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gelles-brandeis committed Jan 9, 2024
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6 changes: 3 additions & 3 deletions imscroll/AOISpotLanding.m
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% You should have received a copy of the GNU General Public License
% along with this software. If not, see <http://www.gnu.org/licenses/>.


%keyboard
FrameRange=handles.AllSpots.FrameVector; % Vector of frames for which spots were found
[frmrose frmcol]=size(FrameRange); % also, frmcol= #rows in AllSpots cell array
[asrose ascol]=size(handles.AllSpots.AllSpotsCells);
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%our AOI and the spots in this
%frame

spotindexhigh=[1:handles.AllSpots.AllSpotsCells{frmindex,2}]; %Vector of spot indices found in this frame
%handles.AllSpots.AllSpotsCells{frmindex,2}= # of frames for which information
spotindexhigh=[1:handles.AllSpots.AllSpotsCells{frmindex,2}]; %making vector of spot indices found in this frame
%handles.AllSpots.AllSpotsCells{frmindex,2}= # of spots for which information
% is stored in AllSpotsCells cell array
% This is for the spots found with the High amplitude threshold
% Distances btwn our AOI and spots found using high amplitude threshold
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163 changes: 163 additions & 0 deletions imscroll/AOISpotLandingXY.m
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function pc=AOISpotLandingXY(AOInum,radiusX,radiusY,radiusXLo, radiusYLo, handles,aoiinfo2,radius_hys)
%
% function AOISpotLandingXY(AOInum,radiusX,radiusXLo, radiusYLo, radiusY,handles,aoiinfo2,radiu_hys)
%
% Will determine whether the spots landing in the field of view (stored in
% handles.AllSpots) occur within the AOI specified by AOInum. Output will
% be an array [(frame number) 0,1] specifying whether the aoi contained a
% spot during each frame number covered by the handles.AllSpots cell array
%
% AOInum == number of the AOI in the handles.AllSpots.aoiinfo2 list
% radiusX == upper limit pixel distance in X coordinate, X coordinate proximity of the
% spot to the AOI center (Xz, Yz) in order to be counted as a landing
% If radiusX is POSITIVE then spot (x,y) must satisfy:
% radiusXlo < (x- Xz) < radiusX to be a landing
% (spot must be close and to the right of the reference AOI)
% If radiusX is NEGATIVE 0 then spot (x, y) must satisfy:
% radiusX < (x-Xz) < radiusXlo to be a landing
% (spot must be close and to the left of the reference AOI)
% radiusY == upper limit pixel distance in Y coordinate, Y coordinate proximity of the
% spot to the AOI center (Xz, Yz) in order to be counted as a landing
% If radiusY is POSITIVE then spot (x,y) must satisfy:
% 0 < (y- Yz) < radiusY to be a landing
% If radiusY is NEGATIVE 0 then spot (x, y) must satisfy:
% radiusY < (y-Yz) < 0 to be a landing
% radiusXLo == lower limit pixel distance in X coordinate
% (must have abs(radiusXlo) < abs(radiusX, and both same sign )
% radiusYLo == lower limit pixel distancee in Y coordinate
% (must have abs(radiusYlo) < abs(radiusY), and both same sign)
% handles == handles structure containing members
% AllSpots, Driftlist
% aoiinfo2 == [frm# ave x y pixnum aoi#] listing of information about the aois in use

% Copyright 2015 Larry Friedman, Brandeis University.

% This is free software: you can redistribute it and/or modify it under the
% terms of the GNU General Public License as published by the Free Software
% Foundation, either version 3 of the License, or (at your option) any later
% version.

% This software is distributed in the hope that it will be useful, but WITHOUT ANY
% WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
% A PARTICULAR PURPOSE. See the GNU General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with this software. If not, see <http://www.gnu.org/licenses/>.

%if (abs(radiusXLo) > abs(radiusX)) | (abs(radiusYLo) > abs(radiusY)) | ((radiusXLo/radiusX)<0) | ((radiusYLo/radiusY)<0)
% error('error in AOISpotLandingXY: radius ranges/signs unacceptable')
%end
FrameRange=handles.AllSpots.FrameVector; % Vector of frames for which spots were found
[frmrose frmcol]=size(FrameRange); % also, frmcol= #rows in AllSpots cell array
[asrose ascol]=size(handles.AllSpots.AllSpotsCells);

%aoiinfo2=handles.AllSpots.aoiinfo2; %'[frm# ave x y pixnum aoi#]';

if asrose~=frmcol
sprintf('Error in AOISpotLanding: FrameRange and AllSpot sizes disagree')

end
pc=zeros(frmcol,2); % Allocate output matrix
logik=aoiinfo2(:,6)==AOInum; % Find row of aoiinfo2 with this AOI
xycoordzero=aoiinfo2(logik,3:4); % [x y] coordinate of our AOI
AmpHighLow=0;
for frmindex=1:frmcol

% Cycle through all frames
OptionalXYshift=[0 0]; % Initialize shift of AOI center due to drift
if any(get(handles.StartParameters,'Value')==[2 3 4])

% Here if we are in a 'moving aoi mode'

% Setting AOI offset if we are in
% moving AOI mode
% OptionalXYshift=ShiftAOI(AOInum,FrameRange(frmindex),handles.AllSpots.aoiinfo2,handles.DriftList);
OptionalXYshift=ShiftAOI(AOInum,FrameRange(frmindex),aoiinfo2,handles.DriftList);
end
%[frame# ave x y pixnum aoinum (danny's original aoi#)]

xycoord=xycoordzero+OptionalXYshift; % This will be [x y] coordinates of our AOI, shifted if necessary
% Need to test all the spots in the
% AllSpots cell array for proximity to the
% xycoord location AllSpots{m,1}=[x y] spot list,
% {m,2}=# of spots found, {m,3}=frm #

%Next, form vector of distances between
%our AOI and the spots in this
%frame

spotindexhigh=[1:handles.AllSpots.AllSpotsCells{frmindex,2}]; %Vector of spot indices found in this frame
%handles.AllSpots.AllSpotsCells{frmindex,2}= # of spots found in frame
% 'frmindex'.
% {frmindex,1}=(x y) list of spots found in frame='frmindex'
% This is for the spots found with the High amplitude threshold
% Distances btwn our AOI and spots found using high amplitude threshold
%distanceshigh=sqrt( (xycoord(1)-handles.AllSpots.AllSpotsCells{frmindex,1}(spotindexhigh,1)).^2 +(xycoord(2)-handles.AllSpots.AllSpotsCells{frmindex,1}(spotindexhigh,2)).^2 );
% deltaX and deltaY Distances btwn our AOI (xycoord) and spots found using high amplitude threshold
distanceX= handles.AllSpots.AllSpotsCells{frmindex,1}(spotindexhigh,1) - xycoord(1);
distanceY= handles.AllSpots.AllSpotsCells{frmindex,1}(spotindexhigh,2) - xycoord(2);
% Vector of spot indices for spots with Low amplitude threshold
% spotindexlow=[1:handles.AllSpotsLow.AllSpotsCells{frmindex,2}];

% Distances btwn our AOI and spots found using Low amplitude threshold
% distanceslow=sqrt( (xycoord(1)-handles.AllSpotsLow.AllSpotsCells{frmindex,1}(spotindexlow,1)).^2 +(xycoord(2)-handles.AllSpotsLow.AllSpotsCells{frmindex,1}(spotindexlow,2)).^2 );
signRadiusX=radiusX/abs(radiusX); % = 1 or -1, sign of radiusX
signRadiusY=radiusY/abs(radiusY); % = 1 or -1, sign of radiusY
diffX=signRadiusX*distanceX; % Use to make single logical if any() statement below work for
% both + and - values of
% radiusX (but at this point it still tests whether spot is
% displaced by + or - radiusX distance)
diffY=signRadiusY*distanceY;
if get(handles.SignX,'Value')==1 % True when we wish to be insensitive to sign of radiusX:
% so spot distance can be w/in either + or - radiusX
% Now if any() statment will be true if spot
% is displaced within + or - radiusX distance regardless of the
% sign of radiusX
diffX=abs(diffX);
end
if get(handles.SignY,'Value')==1 % True when we wish to be insensitive to sign of radiusY
% spot distance can be w/in either + or - radiusY
diffY=abs(diffY);
end

% if any(distanceshigh<radius)
% Here if a spot with high amplitude threshold was close
% [frm# 1/0]
% AmpHighLow=1;
% pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 1]; % Mark as high = 1 b/c spot was close to AOI
% elseif (AmpHighLow==1) & any(distanceslow<radius*radius_hys)
% Here if the last frame was high and this frame
% satisfies only a relaxed criteria (hysterisis) for
% being in a high state (lower amplitude spots, larger
% distance between spots and AOI center)
% Note: radius_hys=str2num(get(handles.UpThreshold,'String'))

% pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 1]; % Mark as high = 1 b/c spot was close to AOI
% else
% Here is there was no spot close to our AOI center
% AmpHighLow=0;
% pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 0]; % Mark as low = 0 b/c no spot was close to AOI
% end
%keyboard
% if any((0<diffX)&(diffX<signRadiusX*radiusX) & (0<diffY)&(diffY<signRadiusY*radiusY) )
if any((signRadiusX*radiusXLo<diffX)&(diffX<signRadiusX*radiusX) & (signRadiusY*radiusYLo<diffY)&(diffY<signRadiusY*radiusY) )
% Here if a spot is w/in specified X and Y region of our AOI
% [frm# 1/0]
AmpHighLow=1;
pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 1]; % Mark as high = 1 b/c spot was close to AOI
% elseif (AmpHighLow==1) & any(distanceslow<radius*radius_hys)
% Here if the last frame was high and this frame
% satisfies only a relaxed criteria (hysterisis) for
% being in a high state (lower amplitude spots, larger
% distance between spots and AOI center)
% Note: radius_hys=str2num(get(handles.UpThreshold,'String'))

% pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 1]; % Mark as high = 1 b/c spot was close to AOI
else
% Here is there was no spot close to our AOI center
AmpHighLow=0;
pc(frmindex,:)=[handles.AllSpots.AllSpotsCells{frmindex,3} 0]; % Mark as low = 0 b/c no spot was close to AOI
end
%keyboard
end

end
95 changes: 95 additions & 0 deletions imscroll/BackgroundAOICircle.m
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function pc=BackgroundAOICircle(InputAoiinfo2, AOIsize, AOIdistance)
%
% function BackgroundAOICircle(InputAoiinfo2, AOIsize, AOIdistance)
%
% This function will output aoiinfo2 and RefAOINearLogik (see
% description in any aoifits file) variables that define background AOIs
% for the reference InputAoiinfo2 AOIs. For each reference AOI listed in
% InputAoiinfo2, the function will calculate the coordinate for several
% AOIs that encircle that reference AOI (based on the parameters
% AOIsize and AOIdistance).
%
% InputAoiinfo2 == aoiinfo2 variable listing a set of reference AOIs. The
% purpose of this function is to calculate a set of backbround AOIs
% appropriate for the reference AOIs listed in InputAoiinfo2.
% AOIsize == the spacing of the background AOIs is based on their size (we
% prefer that they minimally overlap) and the background AOI
% size in pixels will be AOIsize x AOIsize (total area will then
% be AOIsize^2). i.e. AOIsize specifies the length of one side
% (in pixels) of a square AOI
% AOIdistance == the circle of background AOIs that surrond each reference
% AOI will be places with their centers set at a distance of
% AOIdistance (in pixels) away from each reference AOI
% output.aoiinfo2 == an aoiinfo2 variable listing the background AOIs for
% the refernece AOIs specified in InputAoiinfo2
% output.RefAOINearLogik == logical array defined as in the aoifits
% variable. This means that e.g.
% output.aoiinfo2(output.RefAOINearLogik{12},:) will pick out those
% background AOIs in output.aoiinfo2 that are close to refernece
% AOI number 12 in InputAoiinfo2.


