Pybids #284

arokem · 2020-06-30T22:59:16Z

This uses pybids to parse the input.

pep8speaks · 2020-06-30T22:59:22Z

Hello @arokem! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

In the file AFQ/api.py:

Line 683:26: E741 ambiguous variable name 'l'

In the file AFQ/tests/test_api.py:

Line 164:25: E128 continuation line under-indented for visual indent
Line 166:25: E128 continuation line under-indented for visual indent

In the file AFQ/tests/test_viz.py:

Line 11:14: E225 missing whitespace around operator
Line 13:17: E128 continuation line under-indented for visual indent
Line 14:17: E128 continuation line under-indented for visual indent

Comment last updated at 2020-07-13 23:29:16 UTC

Now comes the hard part of generalizing this...

This now seems to resolve yeatmanlab#265, but might still be limited in other ways.

Pandas infers types of columns read from a file and this can go sideways. So, let's focus on the values.

arokem · 2020-07-09T20:37:56Z

Finally passing the tests now. @36000 : would you mind giving this a review?

36000 · 2020-07-13T21:05:50Z

AFQ/data.py

-        my_path = afq_home
-    else:
-        my_path = path
+        os.makedirs(afq_home)


os.makedirs(afq_home, exist_ok=True)

36000 · 2020-07-13T21:06:59Z

AFQ/data.py

-        my_path = afq_home
-    else:
-        my_path = path
+        os.makedirs(afq_home)


os.makedirs(afq_home, exist_ok=True)

36000 · 2020-07-13T21:32:00Z

This looks good! Should simplify setting up the API object.

arokem · 2020-07-13T23:30:50Z

Thanks for the feedback! I'll wait for the CI to finish and then merge.

arokem force-pushed the pybids branch from 7cf7a02 to 2ee36f2 Compare July 1, 2020 19:13

arokem mentioned this pull request Jul 3, 2020

ses-01 is the bids-compliant format #294

Closed

arokem force-pushed the pybids branch 2 times, most recently from 176b883 to 6e6d2b3 Compare July 7, 2020 18:59

arokem added 20 commits July 8, 2020 18:02

WIP: Experiment with pybids.

31e165a

The file has to be called exactly dataset_description.json

635b38b

Separate Freesurfer to a different derivatives directory

1347f08

Heading in the (hopefully) right direction.

06b3f5e

Limits scope in which we look for files (in case raw data is nearby).

68eb730

Ever closer.

38e8ffc

Be consistent about sess => ses

ed11de8

Seems to recapitulate previous functionality.

0b15387

Now comes the hard part of generalizing this...

Allow cases in which there is no session folder.

76e3240

This now seems to resolve yeatmanlab#265, but might still be limited in other ways.

Remove temporary scratch file.

cc7492e

PEP8 in tests.

cac53df

Small cleanups in tests/data.

6387190

Adjust CLI, adjust tests.

47a46fb

Update API in example.

4e00275

Properly name the subject/session directories.

afab5d3

Enable passing an FA threshold as the WM label.

c3e7eb3

Use a more general variable name. Update everywhere.

295b6a9

"sess" => "ses" in tests.

855450c

Fixes CLI.

67621db

One more "sess" => "ses"

b9da927

arokem force-pushed the pybids branch from afbd079 to b9da927 Compare July 9, 2020 01:02

arokem added 4 commits July 8, 2020 18:13

One more change in Boutiques descriptor.

7a26c07

Adapt viz test to new API.

3c217d1

Need to save top level output (tract profile CSV) to top level dir.

0979389

Apply corresponding change in tests.

7633075

Focus on the values in the DataFrame.

70c1f7a

Pandas infers types of columns read from a file and this can go sideways. So, let's focus on the values.

Docstring to include new variables and their defaults.

babb6b5

36000 reviewed Jul 13, 2020

View reviewed changes

AFQ/data.py Outdated

my_path = afq_home

else:

my_path = path

os.makedirs(afq_home)

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36000 Jul 13, 2020

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os.makedirs(afq_home, exist_ok=True)

36000 reviewed Jul 13, 2020

View reviewed changes

AFQ/data.py Outdated

my_path = afq_home

else:

my_path = path

os.makedirs(afq_home)

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36000 Jul 13, 2020

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os.makedirs(afq_home, exist_ok=True)

Avoid error if the directory already exists.

b2aae58

arokem merged commit da585b2 into yeatmanlab:master Jul 14, 2020

arokem deleted the pybids branch July 14, 2020 03:02

arokem mentioned this pull request Jul 24, 2020

Use pybids to manage data #111

Closed

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Pybids #284

Pybids #284

arokem commented Jun 30, 2020 •

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pep8speaks commented Jun 30, 2020 •

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arokem commented Jul 9, 2020

36000 Jul 13, 2020

36000 Jul 13, 2020

36000 commented Jul 13, 2020

arokem commented Jul 13, 2020

Pybids #284

Pybids #284

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arokem commented Jun 30, 2020 • edited Loading

pep8speaks commented Jun 30, 2020 • edited Loading

Comment last updated at 2020-07-13 23:29:16 UTC

arokem commented Jul 9, 2020

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36000 commented Jul 13, 2020

arokem commented Jul 13, 2020

arokem commented Jun 30, 2020 •

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pep8speaks commented Jun 30, 2020 •

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