Skip to content

← diagnostics package

NirsOpticalDensityQualityMetrics

Computes various quality metrics from NIRS data that has been converted to optical density.

This should be preceded with the node IntensityToOpticalDensity. This expects a stream where the Metadata.quantity is set to Quantities.optical_density and Origin.modality set to Modalities.NIRS. This should be set by your importer but otherwise you can use SetStreamProperties to set it. Version 0.3.0

Ports/Properties

data

Data to process.

verbose name
Data
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
INOUT

diagnostic_flatline

All-flat channels.

verbose name
Diagnostic Flatline
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

diagnostic_saturation

Saturating channels.

verbose name
Diagnostic Saturation
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

diagnostic_motion

Motion-artifact presence in channels.

verbose name
Diagnostic Motion
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

diagnostic_explainedvar

Variance explained due to various processes, by channel.

verbose name
Diagnostic Explainedvar
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

diagnostic_anticorr

HbO/HbR anti-correlation in channels (higher is better).

verbose name
Diagnostic Anticorr
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

diagnostic_motionprofile

Motion profile over time (not per-channel).

verbose name
Diagnostic Motionprofile
default value
None
port type
DataPort
value type
Packet (can be None)
data direction
OUT

correlate_streams

Additional streams that shall be used to calculate variance explained by the measures therein.

verbose name
Correlate Streams
default value
[]
port type
ListPort
value type
list (can be None)

exclude_shortsep

Exclude "short" channels with a source-detector distance below this threshold, which is in millimeters. A typical value is 15. If set to 0, no channels are excluded from the analysis.

verbose name
Exclude Short-Separation Channels
default value
0
port type
IntPort
value type
int (can be None)

average_wavelengths

Average measures over wavelengths.

verbose name
Average Wavelengths
default value
True
port type
BoolPort
value type
bool (can be None)

mayer_band

Frequency range for Mayer waves.

verbose name
Mayer Band
default value
[0.06, 0.14]
port type
ListPort
value type
list (can be None)

respiration_band

Frequency range for respiration effects.

verbose name
Respiration Band
default value
[0.2, 0.33]
port type
ListPort
value type
list (can be None)

cardiac_band

Frequency range for cardiac cycle.

verbose name
Cardiac Band
default value
[1, 1.6]
port type
ListPort
value type
list (can be None)

skip_explained_var

Skip the variance explained quality metrics. These can require significant compute resources depending on the size of your file.

verbose name
Skip Explained Var
default value
False
port type
BoolPort
value type
bool (can be None)

hp_cutoff

Frequency cutoff (lower bound) for highpass filter. Leave empty to skip highpass filter.

verbose name
Hp Cutoff
default value
[0.01, 0.02]
port type
ListPort
value type
list (can be None)

lp_cutoff

Frequency cutoff (upper bound) for lowpass filter. Leave empty to skip lowpass filter.

verbose name
Lp Cutoff
default value
[]
port type
ListPort
value type
list (can be None)

set_breakpoint

Set a breakpoint on this node. If this is enabled, your debugger (if one is attached) will trigger a breakpoint.

verbose name
Set Breakpoint (Debug Only)
default value
False
port type
BoolPort
value type
bool (can be None)

metadata

User-definable meta-data associated with the node. Usually reserved for technical purposes.

verbose name
Metadata
default value
{}
port type
DictPort
value type
dict (can be None)