Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of neurofibromatosis.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches

[1] § MATERIALS AND METHODS › Immunohistochemistry and confocal imaging ↔ MakeTheMAPMap.m, lines 1–67 · score 0.81 · MakeTheMAPMap, tERK, image stacks, pERK, CMTK, macro
[2] § MATERIALS AND METHODS › Immunohistochemistry and confocal imaging ↔ MakeTheMAPMap.m, lines 1–67 · score 0.67 · tERK, image stacks, pERK, Pairwise, macro, Pixel
[3] § RESULTS › Cxcr4 signaling has limited effects on canonical Ras-Raf-MEK-ERK signaling in the brain ↔ MakeTheMAPMap.m, lines 421–495 · score 0.57 · Mann Whitney, pERK, discovery, bars, stained, FDR
[4] § RESULTS › Cxcr4 signaling has limited effects on canonical Ras-Raf-MEK-ERK signaling in the brain ↔ MakeTheMAPMap.m, lines 68–213 · score 0.57 · tERK, pERK, contraction, indirect, loss, quantified

Paper

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The authors' code

MATLAB · 2,413 lines · 76 KB · no license · 4 matches

function MakeTheMAPMap
close all
clear all
ncores = 4;
ERKLabel = '*1_warp*';
pERKLabel = '*3_warp*';
nPermutes = 500;
FDRThresh = 0.00005; %
UsingERK = 1;
% This function will create the MAP-Map whole-brain activity map from
% registered pERK/tERK data by performing differential intensity analysis
% at each voxel.
%
% Morphed pERK data from two groups needs to be in two folders, and we are
% propted for the folders when the program starts. Each parwise comparison
% between all the groups is made. The input images need to be single
% channel 8-bit tiff stacks. Any registered stacks registered to any
% reference brain should work, but to keep consistent with the formatting
% of the Z-Brain and subsequent analysis, images should be registered into
% the reference brain ('Ref20131120pt14pl2.nrrd'), downsampled to
% 300x679x80 (x,y,z), and pre-smoothed with a 2D gaussian filter (sigma =
% 2). I use an Imagej macro script 'PrepareStacksForMAPMapping.ijm' to do
% this, which converts the '.nrrd' files output from CMTK into Tiffs,
% downsample and smooths appropriately.
%
% We look for which files are pERK stains, and which are total ERK stains
% based on the naming, where channel 1 has the string '1_warp' within it,
% while channel 2 is '2_warp', etc. This needs to be set appropriately
% before running the script.
% Pairwise comparisons are made between all of the input folders. the two
% groups analyzed (GroupA and GroupB) are combined and then ranked. A
% Mann-Whitney U statistic Z score is calculated at each pixel. To then set an FDR threshold,
% pseudogroups are assembled by randomization such that they have an equal
% number of fish from GroupA and GroupB, randomly assigned, and a Z score
% is calculated as before. This mixing procedure is repeated 500 times,
% creating a distribution of control Zs at each voxel. From this
% distribution we then set a FDR threshold 0.00005 (0.005% probability of
% finding a value greater than this threshold). This is done assuming a
% normal distribution. The GroupA vs GroupB Z score is then thresholded at
% this value of Z (all pixels with lesser value are set to 0. The image is
% normalized such that 10 = 255 in an 8bit tiff, and the image stacks are
% written. I also set a requirement that there is a minimal pERK staining
% intensity at the pixel to get rid of most non-brain pixels (average
% across all brains must be 5/255), and there also needs to be a mininmum
% of 5 warped fish in each group at the relevant pixel, set based on the
% fact that the only '0' pixels in the stack are those missing after
% warping - ie. not real image values.
% The main file output from this analysis is the
% '*SignificantDeltaMedian.tif' file, which we refer to as the MAP-Map .
% This stack depicts the delta Median value, at each pixel foud to be above
% the FDR threshold.
% Significant pixels are assigned a non-0 value. Green signal indicates
% higher signals in the first Group (for example, GroupX in a
% 'GroupX_over_GroupY' comparison), magneta signals indicate higher signals
% in the second group. These signals are mapped linearly between 0 and
% 65535 in a 16-bit stack, where 65535 represents a delta pERK level of
% 0.5. We also write the thresholded Z-score comparison ('*ZScores.tif'),
% which represents is mapped 0-255 = ZScore 0-10 in an 8bit stack, As a
% control we write the final mixed group analysis from which the FDR
% threshold is calculated in order to give a sense of what false signals
% look like (there should be almost none). Finally we also write stacks
% depicting the median pERK level at each voxel, and the standard deviation
% at each voxel, for each group.
%
%%--------------- Variables that can be tweaked
%
% ncores -- number of cores on your computer (i.e., num workers). over
% which to parallelize parfor loops. Make sure not to set too hight that
% you run out of RAM!
%
%
% ERK and pERK labels -- '*N_warp*' where N = post-warp channel number
%
% nPermutes -- the number of times we make pseudogroup comparisons for the
% FDR calculation
%
% FDRThresh -- The FRD thresholding of the Z-score. A value of 0.00005
% gives very clean control comparisons.
%
% UsingERK -- logical, set to 1 to run the total-ERK based normalization to
% calculate pERK levels (pERK/tERK). If you are not using this normalization (for
% example if you dont have the tERK stain, or want to quantify differences
% in another channel, set to 0).
%
% Written by Owen Randlett ([email hidden])
%
% This function uses two non-standard matlab functions, which I gratefully acknowldege the authors of:
%
% uipickfiles.m by Douglas Schwarz
%
% http://www.mathworks.com/matlabcentral/fileexchange/10867-uipickfiles--uigetfile-on-steroids
% http://www.mathworks.com/matlabcentral/fileexchange/view_license?file_info_id=10867
%
% uipickfiles BSD Licence:
% Copyright (c) 2007, Douglas M. Schwarz
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are
% met:
%
% * Redistributions of source code must retain the above copyright
% notice, this list of conditions and the following disclaimer.
% * Redistributions in binary form must reproduce the above copyright
% notice, this list of conditions and the following disclaimer in
% the documentation and/or other materials provided with the distribution
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
% POSSIBILITY OF SUCH DAMAGE.
%
% parfor_progress.m by Jeremy Scheff
%
% http://www.mathworks.com/matlabcentral/fileexchange/32101-progress-monitor--progress-bar--that-works-with-parfor/content/parfor_progress.m
% http://www.mathworks.com/matlabcentral/fileexchange/view_license?file_info_id=32101
%
% parfor_progress BSD licence
% Copyright (c) 2011, Jeremy Scheff
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are
% met:
%
% * Redistributions of source code must retain the above copyright
% notice, this list of conditions and the following disclaimer.
% * Redistributions in binary form must reproduce the above copyright
% notice, this list of conditions and the following disclaimer in
% the documentation and/or other materials provided with the distribution
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
% POSSIBILITY OF SUCH DAMAGE.
%
%---------------------------------------------
disp(strcat('Running with the following settings: ncores = ', num2str(ncores), ' ERKLabel = ', num2str(ERKLabel), ' pERKLabel = ', num2str(pERKLabel), ' nPermutes = ', num2str(nPermutes), ' FDRThresh = ', num2str(FDRThresh), 'UsingERK = ', num2str(UsingERK)))
prompt = 'Select all the groups';
Groups.dirs = uipickfiles('Prompt', prompt);
NumGroups = length(Groups.dirs);
cd(Groups.dirs{1});
cd('..');
prompt = 'select output directory';
dirOut = cell2mat(uipickfiles('Prompt', prompt));
if length(dirOut) < 1
error('Invalide dirOut')
end
ParObject = parpool(ncores); % open up the parallel workers
for i = 1:NumGroups;
[~, name, ext] = fileparts(Groups.dirs{i}); % automatically get the group nape from the folder name
Groups.names{i} = strcat(name, ext);
disp(['Group ',num2str(i),' was selected as: ', Groups.names{i}]);
end
%setup a progress bar
NumComparisons = NumGroups.*(NumGroups-1)./2;
% now we need to define all the group comparisons
for m = 1:NumGroups
for n = m+1:NumGroups % these loops define all the pariwise comparisons
tic
GrA = Groups.names{m};
dirA = Groups.dirs{m};
GrB = Groups.names{n};
dirB = Groups.dirs{n};
ChurnThroughGroups(GrA, dirA, GrB, dirB, dirOut, UsingERK, ERKLabel, pERKLabel, ncores, nPermutes, FDRThresh) % process each two group comparison
toc
end
end
delete(ParObject); %shut down the paralell pool
clear all
end
function ChurnThroughGroups(GrA, dirA, GrB, dirB, dirOut, UsingERK, ERKLabel, pERKLabel, ncores, nPermutes, FDRThresh)
cd(dirA)
if UsingERK == 1;
fnames = dir(ERKLabel); %Get the file names: this relies on the CMTK program to add a "warp" after the channel numnber to the warped file images
else
fnames = dir('*.tif*');
end
info = imfinfo(fnames(1).name); % get the image paramaters from the info file
height = info(1).Height; % assign the image dimesnsions
width = info(1).Width;
Zs = numel(info);
if info(1).BitsPerSample ~=8
error('Input images not of correct bit depth. Should be 8-bit images') % if not using 8-bit images, the thresholds will be different
end
cd(dirA)
if UsingERK == 1;
if length(dir(ERKLabel)) ~= length(dir(pERKLabel)) % check to make sure that there are the same number of pERK and ERK stacks
warndlg('The number of stacks in group A arent equal');
end
end
if UsingERK == 1;
fnamesERKA = dir(ERKLabel);
fnamespERKA = dir(pERKLabel);
else
fnamespERKA = dir(pERKLabel);
fnamesERKA = [];
end
nGroupA = length(fnamespERKA); % get the number of fish from the number of images found
cd(dirB) % do the same for groupB
if UsingERK == 1;
if length(dir(ERKLabel)) ~= length(dir(pERKLabel)) % check to make sure that there are the same number of pERK and ERK stacks
warndlg('The number of stacks in group B arent equal');
end
end
if UsingERK == 1;
fnamesERKB = dir(ERKLabel);
fnamespERKB = dir(pERKLabel);
else
fnamespERKB = dir(pERKLabel);
fnamesERKB = [];
end
nGroupB = length(fnamespERKB);
% preallocate images
Amedian = zeros(height, width, Zs);
AStd = zeros(height, width, Zs);
Bmedian= zeros(height, width, Zs);
BStd = zeros(height, width, Zs);
mwuZScoresImage = zeros(height, width, Zs);
mwuMixedZScoresImageSingleIteration = zeros(height, width, Zs); % when I finally write the file, I dont want the one that is the mean that has been iterated over many times so I will use this single iteration to write as an example image of the FDR thresholding
%Set up the groups for the mixed group analysis
RandMixedGrA = zeros(floor(nGroupA./2)*2,nPermutes);
RandMixedGrB = zeros(floor(nGroupB./2)*2,nPermutes);
for nperm = 1:nPermutes % pre-assign all of the mixed groups. This is done so that the computation is only done once, and so that we have the same exact mixed group comparisons to write as the control image
RandMixedGrA(:,nperm) = datasample(1:nGroupA, floor(nGroupA./2)*2, 'Replace', false); % pick random indicies for the psuedo group
RandMixedGrB(:,nperm) = datasample(nGroupA+1:nGroupB+nGroupA, floor(nGroupB./2)*2, 'Replace', false);
end
cd(dirOut);
parfor_progress(Zs);
parfor (z = 1:Zs, ncores) % loop through each z plane one at a time to build up the final Z-score image stack
BpERK = zeros(height, width, nGroupB);
ApERK = zeros(height, width, nGroupA);
if UsingERK == 1
BERK = zeros(height, width, nGroupB);
AERK = zeros(height, width, nGroupA);
end
cd(dirA);
for j = 1:nGroupA % we loop through load all images from one group into an image stack
infopERKA = imfinfo(fnamespERKA(j).name);
% now we will calculate the pERK signal over the total signal. This
% will be our matrix.
ApERK(:,:,j) = imread(fnamespERKA(j).name, z, 'Info', infopERKA);
if UsingERK == 1
infoERKA = imfinfo(fnamesERKA(j).name);
AERK(:,:,j) = imread(fnamesERKA(j).name, z, 'Info', infoERKA);
end
end
if UsingERK == 1
A = ApERK./AERK; %calculate pERK signal over total signal
elseif UsingERK == 0
A = ApERK;
end
cd (dirB);
for j = 1:nGroupB % we loop through load all images from one group into an image stack
infopERKB = imfinfo(fnamespERKB(j).name);
% now we will calculate the pERK signal over the total signal. This
% will be our matrix.
BpERK(:,:,j) = imread(fnamespERKB(j).name, z, 'Info', infopERKB);
if UsingERK == 1
infoERKB = imfinfo(fnamesERKB(j).name);
BERK(:,:,j) = imread(fnamesERKB(j).name, z, 'Info', infoERKB);
end
end
if UsingERK == 1
B = BpERK./BERK; %calculate pERK signal over total signal
elseif UsingERK == 0
B = BpERK;
end
Amedian(:,:,z) = nanmedian(A, 3);
Bmedian(:,:,z) = nanmedian(B, 3);
AStd(:,:,z) = nanstd(A, 0, 3);
BStd(:,:,z) = nanstd(B, 0, 3);
meanpERK = mean(cat(3, ApERK, BpERK), 3);
% Now we want to calculate a ranksum like statistic for the groups
% rather than caculating a T-statistic
%
%Combine all into one big matrix to rank.
ABCombined = cat(3,A,B);
%Determine which indices are from which group
FishInGroupA = 1:size(A,3);
FishInGroupB = size(A,3)+1:size(A,3)+size(B,3);
ranks = tiedrank(permute(ABCombined, [3,2,1])); % rank the fish. The permute calls are required because tiedrank only works along the first dimension of a matrix
ranks = permute(ranks, [3,2,1]);
%Fisrt we do a kind of boostrapping we randomly mixed data to find
%the false discovery distribution. By mixing the groups with equal
%numbers of fish from each group, we should destroy any of the
%group by group variablility that we are trying to quantify, and
%thus determine the noise level in our analysis. This is done
%'nPermutes' number of times
ZScoresMixedGrA = zeros(height, width, nPermutes);
ZScoresMixedGrB = zeros(height, width, nPermutes);
for perm = 1:nPermutes
% get the vector for the indiecies of the fish in each mixed group
RandMixedGrAThisPerm = squeeze(RandMixedGrA(:,perm))';
RandMixedGrBThisPerm = squeeze(RandMixedGrB(:,perm))';
FishInMixedGrA = [RandMixedGrAThisPerm(1:end/2),RandMixedGrBThisPerm(1:end/2)];
FishInMixedGrB = [RandMixedGrAThisPerm(end/2+1:end), RandMixedGrBThisPerm(end/2+1:end)];
% sum the ranks from each group
SumRanksMixedGrA = nansum(ranks(:,:,FishInMixedGrA),3);
SumRanksMixedGrB = nansum(ranks(:,:,FishInMixedGrB),3);
% determine the number of fish contributing to each pixel. This is
% not always the same, because if for example part of the forebrain
% was not imaged in one fish, after warping there are 0-pixel
% values at this missing region. These are NaN'd out above, but we
% need to keep track of the Ns for the ranksum and Z-score
% statistics
NsInMixedGrA = length(FishInMixedGrA) - sum(isnan(ranks(:,:,FishInMixedGrA)),3);
NsInMixedGrB = length(FishInMixedGrB) - sum(isnan(ranks(:,:,FishInMixedGrB)),3);
%Calculate the Mann-Whitney U-statistic
%(http://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U)
UMixedGrA = SumRanksMixedGrA - (NsInMixedGrA.*(NsInMixedGrA + 1))./2;
UMixedGrB = SumRanksMixedGrB - (NsInMixedGrB.*(NsInMixedGrB + 1))./2;
%Calculate the Z-score. The disribution of Us can be assumed to be
%normal, and from inspection of my data this assumption appears
%valid
%The value of U is the mean between the two groups
MUmixed = (UMixedGrA + UMixedGrB)./2;
SigmaUmixed = sqrt(NsInMixedGrA.*NsInMixedGrB.*(NsInMixedGrA + NsInMixedGrB + 1)./12);
ZScoresMixedGrATemp = (UMixedGrA - MUmixed)./SigmaUmixed;
ZScoresMixedGrBTemp = (UMixedGrB - MUmixed)./SigmaUmixed;
ZScoresMixedGrA(:,:,perm) = ZScoresMixedGrATemp;
ZScoresMixedGrB(:,:,perm) = ZScoresMixedGrBTemp;
end
% now we set the FDR threshold. The distrubition of Zs appears
% normally distributed at each pixel, so I will use norminv to find
% the critical value for Z at each pixel, with an frd rate set
% above (ex 0.00005).
ZScoreThresh = norminv((1-FDRThresh), 0, std(ZScoresMixedGrA, 0, 3));
% now we do the actual comparison between groups. Fist sum the
% ranks;
SumRanksGrA = nansum(ranks(:,:,FishInGroupA),3);
SumRanksGrB = nansum(ranks(:,:,FishInGroupB),3);
%Determine the Ns based on the number of non-NaN values at each
%pixel
NsInGrA = size(A,3) - sum(isnan(ranks(:,:,FishInGroupA)),3);
NsInGrB = size(B,3) - sum(isnan(ranks(:,:,FishInGroupB)),3);
% get the mann-whiteny Us
UGrA = SumRanksGrA - (NsInGrA.*(NsInGrA + 1))./2;
UGrB = SumRanksGrB - (NsInGrB.*(NsInGrB + 1))./2;
%Calculate the Z-score
MU = (UGrA + UGrB)./2;
SigmaU = sqrt(NsInGrA.*NsInGrB.*(NsInGrA + NsInGrB + 1)./12);
ZScoresGrA = (UGrA - MU)./SigmaU;
%throw away any pixel where the mean pERK value is less than 5 (as
%the brain is highly stained, these are mostly non-brain pixels)
ZScoresGrA(meanpERK < 5) = NaN;
%throw away any pixel in which we dont have at least 5 fish
ZScoresGrA(NsInGrA < 5) = NaN;
ZScoresGrA(NsInGrB < 5) = NaN;
%Threshold the ZScores based on the FDR threshold we calculated.
%Note this is done separately at each pixel.
ZScoresGrA(abs(ZScoresGrA)<ZScoreThresh) = NaN;
%Assign these values in the image stack we will wite later
mwuZScoresImage(:,:,z) = ZScoresGrA;
% Do the same thing for the last mixed-group comparison as an
% example of the false discoveries.
ZScoresMixedSigleIterationForWriting = ZScoresMixedGrA(:,:,end); % we will save the last iteration and write to file to show what the control FDR rate images look like.
ZScoresMixedSigleIterationForWriting(meanpERK < 5) = NaN;
ZScoresMixedSigleIterationForWriting(NsInGrA < 5) = NaN;
ZScoresMixedSigleIterationForWriting(NsInGrB < 5) = NaN;
ZScoresMixedSigleIterationForWriting(abs(ZScoresMixedSigleIterationForWriting)<ZScoreThresh) = NaN;
mwuMixedZScoresImageSingleIteration(:,:,z) = ZScoresMixedSigleIterationForWriting;
cd(dirOut);
parfor_progress; %update the lovely parfor progess bar.
end
cd(dirOut);
parfor_progress(0);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
disp(strcat('Completed the comparison of: ', GrA, '-vs-', GrB)) % uodate where we are in the analysis
%now we threshold the images such that a Z-statistic of 10 is saturated. We
%also split into the positive and negative components such that these can
%be written in differnt colours.
mwuZScoresImage = mwuZScoresImage./10;
mwuZScoresImage(mwuZScoresImage > 1) = 1;
mwuZScoresImage(mwuZScoresImage < -1) = -1;
mwuZScoresImagePositive = mwuZScoresImage;
mwuZScoresImagePositive(mwuZScoresImagePositive < 0) = 0;
mwuZScoresImageNegative = mwuZScoresImage.*-1;
mwuZScoresImageNegative(mwuZScoresImageNegative < 0) = 0;
mwuMixedZScoresImageSingleIteration = mwuMixedZScoresImageSingleIteration./10;
mwuMixedZScoresImageSingleIteration(mwuMixedZScoresImageSingleIteration > 1) = 1;
mwuMixedZScoresImageSingleIteration(mwuMixedZScoresImageSingleIteration < -1) = -1;
mwuMixedZScoresImageSingleIterationPositive = mwuMixedZScoresImageSingleIteration;
mwuMixedZScoresImageSingleIterationPositive(mwuMixedZScoresImageSingleIterationPositive < 0) = 0;
mwuMixedZScoresImageSingleIterationNegative = mwuMixedZScoresImageSingleIteration.*-1;
mwuMixedZScoresImageSingleIterationNegative(mwuMixedZScoresImageSingleIterationNegative < 0) = 0;
% Compute the delta Median images thresholded with the ZScores
DeltaMedian = (Amedian - Bmedian)./(Amedian + Bmedian);
DeltaMedianPos = zeros(size(DeltaMedian));
DeltaMedianNeg = zeros(size(DeltaMedian));
DeltaMedianPos(mwuZScoresImagePositive >0) = abs(DeltaMedian(mwuZScoresImagePositive >0));
DeltaMedianNeg(mwuZScoresImageNegative >0) = abs(DeltaMedian(mwuZScoresImageNegative >0));
DeltaMedianPos = uint16(DeltaMedianPos./0.5.*65535);
DeltaMedianNeg = uint16(DeltaMedianNeg./0.5.*65535);
