U
    f»{jŠU  ã                   @   s  d dl mZmZ d dlZd dlZd dlmZ d dlZ	d dl
Z
d dlZddlmZ ddlmZ ddlmZ ddlmZ dd	lmZmZ d
dlmZ d
dlmZ d
dlmZmZ d
dlmZmZm Z m!Z!m"Z"m#Z#m$Z$m%Z% e ddd„ƒZ&dd„ Z'e G dd„ deƒƒZ(ddd„Z)dd„ Z*dd„ Z+dS ) é    )ÚConfigParserÚRawConfigParserNé   )Ú_localized_abbré   )ÚBaseRaw)Ú_mult_cal_one)ÚFIFF)Úcreate_infoÚ_format_dig_pointsé   )ÚAnnotations)Úget_mni_fiducials)Úapply_transÚ
_get_trans)ÚloggerÚverboseÚfill_docÚwarnÚ_check_fnameÚ_validate_typeÚ_check_optionÚ_mask_to_onsets_offsetsÚannotateFc                 C   s   t | |||ƒS )a›  Reader for a NIRX fNIRS recording.

    Parameters
    ----------
    fname : str
        Path to the NIRX data folder or header file.
    %(saturated)s
    %(preload)s
    %(verbose)s

    Returns
    -------
    raw : instance of RawNIRX
        A Raw object containing NIRX data.

    See Also
    --------
    mne.io.Raw : Documentation of attribute and methods.

    Notes
    -----
    %(nirx_notes)s
    )ÚRawNIRX)ÚfnameÚ	saturatedÚpreloadr   © r   úO/var/www/html/bwave/python/venv/lib/python3.8/site-packages/mne/io/nirx/nirx.pyÚread_raw_nirx   s    r    c                 C   s   t | ddd�S )NÚrúlatin-1)Úencoding)Úopen)r   r   r   r   Ú_open6   s    r%   c                       s.   e Zd ZdZed‡ fdd„	ƒZdd„ Z‡  ZS )	r   a9  Raw object from a NIRX fNIRS file.

    Parameters
    ----------
    fname : str
        Path to the NIRX data folder or header file.
    %(saturated)s
    %(preload)s
    %(verbose)s

    See Also
    --------
    mne.io.Raw : Documentation of attribute and methods.

    Notes
    -----
    %(nirx_notes)s
    FNc           P         s.  ddl m} t d| ¡ t|ddƒ t|tdƒ td|dƒ t|ƒ}| d¡r`t 	t 
|¡¡}t|d	d
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tƒ }|D �]$}t d||f ¡|
|< d}t|
| ƒdk�rø|dk�r:td|› dt|
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| D ƒ¡d }t|ƒdk�svt|
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| ƒ› �ƒ‚|d }|dk�rª|}nN|dk�rÈ|dk�rÂdnd}n0|dk�sÖt‚|}|
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| | |
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d ƒ�}| ¡  d ¡d }W 5 Q R X t|
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�r0   Y n2X |jt#j'j(d9�}d
}t "d:|› d;|› �¡  �qf�q|�rZ �qv�qZ|d k�rºtd<t)tƒ› d=t*|ƒ› d>�ƒ t#j$d?dddddt#j'j(d9�}|�rÊd@dAg‰ndBd„ t +dC|dD dE ¡D ƒ‰|�r8t +dF| d ¡dG ¡‰t +dH| d ¡dG ¡‰ dId„ ˆD ƒ‰dJd„ ˆ D ƒ‰ nLt ,dKd„ t +dL|dM dN ¡D ƒt-¡‰t ,dOd„ t +dP|dM dN ¡D ƒt-¡‰ |�rœt.|d& dQ ƒ}nt.|dD dR ƒ}|�rÖt/|
dS ƒ�}t0 1|¡}W 5 Q R X n"t2d
dT�}| |
dU ¡ |j3dV }i } |�r|dW  ¡ }!n|dX  dYd#¡ ¡ }!dZ !|!¡| d[< t|!ƒdk�rT|!d  dYd#¡| d\< t|!ƒdk�rv|!d]  dYd#¡| d^< t|!ƒdk�r˜|!dG  dYd#¡| d_< |d`  dYd#¡| da< | da dbk�rÆt4j5| da< n$| da dck�ràt4j6| da< n
t4j7| da< |dd d#k�r|j8t-|dd ƒ |j9|j:f| de< ||
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q˜tRtS| ƒjT|4||g|g|=g|d‰� t)ƒ t)ƒ t)ƒ t)ƒ f\}A}B}C}D|>d k	�rt?|>ƒD ]ˆ\}E}@tU|@ƒ\}F}G|F|4dŠ  }F|G|4dŠ  }G|G|F8 }G|A V|F¡ |B V|G¡ |C Vd‹gt|Fƒ ¡ |D V| jWd|E d|E d … gt|Fƒ ¡ �qŒ|�s4|
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Loading %sz	path-liker   r   )r   ÚnanÚignorez.hdrÚreadT)Úneed_dirz%s/*%súconfig.jsonF)Úhdrr+   údescription.jsonÚwl1Úwl2úprobeInfo.matÚtri)r,   ÚinfÚsetZtplr.   r/   z
config.txtr0   Zdatr   z>A single dat file was expected in the specified path, but got z^. This may indicate that the file structure has been modified since the measurement was saved.©r.   r/   z	Need one z file, got c                 S   s   g | ]}d t  |¡k‘qS )Znosatflags_)ÚopÚbasename)Ú.0Úxr   r   r   Ú
<listcomp>{   s   ÿz$RawNIRX.__init__.<locals>.<listcomp>r   z%Need one nosatflags and one standard r(   r'   r   r.   Ú
r,   z#.*?#Ú )Úflagsz(\[DataStructure].*)ZGeneralInfoÚVersion)z2021.4.0-34-ge9fdbbc8z2021.9.0-5-g3eb32851z2021.9.0-6-g14ef4a71z,MNE has not been tested with Aurora version ZNIRStar)z"15.0"z"15.2"z"15.3"z.MNE does not support this NIRStar version (%s)ZNIRScoutZDeviceZNIRSportzbOnly import of data from NIRScout devices have been thoroughly tested. You are using a %s device. ÚDateZTimeú ÚweekdayÚmonthzTrying z datetime: )z"%a, %b %d, %Y""%H:%M:%S.%f"z"%a %d %b %Y""%H:%M:%S.%f"z"%a, %d %b %Y""%H:%M:%S.%f"z%Y-%m-%d %H:%M:%S.%f)ÚtzinfozMeasurement date language z detected: z{Extraction of measurement date from NIRX file failed. This can be caused by files saved in certain locales (currently only zj supported). Please report this as a github issue. The date is being set to January 1st, 2000, instead of Ú.iÐ  iø  iR  c                 S   s   g | ]}t |ƒ‘qS r   ©Úint©r7   Úsr   r   r   r9   ê   s     ú(\d+)ZImagingParametersZWavelengthsz	(\d+)-\d+éþÿÿÿz	\d+-(\d+)c                 S   s   g | ]}t |ƒd  ‘qS ©r   rD   rF   r   r   r   r9   ó   s     c                 S   s   g | ]}t |ƒd  ‘qS rJ   rD   )r7   Údr   r   r   r9   ô   s     c                 S   s   g | ]}t |ƒ‘qS r   rD   rF   r   r   r   r9   ÷   s     z(\d+)-\d+:\d+ZDataStructurezS-D-Keyc                 S   s   g | ]}t |ƒ‘qS r   rD   rF   r   r   r   r9   û   s     z\d+-(\d+):\d+zSampling rateZSamplingRater-   )Úallow_no_valuer2   zSubject DemographicsÚsubjectÚnameú"Ú_Zhis_idZ
first_nameéÿÿÿÿÚ	last_nameZmiddle_nameZgenderZsex>   Ú1ÚMÚMale>   ÚFÚFemaleÚ2ZageÚbirthdayr0   Z	probeInfoÚprobes)r   r   Zindex_cZ	coords_s3g      Y@Z	coords_d3Z	coords_c3Z	fsaverageZmriÚhead)r   r!   Úcoord_frame)Úkindr!   Úidentr\   c                    s   g | ]}d ˆ | › �‘qS )ÚSr   ©r7   Úidx)Úsourcesr   r   r9   ^  s     c                    s   g | ]}d ˆ | › �‘qS )Z_Dr   r`   )Ú	detectorsr   r   r9   _  s     c                 S   s   g | ]\}}|t |ƒ ‘qS r   ©Ústr)r7   ÚmÚnr   r   r   r9   `  s     c                    s    g | ]}|d  t ˆ d ƒ ‘qS )r?   r   rd   rF   ©Úfnirs_wavelengthsr   r   r9   a  s     c                    s    g | ]}|d  t ˆ d ƒ ‘qS )r?   r   rd   rF   rh   r   r   r9   b  s     c                 S   s   g | ]}|D ]}|‘qqS r   r   )r7   ÚpairÚvalr   r   r   r9   c  s       Zfnirs_cw_amplitude)Zch_types)Úsubject_infoÚdigÚ	meas_dateZchsÚlocr   é   é	   Úrb)Úsd_indexÚfilesÚboundsÚnan_mask)r   r   Úch_names)Ú	filenamesZ
last_sampsÚ
raw_extrasr   ZsfreqZBAD_SATURATEDéýÿÿÿZevtr1   c                 S   s   g | ]}t  d |¡‘qS )rH   )ÚreÚfindall)r7   Úliner   r   r   r9   ¿  s     g      ð?)rw   )\Zscipy.ior&   r   Úinfor   re   r   Úendswithr5   ÚdirnameÚabspathr   ÚglobÚlenr   ÚdictÚRuntimeErrorÚnpÚwhereÚAssertionErrorr%   r)   Úcountr{   ÚsubÚDOTALLr   Úread_stringr   ÚitemsÚsplitÚreplaceÚrangeÚjoinÚdebugÚdtÚdatetimeÚstrptimeÚ
ValueErrorÚtimezoneÚutcÚlistÚreprr|   ZasarrayrE   Úfloatr$   ÚjsonÚloadr   Ú	_sectionsr	   ZFIFFV_SUBJ_SEX_MALEZFIFFV_SUBJ_SEX_FEMALEZFIFFV_SUBJ_SEX_UNKNOWNÚyearrA   ÚdayÚ_convert_fnirs_to_headr   r   ZFIFFV_COORD_HEADÚ	enumerateÚappendZFIFFV_POINT_EEGr   ÚarrayÚshapeZconcatenateZastypeÚzipr
   Z_unlockÚupdateÚtellÚgetÚisnanÚ_read_csv_rows_colsÚTÚzerosÚboolÚsuperr   Ú__init__r   Úextendrw   ÚisfileÚ_determine_tri_idxsr   Zset_annotations)PÚselfr   r   r   r   r&   Zjson_configZ	is_auroraÚkeysZn_datrt   rv   ÚkeyZfidxZnoidxÚfidZlast_sampleÚfZhdr_str_allZhdr_strr,   Zdatetime_strrn   ro   ZtranslationsZdo_breakZloc_datetime_strrk   ÚiiZdt_codeZsamplingrater2   rl   ÚnamesZmat_datarZ   Zrequested_channelsÚsrc_locsÚdet_locsÚch_locsÚ
mri_head_trm   Zch_locZreq_indZreq_idxZsd_idxZsnamesZdnamesZsdnamesZsd1Zsd2Zchnamesr~   Zch_idx2ÚsrcZdetZmidpointZch_idx3ru   Úoffsetr}   ry   Z
annot_maskZkiÚmaskZonsetÚdurationÚdescriptionrw   ÚciÚonZdurÚtZtf_idxÚdesc_idxZt_Ztrigger_frameÚdescZbinary_valueZannot©Ú	__class__)rc   ri   rb   r   r°   O   sb   


ÿ
ÿÿ ÿ

 ÿ
ÿÿ
þ

ÿ
ÿ
ÿ


ÿ
ÿÿÿ
ÿÿÿý
ÿÿÿý

ÿÿÿ
þ     ÿüÿ
þ
$$$
 ü    ÿ


 ÿ
    þ


.

zRawNIRX.__init__c                 C   sô   | j | d }tƒ }	dD ]t}
t| j | d |
 |||| j | d |
 ƒj}| j | d  |
d¡}|dk	r‚tj||dd…||…f < |	 |¡ qt t	|	d ƒd || f¡}|	d |ddd…dd…f< |	d	 |d	dd…dd…f< t
|||||ƒ |S )
z¬Read a segment of data from a file.

        The NIRX machine records raw data as two different wavelengths.
        The returned data interleaves the wavelengths.
        rs   r4   rt   ru   rv   Nr   r   r   )Z_raw_extrasr™   r«   r¬   r©   r†   r'   r£   r­   rƒ   r   )r´   Údatara   ÚfiÚstartÚstopZcalsZmultrs   Zwlsr¶   rK   rv   Z	this_datar   r   r   Ú_read_segment_fileÑ  s&      ýzRawNIRX._read_segment_file)FN)Ú__name__Ú
__module__Ú__qualname__Ú__doc__r   r°   rÏ   Ú__classcell__r   r   rÉ   r   r   :   s      r   r?   c              	   C   sž   t | dƒ�l}| || ¡ tƒ }|d d k	rB| || ||  ¡ |j|Ž  d¡}	|d k	rb||	ƒ}	tj|	t|d�}
W 5 Q R X || df|
_	|
d d …|f }
|
S )Nrr   r   r"   )ÚseprQ   )
r$   Úseekr™   r£   r)   Údecoder†   Ú
fromstringr›   r¥   )r   rÍ   rÎ   Úcolsru   rÕ   r�   r·   ÚargsrË   r8   r   r   r   r«   î  s    r«   c                 C   s:   t | ||ƒ\}}t||ƒ}t||ƒ}t||ƒ}||||fS )N)r   r   )ZtransZfroÚtor»   r¼   r½   r¾   rP   r   r   r   r¡   þ  s
    


r¡   c                 C   s<   t | ƒdkrd}d}nt | ƒdkr,d}d}ntdƒ‚||fS )z5Determine tri file indexes for frame and description.é   é   é
   rq   é   zUnable to read trigger file.)rƒ   r…   )ÚtriggerZtrigger_frame_idxrÇ   r   r   r   r³     s    r³   )r   FN)r?   N),Úconfigparserr   r   r‚   r{   Úos.pathÚpathr5   r”   r“   rœ   Únumpyr†   r   Úbaser   Úutilsr   Ú	constantsr	   Z	meas_infor
   r   Úannotationsr   Z_freesurferr   Z
transformsr   r   r   r   r   r   r   r   r   r   r    r%   r   r«   r¡   r³   r   r   r   r   Ú<module>   s8   (   7   ÿ
