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Jin Hyun Cheong jcheong0428 Dartmouth College jcheong0428.github.io Graduate student in Psychological and Brain Sciences at Dartmouth College.

cosanlab/nltools 73

Python toolbox for analyzing imaging data

jcheong0428/facesync 12

FaceSync - Open source python toolbox for synchronizing videos by audio and analyzing facial expression data

cosanlab/emotionCF 2

A package to perform collaborative filtering on emotion datasets.

jcheong0428/awesome-public-datasets 1

A topic-centric list of high-quality open datasets in public domains. By everyone, for everyone!

jcheong0428/awesome-rl 1

Reinforcement learning resources curated

jcheong0428/2018_materials 0

Materials for Neurohackademy 2018 lectures, tutorials, etc.

jcheong0428/2018_projects 0

Directory of Neurohackademy 2018 projects

jcheong0428/autocrop 0

:id: Automatically crops faces from batches of pictures

fork jakevdp/MyST-NB

Parse and execute ipynb files in Sphinx

https://myst-nb.readthedocs.io

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ejolly

commit sha c5f874ec8e35f47e7ce3040a90992c8e47278b25

user x item matrix conversion more flexibly handles columns. model training testing splits can now handle fractional values.

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commit sha c789d9935eb7d3aad9382f1d44198ee2354ddd99

models can now handle float n_train_items for percentage splitting

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ejolly

commit sha 5f090dc822405b6e8766c4bdceb335c411371ee2

Make sure updates pass all tests. Fix random to seed for reproducible testing.

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ejolly

commit sha 8aa36f023667d0e328b626ee7d4278f0bf5352e1

Updated __repr__ and removed auto-masking if null values in dataset during model init

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ejolly

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Added some utility functions. Fixed bug where retreiving predictions would fail with numerical column names

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issue openedcosanlab/nltools

Wrong cross validated weight maps in output for lassopcr

In brain_data.py at line 1108 the same (non-cross validated) weight map is returned fort each cross-validation fold because the initial classifier object is used instead of the cross-validated one.

I believe this part

if predictor_settings['algorithm'] == 'lassopcr':
    wt_map_xval.append(np.dot(predictor_settings['_pca'].components_.T, predictor_settings['_lasso'].coef_))
elif predictor_settings['algorithm'] == 'pcr':
    wt_map_xval.append(np.dot(predictor_settings['_pca'].components_.T, predictor_settings['_regress'].coef_))
else:
    wt_map_xval.append(predictor_cv.coef_.squeeze())
output['weight_map_xval'].data = np.array(wt_map_xval)

should be replaced by

if predictor_settings['algorithm'] == 'lassopcr':
    wt_map_xval.append(np.dot(predict_cv['pca'].components_.T, predict_cv['lasso'].coef_))
elif predictor_settings['algorithm'] == 'pcr':
    wt_map_xval.append(np.dot(predict_cv['pca'].components_.T, predict_cv['regress'].coef_))
else:
    wt_map_xval.append(predictor_cv.coef_.squeeze())
output['weight_map_xval'].data = np.array(wt_map_xval)

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issue commentcosanlab/nltools

ttest 'permutation' question

hi @dabinyeum, We are planning on updating that feature soon. Currently that method requires that you have the MNE package installed, which is an optional requirement. This method is fairly limited as most computers can't run this on whole brain. We are (slowly) working on adding some of the accelerated bootstrap/permutation methods

Thank you so much for the reply!

dabinyeum

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issue commentcosanlab/nltools

ttest 'permutation' question

hi @dabinyeum, We are planning on updating that feature soon. Currently that method requires that you have the MNE package installed, which is an optional requirement. This method is fairly limited as most computers can't run this on whole brain. We are (slowly) working on adding some of the accelerated bootstrap/permutation methods

dabinyeum

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issue openedcosanlab/nltools

ttest 'permutation' question

Hi all,

I have a question regarding the permutation test in the ttest function.

I was able to run and plot different thresholds of the ttests such as: Comm_v_Stat_avg_stats_unc = Comm_v_Stat_avg.ttest(threshold_dict={'unc':.001}) Comm_v_Stat_avg_stats_fdr = Comm_v_Stat_avg.ttest(threshold_dict={'fdr':.05})

I was trying to run the permutation test under the same function using this code: Comm_v_Stat_avg_stats_perm = Comm_v_Stat_avg.ttest(threshold_dict = {'permutation':'tfce', 'n_permutations':1000}) and got this error message. Screen Shot 2021-01-11 at 4 46 22 PM

Please provide feedback as to how I can make this code run or if I did anything incorrectly. Thanks for your help!

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added google analytics

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sminyonglee

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Merge pull request #2 from sminyonglee/minor-edits added google analytics tyty - S

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major update

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replace favicon

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Merge pull request #1 from sminyonglee/update major update ty - S

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issue openedcosanlab/nltools

Brain_Data class in Python 3.8

Since upgrading to Python 3.8 I get a cryptic error AttributeError: ‘_io.BytesIO’ object has no attribute ‘mode’ anytime I am working with Brain_Data. I am able to load data in as a Brain_Data object, but any kind of method/operation on it fails with that same error (e.g., .filter, .smooth, and .to_nifti()). Pretty sure Python version is the issue since it still works fine in environments with 3.7.

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PR opened lineatkaf/lineatkaf.github.io

Bump ini from 1.3.5 to 1.3.7

Bumps ini from 1.3.5 to 1.3.7. <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/npm/ini/commit/c74c8af35f32b801a7e82a8309eab792a95932f6"><code>c74c8af</code></a> 1.3.7</li> <li><a href="https://github.com/npm/ini/commit/024b8b55ac1c980c6225607b007714c54eb501ba"><code>024b8b5</code></a> update deps, add linting</li> <li><a href="https://github.com/npm/ini/commit/032fbaf5f0b98fce70c8cc380e0d05177a9c9073"><code>032fbaf</code></a> Use Object.create(null) to avoid default object property hazards</li> <li><a href="https://github.com/npm/ini/commit/2da90391ef70db41d10f013e3a87f9a8c5d01a72"><code>2da9039</code></a> 1.3.6</li> <li><a href="https://github.com/npm/ini/commit/cfea636f534b5ca7550d2c28b7d1a95d936d56c6"><code>cfea636</code></a> better git push script, before publish instead of after</li> <li><a href="https://github.com/npm/ini/commit/56d2805e07ccd94e2ba0984ac9240ff02d44b6f1"><code>56d2805</code></a> do not allow invalid hazardous string as section name</li> <li>See full diff in <a href="https://github.com/isaacs/ini/compare/v1.3.5...v1.3.7">compare view</a></li> </ul> </details> <details> <summary>Maintainer changes</summary> <p>This version was pushed to npm by <a href="https://www.npmjs.com/~isaacs">isaacs</a>, a new releaser for ini since your current version.</p> </details> <br />

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Bump urllib3 from 1.22 to 1.24.2

