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Failed to load stickBot model in the parametric KinDynComputations. #71

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S-Dafarra opened this issue Feb 29, 2024 · 9 comments · Fixed by #72
Closed

Failed to load stickBot model in the parametric KinDynComputations. #71

S-Dafarra opened this issue Feb 29, 2024 · 9 comments · Fixed by #72

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@S-Dafarra
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If I try to load the model https://github.com/icub-tech-iit/ergocub-gazebo-simulations/blob/1179630a88541479df51ebb108a21865ea251302/models/stickBot/model.urdf
in KinDynComputationsParametric I have the following issue:

Traceback (most recent call last):
  File "C:\Software\hippopt\src\hippopt\turnkey_planners\humanoid_kinodynamic\main_periodic_step_parametric.py", line 377, in <module>
    planner = walking_planner.Planner(settings=planner_settings)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Software\hippopt\src\hippopt\turnkey_planners\humanoid_kinodynamic\planner.py", line 27, in __init__
    self.kin_dyn_object = adam.parametric.casadi.KinDynComputationsParametric(
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Software\adam\src\adam\parametric\casadi\computations_parametric.py", line 40, in __init__
    factory = URDFParametricModelFactory(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Software\adam\src\adam\parametric\model\parametric_factories\parametric_model.py", line 32, in __init__
    self.urdf_desc = urdf_parser_py.urdf.URDF.from_xml_file(path)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Software\mambaforge\envs\hippopt\Lib\site-packages\urdf_parser_py\xml_reflection\core.py", line 617, in from_xml_file
    return cls.from_xml_string(xml_string)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Software\mambaforge\envs\hippopt\Lib\site-packages\urdf_parser_py\xml_reflection\core.py", line 610, in from_xml_string
    node = etree.fromstring(xml_string)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "src/lxml/etree.pyx", line 3264, in lxml.etree.fromstring
  File "src/lxml/parser.pxi", line 1984, in lxml.etree._parseMemoryDocument
ValueError: Unicode strings with encoding declaration are not supported. Please use bytes input or XML fragments without declaration.

The normal KinDynComputations instead works fine.

cc @CarlottaSartore
@CarlottaSartore
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Probably related to #49 (comment)

@CarlottaSartore
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This should work

 
 ## Ack to remove the encoding urdf, see https://github.com/icub-tech-iit/ergocub-gazebo-simulations/issues/49
 robot_file_read = open(model_path, "r")
 robot_urdf_string = robot_file_read.read()
 robot_urdf_string = robot_urdf_string.replace("<?xml", "")
 robot_urdf_string = robot_urdf_string.replace("version='1.0'", "")
 robot_urdf_string = robot_urdf_string.replace("encoding='UTF-8'?>", "")
 robot_file_write = open(model_path, "w")

@traversaro
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@S-Dafarra how did you installed adam ?

@S-Dafarra
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@S-Dafarra how did you installed adam ?

conda

now I switched to source installation. I noticed that in the standard case, there is this snippet

adam/src/adam/model/std_factories/std_model.py

Lines 11 to 23 in 2f18e9e

def urdf_remove_sensors_tags(xml_string):
# Parse the XML string
root = ET.fromstring(xml_string)
# Find and remove all tags named "sensor" that are child of
# root node (i.e. robot)
for sensors_tag in root.findall("sensor"):
root.remove(sensors_tag)
# Convert the modified XML back to a string
modified_xml_string = ET.tostring(root)
return modified_xml_string

I have added it with the following diff

index 1a46094..cbcb3ed 100644
--- a/src/adam/parametric/model/parametric_factories/parametric_model.py
+++ b/src/adam/parametric/model/parametric_factories/parametric_model.py
@@ -2,9 +2,9 @@ import pathlib
 from typing import List

 import urdf_parser_py.urdf
-
 from adam.core.spatial_math import SpatialMath
 from adam.model import ModelFactory, StdJoint, StdLink, Link, Joint
+from adam.model.std_factories.std_model import urdf_remove_sensors_tags
 from adam.parametric.model import ParmetricJoint, ParametricLink


