def createListfiles() :
IJ.showMessage("Select a folder with the .tif files")
selectdir=IJ.getDirectory("image")
selectdir=IJ.getDirectory("")
listfiles=glob.glob(selectdir+"*.tif")
#fullprefix = str.rsplit(str(listfiles[0]), "/", 1)
fullprefix = os.path.split(listfiles[0])
root = fullprefix[0]
lastprefix = str.split(fullprefix[1], "_")
del(listfiles)
gdselectfiles = NonBlockingGenericDialog("List files Choice")
gdselectfiles.addMessage("")
gdselectfiles.addStringField("Prefix ?", lastprefix[0], 32)
gdselectfiles.addStringField("Filter (w00001DIA) ?", "1DIA")
gdselectfiles.addStringField("Positions (s0001) ?", "1-2")
gdselectfiles.addStringField("Temps (t0001) ?", "1-11")
#gdselectfiles.addStringField("Files pattern", "*DIA_s*1_t*.tif", 32)
gdselectfiles.showDialog()
prefix = str(gdselectfiles.getNextString())
channel = str(gdselectfiles.getNextString())
temppositions = str(gdselectfiles.getNextString())
positions = str.split(temppositions, "-")
temptimes = str(gdselectfiles.getNextString())
times = str.split(temptimes, "-")
if channel != "" : channel = "_w000"+channel
positionslist=[]
if positions[0] != "" :
for p in range(int(positions[0]), int(positions[1])+1, 1) :
positionslist.append("_s"+"%04i"%(p))
else : positionslist.append("")
timeslist=[]
if times[0] != "" :
for t in range(int(times[0]), int(times[1])+1, 1) :
timeslist.append("_t"+"%04i"%(t))
else : timeslist.append("")
patterns=[]
listfiles = []
for p in positionslist :
files = []
for t in timeslist :
patterns.append(channel+p+t+".tif")
tempfilename = os.path.join(root, prefix+patterns[-1])
files.append(tempfilename)
#files.append(root+"/"+prefix+patterns[-1])
listfiles.append(files)
if len(listfiles)>1 : return (prefix, patterns, listfiles, positionslist)
else : return (prefix, patterns, files, "_s0001")
def runGUI(defaultTargetChannel=2,
defaultdt=1.0,
defaultRadius=0.3,
defaultThreshold=16,
defaultFrameGap=0.01,
defaultLinkingMax=0.01,
defaultClosingMax=0.01):
gd = NonBlockingGenericDialog("ZedMate - v0.18 beta")
gd.addMessage(
"\tZedMate is a TrackMate-based 3D prticle analyzer \n\t\t\t\t\t\t\t\t\t\t\t(copyright Artur Yakimovich 2018-19)\n\n"
)
gd.addStringField("File_extension", ".tif")
gd.addStringField("File_name_contains", "")
gd.addNumericField("Target_Channel", defaultTargetChannel, 0)
gd.addNumericField("dt", defaultdt, 2)
gd.addNumericField("Radius", defaultRadius, 2)
gd.addNumericField("Threshold", defaultThreshold, 2)
gd.addNumericField("Frame_Gap", defaultFrameGap, 0)
gd.addNumericField("Linking_Max", defaultLinkingMax, 2)
gd.addNumericField("Closing_Max", defaultClosingMax, 2)
gd.addMessage("\t\t\t\t\t\t_______________________________________")
gd.addCheckbox("Preview Parameters on the First Image Only", 0)
gd.addMessage("\t\t\t\t\t(Doesn't save results. Re-opens this Dialog).")
