ANTsRNet
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ANTsX
Ssd7 Model
createSsd7Model2D fails for 2D
library(ANTsRNet)
createSsd7Model2D(c(256, 256, 3), 2)
#> Error in py_call_impl(callable, dots$args, dots$keywords): ValueError: Duplicate node name in graph: 'packed'
#>
#> Detailed traceback:
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/backend.py", line 3014, in tile
#> return array_ops.tile(x, n)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/gen_array_ops.py", line 11293, in tile
#> input, multiples, name=name, ctx=_ctx)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/gen_array_ops.py", line 11340, in tile_eager_fallback
#> _attr_Tmultiples, (multiples,) = _execute.args_to_matching_eager([multiples], _ctx, _dtypes.int32)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/eager/execute.py", line 257, in args_to_matching_eager
#> t, dtype, preferred_dtype=default_dtype, ctx=ctx))
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 1296, in internal_convert_to_tensor
#> ret = conversion_func(value, dtype=dtype, name=name, as_ref=as_ref)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/array_ops.py", line 1278, in _autopacking_conversion_function
#> return _autopacking_helper(v, dtype, name or "packed")
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/array_ops.py", line 1214, in _autopacking_helper
#> return gen_array_ops.pack(elems_as_tensors, name=scope)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/gen_array_ops.py", line 6304, in pack
#> "Pack", values=values, axis=axis, name=name)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/op_def_library.py", line 793, in _apply_op_helper
#> op_def=op_def)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/func_graph.py", line 548, in create_op
#> compute_device)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 3429, in _create_op_internal
#> op_def=op_def)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 1773, in __init__
#> control_input_ops)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 1613, in _create_c_op
#> raise ValueError(str(e))
Also fails for 3D
library(ANTsRNet)
createSsd7Model3D(c(256, 256, 100, 3), 2)
#> Error in py_call_impl(callable, dots$args, dots$keywords): ValueError: Negative dimension size caused by subtracting 3 from 1 for 'classes7_1/Conv3D' (op: 'Conv3D') with input shapes: [?,4,4,1,32], [3,3,3,32,10].
#>
#> Detailed traceback:
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/engine/base_layer.py", line 842, in __call__
#> outputs = call_fn(cast_inputs, *args, **kwargs)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/keras/layers/convolutional.py", line 197, in call
#> outputs = self._convolution_op(inputs, self.kernel)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/nn_ops.py", line 1134, in __call__
#> return self.conv_op(inp, filter)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/nn_ops.py", line 639, in __call__
#> return self.call(inp, filter)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/nn_ops.py", line 238, in __call__
#> name=self.name)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/ops/gen_nn_ops.py", line 1553, in conv3d
#> dilations=dilations, name=name)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/op_def_library.py", line 793, in _apply_op_helper
#> op_def=op_def)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/func_graph.py", line 548, in create_op
#> compute_device)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 3429, in _create_op_internal
#> op_def=op_def)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 1773, in __init__
#> control_input_ops)
#> File "/Users/johnmuschelli/.virtualenvs/r-reticulate/lib/python3.7/site-packages/tensorflow_core/python/framework/ops.py", line 1613, in _create_c_op
#> raise ValueError(str(e))
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
Try this:
library( ANTsRNet )
library( tensorflow )
tf$compat$v1$disable_eager_execution()
createSsd7Model2D(c(250, 250, 3), 2)
createSsd7Model3D(c(250, 250, 250, 3), 2)
Does that break other code? Worked for me, but found that disable_eager_execution caused errors elsewhere.
Can't remember - let's see if R CMD check passes on https://travis-ci.org/ANTsX/ANTsRNet/builds/645515832