Merge pull request #413 from Deep-MI/dev

PR for eTIV fix and new stable release

.dockerignore

@@ -1,2 +1,12 @@
 **/.git
 **/.github
+checkpoints
+Singularity
+images
+venv
+Tutorial
+**/*.md
+Docker/Dockerfile*
+*.txt
+venv
+/srun_fastsurfer.sh

.gitignore

@@ -0,0 +1,2 @@
+/BUILD.info
+/.idea/**

CONTRIBUTING.md

@@ -54,6 +54,53 @@ Enhancement suggestions are tracked as [GitHub issues](issues).
 - **Describe the current behavior** and **explain which behavior you expected to see instead** and why.
 - **Explain why this enhancement would be useful** to most users.
 
+## Contributing Code
+
+1. [Fork](https://docs.github.com/en/get-started/quickstart/fork-a-repo) this repository to your github account
+2. Clone your fork to your computer (`git clone https://github.com/<username>/FastSurfer.git`)
+3. Change into the project directory (`cd FastSurfer`)
+4. Add Deep-MI repo as upstream (`git remote add upstream https://github.com/Deep-MI/FastSurfer.git`)
+5. Update information from upstream (`git fetch upstream`)
+6. Checkout the upstream dev branch (`git checkout -b dev upstream/dev`)
+7. Create your feature branch from dev (`git checkout -b my-new-feature`)
+8. Commit your changes (`git commit -am 'Add some feature'`)
+9. Push to the branch to your github (`git push origin my-new-feature`)
+10. Create new pull request on github web interface from that branch into Deep-NI **dev branch** (not into stable, which is default)
+
+If lots of things changed in the meantime or the pull request is showing conflicts you should rebase your branch to the current upstream dev.
+This is the preferred way, but only possible if you are the sole develop or your branch:
+
+10. Switch into dev branch (`git checkout dev`)
+11. Update your dev branch (`git pull upstream dev`)
+12. Switch into your feature (`git chekcout my-new-feature`)
+13. Rebase your branch onto dev (`git rebase dev`), resolve conflicts and continue until complete
+14. Force push the updated feature branch to your gihub (`git push -f origin my-new-feature`)
+
+If other people co-develop the my-new-feature branch, rewriting history with a rebase is not possible.
+Instead you need to merge upstream dev into your branch:
+
+10. Switch into dev branch (`git checkout dev`)
+11. Update your dev branch (`git pull upstream dev`)
+12. Switch into your feature (`git chekcout my-new-feature`)
+13. Merge dev into your feature (`git merge dev`), resolve conflicts and commit
+14. Push to origin (`git push origin my-new-feature`)
+
+Either method updates the pull request and resolves conflicts, so that we can merge it once it is complete.
+Once the pull request is merged by us you can delete the feature branch in your clone and on your fork:
+
+15. Switch into dev branch (`git checkout dev`)
+16. Delete feature branch (`git branch -D my-new-feature`)
+17. Delete the branch on your github fork either via GUI, or via command line (`git push origin --delete my-new-feature`)
+
+This procedure will ensure that your local dev branch always follows our dev branch and will never diverge. You can, once in a while, push the dev branch, or similarly update stable and push it to your fork (origin), but that is not really necessary. 
+
+Next time you contribute a feature, you do not need to go through the steps 1-6 above, but simply:
+- Switch to dev branch (`git checkout dev`)
+- Make sure it is identical to upstream (`git pull upstream dev`)
+- Check out a new feature branch and continue from 7. above. 
+
+Another good command, if for some reasons your dev branch diverged, which should never happen as you never commit to it, you can reset it by `git reset --hard upstream/dev`. Make absolutely sure you are in your dev branch (not the feature branch) and be aware that this will delete any local changes!
+
 ## Attribution
 
 This guide is based on the **contributing-gen**. [Make your own](https://github.com/bttger/contributing-gen)!

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
 

CerebNet/inference.py

@@ -14,9 +14,9 @@
 
 # IMPORTS
 import time
-from os import makedirs, cpu_count
+from os import makedirs
 from os.path import join, dirname, isfile
-from typing import Dict, List, Tuple, Optional, Literal
+from typing import Dict, List, Tuple, Optional
 from concurrent.futures import Future, ThreadPoolExecutor
 
 import nibabel as nib
@@ -26,6 +26,7 @@
 from tqdm import tqdm
 
 from FastSurferCNN.utils import logging
+from FastSurferCNN.utils.threads import get_num_threads
 from FastSurferCNN.utils.mapper import JsonColorLookupTable, TSVLookupTable
 from FastSurferCNN.utils.common import (
     find_device,
@@ -34,8 +35,8 @@
     NoParallelExecutor,
 )
 from CerebNet.data_loader.augmentation import ToTensorTest
-from CerebNet.data_loader.dataset import SubjectDataset, Plane, LocalizerROI, PLANES
-from CerebNet.datasets.utils import crop_transform, load_reorient_lia
+from CerebNet.data_loader.dataset import SubjectDataset, Plane, PLANES
+from CerebNet.datasets.utils import crop_transform
 from CerebNet.models.networks import build_model
 from CerebNet.utils import checkpoint as cp
 
@@ -64,7 +65,7 @@ def __init__(
         self.pool = None
         self._threads = None
         self.threads = threads
-        torch.set_num_threads(cpu_count() if self._threads is None else self._threads)
+        torch.set_num_threads(get_num_threads() if self._threads is None else self._threads)
         self.pool = (
             ThreadPoolExecutor(self._threads) if async_io else NoParallelExecutor()
         )