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  • 02:26
    kushalkolar commented #31
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  • Dec 01 17:31
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  • Dec 01 12:25
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  • Dec 01 12:24
    kushalkolar commented #36
Kushal Kolar
@kushalkolar
try pip install opencv-contrib-python~=3.4.1
smsadegh
@smsadegh
sorry fir not getting back to you. Was taken by some visits
after running.: pip install opencv-contrib-python~=3.4.1
and then again running (in MESmerize directory): pip install -r requirements.txt
I get the same error message:
...Collecting matplotlib==2.1.2
Using cached matplotlib-2.1.2.tar.gz (36.2 MB)
ERROR: Could not find a version that satisfies the requirement opencv-contrib-python==3.4.1.15 (from -r requirements.txt (line 10)) (from versions: 3.4.2.16, 3.4.2.17, 3.4.3.18, 3.4.4.19, 3.4.5.20, 3.4.8.29, 3.4.9.31, 3.4.9.33, 4.0.0.21, 4.0.1.24, 4.1.0.25, 4.1.1.26, 4.1.2.30, 4.2.0.32, 4.2.0.34)
ERROR: No matching distribution found for opencv-contrib-python==3.4.1.15 (from -r requirements.txt (line 10))
Kushal Kolar
@kushalkolar
if you install the available version of opencv-contrib after installing the other requirements that's fine
rem7101
@rem7101
Hello - I appear to be having similar issues as smsadegh - I am trying to install on a Mac version 10.14.6 - I have the full readout pasted here below:

Last login: Sat May 16 11:47:55 on ttys000
(base) macbook-pro-4:~ user1$ conda create --name mesmerize python=3.6
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /anaconda3/envs/mesmerize

added / updated specs:

- python=3.6

The following NEW packages will be INSTALLED:

ca-certificates pkgs/main/osx-64::ca-certificates-2020.1.1-0
certifi pkgs/main/osx-64::certifi-2020.4.5.1-py36_0
libcxx pkgs/main/osx-64::libcxx-10.0.0-1
libedit pkgs/main/osx-64::libedit-3.1.20181209-hb402a30_0
libffi pkgs/main/osx-64::libffi-3.3-h0a44026_1
ncurses pkgs/main/osx-64::ncurses-6.2-h0a44026_1
openssl pkgs/main/osx-64::openssl-1.1.1g-h1de35cc_0
pip pkgs/main/osx-64::pip-20.0.2-py36_3
python pkgs/main/osx-64::python-3.6.10-hf48f09d_2
readline pkgs/main/osx-64::readline-8.0-h1de35cc_0
setuptools pkgs/main/osx-64::setuptools-46.0.0-py36_0
sqlite pkgs/main/osx-64::sqlite-3.31.1-h5c1f38d_1
tk pkgs/main/osx-64::tk-8.6.8-ha441bb4_0
wheel pkgs/main/osx-64::wheel-0.34.2-py36_0
xz pkgs/main/osx-64::xz-5.2.5-h1de35cc_0
zlib pkgs/main/osx-64::zlib-1.2.11-h1de35cc_3

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#

To activate this environment, use

#

$ conda activate mesmerize

#

To deactivate an active environment, use

#

$ conda deactivate

(base) macbook-pro-4:~ user1$ conda activate mesmerize
(mesmerize) macbook-pro-4:~ user1$ conda install cython numpy pandas
Collecting package metadata (current_repodata.json): done
Solving environment: done

Package Plan

environment location: /anaconda3/envs/mesmerize

added / updated specs:

- cython
- numpy
- pandas

The following NEW packages will be INSTALLED:

