TabularInput¶

class TabularInput(file=None, sidecar=None, name=None)[source]: A BIDS tabular tsv file with sidecar.

Methods

`hed.models.tabular_input.TabularInput.__init__`([...])	Constructor for the TabularInput class.
`hed.models.tabular_input.TabularInput.assemble`([...])	Assembles the hed strings
`hed.models.tabular_input.TabularInput.column_metadata`()	Get the metadata for each column
`hed.models.tabular_input.TabularInput.combine_dataframe`(...)	Combines all columns in the given dataframe into a single HED string series,
`hed.models.tabular_input.TabularInput.convert_to_form`(...)	Convert all tags in underlying dataframe to the specified form.
`hed.models.tabular_input.TabularInput.convert_to_long`(...)	Convert all tags in underlying dataframe to long form.
`hed.models.tabular_input.TabularInput.convert_to_short`(...)	Convert all tags in underlying dataframe to short form.
`hed.models.tabular_input.TabularInput.expand_defs`(...)	Shrinks any def-expand found in the underlying dataframe.
`hed.models.tabular_input.TabularInput.get_column_refs`()	Returns a list of column refs for this file.
`hed.models.tabular_input.TabularInput.get_def_dict`(...)	Returns the definition dict for this sidecar.
`hed.models.tabular_input.TabularInput.get_worksheet`([...])	Get the requested worksheet.
`hed.models.tabular_input.TabularInput.reset_column_mapper`([...])	Change the sidecars and settings.
`hed.models.tabular_input.TabularInput.reset_mapper`(...)	Set mapper to a different view of the file.
`hed.models.tabular_input.TabularInput.set_cell`(...)	Replace the specified cell with transformed text.
`hed.models.tabular_input.TabularInput.shrink_defs`(...)	Shrinks any def-expand found in the underlying dataframe.
`hed.models.tabular_input.TabularInput.to_csv`([file])	Write to file or return as a string.
`hed.models.tabular_input.TabularInput.to_excel`(file)	Output to an Excel file.
`hed.models.tabular_input.TabularInput.validate`(...)	Creates a SpreadsheetValidator and returns all issues with this fil

Attributes

`hed.models.tabular_input.TabularInput.COMMA_DELIMITER`
`hed.models.tabular_input.TabularInput.EXCEL_EXTENSION`
`hed.models.tabular_input.TabularInput.FILE_EXTENSION`
`hed.models.tabular_input.TabularInput.FILE_INPUT`
`hed.models.tabular_input.TabularInput.HED_COLUMN_NAME`
`hed.models.tabular_input.TabularInput.STRING_INPUT`
`hed.models.tabular_input.TabularInput.TAB_DELIMITER`
`hed.models.tabular_input.TabularInput.TEXT_EXTENSION`
`hed.models.tabular_input.TabularInput.columns`	Returns a list of the column names.
`hed.models.tabular_input.TabularInput.dataframe`	The underlying dataframe.
`hed.models.tabular_input.TabularInput.dataframe_a`	Return the assembled dataframe
`hed.models.tabular_input.TabularInput.has_column_names`	True if dataframe has column names.
`hed.models.tabular_input.TabularInput.loaded_workbook`	The underlying loaded workbooks.
`hed.models.tabular_input.TabularInput.name`	Name of the data.
`hed.models.tabular_input.TabularInput.onsets`	Returns the onset column if it exists
`hed.models.tabular_input.TabularInput.series_a`	Return the assembled dataframe as a series
`hed.models.tabular_input.TabularInput.series_filtered`	Return the assembled dataframe as a series, with rows that have the same onset combined
`hed.models.tabular_input.TabularInput.worksheet_name`	The worksheet name.

TabularInput.__init__(file=None, sidecar=None, name=None)[source]¶

Constructor for the TabularInput class.

Parameters:

file (str or FileLike) – A tsv file to open.
sidecar (str or Sidecar or FileLike) – A Sidecar or source file/filename.
name (str) – The name to display for this file for error purposes.

Raises:

HedFileError –
- file is blank
- An invalid dataframe was passed with size 0
- An invalid extension was provided
- A duplicate or empty column name appears
OSError –
- Cannot open the indicated file
ValueError –
- This file has no column names

TabularInput.assemble(mapper=None, skip_curly_braces=False)¶

Assembles the hed strings

Parameters:

mapper (ColumnMapper or None) – Generally pass none here unless you want special behavior.
skip_curly_braces (bool) – If True, don’t plug in curly brace values into columns.

Returns:

the assembled dataframe

Return type:

Dataframe

TabularInput.column_metadata()¶

Get the metadata for each column

Returns:: number/ColumnMeta pairs
Return type:: dict

static TabularInput.combine_dataframe(dataframe)¶

Combines all columns in the given dataframe into a single HED string series,: skipping empty columns and columns with empty strings.

Parameters:: dataframe (Dataframe) – The dataframe to combine
Returns:: the assembled series
Return type:: Series

TabularInput.convert_to_form(hed_schema, tag_form)¶

Convert all tags in underlying dataframe to the specified form.

Parameters:

hed_schema (HedSchema) – The schema to use to convert tags.
tag_form (str) – HedTag property to convert tags to. Most cases should use convert_to_short or convert_to_long below.

TabularInput.convert_to_long(hed_schema)¶

Convert all tags in underlying dataframe to long form.

Parameters:: hed_schema (HedSchema or None) – The schema to use to convert tags.

TabularInput.convert_to_short(hed_schema)¶

Convert all tags in underlying dataframe to short form.

Parameters:: hed_schema (HedSchema) – The schema to use to convert tags.

TabularInput.expand_defs(hed_schema, def_dict)¶

Shrinks any def-expand found in the underlying dataframe.

Parameters:

hed_schema (HedSchema or None) – The schema to use to identify defs
def_dict (DefinitionDict) – The definitions to expand

TabularInput.get_column_refs()[source]¶

Returns a list of column refs for this file.

Default implementation returns none.

Returns:: A list of unique column refs found
Return type:: column_refs(list)

TabularInput.get_def_dict(hed_schema, extra_def_dicts=None)[source]¶

Returns the definition dict for this sidecar.

Parameters:

hed_schema (HedSchema) – used to identify tags to find definitions
extra_def_dicts (list, DefinitionDict, or None) – Extra dicts to add to the list.

Returns:

A single definition dict representing all the data(and extra def dicts)

Return type:

DefinitionDict

TabularInput.get_worksheet(worksheet_name=None)¶

Get the requested worksheet.

Parameters:: worksheet_name (str or None) – The name of the requested worksheet by name or the first one if None.
Returns:: The workbook request.
Return type:: openpyxl.workbook.Workbook

Notes

If None, returns the first worksheet.

Raises:

KeyError –

The specified worksheet name does not exist

TabularInput.reset_column_mapper(sidecar=None)[source]¶

Change the sidecars and settings.

Parameters:: sidecar (str or [str] or Sidecar or [Sidecar]) – A list of json filenames to pull sidecar info from.

TabularInput.reset_mapper(new_mapper)¶

Set mapper to a different view of the file.

Parameters:: new_mapper (ColumnMapper) – A column mapper to be associated with this base input.

TabularInput.set_cell(row_number, column_number, new_string_obj, tag_form='short_tag')¶

Replace the specified cell with transformed text.

Parameters:

row_number (int) – The row number of the spreadsheet to set.
column_number (int) – The column number of the spreadsheet to set.
new_string_obj (HedString) – Object with text to put in the given cell.
tag_form (str) – Version of the tags (short_tag, long_tag, base_tag, etc)

Notes

Any attribute of a HedTag that returns a string is a valid value of tag_form.

Raises:

ValueError –
- There is not a loaded dataframe
KeyError –
- the indicated row/column does not exist
AttributeError –
- The indicated tag_form is not an attribute of HedTag

TabularInput.shrink_defs(hed_schema)¶

Shrinks any def-expand found in the underlying dataframe.

Parameters:: hed_schema (HedSchema or None) – The schema to use to identify defs

TabularInput.to_csv(file=None)¶

Write to file or return as a string.

Parameters:

file (str, file-like, or None) – Location to save this file. If None, return as string.

Returns:

None if file is given or the contents as a str if file is None.

Return type:

None or str

Raises:

OSError –

Cannot open the indicated file

TabularInput.to_excel(file)¶

Output to an Excel file.

Parameters:

file (str or file-like) – Location to save this base input.

Raises:

ValueError –
- if empty file object was passed
OSError –
- Cannot open the indicated file

TabularInput.validate(hed_schema, extra_def_dicts=None, name=None, error_handler=None)¶

Creates a SpreadsheetValidator and returns all issues with this fil

Parameters:

hed_schema (HedSchema) – The schema to use for validation
extra_def_dicts (list of DefDict or DefDict) – all definitions to use for validation
name (str) – The name to report errors from this file as
error_handler (ErrorHandler) – Error context to use. Creates a new one if None

Returns:

A list of issues for hed string

Return type:

issues (list of dict)

TabularInput.COMMA_DELIMITER = ','¶

TabularInput.EXCEL_EXTENSION = ['.xlsx']¶

TabularInput.FILE_EXTENSION = ['.tsv', '.txt', '.xlsx']¶

TabularInput.FILE_INPUT = 'file'¶

TabularInput.HED_COLUMN_NAME = 'HED'¶

TabularInput.STRING_INPUT = 'string'¶

TabularInput.TAB_DELIMITER = '\t'¶

TabularInput.TEXT_EXTENSION = ['.tsv', '.txt']¶

TabularInput.columns¶

Returns a list of the column names.

Empty if no column names.

Returns:: the column names
Return type:: columns(list)

TabularInput.dataframe¶: The underlying dataframe.

TabularInput.dataframe_a¶

Return the assembled dataframe: Probably a placeholder name.

Returns:: the assembled dataframe
Return type:: Dataframe

TabularInput.has_column_names¶: True if dataframe has column names.

TabularInput.loaded_workbook¶: The underlying loaded workbooks.

TabularInput.name¶: Name of the data.

TabularInput.onsets¶: Returns the onset column if it exists

TabularInput.series_a¶

Return the assembled dataframe as a series

Returns:: the assembled dataframe with columns merged
Return type:: Series

TabularInput.series_filtered¶

Return the assembled dataframe as a series, with rows that have the same onset combined

Returns:: the assembled dataframe with columns merged, and the rows filtered together
Return type:: Series

TabularInput.worksheet_name¶: The worksheet name.