search

rosinality / knotter

Implementation of Mapper algorithm for Topological Data Analysis
MIT License
45 stars 13 forks source link

error installing #2

Open outlace opened 8 years ago

outlace commented 8 years ago

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/zt/qjk01pyj4hn34zyhq9h50r1c0000gn/T/pip-build-zXfvwJ/knotter

rosinality commented 8 years ago

Hmm I don't found any error in running egg_info command. Can you show me a full error messages or elaborate your situations?

outlace commented 8 years ago

Brandons-MacBook-Air:~ brandon$ pip install knotter Collecting knotter Downloading knotter-0.2.0.tar.gz (750kB) 100% |████████████████████████████████| 757kB 648kB/s Complete output from command python setup.py egg_info: Traceback (most recent call last): File "", line 1, in File "/private/var/folders/zt/qjk01pyj4hn34zyhq9h50r1c0000gn/T/pip-build-ym27_6ob/knotter/setup.py", line 7, in with open(path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f: File "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/codecs.py", line 895, in open file = builtins.open(filename, mode, buffering) FileNotFoundError: [Errno 2] No such file or directory: '/private/var/folders/zt/qjk01pyj4hn34zyhq9h50r1c0000gn/T/pip-build-ym27_6ob/knotter/DESCRIPTION.rst'

----------------------------------------

Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/zt/qjk01pyj4hn34zyhq9h50r1c0000gn/T/pip-build-ym27_6ob/knotter/

outlace commented 8 years ago

Also, what is the roadmap for this project? Looks like its no longer in active development. From the screenshot it looks amazing, better than Ayasdi. I've been looking for a user-friendly TDA tool for a long time, Python Mapper is just not particularly usable.

rosinality commented 8 years ago

Aaargh I got it. This (0c2985cf80590554b24b5c6d2cda050a1ddf5243) will resolve an issue.

I think Ayasdi would offer better functionalities than Knotter. I wanted to explore potentials of TDA for data analysis. But Ayasdi don't offer free or demo version of their tools, so I made this.

Maybe porting to ipywidgets or bokeh as suggested in #1 is way-to-go, but these are seem to be more complicated than I thought (especially bokeh). Anyway I will develop this occasionally.

outlace commented 8 years ago

That fixed it. Can you upload a test data set? I'm not able to get it working with my own data. I browse -> select CSV -> select the columns I want -> modify parameters -> click Analyze and it does nothing

rosinality commented 8 years ago

https://github.com/rosinality/knotter/blob/master/samples/swiss-roll.csv (came from manifold learning example of scikit-learn, http://scikit-learn.org/stable/auto_examples/manifold/plot_compare_methods.html) Maybe you can start with this. Select variable x, y, z, and by adjusting number of covers/overlap you can get analysis result. Also you can color the graph by toggle color panel (palette icon) and select variable color.

outlace commented 8 years ago

This is fantastic. Exactly the user-friendly TDA tool I was looking for. I'd like to help contribute to this project to get it to a point where academic researchers could use it in production. Do you think this can scale with big data sets? I notice it lags and gets slow analyzing my data. Is it possible to utilize the GPU for this analysis?

rosinality commented 8 years ago

Maybe I should clean the code first...:)

I experienced that most slowdown came from current simple and crude find_nerve functions. I will revise it so that it will run more fast especially when # of cover is large. (current algorithm searches (# of clusters combination 2) pairs) GPU can be used in clustering step, but fastcluster of hdbscan can be tried first. Maybe hdbscan is better choice than hierarchical clustering when # of data points is enough large. Another problems is that memory consumption came from pairwise distance matrices. But fixing this will be more difficult than computation-wise speed-ups.

mlnjsh commented 7 years ago

I have installed knotter in Anaconda but i am not able to start it...how do i start it

rosinality commented 7 years ago

Can I get an error message?

mlnjsh commented 7 years ago

I am not able to start Knotter

showing Syntax error

after installing it in anaconda i type

knotter

it says syntax error and moerover i dont know how to initiate it..

regards

On Thu, Apr 20, 2017 at 10:13 AM, Kim Seonghyeon notifications@github.com wrote:

Can I get an error message?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/rosinality/knotter/issues/2#issuecomment-295578776, or mute the thread https://github.com/notifications/unsubscribe-auth/AG4vYG9zsS5RqqBuWvpx1wsfyjDyqRkjks5rxuJsgaJpZM4I5Fg7 .

rosinality commented 7 years ago

I tested, but I cannot find syntax error...can you give me an error message?