Deformetrica GUI on 4.2

fort...@gmail.com

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Jun 13, 2019, 3:50:39 PM6/13/19

to Deformetrica

Hello,

It seems the deformetrica gui no longer works on 4.2, on the same machine in a different environment it is working on 4.1, however, after creating a new environment to install 4.2 I get an error message after running "deformetrica gui"

Traceback (most recent call last):

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovis.py", line 5, in <module>

from .vtkIOInfovisPython import *

ImportError: dlopen(/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovisPython.so, 2): Library not loaded: @rpath/libxml2.2.dylib

Referenced from: /Users/xxxx/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib

Reason: Incompatible library version: libvtkIOInfovis-8.2.1.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/xxxx/vmtk/envs/deformetrica_new/bin/deformetrica", line 6, in <module>

from deformetrica import main

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica.py", line 8, in <module>

import api

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/api/__init__.py", line 1, in <module>

from .deformetrica import Deformetrica

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/api/deformetrica.py", line 16, in <module>

from core.models.affine_atlas import AffineAtlas

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/core/models/affine_atlas.py", line 9, in <module>

from in_out.dataset_functions import create_template_metadata

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/in_out/dataset_functions.py", line 15, in <module>

from in_out.deformable_object_reader import DeformableObjectReader

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/in_out/deformable_object_reader.py", line 11, in <module>

from vtk import vtkPolyDataReader

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtk.py", line 32, in <module>

all_spec.loader.exec_module(all_m)

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/all.py", line 77, in <module>

from .vtkIOInfovis import *

File "/Users/xxxx/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovis.py", line 9, in <module>

from vtkIOInfovisPython import *

ModuleNotFoundError: No module named 'vtkIOInfovisPython'

Benoit Martin

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Jun 17, 2019, 3:24:48 AM6/17/19

to Deformetrica

Hello,

Thank you for your feedback.

I will give this a look and let you know when a fix is available.

May I ask how you installed deformetrica ? Within a Conda environment ? Using the official Conda package ?

Kindly,

Benoit

Benoit Martin

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Jul 9, 2019, 7:51:44 AM7/9/19

to Deformetrica

Hello,

Just letting you know that a new "release candidate" version in available.

This new version fixes a number if issues, including some related to the GUI.

The package can be installed by running the following conda command: conda install -c pytorch -c conda-forge -c anaconda -c aramislab/label/rc deformetrica

Let me know if this fixes your problems.

Bests,

Benoit

ronaldfo...@gmail.com

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Jul 9, 2019, 11:40:46 AM7/9/19

to Deformetrica

Thank you for the update. Sorry for the delayed response but i had installed deformetrica using conda environment and using the official package previously. I have just installed using the commands you suggested for the RC version and can let you know that the gui does not work still on my mac (10.12.6). Below is the following error message:

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovis.py", line 5, in <module>

from .vtkIOInfovisPython import *

ImportError: dlopen(/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovisPython.so, 2): Library not loaded: @rpath/libxml2.2.dylib

Referenced from: /Users/XXXX/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib

Reason: Incompatible library version: libvtkIOInfovis-8.2.1.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/XXXX/vmtk/envs/deformetrica_new/bin/deformetrica", line 6, in <module>

from deformetrica import main

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica.py", line 8, in <module>

import api

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/api/__init__.py", line 1, in <module>

from .deformetrica import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/api/deformetrica.py", line 16, in <module>

from core.models.affine_atlas import AffineAtlas

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/core/models/affine_atlas.py", line 9, in <module>

from in_out.dataset_functions import create_template_metadata

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/in_out/dataset_functions.py", line 15, in <module>

from in_out.deformable_object_reader import DeformableObjectReader

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/in_out/deformable_object_reader.py", line 11, in <module>

from vtk import vtkPolyDataReader

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtk.py", line 32, in <module>

all_spec.loader.exec_module(all_m)

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/all.py", line 77, in <module>

from .vtkIOInfovis import *

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovis.py", line 9, in <module>

Benoit Martin

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Jul 10, 2019, 3:55:57 AM7/10/19

to Deformetrica

Thank you for your feedback.

May I ask that you run 'conda list' from inside your conda environment where deformetrica is installed ?

This will list all the libraries and their version that are installed within that conda environment.

This will help me in identifying the issue.

