Python WindowManager.getFrame方法代码示例

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
def readResults(windowTitle):
   textPanel = WindowManager.getFrame(windowTitle).getTextPanel()
   headings = textPanel.getColumnHeadings()
   
   "get results from TextWindow with java.lang.string title"
   resolver = re.compile('\d+\t(?P<frame>\d+\.0+)\t(?P<fsDistance>\d+\.\d+)\t(?P<ffDistance>\d+\.\d+)\t(?P<ssDistance>\d+\.\d+)\t(?P<fVol>\d+\.\d+)\t(?P<sVol>\d+\.\d+)')
   frameA = []
   distA = []
   volFcA = []
   volScA = []
   #xFcA, yFcA, zFcA, xScA, yScA, zScA
   resPnl = WindowManager.getFrame(windowTitle).getTextPanel()
   for row in range(resPnl.getLineCount()):
      mo = resolver.match(resPnl.getLine(row))
      frameA.append(int(float(mo.group('frame'))))
      distA.append(mo.group("fsDistance"))
      volFcA.append(mo.group("fVol"))
      volScA.append(mo.group("sVol"))
   return frameA, distA, volFcA, volScA

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
def update_menus():
	try:
		IJ.redirectErrorMessages()
		IJ.run('Update Menus')
	except:
		error_message = 'Error updating menus'
		logWindow = WindowManager.getFrame("Log")
		if not logWindow is None:
			error_message = error_message + ': ' \
				+ logWindow.getTextPanel().getText()
			logWindow.close()
		print error_message
		global error
		error += 1

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
    timeInterval = round(calibration.frameInterval)

    #start measurement
    splitCh = CS.split(imp)                        # split channels
    #try:
    ATA().segAndMeasure(splitCh[0], splitCh[1])    # perform segmentation and measurement 
    #else: go to next element in moFileList
    # move image to "segProblem" folder
    # continue

    WindowManager.getImage("binProjMerged").close()
    WindowManager.getImage("DUP_C1-"+image.group()).close()
    WindowManager.getImage("DUP_C2-"+image.group()).close()

    # read the measurements from results tables.
    distance_lines = WindowManager.getFrame("Statistics_Distance").getTextPanel().getText().split("\n")
    ch0_dots = tableToDots(WindowManager.getFrame("Statistics_Ch0").getTextPanel().getText().split("\n"), 0)
    ch1_dots = tableToDots(WindowManager.getFrame("Statistics_Ch1").getTextPanel().getText().split("\n"), 1)

    WindowManager.getFrame("Statistics_Distance").close(False)
    WindowManager.getFrame("Statistics_Ch0").close(False)
    WindowManager.getFrame("Statistics_Ch1").close(False)

    frameList = []
    for l in distance_lines[1:len(distance_lines)-1]:
        index, frame, distance, ch0dist, ch1dist, ch0vol, ch1vol = l.split("\t")
        # find respective frame in ch0 and ch1 dot list. Problem, if both dots have same volume. Vol can be identical!       
        ch0DotList = dotListToSingle( [d for d in ch0_dots if (d.getFrame() == int(float(frame)) and d.getVol() == int(float(ch0vol)) )] )
        ch1DotList = dotListToSingle( [d for d in ch1_dots if (d.getFrame() == int(float(frame)) and d.getVol() == int(float(ch1vol)) )] )

        frameList.append(fr(frame, distance, ch0DotList, ch1DotList))

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]


from ij import IJ, WindowManager
from ij.measure import ResultsTable
from ij.text import TextWindow

bClose = True

IJ.run("Blobs (25K)")
imp = IJ.getImage()
IJ.setAutoThreshold(imp, "Default")
IJ.run(imp, "Convert to Mask", "")
IJ.run(imp, "Set Measurements...", "area center redirect=None decimal=3")
IJ.run(imp, "Analyze Particles...", "display exclude clear include summarize")
tw = WindowManager.getFrame("Summary")
if tw != None:
    st = tw.getTextPanel().getResultsTable()
    IJ.log("1st row of Summary:\n"+ st.getRowAsString(0))
    v = st.getCounter()
    w = st.getLastColumn()
    s = st.size()
    z = st.getValueAsDouble(w, 0)
    af = float(z)
    af /= 100.
    print("Area Fraction: %.3f" % af)
    
else:
    IJ.log("Summary window not found")

if bClose:

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
   mkdir(saveFolder)

for image in moFileList:
   print "starting with cell " + image.group() + " " + "("+ str(moFileList.index(image)) + "/" + str(len(moFileList)) + ")"
   imp = Opener().openImage(path + image.group()) # open Image
   cal = imp.getCalibration()
   splitCh = CS.split(imp)                        # split channels
   #try:
   ATA().segAndMeasure(splitCh[0], splitCh[1])    # perform segmentation and measurement 
   #else: go to next element in moFileList
   
