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CameronBodine / PINGMapper

Open-source interface for processing recreation-grade side scan sonar datasets and reproducibly mapping benthic habitat
https://cameronbodine.github.io/PINGMapper/
MIT License
43 stars 3 forks source link

Shadow removal - `weights` argument not defined in tensorflow/keras model call #54

Closed bthetford closed 1 year ago

bthetford commented 1 year ago

When I try to process a recording (my own, or the example data using test_PINGMapper.py), using remShadow = 1 or 2, I get the following error: 

Automatically detecting shadows for 7 chunks:
MODE: 1 | Remove all shadows...
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
  File "src\class_portstarObj.py", line 483, in _initModel
    model = tf.keras.models.load_model(weights)
NameError: name 'weights' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\externals\loky\process_executor.py", line 436, in _process_worker
    r = call_item()
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\externals\loky\process_executor.py", line 288, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\_parallel_backends.py", line 595, in __call__
    return self.func(*args, **kwargs)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 264, in __call__
    for func, args, kwargs in self.items]
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 264, in <listcomp>
    for func, args, kwargs in self.items]
  File "src\class_portstarObj.py", line 1545, in _detectShadow
    self.shadowModel = self._initModel(USE_GPU)
  File "src\class_portstarObj.py", line 486, in _initModel
    model.load_weights(self.weights)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\engine\training.py", line 234, in load_weights
    return super(Model, self).load_weights(filepath, by_name, skip_mismatch)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\engine\network.py", line 1222, in load_weights
    hdf5_format.load_weights_from_hdf5_group(f, self.layers)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\saving\hdf5_format.py", line 651, in load_weights_from_hdf5_group
    original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
"""

The error is identical whether I try to remove all or only bank shadows.

CameronBodine commented 1 year ago

I'm not able to recreate on my end, but I think I fixed the issue. I updated weights to self.weights. Try updating and let me know if it works for you.

bthetford commented 1 year ago

That fixed changed the resulting error a little bit, but it still ends with the same problem with the string 'utf8' 

Automatically detecting shadows for 48 chunks:
MODE: 1 | Remove all shadows...
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
  File "src\class_portstarObj.py", line 483, in _initModel
    model = tf.keras.models.load_model(self.weights)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\p
    return hdf5_format.load_model_from_hdf5(filepath, custom_objects, compile)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\p
    model_config = json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'
CameronBodine commented 1 year ago

Can you confirm that you have a model folder in the ping mapper directory and that there are hdf and json files in there?

bthetford commented 1 year ago

I have folders bankpick, bedpick and shadow in the folder PINGMapper/models, inside PINGMapper/models/shadow I have 1 .json file and 1.h5 file

CameronBodine commented 1 year ago

With ping environment activated, can you run conda list and post the output?

bthetford commented 1 year ago 
$ conda list
# packages in environment at C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
absl-py                   0.15.0             pyhd3eb1b0_0
affine                    2.3.0              pyhd3eb1b0_0
aiohttp                   3.8.3            py37h2bbff1b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py37haa95532_0
async-timeout             4.0.2            py37haa95532_0
asynctest                 0.13.0                     py_0
attrs                     22.1.0           py37haa95532_0
blas                      1.0                         mkl
blinker                   1.4              py37haa95532_0
blosc                     1.21.0               h19a0ad4_1
bottleneck                1.3.5            py37h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py37h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.10.11           haa95532_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py37haa95532_0
cffi                      1.15.1           py37h2bbff1b_3
cfitsio                   3.470                h2bbff1b_7
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py37haa95532_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.6            py37haa95532_0
cryptography              38.0.1           py37h21b164f_0
cudatoolkit               10.1.243             h74a9793_0
cudnn                     7.6.5                cuda10.1_0
curl                      7.86.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cytoolz                   0.12.0           py37h2bbff1b_0
dask-core                 2021.10.0          pyhd3eb1b0_0
expat                     2.4.9                h6c2663c_0
fftw                      3.3.9                h2bbff1b_1
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               ha860e81_0
freexl                    1.0.6                h2bbff1b_0
frozenlist                1.3.3            py37h2bbff1b_0
fsspec                    2022.11.0        py37haa95532_0
gast                      0.2.2                    py37_0
gdal                      3.0.2            py37hb978731_4
geos                      3.8.0                h33f27b4_0
geotiff                   1.7.0                h4545760_0
giflib                    5.2.1                h62dcd97_0
glib                      2.69.1               h5dc1a3c_2
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.4              pyhd3eb1b0_0
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py37hc60d5dd_0
gst-plugins-base          1.18.5               h9e645db_0
gstreamer                 1.18.5               hd78058f_0
h5py                      3.7.0            py37h3de5c98_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.6               h1756f20_1
icc_rt                    2022.1.0             h6049295_2
icu                       58.2                 ha925a31_3
idna                      3.4              py37haa95532_0
imagecodecs               2021.8.26        py37hc0a7faf_1
imageio                   2.19.3           py37haa95532_0
importlib-metadata        4.11.3           py37haa95532_0
intel-openmp              2021.4.0          haa95532_3556
joblib                    1.1.1            py37haa95532_0
jpeg                      9e                   h2bbff1b_0
kealib                    1.4.14               hde4a422_1
keras-applications        1.0.8                      py_1
keras-preprocessing       1.1.2              pyhd3eb1b0_0
kiwisolver                1.4.4            py37hd77b12b_0
krb5                      1.19.2               h5b6d351_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  12.0.0          default_h627e005_2
libcurl                   7.86.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libffi                    3.4.2                hd77b12b_6
libgdal                   3.0.2                ha304284_4
libiconv                  1.16                 h2bbff1b_2
libnetcdf                 4.8.1                h6685c40_1
libogg                    1.3.5                h2bbff1b_1
libpng                    1.6.37               h2a8f88b_0
libpq                     12.9                 hb652d5d_3
libprotobuf               3.20.1               h23ce68f_0
libspatialite             4.3.0a              h14feca5_20
libssh2                   1.10.0               hcd4344a_0
libtiff                   4.4.0                h8a3f274_2
libvorbis                 1.3.7                he774522_0
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
libzip                    1.8.0                h49b8836_0
libzopfli                 1.0.3                ha925a31_0
locket                    1.0.0            py37haa95532_0
lz4-c                     1.9.4                h2bbff1b_0
m2w64-expat               2.1.1                         2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gettext             0.19.7                        2
m2w64-gmp                 6.1.0                         2
m2w64-libiconv            1.14                          6
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
markdown                  3.4.1            py37haa95532_0
matplotlib                3.5.3            py37haa95532_0
matplotlib-base           3.5.3            py37hd77b12b_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py37h2bbff1b_0
mkl_fft                   1.3.1            py37h277e83a_0
mkl_random                1.2.2            py37hf11a4ad_0
msys2-conda-epoch         20160418                      1
multidict                 6.0.2            py37h2bbff1b_0
munkres                   1.1.4                      py_0
networkx                  2.6.3              pyhd3eb1b0_0
numexpr                   2.8.4            py37h5b0cc5e_0
numpy                     1.21.5           py37h7a0a035_3
numpy-base                1.21.5           py37hca35cd5_3
oauthlib                  3.2.1            py37haa95532_0
openjpeg                  2.4.0                h4fc8c34_0
openssl                   1.1.1s               h2bbff1b_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 22.0             py37haa95532_0
pandas                    1.3.5            py37h6214cd6_0
partd                     1.2.0              pyhd3eb1b0_1
pcre                      8.45                 hd77b12b_0
pillow                    9.3.0            py37hdc2b20a_1
pip                       22.3.1           py37haa95532_0
ply                       3.11                     py37_0
proj                      6.2.1                h3758d61_0
protobuf                  3.20.1           py37hd77b12b_0
psutil                    5.9.4                    pypi_0    pypi
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyjwt                     2.4.0            py37haa95532_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py37haa95532_0
pyproj                    2.6.1.post1      py37h593ac45_1
pyqt                      5.15.7           py37hd77b12b_0
pyqt5-sip                 12.11.0          py37hd77b12b_0
pysocks                   1.7.1                    py37_1
python                    3.7.15               h6244533_1
python-dateutil           2.8.2              pyhd3eb1b0_0
pytz                      2022.7           py37haa95532_0
pywavelets                1.3.0            py37h2bbff1b_0
pyyaml                    6.0              py37h2bbff1b_1
qt-main                   5.15.2               he8e5bd7_7
qt-webengine              5.15.9               hb9a9bb5_4
qtwebkit                  5.212                h3ad3cdb_4
rasterio                  1.2.10           py37h17c1fa0_0
requests                  2.28.1           py37haa95532_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
scikit-image              0.19.3           py37hd77b12b_1
scipy                     1.7.3            py37h7a0a035_2
setuptools                65.5.0           py37haa95532_0
sip                       6.6.2            py37hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h6c2663c_0
snuggs                    1.4.7              pyhd3eb1b0_0
sqlite                    3.40.0               h2bbff1b_0
tensorboard               2.8.0            py37haa95532_0
tensorboard-data-server   0.6.1            py37haa95532_0
tensorboard-plugin-wit    1.8.1            py37haa95532_0
tensorflow                2.1.0           gpu_py37h7db9008_0
tensorflow-base           2.1.0           gpu_py37h55f5790_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
tensorflow-gpu            2.1.0                h0d30ee6_0
termcolor                 1.1.0            py37haa95532_1
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.3                h3649cd2_2
tk                        8.6.12               h2bbff1b_0
toml                      0.10.2             pyhd3eb1b0_0
toolz                     0.12.0           py37haa95532_0
tornado                   6.2              py37h2bbff1b_0
typing-extensions         4.4.0            py37haa95532_0
typing_extensions         4.4.0            py37haa95532_0
urllib3                   1.26.13          py37haa95532_0
vc                        14.2                 h21ff451_1
vs2015_runtime            14.27.29016          h5e58377_2
werkzeug                  0.16.1                     py_0
wheel                     0.37.1             pyhd3eb1b0_0
win_inet_pton             1.1.0            py37haa95532_0
wincertstore              0.2              py37haa95532_2
wrapt                     1.14.1           py37h2bbff1b_0
xerces-c                  3.2.4                hd77b12b_0
xz                        5.2.8                h8cc25b3_0
yaml                      0.2.5                he774522_0
yarl                      1.8.1            py37h2bbff1b_0
zfp                       0.5.5                hd77b12b_6
zipp                      3.11.0           py37haa95532_0
zlib                      1.2.13               h8cc25b3_0
zstd                      1.5.2                h19a0ad4_0
(ping)
CameronBodine commented 1 year ago

Alrighty, can you post the contents of PINGMapper.yml inside ./PINGMapper/conda for me? Your env looks quite a bit different then my windows and ubuntu pc's.

CameronBodine commented 1 year ago

For example, on windows:

(ping) PS C:\Users\bodin> conda list
# packages in environment at C:\Users\bodin\miniconda3\envs\ping:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
abseil-cpp                20210324.2           hd77b12b_0
absl-py                   1.3.0            py39haa95532_0
affine                    2.3.0              pyhd3eb1b0_0
aiohttp                   3.8.3            py39h2bbff1b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py39haa95532_0
astunparse                1.6.3                      py_0
async-timeout             4.0.2            py39haa95532_0
attrs                     22.1.0           py39haa95532_0
blas                      1.0                         mkl
blinker                   1.4              py39haa95532_0
blosc                     1.21.0               h19a0ad4_1
bottleneck                1.3.5            py39h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py39h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.10.11           haa95532_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py39haa95532_0
cffi                      1.15.1           py39h2bbff1b_3
cfitsio                   3.470                h2bbff1b_7
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py39haa95532_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.6            py39haa95532_0
contourpy                 1.0.5            py39h59b6b97_0
cryptography              38.0.4           py39h21b164f_0
cudatoolkit               11.3.1               h59b6b97_2
cudnn                     8.2.1                cuda11.3_0
curl                      7.86.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cytoolz                   0.12.0           py39h2bbff1b_0
dask-core                 2022.7.0         py39haa95532_0
expat                     2.4.9                h6c2663c_0
fftw                      3.3.9                h2bbff1b_1
flatbuffers               2.0.0                h6c2663c_0
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               ha860e81_0
freexl                    1.0.6                h2bbff1b_0
frozenlist                1.3.3            py39h2bbff1b_0
fsspec                    2022.11.0        py39haa95532_0
gast                      0.4.0              pyhd3eb1b0_0
gdal                      3.0.2            py39hb978731_4
geos                      3.8.0                h33f27b4_0
geotiff                   1.7.0                h4545760_0
giflib                    5.2.1                h62dcd97_0
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.1                      py_2
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py39hc60d5dd_0
h5py                      3.7.0            py39h3de5c98_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.6               h1756f20_1
icc_rt                    2022.1.0             h6049295_2
icu                       68.1                 h6c2663c_0
idna                      3.4              py39haa95532_0
imagecodecs               2021.8.26        py39hc0a7faf_1
imageio                   2.19.3           py39haa95532_0
importlib-metadata        4.11.3           py39haa95532_0
intel-openmp              2021.4.0          haa95532_3556
joblib                    1.1.1            py39haa95532_0
jpeg                      9e                   h2bbff1b_0
kealib                    1.4.14               hde4a422_1
keras-preprocessing       1.1.2              pyhd3eb1b0_0
kiwisolver                1.4.4            py39hd77b12b_0
krb5                      1.19.2               h5b6d351_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  11.1.0          default_h5c34c98_1    conda-forge
libcurl                   7.86.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libgdal                   3.0.2                ha304284_4
libiconv                  1.16                 h2bbff1b_2
libnetcdf                 4.8.1                h6685c40_1
libpng                    1.6.37               h2a8f88b_0
libpq                     12.9                 hb652d5d_3
libprotobuf               3.17.2               h23ce68f_1
libspatialite             4.3.0a              h14feca5_20
libssh2                   1.10.0               hcd4344a_0
libtiff                   4.4.0                h8a3f274_2
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libzip                    1.8.0                h49b8836_0
libzopfli                 1.0.3                ha925a31_0
locket                    1.0.0            py39haa95532_0
lz4-c                     1.9.4                h2bbff1b_0
m2w64-expat               2.1.1                         2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gettext             0.19.7                        2
m2w64-gmp                 6.1.0                         2
m2w64-libiconv            1.14                          6
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
markdown                  3.4.1            py39haa95532_0
markupsafe                2.1.1            py39h2bbff1b_0
matplotlib                3.6.2            py39haa95532_0
matplotlib-base           3.6.2            py39h1094b8e_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py39h2bbff1b_0
mkl_fft                   1.3.1            py39h277e83a_0
mkl_random                1.2.2            py39hf11a4ad_0
msys2-conda-epoch         20160418                      1
multidict                 6.0.2            py39h2bbff1b_0
munkres                   1.1.4                      py_0
networkx                  2.8.4            py39haa95532_0
numexpr                   2.8.4            py39h5b0cc5e_0
numpy                     1.23.5           py39h3b20f71_0
numpy-base                1.23.5           py39h4da318b_0
oauthlib                  3.2.1            py39haa95532_0
openjpeg                  2.4.0                h4fc8c34_0
openssl                   1.1.1s               h2bbff1b_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 22.0             py39haa95532_0
pandas                    1.5.2            py39hf11a4ad_0
partd                     1.2.0              pyhd3eb1b0_1
pillow                    9.3.0            py39hdc2b20a_1
pip                       22.3.1           py39haa95532_0
proj                      6.2.1                h3758d61_0
protobuf                  3.17.2           py39hd77b12b_0
psutil                    5.9.4                    pypi_0    pypi
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyjwt                     2.4.0            py39haa95532_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py39haa95532_0
pyproj                    2.6.1.post1      py39h593ac45_1
pyqt                      5.12.3           py39hcbf5309_8    conda-forge
pyqt-impl                 5.12.3           py39h415ef7b_8    conda-forge
pyqt5-sip                 4.19.18          py39h415ef7b_8    conda-forge
pyqtchart                 5.12             py39h415ef7b_8    conda-forge
pyqtwebengine             5.12.1           py39h415ef7b_8    conda-forge
pysocks                   1.7.1            py39haa95532_0
python                    3.9.15               h6244533_2
python-dateutil           2.8.2              pyhd3eb1b0_0
python-flatbuffers        1.12               pyhd3eb1b0_0
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.7           py39haa95532_0
pywavelets                1.4.1            py39h2bbff1b_0
pyyaml                    6.0              py39h2bbff1b_1
qt                        5.12.9               h5909a2a_4    conda-forge
rasterio                  1.2.10           py39h17c1fa0_0
requests                  2.28.1           py39haa95532_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
scikit-image              0.19.3           py39hd77b12b_1
scipy                     1.9.3            py39he11b74f_0
setuptools                65.6.3           py39haa95532_0
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h6c2663c_0
snuggs                    1.4.7              pyhd3eb1b0_0
sqlite                    3.40.1               h2bbff1b_0
tensorboard               2.6.0                      py_1
tensorboard-data-server   0.6.1            py39haa95532_0
tensorboard-plugin-wit    1.8.1            py39haa95532_0
tensorflow                2.6.0           gpu_py39he88c5ba_0
tensorflow-base           2.6.0           gpu_py39hb3da07e_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
tensorflow-gpu            2.6.0                h17022bd_0
termcolor                 2.1.0            py39haa95532_0
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.3                h3649cd2_2
tk                        8.6.12               h2bbff1b_0
toolz                     0.12.0           py39haa95532_0
tornado                   6.2              py39h2bbff1b_0
typing_extensions         4.4.0            py39haa95532_0
tzdata                    2022g                h04d1e81_0
urllib3                   1.26.13          py39haa95532_0
vc                        14.2                 h21ff451_1
versioneer                0.28                     pypi_0    pypi
vs2015_runtime            14.27.29016          h5e58377_2
werkzeug                  2.2.2            py39haa95532_0
wheel                     0.35.1             pyhd3eb1b0_0
win_inet_pton             1.1.0            py39haa95532_0
wincertstore              0.2              py39haa95532_2
wrapt                     1.14.1           py39h2bbff1b_0
xerces-c                  3.2.4                hd77b12b_0
xz                        5.2.8                h8cc25b3_0
yaml                      0.2.5                he774522_0
yarl                      1.8.1            py39h2bbff1b_0
zfp                       0.5.5                hd77b12b_6
zipp                      3.11.0           py39haa95532_0
zlib                      1.2.13               h8cc25b3_0
zstd                      1.5.2                h19a0ad4_0
CameronBodine commented 1 year ago

Here is something to try (since you figured out how to install the environment way faster):

Remove current ping mapper env:

conda deactivate
conda env remove -n ping

Clean up:

conda clean -a

Update base conda environment:

conda update -n base conda

Then try reinstalling:

conda env create --file conda/PINGMapper.yml
bthetford commented 1 year ago 
$ cat PINGMapper.yml
name: ping
channels:
  - defaults
  - conda-forge
dependencies:
  - python
  - pandas
  - rasterio
  - tensorflow-gpu
  - pyproj
  - scikit-image
  - joblib
  - gdal
  - matplotlib
  - pip
  - pip:
      - psutil
bthetford commented 1 year ago

I'll give those steps a shot. PS I'm using windows 10 and Git Bash as my command line

bthetford commented 1 year ago

I ran those steps you suggested and unfortunately got exactly the same error ending in AttributeError: 'str' object has no attribute 'decode'. Here's the package list since I cleaned and reinstalled the ping environment:

$ conda list
# packages in environment at C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
absl-py                   0.15.0             pyhd3eb1b0_0
affine                    2.3.0              pyhd3eb1b0_0
aiohttp                   3.8.3            py37h2bbff1b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py37haa95532_0
async-timeout             4.0.2            py37haa95532_0
asynctest                 0.13.0                     py_0
attrs                     22.1.0           py37haa95532_0
blas                      1.0                         mkl
blinker                   1.4              py37haa95532_0
blosc                     1.21.0               h19a0ad4_1
bottleneck                1.3.5            py37h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py37h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.10.11           haa95532_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py37haa95532_0
cffi                      1.15.1           py37h2bbff1b_3
cfitsio                   3.470                h2bbff1b_7
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py37haa95532_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.6            py37haa95532_0
cryptography              38.0.4           py37h21b164f_0
cudatoolkit               10.1.243             h74a9793_0
cudnn                     7.6.5                cuda10.1_0
curl                      7.86.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cytoolz                   0.12.0           py37h2bbff1b_0
dask-core                 2021.10.0          pyhd3eb1b0_0
expat                     2.4.9                h6c2663c_0
fftw                      3.3.9                h2bbff1b_1
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               ha860e81_0
freexl                    1.0.6                h2bbff1b_0
frozenlist                1.3.3            py37h2bbff1b_0
fsspec                    2022.11.0        py37haa95532_0
gast                      0.2.2                    py37_0
gdal                      3.0.2            py37hb978731_4
geos                      3.8.0                h33f27b4_0
geotiff                   1.7.0                h4545760_0
giflib                    5.2.1                h62dcd97_0
glib                      2.69.1               h5dc1a3c_2
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.4              pyhd3eb1b0_0
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py37hc60d5dd_0
gst-plugins-base          1.18.5               h9e645db_0
gstreamer                 1.18.5               hd78058f_0
h5py                      3.7.0            py37h3de5c98_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.6               h1756f20_1
icc_rt                    2022.1.0             h6049295_2
icu                       58.2                 ha925a31_3
idna                      3.4              py37haa95532_0
imagecodecs               2021.8.26        py37hc0a7faf_1
imageio                   2.19.3           py37haa95532_0
importlib-metadata        4.11.3           py37haa95532_0
intel-openmp              2021.4.0          haa95532_3556
joblib                    1.1.1            py37haa95532_0
jpeg                      9e                   h2bbff1b_0
kealib                    1.4.14               hde4a422_1
keras-applications        1.0.8                      py_1
keras-preprocessing       1.1.2              pyhd3eb1b0_0
kiwisolver                1.4.4            py37hd77b12b_0
krb5                      1.19.2               h5b6d351_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  12.0.0          default_h627e005_2
libcurl                   7.86.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libffi                    3.4.2                hd77b12b_6
libgdal                   3.0.2                ha304284_4
libiconv                  1.16                 h2bbff1b_2
libnetcdf                 4.8.1                h6685c40_1
libogg                    1.3.5                h2bbff1b_1
libpng                    1.6.37               h2a8f88b_0
libpq                     12.9                 hb652d5d_3
libprotobuf               3.20.1               h23ce68f_0
libspatialite             4.3.0a              h14feca5_20
libssh2                   1.10.0               hcd4344a_0
libtiff                   4.5.0                h8a3f274_0
libvorbis                 1.3.7                he774522_0
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
libzip                    1.8.0                h49b8836_0
libzopfli                 1.0.3                ha925a31_0
locket                    1.0.0            py37haa95532_0
lz4-c                     1.9.4                h2bbff1b_0
m2w64-expat               2.1.1                         2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gettext             0.19.7                        2
m2w64-gmp                 6.1.0                         2
m2w64-libiconv            1.14                          6
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
markdown                  3.4.1            py37haa95532_0
matplotlib                3.5.3            py37haa95532_0
matplotlib-base           3.5.3            py37hd77b12b_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py37h2bbff1b_0
mkl_fft                   1.3.1            py37h277e83a_0
mkl_random                1.2.2            py37hf11a4ad_0
msys2-conda-epoch         20160418                      1
multidict                 6.0.2            py37h2bbff1b_0
munkres                   1.1.4                      py_0
networkx                  2.6.3              pyhd3eb1b0_0
numexpr                   2.8.4            py37h5b0cc5e_0
numpy                     1.21.5           py37h7a0a035_3
numpy-base                1.21.5           py37hca35cd5_3
oauthlib                  3.2.1            py37haa95532_0
openjpeg                  2.4.0                h4fc8c34_0
openssl                   1.1.1s               h2bbff1b_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 22.0             py37haa95532_0
pandas                    1.3.5            py37h6214cd6_0
partd                     1.2.0              pyhd3eb1b0_1
pcre                      8.45                 hd77b12b_0
pillow                    9.3.0            py37hdc2b20a_1
pip                       22.3.1           py37haa95532_0
ply                       3.11                     py37_0
proj                      6.2.1                h3758d61_0
protobuf                  3.20.1           py37hd77b12b_0
psutil                    5.9.4                    pypi_0    pypi
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyjwt                     2.4.0            py37haa95532_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py37haa95532_0
pyproj                    2.6.1.post1      py37h593ac45_1
pyqt                      5.15.7           py37hd77b12b_0
pyqt5-sip                 12.11.0          py37hd77b12b_0
pysocks                   1.7.1                    py37_1
python                    3.7.15               h6244533_1
python-dateutil           2.8.2              pyhd3eb1b0_0
pytz                      2022.7           py37haa95532_0
pywavelets                1.3.0            py37h2bbff1b_0
pyyaml                    6.0              py37h2bbff1b_1
qt-main                   5.15.2               he8e5bd7_7
qt-webengine              5.15.9               hb9a9bb5_4
qtwebkit                  5.212                h3ad3cdb_4
rasterio                  1.2.10           py37h17c1fa0_0
requests                  2.28.1           py37haa95532_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
scikit-image              0.19.3           py37hd77b12b_1
scipy                     1.7.3            py37h7a0a035_2
setuptools                65.6.3           py37haa95532_0
sip                       6.6.2            py37hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h6c2663c_0
snuggs                    1.4.7              pyhd3eb1b0_0
sqlite                    3.40.1               h2bbff1b_0
tensorboard               2.8.0            py37haa95532_0
tensorboard-data-server   0.6.1            py37haa95532_0
tensorboard-plugin-wit    1.8.1            py37haa95532_0
tensorflow                2.1.0           gpu_py37h7db9008_0
tensorflow-base           2.1.0           gpu_py37h55f5790_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
tensorflow-gpu            2.1.0                h0d30ee6_0
termcolor                 1.1.0            py37haa95532_1
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.3                h3649cd2_2
tk                        8.6.12               h2bbff1b_0
toml                      0.10.2             pyhd3eb1b0_0
toolz                     0.12.0           py37haa95532_0
tornado                   6.2              py37h2bbff1b_0
typing-extensions         4.4.0            py37haa95532_0
typing_extensions         4.4.0            py37haa95532_0
urllib3                   1.26.13          py37haa95532_0
vc                        14.2                 h21ff451_1
vs2015_runtime            14.27.29016          h5e58377_2
werkzeug                  0.16.1                     py_0
wheel                     0.37.1             pyhd3eb1b0_0
win_inet_pton             1.1.0            py37haa95532_0
wincertstore              0.2              py37haa95532_2
wrapt                     1.14.1           py37h2bbff1b_0
xerces-c                  3.2.4                hd77b12b_0
xz                        5.2.8                h8cc25b3_0
yaml                      0.2.5                he774522_0
yarl                      1.8.1            py37h2bbff1b_0
zfp                       0.5.5                hd77b12b_6
zipp                      3.11.0           py37haa95532_0
zlib                      1.2.13               h8cc25b3_0
zstd                      1.5.2                h19a0ad4_0
(ping)
bthetford commented 1 year ago

PS here's every exception that comes out:

Automatically detecting shadows for 48 chunks:
MODE: 1 | Remove all shadows...
joblib.externals.loky.process_executor._RemoteTraceback:
"""
Traceback (most recent call last):
  File "src\class_portstarObj.py", line 483, in _initModel
    model = tf.keras.models.load_model(self.weights)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\saving\save.py", line 146, in load_model
    return hdf5_format.load_model_from_hdf5(filepath, custom_objects, compile)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\saving\hdf5_format.py", line 166, in load_model_from_hdf5
    model_config = json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object has no attribute 'decode'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\externals\loky\process_executor.py", line 436, in _process_worker
    r = call_item()
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\externals\loky\process_executor.py", line 288, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\_parallel_backends.py", line 595, in __call__
    return self.func(*args, **kwargs)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 264, in __call__
    for func, args, kwargs in self.items]
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 264, in <listcomp>
    for func, args, kwargs in self.items]
  File "src\class_portstarObj.py", line 1545, in _detectShadow
    self.shadowModel = self._initModel(USE_GPU)
  File "src\class_portstarObj.py", line 486, in _initModel
    model.load_weights(self.weights)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\engine\training.py", line 234, in load_weights
    return super(Model, self).load_weights(filepath, by_name, skip_mismatch)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\engine\network.py", line 1222, in load_weights
    hdf5_format.load_weights_from_hdf5_group(f, self.layers)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\tensorflow_core\python\keras\saving\hdf5_format.py", line 651, in load_weights_from_hdf5_group
    original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "main.py", line 123, in <module>
    read_master_func(**params)
  File "src\main_readFiles.py", line 829, in read_master_func
    r = Parallel(n_jobs=np.min([len(chunks), threadCnt]), verbose=10)(delayed(psObj._detectShadow)(remShadow, int(chunk), USE_GPU, False, tileFile) for chunk in chunks)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 1061, in __call__
    self.retrieve()
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\parallel.py", line 938, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\site-packages\joblib\_parallel_backends.py", line 542, in wrap_future_result
    return future.result(timeout=timeout)
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\concurrent\futures\_base.py", line 435, in result
    return self.__get_result()
  File "C:\Users\b.thetford\AppData\Local\miniconda3\envs\ping\lib\concurrent\futures\_base.py", line 384, in __get_result
    raise self._exception
AttributeError: 'str' object has no attribute 'decode'
(ping)
CameronBodine commented 1 year ago

I was able to successfully recreate your error!

TLDR:

Running conda install tensorflow-gpu=2.6 --force-reinstall in the ping env fixed the issue on my end.

Don't do this part! Just for documentation

I changed the PINGMapper.yml to be:

name: ping-tf-2.1
channels:
  - defaults
  - conda-forge
dependencies:
  - python
  - pandas
  - rasterio
  - tensorflow-gpu=2.1
  - pyproj
  - scikit-image
  - joblib
  - gdal
  - matplotlib
  - pip
  - pip:
      - psutil

I then install the new environment:

conda env create -f .\PINGMapper_21.yml

This gives me the following package version, close (I think the exact same) to your env:

(ping-tf-2.1) PS C:\Users\bodin\Python\PINGMapper> conda list
# packages in environment at C:\Users\bodin\miniconda3\envs\ping-tf-2.1:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
absl-py                   0.15.0             pyhd3eb1b0_0
affine                    2.3.0              pyhd3eb1b0_0
aiohttp                   3.8.3            py37h2bbff1b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py37haa95532_0
async-timeout             4.0.2            py37haa95532_0
asynctest                 0.13.0                     py_0
attrs                     22.1.0           py37haa95532_0
blas                      1.0                         mkl
blinker                   1.4              py37haa95532_0
blosc                     1.21.0               h19a0ad4_1
bottleneck                1.3.5            py37h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py37h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.10.11           haa95532_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py37haa95532_0
cffi                      1.15.1           py37h2bbff1b_3
cfitsio                   3.470                h2bbff1b_7
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py37haa95532_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.6            py37haa95532_0
cryptography              38.0.4           py37h21b164f_0
cudatoolkit               10.1.243             h74a9793_0
cudnn                     7.6.5                cuda10.1_0
curl                      7.86.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cytoolz                   0.12.0           py37h2bbff1b_0
dask-core                 2021.10.0          pyhd3eb1b0_0
expat                     2.4.9                h6c2663c_0
fftw                      3.3.9                h2bbff1b_1
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               ha860e81_0
freexl                    1.0.6                h2bbff1b_0
frozenlist                1.3.3            py37h2bbff1b_0
fsspec                    2022.11.0        py37haa95532_0
gast                      0.2.2                    py37_0
gdal                      3.0.2            py37hb978731_4
geos                      3.8.0                h33f27b4_0
geotiff                   1.7.0                h4545760_0
giflib                    5.2.1                h62dcd97_0
glib                      2.69.1               h5dc1a3c_2
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.4              pyhd3eb1b0_0
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py37hc60d5dd_0
gst-plugins-base          1.18.5               h9e645db_0
gstreamer                 1.18.5               hd78058f_0
h5py                      3.7.0            py37h3de5c98_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.6               h1756f20_1
icc_rt                    2022.1.0             h6049295_2
icu                       58.2                 ha925a31_3
idna                      3.4              py37haa95532_0
imagecodecs               2021.8.26        py37hc0a7faf_1
imageio                   2.19.3           py37haa95532_0
importlib-metadata        4.11.3           py37haa95532_0
intel-openmp              2021.4.0          haa95532_3556
joblib                    1.1.1            py37haa95532_0
jpeg                      9e                   h2bbff1b_0
kealib                    1.4.14               hde4a422_1
keras-applications        1.0.8                      py_1
keras-preprocessing       1.1.2              pyhd3eb1b0_0
kiwisolver                1.4.4            py37hd77b12b_0
krb5                      1.19.2               h5b6d351_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  12.0.0          default_h627e005_2
libcurl                   7.86.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libffi                    3.4.2                hd77b12b_6
libgdal                   3.0.2                ha304284_4
libiconv                  1.16                 h2bbff1b_2
libnetcdf                 4.8.1                h6685c40_1
libogg                    1.3.5                h2bbff1b_1
libpng                    1.6.37               h2a8f88b_0
libpq                     12.9                 hb652d5d_3
libprotobuf               3.20.1               h23ce68f_0
libspatialite             4.3.0a              h14feca5_20
libssh2                   1.10.0               hcd4344a_0
libtiff                   4.5.0                h8a3f274_0
libvorbis                 1.3.7                he774522_0
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
libzip                    1.8.0                h49b8836_0
libzopfli                 1.0.3                ha925a31_0
locket                    1.0.0            py37haa95532_0
lz4-c                     1.9.4                h2bbff1b_0
m2w64-expat               2.1.1                         2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gettext             0.19.7                        2
m2w64-gmp                 6.1.0                         2
m2w64-libiconv            1.14                          6
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
markdown                  3.4.1            py37haa95532_0
matplotlib                3.5.3            py37haa95532_0
matplotlib-base           3.5.3            py37hd77b12b_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py37h2bbff1b_0
mkl_fft                   1.3.1            py37h277e83a_0
mkl_random                1.2.2            py37hf11a4ad_0
msys2-conda-epoch         20160418                      1
multidict                 6.0.2            py37h2bbff1b_0
munkres                   1.1.4                      py_0
networkx                  2.6.3              pyhd3eb1b0_0
numexpr                   2.8.4            py37h5b0cc5e_0
numpy                     1.21.5           py37h7a0a035_3
numpy-base                1.21.5           py37hca35cd5_3
oauthlib                  3.2.1            py37haa95532_0
openjpeg                  2.4.0                h4fc8c34_0
openssl                   1.1.1s               h2bbff1b_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 22.0             py37haa95532_0
pandas                    1.3.5            py37h6214cd6_0
partd                     1.2.0              pyhd3eb1b0_1
pcre                      8.45                 hd77b12b_0
pillow                    9.3.0            py37hdc2b20a_1
pip                       22.3.1           py37haa95532_0
ply                       3.11                     py37_0
proj                      6.2.1                h3758d61_0
protobuf                  3.20.1           py37hd77b12b_0
psutil                    5.9.4                    pypi_0    pypi
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyjwt                     2.4.0            py37haa95532_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py37haa95532_0
pyproj                    2.6.1.post1      py37h593ac45_1
pyqt                      5.15.7           py37hd77b12b_0
pyqt5-sip                 12.11.0          py37hd77b12b_0
pysocks                   1.7.1                    py37_1
python                    3.7.15               h6244533_1
python-dateutil           2.8.2              pyhd3eb1b0_0
pytz                      2022.7           py37haa95532_0
pywavelets                1.3.0            py37h2bbff1b_0
pyyaml                    6.0              py37h2bbff1b_1
qt-main                   5.15.2               he8e5bd7_7
qt-webengine              5.15.9               hb9a9bb5_4
qtwebkit                  5.212                h3ad3cdb_4
rasterio                  1.2.10           py37h17c1fa0_0
requests                  2.28.1           py37haa95532_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
scikit-image              0.19.3           py37hd77b12b_1
scipy                     1.7.3            py37h7a0a035_2
setuptools                65.6.3           py37haa95532_0
sip                       6.6.2            py37hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h6c2663c_0
snuggs                    1.4.7              pyhd3eb1b0_0
sqlite                    3.40.1               h2bbff1b_0
tensorboard               2.8.0            py37haa95532_0
tensorboard-data-server   0.6.1            py37haa95532_0
tensorboard-plugin-wit    1.8.1            py37haa95532_0
tensorflow                2.1.0           gpu_py37h7db9008_0
tensorflow-base           2.1.0           gpu_py37h55f5790_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
tensorflow-gpu            2.1.0                h0d30ee6_0
termcolor                 1.1.0            py37haa95532_1
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.3                h3649cd2_2
tk                        8.6.12               h2bbff1b_0
toml                      0.10.2             pyhd3eb1b0_0
toolz                     0.12.0           py37haa95532_0
tornado                   6.2              py37h2bbff1b_0
typing-extensions         4.4.0            py37haa95532_0
typing_extensions         4.4.0            py37haa95532_0
urllib3                   1.26.13          py37haa95532_0
vc                        14.2                 h21ff451_1
vs2015_runtime            14.27.29016          h5e58377_2
werkzeug                  0.16.1                     py_0
wheel                     0.37.1             pyhd3eb1b0_0
win_inet_pton             1.1.0            py37haa95532_0
wincertstore              0.2              py37haa95532_2
wrapt                     1.14.1           py37h2bbff1b_0
xerces-c                  3.2.4                hd77b12b_0
xz                        5.2.8                h8cc25b3_0
yaml                      0.2.5                he774522_0
yarl                      1.8.1            py37h2bbff1b_0
zfp                       0.5.5                hd77b12b_6
zipp                      3.11.0           py37haa95532_0
zlib                      1.2.13               h8cc25b3_0
zstd                      1.5.2                h19a0ad4_0

Then, when I run the test script python .\test_PINGMapper.py 1, I receive the same error as you did:

Traceback (most recent call last):
  File "src\class_portstarObj.py", line 483, in _initModel
    model = tf.keras.models.load_model(weights)
NameError: name 'weights' is not defined

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\externals\loky\process_executor.py", line 436, in _process_worker
    r = call_item()
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\externals\loky\process_executor.py", line 288, in __call__
    return self.fn(*self.args, **self.kwargs)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\_parallel_backends.py", line 595, in __call__
    return self.func(*args, **kwargs)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\parallel.py", line 264, in __call__
    for func, args, kwargs in self.items]
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\parallel.py", line 264, in <listcomp>
    for func, args, kwargs in self.items]
  File "src\class_portstarObj.py", line 607, in _detectDepth
    model = self._initModel(USE_GPU)
  File "src\class_portstarObj.py", line 486, in _initModel
    model.load_weights(self.weights)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\tensorflow_core\python\keras\engine\training.py", line 234, in load_weights
    return super(Model, self).load_weights(filepath, by_name, skip_mismatch)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\tensorflow_core\python\keras\engine\network.py", line 1222, in load_weights
    hdf5_format.load_weights_from_hdf5_group(f, self.layers)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\tensorflow_core\python\keras\saving\hdf5_format.py", line 651, in load_weights_from_hdf5_group
    original_keras_version = f.attrs['keras_version'].decode('utf8')
AttributeError: 'str' object has no attribute 'decode'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File ".\test_PINGMapper.py", line 155, in <module>
    read_master_func(**params)
  File "src\main_readFiles.py", line 730, in read_master_func
    r = Parallel(n_jobs=np.min([len(chunks), threadCnt]), verbose=10)(delayed(psObj._detectDepth)(detectDep, int(chunk), USE_GPU, tileFile) for chunk in chunks)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\parallel.py", line 1061, in __call__
    self.retrieve()
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\parallel.py", line 938, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\site-packages\joblib\_parallel_backends.py", line 542, in wrap_future_result
    return future.result(timeout=timeout)
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\concurrent\futures\_base.py", line 435, in result
    return self.__get_result()
  File "C:\Users\bodin\miniconda3\envs\ping-tf-2.1\lib\concurrent\futures\_base.py", line 384, in __get_result
    raise self._exception
AttributeError: 'str' object has no attribute 'decode'

The Fix

To fix this, I force reinstalled tensorflow-gpu=2.6 by running the following:

conda install tensorflow-gpu=2.6 --force-reinstall

This gave me the following env (note the updated tensorflow-gpu):

(ping-tf-2.1) PS C:\Users\bodin\Python\PINGMapper> conda list
# packages in environment at C:\Users\bodin\miniconda3\envs\ping-tf-2.1:
#
# Name                    Version                   Build  Channel
_tflow_select             2.1.0                       gpu
abseil-cpp                20210324.2           hd77b12b_0
absl-py                   1.3.0            py37haa95532_0
affine                    2.3.0              pyhd3eb1b0_0
aiohttp                   3.8.3            py37h2bbff1b_0
aiosignal                 1.2.0              pyhd3eb1b0_0
astor                     0.8.1            py37haa95532_0
astunparse                1.6.3                      py_0
async-timeout             4.0.2            py37haa95532_0
asynctest                 0.13.0                     py_0
attrs                     22.1.0           py37haa95532_0
blas                      1.0                         mkl
blinker                   1.4              py37haa95532_0
blosc                     1.21.0               h19a0ad4_1
bottleneck                1.3.5            py37h080aedc_0
brotli                    1.0.9                h2bbff1b_7
brotli-bin                1.0.9                h2bbff1b_7
brotlipy                  0.7.0           py37h2bbff1b_1003
bzip2                     1.0.8                he774522_0
ca-certificates           2022.10.11           haa95532_0
cachetools                4.2.2              pyhd3eb1b0_0
certifi                   2022.12.7        py37haa95532_0
cffi                      1.15.1           py37h2bbff1b_3
cfitsio                   3.470                h2bbff1b_7
charls                    2.2.0                h6c2663c_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
click                     8.0.4            py37haa95532_0
click-plugins             1.1.1              pyhd3eb1b0_0
cligj                     0.7.2              pyhd3eb1b0_0
cloudpickle               2.0.0              pyhd3eb1b0_0
colorama                  0.4.6            py37haa95532_0
cryptography              38.0.4           py37h21b164f_0
cudatoolkit               11.3.1               h59b6b97_2
cudnn                     8.2.1                cuda11.3_0
curl                      7.86.0               h2bbff1b_0
cycler                    0.11.0             pyhd3eb1b0_0
cytoolz                   0.12.0           py37h2bbff1b_0
dask-core                 2021.10.0          pyhd3eb1b0_0
expat                     2.4.9                h6c2663c_0
fftw                      3.3.9                h2bbff1b_1
flatbuffers               2.0.0                h6c2663c_0
flit-core                 3.6.0              pyhd3eb1b0_0
fonttools                 4.25.0             pyhd3eb1b0_0
freetype                  2.12.1               ha860e81_0
freexl                    1.0.6                h2bbff1b_0
frozenlist                1.3.3            py37h2bbff1b_0
fsspec                    2022.11.0        py37haa95532_0
gast                      0.4.0              pyhd3eb1b0_0
gdal                      3.0.2            py37hb978731_4
geos                      3.8.0                h33f27b4_0
geotiff                   1.7.0                h4545760_0
gettext                   0.21.1               h5728263_0    conda-forge
giflib                    5.2.1                h62dcd97_0
glib                      2.74.1               h12be248_1    conda-forge
glib-tools                2.74.1               h12be248_1    conda-forge
google-auth               2.6.0              pyhd3eb1b0_0
google-auth-oauthlib      0.4.1                      py_2
google-pasta              0.2.0              pyhd3eb1b0_0
grpcio                    1.42.0           py37hc60d5dd_0
gst-plugins-base          1.18.5               h9e645db_0
gstreamer                 1.18.5               hd78058f_0
h5py                      3.7.0            py37h3de5c98_0
hdf4                      4.2.13               h712560f_2
hdf5                      1.10.6               h1756f20_1
icc_rt                    2022.1.0             h6049295_2
icu                       68.2                 h0e60522_0    conda-forge
idna                      3.4              py37haa95532_0
imagecodecs               2021.8.26        py37hc0a7faf_1
imageio                   2.19.3           py37haa95532_0
importlib-metadata        4.11.3           py37haa95532_0
intel-openmp              2021.4.0          haa95532_3556
joblib                    1.1.1            py37haa95532_0
jpeg                      9e                   h2bbff1b_0
kealib                    1.4.14               hde4a422_1
keras-applications        1.0.8                      py_1
keras-preprocessing       1.1.2              pyhd3eb1b0_0
kiwisolver                1.4.4            py37hd77b12b_0
krb5                      1.19.2               h5b6d351_0
lcms2                     2.12                 h83e58a3_0
lerc                      3.0                  hd77b12b_0
libaec                    1.0.4                h33f27b4_1
libbrotlicommon           1.0.9                h2bbff1b_7
libbrotlidec              1.0.9                h2bbff1b_7
libbrotlienc              1.0.9                h2bbff1b_7
libclang                  13.0.1          default_h81446c8_0    conda-forge
libcurl                   7.86.0               h86230a5_0
libdeflate                1.8                  h2bbff1b_5
libffi                    3.4.2                hd77b12b_6
libgdal                   3.0.2                ha304284_4
libglib                   2.74.1               he8f3873_1    conda-forge
libiconv                  1.17                 h8ffe710_0    conda-forge
libnetcdf                 4.8.1                h6685c40_1
libogg                    1.3.5                h2bbff1b_1
libpng                    1.6.37               h2a8f88b_0
libpq                     12.9                 hb652d5d_3
libprotobuf               3.17.2               h23ce68f_1
libspatialite             4.3.0a              h14feca5_20
libssh2                   1.10.0               hcd4344a_0
libtiff                   4.5.0                h8a3f274_0
libvorbis                 1.3.7                he774522_0
libwebp                   1.2.4                h2bbff1b_0
libwebp-base              1.2.4                h2bbff1b_0
libxml2                   2.9.14               h0ad7f3c_0
libxslt                   1.1.35               h2bbff1b_0
libzip                    1.8.0                h49b8836_0
libzlib                   1.2.13               hcfcfb64_4    conda-forge
libzopfli                 1.0.3                ha925a31_0
locket                    1.0.0            py37haa95532_0
lz4-c                     1.9.4                h2bbff1b_0
m2w64-expat               2.1.1                         2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gettext             0.19.7                        2
m2w64-gmp                 6.1.0                         2
m2w64-libiconv            1.14                          6
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
m2w64-xz                  5.2.2                         2
markdown                  3.4.1            py37haa95532_0
markupsafe                2.1.1            py37h2bbff1b_0
matplotlib                3.5.3            py37haa95532_0
matplotlib-base           3.5.3            py37hd77b12b_0
mkl                       2021.4.0           haa95532_640
mkl-service               2.4.0            py37h2bbff1b_0
mkl_fft                   1.3.1            py37h277e83a_0
mkl_random                1.2.2            py37hf11a4ad_0
msys2-conda-epoch         20160418                      1
multidict                 6.0.2            py37h2bbff1b_0
munkres                   1.1.4                      py_0
networkx                  2.6.3              pyhd3eb1b0_0
numexpr                   2.8.4            py37h5b0cc5e_0
numpy                     1.21.5           py37h7a0a035_3
numpy-base                1.21.5           py37hca35cd5_3
oauthlib                  3.2.1            py37haa95532_0
openjpeg                  2.4.0                h4fc8c34_0
openssl                   1.1.1s               h2bbff1b_0
opt_einsum                3.3.0              pyhd3eb1b0_1
packaging                 22.0             py37haa95532_0
pandas                    1.3.5            py37h6214cd6_0
partd                     1.2.0              pyhd3eb1b0_1
pcre                      8.45                 hd77b12b_0
pcre2                     10.40                h17e33f8_0    conda-forge
pillow                    9.3.0            py37hdc2b20a_1
pip                       22.3.1           py37haa95532_0
ply                       3.11                     py37_0
proj                      6.2.1                h3758d61_0
protobuf                  3.17.2           py37hd77b12b_0
psutil                    5.9.4                    pypi_0    pypi
pyasn1                    0.4.8              pyhd3eb1b0_0
pyasn1-modules            0.2.8                      py_0
pycparser                 2.21               pyhd3eb1b0_0
pyjwt                     2.4.0            py37haa95532_0
pyopenssl                 22.0.0             pyhd3eb1b0_0
pyparsing                 3.0.9            py37haa95532_0
pyproj                    2.6.1.post1      py37h593ac45_1
pyqt                      5.15.7           py37hd77b12b_0
pyqt5-sip                 12.11.0          py37hd77b12b_0
pysocks                   1.7.1                    py37_1
python                    3.7.15               h6244533_1
python-dateutil           2.8.2              pyhd3eb1b0_0
python-flatbuffers        1.12               pyhd3eb1b0_0
pytz                      2022.7           py37haa95532_0
pywavelets                1.3.0            py37h2bbff1b_0
pyyaml                    6.0              py37h2bbff1b_1
qt-main                   5.15.2               he906bfe_0    conda-forge
qt-webengine              5.15.9               hb9a9bb5_4
qtwebkit                  5.212                h3b0e7b7_2    conda-forge
rasterio                  1.2.10           py37h17c1fa0_0
requests                  2.28.1           py37haa95532_0
requests-oauthlib         1.3.0                      py_0
rsa                       4.7.2              pyhd3eb1b0_1
scikit-image              0.19.3           py37hd77b12b_1
scipy                     1.7.3            py37h7a0a035_2
setuptools                65.6.3           py37haa95532_0
sip                       6.6.2            py37hd77b12b_0
six                       1.16.0             pyhd3eb1b0_1
snappy                    1.1.9                h6c2663c_0
snuggs                    1.4.7              pyhd3eb1b0_0
sqlite                    3.40.1               h2bbff1b_0
tensorboard               2.6.0                      py_1
tensorboard-data-server   0.6.1            py37haa95532_0
tensorboard-plugin-wit    1.8.1            py37haa95532_0
tensorflow                2.6.0           gpu_py37h3e8f0e3_0
tensorflow-base           2.6.0           gpu_py37hb3da07e_0
tensorflow-estimator      2.6.0              pyh7b7c402_0
tensorflow-gpu            2.6.0                h17022bd_0
termcolor                 2.1.0            py37haa95532_0
tifffile                  2021.7.2           pyhd3eb1b0_2
tiledb                    2.3.3                h3649cd2_2
tk                        8.6.12               h2bbff1b_0
toml                      0.10.2             pyhd3eb1b0_0
toolz                     0.12.0           py37haa95532_0
tornado                   6.2              py37h2bbff1b_0
typing-extensions         4.4.0            py37haa95532_0
typing_extensions         4.4.0            py37haa95532_0
ucrt                      10.0.20348.0         haa95532_0
urllib3                   1.26.13          py37haa95532_0
vc                        14.2                 h21ff451_1
vs2015_runtime            14.34.31931         h4c5c07a_10    conda-forge
werkzeug                  2.2.2            py37haa95532_0
wheel                     0.35.1             pyhd3eb1b0_0
win_inet_pton             1.1.0            py37haa95532_0
wincertstore              0.2              py37haa95532_2
wrapt                     1.14.1           py37h2bbff1b_0
xerces-c                  3.2.4                hd77b12b_0
xz                        5.2.8                h8cc25b3_0
yaml                      0.2.5                he774522_0
yarl                      1.8.1            py37h2bbff1b_0
zfp                       0.5.5                hd77b12b_6
zipp                      3.11.0           py37haa95532_0
zlib                      1.2.13               hcfcfb64_4    conda-forge
zstd                      1.5.2                h19a0ad4_0
(ping-tf-2.1) PS C:\Users\bodin\Python\PINGMapper>

Everything ran as expected after re-running the test script!!!

Note

You may want to consider updating your python version as well (python=3.9) to try and get your environment as close to mine as possible. I'm still stumped why PING-Mapper didn't install to the same versions as mine. Perhaps you installed an older version of miniconda3? Dunno. But hopefully updating tensorflow will work for you and you can keep on mapping! Please let me know how it goes.

bthetford commented 1 year ago

Hurray thanks Cam! I'm going to try this now. That is weird, I got the latest miniconda3 version on the site, and it says my installed conda version is 22.11.1. I'll try the tensorflow update alone before the python update to see if there's any difference. Note: After running those steps you posted (delete ping env, update base env, conda clean -a, and remake ping env), I got this error:

InvalidArchiveError("Error with archive C:\\Users\\b.thetford\\AppData\\Local\\miniconda3\\pkgs\\tensorflow-base-2.3.0-eigen_py38h75a453f_0.conda.  You probably need to delete and re-download or re-create this file.  Message was:\n\nfailed with error: [Errno 2] No such file or directory: 'C:\\\\Users\\\\b.thetford\\\\AppData\\\\Local\\\\miniconda3\\\\pkgs\\\\tensorflow-base-2.3.0-eigen_py38h75a453f_0\\\\Lib\\\\site-packages\\\\tensorflow\\\\include\\\\external\\\\llvm-project\\\\mlir\\\\_virtual_includes\\\\DerivedAttributeOpInterfaceIncGen\\\\mlir\\\\Interfaces\\\\DerivedAttributeOpInterface.cpp.inc'")

I tried to run conda env create --file conda/PINGMapper.yml again and nothing changed. Then, I ran conda clean -a again, retried conda env create --file conda/PINGMapper.yml, and it worked. Super strange! Especially since I ran conda clean -a right after updating the base env also.

CameronBodine commented 1 year ago

In my experience, uninstalling Anaconda/miniconda doesn't always remove everything. So, in your case, I bet there were old files that were causing you to revert to older package versions. When you told me about libmamba, I did uninstall miniconda, and found that there was still a miniconda3 folder in my user directory. In addition, there were still Anaconda/miniconda start menu items with broken links, as I noted on this issue. After I removed the start menu folder as well as the miniconda3 folder in my user directory, miniconda installation went smoothly.

I think the conda clean -a step is critical and should be run anytime you are updating or installing a new env.

Welcome to the world of open-source computing! You truly get what you pay for ;-)

Let me know once you successfully run the test script, and we can close this issue as a success! 🤜🪵🤛

bthetford commented 1 year ago

Thanks for all your help Cam, I just got loaded with a ton of multibeam work but I'll get back to you on this soon! Beau

CameronBodine commented 1 year ago

Hi @bthetford, I was wondering if you had a chance to check the new changes? If they work for you, I would like to close this issue. Thanks.

bthetford commented 1 year ago

Hi Cameron, I did not get it working but haven't had any time to test it! I can try to look at it again maybe Friday. Thanks, Beau

bthetford commented 1 year ago

I got back to this yesterday and tried to force reinstall tensorflow GPU, and as you said my python version 3.10 is an issue. Going to use 3.9 and retry.

$ conda install tensorflow-gpu=2.6 --force-reinstall
Retrieving notices: ...working... done
Collecting package metadata (current_repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... failed with initial frozen solve. Retrying with flexible solve.
Solving environment: ...working...
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - tensorflow-gpu=2.6 -> python[version='3.7.*|3.8.*|3.9.*']

Your python: python=3.10

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

Note that strict channel priority may have removed packages required for satisfiability.
CameronBodine commented 1 year ago

Hi @bthetford, I have updated PINGMapper.yml installation procedure with 65046d9 today. This may help with your installation. This update uses tensorflow instead of tensorflow-gpu, which others were having issues with (see #60). If you could let me know if you are able to install and run PING-Mapper, I'd appreciate it.

bthetford commented 1 year ago

Thanks I'll try now! I haven't been able to get the environment to create lately, I just got that same tensorflow error and my env list remained empty. I'll let you know how the new YAML does.

bthetford commented 1 year ago

Hurray! It's working now. Tried both the test file and main.py on my own recording.

CameronBodine commented 1 year ago

Good deal! I will go ahead and close this issue. If you have any other problems, feel free to open a new issue.