| """ | |
| 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 |
| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <script src="https://cdnjs.cloudflare.com/ajax/libs/hammer.js/2.0.8/hammer.min.js"></script> | |
| <script src="https://unpkg.com/cornerstone-core/dist/cornerstone.js"></script> <!-- cornerstone-core - 2.6.1 - 2021-11-19 --> | |
| <script src="https://unpkg.com/cornerstone-tools/dist/cornerstoneTools.js"></script> <!-- cornerstone-tools - 6.0.10 - 2023-07-21 --> | |
| <script src="https://unpkg.com/cornerstone-math/dist/cornerstoneMath.js"></script> <!-- cornerstone-math - 0.1.10 - 2022-06-09 --> |
| import os | |
| import numpy as np | |
| from sklearn.metrics import log_loss | |
| """ | |
| - HARDCODED FORMULAE | |
| - In this gist, we shall almost always use probabilities and not unscaled logits | |
| """ | |
| ## BINARY CLASS CROSS ENTROPY | |
| y_true = [0,0,0,1] # 4 observations |
| """ | |
| Step 1 - Read Dose and CT .dcm files | |
| Step 2 - Resample dose to CT | |
| Step 3 - Plot | |
| """ | |
| import pdb | |
| import pydicom | |
| import traceback | |
| import numpy as np | |
| import SimpleITK as sitk |
| import itk | |
| import SimpleITK as sitk | |
| def convert_sitk_to_itk(sitk_img): | |
| img_array = sitk.GetArrayFromImage(sitk_img) | |
| itk_img = itk.GetImageFromArray(img_array) | |
| itk_img.SetOrigin(tuple(sitk_img.GetOrigin())) | |
| itk_img.SetSpacing(tuple(sitk_img.GetSpacing())) | |
| itk_img.SetDirection(itk.GetMatrixFromArray(np.reshape(np.array(sitk_img.GetDirection()), [sitk_img.GetDimension()]*2))) |
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.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
| import connect | |
| RS_CHECK_PREFIX = '_' | |
| RS_STR_TRANSLATE_OBJ = { ord(' ') : ord('_') , ord('(') : ord('_') , ord(')') : ord('_') , ord('-') : ord('_') , ord('+') : ord('_') , ord('<') : ord('_') , ord('>') : ord('_') } | |
| KEYNAME_PATIENT = 'Patient' | |
| def checkForRTPlan(case, planName): | |
| exists = False | |
| if RS_CHECK_PREFIX + str(planName).translate(RS_STR_TRANSLATE_OBJ) in dir(case.TreatmentPlans): | |
| exists = True |
conda create -y -n XOSight-Pattern2 "python=3.8" "mamba>=0.22.1" -c conda-forge
conda activate XOSight-Pattern2
mamba install ros-noetic-desktop -c robostack -c robostack-experimental -c conda-forge --override-channels
mamba install vs2019_win-64
conda deactivate
conda activate XOSight-Pattern2
mamba install rosdep
| # Option 1 | |
| import os | |
| from pathlib import Path | |
| filename = Path(__file__).parts[-1] | |
| mem = os.popen("ps aux | grep %s | awk '{sum=sum+$6}; END {print sum/1024 \" MB\"}'"% (filename)).read() | |
| # Option 2 | |
| import os | |
| import psutil # pip install psutil | |
| import humanize # pip install humanize |
| import sys, time | |
| import requests | |
| def download_file_from_google_drive(id, destination): | |
| def get_confirm_token(response): | |
| for key, value in response.cookies.items(): | |
| if key.startswith('download_warning'): | |
| return value | |
| return None |