   WindowManager.getImage("binProjMerged").close()
   WindowManager.getImage("DUP_C1-"+image.group()).close()
   WindowManager.getImage("DUP_C2-"+image.group()).close()
   frameA, distA, volFcA, volScA = readResults("Statistics_Distance")   # get results from "Statistics_Distance" window
   WindowManager.getFrame("Statistics_Distance").close(False)


   

   frameA, distA, volFcA, volScA = fillUpFrames(frameA, distA, volFcA, volScA)
   tw = makeTw(imp, frameA, distA, volFcA, volScA)
   tw.getTextPanel().saveAs(saveFolder +"/val_" + image.group('name') + ".tsv") # save filledup results as text
   WindowManager.getFrame("Summary").close(False)
   WindowManager.getFrame("Statistics_Ch0").close(False)
   WindowManager.getFrame("Statistics_Ch1").close(False)
   
   detDots = WindowManager.getImage("DetectedDots")
   detDots.copyScale(imp)
   IJ.saveAs(detDots, ".tiff", saveFolder + "/zi_"+image.group('name')) # save the overlay with connecting line
   print "Saving as " +  image.group('name')

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
	'Plugins, "Cello", xyz' + "\n" +
	'Plugins, "Abracadabra", abc')

# reset the plugins folder to the temporary directory

System.setProperty('plugins.dir', temporary_folder);

# Launch ImageJ

IJ.redirectErrorMessages()
ij = ImageJ()
error = 0

# Must show Duplicate command error

logWindow = WindowManager.getFrame("Log")
if logWindow is None:
	print 'No error adding duplicate entries'
	error += 1
else:
	logText = logWindow.getTextPanel().getText()
	if not 'Duplicate command' in logText:
		print 'Error adding duplicate entries, but the wrong one'
		error += 1
	logWindow.close()

# debug functions

def printMenu(menu, indent):
	n = menu.getItemCount()
	for i in range(0, n):

# 需要导入模块: from ij import WindowManager [as 别名]
# 或者: from ij.WindowManager import getFrame [as 别名]
	list_x2.append( x2 )
	#
	#

#3D OBJECTS COUNTER
for i in range(stepNumber):
	x2  = list_x2[i] 	
	x2_aux = x2.duplicate()
	x2_aux.setTitle('x2_aux')
	#run("3D OC Options", "volume surface nb_of_obj._voxels nb_of_surf._voxels integrated_density mean_gray_value std_dev_gray_value median_gray_value minimum_gray_value maximum_gray_value centroid mean_distance_to_surface std_dev_distance_to_surface median_distance_to_surface centre_of_mass bounding_box show_masked_image_(redirection_requiered) dots_size=5 font_size=10 store_results_within_a_table_named_after_the_image_(macro_friendly) redirect_to=x1")
	arguments = "volume centroid bounding_box show_masked_image_(redirection_requiered) dots_size=5 font_size=10 store_results_within_a_table_named_after_the_image_(macro_friendly) redirect_to=x2_aux"
	IJ.run("3D OC Options", arguments)
	IJ.run(x2, "3D Objects Counter", "threshold=0 slice=0 min.=" + repr(p3DOCmin)+" max.=" + repr(p3DOCmax)+ " exclude_objects_on_edges objects statistics")
	#Obtengo la salida estadística de 3D Objects Counter
	title_x2 = x2.getTitle()
	winStats =WindowManager.getFrame("Statistics for "+title_x2)#tomo la ventana con las estadísticas generadas
	textStats = winStats.getTextPanel()#tomo el texto de la ventana
    textStats.saveAs( resultsFileStats )#Guardo externamente la tabla y luego la levanto con GetParameters( resultsFileStats )
	index, vox, X, Y, Z, Bx, By, Bz, B-width, B-height, B-depth = GetParameters( resultsFileStats )
	
	#guardo la mascara en list_x3
	IJ.selectWindow("Objects map of x2_"+repr(i))		
	img = IJ.getImage()
	mask = img.duplicate()#al cerrar la ventana img al final del ciclo for se borran los datos que contiene img aunque no se avisa de esto, por lo tanto si se quiere guardar alguna ventana abierta hay que guardar un duplicado para no tener problemas
	mask.setTitle('mask_'+repr(i))
	list_x3.append( mask )#almaceno la mascara en la lista correspondiente
	#cierro ventanas que no preciso
	x2_aux.close()	
	img.close()
	#