def _get_win_folder_with_jna(csidl):
""" Use the Python Java wrappers to invoke – circuitously,
I might add – a win32 filesystem API call
"""
import array
from com.sun import jna
from com.sun.jna.platform import win32
buf_size = win32.WinDef.MAX_PATH * 2
buf = array.zeros('c', buf_size)
shell = win32.Shell32.INSTANCE
shell.SHGetFolderPath(None, getattr(win32.ShlObj, csidl.fullname),
None, win32.ShlObj.SHGFP_TYPE_CURRENT, buf)
directory = jna.Native.toString(buf.tostring()).rstrip("\0")
# Downgrade to short path name if have highbit chars. See
# <http://bugs.activestate.com/show_bug.cgi?id=85099>.
has_high_char = False
for char in directory:
if ord(char) > 255:
has_high_char = True
break
if has_high_char:
buf = array.zeros('c', buf_size)
kernel = win32.Kernel32.INSTANCE
if kernel.GetShortPathName(directory, buf, buf_size):
directory = jna.Native.toString(buf.tostring()).rstrip("\0")
return directory
def _get_win_folder_with_jna(csidl_name):
import array
from com.sun import jna
from com.sun.jna.platform import win32
buf_size = win32.WinDef.MAX_PATH * 2
buf = array.zeros('c', buf_size)
shell = win32.Shell32.INSTANCE
shell.SHGetFolderPath(None, getattr(win32.ShlObj, csidl_name), None, win32.ShlObj.SHGFP_TYPE_CURRENT, buf)
dir = jna.Native.toString(buf.tostring()).rstrip("\0")
# Downgrade to short path name if have highbit chars. See
# <http://bugs.activestate.com/show_bug.cgi?id=85099>.
has_high_char = False
for c in dir:
if ord(c) > 255:
has_high_char = True
break
if has_high_char:
buf = array.zeros('c', buf_size)
kernel = win32.Kernel32.INSTANCE
if kernal.GetShortPathName(dir, buf, buf_size):
dir = jna.Native.toString(buf.tostring()).rstrip("\0")
return dir
def _get_win_folder_with_jna(csidl_name):
import array
from com.sun import jna
from com.sun.jna.platform import win32
buf_size = win32.WinDef.MAX_PATH * 2
buf = array.zeros('c', buf_size)
shell = win32.Shell32.INSTANCE
shell.SHGetFolderPath(None, getattr(win32.ShlObj, csidl_name), None,
win32.ShlObj.SHGFP_TYPE_CURRENT, buf)
dir = jna.Native.toString(buf.tostring()).rstrip("\0")
# Downgrade to short path name if have highbit chars. See
# <http://bugs.activestate.com/show_bug.cgi?id=85099>.
has_high_char = False
for c in dir:
if ord(c) > 255:
has_high_char = True
break
if has_high_char:
buf = array.zeros('c', buf_size)
kernel = win32.Kernel32.INSTANCE
if kernel.GetShortPathName(dir, buf, buf_size):
dir = jna.Native.toString(buf.tostring()).rstrip("\0")
return dir
def test_array_coercion(self):
self.assertEquals("double", Coercions.takeArray(array.zeros('d', 2)))
self.assertEquals("float", Coercions.takeArray(array.zeros('f', 2)))
self.assertEquals("4", Coercions.takePyObj(1, 2, 3, 4))
c = Coercions()
self.assertEquals("5", c.takePyObjInst(1, 2, 3, 4, 5))
self.assertEquals("OtherSubVisible[]", c.takeArray([OtherSubVisible()]))
self.assertEquals("SubVisible[]", c.takeArray([SubVisible()]))
def test_array_coercion(self):
self.assertEquals("double", Coercions.takeArray(array.zeros('d', 2)))
self.assertEquals("float", Coercions.takeArray(array.zeros('f', 2)))
self.assertEquals("4", Coercions.takePyObj(1, 2, 3, 4))
c = Coercions()
self.assertEquals("5", c.takePyObjInst(1, 2, 3, 4, 5))
self.assertEquals("OtherSubVisible[]", c.takeArray([OtherSubVisible()]))
self.assertEquals("SubVisible[]", c.takeArray([SubVisible()]))
def nearestZProject(imp1):
relicedImp = Slicer().reslice(imp1)
relicedStack = relicedImp.getStack()
width = imp1.getWidth()
height = imp1.getHeight()
depth = imp1.getNSlices()
topPixels = zeros('f', width * height)
stack2 = ImageStack(width, height)
for i in range(1, relicedImp.getNSlices()):
pixels = relicedStack.getPixels(i)
for x in xrange(width):
for pixel in xrange(x, x + width * (depth - 1), width):
#after finding the first pixel above the threshold value, add the value to the list
if pixels[pixel] != 0:
topPixels[i * width + x] = pixels[pixel]
#break from looping the y when 1st threshold pixel is found is met -> increases speed drastically! Otherwise need an if statement every loop...
