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b/notebooks/4_ElastixTransformix_experimenting.ipynb |
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{ |
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"cells": [ |
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{ |
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"cell_type": "code", |
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"execution_count": 1, |
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"metadata": {}, |
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"outputs": [], |
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"source": [ |
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"import sys\n", |
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"sys.path.append('../')\n", |
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"\n", |
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"import os\n", |
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"import json\n", |
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"import time\n", |
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"from glob import glob\n", |
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"\n", |
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"from utils.elastix import excute_cmd, register_elastix, control_points_transformix\n", |
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"from utils.filemanager import create_directory_if_not_exists, replace_text_in_file, add_and_delete_rows, delete_added_rows\n", |
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"from utils.landmarks import get_landmarks_from_txt, write_landmarks_to_list\n", |
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"from utils.metrics import compute_TRE\n", |
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"from utils.utils import format_elapsed_time\n", |
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"\n", |
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"# To allow auto reload to this notebook after modifying any external file imported\n", |
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"%load_ext autoreload\n", |
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"%autoreload 2" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 2, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"data": { |
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"text/plain": [ |
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"['../dataset/train/copd1/copd1_eBHCT.nii.gz',\n", |
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" '../dataset/train/copd2/copd2_eBHCT.nii.gz',\n", |
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" '../dataset/train/copd3/copd3_eBHCT.nii.gz',\n", |
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" '../dataset/train/copd4/copd4_eBHCT.nii.gz']" |
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] |
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}, |
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"execution_count": 2, |
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"metadata": {}, |
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"output_type": "execute_result" |
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} |
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], |
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"source": [ |
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"train_path = '../dataset/train'\n", |
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"\n", |
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"# prepare the paths\n", |
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"exhale_volumes = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*eBHCT.nii.gz\"), recursive=True))]\n", |
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"inhale_volumes = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*iBHCT.nii.gz\"), recursive=True))]\n", |
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"\n", |
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"exhale_seg = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*eBHCT_lung.nii.gz\"), recursive=True))]\n", |
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"inhale_seg = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*iBHCT_lung.nii.gz\"), recursive=True))]\n", |
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"\n", |
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"exhale_volumes" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 4, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"name": "stdout", |
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"output_type": "stream", |
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"text": [ |
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"Experimenting using -p ../elastix-parameters/Par0003/Par0003.affine.txt params command...\n", |
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"Key for the experiment: Par0003.affine.txt...\n", |
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"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
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"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
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"Registering copd1_eBHCT and copd1_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.affine.txt -out \"output/Par0003.affine.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 30 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
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"TRE (After Registration):- (Mean TRE: 11.87) (STD TRE: 6.72). \n", |
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"\n", |
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"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
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"Registering copd2_eBHCT and copd2_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.affine.txt -out \"output/Par0003.affine.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 26 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
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"TRE (After Registration):- (Mean TRE: 10.96) (STD TRE: 4.92). \n", |
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"\n", |
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"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
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"Registering copd3_eBHCT and copd3_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.affine.txt -out \"output/Par0003.affine.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 31 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
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"TRE (After Registration):- (Mean TRE: 4.41) (STD TRE: 2.93). \n", |
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"\n", |
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"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
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"Registering copd4_eBHCT and copd4_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.affine.txt -out \"output/Par0003.affine.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 31 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
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"TRE (After Registration):- (Mean TRE: 7.66) (STD TRE: 3.55). \n", |
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"\n", |
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"Time for overall registrations: 1 minutes and 59 seconds\n" |
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] |
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} |
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], |
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"source": [ |
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"Par_base = '../elastix-parameters/Par0003'\n", |
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"\n", |
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"# Setting the experiment registration parameter\n", |
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"params_list = [\n", |
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" 'Par0003.affine.txt',\n", |
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" ]\n", |
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"\n", |
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"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
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"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
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"\n", |
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"print(f\"Experimenting using {reg_params} params command...\")\n", |
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"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
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"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
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"\n", |
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"overall_start_time = time.time()\n", |
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"\n", |
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"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
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" # get file name\n", |
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" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
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" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
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"\n", |
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" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
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"\n", |
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" # load the dataset dictionary\n", |
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" with open('../dataset/description.json', 'r') as json_file:\n", |
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" dictionary = json.loads(json_file.read())\n", |
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" file_information = dictionary['train'][sample_name]\n", |
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" print(file_information)\n", |
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"\n", |
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" # get control points path from dataset dir\n", |
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" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
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" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
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"\n", |
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" # start the time only when the registration starts\n", |
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" loop_start_time = time.time()\n", |
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"\n", |
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" # elastix registration\n", |
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" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
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" register_elastix(\n", |
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" fixed_path = i_path, \n", |
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" moving_path = e_path, \n", |
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" fMask = i_seg_path,\n", |
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" mMask= e_seg_path,\n", |
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" reg_params = reg_params,\n", |
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" reg_params_key = reg_params_key,\n", |
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" create_dir_callback = create_directory_if_not_exists,\n", |
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" excute_cmd_callback = excute_cmd)\n", |
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"\n", |
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" # transformix control point transformation\n", |
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" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
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" output_path = control_points_transformix(\n", |
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" fixed_path = i_path, \n", |
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" moving_path = e_path,\n", |
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" reg_params_key = reg_params_key,\n", |
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" input_points = i_cntl_pt, \n", |
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" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
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" replace_text_in_file_callback = replace_text_in_file,\n", |
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" create_dir_callback = create_directory_if_not_exists, \n", |
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" excute_cmd_callback = excute_cmd)\n", |
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"\n", |
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" loop_end_time = time.time()\n", |
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" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
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" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
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"\n", |
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" # get the transformed landmarks\n", |
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" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
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" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
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"\n", |
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" # write the landmarks into the output directory of the points\n", |
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" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
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" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
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" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
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"\n", |
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" # evaluate\n", |
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" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
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" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
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" \n", |
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" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
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" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
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" \n", |
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"overall_end_time = time.time()\n", |
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"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
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"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
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] |
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}, |
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{ |
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"cell_type": "code", |
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"execution_count": 5, |
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"metadata": {}, |
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"outputs": [ |
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{ |