Bumps urllib3 from 1.22 to 1.24.2. <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/urllib3/urllib3/blob/master/CHANGES.rst">urllib3's changelog</a>.</em></p> <blockquote> <h2>1.24.2 (2019-04-17)</h2> <ul> <li> <p>Don't load system certificates by default when any other <code>ca_certs</code>, <code>ca_certs_dir</code> or <code>ssl_context</code> parameters are specified.</p> </li> <li> <p>Remove Authorization header regardless of case when redirecting to cross-site. (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1510">#1510</a>)</p> </li> <li> <p>Add support for IPv6 addresses in subjectAltName section of certificates. (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1269">#1269</a>)</p> </li> </ul> <h2>1.24.1 (2018-11-02)</h2> <ul> <li> <p>Remove quadratic behavior within <code>GzipDecoder.decompress()</code> (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1467">#1467</a>)</p> </li> <li> <p>Restored functionality of <code>ciphers</code> parameter for <code>create_urllib3_context()</code>. (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1462">#1462</a>)</p> </li> </ul> <h2>1.24 (2018-10-16)</h2> <ul> <li> <p>Allow key_server_hostname to be specified when initializing a PoolManager to allow custom SNI to be overridden. (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1449">#1449</a>)</p> </li> <li> <p>Test against Python 3.7 on AppVeyor. (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1453">#1453</a>)</p> </li> <li> <p>Early-out ipv6 checks when running on App Engine. (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1450">#1450</a>)</p> </li> <li> <p>Change ambiguous description of backoff_factor (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1436">#1436</a>)</p> </li> <li> <p>Add ability to handle multiple Content-Encodings (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1441">#1441</a> and Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1442">#1442</a>)</p> </li> <li> <p>Skip DNS names that can't be idna-decoded when using pyOpenSSL (Issue <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1405">#1405</a>).</p> </li> <li> <p>Add a server_hostname parameter to HTTPSConnection which allows for overriding the SNI hostname sent in the handshake. (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1397">#1397</a>)</p> </li> <li> <p>Drop support for EOL Python 2.6 (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1429">#1429</a> and Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1430">#1430</a>)</p> </li> <li> <p>Fixed bug where responses with header Content-Type: message/* erroneously raised HeaderParsingError, resulting in a warning being logged. (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1439">#1439</a>)</p> </li> <li> <p>Move urllib3 to src/urllib3 (Pull <a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1409">#1409</a>)</p> </li> </ul> <h2>1.23 (2018-06-04)</h2> <ul> <li>Allow providing a list of headers to strip from requests when redirecting to a different host. Defaults to the <code>Authorization</code> header. Different</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/urllib3/urllib3/commit/1efadf43dc63317cd9eaa3e0fdb9e05ab07254b1"><code>1efadf4</code></a> Release 1.24.2 (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1564">#1564</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/a6ec68a5c5c5743c59fe5c62c635c929586c429b"><code>a6ec68a</code></a> Merging new release version: 1.24.1</li> <li><a href="https://github.com/urllib3/urllib3/commit/0cedb3b0f1e5d79c89c6db767c534b064b794cf2"><code>0cedb3b</code></a> Restore context.set_ciphers() to create_urllib3_context() (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1463">#1463</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/0aeba3be0224a930f6ffef254ed12b41303a86d7"><code>0aeba3b</code></a> Use bytearray to accumulate bytes from gzip (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1468">#1468</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/f8d1c787d9b02a70d66ddbde9c99061d9073d54a"><code>f8d1c78</code></a> Uninstall oclint to ensure gcc can be brew upgraded (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1464">#1464</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/cd7cfa613b2678e700597d098ce9bbdc934863e6"><code>cd7cfa6</code></a> Resolve pytest pluggy version conflict (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1457">#1457</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/b548abc9812a628d3290d0cab83e44f3c31ac6fe"><code>b548abc</code></a> Update changelog for 1.24 release</li> <li><a href="https://github.com/urllib3/urllib3/commit/ef0c74542abe69421a86c4d3c6a86fe43cb809a4"><code>ef0c745</code></a> Merging new release version: 1.24</li> <li><a href="https://github.com/urllib3/urllib3/commit/a0964d9947c07d2b8495726ac23ad251b5d236af"><code>a0964d9</code></a> Add missing key_server_hostname variable (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1449">#1449</a>)</li> <li><a href="https://github.com/urllib3/urllib3/commit/34d8298ecf93c84f9916457d89701d6d5c807780"><code>34d8298</code></a> Test against Python 3.7 on AppVeyor (<a href="https://github-redirect.dependabot.com/urllib3/urllib3/issues/1453">#1453</a>)</li> <li>Additional commits viewable in <a href="https://github.com/urllib3/urllib3/compare/1.22...1.24.2">compare view</a></li> </ul> </details> <br />

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