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registration_params.py
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### Ecosystem Imports ###
import os
import sys
sys.path.append(os.path.join(os.path.dirname(__file__), "."))
sys.path.append(os.path.join(os.path.dirname(__file__), ".."))
import pathlib
import json
### External Imports ###
import numpy as np
### Internal Imports ###
########################
def create_identity():
params = dict()
params['device'] = "cpu"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Identity"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 2048
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = False
preprocessing_params['save_results'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "identity_initial_alignment"
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "identity_nonrigid_registration"
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_initial():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 2048
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "multi_feature"
initial_registration_params['registration_size'] = 620
initial_registration_params['registration_sizes'] = [150, 200, 250, 300, 350, 400, 450, 500]
initial_registration_params['transform_type'] = 'rigid'
initial_registration_params['keypoint_threshold'] = 0.005
initial_registration_params['match_threshold'] = 0.3
initial_registration_params['sinkhorn_iterations'] = 50
initial_registration_params['show'] = False
initial_registration_params['angle_step'] = 60
initial_registration_params['cuda'] = False if params['device'] == "cpu" else True
initial_registration_params['device'] = params['device']
initial_registration_params['echo'] = False
initial_registration_params['run_sift_ransac'] = True
initial_registration_params['run_superpoint_superglue'] = True
initial_registration_params['run_superpoint_ransac'] = False
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = False
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = False
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_initial_fast():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 2048
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "multi_feature"
initial_registration_params['registration_size'] = 620
initial_registration_params['registration_sizes'] = [150, 200, 250, 300, 400]
initial_registration_params['transform_type'] = 'rigid'
initial_registration_params['keypoint_threshold'] = 0.005
initial_registration_params['match_threshold'] = 0.3
initial_registration_params['sinkhorn_iterations'] = 50
initial_registration_params['show'] = False
initial_registration_params['angle_step'] = 180
initial_registration_params['cuda'] = False if params['device'] == "cpu" else True
initial_registration_params['device'] = params['device']
initial_registration_params['echo'] = False
initial_registration_params['run_sift_ransac'] = False
initial_registration_params['run_superpoint_superglue'] = True
initial_registration_params['run_superpoint_ransac'] = False
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = False
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = False
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_nonrigid():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 4096
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "identity_initial_alignment"
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 4096
nonrigid_registration_params['num_levels'] = 8
nonrigid_registration_params['used_levels'] = 8
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100, 200]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0015]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.8]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_nonrigid_fast():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 2048
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "identity_initial_alignment"
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 2048
nonrigid_registration_params['num_levels'] = 7
nonrigid_registration_params['used_levels'] = 7
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_nonrigid_high_resolution():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 8192
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "identity_initial_alignment"
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 8192
nonrigid_registration_params['num_levels'] = 9
nonrigid_registration_params['used_levels'] = 9
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100, 200, 200]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0015, 0.001]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.8, 2.1]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_initial_nonrigid():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 4096
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "multi_feature"
initial_registration_params['registration_size'] = 620
initial_registration_params['registration_sizes'] = [150, 200, 250, 300, 350, 400, 450, 500]
initial_registration_params['transform_type'] = 'rigid'
initial_registration_params['keypoint_threshold'] = 0.005
initial_registration_params['match_threshold'] = 0.3
initial_registration_params['sinkhorn_iterations'] = 50
initial_registration_params['show'] = False
initial_registration_params['angle_step'] = 90
initial_registration_params['cuda'] = False if params['device'] == "cpu" else True
initial_registration_params['device'] = params['device']
initial_registration_params['echo'] = False
initial_registration_params['run_sift_ransac'] = True
initial_registration_params['run_superpoint_superglue'] = True
initial_registration_params['run_superpoint_ransac'] = False
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 4096
nonrigid_registration_params['num_levels'] = 8
nonrigid_registration_params['used_levels'] = 8
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100, 200]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0015]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.8]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_initial_nonrigid_fast():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 2048
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "multi_feature"