Thank you,

Benoit

ronaldfo...@gmail.com

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Jul 10, 2019, 10:11:13 AM7/10/19

to Deformetrica

# packages in environment at /Users/XXX/vmtk/envs/deformetrica_new:

#

# Name Version Build Channel

bz2file 0.98 py_0 conda-forge

bzip2 1.0.6 h1de35cc_1002 conda-forge

ca-certificates 2019.6.16 hecc5488_0 conda-forge

certifi 2019.6.16 py37_0 conda-forge

cffi 1.12.3 py37hccf1714_0 conda-forge

cudatoolkit 8.0 3 anaconda

curl 7.62.0 ha441bb4_0 anaconda

cycler 0.10.0 py_1 conda-forge

dbus 1.13.6 h2f22bb5_0 conda-forge

deformetrica 4.2.0rc0 pypi_0 pypi

expat 2.2.5 h6de7cb9_1003 conda-forge

freetype 2.10.0 h24853df_0 conda-forge

future 0.17.1 py37_1000 conda-forge

gettext 0.19.8.1 h46ab8bc_1002 conda-forge

glib 2.58.3 h9d45998_1001 conda-forge

h5py 2.9.0 nompi_py37h35dc34b_1102 conda-forge

hdf4 4.2.13 hf3c6af0_1002 conda-forge

hdf5 1.10.4 nompi_h0cbb7df_1106 conda-forge

icu 58.2 h0a44026_1000 conda-forge

intel-openmp 2019.4 233 anaconda

jpeg 9c h1de35cc_1001 conda-forge

jsoncpp 1.8.4 h04f5b5a_1001 conda-forge

kiwisolver 1.1.0 py37h770b8ee_0 conda-forge

libblas 3.8.0 10_openblas conda-forge

libcblas 3.8.0 10_openblas conda-forge

libcurl 7.62.0 h051b688_0

libcxx 4.0.1 hcfea43d_1

libcxxabi 4.0.1 hcfea43d_1

libedit 3.1.20181209 hb402a30_0

libffi 3.2.1 h475c297_4

libgfortran 3.0.1 0 conda-forge

libiconv 1.15 h01d97ff_1005 conda-forge

liblapack 3.8.0 10_openblas conda-forge

libnetcdf 4.6.2 h6b88ef6_1001 conda-forge

libopenblas 0.3.6 hd44dcd8_4 conda-forge

libpng 1.6.37 h2573ce8_0 conda-forge

libssh2 1.8.2 hcdc9a53_2 conda-forge

libtiff 4.0.10 hd08fb8f_1003 conda-forge

libxml2 2.9.9 hd80cff7_1 conda-forge

lz4-c 1.8.3 h6de7cb9_1001 conda-forge

matplotlib 2.2.2 py37hbf02d85_2 anaconda

mkl 2019.4 233 anaconda

ncurses 6.1 h0a44026_1

nibabel 2.3.3 py_1 conda-forge

ninja 1.9.0 h04f5b5a_0 conda-forge

numpy 1.16.2 py37hbb3c62a_1 conda-forge

olefile 0.46 py_0 conda-forge

openblas 0.3.6 hd44dcd8_4 conda-forge

openssl 1.1.1b h01d97ff_2 conda-forge

pcre 8.41 h0a44026_1003 conda-forge

pillow 5.4.1 py37hb68e598_0 anaconda

pip 19.1.1 py37_0

psutil 5.4.8 py37h1de35cc_1000 conda-forge

pycparser 2.19 py37_1 conda-forge

pydicom 1.2.2 py_0 conda-forge

pykeops 1.0.1 pypi_0 pypi

pyparsing 2.4.0 py_0 conda-forge

pyqt 5.9.2 py37h2a560b1_0 conda-forge

python 3.7.3 h359304d_0

python-dateutil 2.8.0 py_0 conda-forge

pytorch 1.0.1 py3.7_2 pytorch

pytz 2019.1 py_0 conda-forge

qt 5.9.7 h93ee506_2 conda-forge

readline 7.0 h1de35cc_5

scikit-learn 0.20.3 py37hca23c92_1 conda-forge

scipy 1.3.0 py37hab3da7d_0 conda-forge

setuptools 41.0.1 py37_0

sip 4.19.8 py37h0a44026_1000 conda-forge

six 1.12.0 py37_1000 conda-forge

sqlite 3.28.0 ha441bb4_0

tbb 2019.7 h770b8ee_0 conda-forge

tk 8.6.8 ha441bb4_0

tornado 6.0.3 py37h01d97ff_0 conda-forge

vtk 8.2.0 py37h9382d79_201 conda-forge

wheel 0.33.4 py37_0

xz 5.2.4 h1de35cc_4

zlib 1.2.11 h1de35cc_3

zstd 1.4.0 ha9f0a20_0 conda-forge

(deformetrica_new)

Benoit Martin

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Jul 10, 2019, 11:47:41 AM7/10/19

to Deformetrica

Hi,

Thanks for the console output. It proved to be useful.

I think the issue should be fixed. Could you give it a try ?

You can run the same command as before: conda install -c pytorch -c conda-forge -c anaconda -c aramislab/label/rc deformetrica

Bests,

Benoit

ronaldfo...@gmail.com

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Jul 10, 2019, 1:30:14 PM7/10/19

to Deformetrica

Thank you for the quick update Benoit. However still having trouble with the gui, here is the output:

Traceback (most recent call last):

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovis.py", line 5, in <module>

from .vtkIOInfovisPython import *

ImportError: dlopen(/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/vtkmodules/vtkIOInfovisPython.so, 2): Library not loaded: @rpath/libxml2.2.dylib

Referenced from: /Users/XXXX/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib

Reason: Incompatible library version: libvtkIOInfovis-8.2.1.dylib requires version 12.0.0 or later, but libxml2.2.dylib provides version 10.0.0

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

File "/Users/XXXX/vmtk/envs/deformetrica_new/bin/deformetrica", line 6, in <module>

from deformetrica.__main__ import main

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/__init__.py", line 4, in <module>

from .api import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/__init__.py", line 1, in <module>

from .deformetrica import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/deformetrica.py", line 13, in <module>

from ..core.estimators.gradient_ascent import GradientAscent

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/core/estimators/__init__.py", line 4, in <module>

from .mcmc_saem import McmcSaem

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/core/estimators/mcmc_saem.py", line 9, in <module>

from ...in_out.array_readers_and_writers import *

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/in_out/__init__.py", line 9, in <module>

from .deformable_object_reader import DeformableObjectReader

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/in_out/deformable_object_reader.py", line 11, in <module>

from vtk import vtkPolyDataReader, vtkSTLReader

Benoit Martin

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Jul 11, 2019, 4:59:52 AM7/11/19

to Deformetrica

Hello,

Again, I am sorry you are having issues with deformetrica.

It is the first time this issue you are having is occuring. Furthermore, I cannot seem to reproduce the issue.

That being said, having tried a few things, I have a strong reason to believe that there is a problem with the libxml library that is used by our vtk reader.

Could you run the following 3 commands? :

1) otool -l /Users/XXXX/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib

2) otool -L /Users/XXXX/vmtk/envs/deformetrica_new/lib/libxml2.dylib

3) otool -L /usr/lib/libxml2.dylib

This will let me check where and with what version the libvtkIOInfovis library is linked.

Do you face the same problem when running Deformetrica via the command line interface ?

My hypothesis is that your environment either does not have the proper libxml2 library or the rpath set in the libvtkIOInfovis library is not searching in the right place.

Perhaps you could update your miniconda/anaconda ? or update the libxml library within your conda environment (conda install libxml2) ? update your systems libxml2 library ?

Thank you for your patience,

I hope we'll get a fix out soon !

Bests,

Benoit

Ronald Fortunato

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Jul 11, 2019, 9:54:37 AM7/11/19

to Deformetrica

Thank you for the steps, I had success on the same machine using 4.1 with python 3.6. Below is the from the env in which is no longer working though.

otool -l /Users/XXXX/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib

/Users/XXXX/vmtk/envs/deformetrica_new/lib/libvtkIOInfovis-8.2.1.dylib:

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cmdsize 48

name @rpath/libtbb.dylib (offset 24)

time stamp 2 Wed Dec 31 19:00:02 1969

current version 0.0.0

compatibility version 0.0.0

Load command 21

cmd LC_LOAD_DYLIB

cmdsize 56

name @rpath/libvtksys-8.2.1.dylib (offset 24)

time stamp 2 Wed Dec 31 19:00:02 1969

current version 1.0.0

compatibility version 1.0.0

Load command 22

cmd LC_LOAD_DYLIB

cmdsize 48

name @rpath/libc++.1.dylib (offset 24)

time stamp 2 Wed Dec 31 19:00:02 1969

current version 1.0.0

compatibility version 1.0.0

Load command 23

cmd LC_LOAD_DYLIB

cmdsize 56

name /usr/lib/libSystem.B.dylib (offset 24)

time stamp 2 Wed Dec 31 19:00:02 1969

current version 1197.1.1

compatibility version 1.0.0

Load command 24

cmd LC_RPATH

cmdsize 272

path /Users/XXXX/vmtk/envs/deformetrica_new/lib (offset 12)

