How to use patch_config method in yandex-tank

Best Python code snippet using yandex-tank

xception.py

Source:xception.py

...8    aligned_xception.preprocess_input)9def AlignedXception41Stride16(*args, **kwargs):10    base = AlignedXception41(*args, **kwargs)11    conf = base.get_config()12    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))13    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))14    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))15    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))16    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))17    patch = models.Model.from_config(conf)18    patch.set_weights(base.get_weights())19    return patch20def AlignedXception41Stride8(*args, **kwargs):21    base = AlignedXception41(*args, **kwargs)22    conf = base.get_config()23    conf = patch_config(conf, ['entry_flow/block3/unit1/sepconv3_depthwise'], 'strides', (1, 1))24    conf = patch_config(conf, ['entry_flow/block3/unit1/shortcut'], 'strides', (1, 1))25    for i in range(8):26        conf = patch_config(conf, [27            'middle_flow/block1/unit{}/sepconv1_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))28        conf = patch_config(conf, [29            'middle_flow/block1/unit{}/sepconv2_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))30        conf = patch_config(conf, [31            'middle_flow/block1/unit{}/sepconv3_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))32    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))33    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))34    # Output shape is different when using exit dilation rates like in35    # https://github.com/bonlime/keras-deeplab-v3-plus/blob/master/model.py#L26536    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))37    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))38    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))39    patch = models.Model.from_config(conf)40    patch.set_weights(base.get_weights())41    return patch42AlignedXception65 = partial(43    wrap_bone,44    aligned_xception.Xception65,45    aligned_xception.preprocess_input)46def AlignedXception65Stride16(*args, **kwargs):47    base = AlignedXception65(*args, **kwargs)48    conf = base.get_config()49    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))50    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))51    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))52    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))53    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))54    patch = models.Model.from_config(conf)55    patch.set_weights(base.get_weights())56    return patch57def AlignedXception65Stride8(*args, **kwargs):58    base = AlignedXception65(*args, **kwargs)59    conf = base.get_config()60    conf = patch_config(conf, ['entry_flow/block3/unit1/sepconv3_depthwise'], 'strides', (1, 1))61    conf = patch_config(conf, ['entry_flow/block3/unit1/shortcut'], 'strides', (1, 1))62    for i in range(16):63        conf = patch_config(conf, [64            'middle_flow/block1/unit{}/sepconv1_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))65        conf = patch_config(conf, [66            'middle_flow/block1/unit{}/sepconv2_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))67        conf = patch_config(conf, [68            'middle_flow/block1/unit{}/sepconv3_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))69    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))70    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))71    # Output shape is different when using exit dilation rates like in72    # https://github.com/bonlime/keras-deeplab-v3-plus/blob/master/model.py#L26573    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))74    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))75    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))76    patch = models.Model.from_config(conf)77    patch.set_weights(base.get_weights())78    return patch79AlignedXception71 = partial(80    wrap_bone,81    aligned_xception.Xception71,82    aligned_xception.preprocess_input)83def AlignedXception71Stride16(*args, **kwargs):84    base = AlignedXception71(*args, **kwargs)85    conf = base.get_config()86    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))87    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))88    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))89    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))90    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))91    patch = models.Model.from_config(conf)92    patch.set_weights(base.get_weights())93    return patch94def AlignedXception71Stride8(*args, **kwargs):95    base = AlignedXception71(*args, **kwargs)96    conf = base.get_config()97    conf = patch_config(conf, ['entry_flow/block5/unit1/sepconv3_depthwise'], 'strides', (1, 1))98    conf = patch_config(conf, ['entry_flow/block5/unit1/shortcut'], 'strides', (1, 1))99    for i in range(16):100        conf = patch_config(conf, [101            'middle_flow/block1/unit{}/sepconv1_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))102        conf = patch_config(conf, [103            'middle_flow/block1/unit{}/sepconv2_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))104        conf = patch_config(conf, [105            'middle_flow/block1/unit{}/sepconv3_depthwise'.format(i + 1)], 'dilation_rate', (2, 2))106    conf = patch_config(conf, ['exit_flow/block1/unit1/sepconv3_depthwise'], 'strides', (1, 1))107    conf = patch_config(conf, ['exit_flow/block1/unit1/shortcut'], 'strides', (1, 1))108    # Output shape is different when using exit dilation rates like in109    # https://github.com/bonlime/keras-deeplab-v3-plus/blob/master/model.py#L265110    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv1_depthwise'], 'dilation_rate', (2, 2))111    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv2_depthwise'], 'dilation_rate', (2, 2))112    conf = patch_config(conf, ['exit_flow/block2/unit1/sepconv3_depthwise'], 'dilation_rate', (2, 2))113    patch = models.Model.from_config(conf)114    patch.set_weights(base.get_weights())...

luna_s3_p8.py

Source:luna_s3_p8.py

1import data_transforms2import data_iterators3import pathfinder4import utils5import string6import numpy as np7import lasagne as nn8# IMPORT A CORRECT PATCH MODEL HERE9import lung_segmentation10import configs_seg_patch.luna_p8 as patch_config11# print utils.get_script_name(__file__).split('_')[-1]12# print patch_config.__name__.split('.')[-1]13# assert utils.get_script_name(__file__).replace('_s*_', '_') == patch_config.__name__.split('.')[-1]14rng = patch_config.rng15# calculate the following things correctly!16p_transform = {'patch_size': (416, 416, 416),17               'mm_patch_size': (416, 416, 416),18               'pixel_spacing': patch_config.p_transform['pixel_spacing']19               }20window_size = 16021stride = 12822n_windows = (p_transform['patch_size'][0] - window_size) / stride + 123valid_pids = patch_config.valid_pids24def data_prep_function(data, luna_annotations, pixel_spacing, luna_origin,25                       p_transform=p_transform,26                       p_transform_augment=None):27    # make sure the data is processed the same way28    lung_mask = lung_segmentation.segment_HU_scan(data)29    x, annotations_tf, tf_matrix, lung_mask_out = data_transforms.transform_scan3d(data=data,30                                                                                   pixel_spacing=pixel_spacing,31                                                                                   p_transform=p_transform,32                                                                                   luna_annotations=luna_annotations,33                                                                                   p_transform_augment=None,34                                                                                   luna_origin=luna_origin,35                                                                                   lung_mask=lung_mask)36    x = data_transforms.pixelnormHU(x)37    y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere')38    return x, y, lung_mask_out, annotations_tf, tf_matrix39valid_data_iterator = data_iterators.LunaScanPositiveLungMaskDataGenerator(data_path=pathfinder.LUNA_DATA_PATH,40                                                                           transform_params=p_transform,41                                                                           data_prep_fun=data_prep_function,42                                                                           rng=rng,43                                                                           batch_size=1,44                                                                           patient_ids=valid_pids,45                                                                           full_batch=True,46                                                                           random=False, infinite=False)47def build_model():48    metadata_dir = utils.get_dir_path('models', pathfinder.METADATA_PATH)49    metadata_path = utils.find_model_metadata(metadata_dir, patch_config.__name__.split('.')[-1])50    metadata = utils.load_pkl(metadata_path)51    print 'Build model'52    model = patch_config.build_model(patch_size=(window_size, window_size, window_size))53    all_layers = nn.layers.get_all_layers(model.l_out)54    num_params = nn.layers.count_params(model.l_out)55    print '  number of parameters: %d' % num_params56    print string.ljust('  layer output shapes:', 36),57    print string.ljust('#params:', 10),58    print 'output shape:'59    for layer in all_layers:60        name = string.ljust(layer.__class__.__name__, 32)61        num_param = sum([np.prod(p.get_value().shape) for p in layer.get_params()])62        num_param = string.ljust(num_param.__str__(), 10)63        print '    %s %s %s' % (name, num_param, layer.output_shape)64    nn.layers.set_all_param_values(model.l_out, metadata['param_values'])...

luna_s2_p8.py

Source:luna_s2_p8.py

1import data_transforms2import data_iterators3import pathfinder4import utils5import string6import numpy as np7import lasagne as nn8# IMPORT A CORRECT PATCH MODEL HERE9import configs_seg_patch.luna_p8 as patch_config10# print utils.get_script_name(__file__).split('_')[-1]11# print patch_config.__name__.split('.')[-1]12# assert utils.get_script_name(__file__).replace('_s*_', '_') == patch_config.__name__.split('.')[-1]13rng = patch_config.rng14# calculate the following things correctly!15p_transform = {'patch_size': (416, 416, 416),16               'mm_patch_size': (416, 416, 416),17               'pixel_spacing': patch_config.p_transform['pixel_spacing']18               }19window_size = 16020stride = 12821n_windows = (p_transform['patch_size'][0] - window_size) / stride + 122valid_pids = patch_config.valid_pids23def data_prep_function(data, luna_annotations, pixel_spacing, luna_origin,24                       p_transform=p_transform,25                       p_transform_augment=None):26    # make sure the data is processed the same way 27    x, annotations_tf, tf_matrix = data_transforms.transform_scan3d(data=data,28                                                                    pixel_spacing=pixel_spacing,29                                                                    p_transform=p_transform,30                                                                    luna_annotations=luna_annotations,31                                                                    p_transform_augment=None,32                                                                    luna_origin=luna_origin)33    x = data_transforms.pixelnormHU(x)34    y = data_transforms.make_3d_mask_from_annotations(img_shape=x.shape, annotations=annotations_tf, shape='sphere')35    return x, y, annotations_tf, tf_matrix36valid_data_iterator = data_iterators.LunaScanPositiveDataGenerator(data_path=pathfinder.LUNA_DATA_PATH,37                                                                   transform_params=p_transform,38                                                                   data_prep_fun=data_prep_function,39                                                                   rng=rng,40                                                                   patient_ids=valid_pids,41                                                                   random=False, infinite=False)42def build_model():43    metadata_dir = utils.get_dir_path('models', pathfinder.METADATA_PATH)44    metadata_path = utils.find_model_metadata(metadata_dir, patch_config.__name__.split('.')[-1])45    metadata = utils.load_pkl(metadata_path)46    print 'Build model'47    model = patch_config.build_model(patch_size=(window_size, window_size, window_size))48    all_layers = nn.layers.get_all_layers(model.l_out)49    num_params = nn.layers.count_params(model.l_out)50    print '  number of parameters: %d' % num_params51    print string.ljust('  layer output shapes:', 36),52    print string.ljust('#params:', 10),53    print 'output shape:'54    for layer in all_layers:55        name = string.ljust(layer.__class__.__name__, 32)56        num_param = sum([np.prod(p.get_value().shape) for p in layer.get_params()])57        num_param = string.ljust(num_param.__str__(), 10)58        print '    %s %s %s' % (name, num_param, layer.output_shape)59    nn.layers.set_all_param_values(model.l_out, metadata['param_values'])...

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