% Copyright 2015 Larry Friedman, Brandeis University.
% This is free software: you can redistribute it and/or modify it under the
% terms of the GNU General Public License as published by the Free Software
% Foundation, either version 3 of the License, or (at your option) any later
% version.

% This software is distributed in the hope that it will be useful, but WITHOUT ANY
% WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
% A PARTICULAR PURPOSE. See the GNU General Public License for more details.
% You should have received a copy of the GNU General Public License
% along with this software. If not, see <http://www.gnu.org/licenses/>.

% In polar coordinates (r,theta) the center of the background AOI circle will be
% placed at a distance=AOIdistance from a reference AOI, and will
% spaced by angles theta = 2*delta, where
delta=atan(AOIsize/AOIdistance/sqrt(2));
% Note that AOIsize/sqrt(2) is 1/2 the diagnol of the background
% AOIs we make (square AOIs with sides=AOIsize)

beta=2*delta*1.1; % 1.1 factor and attempt to really insure the AOIs do not overlap
aoinumber=floor(2*pi/beta); % = number of AOIs we will space around the circle
if aoinumber<1
error('AOIsize and AOIdistance are such that no AOI circle will be made')
end
if aoinumber<3
sprintf('only 2 or fewer background AOIs created in circle')
end
[refrose refcol]=size(InputAoiinfo2);
bknumber=aoinumber*refrose; % = total number of background AOIs that will be placed
pc.aoiinfo2=zeros(bknumber,refcol); % Reserve space for output background aoiinfo2
% frm# ave x y pixnum aoi# referenceAOI# (we will not retain referenceAOI# in the output matrix)
bkaoiinfo2=[zeros(bknumber,1) ones(bknumber,1) zeros(bknumber,1) zeros(bknumber,1) AOIsize*ones(bknumber,1) [1:bknumber]' zeros(bknumber,1)];
outindx=1; % Initialize row index of pc.aoiinfo2
for indx=1:refrose
% Looping through all the reference AOIs
xzero=InputAoiinfo2(indx,3);
yzero=InputAoiinfo2(indx,4);
AOIzero=InputAoiinfo2(indx,6);
frmzero=InputAoiinfo2(indx,1);
% Vector of AOIs in the background AOI circle for the current reference AOI
x=xzero+AOIdistance*cos(beta*[0:aoinumber-1]);
y=yzero+AOIdistance*sin(beta*[0:aoinumber-1]);
for subindx=1:aoinumber
% Enter the background AOI coordinates into the output matrix
bkaoiinfo2(outindx,3:4)=[x(subindx) y(subindx)];
bkaoiinfo2(outindx,7)=AOIzero; % Include the reference AOI#
bkaoiinfo2(outindx,1)=frmzero; % Reference AOI frame number
outindx=outindx+1; % Increment the row index
end
end
% Have now written all the xy coordinates for the background AOIs
% Create the output.RefAOINearLogik cell array
pc.RefAOINearLogik=cell(refrose,1);
for refindx=1:refrose
% Loop through all the reference AOIs, finding all their background AOIs in the output aoiinfo2 matrix
logik=InputAoiinfo2(refindx,6)==bkaoiinfo2(:,7); % Logical array, picks out rows
% of bkaoiinfo2 that specify background
% AOIs for the
% current reference AOI#
pc.RefAOINearLogik{refindx,1}=logik;
end


pc.aoiinfo2(:,1:6)=bkaoiinfo2(:,1:6); %
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