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CellMigration.ipf
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CellMigration.ipf
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#pragma TextEncoding = "UTF-8"
#pragma rtGlobals=3 // Use modern global access method and strict wave access
#pragma DefaultTab={3,20,4} // Set default tab width in Igor Pro 9 and later
#pragma version = 1.15 // version number of Migrate()
#pragma ModuleName = CellMigration
#include <Waves Average>
#include <ColorWaveEditor>
// CellMigration will analyse 2D cell migration in IgorPro
// Use ImageJ to track the cells. Outputs from tracking are saved either
// 1) as sheets in an Excel Workbook, 1 per condition, or
// 2) as direct outputs from Manual Tracking, in csv format
//
// Select CellMigr > Cell Migration...
//
// Tell the dialog how many conditions you want to load and the magnification and time resolution
// Next, give each condition a label (name) and then tell Igor where to find the data
// Either an Excel workbook (per condition) or a directory of CSVs (per condition)
// There is also the ability to define "offsetting data", in the case of XY drift during the experiment.
//
// For Excel workbooks:
// NOTE no headers in Excel file. Keep data to columns A-H, max of 2000 rows
// columns are
// A - 0 - ImageJ row
// B - 1 - Track No
// C - 2 - Slice No
// D - 3 - x (in px)
// E - 4 - y (in px)
// F - 5 - distance
// G - 6 - velocity (actually speed)
// H - 7 - pixel value
////////////////////////////////////////////////////////////////////////
// Menu items
////////////////////////////////////////////////////////////////////////
Menu "CellMigr"
"Cell Migration...", /Q, SetUpMigration(0)
"Superplot...", /Q, SetUpMigration(1)
"Save Reports...", /Q, SaveAllReports()
"Recolor Everything", /Q, RecolorAllPlotsWrapper()
"Rerun Analysis", /Q, RerunAnalysis()
Submenu "Manual tracking conversion"
"Excel to Converted CSV", /Q, Excel2CSV()
"CSV to Converted CSV", /Q, CSV2CSV()
End
"About CellMigration", /Q, AboutCellMigr()
End
////////////////////////////////////////////////////////////////////////
// Master functions and wrappers
////////////////////////////////////////////////////////////////////////
Function SetUpMigration(optVar)
Variable optVar
SetDataFolder root:
// kill all windows and waves before we start
CleanSlate()
SetUp_Panel(optVar)
End
Function ProceedToMigrate()
SetDataFolder root:
WAVE/Z paramWave
MakeColorWave(paramWave[0],"colorWave")
if(paramWave[4] > 0)
Superplot_Panel(paramWave[0],paramWave[4])
else
myIO_Panel(paramWave[0])
endif
End
////////////////////////////////////////////////////////////////////////
// Main functions
////////////////////////////////////////////////////////////////////////
// Loads the data and performs migration analysis
Function Migrate()
WAVE/Z paramWave = root:paramWave
if(!WaveExists(paramWave))
DoAlert 0, "Setup has failed. Missing paramWave."
return -1
endif
// pick up global values needed
Variable cond = paramWave[0]
Variable tStep = paramWave[1]
Variable pxSize = paramWave[2]
Variable superPlot = 0, reps
WAVE/Z colorWave = root:colorWave
WAVE/T/Z condWave = root:condWave
WAVE/T/Z condSplitWave = root:condSplitWave
if(WaveExists(condSplitWave) == 1)
if(cond < numpnts(condSplitWave))
superPlot = 1
cond = numpnts(condSplitWave)
reps = cond / paramWave[0]
endif
endif
// because the user may have used illegal characters in condWave, we make a clean version
// for use in Igor and a copy of the original called labelWave to use in plots and layouts
if(superPlot == 1)
WAVE/T labelWave = CleanUpCondWave(condSplitWave)
WAVE/T labelWave = CleanUpCondWave(condWave)
else
WAVE/T labelWave = CleanUpCondWave(condWave)
endif
// make summary plot windows
String fullList = "cdPlot;ivPlot;ivHPlot;dDPlot;MSDPlot;DAPlot;angleHPlot"
Variable nPlots = ItemsInList(fullList)
String name
Variable i,j
for(i = 0; i < nPlots; i += 1)
name = StringFromList(i, fullList)
KillWindow/Z $name
Display/N=$name/HIDE=1
endfor
String dataFolderName = "root:data"
NewDataFolder/O $dataFolderName // make root:data: but don't put anything in it yet
String condName, pref
Variable moviemax1, moviemax2
for(i = 0; i < cond; i += 1)
if(superPlot == 1)
condName = condSplitWave[i]
else
condName = condWave[i]
endif
// make data folder for each condition
dataFolderName = "root:data:" + condName
NewDataFolder/O/S $dataFolderName
// run other procedures
moviemax1 = LoadMigration(i)
moviemax2 = CorrectMigration(i)
if(moviemax1 != moviemax2)
if(moviemax2 == -1)
print "No correction applied to", condName
else
print "Caution: different number of stationary tracks compared with real tracks."
endif
endif
if(superPlot == 0)
// for each condition go and make tracks and plot everything out
MakeTracks(i)
endif
SetDataFolder root:
endfor
// if we are making a superplot, copy the data into folders named by condWave
if(superPlot == 1)
String sourceDF = ""
cond = numpnts(condWave)
for(i = 0; i < cond; i += 1)
condName = condWave[i]
// make data folder for each master condition
dataFolderName = "root:data:" + condName
NewDataFolder/O $dataFolderName
for(j = 0; j < reps; j += 1)
sourceDF = "root:data:" + condSplitWave[i * reps + j]
// merge data into master condition folder
DuplicateDataFolder/O=2 $sourceDF, $dataFolderName
endfor
SetDataFolder $dataFolderName
// as in the main program: for each condition go and make tracks and plot everything out
MakeTracks(i)
SetDataFolder root:
endfor
endif
// make the image quilt, spakline and joint histogram and then sort out the layouts
Variable optDur = MakeImageQuilt(10) // this aims for a quilt of 100 = 10^2 tracks
MakeJointHistogram(optDur)
TidyCondSpecificLayouts()
KillWindow/Z summaryLayout
NewLayout/N=summaryLayout
TidyUpSummaryLayout()
// when we get to the end, print (pragma) version number
Print "*** Executed Migrate v", GetProcedureVersion("CellMigration.ipf")
KillWindow/Z FilePicker
End
// This function will load the tracking data
/// @param ii variable containing row number from condWave
Function LoadMigration(ii)
Variable ii
WAVE/T/Z condSplitWave = root:condSplitWave
WAVE/T/Z condWave = root:condWave
String condName
if(WaveExists(condSplitWave) == 1)
condName = condSplitWave[ii]
else
condName = condWave[ii]
endif
WAVE/T PathWave1 = root:PathWave1
String pathString = PathWave1[ii]
String sheet, prefix, matName, wList
String fileList
Variable moviemax,csvOrNot
Variable i
if(StringMatch(pathString, "*.xls*") == 1)
// set variable to indicate Excel Workbook
csvOrNot = 0
// Works out what sheets are in Excel Workbook and then loads each.
XLLoadWave/J=1 PathWave1[ii]
fileList = S_value
else
// set variable to indicate csv file
csvOrNot = 1
// Work out what files are in directory
NewPath/O/Q ExpDiskFolder, pathString
fileList = IndexedFile(expDiskFolder,-1,".csv")
endif
fileList = SortList(fileList, ";", 16)
moviemax = ItemsInList(fileList)
for(i = 0; i < moviemax; i += 1)
sheet = StringFromList(i, fileList)
prefix = condName + "_c_" + num2str(i)
matName = condName + "_" + num2str(i)
if(csvOrNot == 0)
XLLoadWave/S=sheet/R=(A1,H2000)/O/K=0/N=$prefix/Q PathWave1[ii]
else
LoadWave/A=$prefix/J/K=1/L={0,1,0,0,0}/O/P=expDiskFolder/Q sheet
endif
wList = wavelist(prefix + "*",";","") // make matrix for each sheet
Concatenate/O/KILL wList, $matName
// now we need to check that the matrix is OK
Wave matTrax = $matName
// check we have a valid matrix with 8 columns
CheckColumnsOfMatrix(matTrax)
// make sure 1st point is -1
matTrax[0][5,6] = -1
// check distances and speeds are correct
CheckDistancesAndSpeeds(matTrax)
endfor
Print "*** Condition", condName, "was loaded from", pathString
// return moviemax back to calling function for checking
return moviemax
End
// This was added in v1.12 Dec 2018. At some point in the last year, the output
// of Manual Tracking changed so that there was no longer a first (0) column containing
// the row numbers. Add this column if that is the case.
STATIC Function CheckColumnsOfMatrix(matTrax)
WAVE matTrax
Variable numCols = DimSize(matTrax,1)
if(numCols == 8)
return 1
elseif(numCols == 7)
// insert new 0th column
InsertPoints/M=1 0,1, MatTrax
MatTrax[][0] = p+1
return 0
else
Print NameOfWave(matTrax), "does not have 8 columns of data."
return -1
endif
End
// The purpose of this function is to work out whether the distances (and speeds) in the
// original data are correct. Currently it just corrects them rather than testing and correcting if needed.
STATIC Function CheckDistancesAndSpeeds(matTrax)
WAVE matTrax
WAVE/Z paramWave = root:paramWave
Variable tStep = paramWave[1]
Variable pxSize = paramWave[2]
// make new distance column
Duplicate/O/RMD=[][3,4]/FREE matTrax,tempDist // take offset coords
Differentiate/METH=2/DIM=0 tempDist
tempDist[][] = (matTrax[p][5] == -1) ? 0 : tempDist[p][q]
MatrixOp/O/FREE tempNorm = sqrt(sumRows(tempDist * tempDist))
tempNorm[] *= pxSize // convert to real distance
// MatrixOp/O/FREE tempReal = sumcols(tempNorm - col(matTrax,5)) // for checking
matTrax[][5] = (matTrax[p][5] == -1) ? -1 : tempNorm[p] // going to leave first point as -1
// correct speed column
matTrax[][6] = (matTrax[p][6] == -1) ? -1 : tempNorm[p] / tStep
// make sure 1st point is -1
matTrax[0][5,6] = -1
End
// This function will load the tracking data from an Excel Workbook
/// @param ii variable containing row number from condWave
Function CorrectMigration(ii)
Variable ii
WAVE/T/Z condSplitWave = root:condSplitWave
WAVE/T/Z condWave = root:condWave
String condName
if(WaveExists(condSplitWave) == 1)
condName = condSplitWave[ii]
else
condName = condWave[ii]
endif
WAVE/T PathWave2 = root:PathWave2
String pathString = PathWave2[ii]
Variable len = strlen(pathString)
if(len == 0)
return -1
elseif(numtype(len) == 2)
return -1
endif
String sheet, prefix, matName, wList, mName
String fileList
Variable moviemax,csvOrNot
Variable i
if(StringMatch(pathString, "*.xls*") == 1)
// set variable to indicate Excel Workbook
csvOrNot = 0
// Works out what sheets are in Excel Workbook and then loads each.
XLLoadWave/J=1 PathWave2[ii]
fileList = S_value
else
// set variable to indicate csv file
csvOrNot = 1
// Work out what files are in directory
NewPath/O/Q ExpDiskFolder, pathString
fileList = IndexedFile(expDiskFolder,-1,".csv")
endif
fileList = SortList(fileList, ";", 16)
moviemax = ItemsInList(fileList)
for(i = 0; i < moviemax; i += 1)
sheet = StringFromList(i,fileList)
prefix = "stat_" + "c_" + num2str(i) // use stat prefix
matName = "stat_" + num2str(i)
if(csvOrNot == 0)
XLLoadWave/S=sheet/R=(A1,H2000)/O/K=0/N=$prefix/Q PathWave2[ii]
else
LoadWave/A=$prefix/J/K=1/L={0,1,0,0,0}/O/P=expDiskFolder/Q sheet
endif
wList = wavelist(prefix + "*",";","") // make matrix for each sheet
Concatenate/O/KILL wList, $matName
Wave matStat = $matName
// Find corresponding movie matrix
mName = ReplaceString("stat_",matname,condName + "_")
Wave matTrax = $mName
OffsetAndRecalc(matStat,matTrax)
endfor
Print "*** Offset data for condition", condName, "was loaded from", pathString
// return moviemax back to calling function for checking
return moviemax
End
// This function uses matStat to offset matTrax
Function OffsetAndRecalc(matStat,matTrax)
Wave matStat,matTrax
// Work out offset for the stat_* waves
Variable x0 = matStat[0][3]
Variable y0 = matStat[0][4]
matStat[][3] -= x0
matStat[][4] -= y0
MatrixOp/O/FREE mStat2 = col(matStat,2)
Variable maxFrame = WaveMax(mStat2)
Variable j // because i refers to rows
// offsetting loop
for(j = 1; j < maxFrame + 1; j += 1)
FindValue/V=(j) mStat2
if(V_Value == -1)
x0 = 0
y0 = 0
else
x0 = matStat[V_Value][3]
y0 = matStat[V_Value][4]
endif
matTrax[][3] = (matTrax[p][2] == j) ? matTrax[p][3] - x0 : matTrax[p][3]
matTrax[][4] = (matTrax[p][2] == j) ? matTrax[p][4] - y0 : matTrax[p][4]
endfor
WAVE/Z paramWave = root:paramWave
Variable tStep = paramWave[1]
Variable pxSize = paramWave[2]
// make new distance column
Duplicate/O/RMD=[][3,4]/FREE matTrax,tempDist // take offset coords
Differentiate/METH=2 tempDist
tempDist[][] = (matTrax[p][5] == -1) ? 0 : tempDist[p][q]
MatrixOp/O/FREE tempNorm = sqrt(sumRows(tempDist * tempDist))
tempNorm[] *= pxSize // convert to real distance
matTrax[][5] = (matTrax[p][5] == -1) ? -1 : tempNorm[p] // going to leave first point as -1
// correct speed column
matTrax[][6] = (matTrax[p][6] == -1) ? -1 : tempNorm[p] / tStep
// put 1st point as -1
matTrax[0][5,6] = -1
End
// This function will make cumulative distance waves for each cell. They are called cd_*
/// @param ii variable containing row number from condWave
Function MakeTracks(ii)
Variable ii
WAVE/T condWave = root:condWave
String condName = condWave[ii]
WAVE/Z paramWave = root:paramWave
Variable tStep = paramWave[1]
Variable pxSize = paramWave[2]
Variable minPoints = paramWave[5]
WAVE/Z colorWave = root:colorWave
WAVE/Z/T unitWave = root:unitWave
String wList0 = WaveList(condName + "_*",";","") // find all matrices
Variable nWaves = ItemsInList(wList0)
Variable nTrack,nTrace=0
String mName0, newName, plotName, avList, avName, errName
Variable i, j
String layoutName = condName + "_layout"
KillWindow/Z $layoutName // Kill the layout if it exists
NewLayout/HIDE=1/N=$layoutName
// cumulative distance and plot over time
plotName = condName + "_cdplot"
KillWindow/Z $plotName // set up plot
Display/N=$plotName/HIDE=1
for(i = 0; i < nWaves; i += 1)
mName0 = StringFromList(i,wList0)
WAVE m0 = $mName0
Duplicate/O/RMD=[][5,5] m0, $"tDistW" // distance
Duplicate/O/RMD=[][1,1] m0, $"tCellW" // cell number
WAVE tDistW,tCellW
Redimension/N=-1 tDistW, tCellW // make 1D
nTrack = WaveMax(tCellW) // find maximum track number
for(j = 1; j < (nTrack+1); j += 1) // index is 1-based
newName = "cd_" + mName0 + "_" + num2str(j)
Duplicate/O tDistW, $newName
WAVE w2 = $newName
w2 = (tCellW[p] == j) ? tDistW[p] : NaN
WaveTransform zapnans w2
if(numpnts(w2) < minPoints)
KillWaves/Z w2 // delete short tracks and any tracks that didn't exist
else
w2[0] = 0 // first point in distance trace is -1 so correct this
Integrate/METH=0 w2 // make cumulative distance
SetScale/P x 0,tStep, w2
AppendtoGraph/W=$plotName $newName