cd(dirOut);
%Write the tiffs. The try/catch loop avoids the bug in windows when maltab
%tries to write to the tiff that windows explorer is accessing.
%Currently I write two files for the comparison of GrA over GrB (where what
%is brighter in GrA is green and brighter in GrB is Magenta), and also
%write GrB over GrA (Where GrB is green). This is redundant, but probably
%useful as I am not defining which is control vs experimental, and I like
%to have experimental as green.
if length(dir(strcat(GrA, '_over_', GrB, '_ZScores.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat(GrA, '_over_', GrB, '_ZScores.tif');
for ind = 1:Zs
while true
try
imwrite(cat(3, mwuZScoresImageNegative(:,:,ind), mwuZScoresImagePositive(:,:,ind), mwuZScoresImageNegative(:,:,ind)), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written: ', GrA, '_over_', GrB, '_ZScores.tif, Skipping file write'))
end
if length(dir(strcat(GrB, '_over_', GrA, '_ZScores.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat(GrB, '_over_', GrA, '_ZScores.tif');
for ind = 1:Zs
while true
try
imwrite(cat(3, mwuZScoresImagePositive(:,:,ind), mwuZScoresImageNegative(:,:,ind), mwuZScoresImagePositive(:,:,ind)), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written:', GrB, '_over_', GrA, '_ZScores.tif, Skipping file write'))
end
% write the mixeed control images
if length(dir(strcat('MixedControl', GrA, '_over_', GrB, '_ZScores.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat('MixedControl', GrA, '_over_', GrB, '_ZScores.tif');
for ind = 1:Zs
while true
try
imwrite(cat(3, mwuMixedZScoresImageSingleIterationNegative(:,:,ind), mwuMixedZScoresImageSingleIterationPositive(:,:,ind), mwuMixedZScoresImageSingleIterationNegative(:,:,ind)), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written:', 'MixedControl', GrA, '_over_', GrB, '_ZScores.tif, Skipping file write'))
end
if length(dir(strcat('MixedControl', GrB, '_over_', GrA, '_ZScores.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat('MixedControl', GrB, '_over_', GrA, '_ZScores.tif');
for ind = 1:Zs
while true
try
imwrite(cat(3, mwuMixedZScoresImageSingleIterationPositive(:,:,ind), mwuMixedZScoresImageSingleIterationNegative(:,:,ind), mwuMixedZScoresImageSingleIterationPositive(:,:,ind)), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written:', 'MixedControl', GrB, '_over_', GrA, '_ZScores.tif, Skipping file write'))
end
% Write the median stack to file.
if UsingERK == 0; % if raw averages these should be 8 bit, if pERK/ERK analysis, normalize to 10.
Amedian = uint8(Amedian);
Bmedian = uint8(Bmedian);
else
Amedian = uint16(Amedian.*65535/10);
Bmedian = uint16(Bmedian.*65535/10);
end
if length(dir(strcat(GrA, '_medianStack.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat(GrA, '_medianStack.tif');
for ind = 1:Zs
while true
try
imwrite(Amedian(:,:,ind), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
%warning(strcat('Warning! Already written:',GrA, '_medianStack.tif,
%Skipping file write'))
end
if length(dir(strcat(GrB, '_medianStack.tif')))<1
tiffFile = strcat(GrB, '_medianStack.tif');
for ind = 1:Zs
while true
try
imwrite(Bmedian(:,:,ind), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
%warning(strcat('Warning! Already written:',GrB, '_medianStack.tif,
%Skipping file write'))
end
% Write the std stack to file.
if UsingERK == 0; % if raw averages these should be 8 bit, if pERK/ERK analysis, normalize to 10.
AStd = uint8(AStd);
BStd = uint8(BStd);
elseif UsingERK == 1;
AStd = uint16(AStd.*65535/10);
BStd = uint16(BStd.*65535/10);
end
if length(dir(strcat(GrA, '_StdStack.tif'))) < 1 % check to make sure we havent already written this file
tiffFile = strcat(GrA, '_StdStack.tif');
for ind = 1:Zs
while true
try
imwrite(AStd(:,:,ind), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
%warning(strcat('Warning! Already written:',GrA, '_medianStack.tif,
%Skipping file write'))
end
if length(dir(strcat(GrB, '_StdStack.tif')))<1
tiffFile = strcat(GrB, '_StdStack.tif');
for ind = 1:Zs
while true
try
imwrite(BStd(:,:,ind), tiffFile,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
%warning(strcat('Warning! Already written:',GrB, '_medianStack.tif,
%Skipping file write'))
end
TiffName = strcat(GrA, '_over_', GrB, '_SignificantDeltaMedians.tif');
if length(dir(TiffName)) < 1 % check to make sure we havent already written this file
for ind = 1:Zs
while true
try
imwrite(cat(3, DeltaMedianNeg(:,:,ind), DeltaMedianPos(:,:,ind), DeltaMedianNeg(:,:,ind)), TiffName,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written:', TiffName, 'Skipping file write'))
end
TiffName = strcat(GrB, '_over_', GrA, '_SignificantDeltaMedians.tif');
if length(dir(TiffName)) < 1 % check to make sure we havent already written this file
for ind = 1:Zs
while true
try
imwrite(cat(3, DeltaMedianPos(:,:,ind), DeltaMedianNeg(:,:,ind), DeltaMedianPos(:,:,ind)), TiffName,'WriteMode','append', 'Compression', 'none');
break
catch
disp('Encountered a Tiff write error')
end
end
end
else
warning(strcat('Warning! Already written:', TiffName, 'Skipping file write'))
end
end
function out = uipickfiles(varargin)
%uipickfiles: GUI program to select files and/or folders.
%
% Syntax:
% files = uipickfiles('PropertyName',PropertyValue,...)
%
% The current folder can be changed by operating in the file navigator:
% double-clicking on a folder in the list or pressing Enter to move further
% down the tree, using the popup menu, clicking the up arrow button or
% pressing Backspace to move up the tree, typing a path in the box to move
% to any folder or right-clicking (control-click on Mac) on the path box to
% revisit a previously-visited folder. These folders are listed in order
% of when they were last visited (most recent at the top) and the list is
% saved between calls to uipickfiles. The list can be cleared or its
% maximum length changed with the items at the bottom of the menu.
% (Windows only: To go to a UNC-named resource you will have to type the
% UNC name in the path box, but all such visited resources will be
% remembered and listed along with the mapped drives.) The items in the
% file navigator can be sorted by name, modification date or size by
% clicking on the headers, though neither date nor size are displayed. All
% folders have zero size.
%
% Files can be added to the list by double-clicking or selecting files
% (non-contiguous selections are possible with the control key) and
% pressing the Add button. Control-F will select all the files listed in
% the navigator while control-A will select everything (Command instead of
% Control on the Mac). Since double-clicking a folder will open it,
% folders can be added only by selecting them and pressing the Add button.
% Files/folders in the list can be removed or re-ordered. Recall button
% will insert into the Selected Files list whatever files were returned the
% last time uipickfiles was run. When finished, a press of the Done button
% will return the full paths to the selected items in a cell array,
% structure array or character array. If the Cancel button or the escape
% key is pressed then zero is returned.
%
% The figure can be moved and resized in the usual way and this position is
% saved and used for subsequent calls to uipickfiles. The default position
% can be restored by double-clicking in a vacant region of the figure.
%
% The following optional property/value pairs can be specified as arguments
% to control the indicated behavior:
%
% Property Value
% ---------- ----------------------------------------------------------
% FilterSpec String to specify starting folder and/or file filter.
% Ex: 'C:\bin' will start up in that folder. '*.txt'
% will list only files ending in '.txt'. 'c:\bin\*.txt' will
% do both. Default is to start up in the current folder and
% list all files. Can be changed with the GUI.
%
% REFilter String containing a regular expression used to filter the
% file list. Ex: '\.m$|\.mat$' will list files ending in
% '.m' and '.mat'. Default is empty string. Can be used
% with FilterSpec and both filters are applied. Can be
% changed with the GUI.
%
% REDirs Logical flag indicating whether to apply the regular
% expression filter to folder names. Default is false which
% means that all folders are listed. Can be changed with the
% GUI.
%
% Type Two-column cell array where the first column contains file
% filters and the second column contains descriptions. If
% this property is specified an additional popup menu will
% appear below the File Filter and selecting an item will put
% that item into the File Filter. By default, the first item
% will be entered into the File Filter. For example,
% { '*.m', 'M-files' ;
% '*.mat', 'MAT-files' }.
% Can also be a cell vector of file filter strings in which
% case the descriptions will be the same as the file filters
% themselves.
% Must be a cell array even if there is only one entry.
%
% Prompt String containing a prompt appearing in the title bar of
% the figure. Default is 'Select files'.
%
% NumFiles Scalar or vector specifying number of files that must be
% selected. A scalar specifies an exact value; a two-element
% vector can be used to specify a range, [min max]. The
% function will not return unless the specified number of
% files have been chosen. Default is [] which accepts any
% number of files.
%
% Append Cell array of strings, structure array or char array
% containing a previously returned output from uipickfiles.
% Used to start up program with some entries in the Selected
% Files list. Any included files that no longer exist will
% not appear. Default is empty cell array, {}.
%
% Output String specifying the data type of the output: 'cell',
% 'struct' or 'char'. Specifying 'cell' produces a cell
