Minor fixes #34

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dzenanz wants to merge 11 commits into SarderLab:main from dzenanz:minorFixes

.dockerignore

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@@ -0,0 +1,11 @@
+    # we do not want to copy git metadata
+    .git
+    # nor Python virtual environment
+    .venv
+    # sample images and other files
+    *.svs
+    *.pdf
+    *.pth
+    *.log

.gitignore

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@@ -0,0 +1,16 @@
+    *.py[cod]
+    __pycache__/
+    _build*
+    build
+    logs
+    training
+    .*.swp
+    .*.swo
+    .eggs
+    .tox
+    .vagrant
+    .venv
+    .venv9
+    .DS_Store
+    **/.DS_Store
+    multic.egg-info

Dockerfile

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@@ Expand Up / @@ -12,7 +12,6 @@ LABEL com.nvidia.volumes.needed="nvidia_driver" @@
     LABEL maintainer="Sayat Mimar - Sarder Lab. <sayat.mimar@ufl.edu>"
-    CMD echo !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! STARTING THE BUILD !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     # RUN mkdir /usr/local/nvidia && ln -s /usr/local/cuda-10.0/compat /usr/local/nvidia/lib
     ENV NVIDIA_VISIBLE_DEVICES all
@@ Expand Down Expand Up / @@ -67,8 +66,6 @@ RUN apt-get update && \ @@
         #apt-get autoremove && \
         rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
-    CMD echo !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! CHECKPOINT !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     RUN apt-get update ##[edited]
     RUN apt-get install 'ffmpeg'\
         'libsm6'\
@@ Expand Down @@

multic/cli/MultiCompartmentSegment/MultiCompartmentSegment.py

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@@ Expand Up / @@ -47,7 +47,7 @@ def main(args): @@
         print(f'This is slide path: {file_path}')
         print('new version')
-        _ = os.system("printf '\n---\n\nFOUND: [{}]\n'".format(args.input_file))
+        _ = os.system("echo '\n---\n\nFOUND: [{}]\n'".format(args.input_file))
         cwd = os.getcwd()
         print(cwd)
@@ Expand Down @@

multic/segmentationschool/Codes/InitializeFolderStructure.py

            
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    @@ -59,11 +59,11 @@ def initializeFolderStructure(dirs,args):
  
        folder_base = args.base_dir

        base_directory_id = folder_base.split('/')[-2]

        _ = os.system("printf '\nIn the base directory: {} {}\n'".format(base_directory_id,folder_base))

        _ = os.system("echo '\nIn the base directory: {} {}\n'".format(base_directory_id,folder_base))

        folder_project = args.project

        project_directory_id = folder_project.split('/')[-2]

        _ = os.system("printf '\nIn the base directory: {}{}\n'".format(project_directory_id,folder_base))

        _ = os.system("echo '\nIn the base directory: {}{}\n'".format(project_directory_id,folder_base))

        gc = girder_client.GirderClient(apiUrl=args.girderApiUrl)

        gc.setToken(args.girderToken)

multic/segmentationschool/Codes/IterativePredict_1X.py

-Original file line number
+Diff line change
@@ Expand Up @@
         annots = convert_xml_json(Annotations, NAMES)
         for annot in annots:
             _ = gc.post(path='annotation',parameters={'itemId':args.item_id}, data = json.dumps(annot))
-            print('uploating layers')
+            print('uploading layers')
         print('annotation uploaded...\n')
     def get_contour_points(mask, args, downsample,value, offset={'X': 0,'Y': 0}):
@@ Expand Down @@

multic/segmentationschool/Codes/__pycache__/InitializeFolderStructure.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/InitializeFolderStructure.cpython-39.pyc

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multic/segmentationschool/Codes/__pycache__/IterativePredict_1X.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/IterativeTraining.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/PAS_deconvolution.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/TransformXMLs.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/__init__.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/extract_reference_features.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/extract_reference_features.cpython-39.pyc

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multic/segmentationschool/Codes/__pycache__/generateTrainSet.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/getWsi.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/getWsi.cpython-39.pyc

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multic/segmentationschool/Codes/__pycache__/get_choppable_regions.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/get_choppable_regions.cpython-37.pyc

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multic/segmentationschool/Codes/__pycache__/get_dataset_list.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/get_network_performance.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/randomCropGenerator.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/randomHSVshift.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/utils.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/utils.cpython-37.pyc

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multic/segmentationschool/Codes/__pycache__/wsi_loader_utils.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/xml_to_mask.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/xml_to_mask.cpython-37.pyc

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multic/segmentationschool/Codes/__pycache__/xml_to_mask2.cpython-36.pyc

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multic/segmentationschool/Codes/__pycache__/xml_to_mask2.cpython-39.pyc

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multic/segmentationschool/Codes/__pycache__/xml_to_mask_minmax.cpython-36.pyc

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multic/segmentationschool/Codes/wsi_loader_utils.py

            
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                      Diff line number
                      Diff line change
                  
    @@ -13,7 +13,7 @@
  
    def save_thumb(args,slide_loc):

        print(slide_loc)

        slideID,slideExt=os.path.splitext(slide_loc.split('/')[-1])

        slideID,slideExt=os.path.splitext(slide_loc.split(os.sep)[-1])

        slide=openslide.OpenSlide(slide_loc)

        if slideExt =='.scn':

            dim_x=int(slide.properties['openslide.bounds-width'])## add to columns

    @@ -62,7 +62,7 @@ def __init__(self,args, wsi_directory=None, transform=None):
  
            usable_slides=[]

            for slide_loc in all_slides:

                slideID,slideExt=os.path.splitext(slide_loc.split('/')[-1])

                slideID,slideExt=os.path.splitext(slide_loc.split(os.sep)[-1])

                print("working slide... "+ slideID,end='\r')

                slide=openslide.OpenSlide(slide_loc)

    @@ -88,9 +88,9 @@ def __init__(self,args, wsi_directory=None, transform=None):
  
            print('Getting slide metadata and usable regions...')

            usable_slides=[]

            for slide_loc in all_slides:

                slideID,slideExt=os.path.splitext(slide_loc.split('/')[-1])

                print("working slide... "+ slideID,end='\r')

            for iteration, slide_loc in enumerate(all_slides):

                slideID,slideExt=os.path.splitext(slide_loc.split(os.sep)[-1])

                print(f"slide {iteration + 1}/{len(all_slides)}: {slideID}" ,end='\r')

                slide=openslide.OpenSlide(slide_loc)

                chop_array=get_choppable_regions(slide,args,slideID,slideExt,mask_out_loc)

multic/segmentationschool/Codes/xml_to_json.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,7 @@ def convert_xml_json(root, names, colorList=None, alpha=0.4): @@
         for n, child in enumerate(anns):
             dataDict = dict()
             name = names[n]
-            _ = os.system("printf 'Building JSON layer: [{}]\n'".format(name))
+            _ = os.system("echo 'Building JSON layer: [{}]\n'".format(name))
             element = []
             reg = child.find('Regions')
             for i in reg.findall('Region'):
@@ Expand Down @@

multic/segmentationschool/__pycache__/__init__.cpython-36.pyc

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multic/segmentationschool/hail.out

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setup.py

-Original file line number
+Diff line change
@@ Expand Up / @@ -45,13 +45,14 @@ def prerelease_local_scheme(version): @@
         install_requires=[
             # scientific packages
             'nimfa>=1.3.2',
-            'numpy>=1.21.1',
+            'numpy>=1.21.1,<2.0',
             'scipy>=0.19.0',
             'Pillow==9.5.0',
             'pandas>=0.19.2',
             'imageio>=2.3.0',
             # 'shapely[vectorized]',
-            #'opencv-python-headless<4.7',
+            # 'opencv-python-headless',
+            # 'imgaug==0.4.0',
             #'sqlalchemy',
             # 'matplotlib',
             'pyvips',
@@ Expand All / @@ -78,6 +79,8 @@ def prerelease_local_scheme(version): @@
             'girder-client',
             # cli
             'ctk-cli',
+            # detectron2 is installed in the dockerfile, so it needs to be commented out here
+            # 'detectron2 @ git+https://github.com/facebookresearch/detectron2@main',  # v0.6+patches
         ],
         license='Apache Software License 2.0',
         keywords='multic',
@@ Expand Down @@

‎.gitattributes

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		@@ -0,0 +1,2 @@
		*.sh text eol=lf
		*.conf text eol=lf

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