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mluerig / iso_track

motion detection of isopods with opencv and trackpy
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Conflict during trackpy installation - conda #1

Open rnrpereira opened 5 years ago

rnrpereira commented 5 years ago

Hi Moritz,

I tried to install trackpy as below and I'm getting a conflict! Do you know how to solve it? thanks,

Rodrigo ########################################################################## (neuro-python36) C:\Users\Rodrigo>conda install -c soft-matter -c soft-matter/channel/dev trackpy Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

mluerig commented 5 years ago

Hi Rodrigo, thanks for getting in touch. I have discontinued the development of iso_track a while ago, but I am currently integrating it with other scripts I have written to form a coherent python package - have a look at https://github.com/mluerig/phenopype.

I have not yet integrated iso_track, but I probably will in the next few weeks, so I would just ask you to stay tuned until this works again.

As for the error; I wrote this code under python 3.7 with opencv 3.4.1, so you could try to roll back:

C:\Windows\system32>conda list
#packages in environment at C:\Anaconda3:

#Name                    Version                   Build  Channel
_ipyw_jlab_nb_ext_conf    0.1.0                    py37_0
alabaster                 0.7.11                   py37_0
anaconda                  5.3.0                    py37_0
anaconda-client           1.7.2                    py37_0
anaconda-navigator        1.9.2                    py37_0
anaconda-project          0.8.2                    py37_0
appdirs                   1.4.3            py37h28b3542_0
asn1crypto                0.24.0                   py37_0
astroid                   2.0.4                    py37_0
astropy                   3.0.4            py37hfa6e2cd_0
atomicwrites              1.2.1                    py37_0
attrs                     18.2.0           py37h28b3542_0
automat                   0.7.0                    py37_0
autopep8                  1.4.3                     <pip>
babel                     2.6.0                    py37_0
backcall                  0.1.0                    py37_0
backports                 1.0                      py37_1
backports.shutil_get_terminal_size 1.0.0                    py37_2
beautifulsoup4            4.6.3                    py37_0
bitarray                  0.8.3            py37hfa6e2cd_0
bkcharts                  0.2                      py37_0
blas                      1.0                         mkl
blaze                     0.11.3                   py37_0
bleach                    2.1.4                    py37_0
blosc                     1.14.4               he51fdeb_0
bokeh                     0.13.0                   py37_0
boto                      2.49.0                   py37_0
bottleneck                1.2.1            py37h452e1ab_1
bzip2                     1.0.6                hfa6e2cd_5
ca-certificates           2018.03.07                    0
certifi                   2018.8.24                py37_1
cffi                      1.11.5           py37h74b6da3_1
chardet                   3.0.4                    py37_1
click                     6.7                      py37_0
cloudpickle               0.5.5                    py37_0
clyent                    1.2.2                    py37_1
colorama                  0.3.9                    py37_0
comtypes                  1.1.7                    py37_0
conda                     4.5.11                py37_1000    conda-forge
conda-build               3.15.1                   py37_0
conda-env                 2.6.0                h36134e3_1
console_shortcut          0.1.1                         3
constantly                15.1.0           py37h28b3542_0
contextlib2               0.5.5                    py37_0
cryptography              2.3.1            py37h74b6da3_0
curl                      7.61.0               h7602738_0
cycler                    0.10.0                   py37_0
cython                    0.28.5           py37h6538335_0
cytoolz                   0.9.0.1          py37hfa6e2cd_1
dask                      0.19.1                   py37_0
dask-core                 0.19.1                   py37_0
