neuro_dot.File_IO#
Module Contents#
Functions#
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CHECK_KEYS Checks if entries in dictionary are mat-objects. |
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LOADMAT Loads files with the *.mat extension. |
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LOADMAT7P3 Loads files with the *.mat extension in the "mat 7.3" format. |
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LOADVOLUMETRICDATA Loads a volumetric data file |
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MAKE_NATIVESPACE_4DFP Calculates native space for an incomplete 4dfp header. |
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NIFTI_4DFP Converts between nifti and 4dfp volume and header formats. |
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READ_4DFP_HEADER Reads the .ifh header of a 4dfp file. |
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SAVEVOLUMETRICDATA Saves a volumetric data file. |
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SNIRF2NDOT takes a file with the 'snirf' extension in the SNIRF format and converts it to NeuroDOT formatting. |
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TODICT Recursively constructs from matobjects nested dictionaries |
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WRITE_4DFP_HEADER Writes a 4dfp header to a .ifh file. |
- neuro_dot.File_IO.check_keys(dict)#
CHECK_KEYS Checks if entries in dictionary are mat-objects. If entries are mat objects, todict is called to change them to nested dictionaries
- neuro_dot.File_IO.loadmat(filename)#
LOADMAT Loads files with the *.mat extension.
Function written by ‘mergen’ on Stack Overflow: https://stackoverflow.com/questions/7008608/scipy-io-loadmat-nested-structures-i-e-dictionaries
This function should be called instead of direct spio.loadmat as it cures the problem of not properly recovering python dictionaries from mat files.
Loadmat calls the function check_keys to cure all entries which are still mat-objects.
NOTE:This function does not work for .mat -v7.3 files.
- neuro_dot.File_IO.loadmat7p3(filename)#
LOADMAT7P3 Loads files with the *.mat extension in the “mat 7.3” format.
Function written by ‘mergen’ on Stack Overflow: https://stackoverflow.com/questions/7008608/scipy-io-loadmat-nested-structures-i-e-dictionaries
This function should be called instead of direct spio.loadmat as it cures the problem of not properly recovering python dictionaries from mat files.
Loadmat7p3 calls the function check_keys to cure all entries which are still mat-objects.
NOTE:This function is to be used for .mat -v7.3 files only.
- neuro_dot.File_IO.LoadVolumetricData(filename, pn, file_type)#
LOADVOLUMETRICDATA Loads a volumetric data file
[volume, header] = LOADVOLUMETRICDATA(filename, pn, file_type) loads a file specified by “filename”, path “pn”, and “file_type”, and returns it in two parts: the raw data file “volume”, and the header “header”, containing a number of key-value pairs in 4dfp format.
[volume, header] = LOADVOLUMETRICDATA(filename) supports a full filename input, as long as the extension is included in the file name and matches a supported file type.
Supported File Types/Extensions: ‘.4dfp’ 4dfp, ‘nii’ NIFTI.
NOTE: This function uses the NIFTI_Reader toolbox available on MATLAB Central. This toolbox has been included with NeuroDOT 2.
Dependencies: READ_4DFP_HEADER, READ_NIFTI_HEADER, MAKE_NATIVESPACE_4DFP.
See Also: SAVEVOLUMETRICDATA.
- neuro_dot.File_IO.Make_NativeSpace_4dfp(header_in)#
MAKE_NATIVESPACE_4DFP Calculates native space for an incomplete 4dfp header.
header_out = MAKE_NATIVESPACE_4DFP(header_in) checks whether “header_in” contains the “mmppix” and “center” fields (these are not always present in 4dfp files). If either is absent, a default called the “native space” is calculated from the other fields of the volume.
See Also: LOADVOLUMETRICDATA, SAVEVOLUMETRICDATA.
- neuro_dot.File_IO.nifti_4dfp(header_in, img_in, mode)#
NIFTI_4DFP Converts between nifti and 4dfp volume and header formats.
- Input:
- header_in:
‘struct’ of either a nifti or 4dfp header
- mode:
flag to indicate direction of conversion between nifti and 4dfp formats
‘n’: 4dfp to Nifti
‘4’: Nifti to 4dfp
- Output:
- header_out:
header in Nifti or 4dfp format
- neuro_dot.File_IO.Read_4dfp_Header(filename, pn)#
READ_4DFP_HEADER Reads the .ifh header of a 4dfp file.
header = READ_4DFP_HEADER(filename, pn) reads an .ifh text file specified by “filename”, containing a number of key-value pairs. The specific pairs are parsed and stored as fields of the output structure “header”.
See Also: LOADVOLUMETRICDATA.
- neuro_dot.File_IO.SaveVolumetricData(volume, header, filename, pn, file_type)#
SAVEVOLUMETRICDATA Saves a volumetric data file.
SAVEVOLUMETRICDATA(volume, header, filename, pn, file_type) saves volumetric data defined by “volume” and “header” into a file specified by “filename”, path “pn”, and “file_type”.
SAVEVOLUMETRICDATA(volume, header, filename) supports a full filename input, as long as the extension is included in the file name and matches a supported file type.
Supported File Types/Extensions: ‘.4dfp’ 4dfp, ‘.nii’ NIFTI.
Dependencies: WRITE_4DFP_HEADER, NIFTI_4DFP.
See Also: LOADVOLUMETRICDATA, MAKE_NATIVESPACE_4DFP.
- neuro_dot.File_IO.snirf2ndot(filename, pn, save_file=0, output=None, dtype=[])#
SNIRF2NDOT takes a file with the ‘snirf’ extension in the SNIRF format and converts it to NeuroDOT formatting.
This function depends on the “Snirf” class from pysnirf2.
- Inputs:
- Filename:
the name of the file to be converted, followed by the .snirf extension.
- Save_file:
flag which determines whether the data will be saved to a ‘mat’ file in NeuroDOT format. (default = 1)
- Output:
the filename (without extension) of the .mat file to be saved.
- Type:
optional - the only currently acceptable value is “snirf”
- Outputs:
- data:
NeuroDOT formatted data (# of channels x # of samples)
- info:
NeuroDOT formatted metadata “info”
- neuro_dot.File_IO.todict(matobj)#
TODICT Recursively constructs from matobjects nested dictionaries
- neuro_dot.File_IO.Write_4dfp_Header(header, filename, pn)#
WRITE_4DFP_HEADER Writes a 4dfp header to a .ifh file.
WRITE_4DFP_HEADER(header, filename) writes the input “header” in 4dfp format to an .ifh file specified by “filename”.
See Also: SAVEVOLUMETRICDATA.