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OpenSource
leverjs
Commits
6134ef4a
Commit
6134ef4a
authored
Oct 16, 2017
by
Andrew Cohen
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updated client
parent
380538e4
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+63
-21
matlab/+Client/detectFissionFusion.m
matlab/+Client/detectFissionFusion.m
+63
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matlab/+Client/detectFissionFusion.m
View file @
6134ef4a
% detectFissionFusion
tic
SERVER
=
'https://leverjs.net/Dario/'
url
=
[
SERVER
'lever'
];
leverList
=
webread
(
url
);
fissionEvents
=
{[],[]};
fusionEvents
=
{[],[]};
% set up data partitions
featureList
=
[];
for
f
=
1
:
length
(
leverList
)
if
(
14
==
f
)
||
(
3
==
f
)
continue
% by folder
leverName
=
leverList
{
f
};
idxFolder
=
strfind
(
leverName
,
'*'
);
fname
=
leverName
(
1
:
idxFolder
-
1
);
% see if this feature name already exists
if
~
isempty
(
featureList
)
featureNames
=
{
featureList
.
folderName
};
fidx
=
find
(
cellfun
(
@
(
x
)
strcmp
(
x
,
fname
),
featureNames
));
else
fidx
=
[];
end
if
~
isempty
(
strfind
(
lower
(
leverList
{
f
}),
'ctrl'
))
idx
=
1
;
if
isempty
(
fidx
)
nf
=
[];
nf
.
folderName
=
fname
;
nf
.
leverNames
=
{
leverName
};
nf
.
features
=
[];
% put stats here
featureList
=
[
featureList
nf
];
fidx
=
length
(
featureList
);
else
idx
=
2
;
featureList
(
fidx
)
.
leverNames
=
{
featureList
(
fidx
)
.
leverNames
{:},
leverName
}
;
end
url
=
[
SERVER
leverList
{
f
}
'/trackList/1'
];
url
=
[
SERVER
leverList
{
f
}
'/constants'
];
constants
=
webread
(
url
);
url
=
[
SERVER
leverList
{
f
}
'/trackList/3'
]
;
trackList
=
webread
(
url
);
if
isempty
(
trackList
)
continue
end
% nFusion= length(find([trackList.t0]>1))/length(find(1==[trackList.t0]));
% nFission = length(find([trackList.t1]<max([trackList.t1])))/length(find(1==[trackList.t0]));
movieFeatures
=
[];
for
t
=
1
:
constants
.
imageData
.
NumberOfFrames
url
=
[
SERVER
leverList
{
f
}
'/cellCentroids/'
num2str
(
t
)];
tCells
=
webread
(
url
);
if
isempty
(
tCells
)
continue
end
trackIDcull
=
setdiff
([
tCells
.
trackID
],[
trackList
.
trackID
]);
for
i
=
1
:
length
(
tCells
)
if
isempty
(
intersect
(
tCells
(
i
)
.
trackID
,
trackIDcull
))
movieFeatures
=
[
movieFeatures
,[
tCells
(
i
)
.
area
]];
end
end
end
% featureList(fidx).features=[featureList(fidx).features median(movieFeatures)];
featureList
(
fidx
)
.
features
=
[
featureList
(
fidx
)
.
features
mean
(
movieFeatures
.
/
median
(
movieFeatures
))];
end
for
i
=
1
:
length
(
featureList
)
fprintf
(
1
,
'%s: mean(featureList)=%2.5f\n'
,
featureList
(
i
)
.
folderName
,
median
(
featureList
(
i
)
.
features
));
end
for
i
=
1
:
length
(
featureList
)
for
j
=
i
+
1
:
length
(
featureList
)
[
p
,
h
]
=
ranksum
(
featureList
(
i
)
.
features
,
featureList
(
j
)
.
features
);
fprintf
(
1
,
'%s vs. %s : [p,h]=%2.3f,%2.3f \n'
,
featureList
(
i
)
.
folderName
,
featureList
(
j
)
.
folderName
,
p
,
h
);
end
end
nFusion
=
length
(
find
([
trackList
.
t0
]
>
1
));
nFission
=
length
(
find
([
trackList
.
t1
]
<
max
([
trackList
.
t1
])));
fissionEvents
{
idx
}
=
[
fissionEvents
{
idx
};
nFission
];
fusionEvents
{
idx
}
=
[
fusionEvents
{
idx
};
nFusion
];
nFissionFusion
=
length
(
trackList
)/
length
(
find
([
trackList
.
t0
]
==
1
));
ctrl
=
[];
idh
=
[];
for
i
=
1
:
length
(
featureList
)
if
strfind
(
lower
(
featureList
(
i
)
.
folderName
),
'ctrl'
)
ctrl
=
[
ctrl
featureList
(
i
)
.
features
];
else
idh
=
[
idh
featureList
(
i
)
.
features
];
end
end
ission12
=
[
median
(
fissionEvents
{
1
}),
median
(
fissionEvents
{
2
})]
[
p
,
h
]
=
ranksum
(
fissionEvents
{
1
},
fissionEvents
{
2
})
fusion12
=
[
median
(
fusionEvents
{
1
})
median
(
fusionEvents
{
2
})]
[
p
,
h
]
=
ranksum
(
fusionEvents
{
1
},
fusionEvents
{
2
})
[
median
(
idh
)
median
(
ctrl
)]
[
p
,
h
]
=
ranksum
(
idh
,
ctrl
)
toc
\ No newline at end of file
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