% array of strings, the strings containing the full paths of
% the chosen files. 'Struct' returns a structure array like
% the result of the dir function except that the 'name' field
% contains a full path instead of just the file name. 'Char'
% returns a character array of the full paths. This is most
% useful when you have just one file and want it in a string
% instead of a cell array containing just one string. The
% default is 'cell'.
%
% All properties and values are case-insensitive and need only be
% unambiguous. For example,
%
% files = uipickfiles('num',1,'out','ch')
%
% is valid usage.
% Version: 1.15, 2 March 2012
% Author: Douglas M. Schwarz
% Email: dmschwarz=ieee*org, dmschwarz=urgrad*rochester*edu
% Real_email = regexprep(Email,{'=','*'},{'@','.'})
% Define properties and set default values.
prop.filterspec = '*';
prop.refilter = '';
prop.redirs = false;
prop.type = {};
prop.prompt = 'Select files';
prop.numfiles = [];
prop.append = [];
prop.output = 'cell';
% Process inputs and set prop fields.
prop = parsepropval(prop,varargin{:});
% Validate FilterSpec property.
if isempty(prop.filterspec)
prop.filterspec = '*';
end
if ~ischar(prop.filterspec)
error('FilterSpec property must contain a string.')
end
% Validate REFilter property.
if ~ischar(prop.refilter)
error('REFilter property must contain a string.')
end
% Validate REDirs property.
if ~isscalar(prop.redirs)
error('REDirs property must contain a scalar.')
end
% Validate Type property.
if isempty(prop.type)
elseif iscellstr(prop.type) && isscalar(prop.type)
prop.type = repmat(prop.type(:),1,2);
elseif iscellstr(prop.type) && size(prop.type,2) == 2
else
error(['Type property must be empty or a cellstr vector or ',...
'a 2-column cellstr matrix.'])
end
% Validate Prompt property.
if ~ischar(prop.prompt)
error('Prompt property must contain a string.')
end
% Validate NumFiles property.
if numel(prop.numfiles) > 2 || any(prop.numfiles < 0)
error('NumFiles must be empty, a scalar or two-element vector.')
end
prop.numfiles = unique(prop.numfiles);
if isequal(prop.numfiles,1)
numstr = 'Select exactly 1 file.';
elseif length(prop.numfiles) == 1
numstr = sprintf('Select exactly %d items.',prop.numfiles);
else
numstr = sprintf('Select %d to %d items.',prop.numfiles);
end
% Validate Append property and initialize pick data.
if isstruct(prop.append) && isfield(prop.append,'name')
prop.append = {prop.append.name};
elseif ischar(prop.append)
prop.append = cellstr(prop.append);
end
if isempty(prop.append)
file_picks = {};
full_file_picks = {};
dir_picks = dir(' '); % Create empty directory structure.
elseif iscellstr(prop.append) && isvector(prop.append)
num_items = length(prop.append);
file_picks = cell(1,num_items);
full_file_picks = cell(1,num_items);
dir_fn = fieldnames(dir(' '));
dir_picks = repmat(cell2struct(cell(length(dir_fn),1),dir_fn(:)),...
num_items,1);
for item = 1:num_items
if exist(prop.append{item},'dir') && ...
~any(strcmp(full_file_picks,prop.append{item}))
full_file_picks{item} = prop.append{item};
[unused,fn,ext] = fileparts(prop.append{item});
file_picks{item} = [fn,ext];
temp = dir(fullfile(prop.append{item},'..'));
if ispc || ismac
thisdir = strcmpi({temp.name},[fn,ext]);
else
thisdir = strcmp({temp.name},[fn,ext]);
end
dir_picks(item) = temp(thisdir);
dir_picks(item).name = prop.append{item};
elseif exist(prop.append{item},'file') && ...
~any(strcmp(full_file_picks,prop.append{item}))
full_file_picks{item} = prop.append{item};
[unused,fn,ext] = fileparts(prop.append{item});
file_picks{item} = [fn,ext];
dir_picks(item) = dir(prop.append{item});
dir_picks(item).name = prop.append{item};
else
continue
end
end
% Remove items which no longer exist.
missing = cellfun(@isempty,full_file_picks);
full_file_picks(missing) = [];
file_picks(missing) = [];
dir_picks(missing) = [];
else
error('Append must be a cell, struct or char array.')
end
% Validate Output property.
legal_outputs = {'cell','struct','char'};
out_idx = find(strncmpi(prop.output,legal_outputs,length(prop.output)));
if length(out_idx) == 1
prop.output = legal_outputs{out_idx};
else
error(['Value of ''Output'' property, ''%s'', is illegal or '...
'ambiguous.'],prop.output)
end
% Set style preference for display of folders.
% 1 => folder icon before and filesep after
% 2 => bullet before and filesep after
% 3 => filesep after only
folder_style_pref = 1;
fsdata = set_folder_style(folder_style_pref);
% Initialize file lists.
if exist(prop.filterspec,'dir')
current_dir = prop.filterspec;
filter = '*';
else
[current_dir,f,e] = fileparts(prop.filterspec);
filter = [f,e];
end
if isempty(current_dir)
current_dir = pwd;
end
if isempty(filter)
filter = '*';
end
re_filter = prop.refilter;
full_filter = fullfile(current_dir,filter);
network_volumes = {};
[path_cell,new_network_vol] = path2cell(current_dir);
if exist(new_network_vol,'dir')
network_volumes = unique([network_volumes,{new_network_vol}]);
end
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,[1 0 0]));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
% Initialize some data.
show_full_path = false;
nodupes = true;
% Get history preferences and set history.
history = getpref('uipickfiles','history',...
struct('name',current_dir,'time',now));
default_history_size = 15;
history_size = getpref('uipickfiles','history_size',default_history_size);
history = update_history(history,current_dir,now,history_size);
% Get figure position preference and create figure.
gray = get(0,'DefaultUIControlBackgroundColor');
if ispref('uipickfiles','figure_position');
fig_pos = getpref('uipickfiles','figure_position');
fig = figure('Position',fig_pos,...
'Color',gray,...
'MenuBar','none',...
'WindowStyle','modal',...
'Resize','on',...
'NumberTitle','off',...
'Name',prop.prompt,...
'IntegerHandle','off',...
'CloseRequestFcn',@cancel,...
'ButtonDownFcn',@reset_figure_size,...
'KeyPressFcn',@keypressmisc,...
'Visible','off');
else
fig_pos = [0 0 740 494];
fig = figure('Position',fig_pos,...
'Color',gray,...
'MenuBar','none',...
'WindowStyle','modal',...
'Resize','on',...
'NumberTitle','off',...
'Name',prop.prompt,...
'IntegerHandle','off',...
'CloseRequestFcn',@cancel,...
'CreateFcn',{@movegui,'center'},...
'ButtonDownFcn',@reset_figure_size,...
'KeyPressFcn',@keypressmisc,...
'Visible','off');
end
% Set system-dependent items.
if ismac
set(fig,'DefaultUIControlFontName','Lucida Grande')
set(fig,'DefaultUIControlFontSize',9)
sort_ctrl_size = 8;
mod_key = 'command';
action = 'Control-click';
elseif ispc
set(fig,'DefaultUIControlFontName','Tahoma')
set(fig,'DefaultUIControlFontSize',8)
sort_ctrl_size = 7;
mod_key = 'control';
action = 'Right-click';
else
sort_ctrl_size = get(fig,'DefaultUIControlFontSize') - 1;
mod_key = 'control';
action = 'Right-click';
end
% Create uicontrols.
frame1 = uicontrol('Style','frame',...
'Position',[255 260 110 70]);
frame2 = uicontrol('Style','frame',...
'Position',[275 135 110 100]);
navlist = uicontrol('Style','listbox',...
'Position',[10 10 250 320],...
'String',filenames,...
'Value',[],...
'BackgroundColor','w',...
'Callback',@clicknav,...
'KeyPressFcn',@keypressnav,...
'Max',2);
tri_up = repmat([1 1 1 1 0 1 1 1 1;1 1 1 0 0 0 1 1 1;1 1 0 0 0 0 0 1 1;...
1 0 0 0 0 0 0 0 1],[1 1 3]);
tri_up(tri_up == 1) = NaN;
tri_down = tri_up(end:-1:1,:,:);
tri_null = NaN(4,9,3);
tri_icon = {tri_down,tri_null,tri_up};
sort_state = [1 0 0];
last_sort_state = [1 1 1];
sort_cb = zeros(1,3);
sort_cb(1) = uicontrol('Style','checkbox',...
'Position',[15 331 70 15],...
'String','Name',...
'FontSize',sort_ctrl_size,...
'Value',sort_state(1),...
'CData',tri_icon{sort_state(1)+2},...
'KeyPressFcn',@keypressmisc,...
'Callback',{@sort_type,1});
sort_cb(2) = uicontrol('Style','checkbox',...
'Position',[85 331 70 15],...
'String','Date',...
'FontSize',sort_ctrl_size,...
'Value',sort_state(2),...
'CData',tri_icon{sort_state(2)+2},...
'KeyPressFcn',@keypressmisc,...
'Callback',{@sort_type,2});
sort_cb(3) = uicontrol('Style','checkbox',...
'Position',[155 331 70 15],...
'String','Size',...
'FontSize',sort_ctrl_size,...
'Value',sort_state(3),...
'CData',tri_icon{sort_state(3)+2},...
'KeyPressFcn',@keypressmisc,...
'Callback',{@sort_type,3});
pickslist = uicontrol('Style','listbox',...
'Position',[380 10 350 320],...
'String',file_picks,...
'BackgroundColor','w',...
'Callback',@clickpicks,...
'KeyPressFcn',@keypresslist,...
'Max',2,...
'Value',[]);
openbut = uicontrol('Style','pushbutton',...
'Position',[270 300 80 20],...
'String','Open',...
'Enable','off',...
'KeyPressFcn',@keypressmisc,...
'Callback',@open);
arrow = [ ...
' 1 ';
' 10 ';
' 10 ';
'000000000000';
' 10 ';
' 10 ';
' 1 '];
cmap = NaN(128,3);
cmap(double('10'),:) = [0.5 0.5 0.5;0 0 0];
arrow_im = NaN(7,76,3);
arrow_im(:,45:56,:) = ind2rgb(double(arrow),cmap);
addbut = uicontrol('Style','pushbutton',...
'Position',[270 270 80 20],...
'String','Add ',...
'Enable','off',...
'CData',arrow_im,...
'KeyPressFcn',@keypressmisc,...
'Callback',@add);
removebut = uicontrol('Style','pushbutton',...
'Position',[290 205 80 20],...
'String','Remove',...
'Enable','off',...
'KeyPressFcn',@keypressmisc,...
'Callback',@remove);
moveupbut = uicontrol('Style','pushbutton',...
'Position',[290 175 80 20],...
'String','Move Up',...
'Enable','off',...
'KeyPressFcn',@keypressmisc,...
'Callback',@moveup);
movedownbut = uicontrol('Style','pushbutton',...
'Position',[290 145 80 20],...
'String','Move Down',...
'Enable','off',...
'KeyPressFcn',@keypressmisc,...
'Callback',@movedown);
dir_popup = uicontrol('Style','popupmenu',...
'Position',[10 350 225 20],...
'BackgroundColor','w',...
'String',path_cell,...
'Value',length(path_cell),...
'KeyPressFcn',@keypressmisc,...
'Callback',@dirpopup);
uparrow = [ ...