break
ip2 = FloatProcessor(width, height, topPixels, None)
imp2 = ImagePlus("Nearest point proj", ip2)
imp3 = imp2.resize(imp2.getWidth() * 2, imp2.getHeight() * 2, 'none')
return imp3
def pixel_has_color(x,y, raster):
'''Returns true if pixel has black color'''
get_pixel_parameter = zeros('i', 1)
pixel = raster.getPixel(x,y,get_pixel_parameter)
if pixel[0]==0:
return True
else:
return False
def pixel_has_color(x, y, raster):
'''Returns true if pixel has black color'''
get_pixel_parameter = zeros('i', 1)
pixel = raster.getPixel(x, y, get_pixel_parameter)
if pixel[0] == 0:
return True
else:
return False
def test_java_object_arrays():
jStringArr = array(String, [String("a"), String("b"), String("c")])
verify(Arrays.equals(jStringArr.typecode, str(String)),
"String array typecode of wrong type, expected %s, found %s" %
(jStringArr.typecode, str(String)))
verify(zeros(String, 5) == Array.newInstance(String, 5))
import java # require for eval to work
if jStringArr != eval(str(jStringArr)):
raise TestFailed, "eval(str(%s)) <> %s" % (jStringArr,)*2
def test_java_object_arrays(self):
jStringArr = array(String, [String("a"), String("b"), String("c")])
self.assert_(
Arrays.equals(jStringArr.typecode, 'java.lang.String'),
"String array typecode of wrong type, expected %s, found %s" %
(jStringArr.typecode, str(String)))
self.assertEqual(zeros(String, 5), Array.newInstance(String, 5))
import java.lang.String # require for eval to work
self.assertEqual(jStringArr, eval(str(jStringArr)))
def test_java_object_arrays(self):
jStringArr = array(String, [String("a"), String("b"), String("c")])
self.assert_(
Arrays.equals(jStringArr.typecode, 'java.lang.String'),
"String array typecode of wrong type, expected %s, found %s" %
(jStringArr.typecode, str(String)))
self.assertEqual(zeros(String, 5), Array.newInstance(String, 5))
import java.lang.String # require for eval to work
self.assertEqual(jStringArr, eval(str(jStringArr)))
def test_java_compat(self):
from java import awt
hsb = awt.Color.RGBtoHSB(0, 255, 255, None)
self.assertEqual(hsb, array("f", [0.5, 1, 1]), "output hsb float array does not correspond to input rgb values")
rgb = apply(awt.Color.HSBtoRGB, tuple(hsb))
self.assertEqual(rgb, -0xFF0001, "output rgb bytes don't match input hsb floats")
hsb1 = zeros("f", 3)
awt.Color.RGBtoHSB(0, 255, 255, hsb1)
self.assertEqual(hsb, hsb1, "hsb float arrays were not equal")
def image(self):
w = self.getWidth();
h = self.getHeight();
non_black_withe_image = BufferedImage(w, h, BufferedImage.TYPE_INT_ARGB)
self.paint(non_black_withe_image.getGraphics())
raster=non_black_withe_image.getRaster()
bi = BufferedImage(w, h, BufferedImage.TYPE_BYTE_BINARY)
write_raster = bi.getRaster()
c = array.zeros('i', 4)
on=wc = array.zeros('i', 1)
off=array.zeros('i', 1)
off[0]=1
for x in range(w):
for y in range(h):
c = raster.getPixel(x,y,c)
if sum(c)!=1020:
write_raster.setPixel(x,y, on)
else:
write_raster.setPixel(x,y, off)
return bi;
def image(self):
w = self.getWidth()
h = self.getHeight()
non_black_withe_image = BufferedImage(w, h,
BufferedImage.TYPE_INT_ARGB)
self.paint(non_black_withe_image.getGraphics())
