Nueral response prediction error

[shanggao11]

Hi there!
May I ask a question about the neural response prediction part?
I have a neural response array in firing rate (FRarray)along with camera stamps and neural stamps; both camera stamps(CSarray) and neural stamps(NSarray) are in frames. NSarray.shape==FRarray.shape(if ignore the number of neurons); CSarray.shape match with the input video frames (I input a 5 mins data, but the facemap only read in 4.2 mins data, I tried both the size of 5 and 4.2 mins); It gave me this error when I run the neural response prediction, Please help me about this, thank you very much!:

at non-singleton dimension 1
pose data shape (3, 15, 50531)
xy.shape (50531, 15, 2)
outlier filter shape (50531, 15, 2)
x.shape (50531, 30)
Neural target shape: (300002, 10)
Keypoints shape: (50531, 30)
Inputs: (50531, 30)
Neural: (300002, 10)
Using lr, n_iter, weight_decay: 0.001 300 0.0001
Ignoring window icon 4534162 exceeds maximum xcb request length 4194303
Ignoring window icon 4534162 exceeds maximum xcb request length 4194303
Traceback (most recent call last):
File "/home/isocortex/miniconda3/envs/facemap/lib/python3.8/site-packages/facemap/gui/neural_activity_window.py", line 537, in
lambda clicked: self.run_neural_predictions(clicked, dialog)
File "/home/isocortex/miniconda3/envs/facemap/lib/python3.8/site-packages/facemap/gui/neural_activity_window.py", line 653, in run_neural_predictions
) = prediction_utils.get_keypoints_to_neural_varexp(
File "/home/isocortex/miniconda3/envs/facemap/lib/python3.8/site-packages/facemap/neural_prediction/prediction_utils.py", line 448, in get_keypoints_to_neural_varexp
) = model.train_model(
File "/home/isocortex/miniconda3/envs/facemap/lib/python3.8/site-packages/facemap/neural_prediction/neural_model.py", line 184, in train_model
loss = ((y_pred - Y_train[i][n].unsqueeze(0)) ** 2).mean()
RuntimeError: The size of tensor a (4503) must match the size of tensor b (22500) at non-singleton dimension 1

[Atika-Syeda]

Hi @shanggao11 can you please confirm if you also load the camera and neural stamps when you run the prediction?

[shanggao11]

Hi @shanggao11 can you please confirm if you also load the camera and neural stamps when you run the prediction?

Thanks for your reply! yes,i am sure that I load the camera and neural stamps.

[Atika-Syeda]

Can you please share facemap and other packages version info please?

[shanggao11]

Hi, Thank you for your response, here is the packages in the facemap environment:
name: facemap
channels:

• conda-forge
• defaults
  dependencies:
• _libgcc_mutex=0.1=conda_forge
• _openmp_mutex=4.5=2_gnu
• alsa-lib=1.2.7.2=h166bdaf_0
• attr=2.5.1=h166bdaf_1
• blosc=1.21.1=h83bc5f7_3
• bzip2=1.0.8=h7f98852_4
• c-ares=1.18.1=h7f98852_0
• ca-certificates=2022.9.24=ha878542_0
• dbus=1.13.6=h5008d03_3
• expat=2.4.9=h27087fc_0
• fftw=3.3.10=nompi_hf0379b8_105
• font-ttf-dejavu-sans-mono=2.37=hab24e00_0
• font-ttf-inconsolata=3.000=h77eed37_0
• font-ttf-source-code-pro=2.038=h77eed37_0
• font-ttf-ubuntu=0.83=hab24e00_0
• fontconfig=2.14.0=hc2a2eb6_1
• fonts-conda-ecosystem=1=0
• fonts-conda-forge=1=0
• freetype=2.12.1=hca18f0e_0
• gettext=0.19.8.1=h27087fc_1009
• glib=2.74.0=h6239696_0
• glib-tools=2.74.0=h6239696_0
• gst-plugins-base=1.20.3=h57caac4_2
• gstreamer=1.20.3=hd4edc92_2
• hdbscan=0.8.28=py39hce5d2b2_1
• hdf5=1.12.2=nompi_h2386368_100
• icu=70.1=h27087fc_0
• jack=1.9.18=h8c3723f_1003
• joblib=1.2.0=pyhd8ed1ab_0
• jpeg=9e=h166bdaf_2
• keyutils=1.6.1=h166bdaf_0
• krb5=1.19.3=h3790be6_0
• ld_impl_linux-64=2.36.1=hea4e1c9_2
• libblas=3.9.0=16_linux64_openblas
• libcap=2.65=ha37c62d_0
• libcblas=3.9.0=16_linux64_openblas
• libclang=14.0.6=default_h2e3cab8_0
• libclang13=14.0.6=default_h3a83d3e_0
• libcups=2.3.3=h3e49a29_2
• libcurl=7.85.0=h7bff187_0
• libdb=6.2.32=h9c3ff4c_0
• libedit=3.1.20191231=he28a2e2_2
• libev=4.33=h516909a_1
• libevent=2.1.10=h9b69904_4
• libffi=3.4.2=h7f98852_5
• libflac=1.3.4=h27087fc_0
• libgcc-ng=12.1.0=h8d9b700_16
• libgfortran-ng=12.1.0=h69a702a_16
• libgfortran5=12.1.0=hdcd56e2_16
• libglib=2.74.0=h7a41b64_0
• libgomp=12.1.0=h8d9b700_16
• libiconv=1.17=h166bdaf_0
• liblapack=3.9.0=16_linux64_openblas
• libllvm11=11.1.0=he0ac6c6_4
• libllvm14=14.0.6=he0ac6c6_0
• libnghttp2=1.47.0=hdcd2b5c_1
• libnsl=2.0.0=h7f98852_0
• libogg=1.3.4=h7f98852_1
• libopenblas=0.3.21=pthreads_h78a6416_3
• libopus=1.3.1=h7f98852_1
• libpng=1.6.38=h753d276_0
• libpq=14.5=hd77ab85_0
• libsndfile=1.0.31=h9c3ff4c_1
• libsqlite=3.39.4=h753d276_0
• libssh2=1.10.0=haa6b8db_3
• libstdcxx-ng=12.1.0=ha89aaad_16
• libtool=2.4.6=h9c3ff4c_1008
• libudev1=249=h166bdaf_4
• libuuid=2.32.1=h7f98852_1000
• libvorbis=1.3.7=h9c3ff4c_0
• libxcb=1.13=h7f98852_1004
• libxkbcommon=1.0.3=he3ba5ed_0
• libxml2=2.10.2=h4c7fe37_1
• libzlib=1.2.12=h166bdaf_4
• llvmlite=0.39.1=py39h7d9a04d_0
• lz4-c=1.9.3=h9c3ff4c_1
• lzo=2.10=h516909a_1000
• mysql-common=8.0.30=haf5c9bc_1
• mysql-libs=8.0.30=h28c427c_1
• ncurses=6.3=h27087fc_1
• nomkl=1.0=h5ca1d4c_0
• nspr=4.32=h9c3ff4c_1
• nss=3.78=h2350873_0
• numba=0.56.2=py39h61ddf18_1
• numexpr=2.8.3=py39h194a79d_100
• numpy=1.23.3=py39hba7629e_0
• openssl=1.1.1q=h166bdaf_0
• packaging=21.3=pyhd8ed1ab_0
• pcre2=10.37=hc3806b6_1
• pip=22.2.2=pyhd8ed1ab_0
• ply=3.11=py_1
• portaudio=19.6.0=h8e90077_6
• pthread-stubs=0.4=h36c2ea0_1001
• pulseaudio=14.0=h0868958_9
• pyparsing=3.0.9=pyhd8ed1ab_0
• pyqt=5.15.7=py39h18e9c17_0
• pyqt5-sip=12.11.0=py39h5a03fae_0
• pytables=3.7.0=py39hee6f8ba_2
• python=3.9.13=h9a8a25e_0_cpython
• python_abi=3.9=2_cp39
• qt-main=5.15.6=hc525480_0
• readline=8.1.2=h0f457ee_0
• scikit-learn=1.1.2=py39he5e8d7e_0
• scipy=1.9.1=py39h8ba3f38_0
• setuptools=65.4.1=pyhd8ed1ab_0
• sip=6.6.2=py39h5a03fae_0
• six=1.16.0=pyh6c4a22f_0
• snappy=1.1.9=hbd366e4_1
• sqlite=3.39.4=h4ff8645_0
• threadpoolctl=3.1.0=pyh8a188c0_0
• tk=8.6.12=h27826a3_0
• toml=0.10.2=pyhd8ed1ab_0
• tzdata=2022d=h191b570_0
• wheel=0.37.1=pyhd8ed1ab_0
• xcb-util=0.4.0=h166bdaf_0
• xcb-util-image=0.4.0=h166bdaf_0
• xcb-util-keysyms=0.4.0=h166bdaf_0
• xcb-util-renderutil=0.3.9=h166bdaf_0
• xcb-util-wm=0.4.1=h166bdaf_0
• xorg-libxau=1.0.9=h7f98852_0
• xorg-libxdmcp=1.1.3=h7f98852_0
• xz=5.2.6=h166bdaf_0
• zstd=1.5.2=h6239696_4
• pip:
  • certifi==2022.9.24
  • charset-normalizer==2.1.1
  • contourpy==1.0.5
  • cycler==0.11.0
  • facemap==0.2.0
  • fonttools==4.37.4
  • idna==3.4
  • kiwisolver==1.4.4
  • matplotlib==3.6.1
  • natsort==8.2.0
  • opencv-python-headless==4.6.0.66
  • pandas==1.5.0
  • pillow==9.2.0
  • pynndescent==0.5.7
  • pyqtgraph==0.11.0rc0
  • python-dateutil==2.8.2
  • pytz==2022.4
  • requests==2.28.1
  • torch==1.11.0
  • torchvision==0.12.0
  • tqdm==4.64.1
  • typing-extensions==4.4.0
  • umap-learn==0.5.3
  • urllib3==1.26.12