diff --git a/config15/test_all_class.txt b/config15/test_all_class.txt index f55a35c..62376c3 100755 --- a/config15/test_all_class.txt +++ b/config15/test_all_class.txt @@ -1,7 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/test_names.txt +data_root = /home/guotwang/data/BRATS2015_Training +save_folder = result15 +data_names = config15/test_names.txt modality_postfix = [Flair, T1, T1c, T2] +file_postfix = mha [network1ax] net_type = MSNet @@ -10,7 +12,7 @@ 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 +model_file = model15/msnet_wt32_10000.ckpt [network1sg] net_type = MSNet @@ -19,7 +21,7 @@ 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 +model_file = model15/msnet_wt32sg_5000.ckpt [network1cr] net_type = MSNet @@ -28,7 +30,7 @@ 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 +model_file = model15/msnet_wt32cr_5000.ckpt [network2ax] @@ -38,7 +40,7 @@ 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 +model_file = model15/msnet_tc32_20000.ckpt [network2sg] net_type = MSNet @@ -47,7 +49,7 @@ 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 +model_file = model15/msnet_tc32sg_5000.ckpt [network2cr] net_type = MSNet @@ -56,7 +58,7 @@ 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 +model_file = model15/msnet_tc32cr_5000.ckpt [network3ax] net_type = MSNet @@ -65,7 +67,7 @@ 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 +model_file = model15/msnet_en32_20000.ckpt [network3sg] net_type = MSNet @@ -74,7 +76,7 @@ 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 +model_file = model15/msnet_en32sg_5000.ckpt [network3cr] net_type = MSNet @@ -83,8 +85,8 @@ 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 +model_file = model15/msnet_en32cr_5000.ckpt [testing] test_slice_direction = all -save_folder = result_all + diff --git a/config15/test_names.txt b/config15/test_names.txt index 4d53103..2f6e1d8 100644 --- a/config15/test_names.txt +++ b/config15/test_names.txt @@ -1,50 +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 +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 diff --git a/config15/test_wt.txt b/config15/test_wt.txt index 6dd616b..1226bcf 100755 --- a/config15/test_wt.txt +++ b/config15/test_wt.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17ValidationData_renamed] -data_names = +data_root = /home/guotwang/data/BRATS2015_Training +save_folder = result15 +data_names = config15/test_names.txt +modality_postfix = [Flair, T1, T1c, T2] +file_postfix = mha [network1ax] net_type = MSNet @@ -9,7 +12,7 @@ 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 +model_file = model15/msnet_wt32_10000.ckpt [network1sg] net_type = MSNet @@ -18,7 +21,7 @@ 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 +model_file = model15/msnet_wt32sg_10000.ckpt [network1cr] net_type = MSNet @@ -27,9 +30,8 @@ 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 +model_file = model15/msnet_wt32cr_10000.ckpt [testing] test_slice_direction = all whole_tumor_only = True -save_folder = results_wt diff --git a/config15/train_en_ax.txt b/config15/train_en_ax.txt index 7769393..8150fda 100755 --- a/config15/train_en_ax.txt +++ b/config15/train_en_ax.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT +label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -29,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_en32 +model_save_prefix = model15/msnet_en32 diff --git a/config15/train_en_cr.txt b/config15/train_en_cr.txt index e4be81e..d885530 100755 --- a/config15/train_en_cr.txt +++ b/config15/train_en_cr.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT +label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -28,5 +29,5 @@ 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 +model_pre_trained = model15/msnet_en32cr_init +model_save_prefix = model15/msnet_en32cr \ No newline at end of file diff --git a/config15/train_en_sg.txt b/config15/train_en_sg.txt index 25fff42..cd76f56 100755 --- a/config15/train_en_sg.txt +++ b/config15/train_en_sg.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT +label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -28,5 +29,5 @@ 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 +model_pre_trained = model15/msnet_en32sg_init +model_save_prefix = model15/msnet_en32sg \ No newline at end of file diff --git a/config15/train_names.txt b/config15/train_names.txt index d80eba0..1f74e04 100644 --- a/config15/train_names.txt +++ b/config15/train_names.txt @@ -1,224 +1,224 @@ -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 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LGG/brats_tcia_pat325_0001 LGG/brats_tcia_pat330_0001 LGG/brats_tcia_pat346_0001 LGG/brats_tcia_pat351_0001 LGG/brats_tcia_pat354_0001 LGG/brats_tcia_pat387_0001 LGG/brats_tcia_pat393_0001 LGG/brats_tcia_pat402_0001 LGG/brats_tcia_pat408_0001 LGG/brats_tcia_pat410_0001 LGG/brats_tcia_pat413_0001 LGG/brats_tcia_pat420_0001 LGG/brats_tcia_pat428_0001 LGG/brats_tcia_pat442_0001 LGG/brats_tcia_pat449_0001 LGG/brats_tcia_pat451_0001 LGG/brats_tcia_pat462_0001 LGG/brats_tcia_pat466_0001 LGG/brats_tcia_pat470_0001 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/config15/train_names_temp.txt b/config15/train_names_temp.txt new file mode 100755 index 0000000..8bc8767 --- /dev/null +++ b/config15/train_names_temp.txt @@ -0,0 +1,10 @@ +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 \ No newline at end of file diff --git a/config15/train_tc_ax.txt b/config15/train_tc_ax.txt index 74ee70a..1fa89f4 100755 --- a/config15/train_tc_ax.txt +++ b/config15/train_tc_ax.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 96, 96, 4] @@ -29,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_tc32 \ No newline at end of file +model_save_prefix = model15/msnet_tc32 \ No newline at end of file diff --git a/config15/train_tc_cr.txt b/config15/train_tc_cr.txt index 55782b4..f130ae5 100755 --- a/config15/train_tc_cr.txt +++ b/config15/train_tc_cr.txt @@ -1,9 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT -with_ground_truth = True +label_postfix = OT +file_postfix = mha batch_size = 5 data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] @@ -28,5 +28,5 @@ 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 +model_pre_trained = model15/msnet_tc32cr_init +model_save_prefix = model15/msnet_tc32cr \ No newline at end of file diff --git a/config15/train_tc_sg.txt b/config15/train_tc_sg.txt index 5e5b3eb..56ced00 100755 --- a/config15/train_tc_sg.txt +++ b/config15/train_tc_sg.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all_lggx3.txt modality_postfix = [Flair, T1, T1c, T2] -label_postfix = OT +label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 96, 96, 4] @@ -28,5 +29,5 @@ 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 +model_pre_trained = model15/msnet_tc32sg_init +model_save_prefix = model15/msnet_tc32sg \ No newline at end of file diff --git a/config15/train_wt_ax.txt b/config15/train_wt_ax.txt index 0415f54..f2ed432 100755 --- a/config15/train_wt_ax.txt +++ b/config15/train_wt_ax.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all.txt modality_postfix = [Flair, T1, T1c, T2] label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -29,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_wt32 \ No newline at end of file +model_save_prefix = model15/msnet_wt32 \ No newline at end of file diff --git a/config15/train_wt_cr.txt b/config15/train_wt_cr.txt index 22ef56c..717db72 100755 --- a/config15/train_wt_cr.txt +++ b/config15/train_wt_cr.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all.txt modality_postfix = [Flair, T1, T1c, T2] label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -28,5 +29,5 @@ 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 +model_pre_trained = model15/msnet_wt32cr_init +model_save_prefix = model15/msnet_wt32cr diff --git a/config15/train_wt_sg.txt b/config15/train_wt_sg.txt index 2970c8e..d612605 100755 --- a/config15/train_wt_sg.txt +++ b/config15/train_wt_sg.txt @@ -1,8 +1,9 @@ [data] -data_root = [/home/guotwang/data/brats_docker_data/pre_process] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/BRATS2015_Training +data_names = config15/train_names_all.txt modality_postfix = [Flair, T1, T1c, T2] label_postfix = OT +file_postfix = mha with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -28,5 +29,5 @@ 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 +model_pre_trained = model15/msnet_wt32sg_init +model_save_prefix = model15/msnet_wt32sg \ No newline at end of file diff --git a/config17/test_all_class.txt b/config17/test_all_class.txt index f4de742..82a57c6 100755 --- a/config17/test_all_class.txt +++ b/config17/test_all_class.