blas pkgs/main/osx-64::blas-1.0-mkl
cython pkgs/main/osx-64::cython-0.29.17-py36h0a44026_0
intel-openmp pkgs/main/osx-64::intel-openmp-2019.4-233
libgfortran pkgs/main/osx-64::libgfortran-3.0.1-h93005f0_2
mkl pkgs/main/osx-64::mkl-2019.4-233
mkl-service pkgs/main/osx-64::mkl-service-2.3.0-py36hfbe908c_0
mkl_fft pkgs/main/osx-64::mkl_fft-1.0.15-py36h5e564d8_0
mkl_random pkgs/main/osx-64::mkl_random-1.1.0-py36ha771720_0
numpy pkgs/main/osx-64::numpy-1.18.1-py36h7241aed_0
numpy-base pkgs/main/osx-64::numpy-base-1.18.1-py36h6575580_1
pandas pkgs/main/osx-64::pandas-1.0.3-py36h6c726b0_0
python-dateutil pkgs/main/noarch::python-dateutil-2.8.1-py_0
pytz pkgs/main/noarch::pytz-2020.1-py_0
six pkgs/main/osx-64::six-1.14.0-py36_0

Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(mesmerize) macbook-pro-4:~ user1$ git clond https://github.com/kushalkolar/MESmerize.git
git: 'clond' is not a git command. See 'git --help'.

The most similar command is
clone
(mesmerize) macbook-pro-4:~ user1$ git clone https://github.com/kushalkolar/MESmerize.git
Cloning into 'MESmerize'...
remote: Enumerating objects: 881, done.
remote: Counting objects: 100% (881/881), done.
remote: Compressing objects: 100% (645/645), done.
remote: Total 11621 (delta 503), reused 513 (delta 211), pack-reused 10740
Receiving objects: 100% (11621/11621), 299.72 MiB | 12.83 MiB/s, done.
Resolving deltas: 100% (7651/7651), done.
Checking out files: 100% (1198/1198), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

'mesmerize/plotting/colormaps/Spectral.png'
'mesmerize/plotting/colormaps/spectral.png'
'mesmerize/plotting/widgets/colormaps/Spectral.png'
'mesmerize/plotting/widgets/colormaps/spectral.png'

(mesmerize) macbook-pro-4:~ user1$ cd MESmerize
(mesmerize) macbook-pro-4:MESmerize user1$ git checkout snap
M mesmerize/plotting/colormaps/Spectral.png
M mesmerize/plotting/widgets/colormaps/Spectral.png
Branch 'snap' set up to track remote branch 'snap' from 'origin'.
Switched to a new branch 'snap'
(mesmerize) macbook-pro-4:MESmerize user1$ pip install -r requirements.txt
Collecting cycler==0.10.0
Using cached cycler-0.10.0-py2.py3-none-any.whl (6.5 kB)
Collecting dask==1.1.1
Using cached dask-1.1.1-py2.py3-none-any.whl (701 kB)
Processing /Users/user1/Library/Caches/pip/wheels/c4/f0/e2/8e4ecc9e1b12a428a7657ba683576d3e79d0a75982f63e8fd2/future-0.17.1-py3-none-any.whl
Collecting h5py==2.9.0
Using cached h5py-2.9.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (6.3 MB)
Collecting hickle==3.4.3
Using cached hickle-3.4.3-py3-none-any.whl (40 kB)
Collecting ipython==7.3.0
Using cached ipython-7.3.0-py3-none-any.whl (768 kB)
Collecting ipyparallel==6.2.3
Using cached ipyparallel-6.2.3-py2.py3-none-any.whl (197 kB)
Collecting MarkupSafe==1.1.1
Using cached MarkupSafe-1.1.1-cp36-cp36m-macosx_10_6_intel.whl (18 kB)
Collecting matplotlib==2.1.2
Using cached matplotlib-2.1.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.2 MB)
Collecting opencv-contrib-python==3.4.1.15
Using cached opencv_contrib_python-3.4.1.15-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (47.4 MB)
Collecting opencv-python==3.4.1.15
Using cached opencv_python-3.4.1.15-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (41.9 MB)
Collecting pandas==0.25.3
Using cached pandas-0.25.3-cp36-cp36m-macosx_10_9_x86_64.whl (10.4 MB)
Collecting Pillow==5.4.1
Using cached Pillow-5.4.1-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.7 MB)
Processing /Users/user1/Library/Caches/pip/wheels/55/d9/6e/753ea9b05c8842e1f8d3d745713226395aaa7090b27a4e6293/psutil-5.5.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting PyQt5==5.9.2
Using cached PyQt5-5.9.2-5.9.3-cp35.cp36.cp37-abi3-macosx_10_6_intel.whl (81.7 MB)
Collecting QtPy==1.6.0
Using cached QtPy-1.6.0-py2.py3-none-any.whl (43 kB)
Collecting scikit-image==0.14.2
Using cached scikit_image-0.14.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (28.9 MB)
Collecting scikit-learn==0.20.3
Using cached scikit_learn-0.20.3-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (8.0 MB)
Collecting scipy==1.3.0
Using cached scipy-1.3.0-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (27.7 MB)
Collecting seaborn==0.9.0
Using cached seaborn-0.9.0-py3-none-any.whl (208 kB)
Processing /Users/user1/Library/Caches/pip/wheels/23/9d/42/5ec745cbbb17517000a53cecc49d6a865450d1f5cb16dc8a9c/sklearn-0.0-py2.py3-none-any.whl
Collecting spyder==3.3.3
Using cached spyder-3.3.3-py3-none-any.whl (2.8 MB)
Collecting tifffile==0.15.1
Using cached tifffile-0.15.1-cp36-cp36m-macosx_10_7_x86_64.whl (116 kB)
Collecting tqdm==4.37.0
Using cached tqdm-4.37.0-py2.py3-none-any.whl (53 kB)
Processing /Users/user1/Library/Caches/pip/wheels/f4/16/80/410b5e600f73d21e3cc507ecc5bb970998db55084e3d38fdf4/PeakUtils-1.3.2-py3-none-any.whl
Collecting tables==3.5.2
Using cached tables-3.5.2-cp36-cp36m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (4.4 MB)
Collecting joblib==0.13.2
Using cached joblib-0.13.2-py2.py3-none-any.whl (278 kB)
Collecting graphviz==0.13
Using cached graphviz-0.13-py2.py3-none-any.whl (17 kB)
Collecting numba==0.42.1
Using cached numba-0.42.1-cp36-cp36m-macosx_10_9_x86_64.whl (1.6 MB)
Processing /Users/user1/Library/Caches/pip/wheels/66/97/1a/1df12a9b145ec52cfc551ab4ae669c8eb6ed5e18aefc751ec7/Bottleneck-1.2.1-cp36-cp36m-macosx_10_9_x86_64.whl
Requirement already satisfied: six in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from cycler==0.10.0->-r requirements.txt (line 1)) (1.14.0)
Requirement already satisfied: numpy>=1.7 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from h5py==2.9.0->-r requirements.txt (line 4)) (1.18.1)
Collecting pickleshare
Using cached pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
Collecting appnope; sys_platform == "darwin"
Using cached appnope-0.1.0-py2.py3-none-any.whl (4.0 kB)
Collecting jedi>=0.10
Using cached jedi-0.17.0-py2.py3-none-any.whl (1.1 MB)
Requirement already satisfied: setuptools>=18.5 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipython==7.3.0->-r requirements.txt (line 6)) (46.0.0.post20200309)
Collecting traitlets>=4.2
Using cached traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
Processing /Users/user1/Library/Caches/pip/wheels/b4/cb/f1/d142b3bb45d488612cf3943d8a1db090eb95e6687045ba61d1/backcall-0.1.0-py3-none-any.whl
Collecting prompt-toolkit<2.1.0,>=2.0.0
Using cached prompt_toolkit-2.0.10-py3-none-any.whl (340 kB)
Collecting pygments
Using cached Pygments-2.6.1-py3-none-any.whl (914 kB)
