Renamed module to ddmr

Brain_study/ABSTRACT/figures.py

@@ -10,7 +10,7 @@ from matplotlib import cm
 from matplotlib.colors import ListedColormap, LinearSegmentedColormap, to_rgba, CSS4_COLORS
 import tikzplotlib
 
-from DeepDeformationMapRegistration.utils.misc import segmentation_ohe_to_cardinal
+from ddmr.utils.misc import segmentation_ohe_to_cardinal
 
 # segm_cm = np.asarray([to_rgba(CSS4_COLORS[c], 1) for c in CSS4_COLORS.keys()])
 # # segm_cm.sort()

Brain_study/Build_test_set.py

@@ -14,11 +14,11 @@ import tensorflow as tf
 import numpy as np
 import h5py
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-from DeepDeformationMapRegistration.utils.misc import get_segmentations_centroids, DisplacementMapInterpolator
+import ddmr.utils.constants as C
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers import AugmentationLayer
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+from ddmr.utils.misc import get_segmentations_centroids, DisplacementMapInterpolator
 
 from tqdm import tqdm
 

Brain_study/Evaluate_network.py

@@ -16,14 +16,14 @@ import numpy as np
 import pandas as pd
 import voxelmorph as vxm
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-from DeepDeformationMapRegistration.utils.misc import segmentation_ohe_to_cardinal
+import ddmr.utils.constants as C
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers import AugmentationLayer
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+from ddmr.utils.misc import segmentation_ohe_to_cardinal
 from EvaluationScripts.Evaluate_class import EvaluationFigures, resize_pts_to_original_space, resize_img_to_original_space, resize_transformation
 from scipy.interpolate import RegularGridInterpolator
 from tqdm import tqdm

Brain_study/Evaluate_network__test_fixed.py

@@ -17,16 +17,16 @@ import numpy as np
 import pandas as pd
 import voxelmorph as vxm
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.operators import min_max_norm, safe_medpy_metric
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.layers import AugmentationLayer, UncertaintyWeighting
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-from DeepDeformationMapRegistration.utils.misc import resize_displacement_map, scale_transformation
-from DeepDeformationMapRegistration.utils.misc import DisplacementMapInterpolator, get_segmentations_centroids, segmentation_ohe_to_cardinal
+import ddmr.utils.constants as C
+from ddmr.utils.operators import min_max_norm, safe_medpy_metric
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers import AugmentationLayer, UncertaintyWeighting
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+from ddmr.utils.misc import resize_displacement_map, scale_transformation
+from ddmr.utils.misc import DisplacementMapInterpolator, get_segmentations_centroids, segmentation_ohe_to_cardinal
 from EvaluationScripts.Evaluate_class import EvaluationFigures, resize_pts_to_original_space, resize_img_to_original_space, resize_transformation
 from scipy.ndimage import zoom
 from tqdm import tqdm

Brain_study/MultiTrain_config.py

@@ -7,7 +7,7 @@ import argparse
 from configparser import ConfigParser
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 
 TRAIN_DATASET = '/mnt/EncryptedData1/Users/javier/ext_datasets/IXI_dataset/T1/training'
 

Brain_study/Train_Baseline.py

@@ -19,13 +19,13 @@ import neurite as ne
 import h5py
 import pickle
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.losses import NCC, StructuralSimilarity, StructuralSimilarity_simplified
-from DeepDeformationMapRegistration.utils.misc import try_mkdir, DatasetCopy, function_decorator
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
+import ddmr.utils.constants as C
+from ddmr.losses import NCC, StructuralSimilarity, StructuralSimilarity_simplified
+from ddmr.utils.misc import try_mkdir, DatasetCopy, function_decorator
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.layers import AugmentationLayer
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