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"name": "stdout", |
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"output_type": "stream", |
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"text": [ |
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"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt params command...\n", |
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"Key for the experiment: Par0003.bs-R1-fg.txt...\n", |
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"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
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"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
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"Registering copd1_eBHCT and copd1_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt -out \"output/Par0003.bs-R1-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 10 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
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"TRE (After Registration):- (Mean TRE: 25.97) (STD TRE: 11.5). \n", |
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"\n", |
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"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
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"Registering copd2_eBHCT and copd2_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt -out \"output/Par0003.bs-R1-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 8 seconds\n", |
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"Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
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"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
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"TRE (After Registration):- (Mean TRE: 21.48) (STD TRE: 6.47). \n", |
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"\n", |
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"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
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"Registering copd3_eBHCT and copd3_iBHCT...\n", |
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"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt -out \"output/Par0003.bs-R1-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
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"Accessing the last transform parameter file TransformParameters.0.txt\n", |
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"Time for current registration loop: 0 minutes and 10 seconds\n", |
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|
233 |
"Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
234 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
235 |
"TRE (After Registration):- (Mean TRE: 11.99) (STD TRE: 6.47). \n", |
|
|
236 |
"\n", |
|
|
237 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
238 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
239 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt -out \"output/Par0003.bs-R1-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
240 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
241 |
"Time for current registration loop: 0 minutes and 9 seconds\n", |
|
|
242 |
"Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
243 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
244 |
"TRE (After Registration):- (Mean TRE: 29.3) (STD TRE: 13.05). \n", |
|
|
245 |
"\n", |
|
|
246 |
"Time for overall registrations: 0 minutes and 39 seconds\n" |
|
|
247 |
] |
|
|
248 |
} |
|
|
249 |
], |
|
|
250 |
"source": [ |
|
|
251 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
252 |
"\n", |
|
|
253 |
"# Setting the experiment registration parameter\n", |
|
|
254 |
"params_list = [\n", |
|
|
255 |
" 'Par0003.bs-R1-fg.txt',\n", |
|
|
256 |
" ]\n", |
|
|
257 |
"\n", |
|
|
258 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
259 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
260 |
"\n", |
|
|
261 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
262 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
263 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
264 |
"\n", |
|
|
265 |
"overall_start_time = time.time()\n", |
|
|
266 |
"\n", |
|
|
267 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
268 |
" # get file name\n", |
|
|
269 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
270 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
271 |
"\n", |
|
|
272 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
273 |
"\n", |
|
|
274 |
" # load the dataset dictionary\n", |
|
|
275 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
276 |
" dictionary = json.loads(json_file.read())\n", |
|
|
277 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
278 |
" print(file_information)\n", |
|
|
279 |
"\n", |
|
|
280 |
" # get control points path from dataset dir\n", |
|
|
281 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
282 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
283 |
"\n", |
|
|
284 |
" # start the time only when the registration starts\n", |
|
|
285 |
" loop_start_time = time.time()\n", |
|
|
286 |
"\n", |
|
|
287 |
" # elastix registration\n", |
|
|
288 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
289 |
" register_elastix(\n", |
|
|
290 |
" fixed_path = i_path, \n", |
|
|
291 |
" moving_path = e_path, \n", |
|
|
292 |
" fMask = i_seg_path,\n", |
|
|
293 |
" mMask= e_seg_path,\n", |
|
|
294 |
" reg_params = reg_params,\n", |
|
|
295 |
" reg_params_key = reg_params_key,\n", |
|
|
296 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
297 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
298 |
"\n", |
|
|
299 |
" # transformix control point transformation\n", |
|
|
300 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
301 |
" output_path = control_points_transformix(\n", |
|
|
302 |
" fixed_path = i_path, \n", |
|
|
303 |
" moving_path = e_path,\n", |
|
|
304 |
" reg_params_key = reg_params_key,\n", |
|
|
305 |
" input_points = i_cntl_pt, \n", |
|
|
306 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
307 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
308 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
309 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
310 |
"\n", |
|
|
311 |
" loop_end_time = time.time()\n", |
|
|
312 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
313 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
314 |
"\n", |
|
|
315 |
" # get the transformed landmarks\n", |
|
|
316 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
317 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
318 |
"\n", |
|
|
319 |
" # write the landmarks into the output directory of the points\n", |
|
|
320 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
321 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
322 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
323 |
"\n", |
|
|
324 |
" # evaluate\n", |
|
|
325 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
326 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
327 |
" \n", |
|
|
328 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
329 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
330 |
" \n", |
|
|
331 |
"overall_end_time = time.time()\n", |
|
|
332 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
333 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
334 |
] |
|
|
335 |
}, |
|
|
336 |
{ |
|
|
337 |
"cell_type": "code", |
|
|
338 |
"execution_count": 6, |
|
|
339 |
"metadata": {}, |
|
|
340 |
"outputs": [ |
|
|
341 |
{ |
|
|
342 |
"name": "stdout", |
|
|
343 |
"output_type": "stream", |
|
|
344 |
"text": [ |
|
|
345 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt params command...\n", |
|
|
346 |
"Key for the experiment: Par0003.bs-R1-ug.txt...\n", |
|
|
347 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
348 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
349 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
350 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt -out \"output/Par0003.bs-R1-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
351 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
352 |
"Time for current registration loop: 0 minutes and 9 seconds\n", |
|
|
353 |
"Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
354 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
355 |
"TRE (After Registration):- (Mean TRE: 25.97) (STD TRE: 11.5). \n", |
|
|
356 |
"\n", |
|
|
357 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
358 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
359 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt -out \"output/Par0003.bs-R1-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
360 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
361 |
"Time for current registration loop: 0 minutes and 8 seconds\n", |
|
|
362 |
"Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
363 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
364 |
"TRE (After Registration):- (Mean TRE: 21.48) (STD TRE: 6.47). \n", |
|
|
365 |
"\n", |
|
|
366 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
367 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
368 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt -out \"output/Par0003.bs-R1-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
369 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
370 |
"Time for current registration loop: 0 minutes and 9 seconds\n", |
|
|
371 |
"Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
372 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
373 |
"TRE (After Registration):- (Mean TRE: 11.99) (STD TRE: 6.47). \n", |
|
|
374 |
"\n", |
|
|
375 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
376 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
377 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt -out \"output/Par0003.bs-R1-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
378 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
379 |
"Time for current registration loop: 0 minutes and 9 seconds\n", |
|
|
380 |
"Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
381 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
382 |
"TRE (After Registration):- (Mean TRE: 29.3) (STD TRE: 13.05). \n", |
|
|
383 |
"\n", |
|
|
384 |
"Time for overall registrations: 0 minutes and 37 seconds\n" |
|
|
385 |
] |
|
|
386 |
} |
|
|
387 |
], |
|
|
388 |
"source": [ |
|
|
389 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
390 |
"\n", |
|
|
391 |
"# Setting the experiment registration parameter\n", |
|
|
392 |
"params_list = [\n", |
|
|
393 |
" 'Par0003.bs-R1-ug.txt',\n", |
|
|
394 |
" ]\n", |
|
|
395 |
"\n", |
|
|
396 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
397 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
398 |
"\n", |
|
|
399 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
400 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
401 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
402 |
"\n", |
|
|
403 |
"overall_start_time = time.time()\n", |
|
|
404 |
"\n", |
|
|
405 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
406 |
" # get file name\n", |
|
|
407 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
408 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
409 |
"\n", |
|
|
410 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
411 |
"\n", |
|
|
412 |
" # load the dataset dictionary\n", |
|
|
413 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
414 |
" dictionary = json.loads(json_file.read())\n", |
|
|
415 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
416 |
" print(file_information)\n", |
|
|
417 |
"\n", |
|
|
418 |
" # get control points path from dataset dir\n", |
|
|
419 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
420 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
421 |
"\n", |
|
|
422 |
" # start the time only when the registration starts\n", |
|
|
423 |
" loop_start_time = time.time()\n", |
|
|
424 |
"\n", |
|
|
425 |
" # elastix registration\n", |
|
|
426 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
427 |
" register_elastix(\n", |
|
|
428 |
" fixed_path = i_path, \n", |
|
|
429 |
" moving_path = e_path, \n", |
|
|
430 |
" fMask = i_seg_path,\n", |
|
|
431 |
" mMask= e_seg_path,\n", |
|
|
432 |
" reg_params = reg_params,\n", |
|
|
433 |
" reg_params_key = reg_params_key,\n", |
|
|
434 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
435 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
436 |
"\n", |
|
|
437 |
" # transformix control point transformation\n", |
|
|
438 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
439 |
" output_path = control_points_transformix(\n", |
|
|
440 |
" fixed_path = i_path, \n", |
|
|
441 |
" moving_path = e_path,\n", |
|
|
442 |
" reg_params_key = reg_params_key,\n", |
|
|
443 |
" input_points = i_cntl_pt, \n", |
|
|
444 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
445 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
446 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
447 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
448 |
"\n", |
|
|
449 |
" loop_end_time = time.time()\n", |
|
|
450 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
451 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
452 |
"\n", |
|
|
453 |
" # get the transformed landmarks\n", |
|
|
454 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
455 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
456 |
"\n", |
|
|
457 |
" # write the landmarks into the output directory of the points\n", |
|
|
458 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
459 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
460 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
461 |
"\n", |
|
|
462 |
" # evaluate\n", |
|
|
463 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
464 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
465 |
" \n", |
|
|
466 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
467 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
468 |
" \n", |
|
|
469 |
"overall_end_time = time.time()\n", |
|
|
470 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
471 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
472 |
] |
|
|
473 |
}, |
|
|
474 |
{ |
|
|
475 |
"cell_type": "code", |
|
|
476 |
"execution_count": 7, |
|
|
477 |
"metadata": {}, |
|
|
478 |
"outputs": [ |
|
|
479 |
{ |
|
|
480 |
"name": "stdout", |
|
|
481 |
"output_type": "stream", |
|
|
482 |
"text": [ |
|
|
483 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt params command...\n", |
|
|
484 |
"Key for the experiment: Par0003.bs-R2-fg.txt...\n", |
|
|
485 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
486 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
487 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
488 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt -out \"output/Par0003.bs-R2-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
489 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
490 |
"Time for current registration loop: 0 minutes and 19 seconds\n", |
|
|
491 |
"Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
492 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
493 |
"TRE (After Registration):- (Mean TRE: 25.45) (STD TRE: 11.45). \n", |
|
|
494 |
"\n", |
|
|
495 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
496 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
497 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt -out \"output/Par0003.bs-R2-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
498 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
499 |
"Time for current registration loop: 0 minutes and 15 seconds\n", |
|
|
500 |
"Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
501 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
502 |
"TRE (After Registration):- (Mean TRE: 21.05) (STD TRE: 6.55). \n", |
|
|
503 |
"\n", |
|
|
504 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