Collecting decorator
Using cached decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
Collecting pexpect; sys_platform != "win32"
Using cached pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
Processing /Users/user1/Library/Caches/pip/wheels/37/a7/db/2d592e44029ef817f3ef63ea991db34191cebaef087a96f505/tornado-6.0.4-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting ipython-genutils
Using cached ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
Collecting ipykernel>=4.4
Using cached ipykernel-5.2.1-py3-none-any.whl (118 kB)
Requirement already satisfied: python-dateutil>=2.1 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from ipyparallel==6.2.3->-r requirements.txt (line 7)) (2.8.1)
Collecting jupyter-client
Using cached jupyter_client-6.1.3-py3-none-any.whl (106 kB)
Collecting pyzmq>=13
Using cached pyzmq-19.0.1-cp36-cp36m-macosx_10_9_intel.whl (1.4 MB)
Requirement already satisfied: pytz in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from matplotlib==2.1.2->-r requirements.txt (line 9)) (2020.1)
Collecting pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1
Using cached pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
Collecting sip<4.20,>=4.19.4
Using cached sip-4.19.8-cp36-cp36m-macosx_10_6_intel.whl (51 kB)
Collecting PyWavelets>=0.4.0
Using cached PyWavelets-1.1.1-cp36-cp36m-macosx_10_9_x86_64.whl (4.3 MB)
Collecting networkx>=1.8
Using cached networkx-2.4-py3-none-any.whl (1.6 MB)
Collecting cloudpickle>=0.2.1
Using cached cloudpickle-1.4.1-py3-none-any.whl (26 kB)
Collecting qtconsole>=4.2.0
Using cached qtconsole-4.7.4-py2.py3-none-any.whl (118 kB)
Collecting qtawesome>=0.4.1
Using cached QtAwesome-0.7.2-py2.py3-none-any.whl (832 kB)
Collecting nbconvert
Using cached nbconvert-5.6.1-py2.py3-none-any.whl (455 kB)
Collecting pyflakes
Using cached pyflakes-2.2.0-py2.py3-none-any.whl (66 kB)
Collecting sphinx
Using cached Sphinx-3.0.3-py3-none-any.whl (2.8 MB)
Collecting pycodestyle
Using cached pycodestyle-2.6.0-py2.py3-none-any.whl (41 kB)
Processing /Users/user1/Library/Caches/pip/wheels/7a/97/5e/6885d024ee585fe437a65cc815cbdb10b810ceaa65242ccbea/numpydoc-0.9.2-py3-none-any.whl
Processing /Users/user1/Library/Caches/pip/wheels/f1/90/67/ebd231ce083da4fd4ca67684aa2f0b0e45b135d321335f8598/rope-0.17.0-py3-none-any.whl
Collecting keyring; sys_platform != "linux2"
Using cached keyring-21.2.1-py3-none-any.whl (31 kB)
Collecting pylint
Using cached pylint-2.5.2-py3-none-any.whl (324 kB)
Collecting spyder-kernels<1.0,>=0.4.2
Using cached spyder_kernels-0.5.2-py2.py3-none-any.whl (42 kB)
Collecting chardet>=2.0.0
Using cached chardet-3.0.4-py2.py3-none-any.whl (133 kB)
Collecting mock>=2.0
Using cached mock-4.0.2-py3-none-any.whl (28 kB)
Collecting numexpr>=2.6.2
Using cached numexpr-2.7.1-cp36-cp36m-macosx_10_6_intel.whl (185 kB)
Collecting llvmlite>=0.27.0dev0
Using cached llvmlite-0.32.1-cp36-cp36m-macosx_10_9_x86_64.whl (15.9 MB)
Collecting parso>=0.7.0
Using cached parso-0.7.0-py2.py3-none-any.whl (100 kB)
Collecting wcwidth
Using cached wcwidth-0.1.9-py2.py3-none-any.whl (19 kB)
Collecting ptyprocess>=0.5
Using cached ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
Collecting jupyter-core>=4.6.0
Using cached jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB)
Collecting entrypoints>=0.2.2
Using cached entrypoints-0.3-py2.py3-none-any.whl (11 kB)
Collecting mistune<2,>=0.8.1
Using cached mistune-0.8.4-py2.py3-none-any.whl (16 kB)
Collecting nbformat>=4.4
Using cached nbformat-5.0.6-py3-none-any.whl (170 kB)
Collecting testpath
Using cached testpath-0.4.4-py2.py3-none-any.whl (163 kB)
Collecting defusedxml
Using cached defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
Collecting bleach
Using cached bleach-3.1.5-py2.py3-none-any.whl (151 kB)
Processing /Users/user1/Library/Caches/pip/wheels/46/c4/40/718c6fd14c2129ccaee10e0cf03ef6c4d01d98cad5dbbfda38/pandocfilters-1.4.2-py3-none-any.whl
Collecting jinja2>=2.4
Using cached Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
Collecting sphinxcontrib-applehelp
Using cached sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl (121 kB)
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Using cached sphinxcontrib_jsmath-1.0.1-py2.py3-none-any.whl (5.1 kB)
Collecting babel>=1.3
Using cached Babel-2.8.0-py2.py3-none-any.whl (8.6 MB)
Collecting packaging
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Collecting sphinxcontrib-qthelp
Using cached sphinxcontrib_qthelp-1.0.3-py2.py3-none-any.whl (90 kB)
Collecting requests>=2.5.0
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Collecting alabaster<0.8,>=0.7
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Collecting snowballstemmer>=1.1
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Collecting importlib-metadata; python_version < "3.8"
