def SaveDiffImages(logDir):
diffDir = os.path.join(logDir,'Diff')
if not os.path.exists(diffDir):
os.mkdir(diffDir)
Files = FS.getSortedListOfFiles(logDir,'*.tif')
frameUpdateList = [] # [time,fn,newVal]
for i,f in enumerate(Files):
name = os.path.splitext(os.path.split(f)[1])[0]
frameNumber = int(name.split('_')[-1])
cur = GTL.LoadSingle(f)
final = GTL.LoadSingle(FrameFiles[frameNumber])
d = CreateDiffImage(cur,final)
frameUpdateList.append([timeAxis[i],frameNumber,d.astype(int).sum()])
im = Image.fromarray(d*255)
im.save(os.path.join(diffDir,name+'.png'))
def GetTimeAxisAdj(SegmentsDirectory):
sList = []
timeAdj = 0
count=0
for i in FS.getSortedListOfFiles(SegmentsDirectory,'*.tif'):
count+=1
d,h,m,s=map(int,os.path.split(i)[1].split('_')[2:6])
h += d*24
m += h*60
s += m*60 + timeAdj
if sList!=[]:
if s - sList[-1]>80: # Pretend any large gaps in time are only 1min
print(count)
timeAdj += sList[-1] - s + 80
s = sList[-1] + 80
sList.append(s)
return sList
def SaveOverlayImages(tifStackData,SeedsPyFile,SegmentsDirectory,red=True):
# This function is more-or-less just a template right now, has MAJOR issues...
r = GTL.LoadFileSequence(SegmentsDirectory, wildcard='*.tif')
rgbM = CreateMapPlots(r)
for i in range(len(Files)):
tifDir,nameTif = os.path.split(Files[i])
mapDir = os.path.join(tifDir,'Maps')
overlayDir = os.path.join(tifDir,'Overlay')
for j in [mapDir,overlayDir]:
if not os.path.exists(j):
os.mkdir(j)
name = os.path.splitext(nameTif)[0]
nameSeedsPy = '_'.join(name.split('_')[:-2])+'_Seeds.py'
### GENERATE MAP PLOT
namePng = name+'.png'
rgbMi = CreateMapPlot(r[i])
im = Image.fromarray(rgbMi)
im.save(os.path.join(mapDir,namePng))
### NOW GENERATE OVERLAY IMAGE
# Grab the frame number from the image name...
frameNumber = int(name.split('_')[-1])
# Get the watershed file from the saved tif:
watershed = GTL.LoadSingle(Files[i])
# Find and load the correct original array based on the frame number:
originalDir = '.../2010FEB09_Edge5/TiffStack' # Put in the right directory here...
origFile = FS.getSortedListOfFiles(originalDir)[frameNumber]
original = GTL.LoadSingle(origFile)
SeedsPyFile = os.path.join(tifDir,nameSeedsPy)
overlayIm = CreateOverlay(original,watershed,SeedsPyFile,frameNumber)
# Now, save the overlay as a png
nameSeedsOutl = name+'SO.png'
im = Image.fromarray(overlayIm)
im.save(os.path.join(overlayDir,nameSeedsOutl))