KeyError: 'com' during dannce-train about dannce HOT 3 CLOSED

You can specify the com_file used for prediction in the io.yaml.

com_file: /path/to/com3d.mat

from dannce.

Hey,
same error even if I add the line specified above. I have attached the io.yaml I used and the config file.

io.txt
dannce_mouse_config.txt

2021-07-14 18:42:27.600576: I tensorflow/stream_executor/platform/default/dso_loader.cc:48] Successfully opened dynamic library cudart64_101.dll
io_config not found in io.yaml file, falling back to main config
new_n_channels_out not found in io.yaml file, falling back to main config
batch_size not found in io.yaml file, falling back to main config
epochs not found in io.yaml file, falling back to main config
net_type not found in io.yaml file, falling back to main config
train_mode not found in io.yaml file, falling back to main config
num_validation_per_exp not found in io.yaml file, falling back to main config
vol_size not found in io.yaml file, falling back to main config
nvox not found in io.yaml file, falling back to main config
max_num_samples not found in io.yaml file, falling back to main config
dannce_finetune_weights not found in io.yaml file, falling back to main config
mono not found in io.yaml file, falling back to main config
com_train_dir set to: .\COM\train_results
com_file set to: E:\DANNCE_test_210608\COM\predict_results\com3d.mat
dannce_train_dir set to: .\DANNCE\train_results\AVG
dannce_predict_dir set to: .\DANNCE\predict_results
dannce_predict_model set to: .\DANNCE\train_results\AVG\weights.1200-12.77642.hdf5
exp set to: [{'label3d_file': 'E:/DANNCE_test_210608/20210610_091000_Label3D_dannce.mat'}]
io_config set to: io.yaml
new_n_channels_out set to: 22
batch_size set to: 4
epochs set to: 1200
net_type set to: AVG
train_mode set to: finetune
num_validation_per_exp set to: 4
vol_size set to: 100
nvox set to: 64
max_num_samples set to: max
dannce_finetune_weights set to: C:\Users\realtime\dannce\demo\markerless_mouse_1\DANNCE\train_results
mono set to: True
base_config set to: C:\Users\realtime\dannce\configs\dannce_mouse_config.yaml
viddir set to: videos
crop_height set to: None
crop_width set to: None
camnames set to: None
n_channels_out set to: 20
sigma set to: 10
verbose set to: 1
net set to: None
gpu_id set to: 0
immode set to: vid
mirror set to: False
loss set to: mask_nan_keep_loss
num_train_per_exp set to: None
metric set to: ['euclidean_distance_3D']
lr set to: 0.001
augment_hue set to: False
augment_brightness set to: False
augment_hue_val set to: 0.05
augment_bright_val set to: 0.05
augment_rotation_val set to: 5
data_split_seed set to: None
valid_exp set to: None
com_fromlabels set to: False
medfilt_window set to: None
new_last_kernel_size set to: [3, 3, 3]
n_layers_locked set to: 2
vmin set to: None
vmax set to: None
interp set to: nearest
depth set to: False
comthresh set to: 0
weighted set to: False
com_method set to: median
cthresh set to: None
channel_combo set to: None
predict_mode set to: torch
n_views set to: 6
rotate set to: True
augment_continuous_rotation set to: False
drop_landmark set to: None
use_npy set to: False
rand_view_replace set to: True
n_rand_views set to: 0
multi_gpu_train set to: False
start_batch set to: 0
n_channels_in set to: None
extension set to: None
vid_dir_flag set to: None
chunks set to: None
lockfirst set to: None
load_valid set to: None
raw_im_h set to: None
raw_im_w set to: None
n_instances set to: 1
start_sample set to: None
write_npy set to: None
expval set to: None
com_thresh set to: None
cam3_train set to: None
debug_volume_tifdir set to: None
downfac set to: None
from_weights set to: None
dannce_predict_vol_tifdir set to: None
Using the following *dannce.mat files: .\20210610_091000_Label3D_dannce.mat
Setting vid_dir_flag to True.
Setting extension to .avi.
Setting chunks to {'Camera1': array([0]), 'Camera2': array([0]), 'Camera3': array([0]), 'Camera4': array([0]), 'Camera5': array([0])}.
Setting n_channels_in to 3.
Setting raw_im_h to 600.
Setting raw_im_w to 960.
Setting expval to True.
Setting net to finetune_AVG.
Setting crop_height to [0, 600].
Setting crop_width to [0, 960].
Setting maxbatch to max.
Setting start_batch to 0.
Setting vmin to -50.0.
Setting vmax to 50.0.
Fine-tuning from C:\Users\realtime\dannce\demo\markerless_mouse_1\DANNCE\train_results\weights.12000-0.00014.hdf5
Experiment 0 using videos in E:/DANNCE_test_210608\videos
Experiment 0 using camnames: ['Camera1', 'Camera2', 'Camera3', 'Camera4', 'Camera5']
{'0_Camera1': array([0]), '0_Camera2': array([0]), '0_Camera3': array([0]), '0_Camera4': array([0]), '0_Camera5': array([0])}
E:/DANNCE_test_210608/20210610_091000_Label3D_dannce.mat
The length of the camnames list must divide evenly into 6. Duplicate a subset of the views starting from the first camera (y/n)?y
Duping camnames. Changed from ['Camera1', 'Camera2', 'Camera3', 'Camera4', 'Camera5'] to ['Camera1', 'Camera2', 'Camera3', 'Camera4', 'Camera5', 'Camera1']
Traceback (most recent call last):
File "C:\Users\realtime\anaconda3\envs\dannce\Scripts\dannce-train-script.py", line 33, in
sys.exit(load_entry_point('dannce', 'console_scripts', 'dannce-train')())
File "c:\users\realtime\dannce\dannce\cli.py", line 66, in dannce_train_cli
dannce_train(params)
File "c:\users\realtime\dannce\dannce\interface.py", line 737, in dannce_train
) = do_COM_load(exp, expdict, n_views, e, params)
File "c:\users\realtime\dannce\dannce\interface.py", line 1685, in do_COM_load
c3dfile = io.load_com(exp["com_file"])
File "c:\users\realtime\dannce\dannce\engine\io.py", line 91, in load_com
d = sio.loadmat(path)["com"]
KeyError: 'com'

Thanks!

from dannce.

Sorry about that, I misread and thought you were doing prediction. For training you can add the same com_file: ... line to the experiment dictionary in the io.yaml like this:

...
exp:
    - label3d_file: 'E:/DANNCE_test_210608/20210610_091000_Label3D_dannce.mat'
      com_file: E:/DANNCE_test_210608/COM/predict_results/com3d.mat

Keep the other line though, because you'll eventually need it for prediction.

from dannce.