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"""
To 
 1) upload DICOM (.dcm) data of a patient and 
 2) perform auto-contouring on it and
 3) download the contours

Tested with Raystation1-B and python3.6

Note: The MICCAI2015 dataset only has 1 planning scan/patient
"""

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Steps

0. The following steps show how to run the MONAILabel server on Windows via Docker. I have tested these steps on the following software versions:

   Name	Version	Terminal	Command
   Windows	Microsoft Windows 11 Pro for Workstations	Win Command Prompt	systeminfo | findstr /B /C:"OS Name" /B /C:"OS Version
   Nvidia Driver	527.56	Win Command Prompt	nvidia-smi --query-gpu=driver_version --format=csv
   Nvidia CUDA Driver API	12.0	Win Command Prompt	nvidia-smi
   Nvidia GPU	NVIDIA GeForce RTX 2080 Ti	Win Command Prompt	nvidia-smi --query-gpu=driver_version --format=csv

| WSL | 1.0.3.0 | Win Command Prompt | wsl --version |

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"""
Data: https://drive.google.com/drive/folders/1zPK--rbdnqK2T0NnTrfvujeSg4PkN_bH?usp=sharing (contains normal_001.tif)
Alternatively: https://aws.amazon.com/marketplace/pp/prodview-exkvqrznup6vc?sr=0-1&ref_=beagle&applicationId=AWSMPContessa#resources 
"""

import os
import sys
import timeit
import numpy as np
sys.path.append('C:\\Program Files\\ASAP 2.1\\bin') # https://github.com/computationalpathologygroup/ASAP/releases/tag/ASAP-2.1

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Install ASAP on CentOS Stream (within a conda environment as a non-root user)

Preliminary points

1. The approach here is to first build/install dependencies of ASAP and then define their paths in the cmake command for ASAP. The order in which I build the dependencies is in the same order as defined using the find_package() function in ASAP/CMakeLists.txt.
2. Assumptions
   • Note 1: I assume you have your conda environment installed and activated
   • Note 2: These instruction assume you have cmake installed. Find a basic tutorial here and a quick intuition here.

• Note 3: These instruction also assume that you gcc --version is >=9 since otherwise it leads to issues with compiling #include in some .cpp files like [core/filetools.cpp](https://github.com/computationalpatholo

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"""
CAMELYON 16 DATASET
- Whole Slide Images (WSI) containing histopathological information on breast cancer

1. Download 
 - To view the list of AWS
    - Link: https://aws.amazon.com/marketplace/pp/prodview-exkvqrznup6vc?sr=0-1&ref_=beagle&applicationId=AWSMPContessa#resources
    - Click on Resources on AWS --> View Resources
 - Single Sample
   - aws s3 cp --no-sign-request s3://camelyon-dataset/CAMELYON16/images/tumor_032.tif ./raw/tumor_032.tif

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Datasets present in OHIF dicom server

Samples are writen down with their StudyInstanceUID as the header.

• Extracted from https://d33do7qe4w26qo.cloudfront.net/dicomweb/studies
• Once you have the StudyInstanceUID, you can use Postman client and the TCIA-NBIA api to extract seriesInstanceUID and sopInstanceUID

Other Referrences

1. To get all collections in TCIA: link

Samples

1. [StageII-Colorectal-CT --> CT-005] 1.3.6.1.4.1.14519.5.2.1.256467663913010332776401703474716742458

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"""
Motivation: Understanding Convolution for Semantic Segmentation (https://arxiv.org/pdf/1702.08502.pdf) 
          : https://stats.stackexchange.com/questions/265462/whats-the-receptive-field-of-a-stack-of-dilated-convolutions
"""

import pdb
import traceback
import numpy as np
import matplotlib.pyplot as plt

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import gc
import sys
import humanize # pip install humanize

def actualsize(input_obj):
    # https://towardsdatascience.com/the-strange-size-of-python-objects-in-memory-ce87bdfbb97f
    memory_size = 0
    ids = set()
    objects = [input_obj]
    while objects:

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Useful aliases

Add these aliases in your ~/.bashrc file. To use them, save the updated file and type . ~/.bashrc to reload the bash file

1. View all running jobs

   • alias qq="watch -n 0.1 'squeue -u ppmody -o \"%.10i %.9P %.24j %.8u %.2t %.10M %.5D %R\" ; echo -e \"\n\" ; squeue -p LKEBgpu,highmemgpu,gpu --sort=\"N,-i\" -o \"%.10i %.9P %.12j %.8u %.2t %.10M %.5D %.16R %.3C %.7m %b\"; echo -e \"\n\"; sinfo -a' "
     

2. View resources within the cluster

   • alias qqq="scontrol -o show nodes |grep -e \"lkeb\" -e \"gpu.ai\" -e \"gpu\"| awk '{ print \$1, \$4, \$5, \$9, \$23, \$24, \$25}'"
     

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"""
This script shall plot contours using cv2 on an image
- Useful for plotting organ contours on a medical image
-- Note: Organ Mask should contain labels values in the [0,255] range 
"""

# Standard Libraries
import pdb
import cv2
import numpy as np