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Using cached astroid-2.4.1-py3-none-any.whl (214 kB)
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Using cached wurlitzer-2.0.0-py2.py3-none-any.whl (6.0 kB)
Collecting jsonschema!=2.5.0,>=2.4
Using cached jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
Collecting webencodings
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Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1
Using cached urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
Collecting idna<3,>=2.5
Using cached idna-2.9-py2.py3-none-any.whl (58 kB)
Requirement already satisfied: certifi>=2017.4.17 in /anaconda3/envs/mesmerize/lib/python3.6/site-packages (from requests>=2.5.0->sphinx->spyder==3.3.3->-r requirements.txt (line 22)) (2020.4.5.1)
Collecting zipp>=0.5
Using cached zipp-3.1.0-py3-none-any.whl (4.9 kB)
Processing /Users/user1/Library/Caches/pip/wheels/32/42/7f/23cae9ff6ef66798d00dc5d659088e57dbba01566f6c60db63/wrapt-1.12.1-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting typed-ast<1.5,>=1.4.0; implementation_name == "cpython" and python_version < "3.8"
Using cached typed_ast-1.4.1-cp36-cp36m-macosx_10_9_x86_64.whl (223 kB)
rem7101
@rem7101
Processing /Users/user1/Library/Caches/pip/wheels/74/16/66/f3b601fb6040a9bbc1652bf154faa76f51a84e2f6f850cb7bd/lazy_object_proxy-1.4.3-cp36-cp36m-macosx_10_9_x86_64.whl
Processing /Users/user1/Library/Caches/pip/wheels/d1/8a/1c/32ab9017418a2c64e4fbaf503c08648bed2f8eb311b869a464/pyrsistent-0.16.0-cp36-cp36m-macosx_10_9_x86_64.whl
Collecting attrs>=17.4.0
Using cached attrs-19.3.0-py2.py3-none-any.whl (39 kB)
Installing collected packages: cycler, dask, future, h5py, hickle, pickleshare, appnope, parso, jedi, ipython-genutils, decorator, traitlets, backcall, wcwidth, prompt-toolkit, pygments, ptyprocess, pexpect, ipython, tornado, jupyter-core, pyzmq, jupyter-client, ipykernel, ipyparallel, MarkupSafe, pyparsing, matplotlib, opencv-contrib-python, opencv-python, pandas, Pillow, psutil, sip, PyQt5, QtPy, scipy, PyWavelets, networkx, cloudpickle, scikit-image, scikit-learn, seaborn, sklearn, qtconsole, qtawesome, entrypoints, mistune, pyrsistent, zipp, importlib-metadata, attrs, jsonschema, nbformat, testpath, defusedxml, webencodings, packaging, bleach, pandocfilters, jinja2, nbconvert, pyflakes, sphinxcontrib-applehelp, sphinxcontrib-jsmath, babel, sphinxcontrib-qthelp, urllib3, idna, chardet, requests, alabaster, docutils, imagesize, sphinxcontrib-serializinghtml, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, snowballstemmer, sphinx, pycodestyle, numpydoc, rope, keyring, mccabe, toml, isort, wrapt, typed-ast, lazy-object-proxy, astroid, pylint, wurlitzer, spyder-kernels, spyder, tifffile, tqdm, PeakUtils, mock, numexpr, tables, joblib, graphviz, llvmlite, numba, bottleneck
Attempting uninstall: pandas
Found existing installation: pandas 1.0.3
Uninstalling pandas-1.0.3:
Successfully uninstalled pandas-1.0.3
Successfully installed MarkupSafe-1.1.1 PeakUtils-1.3.2 Pillow-5.4.1 PyQt5-5.9.2 PyWavelets-1.1.1 QtPy-1.6.0 alabaster-0.7.12 appnope-0.1.0 astroid-2.4.1 attrs-19.3.0 babel-2.8.0 backcall-0.1.0 bleach-3.1.5 bottleneck-1.2.1 chardet-3.0.4 cloudpickle-1.4.1 cycler-0.10.0 dask-1.1.1 decorator-4.4.2 defusedxml-0.6.0 docutils-0.16 entrypoints-0.3 future-0.17.1 graphviz-0.13 h5py-2.9.0 hickle-3.4.3 idna-2.9 imagesize-1.2.0 importlib-metadata-1.6.0 ipykernel-5.2.1 ipyparallel-6.2.3 ipython-7.3.0 ipython-genutils-0.2.0 isort-4.3.21 jedi-0.17.0 jinja2-2.11.2 joblib-0.13.2 jsonschema-3.2.0 jupyter-client-6.1.3 jupyter-core-4.6.3 keyring-21.2.1 lazy-object-proxy-1.4.3 llvmlite-0.32.1 matplotlib-2.1.2 mccabe-0.6.1 mistune-0.8.4 mock-4.0.2 nbconvert-5.6.1 nbformat-5.0.6 networkx-2.4 numba-0.42.1 numexpr-2.7.1 numpydoc-0.9.2 opencv-contrib-python-3.4.1.15 opencv-python-3.4.1.15 packaging-20.3 pandas-0.25.3 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-2.0.10 psutil-5.5.1 ptyprocess-0.6.0 pycodestyle-2.6.0 pyflakes-2.2.0 pygments-2.6.1 pylint-2.5.2 pyparsing-2.4.7 pyrsistent-0.16.0 pyzmq-19.0.1 qtawesome-0.7.2 qtconsole-4.7.4 requests-2.23.0 rope-0.17.0 scikit-image-0.14.2 scikit-learn-0.20.3 scipy-1.3.0 seaborn-0.9.0 sip-4.19.8 sklearn-0.0 snowballstemmer-2.0.0 sphinx-3.0.3 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.4 spyder-3.3.3 spyder-kernels-0.5.2 tables-3.5.2 testpath-0.4.4 tifffile-0.15.1 toml-0.10.1 tornado-6.0.4 tqdm-4.37.0 traitlets-4.3.3 typed-ast-1.4.1 urllib3-1.25.9 wcwidth-0.1.9 webencodings-0.5.1 wrapt-1.12.1 wurlitzer-2.0.0 zipp-3.1.0
(mesmerize) macbook-pro-4:MESmerize user1$ CFLAGS='-stdlib=libc++' python setup.py build_ext -i
running build_ext
cythoning tslearn/cygak.pyx to tslearn/cygak.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cygak.pyx

tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cysax.pyx to tslearn/cysax.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cysax.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/cycc.pyx to tslearn/cycc.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/cycc.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
cythoning tslearn/soft_dtw_fast.pyx to tslearn/soft_dtw_fast.c
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/Cython/Compiler/Main.py:369: FutureWarning: Cython directive 'language_level' not set, using 2 for now (Py2). This will change in a later release! File: /Users/user1/MESmerize/tslearn/soft_dtw_fast.pyx
tree = Parsing.p_module(s, pxd, full_module_name)
skipping 'caiman/source_extraction/cnmf/oasis.cpp' Cython extension (up-to-date)
building 'tslearn.cygak' extension
creating build
creating build/temp.macosx-10.9-x86_64-3.6
creating build/temp.macosx-10.9-x86_64-3.6/tslearn
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cygak.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o
In file included from tslearn/cygak.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning:
"Using deprecated NumPy API, disable it with " "#define
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

^
1 warning generated.
gcc -bundle -undefined dynamic_lookup -L/anaconda3/envs/mesmerize/lib -arch x86_64 -L/anaconda3/envs/mesmerize/lib -arch x86_64 -stdlib=libc++ -arch x86_64 build/temp.macosx-10.9-x86_64-3.6/tslearn/cygak.o -o /Users/user1/MESmerize/tslearn/cygak.cpython-36m-darwin.so
building 'tslearn.cysax' extension
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include -I/anaconda3/envs/mesmerize/include/python3.6m -c tslearn/cysax.c -o build/temp.macosx-10.9-x86_64-3.6/tslearn/cysax.o
In file included from tslearn/cysax.c:600:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:
/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning:
"Using deprecated NumPy API, disable it with " "#define
NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]