505 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
506 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt -out \"output/Par0003.bs-R2-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
507 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
508 |
"Time for current registration loop: 0 minutes and 18 seconds\n", |
|
|
509 |
"Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
510 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
511 |
"TRE (After Registration):- (Mean TRE: 11.07) (STD TRE: 6.63). \n", |
|
|
512 |
"\n", |
|
|
513 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
514 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
515 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt -out \"output/Par0003.bs-R2-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
516 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
517 |
"Time for current registration loop: 0 minutes and 17 seconds\n", |
|
|
518 |
"Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
519 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
520 |
"TRE (After Registration):- (Mean TRE: 28.89) (STD TRE: 13.07). \n", |
|
|
521 |
"\n", |
|
|
522 |
"Time for overall registrations: 1 minutes and 10 seconds\n" |
|
|
523 |
] |
|
|
524 |
} |
|
|
525 |
], |
|
|
526 |
"source": [ |
|
|
527 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
528 |
"\n", |
|
|
529 |
"# Setting the experiment registration parameter\n", |
|
|
530 |
"params_list = [\n", |
|
|
531 |
" 'Par0003.bs-R2-fg.txt',\n", |
|
|
532 |
" ]\n", |
|
|
533 |
"\n", |
|
|
534 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
535 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
536 |
"\n", |
|
|
537 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
538 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
539 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
540 |
"\n", |
|
|
541 |
"overall_start_time = time.time()\n", |
|
|
542 |
"\n", |
|
|
543 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
544 |
" # get file name\n", |
|
|
545 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
546 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
547 |
"\n", |
|
|
548 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
549 |
"\n", |
|
|
550 |
" # load the dataset dictionary\n", |
|
|
551 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
552 |
" dictionary = json.loads(json_file.read())\n", |
|
|
553 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
554 |
" print(file_information)\n", |
|
|
555 |
"\n", |
|
|
556 |
" # get control points path from dataset dir\n", |
|
|
557 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
558 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
559 |
"\n", |
|
|
560 |
" # start the time only when the registration starts\n", |
|
|
561 |
" loop_start_time = time.time()\n", |
|
|
562 |
"\n", |
|
|
563 |
" # elastix registration\n", |
|
|
564 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
565 |
" register_elastix(\n", |
|
|
566 |
" fixed_path = i_path, \n", |
|
|
567 |
" moving_path = e_path, \n", |
|
|
568 |
" fMask = i_seg_path,\n", |
|
|
569 |
" mMask= e_seg_path,\n", |
|
|
570 |
" reg_params = reg_params,\n", |
|
|
571 |
" reg_params_key = reg_params_key,\n", |
|
|
572 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
573 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
574 |
"\n", |
|
|
575 |
" # transformix control point transformation\n", |
|
|
576 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
577 |
" output_path = control_points_transformix(\n", |
|
|
578 |
" fixed_path = i_path, \n", |
|
|
579 |
" moving_path = e_path,\n", |
|
|
580 |
" reg_params_key = reg_params_key,\n", |
|
|
581 |
" input_points = i_cntl_pt, \n", |
|
|
582 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
583 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
584 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
585 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
586 |
"\n", |
|
|
587 |
" loop_end_time = time.time()\n", |
|
|
588 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
589 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
590 |
"\n", |
|
|
591 |
" # get the transformed landmarks\n", |
|
|
592 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
593 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
594 |
"\n", |
|
|
595 |
" # write the landmarks into the output directory of the points\n", |
|
|
596 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
597 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
598 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
599 |
"\n", |
|
|
600 |
" # evaluate\n", |
|
|
601 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
602 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
603 |
" \n", |
|
|
604 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
605 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
606 |
" \n", |
|
|
607 |
"overall_end_time = time.time()\n", |
|
|
608 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
609 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
610 |
] |
|
|
611 |
}, |
|
|
612 |
{ |
|
|
613 |
"cell_type": "code", |
|
|
614 |
"execution_count": 8, |
|
|
615 |
"metadata": {}, |
|
|
616 |
"outputs": [ |
|
|
617 |
{ |
|
|
618 |
"name": "stdout", |
|
|
619 |
"output_type": "stream", |
|
|
620 |
"text": [ |
|
|
621 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt params command...\n", |
|
|
622 |
"Key for the experiment: Par0003.bs-R2-ug.txt...\n", |
|
|
623 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
624 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
625 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
626 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt -out \"output/Par0003.bs-R2-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
627 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
628 |
"Time for current registration loop: 0 minutes and 17 seconds\n", |
|
|
629 |
"Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
630 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
631 |
"TRE (After Registration):- (Mean TRE: 23.74) (STD TRE: 11.18). \n", |
|
|
632 |
"\n", |
|
|
633 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
634 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
635 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt -out \"output/Par0003.bs-R2-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
636 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
637 |
"Time for current registration loop: 0 minutes and 15 seconds\n", |
|
|
638 |
"Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
639 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
640 |
"TRE (After Registration):- (Mean TRE: 18.93) (STD TRE: 6.88). \n", |
|
|
641 |
"\n", |
|
|
642 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
643 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
644 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt -out \"output/Par0003.bs-R2-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
645 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
646 |
"Time for current registration loop: 0 minutes and 17 seconds\n", |
|
|
647 |
"Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
648 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
649 |
"TRE (After Registration):- (Mean TRE: 6.38) (STD TRE: 6.02). \n", |
|
|
650 |
"\n", |
|
|
651 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
652 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
653 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt -out \"output/Par0003.bs-R2-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
654 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
655 |
"Time for current registration loop: 0 minutes and 17 seconds\n", |
|
|
656 |
"Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
657 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
658 |
"TRE (After Registration):- (Mean TRE: 27.81) (STD TRE: 13.32). \n", |
|
|
659 |
"\n", |
|
|
660 |
"Time for overall registrations: 1 minutes and 8 seconds\n" |
|
|
661 |
] |
|
|
662 |
} |
|
|
663 |
], |
|
|
664 |
"source": [ |
|
|
665 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
666 |
"\n", |
|
|
667 |
"# Setting the experiment registration parameter\n", |
|
|
668 |
"params_list = [\n", |
|
|
669 |
" 'Par0003.bs-R2-ug.txt',\n", |
|
|
670 |
" ]\n", |
|
|
671 |
"\n", |
|
|
672 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
673 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
674 |
"\n", |
|
|
675 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
676 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
677 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
678 |
"\n", |
|
|
679 |
"overall_start_time = time.time()\n", |
|
|
680 |
"\n", |
|
|
681 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
682 |
" # get file name\n", |
|
|
683 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
684 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
685 |
"\n", |
|
|
686 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
687 |
"\n", |
|
|
688 |
" # load the dataset dictionary\n", |
|
|
689 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
690 |
" dictionary = json.loads(json_file.read())\n", |
|
|
691 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
692 |
" print(file_information)\n", |
|
|
693 |
"\n", |
|
|
694 |
" # get control points path from dataset dir\n", |
|
|
695 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
696 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
697 |
"\n", |
|
|
698 |
" # start the time only when the registration starts\n", |
|
|
699 |
" loop_start_time = time.time()\n", |
|
|
700 |
"\n", |
|
|
701 |
" # elastix registration\n", |
|
|
702 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
703 |
" register_elastix(\n", |
|
|
704 |
" fixed_path = i_path, \n", |
|
|
705 |
" moving_path = e_path, \n", |
|
|
706 |
" fMask = i_seg_path,\n", |
|
|
707 |
" mMask= e_seg_path,\n", |
|
|
708 |
" reg_params = reg_params,\n", |
|
|
709 |
" reg_params_key = reg_params_key,\n", |
|
|
710 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
711 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
712 |
"\n", |
|
|
713 |
" # transformix control point transformation\n", |
|
|
714 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
715 |
" output_path = control_points_transformix(\n", |
|
|
716 |
" fixed_path = i_path, \n", |
|
|
717 |
" moving_path = e_path,\n", |
|
|
718 |
" reg_params_key = reg_params_key,\n", |
|
|
719 |
" input_points = i_cntl_pt, \n", |
|
|
720 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
721 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
722 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
723 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
724 |
"\n", |
|
|
725 |
" loop_end_time = time.time()\n", |
|
|
726 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
727 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
728 |
"\n", |
|
|
729 |
" # get the transformed landmarks\n", |
|
|
730 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
731 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
732 |
"\n", |
|
|
733 |
" # write the landmarks into the output directory of the points\n", |
|
|
734 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
735 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
736 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
737 |
"\n", |
|
|
738 |
" # evaluate\n", |
|
|
739 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
740 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
741 |
" \n", |
|
|
742 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
743 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
744 |
" \n", |
|
|
745 |
"overall_end_time = time.time()\n", |
|
|
746 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
747 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
748 |
] |
|
|
749 |
}, |
|
|
750 |
{ |
|
|
751 |
"cell_type": "code", |
|
|
752 |
"execution_count": 9, |
|
|
753 |
"metadata": {}, |
|
|
754 |
"outputs": [ |
|
|
755 |
{ |
|
|
756 |
"name": "stdout", |
|
|
757 |
"output_type": "stream", |
|
|
758 |
"text": [ |
|
|
759 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt params command...\n", |
|
|
760 |
"Key for the experiment: Par0003.bs-R3-fg.txt...\n", |
|
|
761 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
762 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
763 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
764 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt -out \"output/Par0003.bs-R3-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
765 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
766 |
"Time for current registration loop: 0 minutes and 26 seconds\n", |
|
|
767 |
"Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
768 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
769 |
"TRE (After Registration):- (Mean TRE: 24.91) (STD TRE: 11.26). \n", |
|
|
770 |
"\n", |
|
|
771 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
772 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
773 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt -out \"output/Par0003.bs-R3-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
774 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
775 |
"Time for current registration loop: 0 minutes and 23 seconds\n", |
|
|
776 |
"Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
777 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
778 |
"TRE (After Registration):- (Mean TRE: 20.56) (STD TRE: 6.87). \n", |
|
|
779 |
"\n", |
|
|
780 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
781 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
782 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt -out \"output/Par0003.bs-R3-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
783 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
784 |
"Time for current registration loop: 0 minutes and 26 seconds\n", |
|
|
785 |
"Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
786 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
787 |
"TRE (After Registration):- (Mean TRE: 9.59) (STD TRE: 6.82). \n", |
|
|
788 |
"\n", |
|
|
789 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
790 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
791 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt -out \"output/Par0003.bs-R3-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
792 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
793 |
"Time for current registration loop: 0 minutes and 24 seconds\n", |
|
|
794 |
"Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
795 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
796 |
"TRE (After Registration):- (Mean TRE: 28.37) (STD TRE: 13.12). \n", |
|
|
797 |
"\n", |
|
|
798 |
"Time for overall registrations: 1 minutes and 41 seconds\n" |
|
|
799 |
] |
|
|
800 |
} |
|
|
801 |
], |
|
|
802 |
"source": [ |
|
|
803 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
804 |
"\n", |
|
|
805 |
"# Setting the experiment registration parameter\n", |
|
|
806 |
"params_list = [\n", |
|
|
807 |
" 'Par0003.bs-R3-fg.txt',\n", |
|
|
808 |
" ]\n", |
|
|
809 |
"\n", |
|
|
810 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
811 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
812 |
"\n", |
|
|
813 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
814 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
815 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
816 |
"\n", |
|
|
817 |
"overall_start_time = time.time()\n", |
|
|
818 |
"\n", |
|
|
819 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
820 |
" # get file name\n", |
|
|
821 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
822 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
823 |
"\n", |
|
|
824 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
825 |