nTrace += 1
endif
endfor
KillWaves/Z tDistW
endfor
Variable alphaLevel = DecideOpacity(nTrace)
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
avList = Wavelist("cd*",";","WIN:"+ plotName)
avName = "W_Ave_cd_" + condName
errName = ReplaceString("Ave", avName, "Err")
fWaveAverage(avList, "", 3, 1, avName, errName)
AppendToGraph/W=$plotName $avName
Label/W=$plotName left "Cumulative distance ("+unitWave[1]+")"
Label/W=$plotName bottom "Time ("+unitWave[0]+")"
ErrorBars/W=$plotName $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($ErrName,$ErrName)
ModifyGraph/W=$plotName lsize($avName)=2,rgb($avName)=(0,0,0)
SetAxis/W=$plotName/A/N=1 left
AppendLayoutObject/W=$layoutName graph $plotName
// instantaneous speed over time
plotName = condName + "_ivplot"
KillWindow/Z $plotName // set up plot
Display/N=$plotName/HIDE=1
for(i = 0; i < nWaves; i += 1)
mName0 = StringFromList(i,wList0)
WAVE m0 = $mName0
Duplicate/O/RMD=[][5,5] m0, $"tDistW" // distance
Duplicate/O/RMD=[][1,1] m0, $"tCellW" // cell number
WAVE tDistW,tCellW
Redimension/N=-1 tDistW, tCellW // make 1D
nTrack = WaveMax(tCellW) // find maximum track number
for(j = 1; j < (nTrack+1); j += 1) // index is 1-based
newName = "iv_" + mName0 + "_" + num2str(j)
Duplicate/O tDistW, $newName
WAVE w2 = $newName
w2 = (tCellW[p] == j) ? tDistW[p] : NaN
WaveTransform zapnans w2
if(numpnts(w2) <= minPoints)
KillWaves w2
else
w2[0] = 0 // first point in distance trace is -1, so correct this
w2 /= tStep // make instantaneous speed
SetScale/P x 0,tStep, w2
AppendtoGraph/W=$plotName $newName
endif
endfor
KillWaves/Z tDistW
endfor
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
avList = Wavelist("iv*",";","WIN:"+ plotName)
avName = "W_Ave_iv_" + condName
errName = ReplaceString("Ave", avName, "Err")
fWaveAverage(avList, "", 3, 1, avName, errName)
AppendToGraph/W=$plotName $avName
Label/W=$plotName left "Instantaneous Speed ("+unitWave[2]+")"
Label/W=$plotName bottom "Time ("+unitWave[0]+")"
ErrorBars/W=$plotName $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($ErrName,$ErrName)
ModifyGraph/W=$plotName lsize($avName)=2,rgb($avName)=(0,0,0)
SetAxis/W=$plotName/A/N=1 left
AppendLayoutObject/W=$layoutName graph $plotName
// print a message to say how many valid tracks we have in this condition
Print ItemsInList(avList), "valid tracks plotted for", condName
plotName = condName + "_ivHist"
KillWindow/Z $plotName //set up plot
Display/N=$plotName/HIDE=1
Concatenate/O/NP avList, tempwave
newName = "h_iv_" + condName // note that this makes a name like h_iv_Ctrl
// before v 1.15 we used sqrt((3*pxsize)^2)/tStep
print wavemax(tempwave)
Variable nBins = ceil(1 + log(numpnts(tempwave))/log(2))
Variable binWidth = wavemax(tempwave)/nBins
Make/O/N=(nBins) $newName
Histogram/B={0,binWidth,nBins} tempwave,$newName
AppendToGraph/W=$plotName $newName
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
ModifyGraph/W=$plotName mode=5,hbFill=4
SetAxis/W=$plotName/A/N=1/E=1 left
SetAxis/W=$plotName/A/N=1/E=1 bottom
Label/W=$plotName left "Frequency"
Label/W=$plotName bottom "Instantaneous Speed ("+unitWave[2]+")"
KillWaves/Z tempwave
AppendLayoutObject/W=$layoutName graph $plotName
// plot out tracks
plotName = condName + "_tkplot"
KillWindow/Z $plotName //set up plot
Display/N=$plotName/HIDE=1
Variable off
for(i = 0; i < nWaves; i += 1)
mName0 = StringFromList(i,wList0)
WAVE m0 = $mName0
Duplicate/O/RMD=[][3,3] m0, $"tXW" //x pos
Duplicate/O/RMD=[][4,4] m0, $"tYW" //y pos
Duplicate/O/RMD=[][1,1] m0, $"tCellW" //track number
WAVE tXW,tYW,tCellW
Redimension/N=-1 tXW,tYW,tCellW
nTrack = WaveMax(tCellW) //find maximum track number
for(j = 1; j < (nTrack+1); j += 1) //index is 1-based
newName = "tk_" + mName0 + "_" + num2str(j)
Duplicate/O tXW, $"w3"
WAVE w3
w3 = (tCellW[p] == j) ? w3[p] : NaN
WaveTransform zapnans w3
if(numpnts(w3) <= minPoints)
KillWaves w3
else
off = w3[0]
w3 -= off //set to origin
w3 *= pxSize
// do the y wave
Duplicate/O tYW, $"w4"
WAVE w4
w4 = (tCellW[p] == j) ? w4[p] : NaN
WaveTransform zapnans w4
off = w4[0]
w4 -= off
