stripeExtraction#

Example Usage#

Full Contents:#

stripeExtraction.anteriorMoveSegmentation(bw, placement, minsz, maxsz, msg)#
ANTERIORMOVESEGMENTATION(bw, placement, minsz, maxsz)

Select a region of the BW segmented image that is anterior or posterior

to current selection (indexed by ‘placement’) to find stripe 7 segmentation.

Parameters

  • bw (NxM binary array) – pre-size-filtered binary mask

  • placement (int) – the rank AP position of the segmented region (stripe7, for ex) that is true in the mask

  • minsz (float or int) – the min allowed size of a true region in the mask, in pixels

  • maxsz (float or int) – the max allowed size of a true region in the mask, in pixels

Returns

  • bw (NxM binary array) – pre-size-filtered binary mask

  • bw2 (NxM binary array) – size-filtered binary mask

  • placement (int) – the rank AP position of the segmented region (stripe7, for ex) that is true in the mask

  • button (waitforbuttonpress() output) – what the current

  • NPMitchell 2020

stripeExtraction.autoStripe7()#

default stripe7 finding protocol

NPMitchell 2020

stripeExtraction.cutCurveIntoLeadingTrailingSegments()#

Cut curve into left and right segments (leading and trailing segments) Assume clockwise motion of the curve

Parameters

stripe (N x 2 float array) – the (AP, DV) coordinates of a stripe (both leading and trailing edges) as (x,y) coordinates

Returns

  • segs (length 2 cell array of xy positions) – leading edge and trailing edge curves as separate coorinate positions

  • NPMitchell 2020

stripeExtraction.extractStripeEdges(dat, maskfn, thres, minmaxsz, embryoID)#

Determine the eges of a stripe in an image

Parameters

  • dat (NxM float array) – the image as a grid of intensity values

  • maskfn (str) – the filename where the mask to determine the stripe segmentation is to be saved on disk

  • thres (float) – minimum value to use when binarizing in the segmentation

  • minmaxsz (length 2 float/int array) – the minimum and maximum size of the segmentated region allowed

  • embryoID (str) – ID tag for the embryo whose stripe is being segmented

Returns

  • curv

  • NPMitchell 2020

stripeExtraction.morphologicalOpLoop(bw, dcrop_orig, placement, thres, minmaxsz, msg)#
MORPHOLOGICALOPLOOP(bw, dcrop_orig, placement, thres, minmaxsz)

Loop to extract mask segmentation by iterative dilation & erosion

Parameters

  • bw (NxM binary array) – pre-size-filtered binary mask

  • dcrop_orig (original intensity data) – original intensity data before thresholding to create mask

  • placement (int) – the rank AP position of the segmented region (stripe7, for ex) that is true in the mask

  • thres (numeric threshold) – threshold for binarizing the dcrop_orig data

  • minmaxsz ([minsz maxsz]) – the min and max allowed size of a true region in the mask, in pixels

Returns

  • bw (NxM binary array) – pre-size-filtered binary mask

  • bw2 (NxM binary array) – size-filtered binary mask

  • good_enough (bool) – segmentation is good enough to save, should be true when returned

  • move_on (bool) – whether we are ready to continue with the pipeline

  • placement (int) – the rank AP position of the segmented region (stripe7, for ex) that is true in the mask

  • NPMitchell 2020

stripeExtraction.ssrCurves(curv, refcurv, take_mean, symmetrize)#

Find sum of squared residual

Parameters

  • curv (N x 2 float array) – the curv to match refcurv

  • refcurv (M x 2 float array) – the second curv, reference

  • take_mean (bool (default=false)) – use mean distance between the two (discrete) curves instead of sum

  • symmetrize (bool (default=false)) – return sqrt(ssr_12)* sqrt(ssr_21) so that curve ordering is irrelevant, or sum them together if take_mean==false.

Returns

  • ssr (float)

  • NPMitchell 2020

Indices and tables#