datashape                 0.5.4                    py37_1
decorator                 4.3.0                    py37_0
defusedxml                0.5.0                    py37_1
distributed               1.23.1                   py37_0
docutils                  0.14                     py37_0
entrypoints               0.2.3                    py37_2
et_xmlfile                1.0.1                    py37_0
exifread                  2.1.2                      py_1    conda-forge
fastcache                 1.0.2            py37hfa6e2cd_2
filelock                  3.0.8                    py37_0
flask                     1.0.2                    py37_1
flask-cors                3.0.6                    py37_0
freetype                  2.9.1                ha9979f8_1
future                    0.17.1                    <pip>
get_terminal_size         1.0.0                h38e98db_0
gevent                    1.3.6            py37hfa6e2cd_0
git                       2.19.1            h21ff451_1000    conda-forge
glob2                     0.6                      py37_0
greenlet                  0.4.15           py37hfa6e2cd_0
h5py                      2.8.0            py37h3bdd7fb_2
hdf5                      1.10.2               hac2f561_1
heapdict                  1.0.0                    py37_2
html5lib                  1.0.1                    py37_0
hyperlink                 18.0.0                   py37_0
icc_rt                    2017.0.4             h97af966_0
icu                       58.2                 ha66f8fd_1
idna                      2.7                      py37_0
imageio                   2.4.1                    py37_0
imagesize                 1.1.0                    py37_0
incremental               17.5.0                   py37_0
intel-openmp              2019.0                      118
ipykernel                 4.10.0                   py37_0
ipython                   6.5.0                    py37_0
ipython_genutils          0.2.0                    py37_0
ipywidgets                7.4.1                    py37_0
isort                     4.3.4                    py37_0
itsdangerous              0.24                     py37_1
jdcal                     1.4                      py37_0
jedi                      0.12.1                   py37_0
jinja2                    2.10                     py37_0
jpeg                      9b                   hb83a4c4_2
jsonschema                2.6.0                    py37_0
jupyter                   1.0.0                    py37_7
jupyter_client            5.2.3                    py37_0
jupyter_console           5.2.0                    py37_1
jupyter_core              4.4.0                    py37_0
jupyterlab                0.34.9                   py37_0
jupyterlab_launcher       0.13.1                   py37_0
keyring                   13.2.1                   py37_0
kiwisolver                1.0.1            py37h6538335_0
lazy-object-proxy         1.3.1            py37hfa6e2cd_2
libcurl                   7.61.0               h7602738_0
libiconv                  1.15                 h1df5818_7
libopencv                 3.4.1                h875b8b8_3
libpng                    1.6.34               h79bbb47_0
libsodium                 1.0.16               h9d3ae62_0
libssh2                   1.8.0                hd619d38_4
libtiff                   4.0.9                h36446d0_2
libxml2                   2.9.8                hadb2253_1
libxslt                   1.1.32               hf6f1972_0
llvmlite                  0.24.0           py37h6538335_0
locket                    0.2.0                    py37_1
lxml                      4.2.5            py37hef2cd61_0
lzo                       2.10                 h6df0209_2
m2w64-gcc-libgfortran     5.3.0                         6
m2w64-gcc-libs            5.3.0                         7
m2w64-gcc-libs-core       5.3.0                         7
m2w64-gmp                 6.1.0                         2
m2w64-libwinpthread-git   5.0.0.4634.697f757               2
markupsafe                1.0              py37hfa6e2cd_1
matplotlib                2.2.3            py37hd159220_0
mccabe                    0.6.1                    py37_1
menuinst                  1.4.14           py37hfa6e2cd_0
mistune                   0.8.3            py37hfa6e2cd_1