initial_registration_params['registration_size'] = 620
initial_registration_params['registration_sizes'] = [150, 200, 250, 300, 350, 400]
initial_registration_params['transform_type'] = 'rigid'
initial_registration_params['keypoint_threshold'] = 0.005
initial_registration_params['match_threshold'] = 0.3
initial_registration_params['sinkhorn_iterations'] = 50
initial_registration_params['show'] = False
initial_registration_params['angle_step'] = 180
initial_registration_params['cuda'] = False if params['device'] == "cpu" else True
initial_registration_params['device'] = params['device']
initial_registration_params['echo'] = False
initial_registration_params['run_sift_ransac'] = False
initial_registration_params['run_superpoint_superglue'] = True
initial_registration_params['run_superpoint_ransac'] = False
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 2048
nonrigid_registration_params['num_levels'] = 7
nonrigid_registration_params['used_levels'] = 7
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def default_initial_nonrigid_high_resolution():
params = dict()
params['device'] = "cuda:0"
params['echo'] = False
params['save_final_images'] = True
params['save_final_displacement_field'] = True
params['case_name'] = "Default_Nonrigid"
params['logging_path'] = None
### Loading Params ###
loading_params = dict()
loading_params['final_level'] = 0
loading_params['pad_value'] = 255.0
loading_params['loader'] = 'tiff'
loading_params['source_resample_ratio'] = 0.2
loading_params['target_resample_ratio'] = 0.2
params['loading_params'] = loading_params
### Saving Params ###
saving_params = dict()
saving_params['saver'] = 'pil'
saving_params['final_saver'] = 'tiff'
saving_params['save_params'] = 'pil'
saving_params['extension'] = ".jpg"
saving_params['final_extension'] = ".tiff"
params['saving_params'] = saving_params
### Preprocessing params ###
preprocessing_params = dict()
preprocessing_params['preprocessing_function'] = "basic_preprocessing"
preprocessing_params['initial_resampling'] = True
preprocessing_params['initial_resolution'] = 8192
preprocessing_params['normalization'] = True
preprocessing_params['convert_to_gray'] = True
preprocessing_params['clahe'] = True
preprocessing_params['save_results'] = True
preprocessing_params['flip_intensity'] = True
params['preprocessing_params'] = preprocessing_params
### Initial registration params ###
run_initial_registration = True
initial_registration_params = dict()
initial_registration_params['save_results'] = True
initial_registration_params['initial_registration_function'] = "multi_feature"
initial_registration_params['registration_size'] = 620
initial_registration_params['registration_sizes'] = [150, 200, 250, 300, 350, 400, 450, 500, 600]
initial_registration_params['transform_type'] = 'rigid'
initial_registration_params['keypoint_threshold'] = 0.005
initial_registration_params['match_threshold'] = 0.3
initial_registration_params['sinkhorn_iterations'] = 50
initial_registration_params['show'] = False
initial_registration_params['angle_step'] = 60
initial_registration_params['cuda'] = False if params['device'] == "cpu" else True
initial_registration_params['device'] = params['device']
initial_registration_params['echo'] = False
initial_registration_params['run_sift_ransac'] = True
initial_registration_params['run_superpoint_superglue'] = True
initial_registration_params['run_superpoint_ransac'] = False
params['run_initial_registration'] = run_initial_registration
params['initial_registration_params'] = initial_registration_params
### Nonrigid registration params ###
run_nonrigid_registration = True
nonrigid_registration_params = dict()
nonrigid_registration_params['save_results'] = True
nonrigid_registration_params['nonrigid_registration_function'] = "instance_optimization_nonrigid_registration"
nonrigid_registration_params['device'] = params['device']
nonrigid_registration_params['echo'] = False
nonrigid_registration_params['cost_function'] = "ncc_local"
nonrigid_registration_params['cost_function_params'] = {'win_size' : 7}
nonrigid_registration_params['regularization_function'] = "diffusion_relative"
nonrigid_registration_params['regularization_function_params'] = dict()
nonrigid_registration_params['registration_size'] = 8192
nonrigid_registration_params['num_levels'] = 9
nonrigid_registration_params['used_levels'] = 9
nonrigid_registration_params['iterations'] = [100, 100, 100, 100, 100, 100, 100, 200, 200]
nonrigid_registration_params['learning_rates'] = [0.005, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0025, 0.0015, 0.001]
nonrigid_registration_params['alphas'] = [1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.5, 1.8, 2.1]
params['run_nonrigid_registration'] = run_nonrigid_registration
params['nonrigid_registration_params'] = nonrigid_registration_params
############################################
return params
def save_params(params, parameters_path):
with open(parameters_path, "w") as to_save:
json.dump(params, to_save)
def load_parameters(parameters_path=None):
if parameters_path is None:
return create_identity() #TODO - replace with create_default()
with open(parameters_path, "r") as to_load:
params = json.loads(to_load.read())
return params
if __name__ == "__main__":
# save_params(default_initial(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_initial.json"))
# save_params(default_initial_fast(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_initial_fast.json"))
# save_params(default_nonrigid(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_nonrigid.json"))
# save_params(default_nonrigid_fast(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_nonrigid_fast.json"))
# save_params(default_nonrigid_high_resolution(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_nonrigid_high_resolution.json"))
# save_params(default_initial_nonrigid(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_initial_nonrigid.json"))
# save_params(default_initial_nonrigid_fast(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_initial_nonrigid_fast.json"))
# save_params(default_initial_nonrigid_high_resolution(), os.path.join(os.path.dirname(os.path.abspath(__file__)), "default_initial_nonrigid_high_resolution.json"))
pass