3
d/                 @   s   d dl Z d dlZd dlmZmZmZmZmZmZm	Z	 d dl
mZ d dlZddlmZmZmZmZmZ G dd deZG dd	 d	eZG d
d deZdd ZdS )    N)oneskronmeaneyehstackdottile)pinv   )BaseInterfaceInputSpecTraitedSpecBaseInterfacetraitsFilec               @   s4   e Zd ZejejedddddZedddZdS )ICCInputSpecT)existsz#n subjects m sessions 3D stat files)desc	mandatory)r   r   N)__name__
__module____qualname__r   Listr   subjects_sessionsmask r   r   7/tmp/pip-build-7vycvbft/nipype/nipype/algorithms/icc.pyr      s
   r   c               @   s.   e Zd ZeddZedddZedddZdS )ICCOutputSpecT)r   zvariance between sessions)r   r   zvariance between subjectsN)r   r   r   r   icc_mapsession_var_mapsubject_var_mapr   r   r   r   r      s   
r   c               @   s(   e Zd ZdZeZeZdd Zdd Z	dS )ICCa5  
    Calculates Interclass Correlation Coefficient (3,1) as defined in
    P. E. Shrout & Joseph L. Fleiss (1979). "Intraclass Correlations: Uses in
    Assessing Rater Reliability". Psychological Bulletin 86 (2): 420-428. This
    particular implementation is aimed at relaibility (test-retest) studies.
    c          	      s  t j| jjj  tjtj dktj   fdd| jj	D }dd |D }tj
|}tj|d d j}tj|d d j}tj|d d j}tj|d d j}xPt|jd D ]>}	||	d d d d f }
t|
\||	< ||	< ||	< ||	< }}qW t j| jj	d d }tj|j}|jd	| < t j||j|j}t j|d tj|j}|jd
| < t j||j|j}t j|d tj|j}|jd| < t j||j|j}t j|d |S )Nr   c                s   g | ]} fd d|D qS )c                s&   g | ]}t j|j   jdd qS )   )nbload	get_fdatareshape).0fname)maskdatar   r   
<listcomp>/   s    z1ICC._run_interface.<locals>.<listcomp>.<listcomp>r   )r'   sessions)r)   r   r   r*   /   s   z&ICC._run_interface.<locals>.<listcomp>c             S   s   g | ]}t j|qS r   )npZdstack)r'   Zsession_datar   r   r   r*   2   s    r!   zicc_map.niizsession_var_map.niizsubject_var_map.niir"   r"   r"   )r#   r$   inputsr   r%   r,   Zlogical_not
logical_orisnanr   r   zerosshaperangeICC_rep_anovar&   ZNifti1ImageZaffineheadersave)selfZruntimeZsession_datasZlist_of_sessionsZall_dataZiccZ	session_FZsession_varZsubject_varxY_ZnimZnew_dataZnew_imgr   )r)   r   _run_interface*   s8    

&zICC._run_interfacec             C   s@   | j  j }tjjd|d< tjjd|d< tjjd|d< |S )Nzicc_map.niir   zsession_var_map.niir   zsubject_var_map.niir   )Z_outputsgetospathabspath)r6   outputsr   r   r   _list_outputsQ   s
    zICC._list_outputsN)
r   r   r   __doc__r   Z
input_specr   Zoutput_specr:   r@   r   r   r   r   r       s
   'r    c             C   s<  | j \}}|d }|d | }|d }t| }| | d j }tt|t|df}tt||df}	t||	g}
ttt|
t	t|
j
|
|
j
| jd}| jd| }|d j }| j |_ || }t| d| d j | }|| | }|| }|| | }|| }|| |||   }|}|| | }||||||fS )z
    the data Y are entered as a 'table' ie subjects are in rows and repeated
    measures in columns

    One Sample Repeated measure ANOVA

    Y = XB + E with X = [FaTor / Subjects]
    r!   r
   Fr   )r1   r   sumr   r   r   r   r   r   r	   Tflatten)r8   Znb_subjectsZnb_conditionsZdfcZdfeZdfrZmean_YZSSTr7   Zx0XZpredicted_YZ	residualsZSSEZMSEZSSCZMSCZsession_effect_FZSSRZMSRr    Ze_varZr_varr   r   r   r3   Y   s.    

*r3   )r<   numpyr,   r   r   r   r   r   r   r   Znumpy.linalgr	   Znibabelr#   Zinterfaces.baser   r   r   r   r   r   r   r    r3   r   r   r   r   <module>   s   $		: