uvaSeg not working

[muschellij2]

library(ANTsRNet)
library(ANTsR)
#> Loading required package: ANTsRCore
#> 
#> Attaching package: 'ANTsRCore'
#> The following objects are masked from 'package:stats':
#> 
#>     sd, var
#> The following objects are masked from 'package:base':
#> 
#>     all, any, apply, max, min, prod, range, sum
img <- ri( 1 ) %>% resampleImage( c(4,4) ) %>% iMath( "Normalize" )
mask = randomMask( getMask( img ), 50 )
r = c( 3, 3 )
patch = getNeighborhoodInMask( img, mask, r, boundary.condition = "NA" )
uvaSegModel = uvaSegTrain( patch, 6 )
#> Error in py_call_impl(callable, dots$args, dots$keywords): _SymbolicException: Inputs to eager execution function cannot be Keras symbolic tensors, but found [<tf.Tensor 'dense_2/Identity:0' shape=(None, 6) dtype=float32>, <tf.Tensor 'dense_1/Identity:0' shape=(None, 6) dtype=float32>]
#> 
#> Detailed traceback: 
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training.py", line 728, in fit
#>     use_multiprocessing=use_multiprocessing)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_v2.py", line 324, in fit
#>     total_epochs=epochs)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_v2.py", line 123, in run_one_epoch
#>     batch_outs = execution_function(iterator)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/training_v2_utils.py", line 86, in execution_function
#>     distributed_function(input_fn))
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/def_function.py", line 457, in __call__
#>     result = self._call(*args, **kwds)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/def_function.py", line 520, in _call
#>     return self._stateless_fn(*args, **kwds)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/function.py", line 1823, in __call__
#>     return graph_function._filtered_call(args, kwargs)  # pylint: disable=protected-access
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/function.py", line 1141, in _filtered_call
#>     self.captured_inputs)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/function.py", line 1224, in _call_flat
#>     ctx, args, cancellation_manager=cancellation_manager)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/function.py", line 511, in call
#>     ctx=ctx)
#>   File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/execute.py", line 75, in quick_execute
#>     "tensors, but found {}".format(keras_symbolic_tensors))

^{Created on 2020-01-30 by the reprex package (v0.3.0.9001)}

Session info

sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value                       
#>  version  R version 3.6.0 (2019-04-26)
#>  os       macOS Mojave 10.14.6        
#>  system   x86_64, darwin15.6.0        
#>  ui       X11                         
#>  language (EN)                        
#>  collate  en_US.UTF-8                 
#>  ctype    en_US.UTF-8                 
#>  tz       America/New_York            
#>  date     2020-01-30                  
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package     * version     date       lib source                             
#>  ANTsR       * 0.5.4.2     2019-11-14 [1] local                              
#>  ANTsRCore   * 0.7.3       2019-12-11 [1] Github (ANTsX/ANTsRCore@416d8f1)   
#>  ANTsRNet    * 1.1         2020-01-30 [1] local                              
#>  assertthat    0.2.1       2019-03-21 [1] CRAN (R 3.6.0)                     
#>  backports     1.1.5       2019-10-02 [1] CRAN (R 3.6.0)                     
#>  base64enc     0.1-3       2015-07-28 [1] CRAN (R 3.6.0)                     
#>  cli           2.0.1       2020-01-08 [1] CRAN (R 3.6.0)                     
#>  crayon        1.3.4       2017-09-16 [1] CRAN (R 3.6.0)                     
#>  digest        0.6.23      2019-11-23 [1] CRAN (R 3.6.0)                     
#>  evaluate      0.14        2019-05-28 [1] CRAN (R 3.6.0)                     
#>  fansi         0.4.1       2020-01-08 [1] CRAN (R 3.6.0)                     
#>  fs            1.3.1       2019-05-06 [1] CRAN (R 3.6.0)                     
#>  generics      0.0.2       2018-11-29 [1] CRAN (R 3.6.0)                     
#>  glue          1.3.1       2019-03-12 [1] CRAN (R 3.6.0)                     
#>  highr         0.8         2019-03-20 [1] CRAN (R 3.6.0)                     
#>  htmltools     0.4.0       2019-10-04 [1] CRAN (R 3.6.0)                     
#>  ITKR          0.5.2       2019-11-05 [1] Github (stnava/ITKR@fe97efa)       
#>  jsonlite      1.6         2018-12-07 [1] CRAN (R 3.6.0)                     
#>  keras         2.2.5.0     2019-10-08 [1] CRAN (R 3.6.0)                     
#>  knitr         1.26.1      2020-01-05 [1] Github (muschellij2/knitr@f5af631) 
#>  lattice       0.20-38     2018-11-04 [1] CRAN (R 3.6.0)                     
#>  magrittr      1.5         2014-11-22 [1] CRAN (R 3.6.0)                     
#>  Matrix        1.2-17      2019-03-22 [1] CRAN (R 3.6.0)                     
#>  mvtnorm       1.0-11      2019-06-19 [1] CRAN (R 3.6.0)                     
#>  pillar        1.4.3       2019-12-20 [1] CRAN (R 3.6.0)                     
#>  pkgconfig     2.0.3       2019-09-22 [1] CRAN (R 3.6.0)                     
#>  purrr         0.3.3       2019-10-18 [1] CRAN (R 3.6.0)                     
#>  R6            2.4.1       2019-11-12 [1] CRAN (R 3.6.0)                     
#>  Rcpp          1.0.3       2019-11-08 [1] CRAN (R 3.6.0)                     
#>  RcppEigen     0.3.3.7.0   2019-11-16 [1] CRAN (R 3.6.0)                     
#>  reprex        0.3.0.9001  2020-01-05 [1] Github (tidyverse/reprex@5ae0b29)  
#>  reticulate    1.13        2019-07-24 [1] CRAN (R 3.6.0)                     
#>  rlang         0.4.2       2019-11-23 [1] CRAN (R 3.6.0)                     
#>  rmarkdown     2.0.7       2020-01-17 [1] Github (rstudio/rmarkdown@2faf16a) 
#>  rstudioapi    0.10.0-9003 2020-01-05 [1] Github (rstudio/rstudioapi@abe596d)
#>  sessioninfo   1.1.1       2018-11-05 [1] CRAN (R 3.6.0)                     
#>  stringi       1.4.5       2020-01-11 [1] CRAN (R 3.6.0)                     
#>  stringr       1.4.0       2019-02-10 [1] CRAN (R 3.6.0)                     
#>  styler        1.1.1       2019-05-06 [1] CRAN (R 3.6.0)                     
#>  tensorflow    2.0.0       2019-10-02 [1] CRAN (R 3.6.0)                     
#>  tfruns        1.4         2018-08-25 [1] CRAN (R 3.6.0)                     
#>  tibble        2.1.3       2019-06-06 [1] CRAN (R 3.6.0)                     
#>  whisker       0.4         2019-08-28 [1] CRAN (R 3.6.0)                     
#>  withr         2.1.2       2018-03-15 [1] CRAN (R 3.6.0)                     
#>  xfun          0.11        2019-11-12 [1] CRAN (R 3.6.0)                     
#>  yaml          2.2.0       2018-07-25 [1] CRAN (R 3.6.0)                     
#>  zeallot       0.1.0       2018-01-28 [1] CRAN (R 3.6.0)                     
#> 
#> [1] /Library/Frameworks/R.framework/Versions/3.6/Resources/library