Merge pull request #9 from rg2/devel

Latest changes from devel branch - preparing for next release.

CMakeLists.txt

@@ -28,7 +28,7 @@ cmake_minimum_required(VERSION 3.13.0 FATAL_ERROR)
 #endif ()
 
 # Version format is YYYY.MM.DD for a release and YYYY.MM.DD.1 for devel after the release
-project(xreg VERSION 2020.12.13.1)
+project(xreg VERSION 2021.09.19.0)
 
 set (CMAKE_CXX_STANDARD "11" CACHE STRING "C++ Standard (needs at least 11)")
 mark_as_advanced(CMAKE_CXX_STANDARD)

dist/dist_readme/README.txt

@@ -3,7 +3,7 @@
  | xReg: Modeling and Registration Software for Surgery |
  | |
  | Executable Programs |
- | v2020.12.13.0 |
+ | v2021.09.19.0 |
  | |
  | Robert Grupp ([email protected]) |
  +------------------------------------------------------+
@@ -17,7 +17,7 @@ See the following pages for more information about the library and tools:
 The walkthrough link above contains demonstrations (with data) on example usages of these tools.
 
 Included in this release is a "bin" directory which contains the xReg executable files. Each xReg
-program name is prefixed with "xreg-" (e.g. "xreg-convert-dicom"). The help message of each
+program name is prefixed with "xreg-" (e.g. "xreg-convert-dicom-vols"). The help message of each
 program, obtained by passing the "--help" or "-h" flags, documents the program's interface and
 the available options.
 

docker/README.md

@@ -3,12 +3,17 @@
 ## Introduction
 The files in this directory may be used to create Docker images with builds of the xReg software.
 Ubuntu and CentOS base images are supported.
-The releases of exectuable programs for CentOS 7 and Ubuntu 16.04 were created using this pipeline. 
+The releases of exectuable programs for CentOS 7 and Ubuntu 16.04, 18.04, 20.04 were created using this pipeline. 
 
 The build argument `os_name` is used to choose either Ubuntu or CentOS (e.g. passing `--build-arg os_name=ubuntu` or `--build-arg os_name=centos` to `docker build`).
 The operating system version is specified using the `os_version` build argument (e.g. passing `--build-arg os_version=7` or `--build-arg os_version=16.04` to `docker build`).
 When these arguments are not provided, Ubuntu 16.04 is used by default.
 
+## GitHub Packages
+The images containing all xReg dependencies are available as GitHub packages [here](https://github.com/rg2?tab=packages&repo_name=xreg).
+Although these are primarily intended to be used as part of a continuous integration pipeline, others may find them useful for developing or building xReg.
+More images may be made available as needed/requested.
+
 ## List of Files
 * `Dockerfile.centos_dev_base`
  * Installs packages needed for xReg build on *CentOS* and also builds a recent version of CMake
@@ -26,8 +31,7 @@ A copy/pastable list of shell commands is provided in [`example_commands`](examp
 
 Specific commands are also listed below:
 
-NOTE: all of these commands assume that the xReg repository contents are located in ~/xreg-git.
-These commands were tested on MacOS 10.14.6 with Docker Desktop (community) 2.3.0.5.
+NOTE: all of these commands assume that the xReg repository contents are located in `~/xreg-git`.
 
 ### Ubuntu 16.04 Build
 

docker/example_commands

@@ -18,7 +18,6 @@ docker build -t xreg-deps-${OS_NAME}-${OS_VERSION} --build-arg os_name=${OS_NAME
 
 # Build xReg
 docker build -t xreg-${OS_NAME}-${OS_VERSION} --build-arg os_name=${OS_NAME} --build-arg os_version=${OS_VERSION} -f ~/xreg-git/docker/Dockerfile.xreg ~/xreg-git
-i
 
 # Create xReg distributable
 docker build -t xreg-dist-${OS_NAME}-${OS_VERSION} --build-arg os_name=${OS_NAME} --build-arg os_version=${OS_VERSION} -f ~/xreg-git/docker/Dockerfile.xreg-dist-bin ~/xreg-git

tests/wiki_cmds.py

@@ -132,8 +132,26 @@ def macos_check_for_dyld_vars():
  time.sleep(5)
 
 if __name__ == '__main__':
+ mac_slicer_default_path = '/Applications/Slicer.app/Contents/MacOS/Slicer'
+ win_slicer_default_path = 'C:\\Program Files\\Slicer 4.10.2\\Slicer.exe'
+ linux_slicer_default_path = '$HOME/Slicer-4.10.2-linux-amd64/Slicer'
+
  if ('--help' in sys.argv) or ('-h' in sys.argv):
- print('TODO: help message')
+ print('This script exists for semi-automatic functional testing by executing the commands '
+ 'found on the xReg wiki walkthrough and having the user manually verify the outputs.\n'
+ 'Usage: python {} [<xReg bin directory>]\n'
+ 'xReg binaries will be found via the PATH environment variable when an xReg bin '
+ 'directory is not provided.\n'
+ 'When available on the system, 3D Slicer is automatically invoked to visualize volumes.'
+ 'Depending on the operating system, 3D Slicer is assumed to reside in one of the '
+ 'following locations:\n'
+ ' * MacOS: {}\n'
+ ' * Windows: {}\n'
+ ' * Linux: {}'.format(
+ os.path.basename(sys.argv[0]),
+ mac_slicer_default_path,
+ win_slicer_default_path,
+ linux_slicer_default_path))
  sys.exit(0)
  elif len(sys.argv) > 1:
  xreg_bin_dir = sys.argv[1]
@@ -155,18 +173,14 @@ def macos_check_for_dyld_vars():
  slicer_path = None
 
