adnipy package¶
Submodules¶
adnipy.adni module¶
Pandas dataframe extension for ADNI.
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class
adnipy.adni.
ADNI
(pandas_dataframe)[source]¶ Bases:
object
Dataframe deals with ADNI data.
This class presents methods, which are designed to work with data from the ADNI database.
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DATES
= ['Acq Date', 'Downloaded', 'EXAMDATE', 'EXAMDATE_bl', 'update_stamp', 'USERDATE', 'update_stamp', 'USERDATE', 'USERDATE2', 'SCANDATE', 'TAUTRANDT', 'update_stamp', 'USERDATE', 'USERDATE2', 'SCANDATE', 'TRANDATE', 'update_stamp']¶
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INDEX
= ['Subject ID', 'Image ID']¶
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MAPPER
= {'ASSAYTIME': 'TAUTIME', 'Acq Date': 'SCANDATE', 'Image': 'Image ID', 'Image Data ID': 'Image ID', 'PTID': 'Subject ID', 'Subject': 'Subject ID'}¶
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drop_dynamic
()[source]¶ Remove images which are dynamic.
Drops all rows, in which the Description contains ‘Dynamic’.
Returns: All images that are not dynamic. Return type: pd.DataFrame
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groups
(grouped_mci=True)[source]¶ Create a dataframe for each group and save it to a csv file.
Parameters: grouped_mci (bool, default True) – If true, ‘LMCI’ and ‘EMCI’ are treated like ‘MCI’. However, the original values will stills be in the output. Returns: Dictionnairy with a dataframe for each group. Return type: dict
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longitudinal
()[source]¶ Keep only longitudinal data.
This requires an ‘RID’ or ‘Subject ID’ column in the dataframe. Do not use if multiple images are present for a single timepoint.
Parameters: images (pd.DataFrame) – This dataframe will be modified. Returns: A dataframe with only longitudinal data. Return type: pd.DataFrame See also
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rid
()[source]¶ Add a roster ID column.
Will not work if ‘RID’ is already present or ‘Subject ID’ is missing.
Returns: Dataframe with a ‘RID’ column. Return type: pd.DataFrame Examples
>>> subjects = {"Subject ID": ["100_S_1000", "101_S_1001"]} >>> collection = pd.DataFrame(subjects) >>> collection Subject ID 0 100_S_1000 1 101_S_1001 >>> collection.adni.rid() Subject ID RID 0 100_S_1000 1000 1 101_S_1001 1001
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standard_column_names
()[source]¶ Rename dataframe columns to module standard.
This function helps when working with multiple dataframes, since the same data can have different names. It will also call rid() on the dataframe.
Returns: This will have standardized columns names. Return type: pd.DataFrame See also
Examples
>>> subjects = pd.DataFrame({"Subject": ["101_S_1001", "102_S_1002"]}) >>> subjects Subject 0 101_S_1001 1 102_S_1002 >>> subjects.adni.standard_column_names() "VISCODE2" not included. Subject ID RID 0 101_S_1001 1001 1 102_S_1002 1002
>>> images = pd.DataFrame({"Image": [100001, 100002]}) >>> images Image 0 100001 1 100002 >>> images.adni.standard_column_names() "VISCODE2" not included. Image ID 0 100001 1 100002
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standard_dates
()[source]¶ Change type of date columns to datetime.
Returns: Dates will have the appropriate dtype. Return type: pd.DataFrame
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standard_index
(index=None)[source]¶ Process dataframes into a standardized format.
The output is easy to read. Applying functions the the output may not work as expected.
Parameters: index (list of str, default None) – These columns will be the new index. Returns: An easy to read dataframe for humans. Return type: pd.DataFrame
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adnipy.adnipy module¶
Process ADNI study data with adnipy.
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adnipy.adnipy.
get_matching_images
(left, right)[source]¶ Match different scan types based on closest date.
The columns ‘Subject ID’ and ‘SCANDATE’ are required.
Parameters: - left (pd.DataFrame) – Dataframe containing the tau scans.
- right (pd.DataFrame) – Dataframe containing the mri scans.
Returns: For each timepoint there is a match from both inputs.
Return type: pd.DataFrame
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adnipy.adnipy.
read_csv
(file)[source]¶ Return a csv file as a pandas.DataFrame.
Recognizes missing values used in the ADNI database.
Parameters: file (str, pathlib.Path) – The path to the .csv file. Returns: Returns the file as a dataframe. Return type: pd.DataFrame See also
standard_column_names()
,standard_dates()
,standard_index()
adnipy.data module¶
Process data created in Matlab.
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adnipy.data.
image_id_from_filename
(filename)[source]¶ Extract image ID of single ADNI .nii filename.
Images from the ADNI database have a specific formatting. Using regular expressions the image ID can be extracted from filenames.
Parameters: filename (str) – It must contain the Image ID at the end. Returns: Image as a integer. Return type: numpy.int64 Examples
>>> image_id_from_filename("*_I123456.nii") 123456
Module contents¶
Process ADNI study data with adnipy.