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17ValidationData_renamed] -data_names = +data_root = /home/guotwang/data/Brats17TrainingData +save_folder = result17 +data_names = config17/test_names.txt +modality_postfix = [flair, t1, t1ce, t2] +file_postfix = nii.gz [network1ax] net_type = MSNet @@ -9,7 +12,7 @@ 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 +model_file = model17/msnet_wt32_20000.ckpt [network1sg] net_type = MSNet @@ -18,7 +21,7 @@ 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 +model_file = model17/msnet_wt32sg_20000.ckpt [network1cr] net_type = MSNet @@ -27,7 +30,7 @@ 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 +model_file = model17/msnet_wt32cr_20000.ckpt [network2ax] @@ -37,7 +40,7 @@ downsample_twice = True data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_tc32_20000.ckpt +model_file = model17/msnet_tc32_20000.ckpt [network2sg] net_type = MSNet @@ -46,7 +49,7 @@ downsample_twice = True data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_tc32sg_20000.ckpt +model_file = model17/msnet_tc32sg_20000.ckpt [network2cr] net_type = MSNet @@ -55,7 +58,7 @@ downsample_twice = True data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_tc32cr_20000.ckpt +model_file = model17/msnet_tc32cr_20000.ckpt [network3ax] net_type = MSNet @@ -64,7 +67,7 @@ downsample_twice = False data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_en32_20000.ckpt +model_file = model17/msnet_en32_20000.ckpt [network3sg] net_type = MSNet @@ -73,7 +76,7 @@ downsample_twice = False data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_en32sg_20000.ckpt +model_file = model17/msnet_en32sg_20000.ckpt [network3cr] net_type = MSNet @@ -82,10 +85,7 @@ downsample_twice = False data_shape = [19, 96, 96, 4] label_shape = [11, 96, 96, 1] class_num = 2 -model_file = model_pretrain/msnet_en32cr_20000.ckpt +model_file = model17/msnet_en32cr_20000.ckpt [testing] test_slice_direction = all -label_convert_source = [0, 1, 2, 3] -label_convert_target = [0, 1, 2, 4] -save_folder = results diff --git a/config17/test_names_example.txt b/config17/test_names.txt similarity index 100% rename from config17/test_names_example.txt rename to config17/test_names.txt diff --git a/config17/test_wt.txt b/config17/test_wt.txt index 6dd616b..b9208de 100755 --- a/config17/test_wt.txt +++ b/config17/test_wt.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17ValidationData_renamed] -data_names = +data_root = /home/guotwang/data/Brats17TrainingData +save_folder = result17 +data_names = config17/test_names.txt +modality_postfix = [flair, t1, t1ce, t2] +file_postfix = nii.gz [network1ax] net_type = MSNet @@ -9,7 +12,7 @@ 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 +model_file = model17/msnet_wt32_20000.ckpt [network1sg] net_type = MSNet @@ -18,7 +21,7 @@ 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 +model_file = model17/msnet_wt32sg_20000.ckpt [network1cr] net_type = MSNet @@ -27,9 +30,8 @@ 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 +model_file = model17/msnet_wt32cr_20000.ckpt [testing] test_slice_direction = all whole_tumor_only = True -save_folder = results_wt diff --git a/config17/train_en_ax.txt b/config17/train_en_ax.txt index 50eb304..bed9b44 100755 --- a/config17/train_en_ax.txt +++ b/config17/train_en_ax.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_en32 \ No newline at end of file +model_save_prefix = model17/msnet_en32 \ No newline at end of file diff --git a/config17/train_en_cr.txt b/config17/train_en_cr.txt index e8095a5..4936464 100755 --- a/config17/train_en_cr.txt +++ b/config17/train_en_cr.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_en32cr \ No newline at end of file +model_save_prefix = model17/msnet_en32cr \ No newline at end of file diff --git a/config17/train_en_sg.txt b/config17/train_en_sg.txt index bb310b2..196bcce 100755 --- a/config17/train_en_sg.txt +++ b/config17/train_en_sg.