raster = non_black_withe_image.getRaster()
bi = BufferedImage(w, h, BufferedImage.TYPE_BYTE_BINARY)
write_raster = bi.getRaster()
c = array.zeros('i', 4)
on = wc = array.zeros('i', 1)
off = array.zeros('i', 1)
off[0] = 1
for x in range(w):
for y in range(h):
c = raster.getPixel(x, y, c)
if sum(c) != 1020:
write_raster.setPixel(x, y, on)
else:
write_raster.setPixel(x, y, off)
return bi
def read_all(reader):
arrsize = 8 * 1024
arr = zeros('c', arrsize)
buffer = StringBuilder()
numCharsRead = 0
while numCharsRead != -1:
numCharsRead = reader.read(arr, 0, arrsize)
if numCharsRead != -1:
buffer.append(arr, 0, numCharsRead)
return buffer.toString()
def test_java_compat(self):
from array import zeros
from java.awt import Color
hsb = Color.RGBtoHSB(0,255,255, None)
self.assertEqual(hsb, array('f', [0.5,1,1]),
"output hsb float array does not correspond to input rgb values")
rgb = apply(Color.HSBtoRGB, tuple(hsb))
self.assertEqual(rgb, -0xff0001,
"output rgb bytes don't match input hsb floats")
hsb1 = zeros('f', 3)
Color.RGBtoHSB(0, 255, 255, hsb1)
self.assertEqual(hsb, hsb1, "hsb float arrays were not equal")
def test_java_compat(self):
from java.awt import Color
hsb = Color.RGBtoHSB(0, 255, 255, None)
self.assertEqual(
hsb, array('f', [0.5, 1, 1]),
"output hsb float array does not correspond to input rgb values")
rgb = apply(Color.HSBtoRGB, tuple(hsb))
self.assertEqual(rgb, -0xff0001,
"output rgb bytes don't match input hsb floats")
hsb1 = zeros('f', 3)
Color.RGBtoHSB(0, 255, 255, hsb1)
self.assertEqual(hsb, hsb1, "hsb float arrays were not equal")
def learn(imp):
IJ.run(imp, "Line Width...", "line=10")
IJ.run("Colors...", "foreground=black background=black selection=red")
# Clear ROI manager
roiMan = RoiManager.getInstance()
if roiMan is not None:
roiMan.reset()
# set results table
rt = ResultsTable.getResultsTable()
# set up analyzer
analyzer = Analyzer(imp, 1, rt)
impBrightness = ProcessHSB.getBrightness(imp)
IJ.run(impBrightness, "8-bit", "")
IJ.run(impBrightness, "Auto Threshold", "method=Shanbhag white")
IJ.run(impBrightness, "Analyze Particles...",
"size=50000-Infinity circularity=0.00-1.00 show=Masks add in_situ")
# Pixel running total
pixelTotal = zeros('f', 4)
roiTotal = roiMan.getCount()
if roiMan is not None:
# Iterate throught the ROIs
for roi in xrange(roiTotal):
roiMan.select(roi)
selectRoi = roiMan.getRoi(roi)
option = getOptions()
# measure
analyzer.measure()
meas = rt.getRowAsString(0)
newLine = meas.split(" ", 1)
pixels = float(newLine[1])
# Tag the ROI
IJ.run(imp, "Fill", "slice")
pixelTotal[0] = pixelTotal[0] + (option[0] * pixels)
pixelTotal[1] = pixelTotal[1] + (option[1] * pixels)
pixelTotal[2] = pixelTotal[2] + (option[2] * pixels)
pixelTotal[3] = pixelTotal[3] + (option[3] * pixels)
return pixelTotal
else:
return pixelTotal
def getOptions():
pixels = zeros('f', 4) # 4 elements
# First Dialog Box
item = [
"coralline", "tunicate", "red", "macro", "background", "more than one"
]
gd = GenericDialog("Options")
gd.addRadioButtonGroup("options", item, 3, 2, "coralline")
gd.showDialog()
button = gd.getNextRadioButton()
# Second Dialog Box
gd2 = GenericDialog("Multiple Options")
items = ["coralline", "tunicate", "red", "macro", "garbage"]
defaultVal = [False] * 5
gd2.addCheckboxGroup(2, 3, items, defaultVal)
gd2.addNumericField("coralline %", 0, 0)
gd2.addNumericField("tunicate %", 0, 0)
gd2.addNumericField("red %", 0, 0)
gd2.addNumericField("macro %", 0, 0)
gd2.addNumericField("background %", 0, 0)
if gd.wasCanceled():
return 0
if button == "coralline":
pixels[0] = 1
elif button == "tunicate":
pixels[1] = 1
elif button == "red":
pixels[2] = 1
elif button == "macro":
pixels[3] = 1
elif button == "more than one":
gd2.showDialog()
checklist = gd2.getCheckboxes()
pixels[0] = int(
checklist[0].state) * (float(gd2.getNextNumber()) / 100)
pixels[1] = int(
checklist[1].state) * (float(gd2.getNextNumber()) / 100)
pixels[2] = int(
checklist[2].state) * (float(gd2.getNextNumber()) / 100)
pixels[3] = int(
checklist[3].state) * (float(gd2.getNextNumber()) / 100)
return pixels
def test_java_compat():
print_test('array', 2)
from java import awt
hsb = awt.Color.RGBtoHSB(0,255,255, None)
#print hsb
verify(hsb == array('f', [0.5,1,1]),
"output hsb float array does not correspond to input rgb values")
rgb = apply(awt.Color.HSBtoRGB, tuple(hsb))
#print hex(rgb)
verify(rgb == 0xff00ffff, "output rgb bytes don't match input hsb floats")
print_test('zeros', 2)
hsb1 = zeros('f', 3)
awt.Color.RGBtoHSB(0,255,255, hsb1)
#print hsb, hsb1
verify(hsb == hsb1, "hsb float arrays were not equal")
def getBytes(self, size):
parmStr = self.toString()
if size == Parameter.DATA_SIZE:
dataSize = len(parmStr)
elif size == Parameter.UNKNOWN_SIZE:
dataSize = len(parmStr);
elif size == Parameter.DEFAULT_SIZE:
dataSize = 65000;
elif size == Parameter.OUTPUT_SIZE:
dataSize = Parameter.DEFAULT_OUTPUT_SIZE
else: dataSize = size
nulled = array.zeros( 'b', 3)
nulled[0] = 0
nulled[1] = 0
nulled[2] = 0
convertor = AS400Text(dataSize + 3, 37);
return convertor.toBytes( parmStr + nulled.tostring() );
def NeighborChecker(xar, yar, zar, switch):
""" Check the distance to neighbors, and count the number of neighbors below thdist. """
global thdist
neighborA = zeros('d', len(xar))
if switch:
for i in range(len(xar)):
cx = xar[i]
cy = yar[i]
cz = zar[i]
for j in range(len(xar)):
if j != i :
dist = Math.sqrt( Math.pow((cx - xar[j]), 2) + Math.pow((cy - yar[j]), 2))
if dist < thdist:
if Math.abs(cz - zar[j]) < 2:
logstr = ".... Dot%d - Dot%d too close: dist = %d" % (i, j, dist)
IJ.log(logstr)
print logstr
neighborA[i] += 1
if neighborA[i] > 0:
IJ.log("---> Dot%d rejected" % (i))
print "---> Dot", i, " rejected"
return neighborA
def measureWidth(numberOfWidthMeasurements):
impIn = WindowManager.getCurrentImage()
title = impIn.getTitle()
IJ.run("Duplicate...", " ")
impWork = WindowManager.getCurrentImage()
workTitle = impWork.getTitle()
IJ.run("Clear Results")
IJ.run("Measure")
rt = ResultsTable.getResultsTable()
min = rt.getValue("Min", 0)
IJ.run("Subtract...", "value=" + str(min))
IJ.resetMinAndMax()
imp = WindowManager.getCurrentImage()
width = imp.getWidth()
height = imp.getHeight()
IJ.setAutoThreshold(imp, "Mean dark")
roiManager = RoiManager.getRoiManager()
roiManager.reset()
IJ.run("Analyze Particles...", "size=1000-Infinity add")
IJ.run("Clear Results")
roiManager.select(0)
roiManager.runCommand("Measure")
angle = rt.getValue("Angle", 0)
IJ.run("Select None")
roiManager.runCommand("Delete")
IJ.run("Rotate... ", "angle="+str(angle)+" grid=1 interpolation=Bilinear enlarge")
IJ.setAutoThreshold(imp, "Li dark")
IJ.run("Convert to Mask")
IJ.run("Fill Holes")
roiManager.reset()
IJ.run("Analyze Particles...", "size=1000-Infinity add")
IJ.run("Clear Results")
roiManager.select(0)
IJ.run("Clear Outside")
IJ.selectWindow(title)
IJ.run("Rotate... ", "angle="+str(angle)+" grid=1 interpolation=Bilinear enlarge")
roiManager.select(0)
roiManager.runCommand("Measure")
IJ.run("Select None")
IJ.run("Rotate... ", "angle="+str(-angle)+" grid=1 interpolation=Bilinear enlarge")
IJ.run("Canvas Size...", "width="+str(width)+" height="+str(height)+" position=Center zero")
IJ.selectWindow(workTitle)
xBox = rt.getValue("BX", 0)
lengthBox = rt.getValue("Width", 0)
heightBox = rt.getValue("Height", 0)
lengthEllipse = rt.getValue("Major", 0)
heightEllipse = rt.getValue("Minor", 0)
calibration = imp.getCalibration()
xMiddle = int(round(((lengthBox - xBox) / 2.0) + xBox, 0))
xOuter = xBox + lengthBox
xInner = xBox
widths = zeros('f', numberOfWidthMeasurements)
delta = (xOuter - xInner) / (numberOfWidthMeasurements + 1.0)
for i in range(1,numberOfWidthMeasurements+1):
deltaLen = delta * i;
xM = xInner + deltaLen
widths[i-1] = getWidthAt(xM, imp)
IJ.run("Flatten");
IJ.run("Rotate... ", "angle="+str(-angle)+" grid=1 interpolation=Bilinear enlarge")
IJ.run("Canvas Size...", "width="+str(width)+" height="+str(height)+" position=Center zero")
impFlat = WindowManager.getCurrentImage()
imp.changes = False;
imp.close()
titleIn = impIn.getTitle()
titleFlat = impFlat.getTitle()
IJ.selectWindow(titleIn)
IJ.run("Add Image...", "image=" + titleFlat + " x=0 y=0 opacity=50 zero")
impFlat.changes = False
impFlat.close()
return widths
def zeros(shape, dtype = float):
return new(array.zeros(shape, dtype))
# fillROI_.py
# from A. Cardona
# http://www.ini.uzh.ch/~acardona/fiji-tutorial/#fill-ROI
#
from ij import IJ, ImagePlus
from ij.process import FloatProcessor
from array import zeros
from random import random
from ij.gui import Roi, PolygonRoi
# Create a new ImagePlus filled with noise
width = 1024
height = 1024
pixels = zeros('f', width * height)
for i in xrange(len(pixels)):
pixels[i] = random()
fp = FloatProcessor(width, height, pixels, None)
imp = ImagePlus("Random", fp)
# Fill a rectangular region of interest
# with a value of 2:
roi = Roi(400, 200, 400, 300)
fp.setRoi(roi)
fp.setValue(2.0)
fp.fill()
# Fill a polygonal region of interest
# with a value of -3
xs = [234, 174, 162, 102, 120, 123, 153, 177, 171,
def zeros(shape, dtype=float):
return new(array.zeros(shape, dtype))
# 선택 영역 칠하기
from ij import ImagePlus
from ij.process import FloatProcessor
from array import zeros
from random import random
from ij.gui import Roi, PolygonRoi
# noise로 칠해진 이미지 생성
width = 1024
height = 1024
pixels = zeros('f', width * height)
for i in xrange(len(pixels)):