  if platform.system() == 'Darwin':
- mac_slicer_default_path = '/Applications/Slicer.app/Contents/MacOS/Slicer'
-
  if os.path.exists(mac_slicer_default_path):
  slicer_path = mac_slicer_default_path
  elif platform.system() == 'Windows':
- win_slicer_default_path = 'C:\\Program Files\\Slicer 4.10.2\\Slicer.exe'
-
  if os.path.exists(win_slicer_default_path):
  # enclose the path in quotes to handle any spaces
  slicer_path = '\"{}\"'.format(win_slicer_default_path)
  elif platform.system() == 'Linux':
- linux_slicer_default_path = os.path.expandvars('$HOME/Slicer-4.10.2-linux-amd64/Slicer')
+ linux_slicer_default_path = os.path.expandvars(linux_slicer_default_path)
 
  if os.path.exists(linux_slicer_default_path):
  slicer_path = linux_slicer_default_path
@@ -354,3 +368,52 @@ def macos_check_for_dyld_vars():
  view_movie('edges.mp4')
  view_movie('mov.mp4')
 
+ #################################################################
+ # Based off: https://github.com/rg2/xreg/wiki/Example%3A-TCIA-Hip-Radiograph-Rigid-Registration
+ if True:
+ print('Workflow for 2D/3D registration to real pelvis radiograph...')
+
+ print('3D DICOM conversion/resampling...')
+
+ download_file('https://services.cancerimagingarchive.net/services/v4/TCIA/query/getImage?SeriesInstanceUID=1.3.6.1.4.1.14519.5.2.1.1706.4016.124291161306415775701317569638', 'TCGA-G2-A3VY_ct.zip', True)
+
+ extract_zip('TCGA-G2-A3VY_ct.zip', 'TCGA-G2-A3VY_ct_dcm')
+
+ run_cmd('xreg-convert-dicom-vols --one TCGA-G2-A3VY_ct_dcm TCGA-G2-A3VY_ct.nii.gz')
+
+ view_vol('TCGA-G2-A3VY_ct.nii.gz', slicer_path)
+
+ download_file('https://raw.githubusercontent.com/wiki/rg2/xreg/examples/tcia_hip_radiograph_rigid_2d_3d/TCGA-G2-A3VY_ct_full_pelvis-label.nii.gz', use_existing=True)
+
+ download_file('https://github.com/rg2/xreg/wiki/examples/tcia_hip_radiograph_rigid_2d_3d/pelvis_3d_lands.fcsv', use_existing=True)
+
+ print('Creating 3D mesh of pelvis...')
+ run_cmd('xreg-create-mesh TCGA-G2-A3VY_ct_full_pelvis-label.nii.gz pelvis.ply 1 2')
+
+ print('2D DICOM conversion...')
+
+ download_file('https://services.cancerimagingarchive.net/services/v4/TCIA/query/getImage?SeriesInstanceUID=1.3.6.1.4.1.14519.5.2.1.1706.4016.146872675804132000774592060313', 'TCGA-G2-A3VY_radiographs_1.zip', True)
+
+ extract_zip('TCGA-G2-A3VY_radiographs_1.zip', 'TCGA-G2-A3VY_radiographs')
+
+ download_file('https://github.com/rg2/xreg/wiki/examples/tcia_hip_radiograph_rigid_2d_3d/2-c73e.fcsv', use_existing=True)
+
+ run_cmd('xreg-convert-dicom-radiograph TCGA-G2-A3VY_radiographs/2-c73e4bdf6c7d19772d00acd2891965fa.dcm 2-c73e_pd.h5 2-c73e.fcsv')
+
+ run_cmd('xreg-remap-tile-proj-data -d 0.25 -o 2-c73e_pd.h5 2-c73e_remap.png')
+
+ view_image('2-c73e_remap.png')
+
+ run_cmd('xreg-draw-xray-scene -i -l 2-c73e_pd.h5 pelvis.ply - pelvis_3d_lands.fcsv -')
+
+ print('2D/3D registration of pelvis..')
+
+ run_cmd('xreg-hip-surg-pelvis-single-view-regi-2d-3d TCGA-G2-A3VY_ct.nii.gz pelvis_3d_lands.fcsv 2-c73e_pd.h5 2-c73e_pelvis_regi.h5 2-c73e_regi_debug.h5 --no-log-remap -s TCGA-G2-A3VY_ct_full_pelvis-label.nii.gz')
+
+ run_cmd('xreg-draw-xray-scene -i -l 2-c73e_pd.h5 pelvis.ply 2-c73e_pelvis_regi.h5 pelvis_3d_lands.fcsv 2-c73e_pelvis_regi.h5')
+
+ run_cmd('xreg-regi2d3d-replay --proj-ds 0.5 --video-fps 10 2-c73e_regi_debug.h5')
+
+ view_movie('edges.mp4')
+ view_movie('mov.mp4')
+