gd.addMessage("\t\t\t\t\t\t_______________________________________")
gd.addCheckbox("Save MNIST mimicry embedding (beta)", 0)
gd.showDialog()
if gd.wasCanceled():
return
extension = gd.getNextString()
containString = gd.getNextString()
targetChannel = int(gd.getNextNumber())
dt = gd.getNextNumber()
radius = gd.getNextNumber()
threshold = gd.getNextNumber()
frameGap = int(gd.getNextNumber())
linkingMax = gd.getNextNumber()
closingMax = gd.getNextNumber()
testMode = gd.getNextBoolean()
mimicryEmbd = gd.getNextBoolean()
inputDir = IJ.getDirectory("Input_directory")
if not inputDir:
return
if not testMode:
outputDir = IJ.getDirectory("Output_directory")
if not outputDir:
return
else:
outputDir = inputDir # for the case of test
#if not os.path.exists(outputDir):
# os.makedirs(outputDir)
runBatch(inputDir, outputDir, extension, containString, targetChannel, dt, radius, threshold, frameGap,\
linkingMax, closingMax, testMode, mimicryEmbd)
def showGui(par, title):
"""Updated version discriminates between string and numeric outputs to treat them accordingly"""
numflags = {}
gd = NonBlockingGenericDialog(title)
s_keys = sorted(par.keys())
for nm in s_keys:
if isinstance(par[nm], (int, float, long)):
gd.addNumericField(nm, par[nm], 1)
numflags[nm] = True
else:
gd.addStringField(nm, par[nm])
numflags[nm] = False
gd.setOKLabel("Go on!")
gd.setCancelLabel("Recompute..")
gd.centerDialog(False)
gd.setLocation(50, 100)
gd.showDialog()
if gd.wasCanceled():
rep = True
else:
rep = False
for nm in s_keys:
if numflags[nm]:
par[nm] = gd.getNextNumber()
else:
par[nm] = gd.getNextString().encode("ascii", "replace")
return par, rep
gd.addNumericField("Size_threshold",100,0)
gd.addChoice("Process_filter",["None","Min","Median"],"None")
gd.addCheckbox("Operate_on_tile_subset",False)
gd.addStringField("Which_tile_subset","1-4,9,11",12)
gd.showDialog()
## Parses the information from the dialog box
if (gd.wasOKed()):
analysisChannel = gd.getNextChoiceIndex()+1
bleedingChannel = gd.getNextChoiceIndex()
refChannel = gd.getNextChoiceIndex()
intThreshold = gd.getNextNumber()
sizeThreshold = gd.getNextNumber()
processFilter = gd.getNextChoiceIndex()
doSubset = gd.getNextBoolean()
whichTiles = gd.getNextString()
tileList = []
parsingFailed = False
if doSubset:
try:
whichTilesDespaced = whichTiles.replace(" ","")
tilesListed = whichTilesDespaced.split(",")
for tile in tilesListed:
tilesExpanded = tile.split("-")
tilesExpanded = map(int,tilesExpanded)
if (len(tilesExpanded) == 2):
tilesExpanded = range(tilesExpanded[0],tilesExpanded[1]+1)
tileList = tileList + tilesExpanded
tileList = list(set(tileList))
tileList = filter(lambda x: True if x<nTiles+1 else False,tileList)
print tileList
from ij.measure import Measurements
from ij.gui import NonBlockingGenericDialog
from ij.gui import WaitForUserDialog
# Get input and output directories
dc = DirectoryChooser("Choose an input directory")
inputDirectory = dc.getDirectory()
dc = DirectoryChooser("Choose an output directory")
outputDirectory = dc.getDirectory()
gd = NonBlockingGenericDialog("Channel Options")
gd.addStringField("Enter your name: ", "")
gd.showDialog()
name = gd.getNextString()
if gd.wasCanceled():
print "User canceled dialog!"
# Finds all the subfolders in the main directory
with open(outputDirectory + "annotations_" + name + ".csv", "w") as log:
subfolders = []
# for subfolder in os.listdir(inputDirectory):
# if os.path.isdir(inputDirectory + subfolder):
# subfolders.append(subfolder)
# for subfolder in subfolders:
# user interface
nbgd = NonBlockingGenericDialog("ER Selection")
nbgd.addStringField("Selection radius: ", str(radius), 5)
nbgd.hideCancelButton()
imp = IJ.getImage()
overlay = Overlay()
overlay = imp.getOverlay()
nbgd.showDialog()
if mean_max_det is True:
IJ.setTool("polygon")
else:
IJ.setTool("rectangle")
radius = int(nbgd.getNextString().strip())
imp = IJ.getImage()
# set variables
all_x = []
all_y = []
ER_measurements = []
# function
ER_points(all_x, all_y, overlay, ER_measurements)
# set more variables
ER = []
# merges the x and y lists such that x,y are pairs in a list
x_y = list(zip(all_x, all_y))
# loops through x,y coordinate pairs, draw a circle and measures the average intensity.