From 0cd141b07d50c517e064d793807e48c377878352 Mon Sep 17 00:00:00 2001 From: Guotai Wang Date: Sat, 13 Jan 2018 10:30:46 +0000 Subject: [PATCH] rename config15 and model15 --- config/test_all_class.txt | 90 ------ config/test_names.txt | 50 ---- config/test_wt.txt | 35 --- config/train_en_ax.txt | 32 -- config/train_en_cr.txt | 32 -- config/train_en_sg.txt | 32 -- config/train_names.txt | 224 -------------- config/train_names_all.txt | 274 ------------------ config/train_names_all_lggx3.txt | 3 - config/train_tc_ax.txt | 32 -- config/train_tc_cr.txt | 32 -- config/train_tc_sg.txt | 32 -- config/train_wt_ax.txt | 32 -- config/train_wt_cr.txt | 32 -- config/train_wt_sg.txt | 32 -- {model => model15}/checkpoint | 0 .../msnet_en32_20000.ckpt.data-00000-of-00001 | Bin .../msnet_en32_20000.ckpt.index | Bin {model => model15}/msnet_en32_20000.ckpt.meta | Bin ...msnet_en32cr_5000.ckpt.data-00000-of-00001 | Bin .../msnet_en32cr_5000.ckpt.index | Bin .../msnet_en32cr_5000.ckpt.meta | Bin ...msnet_en32sg_5000.ckpt.data-00000-of-00001 | Bin .../msnet_en32sg_5000.ckpt.index | Bin .../msnet_en32sg_5000.ckpt.meta | Bin .../msnet_tc32_20000.ckpt.data-00000-of-00001 | Bin .../msnet_tc32_20000.ckpt.index | Bin {model => model15}/msnet_tc32_20000.ckpt.meta | Bin ...msnet_tc32cr_5000.ckpt.data-00000-of-00001 | Bin .../msnet_tc32cr_5000.ckpt.index | Bin .../msnet_tc32cr_5000.ckpt.meta | Bin ...msnet_tc32sg_5000.ckpt.data-00000-of-00001 | Bin .../msnet_tc32sg_5000.ckpt.index | Bin .../msnet_tc32sg_5000.ckpt.meta | Bin .../msnet_wt32_10000.ckpt.data-00000-of-00001 | Bin .../msnet_wt32_10000.ckpt.index | Bin {model => model15}/msnet_wt32_10000.ckpt.meta | Bin ...msnet_wt32cr_5000.ckpt.data-00000-of-00001 | Bin .../msnet_wt32cr_5000.ckpt.index | Bin .../msnet_wt32cr_5000.ckpt.meta | Bin ...msnet_wt32sg_5000.ckpt.data-00000-of-00001 | Bin .../msnet_wt32sg_5000.ckpt.index | Bin .../msnet_wt32sg_5000.ckpt.meta | Bin 43 files changed, 964 deletions(-) delete mode 100755 config/test_all_class.txt delete mode 100644 config/test_names.txt delete mode 100755 config/test_wt.txt delete mode 100755 config/train_en_ax.txt delete mode 100755 config/train_en_cr.txt delete mode 100755 config/train_en_sg.txt delete mode 100644 config/train_names.txt delete mode 100755 config/train_names_all.txt delete mode 100755 config/train_names_all_lggx3.txt delete mode 100755 config/train_tc_ax.txt delete mode 100755 config/train_tc_cr.txt delete mode 100755 config/train_tc_sg.txt delete mode 100755 config/train_wt_ax.txt delete mode 100755 config/train_wt_cr.txt delete mode 100755 config/train_wt_sg.txt rename {model => model15}/checkpoint (100%) rename {model => model15}/msnet_en32_20000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_en32_20000.ckpt.index (100%) rename {model => model15}/msnet_en32_20000.ckpt.meta (100%) rename {model => model15}/msnet_en32cr_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_en32cr_5000.ckpt.index (100%) rename {model => model15}/msnet_en32cr_5000.ckpt.meta (100%) rename {model => model15}/msnet_en32sg_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_en32sg_5000.ckpt.index (100%) rename {model => model15}/msnet_en32sg_5000.ckpt.meta (100%) rename {model => model15}/msnet_tc32_20000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_tc32_20000.ckpt.index (100%) rename {model => model15}/msnet_tc32_20000.ckpt.meta (100%) rename {model => model15}/msnet_tc32cr_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_tc32cr_5000.ckpt.index (100%) rename {model => model15}/msnet_tc32cr_5000.ckpt.meta (100%) rename {model => model15}/msnet_tc32sg_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_tc32sg_5000.ckpt.index (100%) rename {model => model15}/msnet_tc32sg_5000.ckpt.meta (100%) rename {model => model15}/msnet_wt32_10000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_wt32_10000.ckpt.index (100%) rename {model => model15}/msnet_wt32_10000.ckpt.meta (100%) rename {model => model15}/msnet_wt32cr_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_wt32cr_5000.ckpt.index (100%) rename {model => model15}/msnet_wt32cr_5000.ckpt.meta (100%) rename {model => model15}/msnet_wt32sg_5000.ckpt.data-00000-of-00001 (100%) rename {model => model15}/msnet_wt32sg_5000.ckpt.index (100%) rename {model => model15}/msnet_wt32sg_5000.ckpt.meta (100%) diff --git a/config/test_all_class.txt b/config/test_all_class.txt deleted file mode 100755 index f55a35c..0000000 --- a/config/test_all_class.txt +++ /dev/null @@ -1,90 +0,0 @@ -[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 diff --git a/config/test_names.txt b/config/test_names.txt deleted file mode 100644 index 4d53103..0000000 --- a/config/test_names.txt +++ /dev/null @@ -1,50 +0,0 @@ -HGG_brats_tcia_pat417_0001 -HGG_brats_tcia_pat205_0001 -HGG_brats_tcia_pat455_0001 -HGG_brats_tcia_pat374_0356 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-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 diff --git a/config/test_wt.txt b/config/test_wt.txt deleted file mode 100755 index 6dd616b..0000000 --- a/config/test_wt.txt +++ /dev/null @@ -1,35 +0,0 @@ -[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 diff --git a/config/train_en_ax.txt b/config/train_en_ax.txt deleted file mode 100755 index 7769393..0000000 --- a/config/train_en_ax.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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 diff --git a/config/train_en_cr.txt b/config/train_en_cr.txt deleted file mode 100755 index e4be81e..0000000 --- a/config/train_en_cr.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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 \ No newline at end of file diff --git a/config/train_en_sg.txt b/config/train_en_sg.txt deleted file mode 100755 index 25fff42..0000000 --- a/config/train_en_sg.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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 \ No newline at end of file diff --git a/config/train_names.txt b/config/train_names.txt deleted file mode 100644 index d80eba0..0000000 --- a/config/train_names.txt +++ /dev/null @@ -1,224 +0,0 @@ -HGG_brats_tcia_pat399_0369 -HGG_brats_tcia_pat448_0001 -HGG_brats_tcia_pat396_0294 -HGG_brats_tcia_pat335_0001 -HGG_brats_tcia_pat208_0001 -HGG_brats_tcia_pat230_0511 -HGG_brats_tcia_pat309_0243 -HGG_brats_tcia_pat242_0001 -HGG_brats_tcia_pat190_0001 -HGG_brats_tcia_pat290_0669 -HGG_brats_2013_pat0011_1 -HGG_brats_tcia_pat171_0387 -HGG_brats_tcia_pat439_0333 -HGG_brats_tcia_pat217_0001 -HGG_brats_2013_pat0015_1 -HGG_brats_tcia_pat290_0001 -LGG_brats_tcia_pat420_0001 -HGG_brats_tcia_pat260_0244 -HGG_brats_tcia_pat463_0001 -HGG_brats_tcia_pat153_0002 -HGG_brats_tcia_pat343_0001 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LGG_brats_tcia_pat480_0001 LGG_brats_tcia_pat483_0001 LGG_brats_tcia_pat490_0001 LGG_brats_tcia_pat493_0001 \ No newline at end of file diff --git a/config/train_tc_ax.txt b/config/train_tc_ax.txt deleted file mode 100755 index 74ee70a..0000000 --- a/config/train_tc_ax.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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, 96, 96, 4] -label_shape = [11, 96, 96, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 0, 1, 1] -batch_slice_direction = axial -train_with_roi_patch = True -label_roi_mask = [1,2,3,4] -roi_patch_margin = 5 - -[network] -net_type = MSNet -net_name = MSNet_TC32 -downsample_twice = True -class_num = 2 - -[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_tc32 \ No newline at end of file diff --git a/config/train_tc_cr.txt b/config/train_tc_cr.txt deleted file mode 100755 index 55782b4..0000000 --- a/config/train_tc_cr.