"\n", |
|
|
826 |
" # load the dataset dictionary\n", |
|
|
827 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
828 |
" dictionary = json.loads(json_file.read())\n", |
|
|
829 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
830 |
" print(file_information)\n", |
|
|
831 |
"\n", |
|
|
832 |
" # get control points path from dataset dir\n", |
|
|
833 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
834 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
835 |
"\n", |
|
|
836 |
" # start the time only when the registration starts\n", |
|
|
837 |
" loop_start_time = time.time()\n", |
|
|
838 |
"\n", |
|
|
839 |
" # elastix registration\n", |
|
|
840 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
841 |
" register_elastix(\n", |
|
|
842 |
" fixed_path = i_path, \n", |
|
|
843 |
" moving_path = e_path, \n", |
|
|
844 |
" fMask = i_seg_path,\n", |
|
|
845 |
" mMask= e_seg_path,\n", |
|
|
846 |
" reg_params = reg_params,\n", |
|
|
847 |
" reg_params_key = reg_params_key,\n", |
|
|
848 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
849 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
850 |
"\n", |
|
|
851 |
" # transformix control point transformation\n", |
|
|
852 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
853 |
" output_path = control_points_transformix(\n", |
|
|
854 |
" fixed_path = i_path, \n", |
|
|
855 |
" moving_path = e_path,\n", |
|
|
856 |
" reg_params_key = reg_params_key,\n", |
|
|
857 |
" input_points = i_cntl_pt, \n", |
|
|
858 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
859 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
860 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
861 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
862 |
"\n", |
|
|
863 |
" loop_end_time = time.time()\n", |
|
|
864 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
865 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
866 |
"\n", |
|
|
867 |
" # get the transformed landmarks\n", |
|
|
868 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
869 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
870 |
"\n", |
|
|
871 |
" # write the landmarks into the output directory of the points\n", |
|
|
872 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
873 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
874 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
875 |
"\n", |
|
|
876 |
" # evaluate\n", |
|
|
877 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
878 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
879 |
" \n", |
|
|
880 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
881 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
882 |
" \n", |
|
|
883 |
"overall_end_time = time.time()\n", |
|
|
884 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
885 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
886 |
] |
|
|
887 |
}, |
|
|
888 |
{ |
|
|
889 |
"cell_type": "code", |
|
|
890 |
"execution_count": 10, |
|
|
891 |
"metadata": {}, |
|
|
892 |
"outputs": [ |
|
|
893 |
{ |
|
|
894 |
"name": "stdout", |
|
|
895 |
"output_type": "stream", |
|
|
896 |
"text": [ |
|
|
897 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt params command...\n", |
|
|
898 |
"Key for the experiment: Par0003.bs-R3-ug.txt...\n", |
|
|
899 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
900 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
901 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
902 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt -out \"output/Par0003.bs-R3-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
903 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
904 |
"Time for current registration loop: 0 minutes and 24 seconds\n", |
|
|
905 |
"Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
906 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
907 |
"TRE (After Registration):- (Mean TRE: 13.2) (STD TRE: 9.19). \n", |
|
|
908 |
"\n", |
|
|
909 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
910 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
911 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt -out \"output/Par0003.bs-R3-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
912 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
913 |
"Time for current registration loop: 0 minutes and 21 seconds\n", |
|
|
914 |
"Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
915 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
916 |
"TRE (After Registration):- (Mean TRE: 4.41) (STD TRE: 5.15). \n", |
|
|
917 |
"\n", |
|
|
918 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
919 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
920 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt -out \"output/Par0003.bs-R3-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
921 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
922 |
"Time for current registration loop: 0 minutes and 25 seconds\n", |
|
|
923 |
"Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
924 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
925 |
"TRE (After Registration):- (Mean TRE: 1.67) (STD TRE: 1.62). \n", |
|
|
926 |
"\n", |
|
|
927 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
928 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
929 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt -out \"output/Par0003.bs-R3-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
930 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
931 |
"Time for current registration loop: 0 minutes and 23 seconds\n", |
|
|
932 |
"Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
933 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
934 |
"TRE (After Registration):- (Mean TRE: 24.22) (STD TRE: 10.83). \n", |
|
|
935 |
"\n", |
|
|
936 |
"Time for overall registrations: 1 minutes and 34 seconds\n" |
|
|
937 |
] |
|
|
938 |
} |
|
|
939 |
], |
|
|
940 |
"source": [ |
|
|
941 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
942 |
"\n", |
|
|
943 |
"# Setting the experiment registration parameter\n", |
|
|
944 |
"params_list = [\n", |
|
|
945 |
" 'Par0003.bs-R3-ug.txt',\n", |
|
|
946 |
" ]\n", |
|
|
947 |
"\n", |
|
|
948 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
949 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
950 |
"\n", |
|
|
951 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
952 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
953 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
954 |
"\n", |
|
|
955 |
"overall_start_time = time.time()\n", |
|
|
956 |
"\n", |
|
|
957 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
958 |
" # get file name\n", |
|
|
959 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
960 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
961 |
"\n", |
|
|
962 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
963 |
"\n", |
|
|
964 |
" # load the dataset dictionary\n", |
|
|
965 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
966 |
" dictionary = json.loads(json_file.read())\n", |
|
|
967 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
968 |
" print(file_information)\n", |
|
|
969 |
"\n", |
|
|
970 |
" # get control points path from dataset dir\n", |
|
|
971 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
972 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
973 |
"\n", |
|
|
974 |
" # start the time only when the registration starts\n", |
|
|
975 |
" loop_start_time = time.time()\n", |
|
|
976 |
"\n", |
|
|
977 |
" # elastix registration\n", |
|
|
978 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
979 |
" register_elastix(\n", |
|
|
980 |
" fixed_path = i_path, \n", |
|
|
981 |
" moving_path = e_path, \n", |
|
|
982 |
" fMask = i_seg_path,\n", |
|
|
983 |
" mMask= e_seg_path,\n", |
|
|
984 |
" reg_params = reg_params,\n", |
|
|
985 |
" reg_params_key = reg_params_key,\n", |
|
|
986 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
987 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
988 |
"\n", |
|
|
989 |
" # transformix control point transformation\n", |
|
|
990 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
991 |
" output_path = control_points_transformix(\n", |
|
|
992 |
" fixed_path = i_path, \n", |
|
|
993 |
" moving_path = e_path,\n", |
|
|
994 |
" reg_params_key = reg_params_key,\n", |
|
|
995 |
" input_points = i_cntl_pt, \n", |
|
|
996 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
997 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
998 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
999 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1000 |
"\n", |
|
|
1001 |
" loop_end_time = time.time()\n", |
|
|
1002 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1003 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1004 |
"\n", |
|
|
1005 |
" # get the transformed landmarks\n", |
|
|
1006 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1007 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1008 |
"\n", |
|
|
1009 |
" # write the landmarks into the output directory of the points\n", |
|
|
1010 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1011 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1012 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1013 |
"\n", |
|
|
1014 |
" # evaluate\n", |
|
|
1015 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1016 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1017 |
" \n", |
|
|
1018 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1019 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1020 |
" \n", |
|
|
1021 |
"overall_end_time = time.time()\n", |
|
|
1022 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1023 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1024 |
] |
|
|
1025 |
}, |
|
|
1026 |
{ |
|
|
1027 |
"cell_type": "code", |
|
|
1028 |
"execution_count": 11, |
|
|
1029 |
"metadata": {}, |
|
|
1030 |
"outputs": [ |
|
|
1031 |
{ |
|
|
1032 |
"name": "stdout", |
|
|
1033 |
"output_type": "stream", |
|
|
1034 |
"text": [ |
|
|
1035 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt params command...\n", |
|
|
1036 |
"Key for the experiment: Par0003.bs-R4-fg.txt...\n", |
|
|
1037 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1038 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1039 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1040 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt -out \"output/Par0003.bs-R4-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1041 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1042 |
"Time for current registration loop: 0 minutes and 34 seconds\n", |
|
|
1043 |
"Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1044 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1045 |
"TRE (After Registration):- (Mean TRE: 24.33) (STD TRE: 10.93). \n", |
|
|
1046 |
"\n", |
|
|
1047 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1048 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1049 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt -out \"output/Par0003.bs-R4-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1050 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1051 |
"Time for current registration loop: 0 minutes and 29 seconds\n", |
|
|
1052 |
"Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1053 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1054 |
"TRE (After Registration):- (Mean TRE: 19.9) (STD TRE: 6.81). \n", |
|
|
1055 |
"\n", |
|
|
1056 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1057 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1058 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt -out \"output/Par0003.bs-R4-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1059 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1060 |
"Time for current registration loop: 0 minutes and 34 seconds\n", |
|
|
1061 |
"Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1062 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1063 |
"TRE (After Registration):- (Mean TRE: 8.18) (STD TRE: 6.89). \n", |
|
|
1064 |
"\n", |
|
|
1065 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1066 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1067 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt -out \"output/Par0003.bs-R4-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1068 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1069 |
"Time for current registration loop: 0 minutes and 31 seconds\n", |
|
|
1070 |
"Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1071 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1072 |
"TRE (After Registration):- (Mean TRE: 28.09) (STD TRE: 12.76). \n", |
|
|
1073 |
"\n", |
|
|
1074 |
"Time for overall registrations: 2 minutes and 10 seconds\n" |
|
|
1075 |
] |
|
|
1076 |
} |
|
|
1077 |
], |
|
|
1078 |
"source": [ |
|
|
1079 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1080 |
"\n", |
|
|
1081 |
"# Setting the experiment registration parameter\n", |
|
|
1082 |
"params_list = [\n", |
|
|
1083 |
" 'Par0003.bs-R4-fg.txt',\n", |
|
|
1084 |
" ]\n", |
|
|
1085 |
"\n", |
|
|
1086 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1087 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1088 |
"\n", |
|
|
1089 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1090 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1091 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1092 |
"\n", |
|
|
1093 |
"overall_start_time = time.time()\n", |
|
|
1094 |
"\n", |
|
|
1095 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1096 |
" # get file name\n", |
|
|
1097 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1098 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1099 |
"\n", |
|
|
1100 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1101 |
"\n", |
|
|
1102 |
" # load the dataset dictionary\n", |
|
|
1103 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1104 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1105 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1106 |
" print(file_information)\n", |
|
|
1107 |
"\n", |
|
|
1108 |
" # get control points path from dataset dir\n", |
|
|
1109 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1110 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1111 |
"\n", |
|
|
1112 |
" # start the time only when the registration starts\n", |
|
|
1113 |
" loop_start_time = time.time()\n", |
|
|
1114 |
"\n", |
|
|
1115 |
" # elastix registration\n", |
|
|
1116 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1117 |
" register_elastix(\n", |
|
|
1118 |
" fixed_path = i_path, \n", |
|
|
1119 |
" moving_path = e_path, \n", |
|
|
1120 |
" fMask = i_seg_path,\n", |
|
|
1121 |
" mMask= e_seg_path,\n", |
|
|
1122 |
" reg_params = reg_params,\n", |
|
|
1123 |
" reg_params_key = reg_params_key,\n", |
|
|
1124 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1125 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1126 |
"\n", |
|
|
1127 |
" # transformix control point transformation\n", |
|
|
1128 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1129 |
" output_path = control_points_transformix(\n", |
|
|
1130 |
" fixed_path = i_path, \n", |
|
|
1131 |
" moving_path = e_path,\n", |
|
|
1132 |
" reg_params_key = reg_params_key,\n", |
|
|
1133 |
" input_points = i_cntl_pt, \n", |
|
|
1134 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1135 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1136 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1137 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1138 |
"\n", |
|
|
1139 |
" loop_end_time = time.time()\n", |
|
|
1140 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1141 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1142 |
"\n", |
|
|
1143 |
" # get the transformed landmarks\n", |
|
|
1144 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1145 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1146 |
"\n", |
|
|
1147 |
" # write the landmarks into the output directory of the points\n", |