@@ -29,7 +29,22 @@ class URDFParametricModelFactory(ModelFactory):
         if not path.exists():
             raise FileExistsError(path)
         self.links_name_list = links_name_list
-        self.urdf_desc = urdf_parser_py.urdf.URDF.from_xml_file(path)
+
+        # Read URDF, but before passing it to urdf_parser_py get rid of all sensor tags
+        # sensor tags are valid elements of URDF (see ),
+        # but they are ignored by urdf_parser_py, that complains every time it sees one.
+        # As there is nothing to be fixed in the used models, and it is not useful
+        # to have a useless and noisy warning, let's remove before hands all the sensor elements,
+        # that anyhow are not parser by urdf_parser_py or adam
+        # See https://github.com/ami-iit/ADAM/issues/59
+        xml_file = open(path, "r")
+        xml_string = xml_file.read()
+        xml_file.close()
+        xml_string_without_sensors_tags = urdf_remove_sensors_tags(xml_string)
+
+        self.urdf_desc = urdf_parser_py.urdf.URDF.from_xml_string(
+            xml_string_without_sensors_tags
+        )
         self.name = self.urdf_desc.name
         self.length_multiplier = length_multiplier
         self.densities = densities

and now the model is loaded correctly

@flferretti
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Have you tried using:

xml_file = open(path, "r", encoding="utf-8")

in

adam/src/adam/model/std_factories/std_model.py

Line 47 in 2f18e9e

xml_file = open(path, "r")

Because using the system default implicitly can create problems on Windows.

@CarlottaSartore
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mmm, I think the error is "hidden" from removing the sensor tag, but it is resolved because now urf_parser_py is loading a file without the declaration.

Which version of urdf_parser_py you are using?
Since it should be fixed ros/urdf_parser_py#83, maybe I am biased and the issue is another one.

@S-Dafarra
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S-Dafarra commented Feb 29, 2024 •
edited
Loading

@S-Dafarra how did you installed adam ?

