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[2023-08-16 11:43:57,980] INFO [main.feature_extractor_inference:475] configuration used in inference:
[2023-08-16 11:43:57,996] INFO [main.feature_extractor_inference:476] split:
reload: true
file: null
train_val_test:
[2023-08-16 11:43:57,996] INFO [main.feature_extractor_inference:481] Latent name used in HDF5 file: resnet18
[2023-08-16 11:43:58,089] INFO [deepethogram.data.augs.get_gpu_transforms:246] GPU transforms: {'train': Sequential(
(0): ToFloat()
(1): VideoSequential(
(RandomHorizontalFlip_0): RandomHorizontalFlip(RandomHorizontalFlip(p=0.5, p_batch=1.0, same_on_batch=False))
(RandomRotation_1): RandomRotation(RandomRotation(degrees=10, p=0.5, p_batch=1.0, same_on_batch=False, resample=bilinear, align_corners=True))
(ColorJitter_2): ColorJitter(ColorJitter(brightness=0.25, contrast=0.1, saturation=0.1, hue=0.1, p=0.5, p_batch=1.0, same_on_batch=False))
(RandomGrayscale_3): RandomGrayscale(RandomGrayscale(p=0.5, p_batch=1.0, same_on_batch=False))
)
(2): NormalizeVideo()
(3): StackClipInChannels()
), 'val': Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
), 'test': Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
), 'denormalize': Sequential(
(0): UnstackClip()
(1): DenormalizeVideo()
)}
[2023-08-16 11:43:58,089] INFO [main.feature_extractor_inference:515] gpu_transform: Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
)
[2023-08-16 11:43:58,293] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,527] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,543] INFO [deepethogram.feature_extractor.train.build_model_from_cfg:220] feature extractor weightfile: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,683] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component spatial from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,074] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component flow from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,433] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230815_232411_flow_generator_train\lightning_checkpoints\epoch=3-step=3999.ckpt
[2023-08-16 11:43:59,433] INFO [deepethogram.utils.load_state:341] loading from checkpoint file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230815_232411_flow_generator_train\lightning_checkpoints\epoch=3-step=3999.ckpt...
[2023-08-16 11:43:59,449] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component fusion from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,558] INFO [main.feature_extractor_inference:545] best epoch from loaded file: 19
Traceback (most recent call last):
File "C:\Users\shahlab\anaconda3\envs\deg\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\shahlab\anaconda3\envs\deg\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\deepethogram\feature_extractor\inference.py", line 586, in
feature_extractor_inference(cfg)
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\deepethogram\feature_extractor\inference.py", line 548, in feature_extractor_inference
thresholds = f['val']['metrics_by_threshold']['optimum'][best_epoch, :]
File "h5py_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\h5py_hl\dataset.py", line 758, in getitem
return self._fast_reader.read(args)
File "h5py_selector.pyx", line 361, in h5py._selector.Reader.read
File "h5py_selector.pyx", line 151, in h5py._selector.Selector.apply_args
IndexError: Index (19) out of range for (0-15)
[2023-08-16 11:44:00,996] INFO [deepethogram.gui.main.featureextractor_infer:462] Inference finished. If you see error messages above, inference did not complete successfully.
Hello, I'm trying to run the deepethogram and it works very well with example videos. However, when I switched to my videos, it gave me the indexError when I was trying to run the featureextractor_inference. How can I fix it? Does anyone have good suggestions? Thanks.
The text was updated successfully, but these errors were encountered:
[2023-08-16 11:43:57,980] INFO [main.feature_extractor_inference:475] configuration used in inference:
[2023-08-16 11:43:57,996] INFO [main.feature_extractor_inference:476] split:
reload: true
file: null
train_val_test:
compute:
fp16: false
num_workers: 8
batch_size: 8
min_batch_size: 8
max_batch_size: 512
distributed: false
gpu_id: 0
dali: false
metrics_workers: 0
reload:
overwrite_cfg: false
latest: false
notes: null
log:
level: info
augs:
brightness: 0.25
contrast: 0.1
hue: 0.1
saturation: 0.1
color_p: 0.5
grayscale: 0.5
crop_size: null
resize:
dali: false
random_resize: false
pad: null
LR: 0.5
UD: 0.0
degrees: 10
normalization:
'N': 345600000
mean:
std:
feature_extractor:
arch: resnet18
fusion: average
sampler: null
final_bn: false
sampling_ratio: null
final_activation: sigmoid
dropout_p: 0.25
n_flows: 10
n_rgb: 1
curriculum: false
inputs: both
weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
train:
steps_per_epoch:
train: 1000
val: 200
test: 20
num_epochs: 10
loss_weight_exp: 1.0
flow_generator:
type: flow_generator
flow_loss: MotionNet
flow_max: 10
input_images: 11
flow_sparsity: false
smooth_weight_multiplier: 1.0
sparsity_weight: 0.0
loss: MotionNet
max: 5
n_rgb: 11
arch: TinyMotionNet
weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230815_232411_flow_generator_train\lightning_checkpoints\epoch=3-step=3999.ckpt
inference:
directory_list:
ignore_error: true
overwrite: true
use_loaded_model_cfg: true
postprocessor:
type: min_bout_per_behavior
min_bout_length: 1
cmap: deepethogram
control_arrow_jump: 31
label_view_width: 31
prediction_opacity: 0.2
project:
class_names:
config_file: project_config.yaml
data_path: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\DATA
labeler: null
model_path: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models
name: habitation_test
path: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram
pretrained_path: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\pretrained_models
run:
type: inference
model: feature_extractor
dir: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_114357_feature_extractor_inference
sequence:
filter_length: 15
unlabeled_alpha: 0.1
vertical_arrow_jump: 3
[2023-08-16 11:43:57,996] INFO [main.feature_extractor_inference:481] Latent name used in HDF5 file: resnet18
[2023-08-16 11:43:58,089] INFO [deepethogram.data.augs.get_gpu_transforms:246] GPU transforms: {'train': Sequential(
(0): ToFloat()
(1): VideoSequential(
(RandomHorizontalFlip_0): RandomHorizontalFlip(RandomHorizontalFlip(p=0.5, p_batch=1.0, same_on_batch=False))
(RandomRotation_1): RandomRotation(RandomRotation(degrees=10, p=0.5, p_batch=1.0, same_on_batch=False, resample=bilinear, align_corners=True))
(ColorJitter_2): ColorJitter(ColorJitter(brightness=0.25, contrast=0.1, saturation=0.1, hue=0.1, p=0.5, p_batch=1.0, same_on_batch=False))
(RandomGrayscale_3): RandomGrayscale(RandomGrayscale(p=0.5, p_batch=1.0, same_on_batch=False))
)
(2): NormalizeVideo()
(3): StackClipInChannels()
), 'val': Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
), 'test': Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
), 'denormalize': Sequential(
(0): UnstackClip()
(1): DenormalizeVideo()
)}
[2023-08-16 11:43:58,089] INFO [main.feature_extractor_inference:515] gpu_transform: Sequential(
(0): ToFloat()
(1): NormalizeVideo()
(2): StackClipInChannels()
)
[2023-08-16 11:43:58,293] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,527] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,543] INFO [deepethogram.feature_extractor.train.build_model_from_cfg:220] feature extractor weightfile: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:58,683] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component spatial from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,074] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component flow from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,433] INFO [deepethogram.projects.get_weightfile_from_cfg:1079] loading specified weights: C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230815_232411_flow_generator_train\lightning_checkpoints\epoch=3-step=3999.ckpt
[2023-08-16 11:43:59,433] INFO [deepethogram.utils.load_state:341] loading from checkpoint file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230815_232411_flow_generator_train\lightning_checkpoints\epoch=3-step=3999.ckpt...
[2023-08-16 11:43:59,449] INFO [deepethogram.utils.load_feature_extractor_components:630] loading component fusion from file C:\Users\shahlab\Desktop\Deepethogram\vole\habitation_test_deepethogram\models\230816_013853_feature_extractor_train\lightning_checkpoints\epoch=19-step=17955.ckpt
[2023-08-16 11:43:59,558] INFO [main.feature_extractor_inference:545] best epoch from loaded file: 19
Traceback (most recent call last):
File "C:\Users\shahlab\anaconda3\envs\deg\lib\runpy.py", line 196, in _run_module_as_main
return _run_code(code, main_globals, None,
File "C:\Users\shahlab\anaconda3\envs\deg\lib\runpy.py", line 86, in _run_code
exec(code, run_globals)
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\deepethogram\feature_extractor\inference.py", line 586, in
feature_extractor_inference(cfg)
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\deepethogram\feature_extractor\inference.py", line 548, in feature_extractor_inference
thresholds = f['val']['metrics_by_threshold']['optimum'][best_epoch, :]
File "h5py_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
File "h5py_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
File "C:\Users\shahlab\anaconda3\envs\deg\lib\site-packages\h5py_hl\dataset.py", line 758, in getitem
return self._fast_reader.read(args)
File "h5py_selector.pyx", line 361, in h5py._selector.Reader.read
File "h5py_selector.pyx", line 151, in h5py._selector.Selector.apply_args
IndexError: Index (19) out of range for (0-15)
[2023-08-16 11:44:00,996] INFO [deepethogram.gui.main.featureextractor_infer:462] Inference finished. If you see error messages above, inference did not complete successfully.
Hello, I'm trying to run the deepethogram and it works very well with example videos. However, when I switched to my videos, it gave me the indexError when I was trying to run the featureextractor_inference. How can I fix it? Does anyone have good suggestions? Thanks.
The text was updated successfully, but these errors were encountered: