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NIST-MNI · Aug 4, 2017 · fc0f9ce · fc0f9ce
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diff --git a/examples/add_configuration/cerebellum_segment_options.json b/examples/add_configuration/cerebellum_segment_options.json
@@ -0,0 +1,10 @@
+{
+  "local_linear_register": true,
+  "non_linear_pairwise": false,
+  "simple_fusion": false,
+  "non_linear_register_level": 2,
+  "resample_order": 2,
+  "resample_baa": true,
+  "library_preselect":10,
+  "fuse_options": {"patch":1,"search":1,"threshold":0.0,"gco_energy":null}
+}
diff --git a/examples/add_configuration/cv_cerebellum.json b/examples/add_configuration/cv_cerebellum.json
@@ -0,0 +1,3 @@
+{
+  "library":"manual_library_cerebellum.lst"
+}
diff --git a/examples/add_configuration/manual_library_cerebellum.json b/examples/add_configuration/manual_library_cerebellum.json
@@ -0,0 +1,46 @@
+{
+  "reference_model": "../../models/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c.mnc",
+  "reference_mask":  "../../models/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_mask.mnc",
+  "library":"manual_library_cerebellum.lst",
+  "build_remap": [  [101,1],
+                    [103,2],
+                    [105,3],
+                    [107,4],
+                    [108,5],
+                    [109,6],
+                    [113,7],
+                    [115,8],
+                    [116,9],
+                    [117,10],
+                    [119,11],
+                    [121,12],
+                    [123,13],
+                    [125,14],
+                    [131,15],
+                    [133,16],
+                    [135,17],
+                    [137,18],
+                    [138,19],
+                    [139,20],
+                    [143,21],
+                    [145,22],
+                    [146,23],
+                    [147,24],
+                    [149,25],
+                    [153,26],
+                    [155,27],
+                    [171,28],
+                    [200,29],
+                    [201,30],
+                    [300,31],
+                    [301,32],
+                    [400,33],
+                    [500,34] ] ,
+  "classes": 35,
+  "linear_register": false,
+  "local_linear_register": true,
+  "non_linear_register": true,
+  "non_linear_register_level": 2,
+  "resample_baa": true,
+  "resample_order": 2
+}
diff --git a/examples/real_tests/test_grading/cv.json b/examples/real_tests/test_grading/cv.json
@@ -0,0 +1,8 @@
+{
+  "validation_library":"snipe_library.lst",
+  "iterations":-1,
+  "cv":1,
+  "fuse_variant":"fuse",
+  "cv_variant":"cv",
+  "regularize_variant":"reg_1"
+}
diff --git a/examples/real_tests/test_grading/cv_results.R b/examples/real_tests/test_grading/cv_results.R
@@ -0,0 +1,70 @@
+library(ggplot2)
+library(jsonlite)
+library(grid)
+library(plyr)
+theme_set(theme_bw(base_size = 14, base_family = "Arial"))
+
+cv_slow<-fromJSON("test_cv/cv_stats.json") 
+cv_fast<-fromJSON("test_cv_fast/cv_stats.json") 
+cv_lin<-fromJSON("test_cv_lin/cv_stats.json") 
+cv_v_slow<-fromJSON("test_cv_slow/cv_stats.json")
+cv_v_slow_1<-fromJSON("test_cv_slow_1/cv_stats.json")
+
+cv_kappa<-data.frame(
+  cv_slow=cv_slow$gkappa,
+  cv_fast=cv_fast$gkappa,
+  cv_lin=cv_lin$gkappa,
+  cv_v_slow=cv_v_slow$gkappa,
+  cv_v_slow_1=cv_v_slow_1$gkappa
+    )
+
+cvv<-stack(cv_kappa)
+
+names(cvv)=c('GenKappa','Method')
+
+png('cv_kappa.png',width=800,height=400,type='cairo')
+
+ggplot(data=cvv,aes(x=Method,y=GenKappa))+
+ geom_boxplot(notch=T)+
+ theme_bw()+
+ theme(
+   axis.text = element_text(face = 'bold', vjust = 0.2, size = 18),
+   axis.title = element_text(face = 'bold', vjust = 0.2, size = 20),
+   plot.margin = unit(c(0.2,2.8,0.2,0.2), "cm")
+   )
+
+
+slen=length(names(cv_slow$result))
+lcv <- vector(mode = "list", length = slen)
+
+for(l in seq(slen)) {
+  i=names(cv_slow$result)[l]
+  cv_grading<-data.frame(
+    grad_slow=cv_slow$result[,i]$grad,
+    grad_fast=cv_fast$result[,i]$grad,
+    grad_lin=cv_lin$result[,i]$grad,
+    grad_v_slow=cv_v_slow$result[,i]$grad,
+    grad_v_slow_1=cv_v_slow_1$result[,i]$grad
+  )
+  lcv[[l]]<-stack(cv_grading)
+  names(lcv[[l]])=c('Grading','Method')
+  lcv[[l]]$group=rep(cv_slow$group,length(names(cv_grading)))
+  lcv[[l]]$struct=rep(i,length(lcv[[l]]$group))
+}
+
+cvv<-rbind.fill(lcv)
+cvv$struct<-as.factor(as.numeric(cvv$struct))
+cvv$group<-as.factor(cvv$group)
+
+png('cv_grading.png',width=800,height=800,type='cairo')
+
+ggplot(data=cvv,aes(x=group,y=Grading,colour=Method))+
+ geom_boxplot(notch=T)+
+ theme_bw()+
+ facet_grid(struct~Method)+
+ geom_abline(intercept=0,slope=0,colour='red',lty=2)+
+ theme(
+   axis.text = element_text(face = 'bold', vjust = 0.2, size = 18),
+   axis.title = element_text(face = 'bold', vjust = 0.2, size = 20),
+   plot.margin = unit(c(0.2,2.8,0.2,0.2), "cm")
+   )
diff --git a/examples/real_tests/test_grading/grade.json b/examples/real_tests/test_grading/grade.json
@@ -0,0 +1,35 @@
+{
+  "initial_local_register": false,
+  "non_linear_pairwise": false,
+  "non_linear_register": true,
+  "non_linear_register_ants": true,
+
+  "non_linear_register_level": 2,
+  "non_linear_register_start": 8,
+
+  "non_linear_register_options": {
+        "conf":   {"8":100,"4":40,"2":40,"1": 20  },
+        "blur":   {"8":8  ,"4":4 ,"2":2, "1": 1   },
+        "shrink": {"8":8  ,"4":4 ,"2":2, "1": 1   },
+
+        "transformation": "SyN[ .25, 1.0 , 1.0 ]",
+        "use_histogram_matching": true,
+        "cost_function":"CC",
+        "cost_function_par":"1,3,Regular,1.0"
+  },  
+
+  "simple_fusion": false,
+  "resample_order": 1,
+  "resample_baa": true,
+  "library_preselect": -1,
+  "segment_symmetric": false,
+
+  "fuse_options":
+  {
+      "patch": 1,
+      "search": 1,
+      "threshold": 0.0,
+      "top": 4
+  }
+
+}
diff --git a/examples/real_tests/test_grading/library_description.json b/examples/real_tests/test_grading/library_description.json
@@ -0,0 +1,50 @@
+{
+  "reference_model": "snipe_library/NC/T1/ADNI.stx_011_S_0002_m00_bbox_snipe.mnc",
+  "reference_mask":  "snipe_library/whole.mnc",
+
+  "reference_local_model" : null,
+  "reference_local_mask" :  null,
+  "library":"snipe_library.lst",
+
+  "build_remap":         [ [2,1],
+                           [4,2],
+                           [19,3],
+                           [21,4]],
+
+  "build_flip_remap":    null,
+  "parts": 0,
+  "classes": 5,
+  "groups": 2,
+  "build_symmetric": false,
+  "build_symmetric_flip": false,
+  "symmetric_lut": null,
+  "denoise": false,
+  "denoise_beta": null,
+
+  "initial_register": false,
+  "initial_local_register": false,
+
+  "non_linear_register": true,
+  "non_linear_register_type": "ants",
+
+  "non_linear_register_level": 2,
+  "non_linear_register_start": 8,
+
+  "non_linear_register_options": {
+        "conf":   {"8":100,"4":40,"2":40,"1": 20  },
+        "blur":   {"8":8  ,"4":4 ,"2":2, "1": 1   },
+        "shrink": {"8":8  ,"4":4 ,"2":2, "1": 1   },
+
+        "transformation": "SyN[ .25, 1.0 , 1.0 ]",