Load command 25

cmd LC_FUNCTION_STARTS

cmdsize 16

dataoff 327184

datasize 872

Load command 26

cmd LC_DATA_IN_CODE

cmdsize 16

dataoff 328056

datasize 0

Load command 27

cmd LC_RPATH

cmdsize 32

path @loader_path/ (offset 12)

________________________________________________________________________________________

otool -L /Users/XXXX/vmtk/envs/deformetrica_new/lib/libxml2.dylib

/Users/XXXX/vmtk/envs/deformetrica_new/lib/libxml2.dylib:

@rpath/libxml2.2.dylib (compatibility version 12.0.0, current version 12.9.0)

@rpath/libicuuc.58.dylib (compatibility version 58.0.0, current version 58.2.0)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1197.1.1)

@rpath/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11)

@rpath/liblzma.5.dylib (compatibility version 8.0.0, current version 8.4.0)

@rpath/libiconv.2.dylib (compatibility version 9.0.0, current version 9.0.0)

________________________________________________________________________________________

otool -L /usr/lib/libxml2.dylib

/usr/lib/libxml2.dylib:

/usr/lib/libxml2.2.dylib (compatibility version 10.0.0, current version 10.9.0)

/usr/lib/libicucore.A.dylib (compatibility version 1.0.0, current version 57.1.0)

/usr/lib/liblzma.5.dylib (compatibility version 6.0.0, current version 6.3.0)

/usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.8)

/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1238.60.2

________________________________________________________________________________________

I ran the conda install libxml2 and now get a new error message after successfully installing libxml2:

Traceback (most recent call last):

File "/Users/XXXX/vmtk/envs/deformetrica_new/bin/deformetrica", line 6, in <module>

from deformetrica.__main__ import main

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/__init__.py", line 4, in <module>

from .api import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/__init__.py", line 1, in <module>

from .deformetrica import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/deformetrica.py", line 9, in <module>

import torch

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/torch/__init__.py", line 84, in <module>

from torch._C import *

ImportError: numpy.core.multiarray failed to import

________________________________________________________________________________________

Maybe an unrelated note but when I ran update conda (conda update -n base -c defaults conda) inside the deformetrica environment after running on the base environment and I got this pretty descriptive error message:

PackagesNotFoundError: The following packages are not available from current channels:

- vmtk/osx-64::vmtk==1.4.0=py36h5f860b4_1 -> python[version='>=3.6,<3.6.2.0a0']

Ronald Fortunato

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Jul 11, 2019, 10:04:07 AM7/11/19

to Deformetrica

It seems like some of my message got cut off so I am attaching a pdf.

DeformetricaLongMessage.pdf

Benoit Martin

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Jul 16, 2019, 6:26:20 AM7/16/19

to Deformetrica

Hello,

Thank you for being so patient.

In order to fix the "ImportError: numpy.core.multiarray failed to import" error, it seems that you need to upgrade numpy: pip install -U numpy

This does however seem rather strange.

As for the "PackagesNotFoundError", you could explicitly specify the conda channels that should be used. Perhaps: conda update -n base -c anaconda -c conda-forge -c aramislab/label/rc -c pytorch conda

Bests,

Benoit

Ronald Fortunato

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Jul 16, 2019, 1:15:23 PM7/16/19

to Deformetrica

:pip install -U numpy

Requirement already up-to-date: numpy in /Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages (1.16.4)

:deformetrica gui

Traceback (most recent call last):

File "/Users/XXXX/vmtk/envs/deformetrica_new/bin/deformetrica", line 6, in <module>

from deformetrica.__main__ import main

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/__init__.py", line 4, in <module>

from .api import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/__init__.py", line 1, in <module>

from .deformetrica import Deformetrica

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/deformetrica/api/deformetrica.py", line 9, in <module>

import torch

File "/Users/XXXX/vmtk/envs/deformetrica_new/lib/python3.7/site-packages/torch/__init__.py", line 84, in <module>

from torch._C import *

ImportError: numpy.core.multiarray failed to import

Ronald Fortunato

unread,

Jul 16, 2019, 1:47:18 PM7/16/19

to Deformetrica

I ran that upgrade command and for some reason that preceded to break my environment and even conda itself. "error message: "ImportError: No yaml library available. To proceed, conda install ruamel_yaml" that even came up when trying to install or remove envs.

Could not deactivate even to get out. Reinstalled fresh anaconda, still have same error as above.

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