' 0 ';
' 000 ';
'00000 ';
' 0 ';
' 0 ';
' 0 ';
' 000000'];
cmap = NaN(128,3);
cmap(double('0'),:) = [0 0 0];
uparrow_im = ind2rgb(double(uparrow),cmap);
up_dir_but = uicontrol('Style','pushbutton',...
'Position',[240 350 20 20],...
'CData',uparrow_im,...
'KeyPressFcn',@keypressmisc,...
'Callback',@dir_up_one,...
'ToolTip','Go to parent folder');
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
hist_cm = uicontextmenu;
pathbox = uicontrol('Style','edit',...
'Position',[10 375 250 26],...
'BackgroundColor','w',...
'String',current_dir,...
'HorizontalAlignment','left',...
'TooltipString',[action,' to display folder history'],...
'KeyPressFcn',@keypressmisc,...
'Callback',@change_path,...
'UIContextMenu',hist_cm);
label1 = uicontrol('Style','text',...
'Position',[10 401 250 16],...
'String','Current Folder',...
'HorizontalAlignment','center',...
'TooltipString',[action,' to display folder history'],...
'UIContextMenu',hist_cm);
hist_menus = [];
make_history_cm()
label2 = uicontrol('Style','text',...
'Position',[10 440+36 80 17],...
'String','File Filter',...
'HorizontalAlignment','left');
label3 = uicontrol('Style','text',...
'Position',[100 440+36 160 17],...
'String','Reg. Exp. Filter',...
'HorizontalAlignment','left');
showallfiles = uicontrol('Style','checkbox',...
'Position',[270 420+32 110 20],...
'String','Show All Files',...
'Value',0,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@togglefilter);
refilterdirs = uicontrol('Style','checkbox',...
'Position',[270 420+10 100 20],...
'String','RE Filter Dirs',...
'Value',prop.redirs,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@toggle_refiltdirs);
filter_ed = uicontrol('Style','edit',...
'Position',[10 420+30 80 26],...
'BackgroundColor','w',...
'String',filter,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@setfilspec);
refilter_ed = uicontrol('Style','edit',...
'Position',[100 420+30 160 26],...
'BackgroundColor','w',...
'String',re_filter,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@setrefilter);
type_value = 1;
type_popup = uicontrol('Style','popupmenu',...
'Position',[10 422 250 20],...
'String','',...
'BackgroundColor','w',...
'Value',type_value,...
'KeyPressFcn',@keypressmisc,...
'Callback',@filter_type_callback,...
'Visible','off');
if ~isempty(prop.type)
set(filter_ed,'String',prop.type{type_value,1})
setfilspec()
set(type_popup,'String',prop.type(:,2),'Visible','on')
end
viewfullpath = uicontrol('Style','checkbox',...
'Position',[380 335 230 20],...
'String','Show full paths',...
'Value',show_full_path,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@showfullpath);
remove_dupes = uicontrol('Style','checkbox',...
'Position',[380 360 280 20],...
'String','Remove duplicates (as per full path)',...
'Value',nodupes,...
'HorizontalAlignment','left',...
'KeyPressFcn',@keypressmisc,...
'Callback',@removedupes);
recall_button = uicontrol('Style','pushbutton',...
'Position',[665 335 65 20],...
'String','Recall',...
'KeyPressFcn',@keypressmisc,...
'Callback',@recall,...
'ToolTip','Add previously selected items');
label4 = uicontrol('Style','text',...
'Position',[380 405 350 20],...
'String','Selected Items',...
'HorizontalAlignment','center');
done_button = uicontrol('Style','pushbutton',...
'Position',[280 80 80 30],...
'String','Done',...
'KeyPressFcn',@keypressmisc,...
'Callback',@done);
cancel_button = uicontrol('Style','pushbutton',...
'Position',[280 30 80 30],...
'String','Cancel',...
'KeyPressFcn',@keypressmisc,...
'Callback',@cancel);
% If necessary, add warning about number of items to be selected.
num_files_warn = uicontrol('Style','text',...
'Position',[380 385 350 16],...
'String',numstr,...
'ForegroundColor',[0.8 0 0],...
'HorizontalAlignment','center',...
'Visible','off');
if ~isempty(prop.numfiles)
set(num_files_warn,'Visible','on')
end
resize()
% Make figure visible and hide handle.
set(fig,'HandleVisibility','off',...
'Visible','on',...
'ResizeFcn',@resize)
% Wait until figure is closed.
uiwait(fig)
% Compute desired output.
switch prop.output
case 'cell'
out = full_file_picks;
case 'struct'
out = dir_picks(:);
case 'char'
out = char(full_file_picks);
case 'cancel'
out = 0;
end
% Update history preference.
setpref('uipickfiles','history',history)
if ~isempty(full_file_picks) && ~strcmp(prop.output,'cancel')
setpref('uipickfiles','full_file_picks',full_file_picks)
end
% Update figure position preference.
setpref('uipickfiles','figure_position',fig_pos)
% ----------------- Callback nested functions ----------------
function add(varargin)
values = get(navlist,'Value');
for i = 1:length(values)
dir_pick = fdir(values(i));
pick = dir_pick.name;
pick_full = fullfile(current_dir,pick);
dir_pick.name = pick_full;
if ~nodupes || ~any(strcmp(full_file_picks,pick_full))
file_picks{end + 1} = pick; %#ok<AGROW>
full_file_picks{end + 1} = pick_full; %#ok<AGROW>
dir_picks(end + 1) = dir_pick; %#ok<AGROW>
end
end
if show_full_path
set(pickslist,'String',full_file_picks,'Value',[]);
else
set(pickslist,'String',file_picks,'Value',[]);
end
set([removebut,moveupbut,movedownbut],'Enable','off');
end
function remove(varargin)
values = get(pickslist,'Value');
file_picks(values) = [];
full_file_picks(values) = [];
dir_picks(values) = [];
top = get(pickslist,'ListboxTop');
num_above_top = sum(values < top);
top = top - num_above_top;
num_picks = length(file_picks);
new_value = min(min(values) - num_above_top,num_picks);
if num_picks == 0
new_value = [];
set([removebut,moveupbut,movedownbut],'Enable','off')
end
if show_full_path
set(pickslist,'String',full_file_picks,'Value',new_value,...
'ListboxTop',top)
else
set(pickslist,'String',file_picks,'Value',new_value,...
'ListboxTop',top)
end
end
function open(varargin)
values = get(navlist,'Value');
if fdir(values).isdir
set(fig,'pointer','watch')
drawnow
% Convert 'My Documents' to 'Documents' when necessary.
if ispc && strcmp(fdir(values).name,'My Documents')
if isempty(dir(fullfile(current_dir,fdir(values).name)))
values = find(strcmp({fdir.name},'Documents'));
end
end
current_dir = fullfile(current_dir,fdir(values).name);
history = update_history(history,current_dir,now,history_size);
make_history_cm()
full_filter = fullfile(current_dir,filter);
path_cell = path2cell(current_dir);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'ListboxTop',1,'Value',[],'String',filenames)
set(addbut,'Enable','off')
set(openbut,'Enable','off')
set(fig,'pointer','arrow')
end
end
function clicknav(varargin)
value = get(navlist,'Value');
nval = length(value);
dbl_click_fcn = @add;
switch nval
case 0
set([addbut,openbut],'Enable','off')
case 1
set(addbut,'Enable','on');
if fdir(value).isdir
set(openbut,'Enable','on')
dbl_click_fcn = @open;
else
set(openbut,'Enable','off')
end
otherwise
set(addbut,'Enable','on')
set(openbut,'Enable','off')
end
if strcmp(get(fig,'SelectionType'),'open')
dbl_click_fcn();
end
end
function keypressmisc(h,evt) %#ok<INUSL>
if strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
% Escape key means Cancel.
cancel()
end
end
function keypressnav(h,evt) %#ok<INUSL>
if length(path_cell) > 1 && strcmp(evt.Key,'backspace') && ...
isequal(evt.Modifier,cell(1,0))
% Backspace means go to parent folder.
dir_up_one()
elseif strcmp(evt.Key,'f') && isequal(evt.Modifier,{mod_key})
% Control-F (Command-F on Mac) means select all files.
value = find(~[fdir.isdir]);
set(navlist,'Value',value)
elseif strcmp(evt.Key,'rightarrow') && ...
isequal(evt.Modifier,cell(1,0))
% Right arrow key means select the file.
add()
elseif strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
% Escape key means Cancel.
cancel()
end
end
function keypresslist(h,evt) %#ok<INUSL>
if strcmp(evt.Key,'backspace') && isequal(evt.Modifier,cell(1,0))
% Backspace means remove item from list.
remove()
elseif strcmp(evt.Key,'escape') && isequal(evt.Modifier,cell(1,0))
% Escape key means Cancel.
cancel()
end
end
function clickpicks(varargin)
value = get(pickslist,'Value');
if isempty(value)
set([removebut,moveupbut,movedownbut],'Enable','off')
else
set(removebut,'Enable','on')
if min(value) == 1
set(moveupbut,'Enable','off')
else
set(moveupbut,'Enable','on')
end
if max(value) == length(file_picks)
set(movedownbut,'Enable','off')
else
set(movedownbut,'Enable','on')
end
end
if strcmp(get(fig,'SelectionType'),'open')
remove();
end
end
function recall(varargin)
if ispref('uipickfiles','full_file_picks')
ffp = getpref('uipickfiles','full_file_picks');
else
ffp = {};
end
for i = 1:length(ffp)
if exist(ffp{i},'dir') && ...
(~nodupes || ~any(strcmp(full_file_picks,ffp{i})))
full_file_picks{end + 1} = ffp{i}; %#ok<AGROW>
[unused,fn,ext] = fileparts(ffp{i});
file_picks{end + 1} = [fn,ext]; %#ok<AGROW>
temp = dir(fullfile(ffp{i},'..'));
if ispc || ismac
thisdir = strcmpi({temp.name},[fn,ext]);
else
thisdir = strcmp({temp.name},[fn,ext]);
end
dir_picks(end + 1) = temp(thisdir); %#ok<AGROW>
dir_picks(end).name = ffp{i};
elseif exist(ffp{i},'file') && ...
(~nodupes || ~any(strcmp(full_file_picks,ffp{i})))
full_file_picks{end + 1} = ffp{i}; %#ok<AGROW>
[unused,fn,ext] = fileparts(ffp{i});
file_picks{end + 1} = [fn,ext]; %#ok<AGROW>
dir_picks(end + 1) = dir(ffp{i}); %#ok<AGROW>
dir_picks(end).name = ffp{i};
end
end
if show_full_path
set(pickslist,'String',full_file_picks,'Value',[]);
else
set(pickslist,'String',file_picks,'Value',[]);
end
set([removebut,moveupbut,movedownbut],'Enable','off');
end
function sort_type(h,evt,cb) %#ok<INUSL>
if sort_state(cb)
sort_state(cb) = -sort_state(cb);
last_sort_state(cb) = sort_state(cb);
else
sort_state = zeros(1,3);
sort_state(cb) = last_sort_state(cb);
end
set(sort_cb,{'CData'},tri_icon(sort_state + 2)')
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(openbut,'Enable','off')
set(fig,'pointer','arrow')
end
function dirpopup(varargin)
value = get(dir_popup,'Value');
container = path_cell{min(value + 1,length(path_cell))};
path_cell = path_cell(1:value);
set(fig,'pointer','watch')
drawnow
if ispc && value == 1
current_dir = '';
full_filter = filter;
drives = getdrives(network_volumes);
num_drives = length(drives);
temp = tempname;
mkdir(temp)
dir_temp = dir(temp);
rmdir(temp)
fdir = repmat(dir_temp(1),num_drives,1);
[fdir.name] = deal(drives{:});
else
current_dir = cell2path(path_cell);
history = update_history(history,current_dir,now,history_size);
make_history_cm()
full_filter = fullfile(current_dir,filter);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
end
filenames = {fdir.name}';
selected = find(strcmp(filenames,container));
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'String',filenames,'Value',selected)
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function dir_up_one(varargin)
value = length(path_cell) - 1;
container = path_cell{value + 1};
path_cell = path_cell(1:value);
set(fig,'pointer','watch')
drawnow
if ispc && value == 1
current_dir = '';
full_filter = filter;
drives = getdrives(network_volumes);
num_drives = length(drives);
temp = tempname;
mkdir(temp)
dir_temp = dir(temp);
rmdir(temp)
fdir = repmat(dir_temp(1),num_drives,1);
[fdir.name] = deal(drives{:});
else
current_dir = cell2path(path_cell);
history = update_history(history,current_dir,now,history_size);
make_history_cm()
full_filter = fullfile(current_dir,filter);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
end
filenames = {fdir.name}';
selected = find(strcmp(filenames,container));
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'String',filenames,'Value',selected)
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function change_path(varargin)
set(fig,'pointer','watch')
drawnow
proposed_path = get(pathbox,'String');
% Process any folders named '..'.
proposed_path_cell = path2cell(proposed_path);
ddots = strcmp(proposed_path_cell,'..');
ddots(find(ddots) - 1) = true;
proposed_path_cell(ddots) = [];
proposed_path = cell2path(proposed_path_cell);
% Check for existance of folder.
if ~exist(proposed_path,'dir')
set(fig,'pointer','arrow')
uiwait(errordlg(['Folder "',proposed_path,...
'" does not exist.'],'','modal'))
return
end
current_dir = proposed_path;
history = update_history(history,current_dir,now,history_size);
make_history_cm()
full_filter = fullfile(current_dir,filter);
[path_cell,new_network_vol] = path2cell(current_dir);
if exist(new_network_vol,'dir')
network_volumes = unique([network_volumes,{new_network_vol}]);
end
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(openbut,'Enable','off')
set(fig,'pointer','arrow')
end
function showfullpath(varargin)
show_full_path = get(viewfullpath,'Value');
if show_full_path
set(pickslist,'String',full_file_picks)
else
set(pickslist,'String',file_picks)
end
end
function removedupes(varargin)
nodupes = get(remove_dupes,'Value');
if nodupes
num_picks = length(full_file_picks);
[unused,rev_order] = unique(full_file_picks(end:-1:1)); %#ok<SETNU>
order = sort(num_picks + 1 - rev_order);
full_file_picks = full_file_picks(order);
file_picks = file_picks(order);
dir_picks = dir_picks(order);
if show_full_path
set(pickslist,'String',full_file_picks,'Value',[])
else
set(pickslist,'String',file_picks,'Value',[])
end
set([removebut,moveupbut,movedownbut],'Enable','off')
end
end
function moveup(varargin)
value = get(pickslist,'Value');
set(removebut,'Enable','on')
n = length(file_picks);
omega = 1:n;
index = zeros(1,n);
index(value - 1) = omega(value);
index(setdiff(omega,value - 1)) = omega(setdiff(omega,value));
file_picks = file_picks(index);
full_file_picks = full_file_picks(index);
dir_picks = dir_picks(index);
value = value - 1;
if show_full_path
set(pickslist,'String',full_file_picks,'Value',value)
else
set(pickslist,'String',file_picks,'Value',value)
end
if min(value) == 1
set(moveupbut,'Enable','off')
end
set(movedownbut,'Enable','on')
end
function movedown(varargin)
value = get(pickslist,'Value');
set(removebut,'Enable','on')
n = length(file_picks);
omega = 1:n;
index = zeros(1,n);
index(value + 1) = omega(value);
index(setdiff(omega,value + 1)) = omega(setdiff(omega,value));
file_picks = file_picks(index);
full_file_picks = full_file_picks(index);
dir_picks = dir_picks(index);
value = value + 1;
if show_full_path
set(pickslist,'String',full_file_picks,'Value',value)
else
set(pickslist,'String',file_picks,'Value',value)
end
if max(value) == n
set(movedownbut,'Enable','off')
end
set(moveupbut,'Enable','on')
end
function togglefilter(varargin)
set(fig,'pointer','watch')
drawnow
value = get(showallfiles,'Value');
if value
filter = '*';
re_filter = '';
set([filter_ed,refilter_ed],'Enable','off')
else
filter = get(filter_ed,'String');
re_filter = get(refilter_ed,'String');
set([filter_ed,refilter_ed],'Enable','on')
end
full_filter = fullfile(current_dir,filter);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function toggle_refiltdirs(varargin)
set(fig,'pointer','watch')
drawnow
value = get(refilterdirs,'Value');
prop.redirs = value;
full_filter = fullfile(current_dir,filter);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function setfilspec(varargin)
set(fig,'pointer','watch')
drawnow
filter = get(filter_ed,'String');
if isempty(filter)
filter = '*';
set(filter_ed,'String',filter)
end
% Process file spec if a subdirectory was included.
[p,f,e] = fileparts(filter);
if ~isempty(p)
newpath = fullfile(current_dir,p,'');
set(pathbox,'String',newpath)
filter = [f,e];
if isempty(filter)
filter = '*';
end
set(filter_ed,'String',filter)
change_path();
end
full_filter = fullfile(current_dir,filter);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function setrefilter(varargin)
set(fig,'pointer','watch')
drawnow
re_filter = get(refilter_ed,'String');
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(navlist,'String',filenames,'Value',[])
set(addbut,'Enable','off')
set(fig,'pointer','arrow')
end
function filter_type_callback(varargin)
type_value = get(type_popup,'Value');
set(filter_ed,'String',prop.type{type_value,1})
setfilspec()
end
function done(varargin)
% Optional shortcut: click on a file and press 'Done'.
% if isempty(full_file_picks) && strcmp(get(addbut,'Enable'),'on')
% add();
% end
numfiles = length(full_file_picks);
if ~isempty(prop.numfiles)
if numfiles < prop.numfiles(1)
msg = {'Too few items selected.',numstr};
uiwait(errordlg(msg,'','modal'))
return
elseif numfiles > prop.numfiles(end)
msg = {'Too many items selected.',numstr};
uiwait(errordlg(msg,'','modal'))
return
end
end
fig_pos = get(fig,'Position');
delete(fig)
end
function cancel(varargin)
prop.output = 'cancel';
fig_pos = get(fig,'Position');
delete(fig)
end
function history_cb(varargin)
set(fig,'pointer','watch')
drawnow
current_dir = history(varargin{3}).name;
history = update_history(history,current_dir,now,history_size);
make_history_cm()
full_filter = fullfile(current_dir,filter);
path_cell = path2cell(current_dir);
fdir = filtered_dir(full_filter,re_filter,prop.redirs,...
@(x)file_sort(x,sort_state));
filenames = {fdir.name}';
filenames = annotate_file_names(filenames,fdir,fsdata);
set(dir_popup,'String',path_cell,'Value',length(path_cell))
if length(path_cell) > 1
set(up_dir_but','Enable','on')
else
set(up_dir_but','Enable','off')
end
set(pathbox,'String',current_dir)
set(navlist,'ListboxTop',1,'Value',[],'String',filenames)
set(addbut,'Enable','off')
set(openbut,'Enable','off')
set(fig,'pointer','arrow')
end
function clear_history(varargin)
history = update_history(history(1),'',[],history_size);
make_history_cm()
end
function set_history_size(varargin)
result_cell = inputdlg('Number of Recent Folders:','',1,...
{sprintf('%g',history_size)});
if isempty(result_cell)
return
end
result = sscanf(result_cell{1},'%f');
if isempty(result) || result < 1
return
end
history_size = result;
history = update_history(history,'',[],history_size);
make_history_cm()
setpref('uipickfiles','history_size',history_size)
end
function resize(varargin)
% Get current figure size.
P = 'Position';
pos = get(fig,P);
w = pos(3); % figure width in pixels
h = pos(4); % figure height in pixels
% Enforce minimum figure size.
w = max(w,564);
h = max(h,443);
if any(pos(3:4) < [w h])
pos(3:4) = [w h];
set(fig,P,pos)
end
% Change positions of all uicontrols based on the current figure
% width and height.
navw_pckw = round([1 1;-350 250]\[w-140;0]);
navw = navw_pckw(1);
pckw = navw_pckw(2);
navp = [10 10 navw h-174];
pckp = [w-10-pckw 10 pckw h-174];
set(navlist,P,navp)
set(pickslist,P,pckp)
set(frame1,P,[navw+5 h-234 110 70])
set(openbut,P,[navw+20 h-194 80 20])
set(addbut,P,[navw+20 h-224 80 20])
frame2y = round((h-234 + 110 - 100)/2);
set(frame2,P,[w-pckw-115 frame2y 110 100])
set(removebut,P,[w-pckw-100 frame2y+70 80 20])
set(moveupbut,P,[w-pckw-100 frame2y+40 80 20])
set(movedownbut,P,[w-pckw-100 frame2y+10 80 20])
set(done_button,P,[navw+30 80 80 30])
set(cancel_button,P,[navw+30 30 80 30])
set(sort_cb(1),P,[15 h-163 70 15])
set(sort_cb(2),P,[85 h-163 70 15])
set(sort_cb(3),P,[155 h-163 70 15])
set(dir_popup,P,[10 h-144 navw-25 20])
set(up_dir_but,P,[navw-10 h-144 20 20])
set(pathbox,P,[10 h-119 navw 26])
set(label1,P,[10 h-93 navw 16])
set(viewfullpath,P,[pckp(1) h-159 230 20])
set(remove_dupes,P,[pckp(1) h-134 280 20])
set(recall_button,P,[w-75 h-159 65 20])
set(label4,P,[w-10-pckw h-89 pckw 20])
set(num_files_warn,P,[w-10-pckw h-109 pckw 16])
set(label2,P,[10 h-18 80 17])
set(label3,P,[100 h-18 160 17])
set(showallfiles,P,[270 h-42 110 20])
set(refilterdirs,P,[270 h-64 100 20])
set(filter_ed,P,[10 h-44 80 26])
set(refilter_ed,P,[100 h-44 160 26])
set(type_popup,P,[10 h-72 250 20])
end
function reset_figure_size(varargin)
if strcmp(get(fig,'SelectionType'),'open')
root_units = get(0,'units');
screen_size = get(0,'ScreenSize');
set(0,'Units',root_units)
hw = [740 494];
pos = [round((screen_size(3:4) - hw - [0 26])/2),hw];
set(fig,'Position',pos)
resize()
end
end
% ------------------ Other nested functions ------------------
function make_history_cm
% Make context menu for history.
if ~isempty(hist_menus)
delete(hist_menus)
end
num_hist = length(history);
hist_menus = zeros(1,num_hist+2);
for i = 1:num_hist
hist_menus(i) = uimenu(hist_cm,'Label',history(i).name,...
'Callback',{@history_cb,i});
end
hist_menus(num_hist+1) = uimenu(hist_cm,...
'Label','Clear Menu',...
'Separator','on',...
'Callback',@clear_history);
hist_menus(num_hist+2) = uimenu(hist_cm,'Label',...
sprintf('Set Number of Recent Folders (%d) ...',history_size),...
'Callback',@set_history_size);
end
end
% -------------------- Subfunctions --------------------
function [c,network_vol] = path2cell(p)
% Turns a path string into a cell array of path elements.
if ispc
p = strrep(p,'/','\');
c1 = regexp(p,'(^\\\\[^\\]+\\[^\\]+)|(^[A-Za-z]+:)|[^\\]+','match');
vol = c1{1};
c = [{'My Computer'};c1(:)];
if strncmp(vol,'\\',2)
network_vol = vol;
else
network_vol = '';
end
else
c = textscan(p,'%s','delimiter','/');
c = [{filesep};c{1}(2:end)];
network_vol = '';
end
end
% --------------------
function p = cell2path(c)
% Turns a cell array of path elements into a path string.
if ispc
p = fullfile(c{2:end},'');
else
p = fullfile(c{:},'');
end
end
% --------------------
function d = filtered_dir(full_filter,re_filter,filter_both,sort_fcn)
% Like dir, but applies filters and sorting.
p = fileparts(full_filter);
if isempty(p) && full_filter(1) == '/'
p = '/';
end
if exist(full_filter,'dir')
dfiles = dir(' ');
else
dfiles = dir(full_filter);
end
if ~isempty(dfiles)
dfiles([dfiles.isdir]) = [];
end
ddir = dir(p);
ddir = ddir([ddir.isdir]);
[unused,index0] = sort(lower({ddir.name})); %#ok<ASGLU>
ddir = ddir(index0);
ddir(strcmp({ddir.name},'.') | strcmp({ddir.name},'..')) = [];
% Additional regular expression filter.
if nargin > 1 && ~isempty(re_filter)
if ispc || ismac
no_match = cellfun('isempty',regexpi({dfiles.name},re_filter));
else
no_match = cellfun('isempty',regexp({dfiles.name},re_filter));
end
dfiles(no_match) = [];
end
if filter_both
if nargin > 1 && ~isempty(re_filter)
if ispc || ismac
no_match = cellfun('isempty',regexpi({ddir.name},re_filter));
else
no_match = cellfun('isempty',regexp({ddir.name},re_filter));
end
ddir(no_match) = [];
end
end
% Set navigator style:
% 1 => list all folders before all files, case-insensitive sorting
% 2 => mix files and folders, case-insensitive sorting
% 3 => list all folders before all files, case-sensitive sorting
nav_style = 1;
switch nav_style
case 1
[unused,index1] = sort_fcn(dfiles); %#ok<ASGLU>
[unused,index2] = sort_fcn(ddir); %#ok<ASGLU>
d = [ddir(index2);dfiles(index1)];
case 2
d = [dfiles;ddir];
[unused,index] = sort(lower({d.name})); %#ok<ASGLU>
d = d(index);
case 3
[unused,index1] = sort({dfiles.name}); %#ok<ASGLU>
[unused,index2] = sort({ddir.name}); %#ok<ASGLU>
d = [ddir(index2);dfiles(index1)];
end
end
% --------------------
function [files_sorted,index] = file_sort(files,sort_state)
switch find(sort_state)
case 1
[files_sorted,index] = sort(lower({files.name}));
if sort_state(1) < 0
files_sorted = files_sorted(end:-1:1);
index = index(end:-1:1);
end
case 2
if sort_state(2) > 0
[files_sorted,index] = sort([files.datenum]);
else
[files_sorted,index] = sort([files.datenum],'descend');
end
case 3
if sort_state(3) > 0
[files_sorted,index] = sort([files.bytes]);
else
[files_sorted,index] = sort([files.bytes],'descend');
end
end
end
% --------------------
function drives = getdrives(other_drives)
% Returns a cell array of drive names on Windows.
letters = char('A':'Z');
num_letters = length(letters);
drives = cell(1,num_letters);
for i = 1:num_letters
if exist([letters(i),':\'],'dir');
drives{i} = [letters(i),':'];
end
end
drives(cellfun('isempty',drives)) = [];
if nargin > 0 && iscellstr(other_drives)
drives = [drives,unique(other_drives)];
end
end
% --------------------
function filenames = annotate_file_names(filenames,dir_listing,fsdata)
% Adds a trailing filesep character to folder names and, optionally,
% prepends a folder icon or bullet symbol.
for i = 1:length(filenames)
if dir_listing(i).isdir
filenames{i} = sprintf('%s%s%s%s',fsdata.pre,filenames{i},...
fsdata.filesep,fsdata.post);
end
end
end
% --------------------
function history = update_history(history,current_dir,time,history_size)
if ~isempty(current_dir)
% Insert or move current_dir to the top of the history.
% If current_dir already appears in the history list, delete it.
match = strcmp({history.name},current_dir);
history(match) = [];
% Prepend history with (current_dir,time).
history = [struct('name',current_dir,'time',time),history];
end
% Trim history to keep at most <history_size> newest entries.
history = history(1:min(history_size,end));
end
% --------------------
function success = generate_folder_icon(icon_path)
% Black = 1, manila color = 2, transparent = 3.
im = [ ...
3 3 3 1 1 1 1 3 3 3 3 3;
3 3 1 2 2 2 2 1 3 3 3 3;
3 1 1 1 1 1 1 1 1 1 1 3;
1 2 2 2 2 2 2 2 2 2 2 1;
1 2 2 2 2 2 2 2 2 2 2 1;
1 2 2 2 2 2 2 2 2 2 2 1;
1 2 2 2 2 2 2 2 2 2 2 1;
1 2 2 2 2 2 2 2 2 2 2 1;
1 2 2 2 2 2 2 2 2 2 2 1;
1 1 1 1 1 1 1 1 1 1 1 1];
cmap = [0 0 0;255 220 130;255 255 255]/255;
fid = fopen(icon_path,'w');
if fid > 0
fclose(fid);
imwrite(im,cmap,icon_path,'Transparency',[1 1 0])
end
success = exist(icon_path,'file');
end
% --------------------
function fsdata = set_folder_style(folder_style_pref)
% Set style to preference.
fsdata.style = folder_style_pref;
% If style = 1, check to make sure icon image file exists. If it doesn't,
% try to create it. If that fails set style = 2.
if fsdata.style == 1
icon_path = fullfile(prefdir,'uipickfiles_folder_icon.png');
if ~exist(icon_path,'file')
success = generate_folder_icon(icon_path);
if ~success
fsdata.style = 2;
end
end
end
% Set pre and post fields.
if fsdata.style == 1
icon_url = ['file://localhost/',...
strrep(strrep(icon_path,':','|'),'\','/')];
fsdata.pre = sprintf('<html><img src="%s"> ',icon_url);
fsdata.post = '</html>';
elseif fsdata.style == 2
fsdata.pre = '<html><b>•</b> ';
fsdata.post = '</html>';
elseif fsdata.style == 3
fsdata.pre = '';
fsdata.post = '';
end
fsdata.filesep = filesep;
end
% --------------------
function prop = parsepropval(prop,varargin)
% Parse property/value pairs and return a structure.
properties = fieldnames(prop);
arg_index = 1;
while arg_index <= length(varargin)
arg = varargin{arg_index};
if ischar(arg)
prop_index = match_property(arg,properties);
prop.(properties{prop_index}) = varargin{arg_index + 1};
arg_index = arg_index + 2;
elseif isstruct(arg)
arg_fn = fieldnames(arg);
for i = 1:length(arg_fn)
prop_index = match_property(arg_fn{i},properties);
prop.(properties{prop_index}) = arg.(arg_fn{i});
end
arg_index = arg_index + 1;
else
error(['Properties must be specified by property/value pairs',...
' or structures.'])
end
end
end
% --------------------
function prop_index = match_property(arg,properties)
% Utility function for parsepropval.
prop_index = find(strcmpi(arg,properties));
if isempty(prop_index)
prop_index = find(strncmpi(arg,properties,length(arg)));
end
if length(prop_index) ~= 1
error('Property ''%s'' does not exist or is ambiguous.',arg)
end
end
function percent = parfor_progress(N)
%PARFOR_PROGRESS Progress monitor (progress bar) that works with parfor.
% PARFOR_PROGRESS works by creating a file called parfor_progress.txt in
% your working directory, and then keeping track of the parfor loop's
% progress within that file. This workaround is necessary because parfor
% workers cannot communicate with one another so there is no simple way
% to know which iterations have finished and which haven't.
%
% PARFOR_PROGRESS(N) initializes the progress monitor for a set of N
% upcoming calculations.
%
% PARFOR_PROGRESS updates the progress inside your parfor loop and
% displays an updated progress bar.
%
% PARFOR_PROGRESS(0) deletes parfor_progress.txt and finalizes progress
% bar.
%
% To suppress output from any of these functions, just ask for a return
% variable from the function calls, like PERCENT = PARFOR_PROGRESS which
% returns the percentage of completion.
%
% Example:
%
% N = 100;
% parfor_progress(N);
% parfor i=1:N
% pause(rand); % Replace with real code
% parfor_progress;
% end
% parfor_progress(0);
%
% See also PARFOR.
% By Jeremy Scheff - [email hidden] - http://www.jeremyscheff.com/
narginchk(0, 1);
if nargin < 1
N = -1;
end
percent = 0;
w = 50; % Width of progress bar
if N > 0
f = fopen('parfor_progress.txt', 'w');
if f<0
error('Do you have write permissions for %s?', pwd);
end
fprintf(f, '%d\n', N); % Save N at the top of progress.txt
fclose(f);
if nargout == 0
disp([' 0%[>', repmat(' ', 1, w), ']']);
end
elseif N == 0
delete('parfor_progress.txt');
percent = 100;
if nargout == 0
disp([repmat(char(8), 1, (w+9)), char(10), '100%[', repmat('=', 1, w+1), ']']);
end
else
if ~exist('parfor_progress.txt', 'file')
error('parfor_progress.txt not found. Run PARFOR_PROGRESS(N) before PARFOR_PROGRESS to initialize parfor_progress.txt.');
end
f = fopen('parfor_progress.txt', 'a');
fprintf(f, '1\n');
fclose(f);
f = fopen('parfor_progress.txt', 'r');
progress = fscanf(f, '%d');
fclose(f);
percent = (length(progress)-1)/progress(1)*100;
if nargout == 0
perc = sprintf('%3.0f%%', percent); % 4 characters wide, percentage
disp([repmat(char(8), 1, (w+9)), char(10), perc, '[', repmat('=', 1, round(percent*w/100)), '>', repmat(' ', 1, w - round(percent*w/100)), ']']);
end
end
end