Brain_study/Train_SegmentationGuided.py

@@ -18,13 +18,13 @@ import h5py
 from datetime import datetime
 import pickle
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.misc import try_mkdir, function_decorator
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.losses import NCC, HausdorffDistanceErosion, GeneralizedDICEScore, StructuralSimilarity_simplified
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
+import ddmr.utils.constants as C
+from ddmr.utils.misc import try_mkdir, function_decorator
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.losses import NCC, HausdorffDistanceErosion, GeneralizedDICEScore, StructuralSimilarity_simplified
+from ddmr.layers import AugmentationLayer
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

Brain_study/Train_UncertaintyWeighted.py

@@ -16,13 +16,13 @@ import h5py
 from datetime import datetime
 import pickle
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.misc import try_mkdir, DatasetCopy, function_decorator
-from DeepDeformationMapRegistration.networks import WeaklySupervised
-from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion, NCC, StructuralSimilarity_simplified, GeneralizedDICEScore
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
-from DeepDeformationMapRegistration.layers import UncertaintyWeighting, AugmentationLayer
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
+import ddmr.utils.constants as C
+from ddmr.utils.misc import try_mkdir, DatasetCopy, function_decorator
+from ddmr.networks import WeaklySupervised
+from ddmr.losses import HausdorffDistanceErosion, NCC, StructuralSimilarity_simplified, GeneralizedDICEScore
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity, _MSSSIM_WEIGHTS
+from ddmr.layers import UncertaintyWeighting, AugmentationLayer
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

Brain_study/data_generator.py

@@ -12,10 +12,10 @@ from skimage.exposure import equalize_adapthist
 from scipy.ndimage import zoom
 import tensorflow as tf
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.operators import min_max_norm
-from DeepDeformationMapRegistration.utils.misc import segmentation_cardinal_to_ohe
-from DeepDeformationMapRegistration.utils.thin_plate_splines import ThinPlateSplines
+import ddmr.utils.constants as C
+from ddmr.utils.operators import min_max_norm
+from ddmr.utils.misc import segmentation_cardinal_to_ohe
+from ddmr.utils.thin_plate_splines import ThinPlateSplines
 from voxelmorph.tf.layers import SpatialTransformer
 from Brain_study.format_dataset import SEGMENTATION_NR2LBL_LUT, SEGMENTATION_LBL2NR_LUT
 

Brain_study/test_datagenerator.py

@@ -1,6 +1,6 @@
 from Brain_study.data_generator import BatchGenerator
 
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 from tqdm import tqdm
 
 from tensorflow import keras
@@ -8,8 +8,8 @@ import tensorflow as tf
 from tensorflow.keras.callbacks import TensorBoard
 import os
 import voxelmorph as vxm
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.losses import NCC, StructuralSimilarity, StructuralSimilarity_simplified
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.losses import NCC, StructuralSimilarity, StructuralSimilarity_simplified
 
 
 def named_logs(model, logs, validation=False):

Brain_study/utils.py

@@ -1,5 +1,5 @@
 import numpy as np
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 
 class SummaryDictionary:
     def __init__(self, model, batch_size, accumulative_gradients_step=None):

COMET/Build_test_set.py

@@ -14,11 +14,11 @@ import tensorflow as tf
 import numpy as np
 import h5py
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-from DeepDeformationMapRegistration.utils.misc import DisplacementMapInterpolator
+import ddmr.utils.constants as C
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers import AugmentationLayer
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+from ddmr.utils.misc import DisplacementMapInterpolator
 from tqdm import tqdm
 
 from Brain_study.data_generator import BatchGenerator

COMET/COMET_train.py

@@ -14,14 +14,14 @@ from tensorflow.keras import Input
 from tensorflow.keras.models import Model
 from tensorflow.python.framework.errors import InvalidArgumentError
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.ms_ssim_tf import _MSSSIM_WEIGHTS
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.misc import function_decorator
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
+import ddmr.utils.constants as C
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.ms_ssim_tf import _MSSSIM_WEIGHTS
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.misc import function_decorator
+from ddmr.layers import AugmentationLayer
+from ddmr.utils.nifti_utils import save_nifti
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

