Python DirectoryChooser.getDirectory方法代码示例

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def ijGUI():
	from ij.io import DirectoryChooser
	dc = DirectoryChooser("Choose directory with Stratec files to scrub")
	dir_in = dc.getDirectory()
	dc = DirectoryChooser("Choose directory to write scrubbed files")
	dir_out = dc.getDirectory()
	idle_task_ij (process_files (dir_in, dir_out))

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def run():
  imp = IJ.getImage()
  if imp is None:
    return
  if not imp.isHyperStack():
    print "Not a hyper stack!"
    return
  if 1 == imp.getNFrames():
    print "There is only one time frame!"
    return
  if 1 == imp.getNSlices():
    print "To register slices of a stack, use 'Register Virtual Stack Slices'"
    return
  dc = DirectoryChooser("Choose target folder")
  target_folder = dc.getDirectory()
  if target_folder is None:
    return # user canceled the dialog
  if not validate(target_folder):
    return
  gd = GenericDialog("Options")
  channels = []
  for ch in range(1, imp.getNChannels()+1 ):
    channels.append(str(ch))
  gd.addChoice("channel:", channels, channels[0])
  gd.showDialog()
  if gd.wasCanceled():
    return
  channel = gd.getNextChoiceIndex() + 1  # zero-based
  vs_imp = create_registered_hyperstack(imp, target_folder, channel)
  vs_imp.show()

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def main():
    #filename = sys.argv[1]
    #exportDir = sys.argv[2]

    inputDir = "/mnt/med-groups-lmu/ls1/users/l/lsalomie/"
    defaultName = "lif.lif"
    outputDir = "/home/hajaalin/tmp/lifexporttest"

    filename = OpenDialog("Choose LIF",inputDir,defaultName).getPath()
    if not filename:
        # user canceled dialog
        return
    
    chooser = DirectoryChooser("Choose export directory")
    chooser.setDefaultDirectory(outputDir)
    exportDir = chooser.getDirectory()
    if not exportDir:
        # user canceled dialog
        return

    # EDF parameters
    params = Parameters()
    params.setQualitySettings(params.QUALITY_HIGH)
    params.nScales = 10

    worker = EdfWorker(exportDir,params)

    iterateLif(filename,worker)

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
    def actionPerformed(self, event):
        dlg = DirectoryChooser("Choose an output directory for the classifier")

        if os.path.exists(self.path):
            dlg.setDefaultDirectory(self.path)

        self.path = dlg.getDirectory()
        IJ.log("Added path: "+self.path)

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def run():
  imp = IJ.getImage()
  if imp is None:
    return
  if not imp.isHyperStack():
    print "Not a hyper stack!"
    return
  if 1 == imp.getNFrames():
    print "There is only one time frame!"
    return
  if 1 == imp.getNSlices():
    print "To register slices of a stack, use 'Register Virtual Stack Slices'"
    return

  options = getOptions(imp)
  if options is not None:
    channel, virtual = options
    print "channel="+str(channel)+" virtual="+str(virtual)
  if virtual is True:
    dc = DirectoryChooser("Choose target folder to save image sequence")
    target_folder = dc.getDirectory()
    if target_folder is None:
      return # user canceled the dialog
    if not validate(target_folder):
      return
  else:
    target_folder = None 

  registered_imp= create_registered_hyperstack(imp, channel, target_folder, virtual)
  if virtual is True:
    if 1 == imp.getNChannels():
      ip=imp.getProcessor()
      ip2=registered_imp.getProcessor()
      ip2.setColorModel(ip.getCurrentColorModel())
      registered_imp.show()
    else:
    	registered_imp.copyLuts(imp)
    	registered_imp.show()
  else:
    if 1 ==imp.getNChannels():
    	registered_imp.show()
    else:
    	registered_imp.copyLuts(imp)
    	registered_imp.show()
  
  registered_imp.show()

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
	def selectInputDir(self):
		inputDialog = DirectoryChooser("Please select a directory contaning your images")
		inputDir = inputDialog.getDirectory()
		for imageFile in os.listdir(inputDir):
			self.files.append(inputDir + imageFile)

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def run():

  IJ.log("Correct_3D_Drift")
    
  imp = IJ.getImage()
  if imp is None:
    return
  if 1 == imp.getNFrames():
    print "There is only one time frame!"
    return

  options = getOptions(imp)
  if options is not None:
    channel, virtual, multi_time_scale, subpixel, process, only_compute = options
    
  if virtual is True:
    dc = DirectoryChooser("Choose target folder to save image sequence")
    target_folder = dc.getDirectory()
    if target_folder is None:
      return # user canceled the dialog
    if not validate(target_folder):
      return
  else:
    target_folder = None 

  # compute shifts
  IJ.log("  computing drifts..."); print("\nCOMPUTING SHIFTS:")

  IJ.log("    at frame shifts of 1"); 
  dt = 1; shifts = compute_and_update_frame_translations_dt(imp, channel, dt, process)
  
  # multi-time-scale computation
  if multi_time_scale is True:
    dt_max = imp.getNFrames()-1
    # computing drifts on exponentially increasing time scales 3^i up to 3^6
    # ..one could also do this with 2^i or 4^i
    # ..maybe make this a user choice? did not do this to keep it simple.
    dts = [3,9,27,81,243,729,dt_max] 
    for dt in dts:
      if dt < dt_max:
        IJ.log("    at frame shifts of "+str(dt)) 
        shifts = compute_and_update_frame_translations_dt(imp, channel, dt, process, shifts)
      else: 
        IJ.log("    at frame shifts of "+str(dt_max));
        shifts = compute_and_update_frame_translations_dt(imp, channel, dt_max, process, shifts)
        break

  # invert measured shifts to make them the correction
  shifts = invert_shifts(shifts)
  print(shifts)
  
  
  # apply shifts
  if not only_compute:
    
    IJ.log("  applying shifts..."); print("\nAPPLYING SHIFTS:")
    
    if subpixel:
      registered_imp = register_hyperstack_subpixel(imp, channel, shifts, target_folder, virtual)
    else:
      shifts = convert_shifts_to_integer(shifts)
      registered_imp = register_hyperstack(imp, channel, shifts, target_folder, virtual)
    
    
    if virtual is True:
      if 1 == imp.getNChannels():
        ip=imp.getProcessor()
        ip2=registered_imp.getProcessor()
        ip2.setColorModel(ip.getCurrentColorModel())
        registered_imp.show()
      else:
    	registered_imp.copyLuts(imp)
    	registered_imp.show()
    else:
      if 1 ==imp.getNChannels():
        registered_imp.show()
      else:
        registered_imp.copyLuts(imp)
        registered_imp.show()
  
    registered_imp.show()
  
  else:
   
    if imp.getRoi(): 
      xmin = imp.getRoi().getBounds().x
      ymin = imp.getRoi().getBounds().y
      zmin = 0
      xmax = xmin + imp.getRoi().getBounds().width - 1
      ymax = ymin + imp.getRoi().getBounds().height - 1
      zmax = imp.getNSlices()-1  
    else:
      xmin = 0
      ymin = 0
      zmin = 0
      xmax = imp.getWidth() - 1
      ymax = imp.getHeight() - 1
      zmax = imp.getNSlices() - 1  
    
    save_shifts(shifts, [xmin, ymin, zmin, xmax, ymax, zmax])
#.........这里部分代码省略.........

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
from ij.io import DirectoryChooser
import ij.ImageStack
from ij import IJ, ImagePlus
import os
import time

# Choose a directory containing the data
dc = DirectoryChooser("Choose directory containing embryo folders...")
srcDir = dc.getDirectory()
print(srcDir)
IJ.log('Root directory: ' + srcDir)

# Prepare output directories...
nowStr = time.strftime('%Y-%m-%d %H%M%S')
outputDir = os.path.join(srcDir, nowStr+ " results")
if not os.path.exists(outputDir):
	os.makedirs(outputDir)

# Loop through embryo sample directories, taking note of date and embryo number
folders=[f for f in os.listdir(srcDir)
	if os.path.isdir(os.path.join(srcDir,f)) and not (f.endswith('results'))]

for folder in folders:
	print(folder)
	IJ.log('Working on data in sample folder: ' + folder)
	(date, embryoNumber) = folder.split('_E')
	
	# Identify the indices of the files where cuts occur
	textFiles=[f for f in os.listdir(os.path.join(srcDir, folder))
	    if (f.endswith('.txt')) and not (f.endswith('para.txt'))]

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def get_files_and_analyze(folder):

  count = 0
  timeseries = []
  for root, directories, filenames in os.walk(folder):
    #print directories
    for directory in sorted(directories):
      #print directory
      if not (("field" in directory)): # "field is specific to the folder where the image files are"
        continue
      else:
        print os.path.join(root, directory)
        analyze(os.path.join(root, directory), 3, 7, 1)

