Merge pull request #6 from rg2/devel

Development leading up to next release

Author: rg2

CMakeLists.txt

@@ -28,7 +28,7 @@ if (APPLE)
 endif ()
 
 # Version format is YYYY.MM.DD for a release and YYYY.MM.DD.1 for devel after the release
-project(xreg VERSION 2020.09.26.1)
+project(xreg VERSION 2020.12.13.0)
 
 set (CMAKE_CXX_STANDARD "11" CACHE STRING "C++ Standard (needs at least 11)")
 mark_as_advanced(CMAKE_CXX_STANDARD)

README.md

@@ -51,7 +51,7 @@ Although the following capabilities currently only exist in an internal version
 ## Building
 A standard CMake configure/generate process is used.
 It is recommended to generate Ninja build files for fast compilation. 
-Example scripts for building all dependencies and the xReg repository are provided for [POSIX systems](example_build_script) (e.g. MacOS and Linux) and [Windows](example_build_script_win.cmd).
+Example scripts for building all dependencies and the xReg repository are provided for POSIX systems (e.g. MacOS and Linux) [here](example_build_script) and [here](example_build_script_2), and also for [Windows](example_build_script_win.cmd).
 The [docker](docker) directory demonstrates how Docker may be used to build the software.
 
 ### Dependencies
@@ -72,82 +72,13 @@ The [docker](docker) directory demonstrates how Docker may be used to build the
     * Included with MacOS
   * Optional: [ffmpeg](https://ffmpeg.org) is used for writing videos when it is found in the system path. The OpenCV video writer is used if ffmpeg is not available.
 
+## Testing
+Functional testing is available in the form of a [python script](tests/wiki_cmds.py) that runs the commands found on the [wiki walkthrough](https://github.com/rg2/xreg/wiki#walkthrough).
+Results of the commands need to be examined by the user and determined to be successful or failures.
+All necessary data is downloaded automatically.
+When the appropriate visualization programs are available on the system, the script also automatically loads the output data for inspection.
+
 ## License and Attribution
 The software is available for use under the [MIT License](LICENSE).
 
-If you have found this software useful in your work, we kindly ask that you cite the most appropriate references below:
-```
-Grupp, Robert B., et al. "Pose estimation of periacetabular osteotomy fragments with intraoperative X-ray navigation." IEEE Transactions on Biomedical Engineering 67.2 (2019): 441-452.
-----------------------------------------------------------------------
-@article{grupp2019pose,
-  title={Pose estimation of periacetabular osteotomy fragments with intraoperative {X}-ray navigation},
-  author={Grupp, Robert B and Hegeman, Rachel A and Murphy, Ryan J and Alexander, Clayton P and Otake, Yoshito and McArthur, Benjamin A and Armand, Mehran and Taylor, Russell H},
-  journal={IEEE Transactions on Biomedical Engineering},
-  volume={67},
-  number={2},
-  pages={441--452},
-  year={2019},
-  publisher={IEEE}
-}
-```
-```
-Grupp, Robert B., Mehran Armand, and Russell H. Taylor. "Patch-based image similarity for intraoperative 2D/3D pelvis registration during periacetabular osteotomy." OR 2.0 Context-Aware Operating Theaters, Computer Assisted Robotic Endoscopy, Clinical Image-Based Procedures, and Skin Image Analysis. Springer, Cham, 2018. 153-163.
-----------------------------------------------------------------------
-@incollection{grupp2018patch,
-  title={Patch-based image similarity for intraoperative {2D}/{3D} pelvis registration during periacetabular osteotomy},
-  author={Grupp, Robert B and Armand, Mehran and Taylor, Russell H},
-  booktitle={OR 2.0 Context-Aware Operating Theaters, Computer Assisted Robotic Endoscopy, Clinical Image-Based Procedures, and Skin Image Analysis},
-  pages={153--163},
-  year={2018},
-  publisher={Springer}
-}
-```
-```
-Grupp, Robert B., et al. "Automatic annotation of hip anatomy in fluoroscopy for robust and efficient 2D/3D registration." International Journal of Computer Assisted Radiology and Surgery (2020): 1-11.
-----------------------------------------------------------------------
-@article{grupp2020automatic,
-  title={Automatic annotation of hip anatomy in fluoroscopy for robust and efficient {2D}/{3D} registration},
-  author={Grupp, Robert B and Unberath, Mathias and Gao, Cong and Hegeman, Rachel A and Murphy, Ryan J and Alexander, Clayton P and Otake, Yoshito and McArthur, Benjamin A and Armand, Mehran and Taylor, Russell H},
-  journal={International Journal of Computer Assisted Radiology and Surgery},
-  pages={1--11},
-  publisher={Springer}
-}
-```
-```
-Grupp, Robert, et al. "Fast and automatic periacetabular osteotomy fragment pose estimation using intraoperatively implanted fiducials and single-view fluoroscopy." Physics in Medicine & Biology (2020).
-----------------------------------------------------------------------
-@article{grupp2020fast,
-  title={Fast and automatic periacetabular osteotomy fragment pose estimation using intraoperatively implanted fiducials and single-view fluoroscopy},
-  author={Grupp, Robert and Murphy, Ryan and Hegeman, Rachel and Alexander, Clayton and Unberath, Mathias and Otake, Yoshito and McArthur, Benjamin and Armand, Mehran and Taylor, Russell H},
-  journal={Physics in Medicine \& Biology},
-  year={2020},
-  publisher={IOP Publishing}
-}
-```
-```
-Grupp, R., et al. "Pelvis surface estimation from partial CT for computer-aided pelvic osteotomies." Orthopaedic Proceedings. Vol. 98. No. SUPP_5. The British Editorial Society of Bone & Joint Surgery, 2016.
-----------------------------------------------------------------------
-@inproceedings{grupp2016pelvis,
-  title={Pelvis surface estimation from partial {CT} for computer-aided pelvic osteotomies},
-  author={Grupp, R and Otake, Y and Murphy, R and Parvizi, J and Armand, M and Taylor, R},
-  booktitle={Orthopaedic Proceedings},
-  volume={98},
-  number={SUPP\_5},
-  pages={55--55},
-  year={2016},
-  organization={The British Editorial Society of Bone \& Joint Surgery}
-}
-```
-```
-Grupp, Robert B., et al. "Smooth extrapolation of unknown anatomy via statistical shape models." Medical Imaging 2015: Image-Guided Procedures, Robotic Interventions, and Modeling. Vol. 9415. International Society for Optics and Photonics, 2015.
-----------------------------------------------------------------------
-@inproceedings{grupp2015smooth,
-  title={Smooth extrapolation of unknown anatomy via statistical shape models},
-  author={Grupp, Robert B and Chiang, H and Otake, Yoshito and Murphy, Ryan J and Gordon, Chad R and Armand, Mehran and Taylor, Russell H},
-  booktitle={Medical Imaging 2015: Image-Guided Procedures, Robotic Interventions, and Modeling},
-  volume={9415},
-  pages={941524},
-  year={2015},
-  organization={International Society for Optics and Photonics}
-}
-```
+If you have found this software useful in your work, we kindly ask that you cite the most appropriate references listed [here](https://github.com/rg2/xreg/wiki/Licensing-and-Attribution).