COMET/COMET_train_UW.py

@@ -12,15 +12,15 @@ from tensorflow.keras import Input
 from tensorflow.keras.models import Model
 from tensorflow.python.framework.errors import InvalidArgumentError
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, \
+import ddmr.utils.constants as C
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, \
     HausdorffDistanceErosion
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.ms_ssim_tf import _MSSSIM_WEIGHTS
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.misc import function_decorator
-from DeepDeformationMapRegistration.layers import AugmentationLayer, UncertaintyWeighting
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.ms_ssim_tf import _MSSSIM_WEIGHTS
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.misc import function_decorator
+from ddmr.layers import AugmentationLayer, UncertaintyWeighting
+from ddmr.utils.nifti_utils import save_nifti
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

COMET/COMET_train_seggguided.py

@@ -14,14 +14,14 @@ from tensorflow.keras import Input
 from tensorflow.keras.models import Model
 from tensorflow.python.framework.errors import InvalidArgumentError
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.ms_ssim_tf import _MSSSIM_WEIGHTS
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.misc import function_decorator
-from DeepDeformationMapRegistration.layers import AugmentationLayer
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
+import ddmr.utils.constants as C
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.ms_ssim_tf import _MSSSIM_WEIGHTS
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.misc import function_decorator
+from ddmr.layers import AugmentationLayer
+from ddmr.utils.nifti_utils import save_nifti
 
 from Brain_study.data_generator import BatchGenerator
 from Brain_study.utils import SummaryDictionary, named_logs

COMET/Evaluate_network.py

@@ -19,16 +19,16 @@ import pandas as pd
 import voxelmorph as vxm
 from voxelmorph.tf.layers import SpatialTransformer
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.operators import min_max_norm, safe_medpy_metric
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.layers import AugmentationLayer, UncertaintyWeighting
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.utils.acummulated_optimizer import AdamAccumulated
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-from DeepDeformationMapRegistration.utils.misc import DisplacementMapInterpolator, get_segmentations_centroids, segmentation_ohe_to_cardinal, segmentation_cardinal_to_ohe
-from DeepDeformationMapRegistration.utils.misc import resize_displacement_map, scale_transformation, GaussianFilter
+import ddmr.utils.constants as C
+from ddmr.utils.operators import min_max_norm, safe_medpy_metric
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers import AugmentationLayer, UncertaintyWeighting
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.utils.acummulated_optimizer import AdamAccumulated
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+from ddmr.utils.misc import DisplacementMapInterpolator, get_segmentations_centroids, segmentation_ohe_to_cardinal, segmentation_cardinal_to_ohe
+from ddmr.utils.misc import resize_displacement_map, scale_transformation, GaussianFilter
 import medpy.metric as medpy_metrics
 from EvaluationScripts.Evaluate_class import EvaluationFigures, resize_pts_to_original_space, resize_img_to_original_space, resize_transformation
 from scipy.interpolate import RegularGridInterpolator

COMET/MultiTrain_config.py

@@ -8,7 +8,7 @@ from configparser import ConfigParser
 from shutil import copy2
 import os
 from datetime import datetime
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 import re
 from COMET.augmentation_constants import LAYER_SELECTION
 TRAIN_DATASET = '/mnt/EncryptedData1/Users/javier/ext_datasets/COMET_dataset/OSLO_COMET_CT/Formatted_128x128x128/train'

COMET/format_dataset.py

@@ -16,8 +16,8 @@ from scipy.ndimage.morphology import binary_dilation, generate_binary_structure
 
 import pandas as pd
 
-from DeepDeformationMapRegistration.utils import constants as C
-from DeepDeformationMapRegistration.utils.misc import segmentation_cardinal_to_ohe, segmentation_ohe_to_cardinal
+from ddmr.utils import constants as C
+from ddmr.utils.misc import segmentation_cardinal_to_ohe, segmentation_ohe_to_cardinal
 
 SEGMENTATION_NR2LBL_LUT = {0: 'background',
                            1: 'parenchyma',

Centerline/centerline.py

@@ -29,8 +29,8 @@ from Centerline.graph_utils import graph_to_ndarray, deform_graph, get_bifurcati
 from Centerline.skeleton_to_graph import get_graph_from_skeleton
 from Centerline.visualization_utils import plot_skeleton, compare_graphs
 
-from DeepDeformationMapRegistration.utils.operators import min_max_norm
-from DeepDeformationMapRegistration.utils import constants as C
+from ddmr.utils.operators import min_max_norm
+from ddmr.utils import constants as C
 
 import cupy
 from cupyx.scipy.ndimage import zoom as zoom_gpu
@@ -39,7 +39,7 @@ from cupyx.scipy.ndimage import map_coordinates
 DATASET_LOCATION = '/mnt/EncryptedData1/Users/javier/vessel_registration/3Dirca/dataset/EVAL'
 DATASET_NAMES = ['Affine', 'None', 'Translation']
 DATASET_FILENAME = 'volume'
-IMGS_FOLDER = '/home/jpdefrutos/workspace/DeepDeformationMapRegistration/Centerline/centerlines'
+IMGS_FOLDER = '/home/jpdefrutos/workspace/ddmr/Centerline/centerlines'
 
 DATASTE_RAW_FILES = '/mnt/EncryptedData1/Users/javier/vessel_registration/3Dirca/nifti3'
 LITS_SEGMENTATION_FILE = 'segmentation'

Centerline/get_vessels.py

@@ -1,8 +1,8 @@
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
+from ddmr.utils.nifti_utils import save_nifti
 from tqdm import tqdm
 import os
 import h5py
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 
 DATASET_LOCATION = '/mnt/EncryptedData1/Users/javier/vessel_registration/3Dirca/dataset/EVAL'
 DATASET_NAMES = ['Affine', 'None', 'Translation']

Centerline/visualization_utils.py

@@ -2,7 +2,7 @@ import matplotlib.pyplot as plt
 from mpl_toolkits.mplot3d import Axes3D
 from matplotlib.lines import Line2D
 import numpy as np
-from DeepDeformationMapRegistration.utils.visualization import add_axes_arrows_3d, remove_tick_labels, set_axes_size
+from ddmr.utils.visualization import add_axes_arrows_3d, remove_tick_labels, set_axes_size
 import os
 
 

Datasets/check_dataset.py

@@ -2,7 +2,7 @@ import os
 import h5py
 import numpy as np
 from tqdm import tqdm
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 
 
 os.environ['CUDA_VISIBLE_DEVICES'] = '0'

Datasets/irca_pre_processing.py

@@ -9,8 +9,8 @@ import zipfile
 import re
 import dicom2nifti as d2n
 import nibabel as nib
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.utils.misc import try_mkdir
 from tqdm import tqdm
 import shutil
 

Datasets/ircad_dataset.py

@@ -26,8 +26,8 @@ import re
 currentdir = os.path.dirname(os.path.realpath(__file__))
 parentdir = os.path.dirname(currentdir)
 sys.path.append(parentdir)  # PYTHON > 3.3 does not allow relative referencing
-from DeepDeformationMapRegistration.utils.cmd_args_parser import parse_arguments
-import DeepDeformationMapRegistration.utils.constants as const
+from ddmr.utils.cmd_args_parser import parse_arguments
+import ddmr.utils.constants as const
 from tools.thinPlateSplines_tf import ThinPlateSplines
 from keras_model.ext.neuron.layers import SpatialTransformer
 from tools.voxelMorph import interpn

EvaluationScripts/Evaluate_3d_weaklySupervised.py

@@ -11,13 +11,13 @@ import voxelmorph as vxm
 import neurite as ne
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.data_generator import DataGeneratorManager
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.networks import WeaklySupervised
-from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion
-from DeepDeformationMapRegistration.layers import UncertaintyWeighting
+import ddmr.utils.constants as C
+from ddmr.data_generator import DataGeneratorManager
+from ddmr.utils.misc import try_mkdir
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.networks import WeaklySupervised
+from ddmr.losses import HausdorffDistanceErosion
+from ddmr.layers import UncertaintyWeighting
 
 
 os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER

EvaluationScripts/Evaluate_class.py

@@ -6,8 +6,8 @@ from medpy.metric.binary import dc, hd95
 import numpy as np
 import pandas as pd
 import os
-from DeepDeformationMapRegistration.utils.constants import EPS
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
+from ddmr.utils.constants import EPS
+from ddmr.utils.nifti_utils import save_nifti
 from skimage.transform import resize
 from skimage.measure import regionprops, label
 

SoA_methods/eval_ants.py

@@ -12,12 +12,12 @@ currentdir = os.path.dirname(os.path.realpath(__file__))
 parentdir = os.path.dirname(currentdir)
 sys.path.append(parentdir)  # PYTHON > 3.3 does not allow relative referencing
 
-from DeepDeformationMapRegistration.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
-from DeepDeformationMapRegistration.ms_ssim_tf import MultiScaleStructuralSimilarity
-from DeepDeformationMapRegistration.utils.misc import DisplacementMapInterpolator, segmentation_ohe_to_cardinal
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.utils.visualization import save_disp_map_img, plot_predictions
-import DeepDeformationMapRegistration.utils.constants as C
+from ddmr.losses import StructuralSimilarity_simplified, NCC, GeneralizedDICEScore, HausdorffDistanceErosion, target_registration_error
+from ddmr.ms_ssim_tf import MultiScaleStructuralSimilarity
+from ddmr.utils.misc import DisplacementMapInterpolator, segmentation_ohe_to_cardinal
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.utils.visualization import save_disp_map_img, plot_predictions
+import ddmr.utils.constants as C
 import shutil
 import medpy.metric as medpy_metrics
 
@@ -30,7 +30,7 @@ import tensorflow as tf
 DATASET_LOCATION = '/mnt/EncryptedData1/Users/javier/vessel_registration/3Dirca/dataset/EVAL'
 DATASET_NAMES = 'test_sample_\d{4}.h5'
 DATASET_FILENAME = 'volume'
-IMGS_FOLDER = '/home/jpdefrutos/workspace/DeepDeformationMapRegistration/Centerline/imgs'
+IMGS_FOLDER = '/home/jpdefrutos/workspace/ddmr/Centerline/imgs'
 
 WARPED_MOV = 'warpedmovout'
 WARPED_FIX = 'warpedfixout'

TrainingScripts/Train_2d.py

@@ -11,10 +11,10 @@ from tensorflow.keras.callbacks import ModelCheckpoint, TensorBoard, EarlyStoppi
 import voxelmorph as vxm
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.data_generator import DataGeneratorManager2D
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
-from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion
+import ddmr.utils.constants as C
+from ddmr.data_generator import DataGeneratorManager2D
+from ddmr.utils.misc import try_mkdir
+from ddmr.losses import HausdorffDistanceErosion
 
 
 os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER

TrainingScripts/Train_2d_uncertaintyWeighting.py

@@ -14,11 +14,11 @@ import neurite as ne
 import h5py
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.data_generator import DataGeneratorManager2D
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
-from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion
-from DeepDeformationMapRegistration.layers import UncertaintyWeighting
+import ddmr.utils.constants as C
+from ddmr.data_generator import DataGeneratorManager2D
+from ddmr.utils.misc import try_mkdir
+from ddmr.losses import HausdorffDistanceErosion
+from ddmr.layers import UncertaintyWeighting
 