pixels[i] = random()
fp = FloatProcessor(width, height, pixels, None)
imp = ImagePlus("Random", fp)
imp.show()
# 직사각형 관심영역(ROI: Region of Interest)를 2로 채우기
fp = FloatProcessor(width, height, pixels, None)
roi = Roi(400, 200, 400, 300) # Roi(int x, int y, int width, int height)
fp.setRoi(roi)
fp.setValue(2.0)
fp.fill()
imp2 = ImagePlus("Rectangle", fp)
imp2.show()
# Polygon ROI를 -3으로 채우기
refImp = IJ.openImage(refpath)
width = refImp.width
height = refImp.height
roim = RoiManager()
roim.runCommand("open", roipath)
roiArray = roim.getRoisAsArray()
nRoi = len(roiArray)
roim.close()
bwStack = ImageStack(width, height, nRoi)
for i in xrange(1, nRoi + 1):
bwStack.setProcessor(
FloatProcessor(width, height, zeros('f', width * height), None), i)
for i in xrange(1, nRoi + 1):
roi = roiArray[i - 1]
fp = bwStack.getProcessor(i)
fp.setValue(1.0)
fp.fill(roi)
roiImp = ImagePlus("roi", bwStack)
outfn = "roi_" + os.path.splitext(roifn)[0] + ".tif"
outpath = os.path.join(roidir, outfn)
if os.path.exists(outpath):
print "Skipped, already exists: ", outfn
else:
IJ.saveAsTiff(roiImp, outpath)
del a[2] xóa phần tử thứ 3. a.remove(1) print(a.pop(1)) Thư viện numpy : import numpy as np mangA=np.array([2,3,4,5,6,8]) mangB=np.arange(25) #tạo một mảng có 25 ptử mangB.reshape(5,5) #tạo mảng 5 5, ma trận mang=np.arange(25).reshape(5,5) ví dụ: abc=np.array([[1,2,3,4,5,6],[1,2,4,67,8,8]]) abc.shape ==>> output is (2,6) Tạo một mảng chứa 5 ptu 0: np.zeros(5) np.ones(10) #tạo 10 phẩn tử có gt 1. np.twos(5) np.zeros(2,1) #tạo mảng 0 hình 2 dòng một ô. +array arithmetic arr + 10 #thêm vào mỗi phần tử 10 đơn vị arr*arr #nhân mỗi phần tử với chính nó arr**2 # mỗi phần tử lũy thừa 2 name.T # đổi dòng thành cột, và ngược lại a1=a[:10] # lấy 10 ptu cua a ve a1 a1[:100]#chuyển ptu cua a1 thanh 100 #khi in a van bao gom ca a1 a1[0]=100 đổi ptu b=a.copy() xem thêm bài 61
from array import array, zeros
from ij import ImagePlus, IJ
# An empty native float array of length 5
a = zeros('f', 5)
print a
# A native float array with values 0 to 9
b = array('f', [0, 1, 2, 3, 4])
print b
# An empty native ImagePlus array of length 5
imps = zeros(ImagePlus, 5)
print imps
# Assign the current image to the first element of the array
imps[0] = IJ.getImage()
print imps
# Length of an array
print "length:", len(imps)
#basename = '141016_155913'
#basename = 'test/DSCF3564'
frame = []
for fn in ['0', '1']:
filename = os.environ['HOME'] + '/' + basename + '_' + fn + '.pgm'
imp = IJ.openImage(filename)
if imp is None:
print "Could not open image from file:", filename
frame.append(imp)
print 'loaded frames'
width = frame[0].width
height = frame[0].height
bpix = zeros('h', (width + height)**2)
for fn in [0, 1]:
pix = frame[fn].getProcessor().getPixels()
for i in range(len(pix)):
x = i % width + i / width + fn # the second frame (fn == 1) is shifted 1px to the right
y = (width - i % width - 1) + (i / width)
bpix[y * (width + height) + x] = pix[i]
print 'wrote frame %s' % fn
ip = ShortProcessor(width + height, width + height, bpix, None)
bayer = ImagePlus("Sensor", ip)
fs = FileSaver(bayer)
