.2,
-    "prob_thresh": 150,
-    "size_thresh": 30,
-    "size_thresh_upper": null,
-    "marker_thresh": null
-  }
-}