Interface and validator for SNIRF files
Project description
pysnirf2
Dynamically generated Python library for reading, writing, and validating Shared Near Infrared Spectroscopy Format (SNIRF) files.
Developed and maintained by the Boston University Neurophotonics Center.
Documentation
Documentation is generated from source using lazydocs
Installation
pip install pysnirf2
pysnirf2 requires Python > 3.6
Features
Open a SNIRF file
Snirf(<path>)
opens a SNIRF file at <path>
or creates a new one if it doesn't exist.
from pysnirf2 import Snirf
>>> snirf = Snirf(r'some\path\subj1_run01.snirf')
Create a SNIRF file object
Snirf()
with no arguments creates a temporary file which can be written later using save()
.
>>> snirf = Snirf()
Closing a SNIRF file
A Snirf
instance wraps a file on disk. It should be closed when you're done reading from it or saving.
>>> snirf.close()
Use a with
statement to ensure that the file is closed when you're done with it:
>>> with Snirf(r'some\path\subj1_run01.snirf') as snirf:
>>> # Read/write
>>> snirf.save()
View or retrieve a file's contents
>>> snirf
Snirf at /
filename:
C:\Users\you\some\path\subj1_run01.snirf
formatVersion: v1.0
nirs: <iterable of 2 <class 'pysnirf2.NirsElement'>>
>>> snirf.nirs[0].probe
Probe at /nirs1/probe
correlationTimeDelayWidths: [0.]
correlationTimeDelays: [0.]
detectorLabels: ['D1' 'D2']
detectorPos2D: [[30. 0.]
[ 0. 30.]]
detectorPos3D: [[30. 0. 0.]
[ 0. 30. 0.]]
filename:
C:\Users\you\some\path\subj1_run01.snirf
frequencies: [1.]
landmarkLabels: None
landmarkPos2D: None
landmarkPos3D: None
location: /nirs/probe
momentOrders: None
sourceLabels: ['S1']
sourcePos2D: [[0. 0.]]
sourcePos3D: [[0.]
[0.]
[0.]]
timeDelayWidths: [0.]
timeDelays: [0.]
useLocalIndex: None
wavelengths: [690. 830.]
wavelengthsEmission: None
Edit a SNIRF file
Assign a new value to a field
>>> snirf.nirs[0].metaDataTags.SubjectID = 'subj1'
>>> snirf.nirs[0].metaDataTags.SubjectID
'subj1'
>>> snirf.nirs[0].probe.detectorPos3D[0, :] = [90, 90, 90]
>>> snirf.nirs[0].probe.detectorPos3D
array([[90., 90., 90.],
[ 0., 30., 0.]])
Note: assignment via slicing is not possible in
dynamic_loading
mode.
Indexed groups
Indexed groups are defined by the SNIRF file format as groups of the same type which are indexed via their name + a 1-based index, i.e. data1
, data2
, ... or stim1
, stim2
, stim3
, ...
pysnirf2 provides an iterable interface for these groups using Pythonic 0-based indexing, i.e. data[0]
, data[1]
, ... or stim[0]
, stim[1]]
, stim[2]
, ...
>>> snirf.nirs[0].stim
<iterable of 0 <class 'pysnirf2.StimElement'>>
>>> len(nirs[0].stim)
0
To add an indexed group, use the appendGroup()
method of any IndexedGroup
class. Indexed groups are created automatically. nirs
is an indexed group.
>>> snirf.nirs[0].stim.appendGroup()
>>> len(nirs[0].stim)
1
>>> snirf.nirs[0].stim[0]
StimElement at /nirs/stim2
data: None
dataLabels: None
filename:
C:\Users\you\some\path\subj1_run01.snirf
name: None
To remove an indexed group
>>> del snirf.nirs[0].stim[0]
Save a SNIRF file
Overwrite the open file
>>> snirf.save()
Save As in a new location
>>> snirf.save(r'some\new\path\subj1_run01_edited.snirf')
The save()
function can be called for any group or indexed group:
>>> snirf.nirs[0].metaDataTags.save('subj1_run01_edited_metadata_only.snirf')
Dynamic loading mode
For larger files, it may be useful to load data dynamically: data will only be loaded on access, and only changed datasets will be written on save()
. When creating a new Snirf
instance, set dynamic_loading
to True
(Default False
).
>>> snirf = Snirf(r'some\path\subj1_run01.snirf', dynamic_loading=True)
Note: in dynamic loading mode, array data cannot be modified with indices like in the example above:
>>> snirf = Snirf(TESTPATH, dynamic_loading=True) >>> snirf.nirs[0].probe.detectorPos3D array([[30., 0., 0.], [ 0., 30., 0.]]) >>> snirf.nirs[0].probe.detectorPos3D[0, :] = [90, 90, 90] >>> snirf.nirs[0].probe.detectorPos3D array([[30., 0., 0.], [ 0., 30., 0.]])To modify an array in
dynamic_loading
mode, assign it, modify it, and assign it back to the Snirf object.>>> detectorPos3D = snirf.nirs[0].probe.detectorPos3D >>> detectorPos3D[0, :] = [90, 90, 90] >>> snirf.nirs[0].probe.detectorPos3D = detectorPos3D array([[90., 90., 90.], [ 0., 30., 0.]])
Validating a SNIRF file
pysnirf2 features functions for validating SNIRF files against the specification and generating detailed error reports.
Validate a Snirf object you have created
>> result = snirf.validate()
Validate a SNIRF file on disk
To validate a SNIRF file on disk
>> from pysnirf2 import validateSnirf
>> result = validateSnirf(r'some\path\subj1_run01.snirf')
Validation results
The validation functions return a ValidationResult
instance which contains details about the SNIRF file.
>> assert valid
To view the validation result:
>> result.display(severity=3)
<pysnirf2.pysnirf2.ValidationResult object at 0x000001C0CCF05A00>
/nirs1/data1/measurementList103/dataType FATAL REQUIRED_DATASET_MISSING
/nirs1/data1/measurementList103/dataTypeIndex FATAL REQUIRED_DATASET_MISSING
/nirs1/data1 FATAL INVALID_MEASUREMENTLIST
Found 668 OK (hidden)
Found 635 INFO (hidden)
Found 204 WARNING (hidden)
Found 3 FATAL
File is INVALID
To look at a particular result:
>> result.errors[2]
<pysnirf2.pysnirf2.ValidationIssue object at 0x000001C0CB502F70>
location: /nirs1/data1
severity: 3 FATAL
name: 8 INVALID_MEASUREMENTLIST
message: The number of measurementList elements does not match the second dimension of dataTimeSeries
The full list of validation results result.issues
can be explored programatically.
Code generation
The interface and validator are generated via metacode that downloads and parses the latest SNIRF specification.
See \gen for details.
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