Merge branch 'docker' into 'master'

Docker

See merge request !2

config15/test_all_class.txt

@@ -0,0 +1,90 @@
+[data]
+data_root         = [/home/guotwang/data/brats_docker_data/pre_process]
+data_names        = config/test_names.txt
+modality_postfix  = [Flair, T1, T1c, T2]
+
+[network1ax]
+net_type            = MSNet
+net_name            = MSNet_WT32
+downsample_twice    = True
+data_shape          = [19, 180, 160, 4]
+label_shape         = [11, 180, 160, 1]
+class_num           = 2
+model_file          = model/msnet_wt32_10000.ckpt
+
+[network1sg]
+net_type            = MSNet
+net_name            = MSNet_WT32sg
+downsample_twice    = True
+data_shape          = [19, 160, 180, 4]
+label_shape         = [11, 160, 180, 1]
+class_num           = 2
+model_file          = model/msnet_wt32sg_5000.ckpt
+
+[network1cr]
+net_type            = MSNet
+net_name            = MSNet_WT32cr
+downsample_twice    = True
+data_shape          = [19, 160, 160, 4]
+label_shape         = [11, 160, 160, 1]
+class_num           = 2
+model_file          = model/msnet_wt32cr_5000.ckpt
+
+
+[network2ax]
+net_type            = MSNet
+net_name            = MSNet_TC32
+downsample_twice    = True
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 2
+model_file          = model/msnet_tc32_20000.ckpt
+
+[network2sg]
+net_type            = MSNet
+net_name            = MSNet_TC32sg
+downsample_twice    = True
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 2
+model_file          = model/msnet_tc32sg_5000.ckpt
+
+[network2cr]
+net_type            = MSNet
+net_name            = MSNet_TC32cr
+downsample_twice    = True
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 2
+model_file          = model/msnet_tc32cr_5000.ckpt
+
+[network3ax]
+net_type            = MSNet
+net_name            = MSNet_EN32
+downsample_twice    = False
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 3
+model_file          = model/msnet_en32_20000.ckpt
+
+[network3sg]
+net_type            = MSNet
+net_name            = MSNet_EN32sg
+downsample_twice    = False
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 3
+model_file          = model/msnet_en32sg_5000.ckpt
+
+[network3cr]
+net_type            = MSNet
+net_name            = MSNet_EN32cr
+downsample_twice    = False
+data_shape          = [19, 96, 96, 4]
+label_shape         = [11, 96, 96, 1]
+class_num           = 3
+model_file          = model/msnet_en32cr_5000.ckpt
+
+[testing]
+test_slice_direction = all
+save_folder = result_all

config15/test_names.txt

@@ -0,0 +1,50 @@
+HGG_brats_tcia_pat417_0001
+HGG_brats_tcia_pat205_0001
+HGG_brats_tcia_pat455_0001
+HGG_brats_tcia_pat374_0356
+HGG_brats_tcia_pat473_0001
+HGG_brats_tcia_pat277_0001
+HGG_brats_tcia_pat396_0117
+LGG_brats_tcia_pat299_0001
+HGG_brats_tcia_pat332_0001
+HGG_brats_tcia_pat178_0002
+HGG_brats_tcia_pat199_0001
+HGG_brats_tcia_pat170_0002
+HGG_brats_tcia_pat156_0001
+HGG_brats_tcia_pat447_0313
+HGG_brats_tcia_pat198_0283
+HGG_brats_tcia_pat105_0001
+HGG_brats_2013_pat0002_1
+HGG_brats_tcia_pat406_0001
+LGG_brats_tcia_pat393_0001
+HGG_brats_tcia_pat274_0001
+LGG_brats_tcia_pat141_0001
+HGG_brats_tcia_pat138_0001
+LGG_brats_2013_pat0006_1
+HGG_brats_tcia_pat314_0001
+LGG_brats_2013_pat0014_1
+HGG_brats_tcia_pat447_0122
+HGG_brats_tcia_pat372_0001
+HGG_brats_tcia_pat230_0637
+HGG_brats_tcia_pat247_0001
+HGG_brats_tcia_pat171_0780
+LGG_brats_tcia_pat351_0001
+HGG_brats_tcia_pat399_0527
+HGG_brats_tcia_pat193_0002
+HGG_brats_tcia_pat374_0557
+HGG_brats_2013_pat0024_1
+HGG_brats_tcia_pat374_0909
+HGG_brats_tcia_pat278_0001
+HGG_brats_tcia_pat180_0001
+HGG_brats_tcia_pat399_0595
+HGG_brats_tcia_pat396_0217
+HGG_brats_tcia_pat257_0001
+HGG_brats_tcia_pat157_0001
+HGG_brats_tcia_pat165_0001
+HGG_brats_2013_pat0022_1
+HGG_brats_tcia_pat444_0001
+HGG_brats_tcia_pat399_0002
+HGG_brats_tcia_pat399_0156
+LGG_brats_tcia_pat428_0001
+HGG_brats_tcia_pat171_0950
+HGG_brats_tcia_pat399_0479