mkl                       2019.0                      118
mkl-service               1.1.2            py37hb217b18_5
mkl_fft                   1.0.4            py37h1e22a9b_1
mkl_random                1.0.1            py37h77b88f5_1
more-itertools            4.3.0                    py37_0
mpmath                    1.0.0                    py37_2
msgpack-python            0.5.6            py37he980bc4_1
msys2-conda-epoch         20160418                      1
multipledispatch          0.6.0                    py37_0
navigator-updater         0.2.1                    py37_0
nbconvert                 5.4.0                    py37_1
nbformat                  4.4.0                    py37_0
networkx                  2.1                      py37_0
nltk                      3.3.0                    py37_0
nose                      1.3.7                    py37_2
notebook                  5.6.0                    py37_0
numba                     0.39.0           py37h830ac7b_0
numexpr                   2.6.8            py37h9ef55f4_0
numpy                     1.15.1           py37ha559c80_0
numpy-base                1.15.1           py37h8128ebf_0
numpydoc                  0.8.0                    py37_0
odo                       0.5.1                    py37_0
olefile                   0.46                     py37_0
opencv                    3.4.1            py37h6fd60c2_3
openpyxl                  2.5.6                    py37_0
openssl                   1.0.2p               hfa6e2cd_0    conda-forge
packaging                 17.1                     py37_0
pandas                    0.23.4           py37h830ac7b_0
pandoc                    1.19.2.1             hb2460c7_1
pandocfilters             1.4.2                    py37_1
parso                     0.3.1                    py37_0
partd                     0.3.8                    py37_0
path.py                   11.1.0                   py37_0
pathlib2                  2.3.2                    py37_0
patsy                     0.5.0                    py37_0
pep8                      1.7.1                    py37_0
phenopype                 0.4.4                     <pip>
pickleshare               0.7.4                    py37_0
pillow                    5.2.0            py37h08bbbbd_0
pip                       10.0.1                   py37_0
pkginfo                   1.4.2                    py37_1
pluggy                    0.7.1            py37h28b3542_0
ply                       3.11                     py37_0
prometheus_client         0.3.1            py37h28b3542_0
prompt_toolkit            1.0.15                   py37_0
psutil                    5.4.7            py37hfa6e2cd_0
py                        1.6.0                    py37_0
py-opencv                 3.4.1            py37h1b0d24d_3
pyasn1                    0.4.4            py37h28b3542_0
pyasn1-modules            0.2.2                    py37_0
pycodestyle               2.4.0                    py37_0
pycosat                   0.6.3            py37hfa6e2cd_0
pycparser                 2.18                     py37_1
pycrypto                  2.6.1            py37hfa6e2cd_9
pycurl                    7.43.0.2         py37h74b6da3_0
pydocstyle                3.0.0                     <pip>
pyflakes                  2.0.0                    py37_0
pygments                  2.2.0                    py37_0
pylint                    2.1.1                    py37_0
pyodbc                    4.0.24           py37h6538335_0
pyopenssl                 18.0.0                   py37_0
pyparsing                 2.2.0                    py37_1
pyqt                      5.9.2            py37h6538335_2
pysocks                   1.6.8                    py37_0
pytables                  3.4.4            py37he6f6034_0
pytest                    3.8.0                    py37_0
pytest-arraydiff          0.2              py37h39e3cac_0
pytest-astropy            0.4.0                    py37_0
pytest-doctestplus        0.1.3                    py37_0
pytest-openfiles          0.3.0                    py37_0
pytest-remotedata         0.3.0                    py37_0
python                    3.7.0                hea74fb7_0
python-dateutil           2.7.3                    py37_0
python-jsonrpc-server     0.0.2                     <pip>
