Segmentation: refactoring

.gitignore

@@ -8,8 +8,6 @@ CMakeFiles
 ITKIOFactoryRegistration
 cmake_install.cmake
 
-/make/itk/itk-config.mk.gen
-
 /ComputeFrangi/Makefile
 /ComputeFrangi/ComputeEigenValue_Sorted_Frangi
 
@@ -21,6 +19,7 @@ ComputeFilter
 /.build
 /.deps
 /bin
+/doxygen-doc
 
 *~
 *.a

.travis.yml

@@ -1,16 +1,19 @@
 language: c
-sudo: false
+os: linux
+dist: trusty
+sudo: required
+addons:
+  apt:
+    packages:
+      - libvtk6-dev
+      - libinsighttoolkit4-dev
 env:
   - PROD=1 TEST_VERBOSE=1
   - PROD=1 TEST_VERBOSE=1 COVERAGE=1
 compiler:
   - gcc
   - clang
 before_install:
-  - mkdir build
-  - git clone https://github.com/CBL-ORION/ITK-builds.git external/ITK
-  # path for CMake to search for built ITK
-  - export ITK_DIR="`( cd external/ITK/usr/local/lib/cmake/ITK-4.9 && pwd )`"
   - if [ "$COVERAGE" = 1 ]; then pip install --user cpp-coveralls;  fi
 script:
   # version of gcc on Travis-CI does not support ASAN flag

Makefile

@@ -7,6 +7,14 @@ BIN_SRC_CONFIG.c   := $(SRCDIR)/config/configurator.c
 BIN_SRC.cc  := $(SRCDIR)/compute-filter/ComputeFilter.cxx $(SRCDIR)/subsample-volume/SubsampleVolume.cxx
 #LIB_SRC.c  := $(LIBDIR)/ndarray/ndarray3.c  # $(LIBDIR)/filter/hdaf/Makefilter.c
 LIB_SRC.c  := $(shell find $(LIBDIR) -path lib/t -prune -o  -type f -name '*.c' \! -name '*_impl.c' -print)
+LIB_SRC.cc  := $(shell find $(LIBDIR) \
+	-path lib/t -prune -o \
+	-path lib/vaa3d-plugin -prune -o \
+	-path lib/config -prune -o \
+	-path lib/filter/vesselness -prune -o \
+	-path lib/integration -prune -o \
+	-type f -name '*.cxx' -print)
+$(echo $(LIB_SRC.cc))
 TEST.c := $(shell find $(TESTDIR) -path lib/t/liborion3mat -prune -o -type f -name "*.c" -print)
 ifdef FEAT_LIBORION3MAT
 TEST.c  += $(TESTDIR)/liborion3mat/test.c
@@ -16,11 +24,13 @@ include make/autodep.mk
 
 ## Target files
 OBJ_PATHSUBST.c  = $(patsubst $(LIBDIR)/%.c,$(BUILDDIR)/%.o,$(1))
+OBJ_PATHSUBST.cc  = $(patsubst $(LIBDIR)/%.cxx,$(BUILDDIR)/%.o,$(1))
 TEST_PATHSUBST.c = $(patsubst $(TESTDIR)/%.c,$(BUILDTESTDIR)/%$(EXEEXT),$(1))
 BIN_PATHSUBST.c  = $(patsubst $(SRCDIR)/%.c,$(BINDIR)/%$(EXEEXT),$(1))
 BIN_PATHSUBST.cc  = $(patsubst $(SRCDIR)/%.cxx,$(BINDIR)/%$(EXEEXT),$(1))
 
-MKDIR_BUILD = mkdir -p `dirname $(call OBJ_PATHSUBST.c,$<)`
+MKDIR_BUILD.c = mkdir -p `dirname $(call OBJ_PATHSUBST.c,$<)`
+MKDIR_BUILD.cc = mkdir -p `dirname $(call OBJ_PATHSUBST.cc,$<)`
 MKDIR_BIN   = mkdir -p `dirname $(call BIN_PATHSUBST.c,$<)`
 MKDIR_BUILDTESTDIR = mkdir -p `dirname $(call TEST_PATHSUBST.c,$<)`
 
@@ -29,9 +39,11 @@ include make/vaa3d-plugin-config.mk
 include make/test-config.mk
 include make/liborion3mat-config.mk
 include make/misc-config.mk
+include make/liborion-config.mk
 
 ## Generate the targets
 LIB_OBJ:= $(call OBJ_PATHSUBST.c,$(LIB_SRC.c))
+LIB_OBJ+= $(call OBJ_PATHSUBST.cc,$(LIB_SRC.cc))
 
 TEST_OBJ:= $(call TEST_PATHSUBST.c,$(TEST.c))
 
@@ -43,7 +55,7 @@ CONFIG_HEADER_FILE := $(LIBDIR)/config/config.h
 $(CONFIG_HEADER_FILE): $(BIN_BIN_CONFIG.c)
 	$(BIN_BIN_CONFIG.c) > $@
 
-.PHONY: tags
+.PHONY: tags $(DOXYGENDIR)
 
 ifdef PROD
   DEV_TARGETS :=
@@ -66,6 +78,7 @@ clean:
 	-find . -type f -name '*.o' -delete
 	-find . -type f \( -name '*.gcda' -o -name '*.gcno' -o -name '*.gcov' \) -delete
 	-rm -Rf $(OUTPUT_DIRS)
+	-rm -Rf $(DOXYGENDIR)
 	-rm -Rf $(ITK_CONFIG_MK)
 	-rm -Rf $(GCOVDIR) $(LCOVDIR)
 	-rm -Rf $(CONFIG_HEADER_FILE)
@@ -78,6 +91,10 @@ include make/00-implicit-rules.mk
 -include $(LIB_SRC.c:$(LIBDIR)/%.c=$(DEPDIR)/$(LIBDIR)/%.P)
 -include $(TEST.c:$(TESTDIR)/%.c=$(DEPDIR)/$(TESTDIR)/%.P)
 