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 64, 64, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_en32sg \ No newline at end of file +model_save_prefix = model17/msnet_en32sg \ No newline at end of file diff --git a/config17/train_names.txt b/config17/train_names.txt new file mode 100755 index 0000000..583289e --- /dev/null +++ b/config17/train_names.txt @@ -0,0 +1,265 @@ +HGG/Brats17_CBICA_AAB_1 +HGG/Brats17_TCIA_314_1 +HGG/Brats17_TCIA_226_1 +HGG/Brats17_TCIA_474_1 +HGG/Brats17_TCIA_331_1 +HGG/Brats17_TCIA_257_1 +HGG/Brats17_2013_18_1 +HGG/Brats17_CBICA_ATP_1 +HGG/Brats17_TCIA_105_1 +HGG/Brats17_TCIA_222_1 +HGG/Brats17_CBICA_APR_1 +HGG/Brats17_CBICA_AOP_1 +HGG/Brats17_CBICA_AQQ_1 +HGG/Brats17_2013_2_1 +HGG/Brats17_CBICA_ABM_1 +HGG/Brats17_TCIA_221_1 +HGG/Brats17_TCIA_203_1 +HGG/Brats17_TCIA_412_1 +HGG/Brats17_TCIA_375_1 +HGG/Brats17_TCIA_328_1 +HGG/Brats17_CBICA_ARF_1 +HGG/Brats17_TCIA_283_1 +HGG/Brats17_2013_12_1 +HGG/Brats17_TCIA_460_1 +HGG/Brats17_TCIA_406_1 +HGG/Brats17_2013_10_1 +HGG/Brats17_CBICA_ASH_1 +HGG/Brats17_TCIA_429_1 +HGG/Brats17_CBICA_ABY_1 +HGG/Brats17_2013_22_1 +HGG/Brats17_CBICA_AQG_1 +HGG/Brats17_CBICA_AXW_1 +HGG/Brats17_TCIA_138_1 +HGG/Brats17_2013_7_1 +HGG/Brats17_TCIA_199_1 +HGG/Brats17_TCIA_335_1 +HGG/Brats17_CBICA_AWG_1 +HGG/Brats17_TCIA_469_1 +HGG/Brats17_CBICA_AOO_1 +HGG/Brats17_CBICA_AQT_1 +HGG/Brats17_TCIA_274_1 +HGG/Brats17_2013_13_1 +HGG/Brats17_CBICA_AXQ_1 +HGG/Brats17_CBICA_AZD_1 +HGG/Brats17_TCIA_117_1 +HGG/Brats17_CBICA_ABE_1 +HGG/Brats17_CBICA_AWI_1 +HGG/Brats17_CBICA_AUR_1 +HGG/Brats17_CBICA_ALN_1 +HGG/Brats17_TCIA_247_1 +HGG/Brats17_TCIA_437_1 +HGG/Brats17_CBICA_AME_1 +HGG/Brats17_CBICA_ABB_1 +HGG/Brats17_TCIA_118_1 +HGG/Brats17_TCIA_409_1 +HGG/Brats17_CBICA_ASK_1 +HGG/Brats17_TCIA_309_1 +HGG/Brats17_TCIA_394_1 +HGG/Brats17_CBICA_ASO_1 +HGG/Brats17_CBICA_BFB_1 +HGG/Brats17_TCIA_265_1 +HGG/Brats17_CBICA_ASE_1 +HGG/Brats17_CBICA_ASW_1 +HGG/Brats17_CBICA_ATB_1 +HGG/Brats17_CBICA_AVV_1 +HGG/Brats17_TCIA_361_1 +HGG/Brats17_CBICA_AOD_1 +HGG/Brats17_TCIA_605_1 +HGG/Brats17_CBICA_AQJ_1 +HGG/Brats17_TCIA_290_1 +HGG/Brats17_CBICA_AYU_1 +HGG/Brats17_TCIA_370_1 +HGG/Brats17_TCIA_448_1 +HGG/Brats17_CBICA_AAL_1 +HGG/Brats17_TCIA_278_1 +HGG/Brats17_2013_4_1 +HGG/Brats17_CBICA_AXO_1 +HGG/Brats17_CBICA_ATV_1 +HGG/Brats17_CBICA_AXL_1 +HGG/Brats17_2013_11_1 +HGG/Brats17_TCIA_234_1 +HGG/Brats17_TCIA_235_1 +HGG/Brats17_TCIA_374_1 +HGG/Brats17_TCIA_208_1 +HGG/Brats17_TCIA_218_1 +HGG/Brats17_CBICA_ANI_1 +HGG/Brats17_TCIA_411_1 +HGG/Brats17_CBICA_AQO_1 +HGG/Brats17_CBICA_BFP_1 +HGG/Brats17_CBICA_AQZ_1 +HGG/Brats17_TCIA_165_1 +HGG/Brats17_TCIA_190_1 +HGG/Brats17_TCIA_343_1 +HGG/Brats17_TCIA_131_1 +HGG/Brats17_CBICA_ASA_1 +HGG/Brats17_2013_21_1 +HGG/Brats17_CBICA_AQD_1 +HGG/Brats17_2013_5_1 +HGG/Brats17_TCIA_372_1 +HGG/Brats17_TCIA_419_1 +HGG/Brats17_TCIA_113_1 +HGG/Brats17_CBICA_AYA_1 +HGG/Brats17_2013_3_1 +HGG/Brats17_CBICA_BHM_1 +HGG/Brats17_TCIA_606_1 +HGG/Brats17_CBICA_AWH_1 +HGG/Brats17_CBICA_AYI_1 +HGG/Brats17_CBICA_AQA_1 +HGG/Brats17_CBICA_ALX_1 +HGG/Brats17_CBICA_AUQ_1 +HGG/Brats17_TCIA_149_1 +HGG/Brats17_TCIA_168_1 +HGG/Brats17_CBICA_AQR_1 +HGG/Brats17_TCIA_368_1 +HGG/Brats17_CBICA_APZ_1 +HGG/Brats17_TCIA_471_1 +HGG/Brats17_TCIA_332_1 +HGG/Brats17_CBICA_ANP_1 +HGG/Brats17_TCIA_321_1 +HGG/Brats17_TCIA_401_1 +HGG/Brats17_TCIA_162_1 +HGG/Brats17_TCIA_498_1 +HGG/Brats17_CBICA_ARZ_1 +HGG/Brats17_TCIA_211_1 +HGG/Brats17_CBICA_ABO_1 +HGG/Brats17_TCIA_192_1 +HGG/Brats17_TCIA_147_1 +HGG/Brats17_TCIA_201_1 +HGG/Brats17_TCIA_608_1 +HGG/Brats17_TCIA_277_1 +HGG/Brats17_2013_23_1 +HGG/Brats17_CBICA_APY_1 +HGG/Brats17_CBICA_AVJ_1 +HGG/Brats17_CBICA_AXJ_1 +HGG/Brats17_2013_27_1 +HGG/Brats17_CBICA_ANG_1 +HGG/Brats17_TCIA_436_1 +HGG/Brats17_TCIA_455_1 +HGG/Brats17_TCIA_479_1 +HGG/Brats17_TCIA_179_1 +HGG/Brats17_TCIA_322_1 +HGG/Brats17_TCIA_478_1 +HGG/Brats17_CBICA_ASU_1 +HGG/Brats17_CBICA_ATF_1 +HGG/Brats17_TCIA_296_1 +HGG/Brats17_TCIA_430_1 +HGG/Brats17_TCIA_121_1 +HGG/Brats17_CBICA_AQU_1 +HGG/Brats17_CBICA_AOH_1 +HGG/Brats17_TCIA_180_1 +HGG/Brats17_CBICA_AZH_1 +HGG/Brats17_CBICA_ARW_1 +HGG/Brats17_TCIA_198_1 +HGG/Brats17_CBICA_AVG_1 +HGG/Brats17_TCIA_473_1 +HGG/Brats17_CBICA_AQP_1 +HGG/Brats17_TCIA_607_1 +HGG/Brats17_CBICA_ABN_1 +HGG/Brats17_CBICA_ALU_1 +HGG/Brats17_TCIA_231_1 +HGG/Brats17_CBICA_AXM_1 +HGG/Brats17_TCIA_111_1 +HGG/Brats17_CBICA_AUN_1 +HGG/Brats17_TCIA_150_1 +HGG/Brats17_CBICA_BHB_1 +HGG/Brats17_CBICA_AYW_1 +HGG/Brats17_CBICA_ASV_1 +HGG/Brats17_TCIA_377_1 +HGG/Brats17_TCIA_499_1 +HGG/Brats17_CBICA_AAG_1 +HGG/Brats17_TCIA_186_1 +HGG/Brats17_TCIA_205_1 +HGG/Brats17_CBICA_AAP_1 +HGG/Brats17_CBICA_ASG_1 +HGG/Brats17_CBICA_BHK_1 +HGG/Brats17_TCIA_319_1 +HGG/Brats17_CBICA_ASY_1 +HGG/Brats17_2013_20_1 +HGG/Brats17_CBICA_ATD_1 +HGG/Brats17_TCIA_167_1 +HGG/Brats17_2013_17_1 +HGG/Brats17_TCIA_300_1 +HGG/Brats17_TCIA_338_1 +HGG/Brats17_CBICA_ANZ_1 +HGG/Brats17_2013_19_1 +HGG/Brats17_TCIA_280_1 +HGG/Brats17_CBICA_AQV_1 +HGG/Brats17_CBICA_AQY_1 +HGG/Brats17_TCIA_425_1 +HGG/Brats17_2013_14_1 +HGG/Brats17_TCIA_133_1 +HGG/Brats17_TCIA_171_1 +HGG/Brats17_TCIA_184_1 +HGG/Brats17_TCIA_242_1 +HGG/Brats17_2013_26_1 +HGG/Brats17_CBICA_ASN_1 +HGG/Brats17_TCIA_444_1 +HGG/Brats17_TCIA_390_1 +HGG/Brats17_CBICA_AMH_1 +HGG/Brats17_TCIA_378_1 +LGG/Brats17_TCIA_442_1 +LGG/Brats17_TCIA_276_1 +LGG/Brats17_TCIA_282_1 +LGG/Brats17_TCIA_130_1 +LGG/Brats17_TCIA_420_1 +LGG/Brats17_TCIA_109_1 +LGG/Brats17_TCIA_325_1 +LGG/Brats17_TCIA_175_1 +LGG/Brats17_TCIA_312_1 +LGG/Brats17_TCIA_633_1 +LGG/Brats17_TCIA_177_1 +LGG/Brats17_2013_6_1 +LGG/Brats17_TCIA_428_1 +LGG/Brats17_TCIA_642_1 +LGG/Brats17_2013_16_1 +LGG/Brats17_TCIA_493_1 +LGG/Brats17_TCIA_266_1 +LGG/Brats17_TCIA_624_1 +LGG/Brats17_TCIA_470_1 +LGG/Brats17_TCIA_307_1 +LGG/Brats17_TCIA_451_1 +LGG/Brats17_TCIA_393_1 +LGG/Brats17_TCIA_408_1 +LGG/Brats17_TCIA_261_1 +LGG/Brats17_TCIA_640_1 +LGG/Brats17_TCIA_402_1 +LGG/Brats17_TCIA_639_1 +LGG/Brats17_TCIA_413_1 +LGG/Brats17_TCIA_615_1 +LGG/Brats17_2013_15_1 +LGG/Brats17_TCIA_141_1 +LGG/Brats17_2013_8_1 +LGG/Brats17_2013_1_1 +LGG/Brats17_TCIA_480_1 +LGG/Brats17_TCIA_351_1 +LGG/Brats17_TCIA_645_1 +LGG/Brats17_TCIA_202_1 +LGG/Brats17_TCIA_103_1 +LGG/Brats17_TCIA_650_1 +LGG/Brats17_TCIA_254_1 +LGG/Brats17_TCIA_410_1 +LGG/Brats17_TCIA_255_1 +LGG/Brats17_TCIA_330_1 +LGG/Brats17_TCIA_101_1 +LGG/Brats17_TCIA_628_1 +LGG/Brats17_TCIA_299_1 +LGG/Brats17_TCIA_241_1 +LGG/Brats17_2013_28_1 +LGG/Brats17_2013_0_1 +LGG/Brats17_TCIA_654_1 +LGG/Brats17_TCIA_298_1 +LGG/Brats17_2013_9_1 +LGG/Brats17_TCIA_653_1 +LGG/Brats17_TCIA_466_1 +LGG/Brats17_TCIA_637_1 +LGG/Brats17_TCIA_632_1 +LGG/Brats17_TCIA_618_1 +LGG/Brats17_TCIA_629_1 +LGG/Brats17_TCIA_644_1 +LGG/Brats17_TCIA_621_1 +LGG/Brats17_TCIA_387_1 +LGG/Brats17_TCIA_249_1 +LGG/Brats17_TCIA_623_1 +LGG/Brats17_TCIA_625_1 +LGG/Brats17_TCIA_462_1 \ No newline at end of file diff --git a/config17/train_names_temp.txt b/config17/train_names_temp.txt new file mode 100755 index 0000000..20ba75a --- /dev/null +++ b/config17/train_names_temp.txt @@ -0,0 +1,10 @@ +HGG/Brats17_CBICA_ATX_1 +HGG/Brats17_CBICA_AXN_1 +HGG/Brats17_TCIA_491_1 +HGG/Brats17_CBICA_AOZ_1 +HGG/Brats17_TCIA_151_1 +HGG/Brats17_2013_25_1 +HGG/Brats17_TCIA_396_1 +HGG/Brats17_CBICA_AQN_1 +HGG/Brats17_TCIA_135_1 +HGG/Brats17_TCIA_603_1 \ No newline at end of file diff --git a/config17/train_tc_ax.txt b/config17/train_tc_ax.txt index c86f2dc..7293d1d 100755 --- a/config17/train_tc_ax.txt +++ b/config17/train_tc_ax.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 96, 96, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_tc32 \ No newline at end of file +model_save_prefix = model17/msnet_tc32 \ No newline at end of file diff --git a/config17/train_tc_cr.txt b/config17/train_tc_cr.txt index b5c0834..3105037 100755 --- a/config17/train_tc_cr.txt +++ b/config17/train_tc_cr.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 96, 96, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_tc32cr \ No newline at end of file +model_save_prefix = model17/msnet_tc32cr \ No newline at end of file diff --git a/config17/train_tc_sg.txt b/config17/train_tc_sg.txt index 7485567..a733167 100755 --- a/config17/train_tc_sg.txt +++ b/config17/train_tc_sg.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all_lggx3.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all_lggx3.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 96, 96, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_tc32sg \ No newline at end of file +model_save_prefix = model17/msnet_tc32sg \ No newline at end of file diff --git a/config17/train_wt_ax.txt b/config17/train_wt_ax.txt index dccfa42..f157b71 100755 --- a/config17/train_wt_ax.txt +++ b/config17/train_wt_ax.