|
|
1148 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1149 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1150 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1151 |
"\n", |
|
|
1152 |
" # evaluate\n", |
|
|
1153 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1154 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1155 |
" \n", |
|
|
1156 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1157 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1158 |
" \n", |
|
|
1159 |
"overall_end_time = time.time()\n", |
|
|
1160 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1161 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1162 |
] |
|
|
1163 |
}, |
|
|
1164 |
{ |
|
|
1165 |
"cell_type": "code", |
|
|
1166 |
"execution_count": 12, |
|
|
1167 |
"metadata": {}, |
|
|
1168 |
"outputs": [ |
|
|
1169 |
{ |
|
|
1170 |
"name": "stdout", |
|
|
1171 |
"output_type": "stream", |
|
|
1172 |
"text": [ |
|
|
1173 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt params command...\n", |
|
|
1174 |
"Key for the experiment: Par0003.bs-R4-ug.txt...\n", |
|
|
1175 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1176 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1177 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1178 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt -out \"output/Par0003.bs-R4-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1179 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1180 |
"Time for current registration loop: 0 minutes and 30 seconds\n", |
|
|
1181 |
"Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1182 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1183 |
"TRE (After Registration):- (Mean TRE: 2.12) (STD TRE: 2.67). \n", |
|
|
1184 |
"\n", |
|
|
1185 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1186 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1187 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt -out \"output/Par0003.bs-R4-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1188 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1189 |
"Time for current registration loop: 0 minutes and 27 seconds\n", |
|
|
1190 |
"Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1191 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1192 |
"TRE (After Registration):- (Mean TRE: 3.58) (STD TRE: 5.25). \n", |
|
|
1193 |
"\n", |
|
|
1194 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1195 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1196 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt -out \"output/Par0003.bs-R4-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1197 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1198 |
"Time for current registration loop: 0 minutes and 32 seconds\n", |
|
|
1199 |
"Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1200 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1201 |
"TRE (After Registration):- (Mean TRE: 1.55) (STD TRE: 1.49). \n", |
|
|
1202 |
"\n", |
|
|
1203 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1204 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1205 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt -out \"output/Par0003.bs-R4-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1206 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1207 |
"Time for current registration loop: 0 minutes and 31 seconds\n", |
|
|
1208 |
"Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1209 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1210 |
"TRE (After Registration):- (Mean TRE: 1.86) (STD TRE: 1.45). \n", |
|
|
1211 |
"\n", |
|
|
1212 |
"Time for overall registrations: 2 minutes and 2 seconds\n" |
|
|
1213 |
] |
|
|
1214 |
} |
|
|
1215 |
], |
|
|
1216 |
"source": [ |
|
|
1217 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1218 |
"\n", |
|
|
1219 |
"# Setting the experiment registration parameter\n", |
|
|
1220 |
"params_list = [\n", |
|
|
1221 |
" 'Par0003.bs-R4-ug.txt',\n", |
|
|
1222 |
" ]\n", |
|
|
1223 |
"\n", |
|
|
1224 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1225 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1226 |
"\n", |
|
|
1227 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1228 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1229 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1230 |
"\n", |
|
|
1231 |
"overall_start_time = time.time()\n", |
|
|
1232 |
"\n", |
|
|
1233 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1234 |
" # get file name\n", |
|
|
1235 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1236 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1237 |
"\n", |
|
|
1238 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1239 |
"\n", |
|
|
1240 |
" # load the dataset dictionary\n", |
|
|
1241 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1242 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1243 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1244 |
" print(file_information)\n", |
|
|
1245 |
"\n", |
|
|
1246 |
" # get control points path from dataset dir\n", |
|
|
1247 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1248 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1249 |
"\n", |
|
|
1250 |
" # start the time only when the registration starts\n", |
|
|
1251 |
" loop_start_time = time.time()\n", |
|
|
1252 |
"\n", |
|
|
1253 |
" # elastix registration\n", |
|
|
1254 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1255 |
" register_elastix(\n", |
|
|
1256 |
" fixed_path = i_path, \n", |
|
|
1257 |
" moving_path = e_path, \n", |
|
|
1258 |
" fMask = i_seg_path,\n", |
|
|
1259 |
" mMask= e_seg_path,\n", |
|
|
1260 |
" reg_params = reg_params,\n", |
|
|
1261 |
" reg_params_key = reg_params_key,\n", |
|
|
1262 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1263 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1264 |
"\n", |
|
|
1265 |
" # transformix control point transformation\n", |
|
|
1266 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1267 |
" output_path = control_points_transformix(\n", |
|
|
1268 |
" fixed_path = i_path, \n", |
|
|
1269 |
" moving_path = e_path,\n", |
|
|
1270 |
" reg_params_key = reg_params_key,\n", |
|
|
1271 |
" input_points = i_cntl_pt, \n", |
|
|
1272 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1273 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1274 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1275 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1276 |
"\n", |
|
|
1277 |
" loop_end_time = time.time()\n", |
|
|
1278 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1279 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1280 |
"\n", |
|
|
1281 |
" # get the transformed landmarks\n", |
|
|
1282 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1283 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1284 |
"\n", |
|
|
1285 |
" # write the landmarks into the output directory of the points\n", |
|
|
1286 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1287 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1288 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1289 |
"\n", |
|
|
1290 |
" # evaluate\n", |
|
|
1291 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1292 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1293 |
" \n", |
|
|
1294 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1295 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1296 |
" \n", |
|
|
1297 |
"overall_end_time = time.time()\n", |
|
|
1298 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1299 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1300 |
] |
|
|
1301 |
}, |
|
|
1302 |
{ |
|
|
1303 |
"cell_type": "code", |
|
|
1304 |
"execution_count": 13, |
|
|
1305 |
"metadata": {}, |
|
|
1306 |
"outputs": [ |
|
|
1307 |
{ |
|
|
1308 |
"name": "stdout", |
|
|
1309 |
"output_type": "stream", |
|
|
1310 |
"text": [ |
|
|
1311 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt params command...\n", |
|
|
1312 |
"Key for the experiment: Par0003.bs-R5-fg.txt...\n", |
|
|
1313 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1314 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1315 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1316 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt -out \"output/Par0003.bs-R5-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1317 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1318 |
"Time for current registration loop: 0 minutes and 39 seconds\n", |
|
|
1319 |
"Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1320 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1321 |
"TRE (After Registration):- (Mean TRE: 23.26) (STD TRE: 10.34). \n", |
|
|
1322 |
"\n", |
|
|
1323 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1324 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1325 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt -out \"output/Par0003.bs-R5-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1326 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1327 |
"Time for current registration loop: 0 minutes and 35 seconds\n", |
|
|
1328 |
"Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1329 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1330 |
"TRE (After Registration):- (Mean TRE: 19.37) (STD TRE: 6.62). \n", |
|
|
1331 |
"\n", |
|
|
1332 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1333 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1334 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt -out \"output/Par0003.bs-R5-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1335 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1336 |
"Time for current registration loop: 0 minutes and 42 seconds\n", |
|
|
1337 |
"Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1338 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1339 |
"TRE (After Registration):- (Mean TRE: 7.61) (STD TRE: 6.38). \n", |
|
|
1340 |
"\n", |
|
|
1341 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1342 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1343 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt -out \"output/Par0003.bs-R5-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1344 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1345 |
"Time for current registration loop: 0 minutes and 39 seconds\n", |
|
|
1346 |
"Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1347 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1348 |
"TRE (After Registration):- (Mean TRE: 27.5) (STD TRE: 12.18). \n", |
|
|
1349 |
"\n", |
|
|
1350 |
"Time for overall registrations: 2 minutes and 37 seconds\n" |
|
|
1351 |
] |
|
|
1352 |
} |
|
|
1353 |
], |
|
|
1354 |
"source": [ |
|
|
1355 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1356 |
"\n", |
|
|
1357 |
"# Setting the experiment registration parameter\n", |
|
|
1358 |
"params_list = [\n", |
|
|
1359 |
" 'Par0003.bs-R5-fg.txt',\n", |
|
|
1360 |
" ]\n", |
|
|
1361 |
"\n", |
|
|
1362 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1363 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1364 |
"\n", |
|
|
1365 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1366 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1367 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1368 |
"\n", |
|
|
1369 |
"overall_start_time = time.time()\n", |
|
|
1370 |
"\n", |
|
|
1371 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1372 |
" # get file name\n", |
|
|
1373 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1374 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1375 |
"\n", |
|
|
1376 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1377 |
"\n", |
|
|
1378 |
" # load the dataset dictionary\n", |
|
|
1379 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1380 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1381 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1382 |
" print(file_information)\n", |
|
|
1383 |
"\n", |
|
|
1384 |
" # get control points path from dataset dir\n", |
|
|
1385 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1386 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1387 |
"\n", |
|
|
1388 |
" # start the time only when the registration starts\n", |
|
|
1389 |
" loop_start_time = time.time()\n", |
|
|
1390 |
"\n", |
|
|
1391 |
" # elastix registration\n", |
|
|
1392 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1393 |
" register_elastix(\n", |
|
|
1394 |
" fixed_path = i_path, \n", |
|
|
1395 |
" moving_path = e_path, \n", |
|
|
1396 |
" fMask = i_seg_path,\n", |
|
|
1397 |
" mMask= e_seg_path,\n", |
|
|
1398 |
" reg_params = reg_params,\n", |
|
|
1399 |
" reg_params_key = reg_params_key,\n", |
|
|
1400 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1401 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1402 |
"\n", |
|
|
1403 |
" # transformix control point transformation\n", |
|
|
1404 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1405 |
" output_path = control_points_transformix(\n", |
|
|
1406 |
" fixed_path = i_path, \n", |
|
|
1407 |
" moving_path = e_path,\n", |
|
|
1408 |
" reg_params_key = reg_params_key,\n", |
|
|
1409 |
" input_points = i_cntl_pt, \n", |
|
|
1410 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1411 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1412 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1413 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1414 |
"\n", |
|
|
1415 |
" loop_end_time = time.time()\n", |
|
|
1416 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1417 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1418 |
"\n", |
|
|
1419 |
" # get the transformed landmarks\n", |
|
|
1420 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1421 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1422 |
"\n", |
|
|
1423 |
" # write the landmarks into the output directory of the points\n", |
|
|
1424 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1425 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1426 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1427 |
"\n", |
|
|
1428 |
" # evaluate\n", |
|
|
1429 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1430 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1431 |
" \n", |
|
|
1432 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1433 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1434 |
" \n", |
|
|
1435 |
"overall_end_time = time.time()\n", |
|
|
1436 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1437 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1438 |
] |
|
|
1439 |
}, |
|
|
1440 |
{ |
|
|
1441 |
"cell_type": "code", |
|
|
1442 |
"execution_count": 14, |
|
|
1443 |
"metadata": {}, |
|
|
1444 |
"outputs": [ |
|
|
1445 |
{ |
|
|
1446 |
"name": "stdout", |
|
|
1447 |
"output_type": "stream", |
|
|
1448 |
"text": [ |
|
|
1449 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt params command...\n", |
|
|
1450 |
"Key for the experiment: Par0003.bs-R5-ug.txt...\n", |
|
|
1451 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1452 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1453 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1454 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt -out \"output/Par0003.bs-R5-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1455 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1456 |
"Time for current registration loop: 0 minutes and 40 seconds\n", |
|
|
1457 |
"Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1458 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1459 |
"TRE (After Registration):- (Mean TRE: 2.03) (STD TRE: 2.64). \n", |
|
|
1460 |
"\n", |
|
|
1461 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1462 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1463 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt -out \"output/Par0003.bs-R5-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1464 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1465 |
