Package bar :: Package rec :: Module index_holder :: Class barReconstructorSlideElem
[hide private]
[frames] | no frames]

Class barReconstructorSlideElem


Nested Classes [hide private]
Instance Methods [hide private]
 
__init__(self, **kwargs)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
int or flaot
getThickness(self, zRes)
Calculate thicknes of the slide in using zRes as quantification unit.
None
defineSpan(self)
Calculate spatial span along plane perpendicular to slide plane.
 
_calculateSlideSpan(self, l)
Slide spans are calculated using following formulas:

Inherited from atlas_indexer.barIndexerSlideElement: getXMLelement

Inherited from base.barObject: __str__, getElementById, writeXMLtoFile

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __subclasshook__

Class Methods [hide private]

Inherited from atlas_indexer.barIndexerSlideElement: fromXML

Static Methods [hide private]

Inherited from base.barObject (private): _getAttributesDict

Class Variables [hide private]
Instance Variables [hide private]
int idx
index in the slide
barIndexerSlideElement next
refrence to the slide with the next index
barIndexerSlideElement prev
reference to the slide with the previous index
(float, float) span
spatial span of the slide
float z
coordinate of the slide plane
Properties [hide private]

Inherited from atlas_indexer.barIndexerSlideElement: coronalcoord, name, slideNumber, slidenumber, transformationmatrix

Inherited from object: __class__

Method Details [hide private]

__init__(self, **kwargs)
(Constructor)

 

x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • coronalcoord - value of the 'coronalcoord' attribute of the represented element
  • slidenumber - value of the 'slidenumber' attribute of the represented element
  • transformationmatrix - value of the 'transformationmatrix' attribute of the represented element
Overrides: object.__init__
(inherited documentation)

getThickness(self, zRes)

 

Calculate thicknes of the slide in using zRes as quantification unit. If zRes == None. Distance without applying quantyfication.

Parameters:
  • zRes (quantification unit) - float
Returns: int or flaot
thicknes of the slide in zRes units

defineSpan(self)

 

Calculate spatial span along plane perpendicular to slide plane.

Returns: None
None

_calculateSlideSpan(self, l)

 

Slide spans are calculated using following formulas:

   s_n=
   \left \langle 
   b_n - \frac{\left | b_{n-1} - b_n \right |}{2}
   ,
   b_n + \frac{\left | b_{n} - b_{n+1} \right |}{2}
    \right \rangle
Parameters:
  • l (list) - list of three values of bregmas: left (the highest value), middle (slide's bregma coordinate) and right (lowest value)
  • eq (Boolean) - Determines wether left and rigth span are the same. If True, left and right spans are the same. Option is implemented but not used.
Returns:
(tuple) Maximal and minimal bregma coordinate of given slide.