 
 os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER

TrainingScripts/Train_3d.py

@@ -13,10 +13,10 @@ import neurite as ne
 import h5py
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.data_generator import DataGeneratorManager
-from DeepDeformationMapRegistration.losses import NCC
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
+import ddmr.utils.constants as C
+from ddmr.data_generator import DataGeneratorManager
+from ddmr.losses import NCC
+from ddmr.utils.misc import try_mkdir
 
 
 os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER

TrainingScripts/Train_3d_weaklySupervised.py

@@ -13,12 +13,12 @@ import neurite as ne
 import h5py
 from datetime import datetime
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.data_generator import DataGeneratorManager
-from DeepDeformationMapRegistration.utils.misc import try_mkdir
-from DeepDeformationMapRegistration.networks import WeaklySupervised
-from DeepDeformationMapRegistration.losses import HausdorffDistanceErosion
-from DeepDeformationMapRegistration.layers import UncertaintyWeighting
+import ddmr.utils.constants as C
+from ddmr.data_generator import DataGeneratorManager
+from ddmr.utils.misc import try_mkdir
+from ddmr.networks import WeaklySupervised
+from ddmr.losses import HausdorffDistanceErosion
+from ddmr.layers import UncertaintyWeighting
 
 
 os.environ['CUDA_DEVICE_ORDER'] = C.DEV_ORDER

{DeepDeformationMapRegistration → ddmr}/data_generator.py

@@ -10,9 +10,9 @@ from skimage.exposure import equalize_adapthist
 from scipy.ndimage import zoom
 import tensorflow as tf
 
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.operators import min_max_norm
-from DeepDeformationMapRegistration.utils.thin_plate_splines import ThinPlateSplines
+import ddmr.utils.constants as C
+from ddmr.utils.operators import min_max_norm
+from ddmr.utils.thin_plate_splines import ThinPlateSplines
 from voxelmorph.tf.layers import SpatialTransformer
 
 

{DeepDeformationMapRegistration → ddmr}/layers.py

@@ -11,7 +11,7 @@ import tensorflow.keras.backend as K
 import tensorflow as tf
 import numpy as np
 
-from DeepDeformationMapRegistration.utils.operators import soft_threshold
+from ddmr.utils.operators import soft_threshold
 
 
 class UncertaintyWeighting(kl.Layer):

{DeepDeformationMapRegistration → ddmr}/layers/SpatialTransformer.py

@@ -4,7 +4,7 @@ import tensorflow as tf
 import neurite as ne
 
 import h5py
-from DeepDeformationMapRegistration.utils.constants import IMG_SHAPE, DISP_MAP_SHAPE
+from ddmr.utils.constants import IMG_SHAPE, DISP_MAP_SHAPE
 
 
 class SpatialTransformer(kl.Layer):

{DeepDeformationMapRegistration → ddmr}/layers/augmentation.py

@@ -10,9 +10,9 @@ import tensorflow.keras.layers as kl
 import tensorflow as tf
 from tensorflow.python.framework.errors import InvalidArgumentError
 
-from DeepDeformationMapRegistration.utils.operators import soft_threshold, gaussian_kernel, sample_unique
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.thin_plate_splines import ThinPlateSplines
+from ddmr.utils.operators import soft_threshold, gaussian_kernel, sample_unique
+import ddmr.utils.constants as C
+from ddmr.utils.thin_plate_splines import ThinPlateSplines
 from voxelmorph.tf.layers import SpatialTransformer
 
 

{DeepDeformationMapRegistration → ddmr}/layers/uncertainty_weighting.py

@@ -12,9 +12,9 @@ import tensorflow as tf
 import numpy as np
 import random
 
-from DeepDeformationMapRegistration.utils.operators import soft_threshold, gaussian_kernel, sample_unique
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.thin_plate_splines import ThinPlateSplines
+from ddmr.utils.operators import soft_threshold, gaussian_kernel, sample_unique
+import ddmr.utils.constants as C
+from ddmr.utils.thin_plate_splines import ThinPlateSplines
 from voxelmorph.tf.layers import SpatialTransformer
 from neurite.tf.utils import resize
 #from cupyx.scipy.ndimage import zoom