warning "Using deprecated NumPy API, disable it with " \

^
1 warning generated.

Kushal Kolar
@kushalkolar
Can you please use the issue tracker for this? Thanks!
And put the outputs into codeblocks so the markdown doesn't format it weirdly :)
rem7101
@rem7101
sorry - I am new to all this - could you please direct me to the issue tracker?
rem7101
@rem7101
thanks
maxrioux100
@maxrioux100
Hello
I am trying to use Mesmerize and cant seem to make it work
First of all: Do we need to install bokeh in our env ? because it isnt in the requirements or in the installation page and it can't seem to work without it
Kushal Kolar
@kushalkolar
No you don't need bokeh
maxrioux100
@maxrioux100
I just ignore the bokeh can't load message ?
Kushal Kolar
@kushalkolar
Yes
maxrioux100
@maxrioux100
btw thanks Kushal it looks amazing (Mesmerize)
Kushal Kolar
@kushalkolar
No worries. If you have more questions don't hesitate
maxrioux100
@maxrioux100
Im on ubuntu and tried both install method and I cant complete motion correction on both
Kushal Kolar
@kushalkolar
Can you use the issue tracker for this
maxrioux100
@maxrioux100
On github ?
Kushal Kolar
@kushalkolar
Yup
maxrioux100
@maxrioux100
Alright
Kushal Kolar
@kushalkolar
Thanks
mbandet
@mbandet
Hi Kushal, I'm currently using Mesmerize to open a tif, and opening manually defined ROIs in order to have data to work with within Mesmerize. I'm wondering whether there is a way to apply Fissa (https://www.nature.com/articles/s41598-018-21640-2) onto the data for use with Mesmerize?
Kushal Kolar
@kushalkolar
I took a quick look at it and it may be possible. If you install it in the same environment as Mesmerize you can use it through the console.

You can access the image data through the viewer work environment in the viewer console.

See the "Splice img seq" example to see how to access, change or update the image data in the viewer work environment. http://mesmerizelab.org/user_guides/viewer/overview.html#splice-img-seq

Here are examples for how to access the ROI data using the ROI mananger via the viewer console http://mesmerizelab.org/user_guides/viewer/modules/roi_manager.html#console
Simon Daste
@sdaste_gitlab
Hi Kushal: I hd the Matplotlib issue and run the command you provided but I cannot open Mesmerize, I get the following (and long error messages)
(mesmerize) sdaste@MacBook-Pro ~ % export PYTHONPATH=/Users/sdaste/MESmerize
(mesmerize) sdaste@MacBook-Pro ~ % python /Users/sdaste/MESmerize/mesmerize
Loading, please wait...
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #2
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #3
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #4
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:962: UserWarning: Duplicate key in file "/Users/sdaste/.matplotlib/matplotlibrc", line #5
(fname, cnt))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/matplotlib/init.py:997: UserWarning: Bad val "qt5" on line #5
"backend: qt5
"
in file "/Users/sdaste/.matplotlib/matplotlibrc"
Key backend: Unrecognized backend string "qt5": valid strings are ['GTK', 'GTKAgg', 'GTKCairo', 'MacOSX', 'Qt4Agg', 'Qt5Agg', 'TkAgg', 'WX', 'WXAgg', 'GTK3Cairo', 'GTK3Agg', 'WebAgg', 'nbAgg', 'agg', 'cairo', 'gdk', 'pdf', 'pgf', 'ps', 'svg', 'template']
(val, error_details, msg))
/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/dask/config.py:168: YAMLLoadWarning: calling yaml.load() without Loader=... is deprecated, as the default Loader is unsafe. Please read https://msg.pyyaml.org/load for full details.
data = yaml.load(f.read()) or {}
===== 2020.07.01 23:07:39 =====
Traceback (most recent call last):
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/Users/sdaste/MESmerize/mesmerize/main.py", line 17, in <module>
from mesmerize.common.window_manager import WindowManager
File "/Users/sdaste/MESmerize/mesmerize/init.py", line 1, in <module>
from .analysis import
File "/Users/sdaste/MESmerize/mesmerize/analysis/init.py", line 3, in <module>
from .math import cross_correlation, drfft_dtw, tvregdiff
File "/Users/sdaste/MESmerize/mesmerize/analysis/math/drfft_dtw.py", line 7, in <module>
from ...plotting.variants.timeseries import TimeseriesPlot
File "/Users/sdaste/MESmerize/mesmerize/plotting/init.py", line 2, in <module>
from .widgets import

