ENH: adding a test using sampled phantom dataset

Test is done on curves extracted from QIN-PROSTATE-001 dataset (see READMEs for
details)

CLI/Testing/Cxx/CMakeLists.txt

@@ -5,6 +5,7 @@ set(TEMP ${PkModeling_BINARY_DIR}/Testing/Temporary)
 #set(DCEMRIDATA ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/DCEMRIData)
 #set(DUKEDATA_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/DukeData)
 #set(SYNDATA ${CMAKE_CURRENT_SOURCE_DIR}/../../Data/SyntheticData)
+set(QINPROSTATE001 ${CMAKE_CURRENT_SOURCE_DIR}/../../../Data/SampledPhantoms/QINProstate001)
 
 set(CLP ${MODULE_NAME})
 
@@ -21,25 +22,78 @@ add_test(NAME ${testname} COMMAND ${Launcher_Command} $<TARGET_FILE:${CLP}Test>
 set_property(TEST ${testname} PROPERTY LABELS ${CLP})
 
 #-----------------------------------------------------------------------------
-if(DUKEDATA_DIR_DIR)
-  set(testname ${CLP}TestDukeSyntheticData)
+if(QINPROSTATE001)
+  set(testname QINProstate001)
   add_test(NAME ${testname} COMMAND ${Launcher_Command} $<TARGET_FILE:${CLP}Test>
+    --compare ${QINPROSTATE001}/Baseline/phantom-ktrans.nrrd
+    ${TEMP}/${testname}-ktrans.nrrd
     ModuleEntryPoint        
-                --T1Tissue 1000
-                --T1Blood 1440
-                --relaxivity 0.0049 
-                --hematocrit 0.45
+                --T1Tissue 1597
+                --T1Blood 1600
+                --relaxivity 0.0039
+                --S0grad 15.0
+                --hematocrit 0.4
                 --aucTimeInterval 90
-                ${DUKEDATA_DIR}/SyntheticDuke.nrrd                   
-                ${DUKEDATA_DIR}/SyntheticDukeMask.nrrd
-                --outputKtrans ${TEMP}/ktransVolumeSyn.nrrd 
-                --outputVe ${TEMP}/veVolumeSyn.nrrd
-                --outputMaxSlope ${TEMP}/maxSlopeVolumeSyn.nrrd
-                --outputAUC ${TEMP}/AUCVolumeSyn.nrrd           
+                --fTolerance 1e-4 
+                --gTolerance 1e-4 
+                --xTolerance 1e-5 
+                --epsilon 1e-9 
+                --maxIter 200 
+                --outputKtrans ${TEMP}/${testname}-ktrans.nrrd 
+                --outputVe ${TEMP}/${testname}-ve.nrrd
+                --outputMaxSlope ${TEMP}/${testname}-maxslope.nrrd
+                --outputAUC ${TEMP}/${testname}-auc.nrrd           
+                --outputBAT ${TEMP}/${testname}-bat.nrrd           
+                --fitted ${TEMP}/${testname}-fit.nrrd
+                --concentrations ${TEMP}/${testname}-conc.nrrd
+                --roiMask ${QINPROSTATE001}/Input/${testname}-phantom-ROI.nrrd
+                --aifMask ${QINPROSTATE001}/Input/${testname}-phantom-AIF.nrrd
+                ${QINPROSTATE001}/Input/${testname}-phantom.nrrd                   
                 )
   set_property(TEST ${testname} PROPERTY LABELS ${CLP})
 endif()
 
+#-----------------------------------------------------------------------------
+#if(DUKEDATA_DIR_DIR)
+#  set(testname ${CLP}TestDukeSyntheticData)
+#  add_test(NAME ${testname} COMMAND ${Launcher_Command} $<TARGET_FILE:${CLP}Test>
+#    ModuleEntryPoint        
+#                --T1Tissue 1000
+#                --T1Blood 1440
+#                --relaxivity 0.0049 
+#                --hematocrit 0.45
+#                --aucTimeInterval 90
+#                ${DUKEDATA_DIR}/SyntheticDuke.nrrd                   
+#                ${DUKEDATA_DIR}/SyntheticDukeMask.nrrd
+#                --outputKtrans ${TEMP}/ktransVolumeSyn.nrrd 
+#                --outputVe ${TEMP}/veVolumeSyn.nrrd
+#                --outputMaxSlope ${TEMP}/maxSlopeVolumeSyn.nrrd
+#                --outputAUC ${TEMP}/AUCVolumeSyn.nrrd           
+#                )
+#  set_property(TEST ${testname} PROPERTY LABELS ${CLP})
+#endif()
+
+
+#-----------------------------------------------------------------------------
+#if(DUKEDATA_DIR_DIR)
+#  set(testname ${CLP}TestDukeSyntheticData)
+#  add_test(NAME ${testname} COMMAND ${Launcher_Command} $<TARGET_FILE:${CLP}Test>
+#    ModuleEntryPoint        
+#                --T1Tissue 1000
+#                --T1Blood 1440
+#                --relaxivity 0.0049 
+#                --hematocrit 0.45
+#                --aucTimeInterval 90
+#                ${DUKEDATA_DIR}/SyntheticDuke.nrrd                   
+#                ${DUKEDATA_DIR}/SyntheticDukeMask.nrrd
+#                --outputKtrans ${TEMP}/ktransVolumeSyn.nrrd 
+#                --outputVe ${TEMP}/veVolumeSyn.nrrd
+#                --outputMaxSlope ${TEMP}/maxSlopeVolumeSyn.nrrd
+#                --outputAUC ${TEMP}/AUCVolumeSyn.nrrd           
+#                )
+#  set_property(TEST ${testname} PROPERTY LABELS ${CLP})
+#endif()
+
 #-----------------------------------------------------------------------------
 # set(testname ${CLP}TestSmallVolumeOfDukeSyntheticData)
 # add_test(NAME ${testname} COMMAND ${Launcher_Command} $<TARGET_FILE:${CLP}Test>

Data/SampledPhantoms/QINProstate001/README

@@ -0,0 +1,5 @@
+qin01-phantom was generated from QIN-PROSTATE dataset available from TCIA, using
+probing.nrrd label.
+
+Details on QIN-PROSTATE collection of TCIA:
+https://wiki.cancerimagingarchive.net/display/Public/QIN+Prostate

Data/SampledPhantoms/README

@@ -0,0 +1,3 @@
+This directory contains phantoms generated from real data using Util/makePhantom.py script.
+These "phantoms" are curves sampled from real data, as should be described in the corresponding
+READMEs in each directory.