  
          
if __name__ == '__main__':
  dc = DirectoryChooser("Choose top directory containing all Matrix Screener images")
  foldername = dc.getDirectory()
  #od = OpenDialog("Click on one of the image files in the folder to be analysed", None	)
  #filename = od.getFileName()
  #foldername = od.getDirectory()
  #print foldername
  
  print "\n\n\n\n\n\n"
  
  #foldername = "/g/almf/software/scripts/imagej/Data_MatrixScreenerImport"
  
  if None != foldername:
    print "foldername = "+foldername
    get_files_and_analyze(foldername)

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
from ij.io import FileSaver, DirectoryChooser
from ij import ImagePlus
from ij.io import FileSaver
import jmFijiGen as jmg

tic = time.time()

sFac = 0.0
barW = 5						# bar width, microns
barH = 6						# bar height, pts
barF = 24						# bar font, pts
barC = "White"			# bar color
barL= "Lower Right"	# bar location

dc = DirectoryChooser("Choose directory")
basePath = dc.getDirectory()

sPngPath = basePath + os.sep + "png" + os.sep
jmg.ensureDir(sPngPath)


names = []

for file in os.listdir(basePath):
	if file.endswith(".tif"):
		name = os.path.splitext(file)[0]
		names.append(name)

names.sort()

sSat = "saturated=%.2f" % sFac

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
import glob
import os.path

from ij import IJ, ImagePlus, ImageStack, WindowManager
from ij.io import DirectoryChooser

from edfgui import ExtendedDepthOfField, Parameters

dc = DirectoryChooser("Set input directory")
files = glob.glob(dc.getDirectory() + "/*.tiff")

dc = DirectoryChooser("Set output directory")
outputDir = dc.getDirectory()

# EDF parameters
params = Parameters()
params.setQualitySettings(params.QUALITY_HIGH)

for f in files:
    imp = ImagePlus(f)

    # output name
    head,tail = os.path.split(f)
    base,ext = os.path.splitext(tail)
    output = os.path.join(outputDir,base + "_edf.tif")
    print output

    # make all-in-focus image
    edf = ExtendedDepthOfField(imp,params)
    edf.process()

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
def run(title):
    gd = GenericDialog("Record Window")
    gd.addMessage("Maximum number of frames to record.\nZero means infinite, interrupt with ESC key.")
    gd.addNumericField("Max. frames:", 50, 0)
    gd.addNumericField("Milisecond interval:", 300, 0)
    gd.addSlider("Start in (seconds):", 0, 20, 5)
    frames = []
    titles = []
    for f in Frame.getFrames():
        if f.isEnabled() and f.isVisible():
            frames.append(f)
            titles.append(f.getTitle())
    gd.addChoice("Window:", titles, titles[0])
    gd.addCheckbox("To file", False)
    gd.showDialog()
    if gd.wasCanceled():
        return
    n_frames = int(gd.getNextNumber())
    interval = gd.getNextNumber() / 1000.0  # in seconds
    frame = frames[gd.getNextChoiceIndex()]
    delay = int(gd.getNextNumber())
    tofile = gd.getNextBoolean()

    dir = None
    if tofile:
        dc = DirectoryChooser("Directory to store image frames")
        dir = dc.getDirectory()
        if dir is None:
            return  # dialog canceled

    snaps = []
    borders = None
    executors = Executors.newFixedThreadPool(1)
    try:
        while delay > 0:
            IJ.showStatus("Starting in " + str(delay) + "s.")
            time.sleep(1)  # one second
            delay -= 1

        IJ.showStatus("Capturing frame borders...")
        bounds = frame.getBounds()
        robot = Robot()
        frame.toFront()
        time.sleep(0.5)  # half a second
        borders = robot.createScreenCapture(bounds)

        IJ.showStatus("Recording " + frame.getTitle())

        # Set box to the inside borders of the frame
        insets = frame.getInsets()
        box = bounds.clone()
        box.x = insets.left
        box.y = insets.top
        box.width -= insets.left + insets.right
        box.height -= insets.top + insets.bottom

        start = System.currentTimeMillis() / 1000.0  # in seconds
        last = start
        intervals = []
        real_interval = 0
        i = 1
        fus = None
        if tofile:
            fus = []

