def findSeptum(root, show, pos, n = 4):
from ij import IJ
corrImg = IJ.openImage(root + "/%s_SegAnalysis/%s/CorrelationImage.tif"% (bf_prefix, pos))
IJ.run(corrImg, "8-bit", "");
#estimate_width extend_line
# these parameters can be added also
cmd = "line_width=10 high_contrast=250 low_contrast=50 show_junction_points show_ids add_to_manager make_binary method_for_overlap_resolution=NONE sigma=3 lower_threshold=0 upper_threshold=1.36 minimum_line_length=30 maximum=60"
if show:
cmd += " displayresults"
IJ.run(corrImg, "Ridge Detection", cmd);
binarylineImg = IJ.getImage()
IJ.run(binarylineImg, "Invert", "");
binaryImg = IJ.openImage(root + "/%s_SegAnalysis/%s/BinaryImage.tif" % (bf_prefix, pos))
binaryImg.show()
IJ.run("Add Image...", "x=0 y=0 opacity=100 zero");
binaryImg.hide()
binarylineImg.hide()
imp2 = binaryImg.flatten();
IJ.run(imp2, "8-bit", "");
for i in range(n):
IJ.run(imp2, "Erode", "");
for j in range(n):
IJ.run(imp2, "Dilate", "");
IJ.saveAsTiff(imp2, d.getPath() + "/%s_SegAnalysis/%s/BinaryImage_with_sep.tif" % (bf_prefix, pos));
def findSeptum(root, show, pos, n=4):
from ij import IJ
corrImg = IJ.openImage(root + "/%s_SegAnalysis/%s/CorrelationImage.tif" %
(bf_prefix, pos))
IJ.run(corrImg, "8-bit", "")
#estimate_width extend_line
# these parameters can be added also
cmd = "line_width=10 high_contrast=250 low_contrast=50 show_junction_points show_ids add_to_manager make_binary method_for_overlap_resolution=NONE sigma=3 lower_threshold=0 upper_threshold=1.36 minimum_line_length=30 maximum=60"
if show:
cmd += " displayresults"
IJ.run(corrImg, "Ridge Detection", cmd)
binarylineImg = IJ.getImage()
IJ.run(binarylineImg, "Invert", "")
binaryImg = IJ.openImage(root + "/%s_SegAnalysis/%s/BinaryImage.tif" %
(bf_prefix, pos))
binaryImg.show()
IJ.run("Add Image...", "x=0 y=0 opacity=100 zero")
binaryImg.hide()
binarylineImg.hide()
imp2 = binaryImg.flatten()
IJ.run(imp2, "8-bit", "")
for i in range(n):
IJ.run(imp2, "Erode", "")
for j in range(n):
IJ.run(imp2, "Dilate", "")
IJ.saveAsTiff(
imp2,
d.getPath() + "/%s_SegAnalysis/%s/BinaryImage_with_sep.tif" %
(bf_prefix, pos))
def run():
global ext, exp, saturated, outputFolder, srcFile
IJ1.batchMode = True
srcDir = srcFile
images, channels = createFileAndChannelsDictionaries(srcDir, exp)
outDir = os.path.join(srcDir, outputFolder)
if not os.path.exists(outDir):
os.makedirs(outDir)
numberOfImages = len(images)
counter = 1
IJ.log("\\Clear")
IJ.log("Convert images from Opera to Hyperstacks...")
for image, filename in images.iteritems():
IJ.log("\\Update1:Processing image " + str(counter) + "/" +
str(numberOfImages))
nrOfChannels = channels[image]
success = openAsHyperstack(filename, image, nrOfChannels)
if (success):
adjustDisplay(nrOfChannels, saturated)
IJ.saveAsTiff(IJ.getImage(), os.path.join(outDir, image + ".tiff"))
IJ.getImage().close()
counter = counter + 1
IJ.log("Finished !")
IJ1.batchMode = False
def run():
helpText = "This program will batch convert any tif image to 8-bit greyscale, " + \
"and empty calibration infomation.\n\n" + \
">> Press OK to Select a directory of TIFF images."
MessageDialog(IJ.getInstance(), "Empty Calibration Guide", helpText)
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPath = os.path.join(root, filename)
outPath = os.path.join(root, "decal-" + filename)
imp = IJ.openImage(imgPath)
imp.setCalibration(Calibration())
ic = ImageConverter(imp)
ic.convertToGray8()
IJ.saveAsTiff(imp, outPath)
print "removed calibration and saved to ", os.path.basename(
outPath)
def subtract_back(file):
"""
ImageJのSubtract backgroundを実行し,
開いた画像のDirectory内にSubtracted_imagesを作成し,
背景画像を減算した画像を保存する。
"""
import os
from ij import IJ
imp = IJ.openImage(file)
img_dir = imp.getOriginalFileInfo().directory
save_dir = os.path.join(img_dir, "Subtracted_images")
if not os.path.exists(save_dir): # もしsave_dirが存在しなければそのディレクトリを作成
os.makedirs(save_dir)
img_file = imp.getOriginalFileInfo().fileName
file_name, ext = os.path.splitext(img_file)
save_path = os.path.join(save_dir, file_name + "-subtracted.tif")
IJ.run(imp, "Subtract Background...", "rolling=30") # Radius 30
IJ.saveAsTiff(imp, save_path)
imp.close()
def save_tif():
# Get the active image, its title, and the directory where it lies
imp = IJ.getImage()
imp_title = imp.getTitle()
path = IJ.getDirectory("image")
IJ.log("Active image source: {}{}".format(path, imp_title))
for i in range(0, len(channel_names)):
current_name = channel_names[i]
if "C={}".format(i) in imp_title:
channel_name = current_name
found_name = True
else:
pass
# In the imp title string, find the index where .nd2 first appears. Everything
# up to this point is kept for use in saving the file.
end_of_title = imp_title.find('.nd2')
tif_title = "{}_{}".format(imp_title[:end_of_title], channel_name)
# Save the image
save_path = "{}{}".format(path, tif_title)
IJ.saveAsTiff(imp, save_path)
IJ.log("Tif saved at {}.tif".format(save_path))
# Close the image
imp.close()
def process(self,imp):
# skip automerged images
if "Merging" in imp.getTitle():
return
title = imp.getTitle() + "_edf"
print "EdfWorker.process: " + title
output = edfProcess(imp, self.params)
IJ.saveAsTiff(output, os.path.join(self.exportDir,title))
def save_separate_tif(f):
if f is not None:
save_dir, pre_save_path = get_presave_path(f, dir_name="Separate")
imp = IJ.openImage(f)
for i in range(imp.getNFrames()):
imp.setT(i + 1)
new_imp = Duplicator().crop(imp)
IJ.saveAsTiff(new_imp, pre_save_path + "_{}.tif".format(i + 1))
def run():
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
outDir = DirectoryChooser("Chose >Output< Dir").getDirectory()
if outDir is None:
IJ.log("Output to same dir as source.")
ourtDir = srcDir
refImageId = getRefIdDialog()
if refImageId is None:
IJ.log("Select Reference Image Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-ND2 files
if not filename.endswith(".nd2"):
continue
inpath = os.path.join(root, filename)
# outfn = "reg_" + os.path.splitext(filename)[0] + ".tif"
# outpath = os.path.join(outDir, outfn)
# if os.path.exists(outpath):
# print "Skipped, already exists: ", outfn
# continue
IJ.log("Registering\n" + filename)
imp = regBf(fn=inpath, refId=refImageId)
if imp is None:
IJ.log("Skipped, wrong with registration:\n" + filename)
continue
else:
# fs = FileSaver(imp)
# fs.saveAsTiffStack(outpath)
# IJ.saveAsTiff(imp, outpath)
# print "Registered and saved to ", outfn
splittedimps = ChannelSplitter.split(imp)
for i, simp in enumerate(splittedimps):
outfn = "reg_" + os.path.splitext(
filename)[0] + "_C_" + str(i) + ".tif"
outpath = os.path.join(outDir, outfn)
if os.path.exists(outpath):
IJ.log("Skipped saving, file already exists:\n" +
outfn)
continue
IJ.saveAsTiff(simp, outpath)
IJ.log("Registered and saved to\n" + outfn)
IJ.log("done!")
def save_registration_image(self):
reg_text_info = self.textfield4.text.split(',')
reg_pir_num = int(reg_text_info[0])
reg_channel = int(reg_text_info[1])
self.reg_final_res = float(reg_text_info[2])
self.forreg_output_path = path.join(self.output_path, "000_Slices_for_ARA_registration")
if path.isdir(self.forreg_output_path):
print("Output path for low resolution slices was already created")
else:
mkdir(self.forreg_output_path)
print("Output path for low resolution slices created")
# check that this slice has not been saved before
reg_slice_name = path.join(self.forreg_output_path, self.name)
if path.isfile(reg_slice_name + '.tif'):
print("Registration slice already exists")
else:
# save otherwise
print("Saving for registration channel {} at {} um/px".format(reg_channel, self.reg_final_res))
# get the Xth resolution image and Xth channel for saving it for registration
series_num = self.high_res_index + reg_pir_num
self.raw_reg_image = open_czi_series(self.input_path, series_num) # read the image
self.regist_image = extractChannel(self.raw_reg_image, reg_channel, 1)
ContrastEnhancer().stretchHistogram(self.regist_image, 0.35)
# self.regist_image.show()
self.regist_image.getProcessor().resetRoi()
# reset min and max automatically
# convert to 8-bit (which also applies the contrast)
# ImageConverter(self.regist_image).convertToGray8()
# convert to Xum/px so that it can be aligned to ARA
reg_im_bin_factor = self.binStep ** reg_pir_num
regres_resolution = reg_im_bin_factor * self.res_xy_size
rescale_factor = regres_resolution / self.reg_final_res
new_width = int(rescale_factor * self.regist_image.getWidth())
# self.lr_dapi_reg.getProcessor().scale(rescale_factor, rescale_factor)
ip = self.regist_image.getProcessor().resize(new_width)
self.regist_image.setProcessor(ip)
# Add the information to the metadata
self.regist_image.getCalibration().pixelWidth = self.reg_final_res
self.regist_image.getCalibration().pixelHeight = self.reg_final_res
self.regist_image.getCalibration().pixelDepth = 1
self.regist_image.getCalibration().setXUnit("micrometer")
self.regist_image.getCalibration().setYUnit("micrometer")
self.regist_image.getCalibration().setZUnit("micrometer")
# self.lr_dapi_reg.getProcessor().resetRoi()
IJ.saveAsTiff(self.regist_image, reg_slice_name)
self.regist_image.close()
self.regist_image.flush()
print("Slice for registration saved")
def make_MAX(cString):
# max projection
print "Running MAX projection..."
IJ.run("Z Project...", "projection=[Max Intensity] all")
# renaming
imp = IJ.getImage() # gets the resulting image
imp.setTitle("MAX_C" + cString + "-" + scanName + "_raw")
imp = IJ.getImage() # gets the resulting image
windowName = imp.getTitle() # gets title
print "Saving MAX..."
IJ.saveAsTiff(imp, os.path.join(scanFolder, windowName))
def run():
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
outDir = DirectoryChooser("Chose >Output< Dir").getDirectory()
if outDir is None:
IJ.log("Output to same dir as source.")
ourtDir = srcDir
refImageId = getRefIdDialog()
if refImageId is None:
IJ.log("Select Reference Image Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-ND2 files
if not filename.endswith(".nd2"):
continue
inpath = os.path.join(root, filename)
# outfn = "reg_" + os.path.splitext(filename)[0] + ".tif"
# outpath = os.path.join(outDir, outfn)
# if os.path.exists(outpath):
# print "Skipped, already exists: ", outfn
# continue
IJ.log("Registering\n" + filename)
imp = regBf(fn=inpath, refId=refImageId)
if imp is None:
IJ.log("Skipped, wrong with registration:\n" + filename)
continue
else:
# fs = FileSaver(imp)
# fs.saveAsTiffStack(outpath)
# IJ.saveAsTiff(imp, outpath)
# print "Registered and saved to ", outfn
splittedimps = ChannelSplitter.split(imp)
for i, simp in enumerate(splittedimps):
outfn = "reg_" + os.path.splitext(filename)[0] + "_C_" + str(i) + ".tif"
outpath = os.path.join(outDir, outfn)
if os.path.exists(outpath):
IJ.log("Skipped saving, file already exists:\n" + outfn)
continue
IJ.saveAsTiff(simp, outpath)
IJ.log("Registered and saved to\n" + outfn)
IJ.log("done!")
def buildStack(saveDir, stacklist):
stacks = {}
for f, s in stacklist.iteritems():
for name in s:
curSlice = IJ.openImage(os.path.join(saveDir, name))
if f not in stacks:
stack = curSlice.createEmptyStack()
stack.addSlice(name, curSlice.getProcessor())
stacks[f] = stack
else:
stacks[f].addSlice(name, curSlice.getProcessor())
call(["/usr/local/bin/rmtrash",os.path.join(saveDir,name)])
for f in stacks:
IJ.saveAsTiff(ImagePlus(f, stacks[f]),os.path.join(saveDir,f))
def save_rois(imp, corners_cleaned, L, OUTDIR):
# parse title
tit = imp.getTitle()
core = '_'.join(tit.split('_')[0:-1])
ending = tit.split('_')[-1]
# save rois
roi_ID = 1
for [x, y] in corners_cleaned:
rect = Roi(x, y, L, L)
imp.setRoi(rect)
imp2 = imp.crop()
# save
IJ.saveAsTiff(
imp2, path.join(OUTDIR,
core + "_ROI-" + str(roi_ID) + "_" + ending))
roi_ID += 1
def processImage(imp, threshold, min_size, max_size, remove_last_slice):
title = imp.title
image_dir = IJ.getDirectory("image")
channel_dir = image_dir + "channel_" + str(channel) + "/"
marker_dir = image_dir + "markers/"
mapped_images_dir = image_dir + "mapped_images/"
makeDir(channel_dir, marker_dir, mapped_images_dir)
IJ.run("Split Channels")
main_channel_image = "C" + str(channel) + "-" + title
IJ.selectWindow(main_channel_image)
imp = IJ.getImage()
if os.path.exists(channel_dir + main_channel_image):
os.remove(channel_dir + main_channel_image)
images_list = WindowManager.getImageTitles()
for image in images_list:
if image != main_channel_image:
IJ.selectWindow(image)
IJ.run("Close")
if remove_last_slice:
imp.setSlice(imp.NSlices)
IJ.run(imp, "Delete Slice", "")
imp.setSlice(1)
IJ.saveAsTiff(imp, channel_dir + main_channel_image)
#time.sleep(5)
IJ.run(
imp, "3D Objects Counter",
"threshold=" + str(threshold) + " slice=1 min.=" + str(min_size) +
" max.=" + str(max_size) + " centres_of_masses statistics")
#title="001-002.tiff"
#time.sleep(10)
image = title.split(".")[0]
restults_window = image + ".csv"
IJ.saveAs("Results", marker_dir + restults_window)
IJ.selectWindow(restults_window)
IJ.run("Close")
imp.close()
imp = IJ.getImage()
title = imp.title
if os.path.exists(mapped_images_dir + title):
os.remove(mapped_images_dir + title)
IJ.saveAsTiff(imp, mapped_images_dir + title)
imp.close()
def draw_centers(data):
pathname = data[1]
filename = data[2]
platename = data[3]
print data[4]
nx = int(data[4])
ny = int(data[5])
nx_com = int(data[6])
ny_com = int(data[7])
ax = int(data[8])
ay = int(data[9])
orientation = 2*math.pi * float(data[10]) / 360.0
line_dy = int(round(math.atan(orientation) * LINE_DX))
ax2 = ax - LINE_DX
ay2 = ay - line_dy
orientation_avg = 2*math.pi * float(data[11]) / 360.0
line_dy = int(round(math.atan(orientation_avg) * LINE_DX))
ax3 = ax - LINE_DX
ay3 = ay - line_dy
imp = IJ.openImage(os.path.join(pathname,filename))
roi_nucleus = PointRoi(nx,ny)
roi_nucleus.setDefaultMarkerSize("Large")
roi_nucleus.setStrokeColor(Color.CYAN)
roi_nucleus_com = PointRoi(nx_com,ny_com)
roi_nucleus_com.setDefaultMarkerSize("Large")
roi_nucleus_com.setStrokeColor(Color.GREEN)
roi_anchor = PointRoi(ax,ay)
roi_anchor.setDefaultMarkerSize("Large")
imp.getProcessor().drawRoi(roi_nucleus)
imp.getProcessor().drawRoi(roi_nucleus_com)
imp.getProcessor().drawRoi(roi_anchor)
imp.setColor(Color.RED)
imp.getProcessor().drawLine(ax,ay,ax2,ay2)
imp.setColor(Color.WHITE)
imp.getProcessor().drawLine(ax,ay,ax3,ay3)
IJ.saveAsTiff(imp,os.path.join(pathname,filename))
def pairwise_stitching(tiff_1, tiff_2, temp_dir):
IJ.open(tiff_1)
tiff_1_title = os.path.basename(tiff_1)
IJ.open(tiff_2)
tiff_2_title = os.path.basename(tiff_2)
new_fused_image = "" + tiff_1_title.split("_")[0] + "-" + tiff_2_title.split("_")[0] + "_.tiff"
IJ.run("Pairwise stitching", "first_image=" + tiff_1_title + " second_image=" + tiff_2_title + " fusion_method=[Linear Blending] fused_image=" + new_fused_image + " check_peaks=1 compute_overlap x=0.0000 y=0.0000 z=0.0000 registration_channel_image_1=[Average all channels] registration_channel_image_2=[Average all channels]")
IJ.selectWindow(tiff_1_title)
IJ.run("Close")
os.remove(tiff_1)
IJ.selectWindow(tiff_2_title)
IJ.run("Close")
os.remove(tiff_2)
IJ.selectWindow(new_fused_image)
imp = IJ.getImage()
IJ.saveAsTiff(imp, os.path.join(temp_dir, new_fused_image))
imp.close()
def trans_to_tif(file_list, overwrite = False):
if file_list is not None:
for path in file_list:
opts = ImporterOptions()
opts.setId(path)
opts.setVirtual(True)
opts.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
opts.setOpenAllSeries(True)
process = ImportProcess(opts)
try:
process.execute()
except:
pass
else:
process.execute()
try:
imps = ImagePlusReader(process).openImagePlus()
except:
IJ.log(path + "\n" + "This file was not properly processed")
pass
else:
dir_name = os.path.dirname(path)
file_name = os.path.basename(os.path.splitext(path)[0])
save_dir = os.path.join(dir_name, file_name)
if not os.path.exists(save_dir):
os.makedirs(save_dir)
imps = ImagePlusReader(process).openImagePlus()
for i, imp in enumerate(imps):
save_path = os.path.join(save_dir, file_name + "_pos{}.tif".format(i + 1))
if not os.path.exists(save_path):
IJ.saveAsTiff(imp, save_path)
IJ.freeMemory()
else:
if overwrite:
IJ.saveAsTiff(imp, save_path)
IJ.freeMemory()
else:
pass
def processImage():
imp = IJ.getImage()
image_name = imp.title
image_dir = IJ.getDirectory("image")
IJ.run(imp, "Measure", "")
marker_dir = os.path.join(image_dir, "markers" + os.path.sep)
processed_marker_dir = os.path.join(image_dir, "processed_markers" + os.path.sep)
makeDir(marker_dir, processed_marker_dir)
csv_file = saveResults(imp, marker_dir)
imp.deleteRoi()
tiff_save_name = os.path.join(processed_marker_dir, image_name)
IJ.saveAsTiff(imp, tiff_save_name)
remove_duplicate_counter(csv_file, processed_marker_dir)
# file_dir = os.path.dirname(os.path.abspath(__file__))
IJ.run(imp, "setRoi ", "");
IJ.run("Save")
imp.close()
return image_dir
def batchProcess(parentpath, theExp):
resarray = []
#for ind in range(8):
for ind in theExp:
cellNo = ind + 1
tracks, cellarea, postcounts, postcounts2, precounts, imp, reallength, secondFrameVirusCounts = main(parentpath, cellNo)
scaledCellArea = cellarea * reallength * reallength
#density = len(tracks) / float(scaledCellArea)
density = secondFrameVirusCounts / float(scaledCellArea)
#ripoffRatio = postcounts / float(len(tracks))
if postcounts > 0:
ripoffRatio = postcounts / float(secondFrameVirusCounts)
else:
ripoffRatio = float('NaN')
if postcounts2 > 0:
ripoffRatio2 = postcounts2 / float(secondFrameVirusCounts)
else:
ripoffRatio2 = float('NaN')
print "Total number of detected dots: ", len(tracks)
print "Second Frame Counts", secondFrameVirusCounts
print "cell area [um2]", scaledCellArea
print "Dot Density:[count / um2]:" , density
print "Number of Ripped off (", preDrug_Starts, " to ", preDrug_Ends, " frame):", precounts
print "Number of Ripped off (", postDrug_Starts, " to ", postDrug_Ends, " frame):", postcounts
print "Number of Ripped off (", postDrug2_Starts, " to ", postDrug2_Ends, " frame):", postcounts2
#resarray.append([cellNo, scaledCellArea, len(tracks), density, precounts, postcounts, ripoffRatio])
resarray.append([cellNo, scaledCellArea, secondFrameVirusCounts, density, precounts, postcounts, postcounts2, ripoffRatio])
outname = "cell" + str(cellNo) + '_dots.tif'
savefilepath = os.path.join(parentpath, outname)
IJ.saveAsTiff(imp, savefilepath)
# exporting results
outcsvpath = os.path.join(parentpath, 'results.csv')
f = open(outcsvpath, 'wb')
writer = csv.writer(f)
writer.writerow(['CellID', 'Area[um2]', 'Dots Total', 'Density', 'RipOff counts2_4', 'RipOff counts5_7', 'RipOff counts8_10', 'RipOff Ratio'])
for arow in resarray:
#arow = [cellNo, cellarea, len(tracks), postcounts, precounts]
writer.writerow(arow)
f.close()
def split_stack():
imp = IJ.getImage()
path = IJ.getDirectory("image")
IJ.run("Stack to Images", "")
# close original image and leave split stacks open
imp.close()
n_images = WindowManager.getImageCount()
for i in range(0, n_images):
frame_imp = IJ.getImage()
imp_title = frame_imp.getTitle()
save_path = "{}{}".format(path, imp_title)
IJ.saveAsTiff(frame_imp, save_path)
IJ.log("{} saved at {}".format(frame_imp, save_path))
frame_imp.close()
def save_summary(self, e):
IJ.selectWindow(self.name)
IJ.run("Flatten")
imp = IJ.getImage()
# downsample
# scale ENLARGING or SHRINKING the canvas dimensions
scale_factor = .2
new_width = str(int(imp.getWidth() * scale_factor))
new_height = str(int(imp.getHeight() * scale_factor))
IJ.selectWindow(self.name + "-1")
str_to_scale = "x=" + str(scale_factor) + " y=" + str(
scale_factor
) + " width=" + new_width + " height=" + new_height + " interpolation=Bilinear average create"
IJ.run("Scale...", str_to_scale)
# save
imp2 = IJ.getImage()
#IJ.saveAs("Tiff", path.join(OUTDIR, self.name + "_summaryOfROIs"))
IJ.saveAsTiff(
imp2, path.join(self.output_path,
self.name + "_summaryOfROIs.tif"))
print "summary image saved"
def make_MAX(singleplane): # singleplane is Boolean True/False
image_titles = [
WindowManager.getImage(id).getTitle()
for id in WindowManager.getIDList()
]
for i in image_titles:
imp = WindowManager.getImage(i)
if singleplane == False: # If the data is not single z-plane, runs max projection
IJ.run(imp, "Z Project...", "projection=[Max Intensity] all")
imp = WindowManager.getImage("MAX_" + i)
windowName = imp.getTitle()
IJ.saveAsTiff(imp, os.path.join(saveFolder,
windowName)) #saves to saveFolder
imp = WindowManager.getImage(i) # Gets the original hyperstack
imp.changes = False # Answers "no" to the dialog asking if you want to save any changes
imp.close() # Closes the hyperstack
# If the data is single plane, it skipes projection and moves to LUT setting
elif singleplane == True:
windowName = imp.getTitle()
print "Single plane data detected. Skipping Z-projection for ", windowName
def run():
helpText = "This program will batch convert any tif image to 8-bit greyscale, " + \
"and empty calibration infomation.\n\n" + \
">> Press OK to Select a directory of TIFF images."
MessageDialog(IJ.getInstance(),"Empty Calibration Guide", helpText)
srcDir = DirectoryChooser("Chose Source Dir").getDirectory()
if srcDir is None:
IJ.log("Choose Dir Canceled!")
return
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
if not filename.endswith(".tif"):
continue
imgPath = os.path.join(root, filename)
outPath = os.path.join(root, "decal-" + filename)
imp = IJ.openImage(imgPath)
imp.setCalibration(Calibration())
ic = ImageConverter(imp)
ic.convertToGray8()
IJ.saveAsTiff(imp, outPath)
print "removed calibration and saved to ", os.path.basename(outPath)
def main():
Interpreter.batchMode = True
if (lambda_flat == 0) ^ (lambda_dark == 0):
print ("ERROR: Both of lambda_flat and lambda_dark must be zero,"
" or both non-zero.")
return
lambda_estimate = "Automatic" if lambda_flat == 0 else "Manual"
print "Loading images..."
# Use BioFormats reader directly to determine dataset dimensions without
# reading every single image. The series count (num_images) is the one value
# we can't easily get any other way, but we might as well grab the others
# while we have the reader available.
bfreader = ImageReader()
bfreader.id = str(filename)
num_images = bfreader.seriesCount
num_channels = bfreader.sizeC
width = bfreader.sizeX
height = bfreader.sizeY
bfreader.close()
# The internal initialization of the BaSiC code fails when we invoke it via
# scripting, unless we explicitly set a the private 'noOfSlices' field.
# Since it's private, we need to use Java reflection to access it.
Basic_noOfSlices = Basic.getDeclaredField('noOfSlices')
Basic_noOfSlices.setAccessible(True)
basic = Basic()
Basic_noOfSlices.setInt(basic, num_images)
# Pre-allocate the output profile images, since we have all the dimensions.
ff_image = IJ.createImage("Flat-field", width, height, num_channels, 32);
df_image = IJ.createImage("Dark-field", width, height, num_channels, 32);
print("\n\n")
# BaSiC works on one channel at a time, so we only read the images from one
# channel at a time to limit memory usage.
for channel in range(num_channels):
print "Processing channel %d/%d..." % (channel + 1, num_channels)
print "==========================="
options = ImporterOptions()
options.id = str(filename)
options.setOpenAllSeries(True)
# concatenate=True gives us a single stack rather than a list of
# separate images.
options.setConcatenate(True)
# Limit the reader to the channel we're currently working on. This loop
# is mainly why we need to know num_images before opening anything.
for i in range(num_images):
options.setCBegin(i, channel)
options.setCEnd(i, channel)
# openImagePlus returns a list of images, but we expect just one (a
# stack).
input_image = BF.openImagePlus(options)[0]
# BaSiC seems to require the input image is actually the ImageJ
# "current" image, otherwise it prints an error and aborts.
WindowManager.setTempCurrentImage(input_image)
basic.exec(
input_image, None, None,
"Estimate shading profiles", "Estimate both flat-field and dark-field",
lambda_estimate, lambda_flat, lambda_dark,
"Ignore", "Compute shading only"
)
input_image.close()
# Copy the pixels from the BaSiC-generated profile images to the
# corresponding channel of our output images.
ff_channel = WindowManager.getImage("Flat-field:%s" % input_image.title)
ff_image.slice = channel + 1
ff_image.getProcessor().insert(ff_channel.getProcessor(), 0, 0)
ff_channel.close()
df_channel = WindowManager.getImage("Dark-field:%s" % input_image.title)
df_image.slice = channel + 1
df_image.getProcessor().insert(df_channel.getProcessor(), 0, 0)
df_channel.close()
print("\n\n")
template = '%s/%s-%%s.tif' % (output_dir, experiment_name)
ff_filename = template % 'ffp'
IJ.saveAsTiff(ff_image, ff_filename)
ff_image.close()
df_filename = template % 'dfp'
IJ.saveAsTiff(df_image, df_filename)
df_image.close()
print "Done!"
headers = ['Original path','Processed path']
csvWriter.writerow(headers)
# Process list of images
for (counter, f) in enumerate(files):
# Display progress
IJ.showStatus("Processing file "+ str(counter+1) +"/"+ str(len(files)))
# Open each image and process it
imp = IJ.openImage(f)
myRoutines(imp)
# Save processed image in out_dir (enforcing .tif extension)
newpath = os.path.splitext(out_dir + imp.getTitle())[0] +".tif"
IJ.saveAsTiff(imp, newpath)
imp.close()
# Log paths of processed files
csvWriter.writerow([f, newpath])
# Display CSV log
csvFile.close()
rt = ResultsTable.open(csvPath)
rt.show("_ProcessedFileList.csv")
# Proudly inform that processing terminated
if IJ.showMessageWithCancel("All done","Reveal output directory?"):
Utils.revealFile(out_dir);
else:
outDir = DirectoryChooser("Batch Splitter: Chose >Output< Dir").getDirectory()
if outDir is None:
print "Output to same dir as source."
ourtDir = srcDir
for root, directories, filenames in os.walk(srcDir):
for filename in filenames:
# Skip non-TIF files
if not filename.endswith(".tif"):
continue
inpath = os.path.join(root, filename)
print "Reading ", filename
imp = IJ.openImage(inpath)
if imp is None:
print "Skipped, wrong with reading: ", filename
continue
else:
splittedimps = ChannelSplitter.split(imp)
for i, simp in enumerate(splittedimps):
outfn = os.path.splitext(filename)[0] + "_C_" + str(i) + ".tif"
outpath = os.path.join(outDir, outfn)
if os.path.exists(outpath):
print "Skipped, already exists: ", outfn
continue
IJ.saveAsTiff(simp, outpath)
print "Splitted and saved to ", outfn
print "done."
for path in filecollection:
theImage = IJ.openImage(path)
calibration = theImage.getCalibration()
scaleXs.append(calibration.pixelWidth)
theImage.close()
lc_scale = max(scaleXs)
print lc_scale
for path in filecollection:
theImage = IJ.openImage(path)
bname1 = os.path.basename(path)
bname2 = os.path.splitext(bname1)[0]
this_cal = theImage.getCalibration()
scale_factor = (this_cal.pixelWidth / lc_scale) * common_scale
params = "x=" + str(scale_factor) + " y=" + str(scale_factor) + " z=1.0 interpolation=Bilinear average process create title=doggie"
IJ.run(theImage,"Scale...",params)
saveImage = WindowManager.getImage("doggie")
pixelWidth = saveImage.getCalibration().pixelWidth
pixelHeight = saveImage.getCalibration().pixelHeight
pixelDepth = saveImage.getCalibration().pixelDepth
if convert_to_rgb:
old_saveImage = saveImage
old_saveImage.changes = False
saveImage = old_saveImage.flatten()
old_saveImage.close()
saveImage.getCalibration().pixelWidth = pixelWidth
saveImage.getCalibration().pixelHeight = pixelHeight
saveImage.getCalibration().pixelDepth = pixelDepth
IJ.saveAsTiff(saveImage,dirPath+"resized/"+bname2+".tif")
theImage.close()
saveImage.close()
def process(self,imp):
# extract nucleus channel, 8-bit and twice binned
imp.setC(self.nucleusChannel)
ip = imp.getChannelProcessor().duplicate()
ip = ip.convertToByteProcessor()
ip = ip.bin(4)
nucleus = ImagePlus("nucleus_channel", ip)
# threshold image and separate clumped nuclei
IJ.run(nucleus, "Auto Threshold", "method=Otsu white setthreshold show");
IJ.run(nucleus, "Make Binary", "thresholded remaining black");
IJ.run(nucleus, "Watershed", "");
directory = imp.getTitle()
directory = directory.replace(" ", "_")\
.replace(",", "_")\
.replace("#", "_series")\
.replace("...", "")\
.replace(".","_")
directory = os.path.join(self.exportDir, directory)
sliceDirectory = os.path.join(directory, "slices")
print directory
print sliceDirectory
if not os.path.exists(sliceDirectory):
os.makedirs(sliceDirectory)
# Create a table to store the results
table = ResultsTable()
# Create a hidden ROI manager, to store a ROI for each blob or cell
#roim = RoiManager(True)
# remove small particles and border particles
pa = ParticleAnalyzer(\
ParticleAnalyzer.ADD_TO_MANAGER | ParticleAnalyzer.EXCLUDE_EDGE_PARTICLES,\
Measurements.CENTER_OF_MASS,\
table,\
self.minArea, self.maxArea,\
0.0,1.0)
if pa.analyze(nucleus):
print "All ok, number of particles: ", table.size()
else:
print "There was a problem in analyzing", imp, nucleus
table.save(os.path.join(directory, "rt.csv"))
# read the center of mass coordinates
cmx = table.getColumn(0)
cmy = table.getColumn(1)
if self.debug:
imp.show()
i=0
for i in range(0, min(self.nCells,table.size())):
# ROI around the cell
cmx = table.getValue("XM",i)
cmy = table.getValue("YM",i)
x = 4 * cmx - (self.boxSize - 1) / 2
y = 4 * cmy - (self.boxSize - 1) / 2
if (x < self.edge or y < self.edge or x > imp.getWidth() - self.edge or y > imp.getHeight() - self.edge):
continue
roi = Roi(x,y,self.boxSize,self.boxSize)
imp.setRoi(roi, False)
cellStack = ImageStack(self.boxSize, self.boxSize)
for z in range(1, imp.getNSlices() + 1):
imp.setSlice(z)
for c in range(1, imp.getNChannels() + 1):
imp.setC(c)
# copy ROI to stack
imp.copy()
impSlice = imp.getClipboard()
cellStack.addSlice(impSlice.getProcessor())
if self.slices:
sliceTitle = "cell_%s_z%s_c%s" % (str(i).zfill(4), str(z).zfill(3), str(c))
print sliceTitle
IJ.saveAsTiff(impSlice, os.path.join(sliceDirectory, sliceTitle))
impSlice.close()
title = "cell_" + str(i).zfill(4)
cell = ImagePlus(title, cellStack)
# save ROI image
IJ.saveAsTiff(cell, os.path.join(directory, title))
cell.close()
if self.debug:
imp.updateAndDraw()
wait = Wait("particle done")
wait.show()
Canceled = False
if not Canceled:
for f in file_path:
# Hyperstackの作成
imp = IJ.openImage(f)
nFrame = imp.getNSlices(
) / n_Channel # 元画像のAttributionがなぜかFrame が Z sliceとなっている
# File 保存のための文字列作成
save_file = imp.getTitle().replace(".tif", "-stack.tif")
save_path = os.path.join(save_dir, save_file)
# Hyper Stackに変換
h_imp = HyperStackConverter.toHyperStack(imp, n_Channel, 1, nFrame,
"Composite")
del imp
# Hyper Stack の Channelカラー変更
for i, color in enumerate(user_color):
h_imp.setC(i + 1)
h_imp.setLut(LUT.createLutFromColor(Colors[color]))
# ファイルを保存
IJ.saveAsTiff(h_imp, save_path)
# IJ.log(save_path)
del h_imp
from ij.io import DirectoryChooser
from ij.plugin import Memory
dc = DirectoryChooser("Choose directory of LSM files...")
dirPath = dc.getDirectory()
if dirPath is not None:
fileList = glob.glob(dirPath+"*.lsm")
for path in fileList:
processImage = False
theSize = os.path.getsize(path) / 1048576.0
print theSize
totFijiMem = Memory().maxMemory() / 1048576.0
print totFijiMem
if (theSize < totFijiMem/3.0):
basename = os.path.splitext(os.path.basename(path))[0]
outputPath = dirPath + basename + ".tif"
if not os.path.exists(outputPath):
processImage = True
params = "type=[Positions from file] order=[Defined by image metadata] browse=[" + path + "] multi_series_file=[" + path + "] fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap ignore_z_stage increase_overlap=10 subpixel_accuracy computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]"
print params
if (processImage):
try:
IJ.run("Grid/Collection stitching", params)
stitchedImage = IJ.getImage()
IJ.saveAsTiff(stitchedImage,outputPath)
stitchedImage.close()
except:
IJ.log("Failed to stitch and save " + path)
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()
# save output
imp = WindowManager.getCurrentImage()
IJ.saveAsTiff(imp,output)
imp.close()
#find the threshold values using the quantiles
percentiles = [98.5, 99.5, 99.9]
thresholds = FindThreholds(In_dir, MouseIDcFos, percentiles)
IJ.log('Thresholds for percentiles ' + str(percentiles) +
' selected to ' + str(thresholds))
#threshold and save images for each threshold value
for i, threshold in enumerate(thresholds):
# create directory
Perc_Out_dir = Out_dir + "percentile_" + str(percentiles[i]) + "/"
if not os.path.exists(Perc_Out_dir):
os.makedirs(Perc_Out_dir)
IJ.log('Processing ' + MouseID + ' for percentile ' +
str(percentiles[i]))
for image in MouseIDcFos:
#open image
imp_orig = Opener().openImage(In_dir + image)
#gaussian blur
imp_GB = blurImage(imp_orig)
imp_orig.close()
#threshold
imp_GB.getProcessor().threshold(threshold)
#save
newname = image.split('.')[0] + '_GPT_' + str(
percentiles[i]) + '.tif'
IJ.saveAsTiff(imp_GB, Perc_Out_dir + newname)
imp_GB.close()
IJ.log('Mouse ' + MouseID + ' processed')
print "DONE, find your results in " + Out_dir
if dirPath is not None:
dc2 = DirectoryChooser("Select output directory...")
outPath = dc2.getDirectory()
if outPath is not None:
gd = GenericDialog("Options...")
gd.addCheckbox("Recolor_images",True)
gd.showDialog()
if (gd.wasOKed()):
doRecolor = gd.getNextBoolean()
for f in os.listdir(dirPath):
if f.endswith(".tif") or f.endswith(".tiff"):
theImage = IJ.openImage(dirPath+f)
IJ.log("Loaded " + f)
palette = [Color.GREEN,Color.RED,Color.BLUE]
if (theImage.getNChannels() < 4):
if doRecolor:
for i in range(theImage.getNChannels()):
theImage.setChannelLut(LUT.createLutFromColor(palette[i]),i+1)
try:
sc = StackConverter(theImage)
sc.convertToRGB()
IJ.saveAsTiff(theImage,outPath+os.path.splitext(f)[0]+"_rgb.tif")
IJ.log("Completed " + f)
except:
IJ.log("Exception thrown during RGB conversion, image skipped")
finally:
theImage.close()
else:
IJ.log("Image has too many color channels")
rm.runCommand("Show All with labels")
#for each image open..
for image in image_titles:
imp = WindowManager.getImage(image)
baseName = os.path.splitext(image)[0] #get the name without extension
roiFile = baseName + "_ROISet.zip" #make the name for the text file
roiFilePath = os.path.join(roiDir,
roiFile) #make the path for the text file
print(roiFilePath)
IJ.openImage(roiFilePath) #open the roi text file
rm.runCommand("Select All") #select all rois
rm.runCommand(imp, "Measure") #measure all rois
rm.runCommand(imp, "Show All") #show all rois
imp2 = imp.flatten() #create a flattened key with rois and labels
imp2.setTitle("labels_" + baseName + ".tif")
imp2.show()
rm.runCommand("Select All")
rm.runCommand("Delete") #delete all rois in manager
imp.close()
rm.runCommand(imp, "Show None")
windowName = imp2.getTitle()
flatPath = os.path.join(roiDir, windowName)
IJ.saveAsTiff(imp2, flatPath) #save flattened image
csvFile = os.path.join(roiDir, "Measurements.csv")
IJ.saveAs("Results", csvFile) #export measurements as csv file
image_path = image_directory + '/' + i;
imp = IJ.openImage(image_path);
imp.show();
for k in match_roi:
IJ.selectWindow(i);
cur_match_roi = k;
m = re.search('(Batch\d+_\d+_XY\d{2}_cropped_singlet\d+).roi', cur_match_roi);
crop_name = m.group(1);
roi_path = roi_directory + '/' + cur_match_roi;
IJ.open(roi_path);
temp_str = 'title=' + crop_name + '.tif duplicate';
IJ.run('Duplicate...', temp_str);
imp_cropped = IJ.getImage();
save_name = crop_dir + '/' + crop_name + '.tif';
print(save_name);
IJ.saveAsTiff(imp_cropped, save_name);
IJ.run('Close All');
gc.collect();
else:
if len(match_roi) >= 1:
for k in match_roi:
image_path = image_directory + '/' + i;
imp = IJ.openImage(image_path);
imp.show();
IJ.selectWindow(i);
cur_match_roi = k;
m = re.search('(Batch\d+_\d+_XY\d{2}_cropped_singlet\d+).roi', cur_match_roi);
crop_name = m.group(1);
roi_path = roi_directory + '/' + cur_match_roi;
IJ.open(roi_path);
IJ.run('Crop');
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)
import glob import os.path import sys from ij import IJ, ImagePlus, ImageStack, WindowManager from ij.io import DirectoryChooser from edfgui import ExtendedDepthOfField, Parameters file_in = sys.argv[1] file_out = sys.argv[2] # EDF parameters params = Parameters() params.setQualitySettings(params.QUALITY_HIGH) params.nScales = 10 # read input image imp = ImagePlus(file_in) # make all-in-focus image edf = ExtendedDepthOfField(imp,params) edf.process() # save output imp = WindowManager.getCurrentImage() IJ.saveAsTiff(imp,file_out) imp.close()
def processOneImage(inputDir):
tmp = glob.glob(os.path.join(inputDir, "fibrone*"))
fibronectin = tmp[0]
tmp = glob.glob(os.path.join(inputDir, "nucleus*"))
nucleus = tmp[0]
tmp = glob.glob(os.path.join(inputDir, "actin*"))
actin = tmp[0]
# read sample name
head,tail = os.path.split(inputDir)
sample = tail.replace(".tif_Files","")
# original images
imp_fn_orig = IJ.openImage(fibronectin)
imp_nuc_orig = IJ.openImage(nucleus)
# work copies
imp_fn = imp_fn_orig.duplicate()
imp_nuc = imp_nuc_orig.duplicate()
IJ.run(imp_fn,"Set Scale...", "distance=1 known=1 pixel=1 unit=pixels")
IJ.run(imp_fn,"Gaussian Blur...","sigma=5")
IJ.run(imp_fn,"Make Binary","")
IJ.run(imp_nuc,"Set Scale...", "distance=1 known=1 pixel=1 unit=pixels")
IJ.run(imp_nuc,"Gaussian Blur...","sigma=5")
IJ.run(imp_nuc,"Make Binary","")
# get moments of the fibronectin image
moments_file = os.path.join(OUTPUT, sample + " moments.txt")
printMoments(fibronectin, moments_file)
moments = readMoments(moments_file)
print moments.m00
sys.exit()
# centroid of fibronectin anchor
centers = getParticleCenters(imp_fn)
cxfn = int(round(centers[0][0]))
cyfn = int(round(centers[1][0]))
fn_centroid_roi = PointRoi(cxfn,cyfn)
fn_centroid_roi.setDefaultMarkerSize("Large")
fn_centroid_roi.setStrokeColor(Color.CYAN)
# center of mass of nucleus
centers = getParticleCenters(imp_nuc)
cxnuc = int(round(centers[2][0]))
cynuc = int(round(centers[3][0]))
nuc_com_roi = PointRoi(cxnuc,cynuc)
nuc_com_roi.setDefaultMarkerSize("Large")
# skeletonize fibronectin anchor to find its orientation
IJ.run(imp_fn,"Skeletonize","")
skel = AnalyzeSkeleton_()
skel.setup("",imp_fn)
skelResult = skel.run(skel.NONE, False, True, None, True, True)
graph = skelResult.getGraph()
print len(graph)
print skelResult.getNumOfTrees()
# find the longest graph
graph = sorted(graph, key=lambda g: getGraphLength(g), reverse=True)
graph = graph[0]
edges = graph.getEdges()
# find longest edge, the main axis of the anchor
edges = sorted(edges, key=lambda edge: edge.getLength(), reverse=True)
#for e in edges:
# print e.getLength()
v1long = edges[0].getV1()
v2long = edges[0].getV2()
x1 = v1long.getPoints()[0].x
y1 = v1long.getPoints()[0].y
x2 = v2long.getPoints()[0].x
y2 = v2long.getPoints()[0].y
anchor_roi = PointRoi(x1,y1)
anchor_roi = anchor_roi.addPoint(x2,y2)
# find top and bottom vertices of the graph
vertices = graph.getVertices()
vertices = sorted(vertices, key=lambda vertex: vertex.getPoints()[0].y)
v1short = vertices[len(vertices)-1]
v2short = vertices[0]
x3 = v1short.getPoints()[0].x
y3 = v1short.getPoints()[0].y
x4 = v2short.getPoints()[0].x
y4 = v2short.getPoints()[0].y
anchor_roi = anchor_roi.addPoint(x3,y3)
anchor_roi = anchor_roi.addPoint(x4,y4)
# calculate angles
a1 = math.atan(abs(float(y2-y1)/float(x2-x1))) / math.pi * 360
a2 = math.atan(abs(float(x4-x3)/float(y4-y3))) / math.pi * 360
amean = float((a1+a2)/2)
dx = cxfn-cxnuc
print sample,cxfn,cyfn,cxnuc,cynuc,dx,math.cos(amean)*dx,x1,y1,x2,y2,x3,y3,x4,y4,a1,a2
# create composite
comp = ImagePlus("composite",imp_nuc_orig.getProcessor().convertToColorProcessor())
comp.getProcessor().setChannel(2,imp_fn_orig.getProcessor())
comp.getProcessor().setChannel(3,imp_fn.getProcessor())
comp.show()
comp.getProcessor().drawRoi(fn_centroid_roi)
comp.getProcessor().drawRoi(nuc_com_roi)
comp.getProcessor().drawRoi(anchor_roi)
comp.repaintWindow()
IJ.saveAsTiff(comp, os.path.join(OUTPUT,sample + ".tif"))
## Outputs each stitched z plane as a separate file
iReader = ImageReader()
iReader.setId(parentLSMFilePath)
for z in range(max_coords[2]+basic_info[4]):
## for z in range(50,51):
IJ.showStatus("z: "+str(z+1)+" of "+str(max_coords[2]+basic_info[4]))
chIps = []
resImages = []
for ch in range(basic_info[0]):
chIps.append(ByteProcessor(max_coords[0]+scale_info[2],max_coords[1]+scale_info[2]))
for ch in range(basic_info[0]):
resImages.append(ImagePlus("ch"+str(ch+1),chIps[ch]))
for se in range(basic_info[1]):
IJ.showProgress(se,basic_info[1])
if z >= coords_upscaled[se][2] and z <= coords_upscaled[se][2]+basic_info[4]-1:
iReader.setSeries(se)
for ch in range(basic_info[0]):
byteArray = iReader.openBytes((z-coords_upscaled[se][2])*basic_info[0]+ch)
testIp = ByteProcessor(scale_info[2],scale_info[2],byteArray)
testImage = ImagePlus("tester",testIp)
Image_stamper.stampStack(testImage,resImages[ch],coords_upscaled[se][0],coords_upscaled[se][1],0)
activeIp = chIps[ch]
testImage.close()
for ch in range(len(resImages)):
IJ.saveAsTiff(resImages[ch],parentLSMFilePath+"_tiles/v_img/img_z_"+str(z+1)+"_c_"+str(ch+1)+".tif")
#outPlaneImage = RGBStackMerge.mergeChannels(resImages,False)
#IJ.saveAsTiff(outPlaneImage,parentLSMFilePath+"_tiles/v_img/img_z_"+str(z+1)+".tif")
#outPlaneImage.close()
parser = OptionParser()
parser.add_option('-o', '--output', help='edf.tiff')
options, args = parser.parse_args()
print options.output
print args
# check input image size
tmp = ImagePlus(args[0])
# put input images in a stack
stack = ImageStack(tmp.getWidth(), tmp.getHeight())
for a in args:
imp = ImagePlus(a)
stack.addSlice(imp.getProcessor())
imp = ImagePlus("focus stack", stack)
IJ.saveAsTiff(imp, options.output.replace("_edf_", "_edf_stack_"))
#sys.exit()
# process input
output = process(imp)
# save output
IJ.saveAsTiff(output, options.output)
# close images
output.close()
imp.close()
categorizer = RangedCategorizer( nImages )
matrices = DenseCorrelationMatricesWithRadius(
wrappedImage,
radii[0],
c,
DoubleType()
)
result = MultiScaleEstimation.estimateZCoordinates( matrices, startingCoordinates, c, radii, steps, visitor, categorizer, opt )
IJ.log("done")
resultFileName = '%s/result.tif' % home.rstrip('/')
imp = ImageJFunctions.wrap( result, 'result' )
IJ.saveAsTiff(imp.duplicate(), resultFileName)
relativeResult = result.copy()
c = relativeResult.cursor()
while c.hasNext():
c.fwd()
cur = c.get()
val = cur.get()
cur.set( val - c.getDoublePosition( 2 ) )
relativeResultFileName = '%s/relativeResult.tif' % home.rstrip('/')
imp = ImageJFunctions.wrap( relativeResult, 'relative result' )
IJ.saveAsTiff(imp.duplicate(), relativeResultFileName)
ratio = [ wrappedImage.dimension( 0 )*1.0/result.dimension( 0 ), wrappedImage.dimension( 1 )*1.0/result.dimension( 1 ) ]
shift = [ 0.0, 0.0 ]
ratio_rec_str = "%.3f" % ratio_rec
gd.addMessage(str(i+1)+"-channel: " + str(mem_recs[i]) + "MB; Ratio: " + ratio_rec_str)
gd.showDialog()
ratioRaw = gd.getNextNumber()