w4 *= pxSize
Concatenate/O/KILL {w3,w4}, $newName
Wave w5 = $newName
AppendtoGraph/W=$plotName w5[][1] vs w5[][0]
endif
endfor
Killwaves/Z tXW,tYW,tCellW //tidy up
endfor
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
// set these graph limits temporarily
SetAxis/W=$plotName left -250,250
SetAxis/W=$plotName bottom -250,250
ModifyGraph/W=$plotName width={Plan,1,bottom,left}
ModifyGraph/W=$plotName mirror=1
ModifyGraph/W=$plotName grid=1
ModifyGraph/W=$plotName gridRGB=(32767,32767,32767)
AppendLayoutObject/W=$layoutName graph $plotName
// calculate d/D directionality ratio
plotName = condName + "_dDplot"
KillWindow/Z $plotName // setup plot
Display/N=$plotName/HIDE=1
String wName0, wName1
Variable len
wList0 = WaveList("tk_" + condName + "_*", ";","")
nWaves = ItemsInList(wList0)
for(i = 0; i < nWaves; i += 1)
wName0 = StringFromList(i,wList0) // tk wave
wName1 = ReplaceString("tk",wName0,"cd") // cd wave
WAVE w0 = $wName0
WAVE w1 = $wName1
newName = ReplaceString("tk",wName0,"dD")
Duplicate/O w1 $newName
WAVE w2 = $newName
len = numpnts(w2)
w2[] = (w1[p] == 0) ? 1 : sqrt(w0[p][0]^2 + w0[p][1]^2) / w1[p]
w2[0] = NaN // d/D at point 0 is not a number
AppendtoGraph/W=$plotName w2
endfor
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
avList = Wavelist("dD*",";","WIN:"+ plotName)
avName = "W_Ave_dD_" + condName
errName = ReplaceString("Ave", avName, "Err")
fWaveAverage(avList, "", 3, 1, avName, errName)
AppendToGraph/W=$plotName $avName
Label/W=$plotName left "Directionality ratio (d/D)"
Label/W=$plotName bottom "Time ("+unitWave[0]+")"
ErrorBars/W=$plotName $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($ErrName,$ErrName)
ModifyGraph/W=$plotName lsize($avName)=2,rgb($avName)=(0,0,0)
AppendLayoutObject/W=$layoutName graph $plotName
// calculate MSD (overlapping method)
plotName = condName + "_MSDplot"
KillWindow/Z $plotName //setup plot
Display/N=$plotName/HIDE=1
wList0 = WaveList("tk_" + condName + "_*", ";","")
nWaves = ItemsInList(wList0)
Variable k
for(i = 0; i < nWaves; i += 1)
wName0 = StringFromList(i,wList0) // tk wave
WAVE w0 = $wName0
len = DimSize(w0,0)
newName = ReplaceString("tk",wName0,"MSD") // for results of MSD per cell
Make/O/N=(len-1,len-1,2)/FREE tempMat0,tempMat1
// make 2 3D waves. 0 is end point to measure MSD, 1 is start point
// layers are x and y
tempMat0[][][] = (p >= q) ? w0[p+1][r] : 0
tempMat1[][][] = (p >= q) ? w0[p-q][r] : 0
MatrixOp/O/FREE tempMat2 = (tempMat0 - tempMat1) * (tempMat0 - tempMat1))
Make/O/N=(len-1)/FREE countOfMSDPnts = (len-1)-p
MatrixOp/O $newName = sumcols(sumbeams(tempMat2))^t / countOfMSDPnts
SetScale/P x 0,tStep, $newName
AppendtoGraph/W=$plotName $newName
endfor
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
avList = Wavelist("MSD*",";","WIN:"+ plotName)
avName = "W_Ave_MSD_" + condName
errName = ReplaceString("Ave", avName, "Err")
fWaveAverage(avList, "", 3, 1, avName, errName)
AppendToGraph/W=$plotName $avName
ModifyGraph/W=$plotName log=1
SetAxis/W=$plotName/A/N=1 left
len = numpnts($avName)*tStep
SetAxis/W=$plotName bottom tStep,(len/2)
Label/W=$plotName left "MSD"
Label/W=$plotName bottom "Time ("+unitWave[0]+")"
ErrorBars/W=$plotName $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=$plotName lsize($avName)=2,rgb($avName)=(0,0,0)
AppendLayoutObject /W=$layoutName graph $plotName
// calculate direction autocorrelation
plotName = condName + "_DAplot"
KillWindow/Z $plotName // setup plot
Display/N=$plotName/HIDE=1
for(i = 0; i < nWaves; i += 1)
wName0 = StringFromList(i,wList0) // tk wave
WAVE w0 = $wName0
len = DimSize(w0,0) // len is number of frames
Differentiate/METH=2/DIM=0/EP=1 w0 /D=vWave // make vector wave (vWave). nVectors is len-1
MatrixOp/O/FREE magWave = sqrt(sumrows(vWave * vWave)) // calculate magnitude of each vector
vWave[][] /= magWave[p] // normalise vectors
newName = ReplaceString("tk",wName0,"DA") // for results of DA per cell
Make/O/N=(len-2,len-2,2)/FREE tempDAMat0,tempDAMat1
tempDAMat0[][][] = (p >= q) ? vWave[p-q][r] : 0
tempDAMat1[][][] = (p >= q) ? vWave[p+1][r] : 0