File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/init.py", line 3, in <module>
from .kshape import KShapeWidget
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/init.py", line 1, in <module>
from .widget import KShapeWidget
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/widget.py", line 13, in <module>
from . import kshape_process
File "/Users/sdaste/MESmerize/mesmerize/plotting/widgets/kshape/kshape_process.py", line 13, in <module>
from tslearn.clustering import KShape
File "/Users/sdaste/MESmerize/tslearn/clustering.py", line 16, in <module>
from tslearn.metrics import cdist_gak, cdist_dtw, cdist_soft_dtw, \
File "/Users/sdaste/MESmerize/tslearn/metrics.py", line 26, in <module>
@njit()
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/decorators.py", line 174, in wrapper
**dispatcher_args)
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/dispatcher.py", line 539, in init
self.targetctx = self.targetdescr.target_context
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/targets/registry.py", line 50, in target_context
return self._toplevel_target_context
File "/Users/sdaste/anaconda3/envs/mesmerize/lib/python3.6/site-packages/numba/utils.py", line 353, in get
res
Any idea what it could be ? many thanks!!
Kushal Kolar
@kushalkolar
@sdaste_gitlab thanks for telling me about this. Could you please post this on the issue tracker on GitHub? Also hard to read tracebacks in gitter
Instructions installation for v0.2 aren't up yet btw for Mac and Linux, might be a library issue so it'd still be great if you could post this on the issue tracker
Kushal Kolar
@kushalkolar
Hi everyone, video tutorials for Mesmerize are finally available! Links are here: https://github.com/kushalkolar/MESmerize#video-tutorials
Serapio M. Baca
@smbaca
Are there updated instructions for the mac/Anaconda install? I have caiman running fine in another environment but I get this error trying to install mesmerize with pip: (mesmerize)% pip install mesmerize
ERROR: Could not find a version that satisfies the requirement mesmerize (from versions: none)
ERROR: No matching distribution found for mesmerize
Kushal Kolar
@kushalkolar
try updating pip wheel & setuptools
5 replies
pip install --upgrade pip setuptools wheel
Eric Melonakos
@emelon8
Hi all, can Mesmerize import .avi files into the viewer for analysis? I saw this video (https://www.youtube.com/watch?v=a1UO2-OhIHw), so I know it's possible with some custom code, but I was wondering if it was already supported through the GUI.
Kushal Kolar
@kushalkolar
you can open an .avi video file as a numpy array using skvideo and then follow the rest here to load it in the Viewer. http://docs.mesmerizelab.org/en/master/user_guides/viewer/overview.html#open-image
you can use skvideo.io.vread, make sure to set as_grey to True http://www.scikit-video.org/stable/modules/generated/skvideo.io.vread.html#skvideo.io.vread
Kushal Kolar
@kushalkolar

We are holding a Mesmerize workshop on Dec 1st & Dec 2nd. For more informtaion please see:
https://www.janelia.org/sites/default/files/You%20%2B%20Janelia/Conferences/22.pdf

Register for the workshop by Nov 20 here:
https://www.janelia.org/you-janelia/conferences/from-images-to-knowledge-with-imagej-friends