deepliif 1.1.12__py3-none-any.whl → 1.1.13__py3-none-any.whl

deepliif/models/__init__.py

@@ -33,7 +33,6 @@ Image.MAX_IMAGE_PIXELS = None
 
 import numpy as np
 from dask import delayed, compute
-import openslide
 
 from deepliif.util import *
 from deepliif.util.util import tensor_to_pil
@@ -592,10 +591,13 @@ def infer_results_for_wsi(input_dir, filename, output_dir, model_dir, tile_size,
 
 def get_wsi_resolution(filename):
     """
-    Use OpenSlide to get the resolution (magnification) of the slide
-    and the corresponding tile size to use by default for DeepLIIF.
+    Try to get the resolution (magnification) of the slide and
+    the corresponding tile size to use by default for DeepLIIF.
     If it cannot be found, return (None, None) instead.
 
+    Note: This will start the javabridge VM, but not kill it.
+          It must be killed elsewhere.
+
     Parameters
     ----------
     filename : str
@@ -604,13 +606,42 @@ def get_wsi_resolution(filename):
     Returns
     -------
     str :
-        Magnification (objective power) as found by OpenSlide.
+        Magnification (objective power) from image metadata.
     int :
         Corresponding tile size for DeepLIIF.
     """
+
+    # make sure javabridge is already set up from with call to get_information()
+    size_x, size_y, size_z, size_c, size_t, pixel_type = get_information(filename)
+
+    mag = None
+    metadata = bioformats.get_omexml_metadata(filename)
+    try:
+        omexml = bioformats.OMEXML(metadata)
+        mag = omexml.instrument().Objective.NominalMagnification
+    except Exception as e:
+        fields = ['AppMag', 'NominalMagnification']
+        try:
+            for field in fields:
+                idx = metadata.find(field)
+                if idx >= 0:
+                    for i in range(idx, len(metadata)):
+                        if metadata[i].isdigit() or metadata[i] == '.':
+                            break
+                    for j in range(i, len(metadata)):
+                        if not metadata[j].isdigit() and metadata[j] != '.':
+                            break
+                    if i == j:
+                        continue
+                    mag = metadata[i:j]
+                    break
+        except Exception as e:
+            pass
+
+    if mag is None:
+        return None, None
+
     try:
-        image = openslide.OpenSlide(filename)
-        mag = image.properties.get(openslide.PROPERTY_NAME_OBJECTIVE_POWER)
         tile_size = round((float(mag) / 40) * 512)
         return mag, tile_size
     except Exception as e:

deepliif/util/__init__.py

@@ -437,7 +437,7 @@ def get_information(filename):
                                                          omexml.image().Pixels.SizeC, \
                                                          omexml.image().Pixels.SizeT, \
                                                          omexml.image().Pixels.PixelType
-    print('SizeX:', size_x, ' SizeY:', size_y, ' SizeZ:', size_z, ' SizeC:', size_c, ' SizeT:', size_t, ' PixelType:', pixel_type)
+    #print('SizeX:', size_x, ' SizeY:', size_y, ' SizeZ:', size_z, ' SizeC:', size_c, ' SizeT:', size_t, ' PixelType:', pixel_type)
     return size_x, size_y, size_z, size_c, size_t, pixel_type
 
 

{deepliif-1.1.12.dist-info → deepliif-1.1.13.dist-info}/METADATA

@@ -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
@@ -9,7 +9,8 @@ Keywords: DeepLIIF,IHC,Segmentation,Classification
 Description-Content-Type: text/markdown
 License-File: LICENSE.md
 Requires-Dist: opencv-python (==4.8.1.78)
-Requires-Dist: torchvision (==0.10.0)
+Requires-Dist: torch (==1.13.1)
+Requires-Dist: torchvision (==0.14.1)
 Requires-Dist: scikit-image (==0.18.3)
 Requires-Dist: dominate (==2.6.0)
 Requires-Dist: numba (==0.57.1)
@@ -18,8 +19,6 @@ Requires-Dist: requests (==2.32.2)
 Requires-Dist: dask (==2021.11.2)
 Requires-Dist: visdom (>=0.1.8.3)
 Requires-Dist: python-bioformats (>=4.0.6)
-Requires-Dist: openslide-bin (==4.0.0.6)
-Requires-Dist: openslide-python (==1.4.1)
 
 
 <!-- PROJECT LOGO -->
@@ -65,7 +64,7 @@ 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.dist-info → deepliif-1.1.13.dist-info}/RECORD

@@ -15,9 +15,11 @@ deepliif/models/CycleGAN_model.py,sha256=WDEa-Zgz57mVc9HbcVDXL5vfHvUDWdWXNLyz8Re
 deepliif/models/DeepLIIFExt_model.py,sha256=HZaX9Z2ue0HQCFFN3guLkBcByCP70i8JvmPY02oOMyU,15022
 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__ - 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__.py,sha256=-R9Em7TVGl36nKzlEI894T0WEONGVMV60aTucqLab5k,30846
+deepliif/models/__init__.py,sha256=EZkZu28f5ju_YiEz4yAMHQ5GAzl1-Mi6AK4kfWe20UA,31934
 deepliif/models/att_unet.py,sha256=tqaFMNbGQUjXObOG309P76c7sIPxEvFR38EyuyHY40o,7116
 deepliif/models/base_model.py,sha256=ezWkmbuuNLGDMjyXe3VzJroj7QR1h0M9ByouzpfCrQg,16843
 deepliif/models/networks.py,sha256=Ijeb7nGf-YFgc_sBR-sIsk--0rTeiUqKZd01k4DMsuM,36614
@@ -26,15 +28,15 @@ 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=-3t8kNolblI33XwpMaRbOPwVkKg1jjtVE8s0DvA2DNs,29145
+deepliif/util/__init__.py,sha256=_b7-t5Z54CJJIy-moeKPPLFHg5BRCKgWo5V18WqRZVo,29146
 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.py,sha256=9MNgqthJZYjl5-TJm5-sjWvMfPBz8F4P5K0RHXRQhfY,5241
 deepliif/util/visualizer.py,sha256=6E1sPbXdgLFB9mnPwtfEjm9O40viG4dfv5MyTpOQQpo,20210
-deepliif-1.1.12.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
-deepliif-1.1.12.dist-info/METADATA,sha256=VX20mfKaSJkgH_OdGJOCbKSp3iahnE3_dnn_MUAMR5Y,35247
-deepliif-1.1.12.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-deepliif-1.1.12.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
-deepliif-1.1.12.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
-deepliif-1.1.12.dist-info/RECORD,,
+deepliif-1.1.13.dist-info/LICENSE.md,sha256=HlZw_UPS6EtJimJ_Ci7xKh-S5Iubs0Z8y8E6EZ3ZNyE,956
+deepliif-1.1.13.dist-info/METADATA,sha256=Ff0QjUBwpZGJcU1YgHfaixVAW6IYyHjV0FUi7QiGaRo,35195
+deepliif-1.1.13.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+deepliif-1.1.13.dist-info/entry_points.txt,sha256=f70-10j2q68o_rDlsE3hspnv4ejlDnXwwGZ9JJ-3yF4,37
+deepliif-1.1.13.dist-info/top_level.txt,sha256=vLDK5YKmDz08E7PywuvEjAo7dM5rnIpsjR4c0ubQCnc,13
+deepliif-1.1.13.dist-info/RECORD,,