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--- a +++ b/notebooks/4_ElastixTransformix_experimenting.ipynb @@ -0,0 +1,2390 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import sys\n", + "sys.path.append('../')\n", + "\n", + "import os\n", + "import json\n", + "import time\n", + "from glob import glob\n", + "\n", + "from utils.elastix import excute_cmd, register_elastix, control_points_transformix\n", + "from utils.filemanager import create_directory_if_not_exists, replace_text_in_file, add_and_delete_rows, delete_added_rows\n", + "from utils.landmarks import get_landmarks_from_txt, write_landmarks_to_list\n", + "from utils.metrics import compute_TRE\n", + "from utils.utils import format_elapsed_time\n", + "\n", + "# To allow auto reload to this notebook after modifying any external file imported\n", + "%load_ext autoreload\n", + "%autoreload 2" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "['../dataset/train/copd1/copd1_eBHCT.nii.gz',\n", + " '../dataset/train/copd2/copd2_eBHCT.nii.gz',\n", + " '../dataset/train/copd3/copd3_eBHCT.nii.gz',\n", + " '../dataset/train/copd4/copd4_eBHCT.nii.gz']" + ] + }, + "execution_count": 2, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "train_path = '../dataset/train'\n", + "\n", + "# prepare the paths\n", + "exhale_volumes = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*eBHCT.nii.gz\"), recursive=True))]\n", + "inhale_volumes = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*iBHCT.nii.gz\"), recursive=True))]\n", + "\n", + "exhale_seg = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*eBHCT_lung.nii.gz\"), recursive=True))]\n", + "inhale_seg = [path.replace('\\\\', '/') for path in sorted(glob(os.path.join(train_path, \"***\" , \"*iBHCT_lung.nii.gz\"), recursive=True))]\n", + "\n", + "exhale_volumes" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.affine.txt params command...\n", + "Key for the experiment: Par0003.affine.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 30 seconds\n", + "Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 11.87) (STD TRE: 6.72). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 26 seconds\n", + "Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 10.96) (STD TRE: 4.92). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 31 seconds\n", + "Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 4.41) (STD TRE: 2.93). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 31 seconds\n", + "Transformed landmarks saved to: output/Par0003.affine.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 7.66) (STD TRE: 3.55). \n", + "\n", + "Time for overall registrations: 1 minutes and 59 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.affine.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R1-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R1-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 10 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 25.97) (STD TRE: 11.5). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 8 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 21.48) (STD TRE: 6.47). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 10 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 11.99) (STD TRE: 6.47). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 9 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 29.3) (STD TRE: 13.05). \n", + "\n", + "Time for overall registrations: 0 minutes and 39 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R1-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R1-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R1-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 9 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 25.97) (STD TRE: 11.5). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 8 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 21.48) (STD TRE: 6.47). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 9 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 11.99) (STD TRE: 6.47). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 9 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R1-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 29.3) (STD TRE: 13.05). \n", + "\n", + "Time for overall registrations: 0 minutes and 37 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R1-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R2-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R2-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 19 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 25.45) (STD TRE: 11.45). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 15 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 21.05) (STD TRE: 6.55). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 18 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 11.07) (STD TRE: 6.63). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 17 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 28.89) (STD TRE: 13.07). \n", + "\n", + "Time for overall registrations: 1 minutes and 10 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R2-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R2-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R2-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 17 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 23.74) (STD TRE: 11.18). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 15 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 18.93) (STD TRE: 6.88). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 17 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 6.38) (STD TRE: 6.02). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 17 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R2-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 27.81) (STD TRE: 13.32). \n", + "\n", + "Time for overall registrations: 1 minutes and 8 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R2-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R3-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R3-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 26 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 24.91) (STD TRE: 11.26). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 23 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 20.56) (STD TRE: 6.87). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 26 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 9.59) (STD TRE: 6.82). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 24 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 28.37) (STD TRE: 13.12). \n", + "\n", + "Time for overall registrations: 1 minutes and 41 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R3-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 10, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R3-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R3-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 24 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 13.2) (STD TRE: 9.19). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 21 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 4.41) (STD TRE: 5.15). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 25 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 1.67) (STD TRE: 1.62). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 23 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R3-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 24.22) (STD TRE: 10.83). \n", + "\n", + "Time for overall registrations: 1 minutes and 34 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R3-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R4-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R4-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 34 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 24.33) (STD TRE: 10.93). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 29 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 19.9) (STD TRE: 6.81). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 34 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 8.18) (STD TRE: 6.89). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 31 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 28.09) (STD TRE: 12.76). \n", + "\n", + "Time for overall registrations: 2 minutes and 10 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R4-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R4-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R4-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 30 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 2.12) (STD TRE: 2.67). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 27 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 3.58) (STD TRE: 5.25). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 32 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 1.55) (STD TRE: 1.49). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 31 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R4-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 1.86) (STD TRE: 1.45). \n", + "\n", + "Time for overall registrations: 2 minutes and 2 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R4-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 13, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R5-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R5-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 39 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 23.26) (STD TRE: 10.34). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 35 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 19.37) (STD TRE: 6.62). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 42 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 7.61) (STD TRE: 6.38). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 39 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 27.5) (STD TRE: 12.18). \n", + "\n", + "Time for overall registrations: 2 minutes and 37 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R5-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R5-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R5-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 40 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 2.03) (STD TRE: 2.64). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 35 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 3.58) (STD TRE: 5.3). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 39 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 1.53) (STD TRE: 1.5). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 38 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R5-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 1.8) (STD TRE: 1.4). \n", + "\n", + "Time for overall registrations: 2 minutes and 34 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R5-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R6-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R6-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 54 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 22.67) (STD TRE: 9.65). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 45 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 19.29) (STD TRE: 7.28). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 50 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 7.23) (STD TRE: 5.93). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 46 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 26.71) (STD TRE: 11.71). \n", + "\n", + "Time for overall registrations: 3 minutes and 17 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R6-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R6-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R6-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 46 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 2.04) (STD TRE: 2.54). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 40 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 3.67) (STD TRE: 5.46). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 47 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 1.54) (STD TRE: 1.51). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 46 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R6-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 1.77) (STD TRE: 1.37). \n", + "\n", + "Time for overall registrations: 3 minutes and 1 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R6-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 17, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R7-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R7-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 55 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 22.37) (STD TRE: 9.43). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 50 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 19.28) (STD TRE: 7.45). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 1 minutes and 0 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 7.14) (STD TRE: 5.82). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 54 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 25.81) (STD TRE: 11.66). \n", + "\n", + "Time for overall registrations: 3 minutes and 40 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R7-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R7-ug.txt params command...\n", + "Key for the experiment: Par0003.bs-R7-ug.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 51 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 2.05) (STD TRE: 2.56). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 46 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 3.64) (STD TRE: 5.48). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 54 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 1.53) (STD TRE: 1.48). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 53 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R7-ug.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 1.77) (STD TRE: 1.37). \n", + "\n", + "Time for overall registrations: 3 minutes and 26 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R7-ug.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 19, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Experimenting using -p ../elastix-parameters/Par0003/Par0003.bs-R8-fg.txt params command...\n", + "Key for the experiment: Par0003.bs-R8-fg.txt...\n", + "-----------------------------------------------------------------------------------------------------------------------------------------------\n", + "{'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", + "Registering copd1_eBHCT and copd1_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 1 minutes and 3 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd1_iBHCT/copd1_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 25.9) (STD TRE: 11.57).\n", + "TRE (After Registration):- (Mean TRE: 22.45) (STD TRE: 9.52). \n", + "\n", + "{'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", + "Registering copd2_eBHCT and copd2_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 0 minutes and 56 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd2_iBHCT/copd2_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 21.77) (STD TRE: 6.46).\n", + "TRE (After Registration):- (Mean TRE: 19.06) (STD TRE: 7.25). \n", + "\n", + "{'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", + "Registering copd3_eBHCT and copd3_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 1 minutes and 5 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd3_iBHCT/copd3_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 12.29) (STD TRE: 6.39).\n", + "TRE (After Registration):- (Mean TRE: 8.15) (STD TRE: 5.75). \n", + "\n", + "{'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", + "Registering copd4_eBHCT and copd4_iBHCT...\n", + "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", + "Accessing the last transform parameter file TransformParameters.0.txt\n", + "Time for current registration loop: 1 minutes and 4 seconds\n", + "Transformed landmarks saved to: output/Par0003.bs-R8-fg.txt/points/output_copd4_iBHCT/copd4_eBHCT\\outputpoints_transformed.txt\n", + "TRE (Before Registration):- (Mean TRE: 30.9) (STD TRE: 13.49).\n", + "TRE (After Registration):- (Mean TRE: 27.31) (STD TRE: 10.6). \n", + "\n", + "Time for overall registrations: 4 minutes and 9 seconds\n" + ] + } + ], + "source": [ + "Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# Setting the experiment registration parameter\n", + "params_list = [\n", + " 'Par0003.bs-R8-fg.txt',\n", + " ]\n", + "\n", + "reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "print(f\"Experimenting using {reg_params} params command...\")\n", + "print(f\"Key for the experiment: {reg_params_key}...\")\n", + "print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "overall_start_time = time.time()\n", + "\n", + "for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + " # get file name\n", + " e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + " i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + " sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + " # load the dataset dictionary\n", + " with open('../dataset/description.json', 'r') as json_file:\n", + " dictionary = json.loads(json_file.read())\n", + " file_information = dictionary['train'][sample_name]\n", + " print(file_information)\n", + "\n", + " # get control points path from dataset dir\n", + " e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + " i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + " # start the time only when the registration starts\n", + " loop_start_time = time.time()\n", + "\n", + " # elastix registration\n", + " print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + " register_elastix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path, \n", + " fMask = i_seg_path,\n", + " mMask= e_seg_path,\n", + " reg_params = reg_params,\n", + " reg_params_key = reg_params_key,\n", + " create_dir_callback = create_directory_if_not_exists,\n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " # transformix control point transformation\n", + " print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + " output_path = control_points_transformix(\n", + " fixed_path = i_path, \n", + " moving_path = e_path,\n", + " reg_params_key = reg_params_key,\n", + " input_points = i_cntl_pt, \n", + " transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + " replace_text_in_file_callback = replace_text_in_file,\n", + " create_dir_callback = create_directory_if_not_exists, \n", + " excute_cmd_callback = excute_cmd)\n", + "\n", + " loop_end_time = time.time()\n", + " loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + " print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + " # get the transformed landmarks\n", + " landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + " transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + " # write the landmarks into the output directory of the points\n", + " output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + " write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + " print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + " # evaluate\n", + " # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + " TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + " print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "overall_end_time = time.time()\n", + "overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")" + ] + }, + { + "cell_type": "code", + "execution_count": 24, + "metadata": {}, + "outputs": [], + "source": [ + "# Par_base = '../elastix-parameters/Par0003'\n", + "\n", + "# # Setting the experiment registration parameter\n", + "# params_list = [\n", + "# 'Par0003.bs-R8-ug.txt',\n", + "# ]\n", + "\n", + "# reg_params = ' '.join(['-p {}'.format(os.path.join(Par_base,param)) for param in params_list]).replace('\\\\', '/')\n", + "# reg_params_key = '+'.join(['{}'.format(param) for param in params_list])\n", + "\n", + "# print(f\"Experimenting using {reg_params} params command...\")\n", + "# print(f\"Key for the experiment: {reg_params_key}...\")\n", + "# print( \"-----------------------------------------------------------------------------------------------------------------------------------------------\")\n", + "\n", + "# overall_start_time = time.time()\n", + "\n", + "# for e_path, i_path, e_seg_path, i_seg_path in zip(exhale_volumes, inhale_volumes, exhale_seg, inhale_seg):\n", + "# # get file name\n", + "# e_filename_full = e_path.split('/')[-1].split('.')[0] #copd1_eBHCT, ..\n", + "# i_filename_full = i_path.split('/')[-1].split('.')[0] #copd1_iBHCT, ..\n", + "\n", + "# sample_name = i_path.split('/')[-1].split('_')[0] #copd1, copd2, ...\n", + "\n", + "# # load the dataset dictionary\n", + "# with open('../dataset/description.json', 'r') as json_file:\n", + "# dictionary = json.loads(json_file.read())\n", + "# file_information = dictionary['train'][sample_name]\n", + "# print(file_information)\n", + "\n", + "# # get control points path from dataset dir\n", + "# e_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_eBH_xyz_r1.txt'\n", + "# i_cntl_pt = f'../dataset/train/{sample_name}/{sample_name}_300_iBH_xyz_r1.txt'\n", + "\n", + "# # start the time only when the registration starts\n", + "# loop_start_time = time.time()\n", + "\n", + "# # elastix registration\n", + "# print(f\"Registering {e_filename_full} and {i_filename_full}...\") \n", + "# register_elastix(\n", + "# fixed_path = i_path, \n", + "# moving_path = e_path, \n", + "# fMask = i_seg_path,\n", + "# mMask= e_seg_path,\n", + "# reg_params = reg_params,\n", + "# reg_params_key = reg_params_key,\n", + "# create_dir_callback = create_directory_if_not_exists,\n", + "# excute_cmd_callback = excute_cmd)\n", + "\n", + "# # transformix control point transformation\n", + "# print(f\"Accessing the last transform parameter file TransformParameters.{len(params_list)-1}.txt\")\n", + "# output_path = control_points_transformix(\n", + "# fixed_path = i_path, \n", + "# moving_path = e_path,\n", + "# reg_params_key = reg_params_key,\n", + "# input_points = i_cntl_pt, \n", + "# transform_path = f'output/{reg_params_key}/images/output_{i_filename_full}/{e_filename_full}/TransformParameters.{len(params_list)-1}.txt',\n", + "# replace_text_in_file_callback = replace_text_in_file,\n", + "# create_dir_callback = create_directory_if_not_exists, \n", + "# excute_cmd_callback = excute_cmd)\n", + "\n", + "# loop_end_time = time.time()\n", + "# loop_elapsed_minutes, loop_elapsed_seconds = format_elapsed_time(loop_start_time, loop_end_time)\n", + "# print(f\"Time for current registration loop: {loop_elapsed_minutes} minutes and {loop_elapsed_seconds} seconds\")\n", + "\n", + "# # get the transformed landmarks\n", + "# landmarks_path = os.path.join(output_path, 'outputpoints.txt')\n", + "# transformed_landmarks = get_landmarks_from_txt(landmarks_path, search_key='OutputIndexFixed')\n", + "\n", + "# # write the landmarks into the output directory of the points\n", + "# output_landmarks_path = os.path.join(output_path, 'outputpoints_transformed.txt')\n", + "# write_landmarks_to_list(transformed_landmarks, output_landmarks_path)\n", + "# print(\"Transformed landmarks saved to: \", output_landmarks_path)\n", + "\n", + "# # evaluate\n", + "# # TRE_mean, TRE_std = compute_TRE(i_cntl_pt, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + "# print(\"TRE (Before Registration):- \", f\"(Mean TRE: {file_information['displacement_mean']})\", f\"(STD TRE: {file_information['displacement_std']}).\")\n", + " \n", + "# TRE_mean, TRE_std = compute_TRE(output_landmarks_path, e_cntl_pt, tuple(file_information['voxel_dim']))\n", + "# print(\"TRE (After Registration):- \", f\"(Mean TRE: {TRE_mean})\", f\"(STD TRE: {TRE_std}). \\n\")\\\n", + " \n", + "# overall_end_time = time.time()\n", + "# overall_elapsed_minutes, overall_elapsed_seconds = format_elapsed_time(overall_start_time, overall_end_time)\n", + "# print(f\"Time for overall registrations: {overall_elapsed_minutes} minutes and {overall_elapsed_seconds} seconds\")\n", + "\n", + "# command fails: Description: itk::ERROR: AdvancedMattesMutualInformationMetric(0000000002B00790): Too many samples map outside moving image buffer: 499 / 2000" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "env", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.10.4" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +}