new option for no apical + str for yaml #200
Conversation
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can we increase the lengths of line to at least 100? |
| ) | ||
| try: | ||
| apical_points_isec = tools.load_json( | ||
| os.path.join(one_row['morph_dir'], "apical_points_isec.json") |
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Don't you need the apical for MM?
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Well, the idea is that for the current release we don't use the bAP feature for the selection, so we don't need the values.
But I consider this fix fairly dangerous. I'd propose we add an option to the config file to actively disable the apical points
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the features using apical points are called bAP, and theu are discared after the computation when the extneuron.db is prioduced. So better not use them at all to speed things up.
…On Jun 25 2020, at 1:35 pm, MikeG ***@***.***> wrote:
@mgeplf commented on this pull request.
In bluepymm/run_combos/calculate_scores.py (#200 (comment)):
> @@ -218,9 +217,13 @@ def create_arg_list(scores_db_filename, emodel_dirs, final_dict,
apical_points_isec = {}
setup = tools.load_module('setup', emodel_dirs[one_row['emodel']])
if hasattr(setup, 'multieval'):
- apical_points_isec = tools.load_json(
- os.path.join(one_row['morph_dir'], "apical_points_isec.json")
- )
+ try:
+ apical_points_isec = tools.load_json(
+ os.path.join(one_row['morph_dir'], "apical_points_isec.json")
Don't you need the apical for MM?
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| ) | ||
| try: | ||
| apical_points_isec = tools.load_json( | ||
| os.path.join(one_row['morph_dir'], "apical_points_isec.json") |
There was a problem hiding this comment.
Well, the idea is that for the current release we don't use the bAP feature for the selection, so we don't need the values.
But I consider this fix fairly dangerous. I'd propose we add an option to the config file to actively disable the apical points
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Ok, I'll add the option in the config file! |
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it is not so obvious, the dict is not used in the run step, only in the prepare I think |
arnaudon
changed the title
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There is a weird bug I can't quite understand how to fix, @anilbey, could you have a look, thanks! |
Do you mean the sqlite error below that's making travis fail?
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Yeah, I think so |
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yes! |
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Ok, I'm on it. |
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That's the error |
Codecov Report
@@ Coverage Diff @@
## master #200 +/- ##
==========================================
+ Coverage 72.06% 72.12% +0.06%
==========================================
Files 21 21
Lines 1353 1356 +3
==========================================
+ Hits 975 978 +3
Misses 378 378
Continue to review full report at Codecov.
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This reverts commit 0114eb0.
New parameter use_apical_points in the config dict to disable the use of apical_points.
Small bug from previous PR on allowing for yaml recipe file, the layer info should be a str so that dataframe.merge can add the etypes to the dataframes.