config15/test_wt.txt

@@ -0,0 +1,35 @@
+[data]
+data_root         = [data/Brats17ValidationData_renamed]
+data_names        =
+
+[network1ax]
+net_type            = MSNet
+net_name            = MSNet_WT32
+downsample_twice    = True
+data_shape          = [19, 180, 160, 4]
+label_shape         = [11, 180, 160, 1]
+class_num           = 2
+model_file          = model_pretrain/msnet_wt32_20000.ckpt
+
+[network1sg]
+net_type            = MSNet
+net_name            = MSNet_WT32sg
+downsample_twice    = True
+data_shape          = [19, 160, 180, 4]
+label_shape         = [11, 160, 180, 1]
+class_num           = 2
+model_file          = model_pretrain/msnet_wt32sg_20000.ckpt
+
+[network1cr]
+net_type            = MSNet
+net_name            = MSNet_WT32cr
+downsample_twice    = True
+data_shape          = [19, 160, 160, 4]
+label_shape         = [11, 160, 160, 1]
+class_num           = 2
+model_file          = model_pretrain/msnet_wt32cr_20000.ckpt
+
+[testing]
+test_slice_direction = all
+whole_tumor_only     = True
+save_folder          = results_wt

config15/train_en_ax.txt

@@ -0,0 +1,32 @@
+[data]
+data_root             = [/home/guotwang/data/brats_docker_data/pre_process]
+data_names            = config/train_names_all_lggx3.txt 
+modality_postfix      = [Flair, T1, T1c, T2]
+label_postfix         = OT  
+with_ground_truth     = True
+batch_size            = 5
+data_shape            = [19, 64, 64, 4]
+label_shape           = [11, 64, 64, 1]
+label_convert_source  = [0, 1, 2, 3, 4]
+label_convert_target  = [0, 1, 0, 0, 2] 
+batch_slice_direction = axial
+train_with_roi_patch  = True
+label_roi_mask        = [1,3,4]
+roi_patch_margin      = 5
+
+[network]
+net_type            = MSNet
+net_name            = MSNet_EN32
+downsample_twice    = False
+class_num           = 3
+
+[training]
+learning_rate      = 1e-3
+decay              = 1e-7
+maximal_iteration  = 20000
+snapshot_iteration = 5000
+start_iteration    = 0
+test_iteration     = 100
+test_step          = 10
+model_pre_trained  = 
+model_save_prefix  = model/msnet_en32

config15/train_en_cr.txt

@@ -0,0 +1,32 @@
+[data]
+data_root             = [/home/guotwang/data/brats_docker_data/pre_process]
+data_names            = config/train_names_all_lggx3.txt 
+modality_postfix      = [Flair, T1, T1c, T2]
+label_postfix         = OT  
+with_ground_truth     = True
+batch_size            = 5
+data_shape            = [19, 64, 64, 4]
+label_shape           = [11, 64, 64, 1]
+label_convert_source  = [0, 1, 2, 3, 4]
+label_convert_target  = [0, 1, 0, 0, 2] 
+batch_slice_direction = coronal
+train_with_roi_patch  = True
+label_roi_mask        = [1,3,4]
+roi_patch_margin      = 5
+
+[network]
+net_type            = MSNet
+net_name            = MSNet_EN32cr
+downsample_twice    = False
+class_num           = 3
+
+[training]
+learning_rate      = 1e-3
+decay              = 1e-7
+maximal_iteration  = 5000
+snapshot_iteration = 5000
+start_iteration    = 1
+test_iteration     = 100
+test_step          = 10
+model_pre_trained  = model/msnet_en32cr_init
+model_save_prefix  = model/msnet_en32cr

config15/train_en_sg.txt

@@ -0,0 +1,32 @@
+[data]
+data_root             = [/home/guotwang/data/brats_docker_data/pre_process]
+data_names            = config/train_names_all_lggx3.txt 
+modality_postfix      = [Flair, T1, T1c, T2]
+label_postfix         = OT  
+with_ground_truth     = True
+batch_size            = 5
+data_shape            = [19, 64, 64, 4]
+label_shape           = [11, 64, 64, 1]
+label_convert_source  = [0, 1, 2, 3, 4]
+label_convert_target  = [0, 1, 0, 0, 2] 
+batch_slice_direction = sagittal
+train_with_roi_patch  = True
+label_roi_mask        = [1,3,4]
+roi_patch_margin      = 5
+
+[network]
+net_type            = MSNet
+net_name            = MSNet_EN32sg
+downsample_twice    = False
+class_num           = 3
+
+[training]
+learning_rate      = 1e-3
+decay              = 1e-7
+maximal_iteration  = 5000
+snapshot_iteration = 5000
+start_iteration    = 1
+test_iteration     = 100
+test_step          = 10
+model_pre_trained  = model/msnet_en32sg_init
+model_save_prefix  = model/msnet_en32sg