{DeepDeformationMapRegistration → ddmr}/losses.py

@@ -3,9 +3,9 @@ import tensorflow.keras.backend as K
 from scipy.ndimage import generate_binary_structure
 from sklearn.utils.extmath import cartesian
 
-from DeepDeformationMapRegistration.utils.operators import soft_threshold, min_max_norm, hard_threshold
-from DeepDeformationMapRegistration.utils.constants import EPS_tf
-from DeepDeformationMapRegistration.utils.misc import function_decorator
+from ddmr.utils.operators import soft_threshold, min_max_norm, hard_threshold
+from ddmr.utils.constants import EPS_tf
+from ddmr.utils.misc import function_decorator
 
 import numpy as np
 import warnings

{DeepDeformationMapRegistration → ddmr}/main.py

@@ -14,13 +14,13 @@ from scipy.ndimage import gaussian_filter, zoom
 from skimage.measure import regionprops
 import SimpleITK as sitk
 
-from DeepDeformationMapRegistration.layers.SpatialTransformer import SpatialTransformer
-import DeepDeformationMapRegistration.utils.constants as C
-from DeepDeformationMapRegistration.utils.nifti_utils import save_nifti
-from DeepDeformationMapRegistration.utils.operators import min_max_norm
-from DeepDeformationMapRegistration.utils.misc import resize_displacement_map
-from DeepDeformationMapRegistration.utils.model_utils import get_models_path, load_model, get_spatialtransformer_model
-from DeepDeformationMapRegistration.utils.logger import LOGGER
+import ddmr.utils.constants as C
+from ddmr.utils.nifti_utils import save_nifti
+from ddmr.layers.SpatialTransformer import SpatialTransformer
+from ddmr.utils.operators import min_max_norm
+from ddmr.utils.misc import resize_displacement_map
+from ddmr.utils.model_utils import get_models_path, load_model, get_spatialtransformer_model
+from ddmr.utils.logger import LOGGER
 
 from importlib.util import find_spec
 
@@ -282,8 +282,7 @@ def main():
     ST_MODEL_FILE = get_spatialtransformer_model()
 
     network, registration_model = load_model(MODEL_FILE, False, True)
-    spatialtransformer_model = tf.keras.models.load_model(ST_MODEL_FILE,
-                                                          custom_objects={'SpatialTransformer': SpatialTransformer})
+    spatialtransformer_model = tf.keras.models.load_model(ST_MODEL_FILE, custom_objects={'SpatialTransformer': SpatialTransformer})
 
     LOGGER.info('Computing registration')
     with sess.as_default():

{DeepDeformationMapRegistration → ddmr}/ms_ssim_tf.py

@@ -9,7 +9,7 @@ from tensorflow.python.ops import control_flow_ops
 from tensorflow.python.ops import nn
 from tensorflow.python.util.tf_export import tf_export
 from tensorflow.python.util import dispatch
-from DeepDeformationMapRegistration.utils.misc import function_decorator
+from ddmr.utils.misc import function_decorator
 
 
 @tf_export('image.convert_image_dtype')
@@ -606,7 +606,7 @@ if __name__ == '__main__':
     tf.enable_eager_execution()
     import nibabel as nib
     import numpy as np
-    from DeepDeformationMapRegistration.utils.operators import min_max_norm
+    from ddmr.utils.operators import min_max_norm
     from skimage.metrics import structural_similarity
 
     img1 = nib.load('test_images/ixi_image.nii.gz')

{DeepDeformationMapRegistration → ddmr}/utils/cmd_args_parser.py

@@ -1,5 +1,5 @@
 import sys, getopt
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 import os
 
 

{DeepDeformationMapRegistration → ddmr}/utils/conf_file_utils.py

@@ -1,4 +1,4 @@
-import DeepDeformationMapRegistration.utils.constants as C
+import ddmr.utils.constants as C
 import re
 import os