+        "use_histogram_matching": true,
+        "cost_function":"CC",
+        "cost_function_par":"1,3,Regular,1.0"
+  },
+
+  "resample_order": 1,
+  "resample_baa": true,
+  "extend_boundary": 4,
+  "op_mask": "E[2] D[4]",
+
+  "create_patch_norm_lib": false
+}
diff --git a/examples/real_tests/test_grading/run_test.sh b/examples/real_tests/test_grading/run_test.sh
@@ -0,0 +1,131 @@
+#! /bin/sh
+set -e
+
+PREFIX=$(pwd)/../../python
+
+export PYTHONPATH=$PREFIX:$PYTHONPATH
+
+
+cat - > library_description.json <<END
+{
+  "reference_model": "snipe_library/NC/T1/ADNI.stx_011_S_0002_m00_bbox_snipe.mnc",
+  "reference_mask":  "snipe_library/whole.mnc",
+  
+  "reference_local_model" : null,
+  "reference_local_mask" :  null,
+  "library":"snipe_library.lst",
+
+  "build_remap":         [ [2,1],
+                           [4,2],
+                           [19,3],
+                           [21,4]],
+                            
+  "build_flip_remap":    null,
+  "parts": 0,
+  "classes": 5,
+  "groups": 2,
+  "build_symmetric": false,
+  "build_symmetric_flip": false,
+  "symmetric_lut": null,
+  "denoise": false,
+  "denoise_beta": null,
+  
+  "initial_register": false,
+  "initial_local_register": false,
+  
+  "non_linear_register": true,
+  "non_linear_register_type": "ants",
+  
+  "non_linear_register_level": 2,
+  "non_linear_register_start": 8,
+  
+  "non_linear_register_options": {
+        "conf":   {"8":100,"4":40,"2":40,"1": 20  },
+        "blur":   {"8":8  ,"4":4 ,"2":2, "1": 1   },
+        "shrink": {"8":8  ,"4":4 ,"2":2, "1": 1   },
+
+        "transformation": "SyN[ .25, 1.0 , 1.0 ]",
+        "use_histogram_matching": true,
+        "cost_function":"CC",
+        "cost_function_par":"1,3,Regular,1.0"
+  },
+  
+  "resample_order": 1,
+  "resample_baa": true,
+  "extend_boundary": 4,
+  "op_mask": "E[2] D[4]",
+  
+  "create_patch_norm_lib": false
+}
+END
+
+
+if [ ! -e test_lib/library.json ];then
+# create the library
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+
+python -m scoop -n 4 $PREFIX/iplScoopFusionGrading.py  \
+  --create library_description.json --output test_lib --debug
+fi
+# run cross-validation
+
+cat - > cv.json <<END
+{
+  "validation_library":"snipe_library.lst",
+  "iterations":-1,
+  "cv":1,
+  "fuse_variant":"fuse",
+  "cv_variant":"cv",
+  "regularize_variant":"reg_1"
+}
+END
+
+
+cat - > grade.json <<END
+{
+  "initial_local_register": false,
+  "non_linear_pairwise": false,
+  "non_linear_register": true,
+  "non_linear_register_ants": true,
+  
+  "non_linear_register_level": 2,
+  "non_linear_register_start": 8,
+
+  "non_linear_register_options": {
+        "conf":   {"8":100,"4":40,"2":40,"1": 20  },
+        "blur":   {"8":8  ,"4":4 ,"2":2, "1": 1   },
+        "shrink": {"8":8  ,"4":4 ,"2":2, "1": 1   },
+
+        "transformation": "SyN[ .25, 1.0 , 1.0 ]",
+        "use_histogram_matching": true,
+        "cost_function":"CC",
+        "cost_function_par":"1,3,Regular,1.0"
+  },  
+
+  "simple_fusion": false,
+  "resample_order": 1,
+  "resample_baa": true,
+  "library_preselect": -1,
+  "segment_symmetric": false,
+
+  "fuse_options":
+  {
+      "patch": 1,
+      "search": 1,
+      "threshold": 0.0,
+      "top": 4
+  }
+
+}
+END
+
+mkdir -p test_cv
+
+export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+python -m scoop -n 4 -vvv \
+  $PREFIX/iplScoopFusionGrading.py \
+   --output test_cv \
+   --debug  \
+   --grade test_lib \
+   --cv cv.json \
+   --options grade.json