python-language-server    0.21.4                    <pip>
pytz                      2018.5                   py37_0
pywavelets                1.0.0            py37h452e1ab_0
pywin32                   223              py37hfa6e2cd_1
pywinpty                  0.5.4                    py37_0
pyyaml                    3.13             py37hfa6e2cd_0
pyzmq                     17.1.2           py37hfa6e2cd_0
qt                        5.9.6            vc14h1e9a669_2  [vc14]
qtawesome                 0.4.4                    py37_0
qtconsole                 4.4.1                    py37_0
qtpy                      1.5.0                    py37_0
requests                  2.19.1                   py37_0
rope                      0.11.0                   py37_0
ruamel_yaml               0.15.46          py37hfa6e2cd_0
scikit-image              0.14.0           py37h6538335_1
scikit-learn              0.19.2           py37heebcf9a_0
scipy                     1.1.0            py37h4f6bf74_1
seaborn                   0.9.0                    py37_0
selenium                  3.141.0                   <pip>
send2trash                1.5.0                    py37_0
service_identity          17.0.0           py37h28b3542_0
setuptools                40.2.0                   py37_0
simplegeneric             0.8.1                    py37_2
singledispatch            3.4.0.3                  py37_0
sip                       4.19.8           py37h6538335_0
six                       1.11.0                   py37_1
snappy                    1.1.7                h777316e_3
snowballstemmer           1.2.1                    py37_0
sortedcollections         1.0.1                    py37_0
sortedcontainers          2.0.5                    py37_0
sphinx                    1.7.9                    py37_0
sphinxcontrib             1.0                      py37_1
sphinxcontrib-websupport  1.1.0                    py37_1
spyder                    3.3.1                    py37_1
spyder-kernels            0.2.6                    py37_0
sqlalchemy                1.2.11           py37hfa6e2cd_0
sqlite                    3.24.0               h7602738_0
statsmodels               0.9.0            py37h452e1ab_0
sympy                     1.1.1                    py37_0
tblib                     1.3.2                    py37_0
terminado                 0.8.1                    py37_1
testpath                  0.3.1                    py37_0
tk                        8.6.8                hfa6e2cd_0
toolz                     0.9.0                    py37_0
tornado                   5.1              py37hfa6e2cd_0
tqdm                      4.26.0           py37h28b3542_0
trackpy                   0.4.1                      py_1    conda-forge
traitlets                 4.3.2                    py37_0
twisted                   18.7.0           py37hfa6e2cd_1
unicodecsv                0.14.1                   py37_0
urllib3                   1.23                     py37_0
vc                        14.1                 h0510ff6_4
vs2015_runtime            14.15.26706          h3a45250_0
wcwidth                   0.1.7                    py37_0
webencodings              0.5.1                    py37_1
werkzeug                  0.14.1                   py37_0
wheel                     0.31.1                   py37_0
widgetsnbextension        3.4.1                    py37_0
win_inet_pton             1.0.1                    py37_1
win_unicode_console       0.5                      py37_0
wincertstore              0.2                      py37_0
winpty                    0.4.3                         4
wrapt                     1.10.11          py37hfa6e2cd_2
xlrd                      1.1.0                    py37_1
xlsxwriter                1.1.0                    py37_0
xlwings                   0.11.8                   py37_0
xlwt                      1.3.0                    py37_0
yaml                      0.1.7                hc54c509_2
yapf                      0.25.0                    <pip>
zeromq                    4.2.5                he025d50_1
zict                      0.1.3                    py37_0
zlib                      1.2.11               h8395fce_2
zope                      1.0                      py37_1
zope.interface            4.5.0            py37hfa6e2cd_0
rnrpereira commented 5 years ago

