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CBICA / niCHART

The neuro-imaging brain aging chart [niCHART] is a comprehensive solution to analyze standard structural and functional brain MRI data across studies. [niCHART] and the associated pre-processing tools implement computational morphometry, functional signal analysis, quality control, statistical harmonization, data standardization, interactive visual
https://cbica.github.io/niCHART/
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Harmonization plotting function controls #177

Closed melhemr closed 2 years ago

melhemr commented 2 years ago

Harmonization plotting function ignores 'isTrainMUSEHarmonization' column, does not initially plot controls until after pressing 'Add to DataFrame' and showing the plots again.

v1.2 istaging.pkl.gz and harmonization model were used for example

initial plot output

(.env) ➜  NiBAx git:(harmonization_bugs) ✗ NiBAx
[2022-03-04 10:11:48,689 — NiBAx.mainwindow — mainwindow.py: Line:28 —             __init__() ] — INFO — New NiBAx session starting...
[2022-03-04 10:11:50,157 — NiBAx.mainwindow — mainwindow.py: Line:54 —             __init__() ] — INFO — Loaded Plugins: dict_keys(['Age Trends', 'Harmonization', 'Load and Save Data', 'Data Characteristics', 'SPARE-*'])
[2022-03-04 10:12:22,634 — yapsy_loaded_plugin_Load_and_Save_Data_0 — loadsave.py: Line:107 —             ReadData() ] — INFO — New data read from file: /Users/randamelhem/NiBAx/Datasets/istaging_v1.2.pkl.gz
[2022-03-04 10:12:22,659 — NiBAx.plugins.loadsave.dataio — dataio.py: Line:41 —   ReadMUSEDictionary() ] — INFO — MUSE dictionary read from file: /Users/randamelhem/NiBAx/NiBAx/plugins/loadsave/MUSE_ROI_Dictionary.csv
/Users/randamelhem/NiBAx/NiBAx/plugins/loadsave/dataio.py:48: PerformanceWarning: DataFrame is highly fragmented.  This is usually the result of calling `frame.insert` many times, which has poor performance.  Consider joining all columns at once using pd.concat(axis=1) instead.  To get a de-fragmented frame, use `newframe = frame.copy()`
  DerivedMUSEMap = pd.read_csv(DerivedMapfile,
[2022-03-04 10:12:22,805 — NiBAx.plugins.loadsave.dataio — dataio.py: Line:51 —   ReadDerivedMUSEMap() ] — INFO — Derived MUSE dictionary read from file: /Users/randamelhem/NiBAx/NiBAx/plugins/loadsave/MUSE_DerivedROIs_Mappings.csv
[2022-03-04 10:12:22,805 — NiBAx.core.model.datamodel — datamodel.py: Line:86 —              SetData() ] — INFO — Data changed in datamodel
2022-03-04 10:12:27.263 Python[17559:23064063] Persistent UI failed to open file file:///Users/randamelhem/Library/Saved%20Application%20State/org.python.python.savedState/window_1.data: No such file or directory (2)
Running harmonization.
Skipping out-of-sample harmonization because `UseForComBatGAMHarmonization` does not exist.
Harmonization done.
Creating color palette from model...

Saving and second plot output

Saving modified data to pickle file...
Plotting controls only
/Users/randamelhem/NiBAx/.env/lib/python3.8/site-packages/pandas/core/indexing.py:1773: SettingWithCopyWarning: 
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  self._setitem_single_column(ilocs[0], value, pi)
Creating color palette from model...