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##### Activity
• Sep 18 17:21
auag92 synchronize #522
• Sep 18 14:03
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• Sep 08 17:42

wd15 on master

docs: add conda-forge to instal… ci(circle): add conda-forge bui… docs(notebooks): relax testing … and 1 more (compare)

• Sep 08 17:42
wd15 closed #521
• Sep 08 17:41
wd15 commented #521
auag92
@auag92
Okay... then I will work on the two point stats workflow and push it to you for review
Daniel Wheeler
@wd15
I think I know what I need to do. We're not doing much CNN then?
Which is fine as we have a ton of work
auag92
@auag92
Yeah, let's conclude this so we can wrap it into a paper
I have been tinkering with CNNs using keras-tensorflow on the sidelines-- will show results once I am there. We can take that as the next project after wrapping up pymks update.
Daniel Wheeler
@wd15
ok, we have a lot to do over the summer, I just need to get started
anything esle?
auag92
@auag92
yeah... looking forward to it
Also... I would be presenting a poster
at MLSE2018 conference in Carnegie Mellon on PyMKS
It's from 6th to 8th of June - will share the poster for review by last week of May.
Daniel Wheeler
@wd15
ok, very cool, happy to review
auag92
@auag92
thanks... that's all from my end for now
Daniel Wheeler
@wd15
I won't see you much for that first week of your visit as I'm out on June 4 and 5 so we'll start properly the following week
auag92
@auag92
Cool...then I will directly come by to office on the Monday of the following week--- I have cluster access so I will continue working from home
Daniel Wheeler
@wd15
ok, that makes sense
that's all then
auag92
@auag92
yeps... good day
A. M. Jokisaari
@amjokisaari
hi Daniel & company... I'm pondering doing two-point statistics on a 3D microstructure (data is in exodus file format). can I do this with PyMKS?
Daniel Wheeler
@wd15
@amjokisaari, Hi!. You could try using PyMKS. We'll see what the issues are. Firstly you'll need to get the data into a grid format in a Numpy array. This seems like a promising package for importing Exodus file formats into Numpy.
A. M. Jokisaari
@amjokisaari
@wd15 , ah okay, thanks! I was wondering about the data structure for PyMKS. the two-point correlation function would work in 3D, I'm assuming, but I'm wondering how it would be visualized. (In 2D you get the 2D graph, thinking of the first PyMKS example). Any thoughts?
Daniel Wheeler
@wd15
PyMKS is a very simple package. It's just some simple helper classes that manipulate numpy arrays. It doesn't do any visualization apart from some simple Matplotlib plots. PyMKS should work in 1D, 2D or 3D. I'm not sure about the best way to visualize 2-point correlations in 3D. It's probably better to do a dimensionality reduction and then create visualizations from the follow up data IMO.
A. M. Jokisaari
@amjokisaari
okay, I see, so I might want to pipeline the data into something else or do additional manipulation on it. I'll have to give it a try and report back.
Daniel Wheeler
@wd15
The 2-points stats themselves are not the final result, in general, but a stage in the process to more tractable data.
A. M. Jokisaari
@amjokisaari
I might just want that, though. I actually want to do exactly what's in the first example - showing anisotropy of some feature.
A. M. Jokisaari
@amjokisaari
thanks for the help!
Daniel Wheeler
@wd15
No worries, let me know if you get stuck.
Amir1361
@Amir1361
Hi Daniel, Please let me know that how can load my micro-structure image in PyMKS. Can I directly load it and use it? Also, please let me know when I built my process-structure link, how can I use it for prediction of new microstructure from new inputs? In fact I am looking for how it can produce microstructure with predicted principal components? Is it possible to predict microstructure? Thanks for your help!
Daniel Wheeler
@wd15

# November PyMKS Meeting

Please fill out the whenisgood when you get a chance

Daniel Wheeler
@wd15

# November PyMKS Meeting

WhenIsGood Results

Event: November PyMKS Meeting
Date: November 19, 2019
Time: 3:00:00 PM
Can make it: Amir Abbas Kazemzadeh, Apaar Shanker, Berkay Yucel, Berkay Yucel, Daniel Wheeler
Timezone: US/Eastern

US/Eastern
Date: November 19, 2019
Time: 3:00:00 PM
Invitees: Amir Abbas Kazemzadeh, Apaar Shanker, Berkay Yucel, Berkay Yucel, Daniel Wheeler

rik4
@shibashisG
Hi,
While running the homogenization_fiber_2D.ipynb notebook , i am getting the error: AttributeError: 'GridSearchCV' object has no attribute 'gridscores'
Daniel Wheeler
@wd15
Hi @rik4, can you let us know which version of PyMKS you are using? We haven't been keeping the "master" branch up to date. I would suggest using the "develop" branch of PyMKS as that's what we're currently maintaining. It will also be released soon.
Sorry, that's meant for @shibashisG
rik4
@shibashisG
Thanks, Daniel for your response, I am using the Master.
Would conda install -c conda-forge pymks install the develop branch?
Daniel Wheeler
@wd15
No, you need to clone the repository with git clone https://github.com/materialsinnovation/pymks.git; cd pymks; git checkout develop to get the develop branch.
There is an enivonment.yml file in the base of the repository that will create a pymks environment for you to work in. Use conda env create -f environment.yml; conda activate pymks to create that. You might need to run python setup.py develop in the base of the repository to get the correct version of pymks.
rik4
@shibashisG
Thanks, Daniel, Let me try
rik4
@shibashisG
HI, Daniel, I could now run all the notebooks successfully, thanks
It would be great if we share this installation info here: http://pymks.org/en/latest/rst/INSTALLATION.html
Daniel Wheeler
@wd15
@shibashisG glad that it worked out. We do need to update that. Hopefully, shortly that will be done.
Alexander_Konstantinidis
@AlexanderKonstantinidis
I just installed pymks on my Windows10 Notebook. I am running Anaconda 3 and Python 3.7. I have followed the instructions successfully using the pip install option. I can import pymks but I am getting an error when I try to execute the command: from pymks import (
generate_multiphase,
solve_fe,
plot_microstructures,
PrimitiveTransformer,
TwoPointCorrelation,
FlattenTransformer
). I am getting
*I am getting an error message, informing that these packages can not be imported from pymsk
Alexander_Konstantinidis
@AlexanderKonstantinidis

## Moreover all commands that involve importing something from fmks fail:

ModuleNotFoundError Traceback (most recent call last)

<ipython-input-4-03e6c46061c0> in <module>
1 from mpl_toolkits.mplot3d import Axes3D
2
----> 3 from pymks.fmks.data.multiphase import generate
4 from pymks.fmks.data.elastic_fe import solve
5 from pymks.fmks.plot import plot_microstructures

ModuleNotFoundError: No module named 'pymks.fmks'

Daniel Wheeler
@wd15
What happens when you do python -c "import pymks; print(pymks.__version__)"
Alexander_Konstantinidis
@AlexanderKonstantinidis
(tf2) C:\Users\Alienware\sfepy>python -c "import pymks; print(pymks.version)"
C:\Users\Alienware\Anaconda3\envs\tf2\lib\site-packages\numpy_distributor_init.py:32: UserWarning: loaded more than 1 DLL from .libs:
C:\Users\Alienware\Anaconda3\envs\tf2\lib\site-packages\numpy.libs\libopenblas.NOIJJG62EMASZI6NYURL6JBKM4EVBGM7.gfortran-win_amd64.dll