"Time for current registration loop: 0 minutes and 35 seconds\n", |
|
|
1466 |
"Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1467 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1468 |
"TRE (After Registration):- (Mean TRE: 3.58) (STD TRE: 5.3). \n", |
|
|
1469 |
"\n", |
|
|
1470 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1471 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1472 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt -out \"output/Par0003.bs-R5-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1473 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1474 |
"Time for current registration loop: 0 minutes and 39 seconds\n", |
|
|
1475 |
"Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1476 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1477 |
"TRE (After Registration):- (Mean TRE: 1.53) (STD TRE: 1.5). \n", |
|
|
1478 |
"\n", |
|
|
1479 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1480 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1481 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt -out \"output/Par0003.bs-R5-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1482 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1483 |
"Time for current registration loop: 0 minutes and 38 seconds\n", |
|
|
1484 |
"Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1485 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1486 |
"TRE (After Registration):- (Mean TRE: 1.8) (STD TRE: 1.4). \n", |
|
|
1487 |
"\n", |
|
|
1488 |
"Time for overall registrations: 2 minutes and 34 seconds\n" |
|
|
1489 |
] |
|
|
1490 |
} |
|
|
1491 |
], |
|
|
1492 |
"source": [ |
|
|
1493 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1494 |
"\n", |
|
|
1495 |
"# Setting the experiment registration parameter\n", |
|
|
1496 |
"params_list = [\n", |
|
|
1497 |
" 'Par0003.bs-R5-ug.txt',\n", |
|
|
1498 |
" ]\n", |
|
|
1499 |
"\n", |
|
|
1500 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1501 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1502 |
"\n", |
|
|
1503 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1504 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1505 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1506 |
"\n", |
|
|
1507 |
"overall_start_time = time.time()\n", |
|
|
1508 |
"\n", |
|
|
1509 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1510 |
" # get file name\n", |
|
|
1511 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1512 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1513 |
"\n", |
|
|
1514 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1515 |
"\n", |
|
|
1516 |
" # load the dataset dictionary\n", |
|
|
1517 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1518 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1519 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1520 |
" print(file_information)\n", |
|
|
1521 |
"\n", |
|
|
1522 |
" # get control points path from dataset dir\n", |
|
|
1523 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1524 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1525 |
"\n", |
|
|
1526 |
" # start the time only when the registration starts\n", |
|
|
1527 |
" loop_start_time = time.time()\n", |
|
|
1528 |
"\n", |
|
|
1529 |
" # elastix registration\n", |
|
|
1530 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1531 |
" register_elastix(\n", |
|
|
1532 |
" fixed_path = i_path, \n", |
|
|
1533 |
" moving_path = e_path, \n", |
|
|
1534 |
" fMask = i_seg_path,\n", |
|
|
1535 |
" mMask= e_seg_path,\n", |
|
|
1536 |
" reg_params = reg_params,\n", |
|
|
1537 |
" reg_params_key = reg_params_key,\n", |
|
|
1538 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1539 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1540 |
"\n", |
|
|
1541 |
" # transformix control point transformation\n", |
|
|
1542 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1543 |
" output_path = control_points_transformix(\n", |
|
|
1544 |
" fixed_path = i_path, \n", |
|
|
1545 |
" moving_path = e_path,\n", |
|
|
1546 |
" reg_params_key = reg_params_key,\n", |
|
|
1547 |
" input_points = i_cntl_pt, \n", |
|
|
1548 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1549 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1550 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1551 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1552 |
"\n", |
|
|
1553 |
" loop_end_time = time.time()\n", |
|
|
1554 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1555 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1556 |
"\n", |
|
|
1557 |
" # get the transformed landmarks\n", |
|
|
1558 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1559 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1560 |
"\n", |
|
|
1561 |
" # write the landmarks into the output directory of the points\n", |
|
|
1562 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1563 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1564 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1565 |
"\n", |
|
|
1566 |
" # evaluate\n", |
|
|
1567 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1568 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1569 |
" \n", |
|
|
1570 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1571 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1572 |
" \n", |
|
|
1573 |
"overall_end_time = time.time()\n", |
|
|
1574 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1575 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1576 |
] |
|
|
1577 |
}, |
|
|
1578 |
{ |
|
|
1579 |
"cell_type": "code", |
|
|
1580 |
"execution_count": 15, |
|
|
1581 |
"metadata": {}, |
|
|
1582 |
"outputs": [ |
|
|
1583 |
{ |
|
|
1584 |
"name": "stdout", |
|
|
1585 |
"output_type": "stream", |
|
|
1586 |
"text": [ |
|
|
1587 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt params command...\n", |
|
|
1588 |
"Key for the experiment: Par0003.bs-R6-fg.txt...\n", |
|
|
1589 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1590 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1591 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1592 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt -out \"output/Par0003.bs-R6-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1593 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1594 |
"Time for current registration loop: 0 minutes and 54 seconds\n", |
|
|
1595 |
"Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1596 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1597 |
"TRE (After Registration):- (Mean TRE: 22.67) (STD TRE: 9.65). \n", |
|
|
1598 |
"\n", |
|
|
1599 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1600 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1601 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt -out \"output/Par0003.bs-R6-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1602 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1603 |
"Time for current registration loop: 0 minutes and 45 seconds\n", |
|
|
1604 |
"Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1605 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1606 |
"TRE (After Registration):- (Mean TRE: 19.29) (STD TRE: 7.28). \n", |
|
|
1607 |
"\n", |
|
|
1608 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1609 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1610 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt -out \"output/Par0003.bs-R6-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1611 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1612 |
"Time for current registration loop: 0 minutes and 50 seconds\n", |
|
|
1613 |
"Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1614 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1615 |
"TRE (After Registration):- (Mean TRE: 7.23) (STD TRE: 5.93). \n", |
|
|
1616 |
"\n", |
|
|
1617 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1618 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1619 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt -out \"output/Par0003.bs-R6-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1620 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1621 |
"Time for current registration loop: 0 minutes and 46 seconds\n", |
|
|
1622 |
"Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1623 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1624 |
"TRE (After Registration):- (Mean TRE: 26.71) (STD TRE: 11.71). \n", |
|
|
1625 |
"\n", |
|
|
1626 |
"Time for overall registrations: 3 minutes and 17 seconds\n" |
|
|
1627 |
] |
|
|
1628 |
} |
|
|
1629 |
], |
|
|
1630 |
"source": [ |
|
|
1631 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1632 |
"\n", |
|
|
1633 |
"# Setting the experiment registration parameter\n", |
|
|
1634 |
"params_list = [\n", |
|
|
1635 |
" 'Par0003.bs-R6-fg.txt',\n", |
|
|
1636 |
" ]\n", |
|
|
1637 |
"\n", |
|
|
1638 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1639 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1640 |
"\n", |
|
|
1641 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1642 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1643 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1644 |
"\n", |
|
|
1645 |
"overall_start_time = time.time()\n", |
|
|
1646 |
"\n", |
|
|
1647 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1648 |
" # get file name\n", |
|
|
1649 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1650 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1651 |
"\n", |
|
|
1652 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1653 |
"\n", |
|
|
1654 |
" # load the dataset dictionary\n", |
|
|
1655 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1656 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1657 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1658 |
" print(file_information)\n", |
|
|
1659 |
"\n", |
|
|
1660 |
" # get control points path from dataset dir\n", |
|
|
1661 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1662 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1663 |
"\n", |
|
|
1664 |
" # start the time only when the registration starts\n", |
|
|
1665 |
" loop_start_time = time.time()\n", |
|
|
1666 |
"\n", |
|
|
1667 |
" # elastix registration\n", |
|
|
1668 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1669 |
" register_elastix(\n", |
|
|
1670 |
" fixed_path = i_path, \n", |
|
|
1671 |
" moving_path = e_path, \n", |
|
|
1672 |
" fMask = i_seg_path,\n", |
|
|
1673 |
" mMask= e_seg_path,\n", |
|
|
1674 |
" reg_params = reg_params,\n", |
|
|
1675 |
" reg_params_key = reg_params_key,\n", |
|
|
1676 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1677 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1678 |
"\n", |
|
|
1679 |
" # transformix control point transformation\n", |
|
|
1680 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1681 |
" output_path = control_points_transformix(\n", |
|
|
1682 |
" fixed_path = i_path, \n", |
|
|
1683 |
" moving_path = e_path,\n", |
|
|
1684 |
" reg_params_key = reg_params_key,\n", |
|
|
1685 |
" input_points = i_cntl_pt, \n", |
|
|
1686 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1687 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1688 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1689 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1690 |
"\n", |
|
|
1691 |
" loop_end_time = time.time()\n", |
|
|
1692 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1693 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1694 |
"\n", |
|
|
1695 |
" # get the transformed landmarks\n", |
|
|
1696 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1697 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1698 |
"\n", |
|
|
1699 |
" # write the landmarks into the output directory of the points\n", |
|
|
1700 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1701 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1702 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1703 |
"\n", |
|
|
1704 |
" # evaluate\n", |
|
|
1705 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1706 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1707 |
" \n", |
|
|
1708 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1709 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1710 |
" \n", |
|
|
1711 |
"overall_end_time = time.time()\n", |
|
|
1712 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1713 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1714 |
] |
|
|
1715 |
}, |
|
|
1716 |
{ |
|
|
1717 |
"cell_type": "code", |
|
|
1718 |
"execution_count": 16, |
|
|
1719 |
"metadata": {}, |
|
|
1720 |
"outputs": [ |
|
|
1721 |
{ |
|
|
1722 |
"name": "stdout", |
|
|
1723 |
"output_type": "stream", |
|
|
1724 |
"text": [ |
|
|
1725 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt params command...\n", |
|
|
1726 |
"Key for the experiment: Par0003.bs-R6-ug.txt...\n", |
|
|
1727 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1728 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1729 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1730 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt -out \"output/Par0003.bs-R6-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1731 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1732 |
"Time for current registration loop: 0 minutes and 46 seconds\n", |
|
|
1733 |
"Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1734 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1735 |
"TRE (After Registration):- (Mean TRE: 2.04) (STD TRE: 2.54). \n", |
|
|
1736 |
"\n", |
|
|
1737 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1738 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1739 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt -out \"output/Par0003.bs-R6-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1740 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1741 |
"Time for current registration loop: 0 minutes and 40 seconds\n", |
|
|
1742 |
"Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1743 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1744 |
"TRE (After Registration):- (Mean TRE: 3.67) (STD TRE: 5.46). \n", |
|
|
1745 |
"\n", |
|
|
1746 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1747 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1748 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt -out \"output/Par0003.bs-R6-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1749 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1750 |
"Time for current registration loop: 0 minutes and 47 seconds\n", |
|
|
1751 |
"Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1752 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1753 |
"TRE (After Registration):- (Mean TRE: 1.54) (STD TRE: 1.51). \n", |
|
|
1754 |
"\n", |
|
|
1755 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1756 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1757 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt -out \"output/Par0003.bs-R6-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1758 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1759 |
"Time for current registration loop: 0 minutes and 46 seconds\n", |
|
|
1760 |
"Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1761 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1762 |
"TRE (After Registration):- (Mean TRE: 1.77) (STD TRE: 1.37). \n", |
|
|
1763 |
"\n", |
|
|
1764 |
"Time for overall registrations: 3 minutes and 1 seconds\n" |
|
|
1765 |
] |
|
|
1766 |
} |
|
|
1767 |
], |
|
|
1768 |
"source": [ |
|
|
1769 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1770 |
"\n", |
|
|
1771 |
"# Setting the experiment registration parameter\n", |
|
|
1772 |
"params_list = [\n", |
|
|
1773 |
" 'Par0003.bs-R6-ug.txt',\n", |
|
|
1774 |
" ]\n", |
|
|
1775 |
"\n", |
|
|
1776 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1777 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1778 |
"\n", |
|
|