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_wt32 \ No newline at end of file +model_save_prefix = model17/msnet_wt32 \ No newline at end of file diff --git a/config17/train_wt_cr.txt b/config17/train_wt_cr.txt index b4c17ae..d889f68 100755 --- a/config17/train_wt_cr.txt +++ b/config17/train_wt_cr.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_wt32cr \ No newline at end of file +model_save_prefix = model17/msnet_wt32cr \ No newline at end of file diff --git a/config17/train_wt_sg.txt b/config17/train_wt_sg.txt index 9e6bd59..b77e1e3 100755 --- a/config17/train_wt_sg.txt +++ b/config17/train_wt_sg.txt @@ -1,6 +1,9 @@ [data] -data_root = [data/Brats17TrainingData_crop_renamed] -data_names = config/train_names_all.txt +data_root = /home/guotwang/data/Brats17TrainingData +data_names = config17/train_names_all.txt +modality_postfix = [flair, t1, t1ce, t2] +label_postfix = seg +file_postfix = nii.gz with_ground_truth = True batch_size = 5 data_shape = [19, 144, 144, 4] @@ -27,4 +30,4 @@ start_iteration = 0 test_iteration = 100 test_step = 10 model_pre_trained = -model_save_prefix = model/msnet_wt32sg \ No newline at end of file +model_save_prefix = model17/msnet_wt32sg \ No newline at end of file diff --git a/convert_brats_image.py b/convert_brats_image.py deleted file mode 100644 index 26b7e27..0000000 --- a/convert_brats_image.py +++ /dev/null @@ -1,38 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import absolute_import, print_function -import os -import numpy as np -import SimpleITK as sitk -from util.parse_config import parse_config - -def convert_brats15_data(input_folder, output_folder, modalities): - """ - Copy the brats dataset to a single folder, and convert .mha files into .nii.gz files - inputs: - input_folder: the root folder of brats data, e.g. */BRATS2015_Training - output_folder: the folder where the converted files will be writen - modalities: modalities of files, e.g., ['Flair', 'T1c', 'T1', 'OT'] - """ - sub_folders = ['HGG', 'LGG'] - if(not os.path.isdir(output_folder)): - os.mkdir(output_folder) - for sub_folder in sub_folders: - sub_dir = input_folder + '/' + sub_folder - patients = os.listdir(sub_dir) - for patient in patients: - if 'brats' in patient: - patient_dir = sub_dir + '/' + patient - scan_dirs = os.listdir(patient_dir) - for mod in modalities: - for scan_dir in scan_dirs: - if mod + '.' in scan_dir: - input_name = patient_dir + '/' + scan_dir + '/' + scan_dir + ".mha" - img = sitk.ReadImage(input_name) - save_name = "{0:}/{1:}_{2:}_{3:}.nii.gz".format(output_folder, sub_folder, patient, mod) - sitk.WriteImage(img, save_name) - -if __name__ == "__main__": - brats15_data_root = "/mnt/shared/guotai/data/BRATS2015_Training" - data_save_root = "/home/guotai/data/brats_docker_data/origin" - modalities = ['Flair', 'T1c', 'T1', 'T2', 'OT'] - convert_brats15_data(brats15_data_root, data_save_root, modalities) diff --git a/pre_process.py b/pre_process.py deleted file mode 100644 index 973fb3e..0000000 --- a/pre_process.py +++ /dev/null @@ -1,49 +0,0 @@ -# -*- coding: utf-8 -*- -from __future__ import absolute_import, print_function -import os -import nibabel -import numpy as np -from util.data_process import * -from util.parse_config import parse_config - -def data_set_crop(read_folder, save_folder, modalities): - """ - Crop the data with a bounding box that is automatically calculated based on the nonzero region - inputs: - read_folder: the folder containing the input data - save_folder: the folder to save the cropped data - modalities: modalities of the data, e.g., ['Flair', 'T1c', 'OT'] - """ - if(not os.path.isdir(save_folder)): - os.mkdir(save_folder) - patient_list = os.listdir(read_folder) - patient_list = [x for x in patient_list if modalities[0] in x] - patient_list = ['_'.join(x.split('_')[:-1]) for x in patient_list] - margin = 5 - - print('patient number ', len(patient_list)) - for patient_name in patient_list: - print(patient_name) - imgs = [] - for mod in modalities: - img_name = os.path.join(read_folder, "{0:}_{1:}.nii.gz".format(patient_name, mod)) - img = load_nifty_volume_as_array(img_name) - imgs.append(img) - - [d_idxes, h_idxes, w_idxes] = np.nonzero(imgs[0]) - mind = d_idxes.min() - margin; maxd = d_idxes.max() + margin - minh = h_idxes.min() - margin; maxh = h_idxes.max() + margin - minw = w_idxes.min() - margin; maxw = w_idxes.max() + margin - for mod_idx in range(len(modalities)): - roi_volume = imgs[mod_idx][np.ix_(range(mind, maxd), range(minh, maxh), range(minw, maxw))] - save_name = "{0:}_{1:}.nii.gz".format(patient_name, modalities[mod_idx]) - save_name = os.path.join(save_folder, save_name) - save_array_as_nifty_volume(roi_volume, save_name) - -if __name__ == "__main__": - data_read_root = "/home/guotai/data/brats_docker_data/origin" - data_save_root = "/home/guotai/data/brats_docker_data/pre_process" - modalities = ['Flair', 'T1c', 'T1', 'T2', 'OT'] - data_set_crop(data_read_root,data_save_root, modalities) - - diff --git a/test.py b/test.py index 724a080..2719be0 100644 --- a/test.py +++ b/test.py @@ -425,18 +425,17 @@ def test(config_file): print('ignored voxel number ', vox_3) label3 = np.zeros_like(label2) - out_label = label1 * 2 - out_label[label2>0] = 3 - out_label[label3==1] = 1 - out_label[label3==2] = 4 + # 5.5, convert label and save output + out_label = label1 * 2 + if('Flair' in config_data['modality_postfix'] and 'mha' in config_data['file_postfix']): + out_label[label2>0] = 3 + out_label[label3==1] = 1 + out_label[label3==2] = 4 + elif('flair' in config_data['modality_postfix'] and 'nii' in config_data['file_postfix']): + out_label[label2>0] = 1 + out_label[label3>0] = 4 out_label = np.asarray(out_label, np.int16) - # 5.5, convert label and save output - label_convert_source = config_test.get('label_convert_source', None) - label_convert_target = config_test.get('label_convert_target', None) - if(label_convert_source and label_convert_target): - assert(len(label_convert_source) == len(label_convert_target)) - out_label = convert_label(out_label, label_convert_source, label_convert_target) test_time.append(time.time() - t0) final_label = np.zeros_like(weight, np.int16) @@ -450,11 +449,11 @@ def test(config_file): sess.close() if __name__ == '__main__': -# if(len(sys.argv) != 2): -# print('Number of arguments should be 2. e.g.') -# print(' python test.py config.txt') -# exit() - config_file = './test_data.txt' + if(len(sys.argv) != 2): + print('Number of arguments should be 2. e.g.') + print(' python test.py config.txt') + exit() + config_file = str(sys.argv[1]) assert(os.path.isfile(config_file)) test(config_file) diff --git a/test_data.txt b/test_data.txt deleted file mode 100755 index 51e0c24..0000000 --- a/test_data.txt +++ /dev/null @@ -1,90 +0,0 @@ -[data] -data_root = /input_dir/Testing/HGG_LGG -save_folder = /output_dir -modality_postfix = [Flair, T1, T1c, T2] -file_post_fix = mha - -[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 diff --git a/util/data_loader.py b/util/data_loader.py index c03a372..3d8a7b8 100644 --- a/util/data_loader.py +++ b/util/data_loader.py @@ -23,7 +23,7 @@ def __init__(self, config): self.label_convert_source = config.get('label_convert_source', None) self.label_convert_target = config.get('label_convert_target', None) self.label_postfix = config.get('label_postfix', 'seg') - self.file_postfix = config.get('file_post_fix', 'nii.gz') + self.file_postfix = config.get('file_postfix', 'nii.gz') self.data_names = config.get('data_names', None) self.data_num = config.get('data_num', None) self.data_resize = config.get('data_resize', None) @@ -37,60 +37,42 @@ def __get_patient_names(self): get the list of patient names, if self.data_names id not None, then load patient names from that file, otherwise search all the names automatically in data_root """ - if('.nii' in self.file_postfix): - if(self.data_names is not None): - assert(os.path.isfile(self.data_names)) - with open(self.data_names) as f: - content = f.readlines() - patient_names = [x.strip() for x in content] - else: # load all image in data_root - sub_dirs = [x[0] for x in os.walk(self.data_root[0])] - patient_names = [] - for sub_dir in sub_dirs: - names = os.listdir(sub_dir) - if(sub_dir == self.data_root[0]): - sub_patient_names = [] - for x in names: - if(self.file_postfix in x): - idx = x.rfind('_') - xsplit = x[:idx] - sub_patient_names.append(xsplit) - else: - sub_dir_name = sub_dir[len(self.data_root[0])+1:] - sub_patient_names = [] - for x in names: - if(self.file_postfix in x): - idx = x.rfind('_') - xsplit = os.path.join(sub_dir_name,x[:idx]) - sub_patient_names.append(xsplit) - sub_patient_names = list(set(sub_patient_names)) - sub_patient_names.sort() - patient_names.extend(sub_patient_names) - + # use pre-defined patient names + if(self.data_names is not None): + assert(os.path.isfile(self.data_names)) + with open(self.data_names) as f: + content = f.readlines() + patient_names = [x.strip() for x in content] + # use all the patient names in data_root else: patient_names = os.listdir(self.data_root[0]) - patient_names = [name for name in patient_names if 'brats' in name] + patient_names = [name for name in patient_names if 'brats' in name.lower()] return patient_names def __load_one_volume(self, patient_name, mod): - if('.nii' in self.file_postfix): - volume_name_short = patient_name + '_' + mod + '.' + self.file_postfix - volume_name = search_file_in_folder_list(self.data_root, volume_name_short) - volume = load_nifty_volume_as_array(volume_name) + patient_dir = os.path.join(self.data_root[0], patient_name) + # for bats17 + if('nii' in self.file_postfix): + image_names = os.listdir(patient_dir) + volume_name = None + for image_name in image_names: + if(mod + '.' in image_name): + volume_name = image_name + break + # for brats15 else: - patient_dir = os.path.join(self.data_root[0], patient_name) img_file_dirs = os.listdir(patient_dir) volume_name = None for img_file_dir in img_file_dirs: if(mod+'.' in img_file_dir): volume_name = img_file_dir + '/' + img_file_dir + '.' + self.file_postfix break - assert(volume_name is not None) - volume_name = os.path.join(patient_dir, volume_name) - volume = load_3d_volume_as_array(volume_name) + assert(volume_name is not None) + volume_name = os.path.join(patient_dir, volume_name) + volume = load_3d_volume_as_array(volume_name) return volume - def load_data(self): + def load_data(self, stage='train'): """ load all the training/testing data """ @@ -107,6 +89,15 @@ def load_data(self): if(self.data_resize): volume = resize_3D_volume_to_given_shape(volume, self.data_resize, 1) if(mod_idx == 0): + margin = 5 + [d_idxes, h_idxes, w_idxes] = np.nonzero(volume) + mind = d_idxes.min() - margin; maxd = d_idxes.max() + margin + minh = h_idxes.min() - margin; maxh = h_idxes.max() + margin + minw = w_idxes.min() - margin; maxw = w_idxes.max() + margin + + if(stage == 'train'): + volume = volume[np.ix_(range(mind, maxd), range(minh, maxh), range(minw, maxw))] + if(mod_idx ==0): weight = np.asarray(volume > 0, np.float32) if(self.intensity_normalize[mod_idx]): volume = itensity_normalize_one_volume(volume) @@ -117,6 +108,8 @@ def load_data(self): label = self.__load_one_volume(self.patient_names[i], self.label_postfix) if(self.data_resize): label = resize_3D_volume_to_given_shape(label, self.data_resize, 0) + if(stage == 'train'): + label = label[np.ix_(range(mind, maxd), range(minh, maxh), range(minw, maxw))] Y.append(label) if((i+1)%50 == 0 or (i+1) == data_num): print('Data load, {0:}% finished'.format((i+1)*100.0/data_num)) diff --git a/evaluation.py b/util/evaluation.py similarity index 100% rename from evaluation.py rename to util/evaluation.py diff --git a/rename_variables.py b/util/rename_variables.py similarity index 82% rename from rename_variables.py rename to util/rename_variables.py index 57cfd26..bf59970 100644 --- a/rename_variables.py +++ b/util/rename_variables.py @@ -1,5 +1,5 @@ import tensorflow as tf -# https://gist.github.com/batzner/7c24802dd9c5e15870b4b56e22135c96 + def rename(checkpoint_from, checkpoint_to, replace_from, replace_to): checkpoint = tf.train.get_checkpoint_state(checkpoint_from) with tf.Session() as sess: @@ -25,8 +25,8 @@ def rename(checkpoint_from, checkpoint_to, replace_from, replace_to): num_pretrain = [10000, 20000, 20000] for i in range(3): for view in ['sg', 'cr']: - checkpoint_from = "model_part/msnet_{0:}32_{1:}.ckpt".format(net_name[i], num_pretrain[i]) - checkpoint_to = "model_part/msnet_{0:}32{1:}_init".format(net_name[i], view) + checkpoint_from = "model15/msnet_{0:}32_{1:}.ckpt".format(net_name[i], num_pretrain[i]) + checkpoint_to = "model15/msnet_{0:}32{1:}_init".format(net_name[i], view) replace_from = "MSNet_{0:}32".format(net_name_c[i]) replace_to = "MSNet_{0:}32{1:}".format(net_name_c[i], view) rename(checkpoint_from, checkpoint_to, replace_from, replace_to)