MatrixOp/O/FREE dotWave = (tempDAMat0 * tempDAMat1)
MatrixOp/O/FREE alphaWave = sumBeams(dotWave)
// Make average. Previously we did this:
// Make/O/N=(len-2)/FREE countOfDAPnts = (len-2)-p
// MatrixOp/O $newName = sumcols(alphaWave)^t / countOfDAPnts
// Now we need to get rid of NaNs in the alphaWave and count the non-NaN points
MatrixOp/O/FREE alphaWave = replaceNans(alphaWave,0)
Make/O/FREE/N=(dimsize(alphaWave,0),dimsize(alphaWave,1)) countOfDAPnts
countOfDAPnts[][] = (abs(alphaWave[p][q]) > 0) ? 1 : 0
MatrixOp/O $newName = sumcols(alphaWave)^t / sumCols(countOfDAPnts)^t
SetScale/P x 0,tStep, $newName
AppendtoGraph/W=$plotName $newName
endfor
Killwaves/Z vWave
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2],alphaLevel)
avList = Wavelist("DA*",";","WIN:"+ plotName)
avName = "W_Ave_DA_" + condName
errName = ReplaceString("Ave", avName, "Err")
fWaveAverage(avList, "", 3, 1, avName, errName)
AppendToGraph/W=$plotName $avName
SetAxis/W=$plotName left -1,1
Label/W=$plotName left "Direction autocorrelation"
Label/W=$plotName bottom "Time ("+unitWave[0]+")"
ErrorBars/W=$plotName $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=$plotName lsize($avName)=2,rgb($avName)=(0,0,0)
AppendLayoutObject/W=$layoutName graph $plotName
// calculate the angle distribution
plotName = condName + "_anglePlot"
KillWindow/Z $plotName // setup plot
Display/N=$plotName/HIDE=1
wList0 = WaveList(condName + "_*",";","") // find all matrices
nWaves = ItemsInList(wList0)
Concatenate/O/NP=0 wList0, allTempW // make long matrix of all tracks
Variable nSteps = dimsize(allTempW,0)
Make/O/N=(nSteps)/FREE tempDistThreshW
Make/O/D/N=(nSteps) angleWave = NaN
// quality filter so that minimal steps are not analysed
tempDistThreshW[] = (allTempW[p][5] > 4 * pxSize) ? 1 : 0
Variable successVar = 0
// this will find angles for all tracks even short tracks
// valid track length has a lower bound defined by user, minimum is 6 points (v. 1.15)
// at tStep = 10 this will find max 4 angles in a track that is not found elsewhere
for(i = 0; i < nSteps; i += 1)
// find a proper step
if(tempDistThreshW[i] == 1)
Make/O/N=(2,2)/FREE matAA,matBB
// set first vector offset to origin (need to transpose later)
matAA[][] = allTempW[p + (i-1)][q+3] - allTempW[i-1][q+3]
for(j = i+1; j < nSteps; j += 1)
if(allTempW[j][1] != allTempW[i][1])
// check there is another proper step from the same cell
successVar = 0
break
elseif(tempDistThreshW[j] == 1)
// find a proper step from same cell and set second vector as this, offset to origin
successVar = 1
matBB[][] = allTempW[p + (j-1)][q+3] - allTempW[j-1][q+3]
break
else
successVar = 0
endif
endfor
if(successVar == 1)
// matrices need transposing
MatrixTranspose matAA
MatrixTranspose matBB
// find cos(theta)
MatrixOp/O/FREE matCC = matAA . matBB / (sqrt(sum(matAA * matAA)) * sqrt(sum(matBB * matBB)))
// angle in radians
AngleWave[i] = acos(matCC[0])
endif
endif
endfor
KillWaves/Z allTempW
// zapnans on AngleWave so I can count valid angles
WaveTransform zapnans AngleWave
newName = "h_angle_" + condName
Make/N=41/O $newName
Histogram/B={0,pi/40,41} angleWave,$newName
AppendToGraph/W=$plotName $newName
ModifyGraph/W=$plotName rgb=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
ModifyGraph/W=$plotName mode=5, hbFill=4
SetAxis/W=$plotName/A/N=1/E=1 left
SetAxis/W=$plotName bottom 0,pi
Make/O/N=5 axisW = {0,pi/4,pi/2,3*pi/4,pi}
// vulgar fractions and pi as Unicode
Make/O/N=5/T axisTW = {"0","\u00BC\u03C0","\u00BD\u03C0","\u00BE\u03C0","\u03C0"}
ModifyGraph/W=$plotName userticks(bottom)={axisW,axisTW}
Label/W=$plotName left "Density"
Label/W=$plotName bottom "Cell turning"
AppendLayoutObject/W=$layoutName graph $plotName
// print message about number of angles
Print numpnts(AngleWave), "valid angles found from all tracks for", condName
// Plot these averages to summary windows at the end
avName = "W_Ave_cd_" + condName
errName = ReplaceString("Ave", avName, "Err")
AppendToGraph/W=cdPlot $avName
ErrorBars/W=cdPlot $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=cdPlot lsize($avName)=2,rgb($avName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
avName = "W_Ave_iv_" + condName
errName = ReplaceString("Ave", avName, "Err")
AppendToGraph/W=ivPlot $avName
ErrorBars/W=ivPlot $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=ivPlot lsize($avName)=2,rgb($avName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
newName = "h_iv_" + condName
AppendToGraph/W=ivHPlot $newName
ModifyGraph/W=ivHPlot rgb($newName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
avName = "W_Ave_dD_" + condName
errName = ReplaceString("Ave", avName, "Err")
AppendToGraph/W=dDPlot $avName
ErrorBars/W=dDPlot $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=dDPlot lsize($avName)=2,rgb($avName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
avName = "W_Ave_MSD_" + condName
errName = ReplaceString("Ave", avName, "Err")
AppendToGraph/W=MSDPlot $avName
ErrorBars/W=MSDPlot $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=MSDPlot lsize($avName)=2,rgb($avName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
avName = "W_Ave_DA_" + condName
errName = ReplaceString("Ave", avName, "Err")
AppendToGraph/W=DAPlot $avName
ErrorBars/W=DAPlot $avName SHADE= {0,0,(0,0,0,0),(0,0,0,0)},wave=($errName,$errName)
ModifyGraph/W=DAPlot lsize($avName)=2,rgb($avName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
newName = "h_angle_" + condName
AppendToGraph/W=angleHPlot $newName
ModifyGraph/W=angleHPlot rgb($newName)=(colorWave[ii][0],colorWave[ii][1],colorWave[ii][2])
End
/// @param plotString String such as "*_tkPlot" to determine which plot get rescaled
/// @param limitVar Variable containing the furthest point
STATIC Function RescalePlotsToLimits(plotString,limitVar)
String plotString
Variable limitVar
// previously a temporary limit of -250,250 was set to all tkPlots and then expanded here if necessary
// as of v 1.15, we just use the furthest point
if(limitVar > 1000)
limitVar = ceil(limitVar / 100) * 100
elseif(limitVar >= 10 && limitVar < 100)
limitVar = ceil(limitVar / 10) * 10
elseif(limitVar >= 1 && limitVar < 10)
limitVar = ceil(limitVar / 1) * 1
elseif(limitVar >= 0.1 && limitVar < 1)
limitVar = ceil(limitVar / 0.1) * 0.1
elseif(limitVar < 0.1)
limitVar = limitVar
else
limitVar = ceil(limitVar / 50) * 50 // we expect values of 150-300
endif
String plotList = WinList(plotString,";","WIN:1")
String plotName
Variable i
for(i = 0; i < ItemsInList(plotList); i += 1)
plotName = StringFromList(i,plotList)
SetAxis/W=$plotName left -limitVar,limitVar
SetAxis/W=$plotName/Z bottom -limitVar,limitVar
SetAxis/W=$plotName/Z top -limitVar,limitVar
endfor
return 1
End
// This function will make ImageQuilts and sparklines of 2D tracks for all conditions
/// @param qSize Variable to indicate desired size of image quilt (qSize^2 tracks)
Function MakeImageQuilt(qSize)
Variable qSize
WAVE/T condWave = root:condWave
Variable cond = numpnts(condWave)
Wave paramWave = root:paramWave
Variable tStep = paramWave[1]
Variable pxSize = paramWave[2]
Wave colorWave = root:colorWave
String condName, dataFolderName, wName
Variable longestCond = 0 , mostFrames = 0
Variable i
for(i = 0; i < cond; i += 1)
condName = condWave[i]
dataFolderName = "root:data:" + condName
SetDataFolder datafolderName
mostFrames = FindSolution()
longestCond = max(longestCond,mostFrames)
endfor
SetDataFolder root:
// Now they're all done, cycle again to find optimum quilt size
Make/O/N=(longestCond,qSize+1,cond)/FREE optiMat
for(i = 0; i < cond; i += 1)
condName = condWave[i]
wName = "root:data:" + condName + ":solutionWave"
Wave w0 = $wName
optiMat[][][i] = (w0[p][0] >= q^2) ? 1 : 0
endfor
optiMat /= cond
// make a 1D wave where row = qSize and value = frames that can be plotted for all cond
MatrixOp/O/FREE quiltSizeMat = sumcols(floor(sumBeams(optiMat)))^t
// find optimum
quiltSizeMat *= p^2
WaveStats/Q quiltSizeMat
Variable optQSize = V_maxRowLoc
Variable optDur = (V_max / V_maxRowLoc^2) - 1 // because 0-based
Print qSize, "x", qSize, "quilt requested.", optQSize, "x", optQSize, "quilt with", optDur, "frames shown (", optDur * tStep, "min)."