1779 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1780 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1781 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1782 |
"\n", |
|
|
1783 |
"overall_start_time = time.time()\n", |
|
|
1784 |
"\n", |
|
|
1785 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1786 |
" # get file name\n", |
|
|
1787 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1788 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1789 |
"\n", |
|
|
1790 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1791 |
"\n", |
|
|
1792 |
" # load the dataset dictionary\n", |
|
|
1793 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1794 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1795 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1796 |
" print(file_information)\n", |
|
|
1797 |
"\n", |
|
|
1798 |
" # get control points path from dataset dir\n", |
|
|
1799 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1800 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1801 |
"\n", |
|
|
1802 |
" # start the time only when the registration starts\n", |
|
|
1803 |
" loop_start_time = time.time()\n", |
|
|
1804 |
"\n", |
|
|
1805 |
" # elastix registration\n", |
|
|
1806 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1807 |
" register_elastix(\n", |
|
|
1808 |
" fixed_path = i_path, \n", |
|
|
1809 |
" moving_path = e_path, \n", |
|
|
1810 |
" fMask = i_seg_path,\n", |
|
|
1811 |
" mMask= e_seg_path,\n", |
|
|
1812 |
" reg_params = reg_params,\n", |
|
|
1813 |
" reg_params_key = reg_params_key,\n", |
|
|
1814 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1815 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1816 |
"\n", |
|
|
1817 |
" # transformix control point transformation\n", |
|
|
1818 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1819 |
" output_path = control_points_transformix(\n", |
|
|
1820 |
" fixed_path = i_path, \n", |
|
|
1821 |
" moving_path = e_path,\n", |
|
|
1822 |
" reg_params_key = reg_params_key,\n", |
|
|
1823 |
" input_points = i_cntl_pt, \n", |
|
|
1824 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1825 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1826 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1827 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1828 |
"\n", |
|
|
1829 |
" loop_end_time = time.time()\n", |
|
|
1830 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1831 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1832 |
"\n", |
|
|
1833 |
" # get the transformed landmarks\n", |
|
|
1834 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1835 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1836 |
"\n", |
|
|
1837 |
" # write the landmarks into the output directory of the points\n", |
|
|
1838 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1839 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1840 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1841 |
"\n", |
|
|
1842 |
" # evaluate\n", |
|
|
1843 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1844 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1845 |
" \n", |
|
|
1846 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1847 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1848 |
" \n", |
|
|
1849 |
"overall_end_time = time.time()\n", |
|
|
1850 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1851 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1852 |
] |
|
|
1853 |
}, |
|
|
1854 |
{ |
|
|
1855 |
"cell_type": "code", |
|
|
1856 |
"execution_count": 17, |
|
|
1857 |
"metadata": {}, |
|
|
1858 |
"outputs": [ |
|
|
1859 |
{ |
|
|
1860 |
"name": "stdout", |
|
|
1861 |
"output_type": "stream", |
|
|
1862 |
"text": [ |
|
|
1863 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt params command...\n", |
|
|
1864 |
"Key for the experiment: Par0003.bs-R7-fg.txt...\n", |
|
|
1865 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
1866 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
1867 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
1868 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt -out \"output/Par0003.bs-R7-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
1869 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1870 |
"Time for current registration loop: 0 minutes and 55 seconds\n", |
|
|
1871 |
"Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1872 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
1873 |
"TRE (After Registration):- (Mean TRE: 22.37) (STD TRE: 9.43). \n", |
|
|
1874 |
"\n", |
|
|
1875 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
1876 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
1877 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt -out \"output/Par0003.bs-R7-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
1878 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1879 |
"Time for current registration loop: 0 minutes and 50 seconds\n", |
|
|
1880 |
"Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1881 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
1882 |
"TRE (After Registration):- (Mean TRE: 19.28) (STD TRE: 7.45). \n", |
|
|
1883 |
"\n", |
|
|
1884 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
1885 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
1886 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt -out \"output/Par0003.bs-R7-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
1887 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1888 |
"Time for current registration loop: 1 minutes and 0 seconds\n", |
|
|
1889 |
"Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1890 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
1891 |
"TRE (After Registration):- (Mean TRE: 7.14) (STD TRE: 5.82). \n", |
|
|
1892 |
"\n", |
|
|
1893 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
1894 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
1895 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt -out \"output/Par0003.bs-R7-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
1896 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
1897 |
"Time for current registration loop: 0 minutes and 54 seconds\n", |
|
|
1898 |
"Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
1899 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
1900 |
"TRE (After Registration):- (Mean TRE: 25.81) (STD TRE: 11.66). \n", |
|
|
1901 |
"\n", |
|
|
1902 |
"Time for overall registrations: 3 minutes and 40 seconds\n" |
|
|
1903 |
] |
|
|
1904 |
} |
|
|
1905 |
], |
|
|
1906 |
"source": [ |
|
|
1907 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
1908 |
"\n", |
|
|
1909 |
"# Setting the experiment registration parameter\n", |
|
|
1910 |
"params_list = [\n", |
|
|
1911 |
" 'Par0003.bs-R7-fg.txt',\n", |
|
|
1912 |
" ]\n", |
|
|
1913 |
"\n", |
|
|
1914 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
1915 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
1916 |
"\n", |
|
|
1917 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
1918 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
1919 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
1920 |
"\n", |
|
|
1921 |
"overall_start_time = time.time()\n", |
|
|
1922 |
"\n", |
|
|
1923 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
1924 |
" # get file name\n", |
|
|
1925 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
1926 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
1927 |
"\n", |
|
|
1928 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
1929 |
"\n", |
|
|
1930 |
" # load the dataset dictionary\n", |
|
|
1931 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
1932 |
" dictionary = json.loads(json_file.read())\n", |
|
|
1933 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
1934 |
" print(file_information)\n", |
|
|
1935 |
"\n", |
|
|
1936 |
" # get control points path from dataset dir\n", |
|
|
1937 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
1938 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
1939 |
"\n", |
|
|
1940 |
" # start the time only when the registration starts\n", |
|
|
1941 |
" loop_start_time = time.time()\n", |
|
|
1942 |
"\n", |
|
|
1943 |
" # elastix registration\n", |
|
|
1944 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
1945 |
" register_elastix(\n", |
|
|
1946 |
" fixed_path = i_path, \n", |
|
|
1947 |
" moving_path = e_path, \n", |
|
|
1948 |
" fMask = i_seg_path,\n", |
|
|
1949 |
" mMask= e_seg_path,\n", |
|
|
1950 |
" reg_params = reg_params,\n", |
|
|
1951 |
" reg_params_key = reg_params_key,\n", |
|
|
1952 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
1953 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1954 |
"\n", |
|
|
1955 |
" # transformix control point transformation\n", |
|
|
1956 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
1957 |
" output_path = control_points_transformix(\n", |
|
|
1958 |
" fixed_path = i_path, \n", |
|
|
1959 |
" moving_path = e_path,\n", |
|
|
1960 |
" reg_params_key = reg_params_key,\n", |
|
|
1961 |
" input_points = i_cntl_pt, \n", |
|
|
1962 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
1963 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
1964 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
1965 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
1966 |
"\n", |
|
|
1967 |
" loop_end_time = time.time()\n", |
|
|
1968 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
1969 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
1970 |
"\n", |
|
|
1971 |
" # get the transformed landmarks\n", |
|
|
1972 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
1973 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
1974 |
"\n", |
|
|
1975 |
" # write the landmarks into the output directory of the points\n", |
|
|
1976 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
1977 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
1978 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
1979 |
"\n", |
|
|
1980 |
" # evaluate\n", |
|
|
1981 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1982 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
1983 |
" \n", |
|
|
1984 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
1985 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
1986 |
" \n", |
|
|
1987 |
"overall_end_time = time.time()\n", |
|
|
1988 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
1989 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
1990 |
] |
|
|
1991 |
}, |
|
|
1992 |
{ |
|
|
1993 |
"cell_type": "code", |
|
|
1994 |
"execution_count": 18, |
|
|
1995 |
"metadata": {}, |
|
|
1996 |
"outputs": [ |
|
|
1997 |
{ |
|
|
1998 |
"name": "stdout", |
|
|
1999 |
"output_type": "stream", |
|
|
2000 |
"text": [ |
|
|
2001 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt params command...\n", |
|
|
2002 |
"Key for the experiment: Par0003.bs-R7-ug.txt...\n", |
|
|
2003 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
2004 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
2005 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
2006 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt -out \"output/Par0003.bs-R7-ug.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
2007 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2008 |
"Time for current registration loop: 0 minutes and 51 seconds\n", |
|
|
2009 |
"Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2010 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
2011 |
"TRE (After Registration):- (Mean TRE: 2.05) (STD TRE: 2.56). \n", |
|
|
2012 |
"\n", |
|
|
2013 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
2014 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
2015 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt -out \"output/Par0003.bs-R7-ug.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
2016 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2017 |
"Time for current registration loop: 0 minutes and 46 seconds\n", |
|
|
2018 |
"Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2019 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
2020 |
"TRE (After Registration):- (Mean TRE: 3.64) (STD TRE: 5.48). \n", |
|
|
2021 |
"\n", |
|
|
2022 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
2023 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
2024 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt -out \"output/Par0003.bs-R7-ug.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
2025 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2026 |
"Time for current registration loop: 0 minutes and 54 seconds\n", |
|
|
2027 |
"Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2028 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
2029 |
"TRE (After Registration):- (Mean TRE: 1.53) (STD TRE: 1.48). \n", |
|
|
2030 |
"\n", |
|
|
2031 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
2032 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
2033 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt -out \"output/Par0003.bs-R7-ug.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
2034 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2035 |
"Time for current registration loop: 0 minutes and 53 seconds\n", |
|
|
2036 |
"Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2037 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
2038 |
"TRE (After Registration):- (Mean TRE: 1.77) (STD TRE: 1.37). \n", |
|
|
2039 |
"\n", |
|
|
2040 |
"Time for overall registrations: 3 minutes and 26 seconds\n" |
|
|
2041 |
] |
|
|
2042 |
} |
|
|
2043 |
], |
|
|
2044 |
"source": [ |
|
|
2045 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
2046 |
"\n", |
|
|
2047 |
"# Setting the experiment registration parameter\n", |
|
|
2048 |
"params_list = [\n", |
|
|
2049 |
" 'Par0003.bs-R7-ug.txt',\n", |
|
|
2050 |
" ]\n", |
|
|
2051 |
"\n", |
|
|
2052 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
2053 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
2054 |
"\n", |
|
|
2055 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
2056 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
2057 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
2058 |
"\n", |
|
|
2059 |
"overall_start_time = time.time()\n", |
|
|
2060 |
"\n", |
|
|
2061 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
2062 |
" # get file name\n", |
|
|
2063 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
2064 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
2065 |
"\n", |
|
|
2066 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
2067 |
"\n", |
|
|
2068 |
" # load the dataset dictionary\n", |
|
|
2069 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
2070 |
" dictionary = json.loads(json_file.read())\n", |
|
|
2071 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
2072 |
" print(file_information)\n", |
|
|
2073 |
"\n", |
|
|
2074 |
" # get control points path from dataset dir\n", |
|
|
2075 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
2076 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
2077 |
"\n", |
|
|
2078 |
" # start the time only when the registration starts\n", |
|
|
2079 |
" loop_start_time = time.time()\n", |
|
|
2080 |
"\n", |
|
|
2081 |
" # elastix registration\n", |
|
|
2082 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
2083 |
" register_elastix(\n", |
|
|
2084 |
" fixed_path = i_path, \n", |
|
|
2085 |
" moving_path = e_path, \n", |
|
|
2086 |
" fMask = i_seg_path,\n", |
|
|
2087 |
" mMask= e_seg_path,\n", |
|
|
2088 |
" reg_params = reg_params,\n", |
|
|
2089 |
" reg_params_key = reg_params_key,\n", |
|
|
2090 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
2091 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
2092 |
"\n", |
|
|
2093 |
" # transformix control point transformation\n", |
|
|
2094 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
2095 |
" output_path = control_points_transformix(\n", |
|
|
2096 |
" fixed_path = i_path, \n", |
|
|
2097 |
" moving_path = e_path,\n", |
|
|
2098 |
" reg_params_key = reg_params_key,\n", |
|
|
2099 |
" input_points = i_cntl_pt, \n", |