+doc: $(DOXYGENDIR)
+
+$(DOXYGENDIR): make/Doxyfile
+	doxygen $<
 tags:
 	ctags --exclude=external -R .
 	# add the ORION 3 code to the tags so that it is easy to jump to the other codebase

debian-packages

@@ -0,0 +1,2 @@
+cmake
+libinsighttoolkit4-dev

lib/config/platform.h

@@ -0,0 +1,41 @@
+#ifndef CONFIG_PLATFORM_H
+#define CONFIG_PLATFORM_H 1
+
+/* define OS_* macros */
+#if defined(_WIN32)
+  #define OS_WINDOWS 1
+#else
+  #define OS_UNIX 1
+#endif
+
+
+/* Platform specific settings */
+
+/* On Windows */
+#if OS_WINDOWS
+  #if _MSC_VER && !__INTEL_COMPILER
+    /* Microsoft compiler */
+
+    /* needed for the secure rand_s function */
+    #define _CRT_RAND_S 1
+    #include <stdlib.h>
+
+  #endif
+
+  /* the extension used for executables */
+  #ifndef PLATFORM_EXE_EXT
+    #define PLATFORM_EXE_EXT ".exe"
+  #endif /* PLATFORM_EXE_EXT */
+
+#endif /* OS_WINDOWS */
+
+#if OS_UNIX
+
+  /* the extension used for executables */
+  #ifndef PLATFORM_EXE_EXT
+    #define PLATFORM_EXE_EXT ""
+  #endif /* PLATFORM_EXE_EXT */
+
+#endif /* OS_UNIX */
+
+#endif /* CONFIG_PLATFORM_H */

lib/container/array_impl.c

@@ -67,3 +67,8 @@ void TYPED_NAME(array_resize) ( TYPED_NAME(array)* array, size_t new_capacity )
 	RESIZE_COUNT(array->data, TYPE, new_capacity);
 	array->capacity = new_capacity;
 }
+
+void TYPED_NAME(array_reset) ( TYPED_NAME(array)* array ) {
+	assert( array != NULL );
+	array->length = 0;
+}

lib/container/array_impl.h

@@ -33,6 +33,8 @@ extern void TYPED_NAME(array_add) ( TYPED_NAME(array)* array, TYPE data );
 
 /* ==== memory management ==== */
 extern void TYPED_NAME(array_resize) ( TYPED_NAME(array)* array, size_t new_capacity );
+/* Resets the length of the array to zero. Does not free elements! */
+extern void TYPED_NAME(array_reset) ( TYPED_NAME(array)* array );
 
 #ifdef __cplusplus
 };

lib/io/path/path.c

@@ -21,7 +21,6 @@ orion_filepath* orion_filepath_new_from_string(const char* fp_string) {
 	char* fp_string_norm;
 	size_t fp_string_norm_len;
 	safe_malloc_and_strcpy(&fp_string_norm, fp_string);
-	size_t fp_string_len = strlen( fp_string );
 
 	orion_filepath* fp = _orion_filepath_init();
 

lib/io/path/path.h

@@ -39,6 +39,7 @@ extern char* orion_filepath_to_string(orion_filepath* fp);
 extern orion_filepath* orion_filepath_base( orion_filepath* fp );
 extern orion_filepath* orion_filepath_dir( orion_filepath* fp );
 
+extern orion_filepath* orion_filepath_cat( orion_filepath* fp1, orion_filepath* fp2 );
 extern orion_filepath* orion_filepath_sibling( orion_filepath* base, orion_filepath* relative);
 
 #ifdef __cplusplus

lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.c

@@ -1,4 +1,6 @@
-/* dead code
+/* TODO turn into test
  *
  * Refactor testSigma
+ *
+ * external/orion3mat/01_Segmentation/dendrites_main/DetectTrainingSet/How_sigma_relates_to_radii/testSigma.m
  */

lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.c

@@ -1,6 +1,3 @@
-/*
- * Refactor: Makefilter
- */
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/Makefilter.h"
 
@@ -11,6 +8,10 @@
 
 #include "kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.h"
 
+/* MATLAB version: Makefilter */
+
+/* TODO document
+ */
 ndarray3* orion_Makefilter(
 		size_t nx, size_t ny, size_t nz,
 		int hdaf_approx_degree,

lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_LP.c

@@ -1,4 +1,4 @@
-/* TODO
+/* TODO: part of testing
  *
  * Refactor: compute_LP
  */

lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/compute_Laplacian.c

@@ -1,4 +1,4 @@
-/* TODO
+/* dead code
  *
  * Refactor: compute_Laplacian
  */

lib/kitchen-sink/01_Segmentation/dendrites_main/DetectTrainingSet/IsotropicFilter/hdaf.c

@@ -1,12 +1,11 @@
-/*
- * Refactor: hdaf
- */
 #include "hdaf.h"
 
 #include <math.h>
 
 #include "numeric/func.h"
 
+/* MATLAB version: hdaf */
+
 /*
  * orion_hdaf( hdaf_approx_degree, scaling_constant, x)
  *