Hi Moritz,

Sure, I'll check phenopype... Thanks a lot... It's an amazing work, congrats!

PS. I have a lab in Brazil where we do experiments on behavior & electrophysiology of rat models of autism. But I have a friend collaborator who works in zebrafish. So, your tool may be very useful ! Thank you again for replying...

Em qua, 23 de jan de 2019 às 12:26, Moritz Lürig notifications@github.com escreveu:

Hi Rodrigo, thanks for getting in touch. I have discontinued the development of iso_track a while ago, but I am currently integrating it with other scripts I have written to form a coherent python package - have a look at https://github.com/mluerig/phenopype.

I have not yet integrated iso_track, but I probably will in the next few weeks, so I would just ask you to stay tuned until this works again.

As for the error; I wrote this code under python 3.7 with opencv 3.4.1, so you could try to roll back:

C:\Windows\system32>conda list

packages in environment at C:\Anaconda3:

Name Version Build Channel

_ipyw_jlab_nb_ext_conf 0.1.0 py37_0 alabaster 0.7.11 py37_0 anaconda 5.3.0 py37_0 anaconda-client 1.7.2 py37_0 anaconda-navigator 1.9.2 py37_0 anaconda-project 0.8.2 py37_0 appdirs 1.4.3 py37h28b3542_0 asn1crypto 0.24.0 py37_0 astroid 2.0.4 py37_0 astropy 3.0.4 py37hfa6e2cd_0 atomicwrites 1.2.1 py37_0 attrs 18.2.0 py37h28b3542_0 automat 0.7.0 py37_0 autopep8 1.4.3 babel 2.6.0 py37_0 backcall 0.1.0 py37_0 backports 1.0 py37_1 backports.shutil_get_terminal_size 1.0.0 py37_2 beautifulsoup4 4.6.3 py37_0 bitarray 0.8.3 py37hfa6e2cd_0 bkcharts 0.2 py37_0 blas 1.0 mkl blaze 0.11.3 py37_0 bleach 2.1.4 py37_0 blosc 1.14.4 he51fdeb_0 bokeh 0.13.0 py37_0 boto 2.49.0 py37_0 bottleneck 1.2.1 py37h452e1ab_1 bzip2 1.0.6 hfa6e2cd_5 ca-certificates 2018.03.07 0 certifi 2018.8.24 py37_1 cffi 1.11.5 py37h74b6da3_1 chardet 3.0.4 py37_1 click 6.7 py37_0 cloudpickle 0.5.5 py37_0 clyent 1.2.2 py37_1 colorama 0.3.9 py37_0 comtypes 1.1.7 py37_0 conda 4.5.11 py37_1000 conda-forge conda-build 3.15.1 py37_0 conda-env 2.6.0 h36134e3_1 console_shortcut 0.1.1 3 constantly 15.1.0 py37h28b3542_0 contextlib2 0.5.5 py37_0 cryptography 2.3.1 py37h74b6da3_0 curl 7.61.0 h7602738_0 cycler 0.10.0 py37_0 cython 0.28.5 py37h6538335_0 cytoolz 0.9.0.1 py37hfa6e2cd_1 dask 0.19.1 py37_0 dask-core 0.19.1 py37_0 datashape 0.5.4 py37_1 decorator 4.3.0 py37_0 defusedxml 0.5.0 py37_1 distributed 1.23.1 py37_0 docutils 0.14 py37_0 entrypoints 0.2.3 py37_2 et_xmlfile 1.0.1 py37_0 exifread 2.1.2 py_1 conda-forge fastcache 1.0.2 py37hfa6e2cd_2 filelock 3.0.8 py37_0 flask 1.0.2 py37_1 flask-cors 3.0.6 py37_0 freetype 2.9.1 ha9979f8_1 future 0.17.1 get_terminal_size 1.0.0 h38e98db_0 gevent 1.3.6 py37hfa6e2cd_0 git 2.19.1 h21ff451_1000 conda-forge glob2 0.6 py37_0 greenlet 0.4.15 py37hfa6e2cd_0 h5py 2.8.0 py37h3bdd7fb_2 hdf5 1.10.2 hac2f561_1 heapdict 1.0.0 py37_2 html5lib 1.0.1 py37_0 hyperlink 18.0.0 py37_0 icc_rt 2017.0.4 h97af966_0 icu 58.2 ha66f8fd_1 idna 2.7 py37_0 imageio 2.4.1 py37_0 imagesize 1.1.0 py37_0 incremental 17.5.0 py37_0 intel-openmp 2019.0 118 ipykernel 4.10.0 py37_0 ipython 6.5.0 py37_0 ipython_genutils 0.2.0 py37_0 ipywidgets 7.4.1 py37_0 isort 4.3.4 py37_0 itsdangerous 0.24 py37_1 