For reference, this is my current

mamba list 
(hippopt) C:\Software\hippopt>mamba list
# packages in environment at C:\Software\mambaforge\envs\hippopt:
#
# Name                    Version                   Build  Channel
adam-robotics             0.1.1.dev4+dirty          pypi_0    pypi
aom                       3.8.1                h63175ca_0    conda-forge
assimp                    5.3.1                h81f0834_2    conda-forge
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
black                     24.2.0          py311h1ea47a8_0    conda-forge
blis                      0.9.0                hcfcfb64_1    conda-forge
brotli                    1.1.0                hcfcfb64_1    conda-forge
brotli-bin                1.1.0                hcfcfb64_1    conda-forge
bzip2                     1.0.8                hcfcfb64_5    conda-forge
ca-certificates           2024.2.2             h56e8100_0    conda-forge
cairo                     1.18.0               h1fef639_0    conda-forge
casadi                    3.6.3           py311h4930016_5    conda-forge
certifi                   2024.2.2           pyhd8ed1ab_0    conda-forge
click                     8.1.7           win_pyh7428d3b_0    conda-forge
cmake                     3.28.3               hf0feee3_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0           py311h005e61a_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
dav1d                     1.2.1                hcfcfb64_0    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
eigen                     3.4.0                h91493d7_0    conda-forge
exceptiongroup            1.2.0              pyhd8ed1ab_2    conda-forge
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
expat                     2.5.0                h63175ca_1    conda-forge
ffmpeg                    6.1.1           gpl_hb766fab_104    conda-forge
ffmpeg-python             0.2.0                      py_0    conda-forge
font-ttf-dejavu-sans-mono 2.37                 hab24e00_0    conda-forge
font-ttf-inconsolata      3.000                h77eed37_0    conda-forge
font-ttf-source-code-pro  2.038                h77eed37_0    conda-forge
font-ttf-ubuntu           0.83                 h77eed37_1    conda-forge
fontconfig                2.14.2               hbde0cde_0    conda-forge
fonts-conda-ecosystem     1                             0    conda-forge
fonts-conda-forge         1                             0    conda-forge
fonttools                 4.49.0          py311ha68e1ae_0    conda-forge
freetype                  2.12.1               hdaf720e_2    conda-forge
future                    1.0.0              pyhd8ed1ab_0    conda-forge
gettext                   0.21.1               h5728263_0    conda-forge
git                       2.44.0               h57928b3_0    conda-forge
git-filter-repo           2.38.0             pyhd8ed1ab_0    conda-forge
glfw                      3.4                  hcfcfb64_0    conda-forge
glib                      2.78.4               h12be248_0    conda-forge
glib-tools                2.78.4               h12be248_0    conda-forge
graphite2                 1.3.13                     1000    conda-forge
gst-plugins-base          1.22.9               h001b923_0    conda-forge
gstreamer                 1.22.9               hb4038d2_0    conda-forge
harfbuzz                  8.3.0                h7ab893a_0    conda-forge
hippopt                   0.1.dev373+dirty          pypi_0    pypi
icu                       73.2                 h63175ca_0    conda-forge
idyntree                  10.3.0          py311heed4631_0    conda-forge
iniconfig                 2.0.0              pyhd8ed1ab_0    conda-forge
intel-openmp              2024.0.0         h57928b3_49841    conda-forge
ipopt                     3.14.14              h1709daf_1    conda-forge
ipython                   8.22.1             pyh7428d3b_0    conda-forge
irrlicht                  1.8.5                h65f4d7e_4    conda-forge
isort                     5.13.2             pyhd8ed1ab_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.5           py311h005e61a_1    conda-forge
krb5                      1.21.2               heb0366b_0    conda-forge
lcms2                     2.16                 h67d730c_0    conda-forge
lerc                      4.0.0                h63175ca_0    conda-forge
libblas                   3.9.0             21_win64_blis    conda-forge
libboost                  1.82.0               h65993cd_6    conda-forge
libbrotlicommon           1.1.0                hcfcfb64_1    conda-forge
libbrotlidec              1.1.0                hcfcfb64_1    conda-forge
libbrotlienc              1.1.0                hcfcfb64_1    conda-forge
libcblas                  3.9.0             21_win64_blis    conda-forge
libclang                  15.0.7          default_hde6756a_4    conda-forge
libclang13                15.0.7          default_h85b4d89_4    conda-forge
libcurl                   8.5.0                hd5e4a3a_0    conda-forge
libdeflate                1.19                 hcfcfb64_0    conda-forge
libexpat                  2.5.0                h63175ca_1    conda-forge
libffi                    3.4.2                h8ffe710_5    conda-forge
libflang                  5.0.0           h6538335_20180525    conda-forge
libglib                   2.78.4               h16e383f_0    conda-forge
libhwloc                  2.9.3           default_haede6df_1009    conda-forge
libiconv                  1.17                 hcfcfb64_2    conda-forge
libjpeg-turbo             3.0.0                hcfcfb64_1    conda-forge
liblapack                 3.9.0           5_hd5c7e75_netlib    conda-forge
libogg                    1.3.4                h8ffe710_1    conda-forge
libopus                   1.3.1                h8ffe710_1    conda-forge
libosqp                   0.6.3                h63175ca_0    conda-forge
libpng                    1.6.43               h19919ed_0    conda-forge
libqdldl                  0.1.5                h63175ca_1    conda-forge
libsodium                 1.0.18               h8d14728_1    conda-forge
libsqlite                 3.45.1               hcfcfb64_0    conda-forge
libssh2                   1.11.0               h7dfc565_0    conda-forge
libtiff                   4.6.0                h6e2ebb7_2    conda-forge
libuv                     1.47.0               hcfcfb64_0    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.3.2                hcfcfb64_0    conda-forge
libxcb                    1.15                 hcd874cb_0    conda-forge
libxml2                   2.12.5               hc3477c8_0    conda-forge