dist/build_all_docker.py

@@ -0,0 +1,74 @@
+# MIT License
+#
+# Copyright (c) 2020 Robert Grupp
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+import os.path
+import sys
+
+import subprocess as sp
+
+def build_dev_base(os_name, os_version, xreg_git_dir):
+    sp.check_call('docker build -t xreg-dev-base-{0}-{1} --build-arg os_name={0} --build-arg os_version={1} -f {2}/docker/Dockerfile.{0}_dev_base {2}'.format(os_name, os_version, xreg_git_dir), shell=True)
+
+def build_deps(os_name, os_version, xreg_git_dir):
+    sp.check_call('docker build -t xreg-deps-{0}-{1} --build-arg os_name={0} --build-arg os_version={1} -f {2}/docker/Dockerfile.xreg-deps {2}'.format(os_name, os_version, xreg_git_dir), shell=True)
+
+def build_xreg(os_name, os_version, xreg_git_dir):
+    sp.check_call('docker build -t xreg-{0}-{1} --build-arg os_name={0} --build-arg os_version={1} -f {2}/docker/Dockerfile.xreg {2}'.format(os_name, os_version, xreg_git_dir), shell=True)
+
+def build_xreg_dist(os_name, os_version, xreg_git_dir, xreg_dist_str):
+    dist_img_name = 'xreg-dist-{0}-{1}'.format(os_name, os_version)
+
+    sp.check_call('docker build -t {4} --build-arg os_name={0} --build-arg os_version={1} --build-arg xreg_dist_str={3} -f {2}/docker/Dockerfile.xreg-dist-bin {2}'.format(os_name, os_version, xreg_git_dir, xreg_dist_str, dist_img_name), shell=True)
+
+    cont_id = sp.check_output('docker create {}'.format(dist_img_name), shell=True).decode().strip()
+    
+    dist_file_name = '{}-{}-{}.tar.gz'.format(xreg_dist_str, os_name, os_version)
+
+    sp.check_output('docker cp {}:/{} .'.format(cont_id, dist_file_name), shell=True)
+    
+    sp.check_call('docker rm {}'.format(cont_id), shell=True)
+
+if __name__ == '__main__':
+    if len(sys.argv) < 2:
+        sys.stderr.write('Usage: {} <xreg src dir> [<xreg ver string>]\n'.format(os.path.basename(sys.argv[0])))
+        sys.stderr.flush()
+        sys.exit(1)
+    
+    xreg_src_dir = sys.argv[1]
+
+    xreg_dist_prefix = 'xreg'
+    
+    if len(sys.argv) > 2:
+        xreg_dist_prefix = '{}-{}'.format(xreg_dist_prefix, sys.argv[2])
+
+    # os name --> list of os version
+    configs_to_build = { 'ubuntu' : [ '16.04', '18.04', '20.04' ], 'centos' : [ '7' ] }
+    
+    for os_name, os_versions in configs_to_build.items():
+        for os_ver in os_versions:
+            build_dev_base(os_name, os_ver, xreg_src_dir)
+            build_deps(os_name, os_ver, xreg_src_dir)
+            build_xreg(os_name, os_ver, xreg_src_dir)
+
+            build_xreg_dist(os_name, os_ver, xreg_src_dir, xreg_dist_prefix)
+
+

dist/dist_readme/README.txt

@@ -3,7 +3,7 @@
             | xReg: Modeling and Registration Software for Surgery |
             |                                                      |
             |                  Executable Programs                 |
-            |                     v2020.09.26.0                    |
+            |                     v2020.12.13.0                    |
             |                                                      |
             |              Robert Grupp (grupp@jhu.edu)            |
             +------------------------------------------------------+
@@ -40,7 +40,8 @@ This software is provided under the terms of the MIT license and a copy of the l
 found in the "LICENSE" file.
 
 If you have found this software useful in your work, we kindly ask that you cite the most
-appropriate references below:
+appropriate references listed below. If you are unsure which work to cite, please see this wiki
+page for guidance: https://github.com/rg2/xreg/wiki/Licensing-and-Attribution.
 
 
     Grupp, Robert B., et al. "Pose estimation of periacetabular osteotomy fragments with intraoperative X-ray navigation." IEEE Transactions on Biomedical Engineering 67.2 (2019): 441-452.

dist/make_linux_dist.py

@@ -27,6 +27,12 @@
 import glob
 import subprocess as sp
 
+kDEBUG = False
+
+def dbg_print(s):
+    if kDEBUG:
+        print(s)
+
 def get_lib_deps(exe_path):
     ldd_lines = sp.check_output('ldd {}'.format(exe_path), shell=True).decode().splitlines()
 
@@ -35,6 +41,9 @@ def get_lib_deps(exe_path):
     for l in ldd_lines:
         toks = l.split('=>')
         if len(toks) > 1:
+            if toks[1].strip() == 'not found':
+                raise ValueError('dep. not found for: {}'.format(toks[0].strip()))
+
             lib_path = toks[1][:toks[1].find('(0x')].strip()
 
             if lib_path:
@@ -63,11 +72,20 @@ def update_rpath(exe_path):
     xreg_exes = glob.glob('{}/bin/xreg-*'.format(xreg_install_prefix))
 
     for exe in xreg_exes:
+        dbg_print('copying exe: {}'.format(exe))
         shutil.copy(exe, dst_bin_path)
-
+        
+        dbg_print('  checking deps...')
         for dep_src_path in get_lib_deps(exe):
-            if not os.path.exists('{}/{}'.format(dst_lib_path,os.path.basename(dep_src_path))):
+            lib_name = os.path.basename(dep_src_path)
+
+            dbg_print('    {}'.format(lib_name))
+            if not os.path.exists('{}/{}'.format(dst_lib_path, lib_name)):
+                dbg_print('      copying...')
                 shutil.copy(dep_src_path, dst_lib_path)
+
+                update_rpath('{}/{}'.format(dst_lib_path, lib_name))
 
+        dbg_print('  updating RPATH...')
         update_rpath('{}/{}'.format(dst_bin_path, os.path.basename(exe)))