|
|
2100 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
2101 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
2102 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
2103 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
2104 |
"\n", |
|
|
2105 |
" loop_end_time = time.time()\n", |
|
|
2106 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
2107 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
2108 |
"\n", |
|
|
2109 |
" # get the transformed landmarks\n", |
|
|
2110 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
2111 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
2112 |
"\n", |
|
|
2113 |
" # write the landmarks into the output directory of the points\n", |
|
|
2114 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
2115 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
2116 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
2117 |
"\n", |
|
|
2118 |
" # evaluate\n", |
|
|
2119 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2120 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
2121 |
" \n", |
|
|
2122 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2123 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
2124 |
" \n", |
|
|
2125 |
"overall_end_time = time.time()\n", |
|
|
2126 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
2127 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
2128 |
] |
|
|
2129 |
}, |
|
|
2130 |
{ |
|
|
2131 |
"cell_type": "code", |
|
|
2132 |
"execution_count": 19, |
|
|
2133 |
"metadata": {}, |
|
|
2134 |
"outputs": [ |
|
|
2135 |
{ |
|
|
2136 |
"name": "stdout", |
|
|
2137 |
"output_type": "stream", |
|
|
2138 |
"text": [ |
|
|
2139 |
"Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt params command...\n", |
|
|
2140 |
"Key for the experiment: Par0003.bs-R8-fg.txt...\n", |
|
|
2141 |
"-----------------------------------------------------------------------------------------------------------------------------------------------\n", |
|
|
2142 |
"{'name': 'copd1', 'image_dim': [512, 512, 121], 'voxel_dim': [0.625, 0.625, 2.5], 'features': 773, 'displacement_mean': 25.9, 'displacement_std': 11.57, 'origin': [1, 1, 1]}\n", |
|
|
2143 |
"Registering copd1_eBHCT and copd1_iBHCT...\n", |
|
|
2144 |
"Excuting command: elastix -f \"../dataset/train/copd1/copd1_iBHCT.nii.gz\" -m \"../dataset/train/copd1/copd1_eBHCT.nii.gz\" -fMask ../dataset/train/copd1/copd1_iBHCT_lung.nii.gz -mMask ../dataset/train/copd1/copd1_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt -out \"output/Par0003.bs-R8-fg.txt/images/output_copd1_iBHCT/copd1_eBHCT\"\n", |
|
|
2145 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2146 |
"Time for current registration loop: 1 minutes and 3 seconds\n", |
|
|
2147 |
"Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2148 |
"TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", |
|
|
2149 |
"TRE (After Registration):- (Mean TRE: 22.45) (STD TRE: 9.52). \n", |
|
|
2150 |
"\n", |
|
|
2151 |
"{'name': 'copd2', 'image_dim': [512, 512, 102], 'voxel_dim': [0.645, 0.645, 2.5], 'features': 612, 'displacement_mean': 21.77, 'displacement_std': 6.46, 'origin': [1, 1, 1]}\n", |
|
|
2152 |
"Registering copd2_eBHCT and copd2_iBHCT...\n", |
|
|
2153 |
"Excuting command: elastix -f \"../dataset/train/copd2/copd2_iBHCT.nii.gz\" -m \"../dataset/train/copd2/copd2_eBHCT.nii.gz\" -fMask ../dataset/train/copd2/copd2_iBHCT_lung.nii.gz -mMask ../dataset/train/copd2/copd2_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt -out \"output/Par0003.bs-R8-fg.txt/images/output_copd2_iBHCT/copd2_eBHCT\"\n", |
|
|
2154 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2155 |
"Time for current registration loop: 0 minutes and 56 seconds\n", |
|
|
2156 |
"Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2157 |
"TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", |
|
|
2158 |
"TRE (After Registration):- (Mean TRE: 19.06) (STD TRE: 7.25). \n", |
|
|
2159 |
"\n", |
|
|
2160 |
"{'name': 'copd3', 'image_dim': [512, 512, 126], 'voxel_dim': [0.652, 0.652, 2.5], 'features': 1172, 'displacement_mean': 12.29, 'displacement_std': 6.39, 'origin': [1, 1, 1]}\n", |
|
|
2161 |
"Registering copd3_eBHCT and copd3_iBHCT...\n", |
|
|
2162 |
"Excuting command: elastix -f \"../dataset/train/copd3/copd3_iBHCT.nii.gz\" -m \"../dataset/train/copd3/copd3_eBHCT.nii.gz\" -fMask ../dataset/train/copd3/copd3_iBHCT_lung.nii.gz -mMask ../dataset/train/copd3/copd3_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt -out \"output/Par0003.bs-R8-fg.txt/images/output_copd3_iBHCT/copd3_eBHCT\"\n", |
|
|
2163 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2164 |
"Time for current registration loop: 1 minutes and 5 seconds\n", |
|
|
2165 |
"Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2166 |
"TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", |
|
|
2167 |
"TRE (After Registration):- (Mean TRE: 8.15) (STD TRE: 5.75). \n", |
|
|
2168 |
"\n", |
|
|
2169 |
"{'name': 'copd4', 'image_dim': [512, 512, 126], 'voxel_dim': [0.59, 0.59, 2.5], 'features': 786, 'displacement_mean': 30.9, 'displacement_std': 13.49, 'origin': [1, 1, 1]}\n", |
|
|
2170 |
"Registering copd4_eBHCT and copd4_iBHCT...\n", |
|
|
2171 |
"Excuting command: elastix -f \"../dataset/train/copd4/copd4_iBHCT.nii.gz\" -m \"../dataset/train/copd4/copd4_eBHCT.nii.gz\" -fMask ../dataset/train/copd4/copd4_iBHCT_lung.nii.gz -mMask ../dataset/train/copd4/copd4_eBHCT_lung.nii.gz -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt -out \"output/Par0003.bs-R8-fg.txt/images/output_copd4_iBHCT/copd4_eBHCT\"\n", |
|
|
2172 |
"Accessing the last transform parameter file TransformParameters.0.txt\n", |
|
|
2173 |
"Time for current registration loop: 1 minutes and 4 seconds\n", |
|
|
2174 |
"Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", |
|
|
2175 |
"TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", |
|
|
2176 |
"TRE (After Registration):- (Mean TRE: 27.31) (STD TRE: 10.6). \n", |
|
|
2177 |
"\n", |
|
|
2178 |
"Time for overall registrations: 4 minutes and 9 seconds\n" |
|
|
2179 |
] |
|
|
2180 |
} |
|
|
2181 |
], |
|
|
2182 |
"source": [ |
|
|
2183 |
"Par_base = '../elastix-parameters/Par0003'\n", |
|
|
2184 |
"\n", |
|
|
2185 |
"# Setting the experiment registration parameter\n", |
|
|
2186 |
"params_list = [\n", |
|
|
2187 |
" 'Par0003.bs-R8-fg.txt',\n", |
|
|
2188 |
" ]\n", |
|
|
2189 |
"\n", |
|
|
2190 |
"reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
2191 |
"reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
2192 |
"\n", |
|
|
2193 |
"print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
2194 |
"print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
2195 |
"print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
2196 |
"\n", |
|
|
2197 |
"overall_start_time = time.time()\n", |
|
|
2198 |
"\n", |
|
|
2199 |
"for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
2200 |
" # get file name\n", |
|
|
2201 |
" e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
2202 |
" i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
2203 |
"\n", |
|
|
2204 |
" sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
2205 |
"\n", |
|
|
2206 |
" # load the dataset dictionary\n", |
|
|
2207 |
" with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
2208 |
" dictionary = json.loads(json_file.read())\n", |
|
|
2209 |
" file_information = dictionary['train'][sample_name]\n", |
|
|
2210 |
" print(file_information)\n", |
|
|
2211 |
"\n", |
|
|
2212 |
" # get control points path from dataset dir\n", |
|
|
2213 |
" e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
2214 |
" i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
2215 |
"\n", |
|
|
2216 |
" # start the time only when the registration starts\n", |
|
|
2217 |
" loop_start_time = time.time()\n", |
|
|
2218 |
"\n", |
|
|
2219 |
" # elastix registration\n", |
|
|
2220 |
" print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
2221 |
" register_elastix(\n", |
|
|
2222 |
" fixed_path = i_path, \n", |
|
|
2223 |
" moving_path = e_path, \n", |
|
|
2224 |
" fMask = i_seg_path,\n", |
|
|
2225 |
" mMask= e_seg_path,\n", |
|
|
2226 |
" reg_params = reg_params,\n", |
|
|
2227 |
" reg_params_key = reg_params_key,\n", |
|
|
2228 |
" create_dir_callback = create_directory_if_not_exists,\n", |
|
|
2229 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
2230 |
"\n", |
|
|
2231 |
" # transformix control point transformation\n", |
|
|
2232 |
" print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
2233 |
" output_path = control_points_transformix(\n", |
|
|
2234 |
" fixed_path = i_path, \n", |
|
|
2235 |
" moving_path = e_path,\n", |
|
|
2236 |
" reg_params_key = reg_params_key,\n", |
|
|
2237 |
" input_points = i_cntl_pt, \n", |
|
|
2238 |
" transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
2239 |
" replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
2240 |
" create_dir_callback = create_directory_if_not_exists, \n", |
|
|
2241 |
" excute_cmd_callback = excute_cmd)\n", |
|
|
2242 |
"\n", |
|
|
2243 |
" loop_end_time = time.time()\n", |
|
|
2244 |
" loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
2245 |
" print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
2246 |
"\n", |
|
|
2247 |
" # get the transformed landmarks\n", |
|
|
2248 |
" landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
2249 |
" transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
2250 |
"\n", |
|
|
2251 |
" # write the landmarks into the output directory of the points\n", |
|
|
2252 |
" output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
2253 |
" write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
2254 |
" print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
2255 |
"\n", |
|
|
2256 |
" # evaluate\n", |
|
|
2257 |
" # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2258 |
" print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
2259 |
" \n", |
|
|
2260 |
" TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2261 |
" print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
2262 |
" \n", |
|
|
2263 |
"overall_end_time = time.time()\n", |
|
|
2264 |
"overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
2265 |
"print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" |
|
|
2266 |
] |
|
|
2267 |
}, |
|
|
2268 |
{ |
|
|
2269 |
"cell_type": "code", |
|
|
2270 |
"execution_count": 24, |
|
|
2271 |
"metadata": {}, |
|
|
2272 |
"outputs": [], |
|
|
2273 |
"source": [ |
|
|
2274 |
"# Par_base = '../elastix-parameters/Par0003'\n", |
|
|
2275 |
"\n", |
|
|
2276 |
"# # Setting the experiment registration parameter\n", |
|
|
2277 |
"# params_list = [\n", |
|
|
2278 |
"# 'Par0003.bs-R8-ug.txt',\n", |
|
|
2279 |
"# ]\n", |
|
|
2280 |
"\n", |
|
|
2281 |
"# reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", |
|
|
2282 |
"# reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", |
|
|
2283 |
"\n", |
|
|
2284 |
"# print(f\"Experimenting using {reg_params} params command...\")\n", |
|
|
2285 |
"# print(f\"Key for the experiment: {reg_params_key}...\")\n", |
|
|
2286 |
"# print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", |
|
|
2287 |
"\n", |
|
|
2288 |
"# overall_start_time = time.time()\n", |
|
|
2289 |
"\n", |
|
|
2290 |
"# for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", |
|
|
2291 |
"# # get file name\n", |
|
|
2292 |
"# e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", |
|
|
2293 |
"# i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", |
|
|
2294 |
"\n", |
|
|
2295 |
"# sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", |
|
|
2296 |
"\n", |
|
|
2297 |
"# # load the dataset dictionary\n", |
|
|
2298 |
"# with open('../dataset/description.json', 'r') as json_file:\n", |
|
|
2299 |
"# dictionary = json.loads(json_file.read())\n", |
|
|
2300 |
"# file_information = dictionary['train'][sample_name]\n", |
|
|
2301 |
"# print(file_information)\n", |
|
|
2302 |
"\n", |
|
|
2303 |
"# # get control points path from dataset dir\n", |
|
|
2304 |
"# e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", |
|
|
2305 |
"# i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", |
|
|
2306 |
"\n", |
|
|
2307 |
"# # start the time only when the registration starts\n", |
|
|
2308 |
"# loop_start_time = time.time()\n", |
|
|
2309 |
"\n", |
|
|
2310 |
"# # elastix registration\n", |
|
|
2311 |
"# print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", |
|
|
2312 |
"# register_elastix(\n", |
|
|
2313 |
"# fixed_path = i_path, \n", |
|
|
2314 |
"# moving_path = e_path, \n", |
|
|
2315 |
"# fMask = i_seg_path,\n", |
|
|
2316 |
"# mMask= e_seg_path,\n", |
|
|
2317 |
"# reg_params = reg_params,\n", |
|
|
2318 |
"# reg_params_key = reg_params_key,\n", |
|
|
2319 |
"# create_dir_callback = create_directory_if_not_exists,\n", |
|
|
2320 |
"# excute_cmd_callback = excute_cmd)\n", |
|
|
2321 |
"\n", |
|
|
2322 |
"# # transformix control point transformation\n", |
|
|
2323 |
"# print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", |
|
|
2324 |
"# output_path = control_points_transformix(\n", |
|
|
2325 |
"# fixed_path = i_path, \n", |
|
|
2326 |
"# moving_path = e_path,\n", |
|
|
2327 |
"# reg_params_key = reg_params_key,\n", |
|
|
2328 |
"# input_points = i_cntl_pt, \n", |
|
|
2329 |
"# transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", |
|
|
2330 |
"# replace_text_in_file_callback = replace_text_in_file,\n", |
|
|
2331 |
"# create_dir_callback = create_directory_if_not_exists, \n", |
|
|
2332 |
"# excute_cmd_callback = excute_cmd)\n", |
|
|
2333 |
"\n", |
|
|
2334 |
"# loop_end_time = time.time()\n", |
|
|
2335 |
"# loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", |
|
|
2336 |
"# print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", |
|
|
2337 |
"\n", |
|
|
2338 |
"# # get the transformed landmarks\n", |
|
|
2339 |
"# landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", |
|
|
2340 |
"# transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", |
|
|
2341 |
"\n", |
|
|
2342 |
"# # write the landmarks into the output directory of the points\n", |
|
|
2343 |
"# output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", |
|
|
2344 |
"# write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", |
|
|
2345 |
"# print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", |
|
|
2346 |
"\n", |
|
|
2347 |
"# # evaluate\n", |
|
|
2348 |
"# # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2349 |
"# print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", |
|
|
2350 |
" \n", |
|
|
2351 |
"# TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", |
|
|
2352 |
"# print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", |
|
|
2353 |
" \n", |
|
|
2354 |
"# overall_end_time = time.time()\n", |
|
|
2355 |
"# overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", |
|
|
2356 |
"# print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")\n", |
|
|
2357 |
"\n", |
|
|
2358 |
"# command fails: Description: itk::ERROR: AdvancedMattesMutualInformationMetric(0000000002B00790): Too many samples map outside moving image buffer: 499 / 2000" |
|
|
2359 |
] |
|
|
2360 |
}, |
|
|
2361 |
{ |
|
|
2362 |
"cell_type": "code", |
|
|
2363 |
"execution_count": null, |
|
|
2364 |
"metadata": {}, |
|
|
2365 |
"outputs": [], |
|
|
2366 |
"source": [] |
|
|
2367 |
} |
|
|
2368 |
], |
|
|
2369 |
"metadata": { |
|
|
2370 |
"kernelspec": { |
|
|
2371 |
"display_name": "env", |
|
|
2372 |
"language": "python", |
|
|
2373 |
"name": "python3" |
|
|
2374 |
}, |
|
|
2375 |
"language_info": { |
|
|
2376 |
"codemirror_mode": { |
|
|
2377 |
"name": "ipython", |
|
|
2378 |
"version": 3 |
|
|
2379 |
}, |
|
|
2380 |
"file_extension": ".py", |
|
|
2381 |
"mimetype": "text/x-python", |
|
|
2382 |
"name": "python", |
|
|
2383 |
"nbconvert_exporter": "python", |
|
|
2384 |
"pygments_lexer": "ipython3", |
|
|
2385 |
"version": "3.10.4" |
|
|
2386 |
} |
|
|
2387 |
}, |
|
|
2388 |
"nbformat": 4, |
|
|
2389 |
"nbformat_minor": 2 |
|
|
2390 |
} |