String plotName,sampleWName
Variable startVar,endVar,xShift,yShift
Variable spaceVar = WorkOutSpacing(pxSize)
Variable j,k
for(i = 0; i < cond; i += 1)
condName = condWave[i]
dataFolderName = "root:data:" + condName
SetDataFolder datafolderName
// make image quilt for each condition
plotName = condName + "_quilt"
KillWindow/Z $plotName
Display/N=$plotName/HIDE=1
WAVE segValid, trackDurations
WAVE/T trackNames
segValid[] = (trackDurations[p] > optDur * tStep) ? p : NaN
WaveTransform zapnans segValid
StatsSample/N=(optQSize^2) segValid
WAVE/Z W_Sampled
sampleWName = "segSelected_" + condName
Duplicate/O W_Sampled, $sampleWName
Wave segSelected = $sampleWName
Make/O/N=(optQSize^2)/T segNames
Make/O/N=(optQSize^2) segLengths
for(j = 0; j < optQSize^2; j += 1)
segNames[j] = trackNames[segSelected[j]]
wName = ReplaceString("tk_",segNames[j],"cd_") // get cum dist wave name
Wave cdW0 = $wName
segLengths[j] = cdW0[optDur] // store cum dist at point optDur
endfor
Sort segLengths, segLengths, segNames
// plot segNamed waves out
Make/O/N=(optQSize^2*(optDur+1),2) quiltBigMat = NaN
for(j = 0; j < optQSize^2; j += 1)
wName = segNames[j]
Wave tkW0 = $wName
// put each track into the big quilt wave leaving a NaN between each
startVar = j * optDur + (j * 1)
endVar = startVar + optDur - 1
quiltBigMat[startVar,endVar][] = tkW0[p-startVar][q]
xShift = mod(j,optQSize) * spaceVar
yShift = floor(j/optQSize) * spaceVar
quiltBigMat[startVar,endVar][0] += xShift
quiltBigMat[startVar,endVar][1] += yShift
endfor
// Add to plot and then format
AppendToGraph/W=$plotName quiltBigMat[][1] vs quiltBigMat[][0]
SetAxis/W=$plotName left (optQsize+1.5) * spaceVar,-2.5*spaceVar
SetAxis/W=$plotName bottom -2.5*spaceVar,(optQsize+1.5) * spaceVar
ModifyGraph/W=$plotName width={Aspect,1}
ModifyGraph/W=$plotName manTick={0,spaceVar,0,0},manMinor={0,0}
ModifyGraph/W=$plotName noLabel=2,mirror=1,standoff=0,tick=3
ModifyGraph/W=$plotName grid=1,gridRGB=(34952,34952,34952)
ModifyGraph axRGB=(65535,65535,65535)
ModifyGraph/W=$plotName rgb=(colorWave[i][0],colorWave[i][1],colorWave[i][2])
ModifyGraph/W=$plotName margin=14
// Append to appropriate layout (page 2)
String layoutName = condName + "_layout"
LayoutPageAction/W=$layoutName appendPage
AppendLayoutObject/W=$layoutName/PAGE=(2) graph $plotName
ModifyLayout/W=$layoutName/PAGE=(2) left($plotName)=21,top($plotName)=291,width($plotName)=261,height($plotName)=261
// make sparkline graphic
plotName = condName + "_sprkln"
KillWindow/Z $plotName
Display/N=$plotName/HIDE=1
// plot the diagonal of segNamed waves out laterally
Make/O/N=(optQSize*(optDur+1),2) sprklnBigMat = NaN
Variable theta
k = 0
for(j = 0; j < optQSize^2; j += optQsize+1)
wName = segNames[j]
Wave tkW0 = $wName
Duplicate/O/FREE tkW0, sprkW0
theta = (1.5 * pi) - atan2(sprkW0[optDur-1][1],sprkW0[optDur-1][0])
Make/O/N=(2,2)/FREE rotMat = {{cos(theta),-sin(theta)},{sin(theta),cos(theta)}}
MatrixMultiply sprkW0, rotMat
WAVE/Z M_product
// put each track into the big quilt wave leaving a NaN between each
startVar = k * optDur + (k * 1)
endVar = startVar + optDur - 1
sprklnBigMat[startVar,endVar][] = M_Product[p-startVar][q]
xShift = mod(k,optQSize) * spaceVar
sprklnBigMat[startVar,endVar][0] += xShift
k += 1
endfor
KillWaves/Z M_product
// Add to plot and then format
AppendToGraph/W=$plotName sprklnBigMat[][1] vs sprklnBigMat[][0]
SetAxis/W=$plotName left 0.75 * spaceVar,-2.5*spaceVar
SetAxis/W=$plotName bottom -0.5*spaceVar,(optQsize+0.5) * spaceVar
ModifyGraph/W=$plotName width={Plan,1,bottom,left}
ModifyGraph/W=$plotName manTick={0,spaceVar,0,0},manMinor={0,0}
ModifyGraph/W=$plotName noLabel=2,mirror=1,standoff=0,tick=3
ModifyGraph/W=$plotName grid=1,gridRGB=(34952,34952,34952)
ModifyGraph axRGB=(65535,65535,65535)
ModifyGraph/W=$plotName rgb=(colorWave[i][0],colorWave[i][1],colorWave[i][2])
ModifyGraph/W=$plotName margin=14
SetDrawLayer/W=$plotName UserBack