Merge pull request #415 from dkuegler/fix/cerebnet/typos

"Small" changes to the CerebNet traning pipeline (missing apply_warp.py and shell errors in realistic_deformations)

CerebNet/apply_warp.py

@@ -0,0 +1,85 @@
+
+# Copyright 2022 Image Analysis Lab, German Center for Neurodegenerative Diseases (DZNE), Bonn
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# IMPORTS
+from os.path import join
+import numpy as np
+import nibabel as nib
+
+from CerebNet.datasets import utils
+
+
+def save_nii_image(img_data, save_path, header, affine):
+    img_out = nib.Nifti1Image(img_data, header=header, affine=affine)
+    print(f"Saving {save_path}")
+    nib.save(img_out, save_path)
+
+
+def store_warped_data(img_path, lbl_path, warp_path, result_path, patch_size):
+
+    img, img_file = utils.load_reorient_rescale_image(img_path)
+
+    lbl_file = nib.load(lbl_path)
+    label = np.asarray(lbl_file.get_fdata(), dtype=np.int16)
+
+    warp_field = np.asarray(nib.load(warp_path).get_fdata())
+    img = utils.map_size(img, base_shape=warp_field.shape[:3])
+    label = utils.map_size(label, base_shape=warp_field.shape[:3])
+    warped_img = utils.apply_warp_field(warp_field, img, interpol_order=3)
+    warped_lbl = utils.apply_warp_field(warp_field, label, interpol_order=0)
+    utils.map_subseg2label(warped_lbl, label_type='cereb_subseg')
+    roi = utils.bounding_volume(label, patch_size)
+
+    img = utils.map_size(warped_img[roi], patch_size)
+    label = utils.map_size(warped_lbl[roi], patch_size)
+
+    img_file.header['dim'][1:4] = patch_size
+    img_file.set_data_dtype(img.dtype)
+    lbl_file.header['dim'][1:4] = patch_size
+    save_nii_image(img,
+                   join(result_path, "T1_warped_cropped.nii.gz"),
+                   header=img_file.header,
+                   affine=img_file.affine)
+    save_nii_image(label,
+                   join(result_path, "label_warped_cropped.nii.gz"),
+                   header=lbl_file.header,
+                   affine=lbl_file.affine)
+
+
+if __name__ == '__main__':
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--img_path",
+                        help="path to T1 image",
+                        type=str)
+    parser.add_argument("--lbl_path",
+                        help="path to label image",
+                        type=str)
+    parser.add_argument("--result_path",
+                        help="folder to store the results",
+                        type=str)
+
+    parser.add_argument("--warp_filename",
+                        help="Warp field file",
+                        default='1Warp.nii.gz',
+                        type=str)
+
+    args = parser.parse_args()
+    warp_path = join(args.result_path, args.warp_filename)
+    store_warped_data(args.img_path,
+                      args.lbl_path,
+                      warp_path=warp_path,
+                      result_path=args.result_path,
+                      patch_size=(128, 128, 128))

CerebNet/datasets/realistic_deformations.sh

@@ -15,7 +15,7 @@
 
 
 # IMPORTS
-if ["$ANTSPATH" = "" ] || [ -f "$ANTSPATH/antsRegistrationSyNQuick.sh" ]
+if [ "$ANTSPATH" = "" ] || [ -f "$ANTSPATH/antsRegistrationSyNQuick.sh" ]
 then
   exit "environment \$ANTSPATH not defined or invalid. \$ANTSPATH must contain antsRegistrationSyNQuick.sh."
 fi
@@ -114,14 +114,16 @@ output_dir=$moving_dataroot/subj2subj_reg
 mkdir -p $output_dir
 
 if [ "$unlabeled_subject" != "UNDEFINED" ]
+then
     IFS=',' read -r -a unlabeled_subject_array <<< "$unlabeled_subject"
 fi
 
 if [ "$labeled_subject" != "UNDEFINED" ]
+then
     IFS=',' read -r -a labeled_subject_array <<< "$labeled_subject"
 fi
 
-if [ ${#labeled_subject_array} != 1 ] && [ ${#unlabeled_subject_array} != 1 ] &&  [ ${#labeled_subject_array} != ${#unlabeled_subject_array}]
+if [ ${#labeled_subject_array} != 1 ] && [ ${#unlabeled_subject_array} != 1 ] && [ ${#labeled_subject_array} != ${#unlabeled_subject_array} ]
 then
     exit "invalid parameters for labeled_subject and unlabeled_subject"
 fi
@@ -179,7 +181,7 @@ do
         else
             echo "$result_path$output_warp already exists, skipping $sub1 -> $sub2."
         fi
-    elif
+    else
         echo "WARNING: $lab_img or $unlab_img does not exist, skipping $sub1 -> $sub2."
     fi