            # 0 n_frames means continuous acquisition
        while 0 == n_frames or (len(snaps) < n_frames and last - start < n_frames * interval):
            now = System.currentTimeMillis() / 1000.0  # in seconds
            real_interval = now - last
            if real_interval >= interval:
                last = now
                img = snapshot(frame, box)
                if tofile:
                    fus.append(executors.submit(Saver(i, dir, bounds, borders, img, insets)))  # will flush img
                    i += 1
                else:
                    snaps.append(img)
                intervals.append(real_interval)
            else:
                time.sleep(interval / 5)
                # interrupt capturing:
            if IJ.escapePressed():
                IJ.showStatus("Recording user-interrupted")
                break

                # debug:
                # print "insets:", insets
                # print "bounds:", bounds
                # print "box:", box
                # print "snap dimensions:", snaps[0].getWidth(), snaps[0].getHeight()

                # Create stack
        stack = None
        if tofile:
            for fu in snaps:
                fu.get()  # wait on all
            stack = VirtualStack(bounds.width, bounds.height, None, dir)
            files = File(dir).list(TifFilter())
            Arrays.sort(files)
            for f in files:
#.........这里部分代码省略.........

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
		sumSize = sumSize + theSize
	return sumSize

def calculate_memory_recs(dirsize,maxmem):
	values = []
	maxchannel = maxmem / 10
	maxtot = long(maxmem * 0.3)
	for i in range(1,6):
		if (maxtot/i > maxchannel):
			values.append((maxchannel*i)/1048576)
		else:
			values.append(maxtot/1048576)
	return values

dc = DirectoryChooser("Choose directory with OME.TIF files...")
sourceDir = dc.getDirectory()

if not(sourceDir is None):
	if not os.path.exists(sourceDir + "resized"):
		os.mkdir(sourceDir + "resized")

	dirSize = get_directory_size(sourceDir)
	dirSizeMB = dirSize / 1048576
	memoryObj = Memory()
	memFiji = memoryObj.maxMemory()
	memFijiMB = memFiji / 1048576

	gd = GenericDialog("Set Parameters...")
	gd.addNumericField("Sizing_ratio (Final disk space / Initial disk space):",0.25,2)
	gd.addMessage("Directory size: " + str(dirSizeMB) + "MB")
	gd.addMessage("Maximum memory: " + str(memFijiMB) + "MB")

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
	arr2 = [x - ma for x in arr]
	start = find_index_greater_zero(arr1)
	end = find_index_greater_zero(arr2)
	length = end-start+1
	return [start,end,length]

def make_tile_series(xs,ys,xlen,ylen):
	arr = []
	for y in range(ys[0],ys[1]+1):
		arr.extend(range(xlen*y+xs[0],xlen*y+xs[1]+1))
	arr = [m+1 for m in arr]
	return arr

##### Sets directory of full-res tiles and gets metadata ######
dc = DirectoryChooser("Choose directory where full-res tiles are stored...")
imgDir = dc.getDirectory()
metadata = IJ.openAsString(imgDir+"tile_info.txt")
p = re.compile(r'X Tiles: (\d+)')
m = p.search(metadata)
if m is None:
	xtiles = 0
else:
	xtiles = int(m.group(1))
p = re.compile(r'Y Tiles: (\d+)')
m = p.search(metadata)
if m is None:
	ytiles = 0
else:
	ytiles = int(m.group(1))
if not os.path.exists(imgDir + "temp"):
	os.mkdir(imgDir + "temp")

# 需要导入模块: from ij.io import DirectoryChooser [as 别名]
# 或者: from ij.io.DirectoryChooser import getDirectory [as 别名]
from ij.plugin.frame import RoiManager
from ij.measure import Calibration
from loci.plugins import BF
from ij.io import FileSaver
from ij.measure import Measurements
from ij.process import ImageStatistics as IS
from java.awt import Color
from ij.io import DirectoryChooser
# Python imports
import os
import math
import sys

# Choose a folder that you want the images resized to the same scale
input_dc = DirectoryChooser("Choose a folder with images to be rescaled.")
inputDir = input_dc.getDirectory()

output_dc = DirectoryChooser("Choose output folder.")
outputDir = output_dc.getDirectory()

# What we need to do is crop EQUAL AREAS. First find the smallest
# image area.

# Find the minimum area per pixel
minArea = 999999
for filename in os.listdir(inputDir):
	if '.tif' in filename:
		print 'Opening ' , filename , '...'
		image = IJ.openImage(inputDir + '/' + filename)
		ip = image.getProcessor()