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import os |
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import shutil |
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import subprocess |
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import pytest |
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from deepreg import log |
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logger = log.get(__name__) |
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def remove_files(name): |
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dir_name = os.path.join("demos", name) |
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# remove zip files |
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files = os.listdir(dir_name) |
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for file in files: |
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if file.endswith(".zip"): |
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os.remove(os.path.join(dir_name, file)) |
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# remove output folders |
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paths = [ |
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os.path.join(dir_name, x) |
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for x in ["dataset", "logs_train", "logs_predict", "logs_reg"] |
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] |
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for path in paths: |
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if os.path.exists(path): |
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shutil.rmtree(path) |
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def check_files(name): |
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"""make sure dataset folder exist but there is no zip files""" |
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dir_name = os.path.join("demos", name) |
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# assert dataset folder exists |
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assert os.path.exists(os.path.join(dir_name, "dataset")) |
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# assert no zip files |
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files = os.listdir(dir_name) |
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files = [x for x in files if x.endswith(".zip")] |
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assert len(files) == 0 |
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def check_vis_single_config_demo(name): |
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time_stamp = sorted(os.listdir(f"demos/{name}/logs_predict"))[0] |
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pair_number = sorted(os.listdir(f"demos/{name}/logs_predict/{time_stamp}/test"))[-1] |
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cmd = [ |
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f"deepreg_vis -m 2 -i 'demos/{name}/logs_predict/{time_stamp}/test/{pair_number}/moving_image.nii.gz, demos/{name}/logs_predict/{time_stamp}/test/{pair_number}/pred_fixed_image.nii.gz, demos/{name}/logs_predict/{time_stamp}/test/{pair_number}/fixed_image.nii.gz' --slice-inds '0,1,2' -s demos/{name}/logs_predict" |
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] |
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execute_commands([cmd]) |
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assert os.path.exists(f"demos/{name}/logs_predict/visualisation.png") |
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def check_vis_unpaired_ct_abdomen(name, method): |
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time_stamp = sorted(os.listdir(f"demos/{name}/logs_predict/{method}"))[0] |
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pair_number = sorted( |
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os.listdir(f"demos/{name}/logs_predict/{method}/{time_stamp}/test") |
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)[-1] |
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cmd = [ |
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f"deepreg_vis -m 2 -i 'demos/{name}/logs_predict/{method}/{time_stamp}/test/{pair_number}/moving_image.nii.gz, demos/{name}/logs_predict/{method}/{time_stamp}/test/{pair_number}/pred_fixed_image.nii.gz, demos/{name}/logs_predict/{method}/{time_stamp}/test/{pair_number}/fixed_image.nii.gz' --slice-inds '0,1,2' -s demos/{name}/logs_predict" |
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] |
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execute_commands([cmd]) |
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assert os.path.exists(f"demos/{name}/logs_predict/visualisation.png") |
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def check_vis_classical_demo(name): |
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cmd = [ |
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f"deepreg_vis -m 2 -i 'demos/{name}/logs_reg/moving_image.nii.gz, demos/{name}/logs_reg/warped_moving_image.nii.gz, demos/{name}/logs_reg/fixed_image.nii.gz' --slice-inds '0,1,2' -s demos/{name}/logs_reg" |
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] |
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execute_commands([cmd]) |
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assert os.path.exists(f"demos/{name}/logs_reg/visualisation.png") |
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def execute_commands(cmds): |
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for cmd in cmds: |
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try: |
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logger.info(f"Running {cmd}") |
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out = subprocess.check_output(cmd, shell=True).decode("utf-8") |
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logger.info(out) |
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except subprocess.CalledProcessError as e: |
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raise RuntimeError( |
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f"Command {cmd} return with err {e.returncode} {e.output}" |
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) |
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class TestDemo: |
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@pytest.mark.parametrize( |
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"name", |
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[ |
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"grouped_mask_prostate_longitudinal", |
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"grouped_mr_heart", |
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"paired_ct_lung", |
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"paired_mrus_brain", |
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"paired_mrus_prostate", |
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"unpaired_ct_lung", |
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"unpaired_mr_brain", |
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"unpaired_us_prostate_cv", |
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], |
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) |
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def test_single_config_demo(self, name): |
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"""each demo has one single configuration file""" |
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remove_files(name) |
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# execute data |
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cmds = [f"python demos/{name}/demo_data.py"] |
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execute_commands(cmds) |
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# check temporary files are removed |
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check_files(name) |
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# execute train, predict sequentially |
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cmds = [f"python demos/{name}/demo_{x}.py --test" for x in ["train", "predict"]] |
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execute_commands(cmds) |
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check_vis_single_config_demo(name) |
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@pytest.mark.parametrize( |
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"method", |
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["comb", "unsup", "weakly"], |
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) |
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def test_unpaired_ct_abdomen(self, method): |
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"""this demo has multiple configuration file""" |
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name = "unpaired_ct_abdomen" |
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remove_files(name) |
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# execute data |
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cmds = [f"python demos/{name}/demo_data.py"] |
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execute_commands(cmds) |
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# check temporary files are removed |
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check_files(name) |
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# execute train, predict sequentially |
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cmds = [ |
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f"python demos/{name}/demo_{x}.py --method {method} --test" |
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for x in ["train", "predict"] |
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] |
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execute_commands(cmds) |
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check_vis_unpaired_ct_abdomen(name, method) |
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@pytest.mark.parametrize( |
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"name", |
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[ |
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"classical_ct_headneck_affine", |
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"classical_mr_prostate_nonrigid", |
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], |
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) |
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def test_classical_demo(self, name): |
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remove_files(name) |
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# execute data |
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cmds = [f"python demos/{name}/demo_data.py"] |
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execute_commands(cmds) |
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# check temporary files are removed |
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check_files(name) |
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# execute data, register |
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cmds = [f"python demos/{name}/demo_register.py --test"] |
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execute_commands(cmds) |
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check_vis_classical_demo(name) |
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DeepRegNet /
DeepReg