jdcal 1.4 py37_0 jedi 0.12.1 py37_0 jinja2 2.10 py37_0 jpeg 9b hb83a4c4_2 jsonschema 2.6.0 py37_0 jupyter 1.0.0 py37_7 jupyter_client 5.2.3 py37_0 jupyter_console 5.2.0 py37_1 jupyter_core 4.4.0 py37_0 jupyterlab 0.34.9 py37_0 jupyterlab_launcher 0.13.1 py37_0 keyring 13.2.1 py37_0 kiwisolver 1.0.1 py37h6538335_0 lazy-object-proxy 1.3.1 py37hfa6e2cd_2 libcurl 7.61.0 h7602738_0 libiconv 1.15 h1df5818_7 libopencv 3.4.1 h875b8b8_3 libpng 1.6.34 h79bbb47_0 libsodium 1.0.16 h9d3ae62_0 libssh2 1.8.0 hd619d38_4 libtiff 4.0.9 h36446d0_2 libxml2 2.9.8 hadb2253_1 libxslt 1.1.32 hf6f1972_0 llvmlite 0.24.0 py37h6538335_0 locket 0.2.0 py37_1 lxml 4.2.5 py37hef2cd61_0 lzo 2.10 h6df0209_2 m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gmp 6.1.0 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 markupsafe 1.0 py37hfa6e2cd_1 matplotlib 2.2.3 py37hd159220_0 mccabe 0.6.1 py37_1 menuinst 1.4.14 py37hfa6e2cd_0 mistune 0.8.3 py37hfa6e2cd_1 mkl 2019.0 118 mkl-service 1.1.2 py37hb217b18_5 mkl_fft 1.0.4 py37h1e22a9b_1 mkl_random 1.0.1 py37h77b88f5_1 more-itertools 4.3.0 py37_0 mpmath 1.0.0 py37_2 msgpack-python 0.5.6 py37he980bc4_1 msys2-conda-epoch 20160418 1 multipledispatch 0.6.0 py37_0 navigator-updater 0.2.1 py37_0 nbconvert 5.4.0 py37_1 nbformat 4.4.0 py37_0 networkx 2.1 py37_0 nltk 3.3.0 py37_0 nose 1.3.7 py37_2 notebook 5.6.0 py37_0 numba 0.39.0 py37h830ac7b_0 numexpr 2.6.8 py37h9ef55f4_0 numpy 1.15.1 py37ha559c80_0 numpy-base 1.15.1 py37h8128ebf_0 numpydoc 0.8.0 py37_0 odo 0.5.1 py37_0 olefile 0.46 py37_0 opencv 3.4.1 py37h6fd60c2_3 openpyxl 2.5.6 py37_0 openssl 1.0.2p hfa6e2cd_0 conda-forge packaging 17.1 py37_0 pandas 0.23.4 py37h830ac7b_0 pandoc 1.19.2.1 hb2460c7_1 pandocfilters 1.4.2 py37_1 parso 0.3.1 py37_0 partd 0.3.8 py37_0 path.py 11.1.0 py37_0 pathlib2 2.3.2 py37_0 patsy 0.5.0 py37_0 pep8 1.7.1 py37_0 phenopype 0.4.4 pickleshare 0.7.4 py37_0 pillow 5.2.0 py37h08bbbbd_0 pip 10.0.1 py37_0 pkginfo 1.4.2 py37_1 pluggy 0.7.1 py37h28b3542_0 ply 3.11 py37_0 prometheus_client 0.3.1 py37h28b3542_0 prompt_toolkit 1.0.15 py37_0 psutil 5.4.7 py37hfa6e2cd_0 py 1.6.0 py37_0 py-opencv 3.4.1 py37h1b0d24d_3 pyasn1 0.4.4 py37h28b3542_0 pyasn1-modules 0.2.2 py37_0 pycodestyle 2.4.0 py37_0 pycosat 0.6.3 py37hfa6e2cd_0 pycparser 2.18 py37_1 pycrypto 2.6.1 py37hfa6e2cd_9 pycurl 7.43.0.2 py37h74b6da3_0 pydocstyle 3.0.0 pyflakes 2.0.0 py37_0 pygments 2.2.0 py37_0 pylint 2.1.1 py37_0 pyodbc 4.0.24 py37h6538335_0 pyopenssl 18.0.0 py37_0 pyparsing 2.2.0 py37_1 pyqt 5.9.2 py37h6538335_2 pysocks 1.6.8 py37_0 pytables 3.4.4 py37he6f6034_0 pytest 3.8.0 py37_0 pytest-arraydiff 0.2 py37h39e3cac_0 pytest-astropy 0.4.0 py37_0 pytest-doctestplus 0.1.3 py37_0 pytest-openfiles 0.3.0 py37_0 pytest-remotedata 0.3.0 py37_0 python 3.7.0 hea74fb7_0 python-dateutil 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-- Rodrigo Neves Romcy Pereira, PhD Associate Professor Brain Institute Federal University of Rio Grande do Norte Natal - RN, Brazil phone: +55 (84)3215-4592 email: rnrpereira@neuro.ufrn.br rnrpereira@neuro.ufrn.br

mluerig commented 5 years ago

thanks for your feedback, glad it's useful to someone. if you or you colleague have questions don't hestitate to get in touch