i'm confused by motion_estimate_filter configuration comments

[shnizzedy]

How can options be mutually exclusive with required options?

C-PAC/dev/docker_data/default_pipeline.yml

Lines 775 to 799 in 23d86fa

	# Dataset-wide respiratory rate data from breathing belt required.
	# mutually exclusive with cutoff, center frequency, and bandwidth options further below
	# Lowest Breaths-Per-Minute in dataset.
	# Required for both notch and lowpass filters.
	breathing_rate_min:
	# Highest Breaths-Per-Minute in dataset.
	# Required for the notch filter.
	breathing_rate_max:
	# notch filter direct customization parameters
	# mutually exclusive with breathing_rate options above
	# the center frequency of the notch filter
	center_frequency:
	# the width of the notch filter
	filter_bandwidth:
	# lowpass filter direct customization parameters
	# mutually exclusive with breathing_rate options above
	# the frequency cutoff of the filter
	lowpass_cutoff:

[shnizzedy]

Like this?

C-PAC/CPAC/pipeline/schema.py

Lines 334 to 383 in d569963

	Any({
	'run': Maybe(Any([False], False)),
	'filter_type': Maybe(In({'notch', 'lowpass'})),
	'filter_order': Maybe(int),
	'breathing_rate_min': Maybe(Any(float, int)),
	'breathing_rate_max': Maybe(Any(float, int)),
	'center_frequency': Maybe(Any(float, int)),
	'filter_bandwidth': Maybe(Any(float, int)),
	'lowpass_cutoff': Maybe(Any(float, int)),
	},
	{
	'run': forkable,
	'filter_type': 'notch',
	'filter_order': int,
	'breathing_rate_min': Any(float, int),
	'breathing_rate_max': Any(float, int),
	'center_frequency': None,
	'filter_bandwidth': None,
	'lowpass_cutoff': Maybe(Any(float, int)),
	},
	{
	'run': forkable,
	'filter_type': 'notch',
	'filter_order': int,
	'breathing_rate_min': None,
	'breathing_rate_max': None,
	'center_frequency': Any(float, int),
	'filter_bandwidth': Any(float, int),
	'lowpass_cutoff': Maybe(Any(float, int)),
	},
	{
	'run': forkable,
	'filter_type': 'lowpass',
	'filter_order': int,
	'breathing_rate_min': Any(float, int),
	'breathing_rate_max': Maybe(Any(float, int)),
	'center_frequency': Maybe(Any(float, int)),
	'filter_bandwidth': Maybe(Any(float, int)),
	'lowpass_cutoff': None,
	},
	{
	'run': forkable,
	'filter_type': 'lowpass',
	'filter_order': int,
	'breathing_rate_min': None,
	'breathing_rate_max': Maybe(Any(float, int)),
	'center_frequency': Maybe(Any(float, int)),
	'filter_bandwidth': Maybe(Any(float, int)),
	'lowpass_cutoff': Maybe(Any(float, int)),
	},),

run	filter_type	breathing_rate_min	breathing_rate_max	center_frequency	filter_bandwidth	lowpass_cutoff
off	doesn't matter	doesn't matter	doesn't matter	doesn't matter	doesn't matter	doesn't matter
on	notch	required	required	None	None	doesn't matter
on	notch	None	None	required	required	doesn't matter
on	lowpass	required	doesn't matter	doesn't matter	doesn't matter	None
on	lowpass	None	doesn't matter	doesn't matter	doesn't matter	required

[sgiavasis]

Okay yeah, "required" is bad wording that wasn't updated. It was originally required. Then the ability to manually design the filters came in.

In the code, if the breathing rates are provided, the filter design attributes (center frequency, bandwidth, cutoff) are automatically configured. But if you provide these directly, you don't need the breathing rates.

[shnizzedy]

What if you provide both?

[sgiavasis]

The way it works now - it will always defer to breathing rate input, but only if both max and min are provided:

https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/func_preproc/utils.py#L135-L147
https://github.com/FCP-INDI/C-PAC/blob/master/CPAC/func_preproc/utils.py#L167-L175

I think we should throw a warning telling the user that's what's happening, when it happens.
I just created an issue for this: #1430

[shnizzedy]

#1432:

C-PAC/dev/docker_data/default_pipeline.yml

Lines 891 to 933 in e8e6eec

	# Dataset-wide respiratory rate data from breathing belt.
	# Notch filter requires either:
	# "breathing_rate_min" and "breathing_rate_max"
	# or
	# "center_frequency" and "filter_bandwitdh".
	# Lowpass filter requires either:
	# "breathing_rate_min"
	# or
	# "lowpass_cutoff".
	# If "breathing_rate_min" (for lowpass and notch filter)
	# and "breathing_rate_max" (for notch filter) are set,
	# the values set in "lowpass_cutoff" (for lowpass filter),
	# "center_frequency" and "filter_bandwidth" (for notch filter)
	# options are ignored.
	# Lowest Breaths-Per-Minute in dataset.
	# For both notch and lowpass filters.
	breathing_rate_min:
	# Highest Breaths-Per-Minute in dataset.
	# For notch filter.
	breathing_rate_max:
	# notch filter direct customization parameters
	# mutually exclusive with breathing_rate options above.
	# If breathing_rate_min and breathing_rate_max are provided,
	# the following parameters will be ignored.
	# the center frequency of the notch filter
	center_frequency:
	# the width of the notch filter
	filter_bandwidth:
	# lowpass filter direct customization parameter
	# mutually exclusive with breathing_rate options above.
	# If breathing_rate_min is provided, the following
	# parameter will be ignored.
	# the frequency cutoff of the filter
	lowpass_cutoff:

run	filter_type	breathing_rate_min	breathing_rate_max	center_frequency	filter_bandwidth	lowpass_cutoff
off	doesn't matter	doesn't matter	doesn't matter	doesn't matter	doesn't matter	doesn't matter
on	notch	required	required	doesn't matter	doesn't matter	doesn't matter
on	notch	None	None	required	required	doesn't matter
on	lowpass	required	doesn't matter	doesn't matter	doesn't matter	doesn't matter
on	lowpass	None	doesn't matter	doesn't matter	doesn't matter	required