Merge pull request #7 from rg2/devel

Merging Latest Development Branch

CMakeLists.txt

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020 Robert Grupp
+# Copyright (c) 2020-2021 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
@@ -22,13 +22,13 @@
 
 cmake_minimum_required(VERSION 3.13.0 FATAL_ERROR)
 
-if (APPLE)
-  # Target MacOS 10.14, Mojave
-  set (CMAKE_OSX_DEPLOYMENT_TARGET "10.14" CACHE STRING "MacOS Deployment Target")
-endif ()
+#if (APPLE)
+#  # Target MacOS 10.14, Mojave
+#  set (CMAKE_OSX_DEPLOYMENT_TARGET "10.14" CACHE STRING "MacOS Deployment Target")
+#endif ()
 
 # Version format is YYYY.MM.DD for a release and YYYY.MM.DD.1 for devel after the release
-project(xreg VERSION 2020.12.13.0)
+project(xreg VERSION 2020.12.13.1)
 
 set (CMAKE_CXX_STANDARD "11" CACHE STRING "C++ Standard (needs at least 11)")
 mark_as_advanced(CMAKE_CXX_STANDARD)

README.md

@@ -70,7 +70,9 @@ The [docker](docker) directory demonstrates how Docker may be used to build the
   * Highly recomended for GPU acceleration: OpenCL (1.x)
     * Only needed at runtime on Windows and Linux and is typically provided with your graphics drivers or CUDA SDK
     * 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.
+  * Optional: [ffmpeg](https://ffmpeg.org) is used for writing videos when it is found in the system path. When ffmpeg is not found, the following fallbacks are used:
+    * MacOS: a video writer using AVFoundation,
+    * Windows, Linux, something else: a writer using OpenCV.
 
 ## 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).

apps/hip_surgery/pelvis_single_view_regi_2d_3d/xreg_hip_surg_pelvis_single_view_regi_2d_3d_main.cpp

@@ -87,6 +87,10 @@ int main(int argc, char* argv[])
          "Do NOT convert RAS to LPS (or LPS to RAS) for the 3D landmarks; "
          "RAS to LPS conversion negates the first and second components.")
     << false;
+
+  po.add("no-log-remap", ProgOpts::kNO_SHORT_FLAG, ProgOpts::kSTORE_TRUE, "no-log-remap",
+         "Do NOT perform log remapping of the projection intensities during pre-processing.")
+    << false;
 
   po.add_backend_flags();
 
@@ -130,6 +134,8 @@ int main(int argc, char* argv[])
 
   const unsigned char pelvis_label = static_cast<unsigned char>(po.get("pelvis-label").as_uint32());
 
+  const bool no_log_remap = po.get("no-log-remap");
+
   //////////////////////////////////////////////////////////////////////////////
   // Read in input intensity volume
 
@@ -167,6 +173,7 @@ int main(int argc, char* argv[])
   PrintLandmarkMap(lands_3d, vout);
 
   ProjPreProc proj_preproc;
+  proj_preproc.params.no_log_remap = no_log_remap;
 
   {
     vout << "reading projection data..." << std::endl;

apps/image_io/CMakeLists.txt

@@ -1,6 +1,6 @@
 # MIT License
 #
-# Copyright (c) 2020 Robert Grupp
+# Copyright (c) 2020-2021 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
@@ -28,4 +28,9 @@ add_subdirectory(extract_nii_from_proj_data)
 add_subdirectory(add_lands_to_proj_data)
 add_subdirectory(draw_xray_scene)
 add_subdirectory(regi2d3d_replay)
+add_subdirectory(convert_rad_raw_to_proj_data)
+add_subdirectory(convert_sta_raw_to_itk)
+add_subdirectory(convert_radiograph_dicom_to_proj_data)
+add_subdirectory(make_video_from_image_dir)
+add_subdirectory(remap_dicom_dir)
 

apps/image_io/add_lands_to_proj_data/xreg_add_lands_to_proj_data_main.cpp

@@ -1,7 +1,7 @@
 /*
  * MIT License
  *
- * Copyright (c) 2020 Robert Grupp
+ * Copyright (c) 2020-2021 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
@@ -55,6 +55,18 @@ int main(int argc, char* argv[])
   po.add("no-pat-rot-up", ProgOpts::kNO_SHORT_FLAG, ProgOpts::kSTORE_TRUE, "no-pat-rot-up",
          "Ignore any flags for rotating the image to achieve patient \"up\" orientation.")
     << false;
+
+  po.add("fcsv-spacing", ProgOpts::kNO_SHORT_FLAG, ProgOpts::kSTORE_DOUBLE, "fcsv-spacing",
+         "Default (isotopic) pixel spacing to assume when parsing FCSV landmarks when no 2D pixel "
+         "spacing is provided by the 2D image metadata.")
+    << 1.0;
+
+  po.add("use-pd-spacing", ProgOpts::kNO_SHORT_FLAG, ProgOpts::kSTORE_TRUE, "use-pd-spacing",
+         "Always use the pixel spacings encoded in the projection data file when interpreting "
+         "FCSV files, even when the pixel spacings were not explicitly provided by the source "
+         "image format. This is useful when an FCSV file was created using a NIFTI file which "
+         "was extracted from a projection data file with estimated spacings.")
+    << false;
 
   try
   {
@@ -78,6 +90,10 @@ int main(int argc, char* argv[])
 
   const bool ignore_pat_rot_up = po.get("no-pat-rot-up");
 
+  const double default_fcsv_spacing = po.get("fcsv-spacing");
+
+  const bool use_pd_spacing = po.get("use-pd-spacing");
+
   vout << "opening proj data for reading/writing..." << std::endl;
   H5::H5File h5(po.pos_args()[0], H5F_ACC_RDWR);
 