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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, 96, 96, 4] -label_shape = [11, 96, 96, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 0, 1, 1] -batch_slice_direction = coronal -train_with_roi_patch = True -label_roi_mask = [1,2,3,4] -roi_patch_margin = 5 - -[network] -net_type = MSNet -net_name = MSNet_TC32cr -downsample_twice = True -class_num = 2 - -[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_tc32cr_init -model_save_prefix = model/msnet_tc32cr \ No newline at end of file diff --git a/config/train_tc_sg.txt b/config/train_tc_sg.txt deleted file mode 100755 index 5e5b3eb..0000000 --- a/config/train_tc_sg.txt +++ /dev/null @@ -1,32 +0,0 @@ -[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, 96, 96, 4] -label_shape = [11, 96, 96, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 0, 1, 1] -batch_slice_direction = sagittal -train_with_roi_patch = True -label_roi_mask = [1,2,3,4] -roi_patch_margin = 5 - -[network] -net_type = MSNet -net_name = MSNet_TC32sg -downsample_twice = True -class_num = 2 - -[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_tc32sg_init -model_save_prefix = model/msnet_tc32sg \ No newline at end of file diff --git a/config/train_wt_ax.txt b/config/train_wt_ax.txt deleted file mode 100755 index 0415f54..0000000 --- a/config/train_wt_ax.txt +++ /dev/null @@ -1,32 +0,0 @@ -[data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt -modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT -with_ground_truth = True -batch_size = 5 -data_shape = [19, 144, 144, 4] -label_shape = [11, 144, 144, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 1, 1, 1] -batch_slice_direction = axial -train_with_roi_patch = False -label_roi_mask = -roi_patch_margin = - -[network] -net_type = MSNet -net_name = MSNet_WT32 -downsample_twice = True -class_num = 2 - -[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_wt32 \ No newline at end of file diff --git a/config/train_wt_cr.txt b/config/train_wt_cr.txt deleted file mode 100755 index 22ef56c..0000000 --- a/config/train_wt_cr.txt +++ /dev/null @@ -1,32 +0,0 @@ -[data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt -modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT -with_ground_truth = True -batch_size = 5 -data_shape = [19, 144, 144, 4] -label_shape = [11, 144, 144, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 1, 1, 1] -batch_slice_direction = coronal -train_with_roi_patch = False -label_roi_mask = -roi_patch_margin = - -[network] -net_type = MSNet -net_name = MSNet_WT32cr -downsample_twice = True -class_num = 2 - -[training] -learning_rate = 1e-3 -decay = 1e-7 -maximal_iteration = 5000 -snapshot_iteration = 1000 -start_iteration = 1 -test_iteration = 100 -test_step = 10 -model_pre_trained = model/msnet_wt32cr_init -model_save_prefix = model/msnet_wt32cr diff --git a/config/train_wt_sg.txt b/config/train_wt_sg.txt deleted file mode 100755 index 2970c8e..0000000 --- a/config/train_wt_sg.txt +++ /dev/null @@ -1,32 +0,0 @@ -[data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt -modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT -with_ground_truth = True -batch_size = 5 -data_shape = [19, 144, 144, 4] -label_shape = [11, 144, 144, 1] -label_convert_source = [0, 1, 2, 3, 4] -label_convert_target = [0, 1, 1, 1, 1] -batch_slice_direction = sagittal -train_with_roi_patch = False -label_roi_mask = -roi_patch_margin = - -[network] -net_type = MSNet -net_name = MSNet_WT32sg -downsample_twice = True -class_num = 2 - -[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_wt32sg_init -model_save_prefix = model/msnet_wt32sg \ No newline at end of file diff --git a/model/checkpoint b/model15/checkpoint similarity index 100% rename from model/checkpoint rename to model15/checkpoint diff --git a/model/msnet_en32_20000.ckpt.data-00000-of-00001 b/model15/msnet_en32_20000.ckpt.data-00000-of-00001 similarity index 100% rename from model/msnet_en32_20000.ckpt.data-00000-of-00001 rename to model15/msnet_en32_20000.ckpt.data-00000-of-00001 diff --git a/model/msnet_en32_20000.ckpt.index b/model15/msnet_en32_20000.ckpt.index similarity index 100% rename from model/msnet_en32_20000.ckpt.index rename to model15/msnet_en32_20000.ckpt.index diff --git a/model/msnet_en32_20000.ckpt.meta b/model15/msnet_en32_20000.ckpt.meta similarity index 100% rename from model/msnet_en32_20000.ckpt.meta rename to model15/msnet_en32_20000.ckpt.meta diff --git a/model/msnet_en32cr_5000.ckpt.data-00000-of-00001 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