fs.saveAsTiff(os.path.dirname(filename) + '/' + 'raw.tiff')
def processCurrentImage(table):
imp = WindowManager.getCurrentImage()
fileName = imp.getTitle()
middleSlice = int(math.floor(imp.getNFrames() / 2.0) + (imp.getNFrames() % 2))
imp.setSlice(middleSlice)
IJ.run("Duplicate...", " ")
imp.close()
imp = WindowManager.getCurrentImage()
dir = fiji.analyze.directionality.Directionality_()
dir.setImagePlus(imp)
dir.setMethod(fiji.analyze.directionality.Directionality_.AnalysisMethod.FOURIER_COMPONENTS)
dir.setBinNumber(90)
dir.setBinStart(-90)
dir.setBuildOrientationMapFlag(False)
dir.computeHistograms()
dir.fitHistograms()
results = dir.getFitAnalysis()
direction = math.degrees(results[0][0])
dispersion = math.degrees(results[0 ][1])
amount = results[0][2]
goodness = results[0][3]
IJ.run("Clear Results")
IJ.run("FFT")
fftImp = WindowManager.getCurrentImage()
IJ.run("Mean...", "radius=2");
IJ.run("Find Maxima...", "noise=15 output=[Point Selection]")
IJ.run("Measure")
fftImp.changes = False
fftImp.close()
rt = ResultsTable.getResultsTable()
size = rt.size()
numberOfFrequences = size
if size>=5:
numberOfFrequences = 5
R = zeros('f', numberOfFrequences)
Theta = zeros('f', numberOfFrequences)
for i in range(0, numberOfFrequences):
R[i] = rt.getValue("R", i)
Theta[i] = rt.getValue("Theta", i)
table.incrementCounter()
table.addValue('image', fileName)
table.addValue('Direction', direction)
table.addValue('Dispersion', dispersion)
table.addValue('Amount', amount)
table.addValue('Goodness', goodness)
for i in range(0, numberOfFrequences):
table.addValue('R'+str(i), R[i])
table.addValue('Theta'+str(i), Theta[i])
widths = measureWidth(numberOfWidthMeasurements)
i = 1;
for width in widths:
table.addValue("width" + str(i), width)
i = i + 1
headings = rt.getHeadings()
for heading in headings:
if heading != "Label":
value = rt.getValue(heading, 0)
table.addValue(heading, value)
table.show('Directonality analysis')
# 밑바닥부터 이미지 만들기
from ij import ImagePlus
from ij.process import FloatProcessor
from array import zeros
from random import random
width = 1024
height = 1024
# Jython으로 array 만들기
# http://fiji.sc/wiki/index.php/Jython_Scripting_Examples#Creating_multi-dimensional_native_java_arrays
pixels = zeros('f', width * height) # f: "float"
for i in xrange(len(pixels)):
pixels[i] = random()
fp = FloatProcessor(width, height, pixels, None)
imp = ImagePlus("White noise", fp)
imp.show()
refpath = os.path.join(refdir, reffn)
refImp = IJ.openImage(refpath)
width = refImp.width
height = refImp.height
roim = RoiManager()
roim.runCommand("open", roipath)
roiArray = roim.getRoisAsArray()
nRoi = len(roiArray)
roim.close()
bwStack = ImageStack(width, height, nRoi)
for i in xrange(1, nRoi+1):
bwStack.setProcessor(FloatProcessor(width, height, zeros('f', width * height), None), i)
for i in xrange(1, nRoi+1):
roi = roiArray[i-1]
fp = bwStack.getProcessor(i)
fp.setValue(1.0)
fp.fill(roi)
roiImp = ImagePlus("roi", bwStack)
outfn = "roi_" + os.path.splitext(roifn)[0] + ".tif"
outpath = os.path.join(roidir, outfn)
if os.path.exists(outpath):
print "Skipped, already exists: ", outfn
else:
IJ.saveAsTiff(roiImp, outpath)
