From b1198c42b4e6437830a3da35a745d92bff003f03 Mon Sep 17 00:00:00 2001 From: Dong Yang Date: Thu, 5 Jan 2023 00:04:54 -0700 Subject: [PATCH] correct typo in auto3dseg (#178) --- .../algorithm_templates/dints/configs/hyper_parameters.yaml | 4 ++-- auto3dseg/algorithm_templates/dints/scripts/infer.py | 2 +- auto3dseg/algorithm_templates/dints/scripts/validate.py | 2 +- .../segresnet2d/configs/hyper_parameters.yaml | 4 ++-- auto3dseg/algorithm_templates/segresnet2d/scripts/infer.py | 2 +- auto3dseg/algorithm_templates/segresnet2d/scripts/validate.py | 2 +- .../swinunetr/configs/hyper_parameters.yaml | 4 ++-- auto3dseg/algorithm_templates/swinunetr/scripts/infer.py | 2 +- auto3dseg/algorithm_templates/swinunetr/scripts/validate.py | 2 +- 9 files changed, 12 insertions(+), 12 deletions(-) diff --git a/auto3dseg/algorithm_templates/dints/configs/hyper_parameters.yaml b/auto3dseg/algorithm_templates/dints/configs/hyper_parameters.yaml index 67d24e2e..1cbe0f0d 100644 --- a/auto3dseg/algorithm_templates/dints/configs/hyper_parameters.yaml +++ b/auto3dseg/algorithm_templates/dints/configs/hyper_parameters.yaml @@ -63,11 +63,11 @@ finetune: validate: ckpt_name: "$@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt'" save_mask: true - ouptut_path: "$@bundle_root + '/prediction_fold' + str(@fold)" + output_path: "$@bundle_root + '/prediction_fold' + str(@fold)" # inference infer: ckpt_name: "$@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt'" fast: false data_list_key: testing - ouptut_path: "$@bundle_root + '/prediction_' + @infer#data_list_key" + output_path: "$@bundle_root + '/prediction_' + @infer#data_list_key" diff --git a/auto3dseg/algorithm_templates/dints/scripts/infer.py b/auto3dseg/algorithm_templates/dints/scripts/infer.py index 3e0fb056..5d66393e 100644 --- a/auto3dseg/algorithm_templates/dints/scripts/infer.py +++ b/auto3dseg/algorithm_templates/dints/scripts/infer.py @@ -45,7 +45,7 @@ def __init__(self, config_file: Optional[Union[str, Sequence[str]]] = None, **ov ckpt_name = parser.get_parsed_content("infer")["ckpt_name"] data_list_key = parser.get_parsed_content("infer")["data_list_key"] - output_path = parser.get_parsed_content("infer")["ouptut_path"] + output_path = parser.get_parsed_content("infer")["output_path"] if not os.path.exists(output_path): os.makedirs(output_path, exist_ok=True) diff --git a/auto3dseg/algorithm_templates/dints/scripts/validate.py b/auto3dseg/algorithm_templates/dints/scripts/validate.py index dcc26d98..b52d4229 100644 --- a/auto3dseg/algorithm_templates/dints/scripts/validate.py +++ b/auto3dseg/algorithm_templates/dints/scripts/validate.py @@ -48,7 +48,7 @@ def run(config_file: Optional[Union[str, Sequence[str]]] = None, **override): softmax = parser.get_parsed_content("training#softmax") ckpt_name = parser.get_parsed_content("validate")["ckpt_name"] - output_path = parser.get_parsed_content("validate")["ouptut_path"] + output_path = parser.get_parsed_content("validate")["output_path"] save_mask = parser.get_parsed_content("validate")["save_mask"] if not os.path.exists(output_path): diff --git a/auto3dseg/algorithm_templates/segresnet2d/configs/hyper_parameters.yaml b/auto3dseg/algorithm_templates/segresnet2d/configs/hyper_parameters.yaml index aa750b65..587e518e 100644 --- a/auto3dseg/algorithm_templates/segresnet2d/configs/hyper_parameters.yaml +++ b/auto3dseg/algorithm_templates/segresnet2d/configs/hyper_parameters.yaml @@ -61,11 +61,11 @@ finetune: validate: ckpt_name: "$@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt'" save_mask: true - ouptut_path: "$@bundle_root + '/prediction_fold' + str(@fold)" + output_path: "$@bundle_root + '/prediction_fold' + str(@fold)" # inference infer: ckpt_name: "$@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt'" fast: false data_list_key: testing - ouptut_path: "$@bundle_root + '/prediction_' + @infer#data_list_key" + output_path: "$@bundle_root + '/prediction_' + @infer#data_list_key" diff --git a/auto3dseg/algorithm_templates/segresnet2d/scripts/infer.py b/auto3dseg/algorithm_templates/segresnet2d/scripts/infer.py index 4d8de10b..45dce10f 100644 --- a/auto3dseg/algorithm_templates/segresnet2d/scripts/infer.py +++ b/auto3dseg/algorithm_templates/segresnet2d/scripts/infer.py @@ -47,7 +47,7 @@ def __init__(self, config_file: Optional[Union[str, Sequence[str]]] = None, **ov ckpt_name = parser.get_parsed_content("infer")["ckpt_name"] data_list_key = parser.get_parsed_content("infer")["data_list_key"] - output_path = parser.get_parsed_content("infer")["ouptut_path"] + output_path = parser.get_parsed_content("infer")["output_path"] if not os.path.exists(output_path): os.makedirs(output_path, exist_ok=True) diff --git a/auto3dseg/algorithm_templates/segresnet2d/scripts/validate.py b/auto3dseg/algorithm_templates/segresnet2d/scripts/validate.py index dc0960cd..730c11d4 100644 --- a/auto3dseg/algorithm_templates/segresnet2d/scripts/validate.py +++ b/auto3dseg/algorithm_templates/segresnet2d/scripts/validate.py @@ -49,7 +49,7 @@ def run(config_file: Optional[Union[str, Sequence[str]]] = None, **override): softmax = parser.get_parsed_content("softmax") ckpt_name = parser.get_parsed_content("validate")["ckpt_name"] - output_path = parser.get_parsed_content("validate")["ouptut_path"] + output_path = parser.get_parsed_content("validate")["output_path"] save_mask = parser.get_parsed_content("validate")["save_mask"] if not os.path.exists(output_path): diff --git a/auto3dseg/algorithm_templates/swinunetr/configs/hyper_parameters.yaml b/auto3dseg/algorithm_templates/swinunetr/configs/hyper_parameters.yaml index 9940c2cb..b48c37e0 100644 --- a/auto3dseg/algorithm_templates/swinunetr/configs/hyper_parameters.yaml +++ b/auto3dseg/algorithm_templates/swinunetr/configs/hyper_parameters.yaml @@ -19,7 +19,7 @@ infer: ckpt_name: $@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt' data_list_key: testing fast: false - ouptut_path: $@bundle_root + '/prediction_' + @infer#data_list_key + output_path: $@bundle_root + '/prediction_' + @infer#data_list_key input_channels: 1 learning_rate: 0.0001 loss: @@ -62,5 +62,5 @@ resample_to_spacing: null softmax: true validate: ckpt_name: $@bundle_root + '/model_fold' + str(@fold) + '/best_metric_model.pt' - ouptut_path: $@bundle_root + '/prediction_fold' + str(@fold) + output_path: $@bundle_root + '/prediction_fold' + str(@fold) save_mask: true diff --git a/auto3dseg/algorithm_templates/swinunetr/scripts/infer.py b/auto3dseg/algorithm_templates/swinunetr/scripts/infer.py index cdc0825b..e1feb5b5 100644 --- a/auto3dseg/algorithm_templates/swinunetr/scripts/infer.py +++ b/auto3dseg/algorithm_templates/swinunetr/scripts/infer.py @@ -45,7 +45,7 @@ def __init__(self, config_file: Optional[Union[str, Sequence[str]]] = None, **ov ckpt_name = parser.get_parsed_content("infer")["ckpt_name"] data_list_key = parser.get_parsed_content("infer")["data_list_key"] - output_path = parser.get_parsed_content("infer")["ouptut_path"] + output_path = parser.get_parsed_content("infer")["output_path"] if not os.path.exists(output_path): os.makedirs(output_path, exist_ok=True) diff --git a/auto3dseg/algorithm_templates/swinunetr/scripts/validate.py b/auto3dseg/algorithm_templates/swinunetr/scripts/validate.py index e739dd6d..27afb650 100644 --- a/auto3dseg/algorithm_templates/swinunetr/scripts/validate.py +++ b/auto3dseg/algorithm_templates/swinunetr/scripts/validate.py @@ -48,7 +48,7 @@ def run(config_file: Optional[Union[str, Sequence[str]]] = None, **override): softmax = parser.get_parsed_content("softmax") ckpt_name = parser.get_parsed_content("validate")["ckpt_name"] - output_path = parser.get_parsed_content("validate")["ouptut_path"] + output_path = parser.get_parsed_content("validate")["output_path"] save_mask = parser.get_parsed_content("validate")["save_mask"] if not os.path.exists(output_path):