@@ -123,6 +139,27 @@ int main(int argc, char* argv[])
       CoordScalar spacing_for_phys_to_ind_x = cur_cam.det_col_spacing;
       CoordScalar spacing_for_phys_to_ind_y = cur_cam.det_row_spacing;
 
+      // The following conditional addresses the UNCOMMON problem listed below:
+      // Suppose that our source data does not have explicit metadata listing pixel spacings,
+      // so the conversion to projection data HDF5 format used some additional information to
+      // estimate the pixel spacings. Now, also suppose that 3D Slicer is not able to read in
+      // the source data - this has happened with certain DICOMs from TCIA with RF modality.
+      // In order to annotate landmarks, a NIFTI (.nii.gz) file is extracted from the projection
+      // HDF5 file and then loaded into 3D Slicer for landmark annotation. This NIFTI file has
+      // the estimated pixel spacings embedded, and therefore the FCSV annotations are physical
+      // points calculated using these spacings. When the contents of the FCSV are then loaded
+      // back into the HDF5 projection data (e.g. using THIS TOOL), the current behavior is to use
+      // a user-provided spacing when the original source data did not have explicit pixel spacings
+      // provided. Although this is the most common case and default desired behavior, for the
+      // previously identified scenario we need to use the estimated pixel spacings present in the
+      // HDF5 file.
+      if (!use_pd_spacing && cur_proj_meta.det_spacings_from_orig_meta &&
+          !*cur_proj_meta.det_spacings_from_orig_meta)
+      {
+        spacing_for_phys_to_ind_x = default_fcsv_spacing;
+        spacing_for_phys_to_ind_y = default_fcsv_spacing;
+      }
+
       bool need_to_rot = false;
 
       const bool check_rot_field = !ignore_pat_rot_up && cur_proj_meta.rot_to_pat_up;

apps/image_io/convert_rad_raw_to_proj_data/CMakeLists.txt

@@ -0,0 +1,30 @@
+# MIT License
+#
+# Copyright (c) 2021 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.
+
+set(EXE_NAME "${XREG_EXE_PREFIX}convert-rad-raw-to-proj-data")
+
+add_executable(${EXE_NAME} xreg_convert_rad_raw_to_proj_data_main.cpp)
+
+target_link_libraries(${EXE_NAME} PUBLIC ${XREG_EXE_LIBS_TO_LINK})
+
+install(TARGETS ${EXE_NAME})
+

apps/image_io/convert_rad_raw_to_proj_data/xreg_convert_rad_raw_to_proj_data_main.cpp

@@ -0,0 +1,91 @@
+/*
+ * MIT License
+ *
+ * Copyright (c) 2021 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.
+ */
+
+#include "xregProgOptUtils.h"
+#include "xregH5ProjDataIO.h"
+#include "xregRadRawProj.h"
+
+using namespace xreg;
+
+int main(int argc, char* argv[])
+{
+  constexpr int kEXIT_VAL_SUCCESS  = 0;
+  constexpr int kEXIT_VAL_BAD_USE  = 1;
+
+  ProgOpts po;
+
+  xregPROG_OPTS_SET_COMPILE_DATE(po);
+
+  po.set_help("Converts a collection of 2D projection images from .rad/.raw format "
+              "into an HDF5 projection data file for use by xReg. "
+              "This may be used to convert projections from the Ljubljana 2D/3D datasets "
+              "located at: http://lit.fe.uni-lj.si/tools.php?lang=eng.");
+  po.set_arg_usage("<Output Proj. Data File> <.rad path #1> [<.rad path #2> [... <.rad path #N>]]");
+  po.set_min_num_pos_args(2);
+
+  try
+  {
+    po.parse(argc, argv);
+  }
+  catch (const ProgOpts::Exception& e)
+  {
+    std::cerr << "Error parsing command line arguments: " << e.what() << std::endl;
+    po.print_usage(std::cerr);
+    return kEXIT_VAL_BAD_USE;
+  }
+
+  if (po.help_set())
+  {
+    po.print_usage(std::cout);
+    po.print_help(std::cout);
+    return kEXIT_VAL_SUCCESS;
+  }
+
+  std::ostream& vout = po.vout();
+
+  const std::string& dst_pd_path = po.pos_args()[0];
+
+  const size_type num_rad_files = po.pos_args().size() - 1;
+
+  vout << "number of .rad files to read: " << num_rad_files << std::endl;
+
+  ProjDataF32List pd;
+  pd.reserve(num_rad_files);
+
+  for (size_type i = 0; i < num_rad_files; ++i)
+  {
+    const std::string& cur_rad_path = po.pos_args()[i+1]; 
+
+    vout << "reading .rad file #" << (i + 1) << ": " << cur_rad_path << std::endl;
+
+    pd.push_back(ReadRawProjAsProjData(cur_rad_path));
+  }
+
+  vout << "saving to proj data HDF5..." << std::endl;
+  WriteProjDataH5ToDisk(pd, dst_pd_path);
+
+  vout << "exiting..." << std::endl;
+  return kEXIT_VAL_SUCCESS;
+}
+

apps/image_io/convert_radiograph_dicom_to_proj_data/CMakeLists.txt

@@ -0,0 +1,30 @@
+# MIT License
+#
+# Copyright (c) 2021 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.
+
+set(EXE_NAME "${XREG_EXE_PREFIX}convert-radiograph-dcm-to-proj-data")
+
+add_executable(${EXE_NAME} xreg_convert_radiograph_dcm_to_proj_data_main.cpp)
+
+target_link_libraries(${EXE_NAME} PUBLIC ${XREG_EXE_LIBS_TO_LINK})
+
+install(TARGETS ${EXE_NAME})
+