libxslt                   1.1.39               h3df6e99_0    conda-forge
libzlib                   1.2.13               hcfcfb64_5    conda-forge
liecasadi                 0.0.6              pyhd8ed1ab_0    conda-forge
llvm-meta                 5.0.0                         0    conda-forge
lxml                      5.1.0           py311h064e5ff_0    conda-forge
m2w64-gcc-libgfortran     5.3.0                         6    conda-forge
m2w64-gcc-libs            5.3.0                         7    conda-forge
m2w64-gcc-libs-core       5.3.0                         7    conda-forge
m2w64-gmp                 6.1.0                         2    conda-forge
m2w64-libwinpthread-git   5.0.0.4634.697f757               2    conda-forge
matplotlib                3.8.3           py311h1ea47a8_0    conda-forge
matplotlib-base           3.8.3           py311h6e989c2_0    conda-forge
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
meshcat-python            0.3.2              pyhd8ed1ab_0    conda-forge
meson                     1.3.2              pyhd8ed1ab_0    conda-forge
metis                     5.1.0             h63175ca_1007    conda-forge
mkl                       2024.0.0         h66d3029_49658    conda-forge
msys2-conda-epoch         20160418                      1    conda-forge
mumps-seq                 5.6.2                h1f49738_4    conda-forge
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
mypy_extensions           1.0.0              pyha770c72_0    conda-forge
ninja                     1.11.1               h91493d7_0    conda-forge
numpy                     1.26.4          py311h0b4df5a_0    conda-forge
openh264                  2.4.1                h63175ca_0    conda-forge
openjpeg                  2.5.0                h3d672ee_3    conda-forge
openmp                    5.0.0                    vc14_1    conda-forge
openssl                   3.2.1                hcfcfb64_0    conda-forge
osqp-eigen                0.8.1                h6d7489e_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pathspec                  0.12.1             pyhd8ed1ab_0    conda-forge
pcre2                     10.42                h17e33f8_0    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    10.2.0          py311h4dd8a23_0    conda-forge
pip                       24.0               pyhd8ed1ab_0    conda-forge
pixman                    0.43.2               h63175ca_0    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pluggy                    1.4.0              pyhd8ed1ab_0    conda-forge
ply                       3.11                       py_1    conda-forge
prettytable               3.10.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.42             pyha770c72_0    conda-forge
proxsuite                 0.6.3           py311h1ea47a8_0    conda-forge
pthread-stubs             0.4               hcd874cb_1001    conda-forge
pthreads-win32            2.9.1                hfa6e2cd_3    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pyngrok                   7.1.2              pyhd8ed1ab_0    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pyqt                      5.15.9          py311h125bc19_5    conda-forge
pyqt5-sip                 12.12.2         py311h12c1d0e_5    conda-forge
pytest                    8.0.2              pyhd8ed1ab_0    conda-forge
python                    3.11.8          h2628c8c_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python_abi                3.11                    4_cp311    conda-forge
pyyaml                    6.0.1           py311ha68e1ae_1    conda-forge
pyzmq                     25.1.2          py311h9250fbb_0    conda-forge
qt-main                   5.15.8              h9e85ed6_19    conda-forge
resolve-robotics-uri-py   0.1.0              pyhd8ed1ab_0    conda-forge
scipy                     1.12.0          py311h0b4df5a_2    conda-forge
sdl                       1.2.68               h21dd15a_0    conda-forge
sdl2                      2.28.5               h63175ca_1    conda-forge
setuptools                69.1.1             pyhd8ed1ab_0    conda-forge
simde                     0.7.6                h91493d7_0    conda-forge
sip                       6.7.12          py311h12c1d0e_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
svt-av1                   1.8.0                h63175ca_0    conda-forge
tbb                       2021.11.0            h91493d7_1    conda-forge
tinyxml2                  10.0.0               h63175ca_0    conda-forge
tk                        8.6.13               h5226925_1    conda-forge
toml                      0.10.2             pyhd8ed1ab_0    conda-forge
tomli                     2.0.1              pyhd8ed1ab_0    conda-forge
tornado                   6.4             py311ha68e1ae_0    conda-forge
traitlets                 5.14.1             pyhd8ed1ab_0    conda-forge
typing_extensions         4.10.0             pyha770c72_0    conda-forge
tzdata                    2024a                h0c530f3_0    conda-forge
u-msgpack-python          2.8.0              pyhd8ed1ab_0    conda-forge
ucrt                      10.0.22621.0         h57928b3_0    conda-forge
urdfdom-py                1.2.1           py311h1ea47a8_3    conda-forge
vc                        14.3                hcf57466_18    conda-forge
vc14_runtime              14.38.33130         h82b7239_18    conda-forge
vs2015_runtime            14.38.33130         hcb4865c_18    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
x264                      1!164.3095           h8ffe710_2    conda-forge
x265                      3.5                  h2d74725_3    conda-forge
xorg-libxau               1.0.11               hcd874cb_0    conda-forge
xorg-libxdmcp             1.1.3                hcd874cb_0    conda-forge
xz                        5.2.6                h8d14728_0    conda-forge
yaml                      0.2.5                h8ffe710_2    conda-forge
zeromq                    4.3.5                h63175ca_0    conda-forge
zlib                      1.2.13               hcfcfb64_5    conda-forge
zstd                      1.5.5                h12be248_0    conda-forge

@S-Dafarra
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Relevant PR: #72

@traversaro
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Since it should be fixed ros/urdf_parser_py#83, maybe I am biased and the issue is another one.

Actually the issue is still there as the fix still needs to be released.

@S-Dafarra S-Dafarra mentioned this issue Mar 8, 2024
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Parametric improvements S-Dafarra/adam
4 participants
@traversaro @S-Dafarra @CarlottaSartore @flferretti