MakeTheMAPMap.m at commit ee4e50d, no license · at the source

Overview

Authors: Andrew H. Miller^1,2,3, Yeng Yang¹, Natalie Schmidt¹, Jaffna Mathiaparanam¹, Mark E. Berres⁴, Mary C. Halloran^1,2

ORCID iDs: Andrew H. Miller, Mary C. Halloran

Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
Department of Neuroscience, University of Wisconsin-Madison, Madison, WI 53706, USA
Neuroscience Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
Biotechnology Center, University of Wisconsin-Madison, Madison, WI 53706, USA

Institutions: University of Wisconsin–Madison (United States)

Journal: Disease models & mechanisms, volume 19, issue 3, article dmm052509

Dates: received 3 June 2025; accepted 13 January 2026; published online 12 March 2026; in print March 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1242/dmm.052509 · PMID 41582719 · PMCID PMC13035064 · OpenAlex W7125700144

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: zebrafish (organism), cellular / molecular (subfield)

Methods: Connectivity, Statistics, Preprocessing, fMRI & imaging

Keywords: Neurofibromatosis, Habituation, cxcr4, cAMP, Zebrafish

MeSH: Habituation, Psychophysiologic*, Learning*, Neurofibromatosis 1*, Receptors, CXCR4*, Signal Transduction*, Zebrafish*, Zebrafish Proteins*, Animals, Benzylamines, Brain, Cyclams, Cyclic AMP, Cyclic AMP-Dependent Protein Kinases, Disease Models, Animal, Extracellular Signal-Regulated MAP Kinases, Larva, Mutation, Neurofibromin 1, raf Kinases, ras Proteins (* major topic)

Topic: Neurofibromatosis and Schwannoma Cases (Neurology, Medicine), according to OpenAlex

Funding: NIH (T32GM007507, R56NS132890, 1R01NS086934); DOD (W81XWH-16-1-0091); University of Wisconsin

Citations: not cited yet (Europe PMC); 97 references in the paper

Research resources: Gene Expression Center RRID:SCR_017757, DNA Sequencing Facility RRID:SCR_017759, Bioinformatics Resource Center RRID:SCR_017799

Abstract

Neurofibromatosis type 1 (NF1) is a neurogenetic disorder caused by loss-of-function mutations in the gene neurofibromin 1 (NF1). NF1 encodes neurofibromin, a multifunctional tumor-suppressing protein that regulates Ras, cAMP and dopamine signaling. NF1 predisposes patients to a wide range of symptoms, including peripheral nerve tumors, brain tumors and cognitive dysfunction. Despite considerable work using animal models to investigate the role of neurofibromin in behavior, translating research into treatment for NF1-associated cognitive dysfunction has not yet been successful. Here, we provide evidence that Cxcr4 chemokine receptor signaling is a regulator of habituation learning and modulator of cAMP-PKA signaling in nf1 mutant larval zebrafish. Combining a small-molecule drug screen and RNAseq analysis, we show that cxcr4b expression is increased in nf1 mutants and that pharmacological inhibition of Cxcr4 with AMD3100 (plerixafor) improves habituation learning. We further demonstrate that plerixafor activates cAMP-PKA pathway signaling but has limited effects on Ras-Raf-MEK-ERK pathway signaling in the nf1 mutant brain. CXCR4 has previously been identified as a potential therapeutic target for neurofibromin-deficient tumorigenesis. Our results suggest that Cxcr4 signaling also regulates neurofibromin-dependent cognitive function.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

zebrafishexplorer.zib.de/home

License: none: the authors keep all their rights

State: unreachable at the last attempt, verified on 30 September 2026

Evidence: found in the paper

Software Heritage: not checked

Found in: the text, “Immunohistochemistry and confocal imaging”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Availability: 1 check, the latest on 30 September 2026: unreachable at the last attempt

30 September 2026: unreachable at the last attempt

At the source: zebrafishexplorer.zib.de/home/

owenrandlett/Z-Brain

License: none: the authors keep all their rights

State: the link answers, verified on 30 September 2026

Evidence: files inventoried

Commit: ee4e50de635daedbc3c5ca0b89ff82d313dc9dce, 11 April 2025

Languages: MATLAB (3), Python (3)

Size: 12 files, 6 scripts

Software Heritage: not archived

Found in: the end of the paper

Holds: README

Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Matplotlib (3 files), NumPy (3 files), scikit-image (3 files), SciPy (3 files), Image Processing Toolbox (2 files), Pillow (2 files), Parallel Computing Toolbox (1 file), Statistics and Machine Learning Toolbox (1 file)

Availability: 1 check, the latest on 30 September 2026: the link answers

30 September 2026: the link answers

7 files

MakeTheMAPMap.m, MATLAB, 2,413 lines, 4 matches
ZBrainAnalysisOfMAPMaps.m, MATLAB, 2,279 lines
ZBrainViewer.m, MATLAB, 2,394 lines
basic_python_MAPMapping_scripts/MakeTheMapMap.py, Python, 375 lines
basic_python_MAPMapping_scripts/PrepareStacksForMAPMapping.py, Python, 49 lines
basic_python_MAPMapping_scripts/make_MAPMAP_projections.py, Python, 133 lines
README.md, Text, 39 lines

At the source: github.com/owenrandlett/Z-Brain

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

2 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
6 scripts, each with its path and the digest of its content;
4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

Datasets cited

geo:GSE317922, at NCBI GEO; found in the end of the paper

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 5 keywords, 20 MeSH terms, 3 funders, 96 references, 3 RRIDs.

Cite

This paper

Miller, A. H., Yang, Y., Schmidt, N., Mathiaparanam, J., Berres, M. E., & Halloran, M. C. (2026). Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of neurofibromatosis. Disease models & mechanisms, 19(3), dmm052509. https://doi.org/10.1242/dmm.052509

BibTeX

@article{miller2026inhibition, author = {Miller, Andrew H. and Yang, Yeng and Schmidt, Natalie and Mathiaparanam, Jaffna and Berres, Mark E. and Halloran, Mary C.}, title = {{Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of neurofibromatosis}}, journal = {Disease models \& mechanisms}, year = {2026}, month = mar, volume = {19}, number = {3}, pages = {dmm052509}, publisher = {Company of Biologists}, issn = {1754-8403}, doi = {10.1242/dmm.052509}, url = {https://doi.org/10.1242/dmm.052509}, pmid = {41582719}, pmcid = {PMC13035064} }

RIS

TY - JOUR AU - Miller, Andrew H. AU - Yang, Yeng AU - Schmidt, Natalie AU - Mathiaparanam, Jaffna AU - Berres, Mark E. AU - Halloran, Mary C. TI - Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of neurofibromatosis T2 - Disease models & mechanisms J2 - Dis Model Mech PY - 2026 DA - 2026/03/12 VL - 19 IS - 3 SP - dmm052509 SN - 1754-8403 PB - Company of Biologists DO - 10.1242/dmm.052509 UR - https://doi.org/10.1242/dmm.052509 LA - en ER -

CSL-JSON

{ "id": "10.1242/dmm.052509", "type": "article-journal", "title": "Inhibition of Cxcr4 chemokine receptor signaling improves habituation learning in a zebrafish model of neurofibromatosis", "container-title": "Disease models & mechanisms", "author": [ { "family": "Miller", "given": "Andrew H." }, { "family": "Yang", "given": "Yeng" }, { "family": "Schmidt", "given": "Natalie" }, { "family": "Mathiaparanam", "given": "Jaffna" }, { "family": "Berres", "given": "Mark E." }, { "family": "Halloran", "given": "Mary C." } ], "container-title-short": "Dis Model Mech", "volume": "19", "issue": "3", "page": "dmm052509", "DOI": "10.1242/dmm.052509", "PMID": "41582719", "PMCID": "PMC13035064", "ISSN": "1754-8403", "publisher": "Company of Biologists", "URL": "https://doi.org/10.1242/dmm.052509", "language": "en", "issued": { "date-parts": [ [ 2026, 3, 12 ] ] } }

The tracing map gets a citation of its own once an author has validated it and it has a DOI.

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