ratio = math.sqrt(ratioRaw)
if (gd.wasOKed()):
filecollection = glob.glob(os.path.join(sourceDir, '*.ome.tif'))
numFiles = len(filecollection)
count = 1
for f in filecollection:
bname1 = os.path.basename(f)
bname2 = os.path.splitext(bname1)[0]
bname3 = os.path.splitext(bname2)[0]
print bname3
params = "open=[" + f + "] color_mode=Default view=Hyperstack stack_order=XYCZT"
IJ.run("Bio-Formats Importer",params)
theImage = WindowManager.getCurrentImage()
params2 = "x=" + str(ratio) + " y=" + str(ratio) + " z=1.0 interpolation=Bilinear average process create title=doggie"
IJ.run(theImage,"Scale...",params2)
theImage.close()
saveImage = WindowManager.getImage("doggie")
savePath = sourceDir+"resized/"+bname3+".tif"
IJ.saveAsTiff(saveImage,sourceDir+"resized/"+bname3+".tif")
saveImage.close()
IJ.showStatus("Tile: " + str(count) + "/" + str(numFiles))
count = count + 1
imageHeight = 1024
imageDepth = 151
pixelWidth = 0.52
pixelHeight = 0.52
pixelDepth = 1.9867549668874172
print(folder)
images = []
# load all images, collect them in a list
for root, directories, filenames in os.walk(folder):
filenames.sort()
for filename in filenames:
print(filename)
if (filename.endswith(".raw")):
if (not File(os.path.join(targetFolder,
filename + ".tif")).exists()):
IJ.run(
"Raw...", "open=[" + os.path.join(folder, filename) +
"] image=[16-bit Signed] width=" + str(imageWidth) +
" height=" + str(imageHeight) + " number=" +
str(imageDepth) + " little-endian")
imp = IJ.getImage()
imp.getCalibration().pixelWidth = pixelWidth
imp.getCalibration().pixelHeight = pixelHeight
imp.getCalibration().pixelDepth = pixelDepth
IJ.saveAsTiff(imp, os.path.join(targetFolder,
filename + ".tif"))
imp.close()
# Copies tiles for stitching into temp directory and stitches, if necessary
if len(tiles)==1:
params = "open=["+ imgDir +"tile_"+str(tiles[0])+".ome.tif] color_mode=Default view=Hyperstack stack_order=XYCZT"
IJ.run("Bio-Formats Importer", params);
tileImage = WindowManager.getImage("tile_"+str(tiles[0])+".ome.tif")
tileImage.setSlice(int(tileImage.getNSlices()/2))
else:
ind = 1
for t in tiles:
shutil.copyfile(imgDir+"tile_"+str(t)+".ome.tif",imgDir+"temp/tile_"+str(ind)+".ome.tif")
ind = ind + 1
IJ.showStatus("Beginning stitch...")
params = "type=[Grid: row-by-row] order=[Right & Down ] grid_size_x=" + str(xs[2]) + " grid_size_y=" + str(ys[2]) + " tile_overlap=10 first_file_index_i=1 directory=[" + imgDir + "temp] file_names=tile_{i}.ome.tif output_textfile_name=TileConfiguration.txt fusion_method=[Linear Blending] regression_threshold=0.30 max/avg_displacement_threshold=2.50 absolute_displacement_threshold=3.50 compute_overlap ignore_z_stage subpixel_accuracy computation_parameters=[Save memory (but be slower)] image_output=[Fuse and display]"
IJ.run("Grid/Collection stitching", params)
fusedImage = WindowManager.getImage("Fused")
IJ.saveAsTiff(fusedImage,imgDir+"temp/Fused.tif")
fusedImage.close()
IJ.open(imgDir+"temp/Fused.tif")
tileImage = WindowManager.getImage("Fused.tif")
tileImage.setSlice(int(tileImage.getNSlices()/2))
gd = NonBlockingGenericDialog("Explore full resolution...")
gd.addMessage("Select ROI for visualization at full resolution")
gd.showDialog()
doContinue = gd.wasOKed()
##### Removes temporary tile files ######
# filelist = [f for f in os.listdir(imgDir+"temp") if f.endswith(".tif")]
# for f in filelist:
# os.remove(f)
from ij import IJ
from ij.gui import GenericDialog
from ij.plugin import ChannelSplitter
import os
path = IJ.getDirectory("Select source directory:")
if not os.path.exists(path + "\\output"):
os.mkdir(path + "\\output")
filenames = list(name for name in os.listdir(path) if name.endswith(".lsm"))
for filename in filenames:
img = IJ.openImage(path + "\\" + filename)
#IJ.saveAsTiff(img, path + "\\output\\" + filename[:-4])
channels = ChannelSplitter.split(img)
for i, c in enumerate(channels):
IJ.saveAsTiff(
c, path + "\\output\\" + filename[:-4] + "_channel" + str(i))
IJ.beep()
gd = GenericDialog("Success!")
gd.addMessage("Successfully split " + str(len(filenames)) + " hyperstacks.")
gd.showDialog()
# Create the overlay image
overlayImage = image.duplicate()
IJ.run(overlayImage, "RGB Color", "")
IJ.run(overlayImage, 'Specify...', 'width=' + str(2*mean_radius) + \
' height=' + str(2*mean_radius) + \
' x=' + str(mean_cx) + \
' y=' + str(mean_cy) + ' oval centered');
roi = overlayImage.getRoi()
overlayImage.setOverlay(roi, Color(246, 27, 27), 10, None)
overlayImage = overlayImage.flatten();
# Now add the overlay image as the first stack
newStack = image.createEmptyStack()
newStack.addSlice(overlayImage.getProcessor())
newStack.addSlice(image.getProcessor())
image.setStack(newStack)
directory = IJ.getDirectory('image')
print directory
name = image.getShortTitle()
print name
# Now save results table. Then done.
IJ.saveAs('Measurements', directory + name + '.txt')
print 'Done saving measurement table!'
# Now overwrite the original image
IJ.saveAsTiff(image, directory + name + '.tif')
def main():
Interpreter.batchMode = True
if (lambda_flat == 0) ^ (lambda_dark == 0):
print ("ERROR: Both of lambda_flat and lambda_dark must be zero,"
" or both non-zero.")
return
lambda_estimate = "Automatic" if lambda_flat == 0 else "Manual"
print "Loading images..."
options = ImporterOptions()
options.setId(str(filename))
options.setOpenAllSeries(True)
options.setConcatenate(True)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
num_channels = len(imps)
w = imps[0].getWidth()
h = imps[0].getHeight()
ff_imp = IJ.createImage("Flat-field", w, h, num_channels, 32);
df_imp = IJ.createImage("Dark-field", w, h, num_channels, 32);
basic = Basic()
Basic_noOfSlices = Basic.getDeclaredField('noOfSlices')
Basic_noOfSlices.setAccessible(True)
for channel, imp in enumerate(imps):
title = imp.getTitle()
print "Processing:", title
x, y, c, z, t = imp.getDimensions()
assert z == 1 and c == 1
imp.setDimensions(1, t, 1)
WindowManager.setTempCurrentImage(imp)
Basic_noOfSlices.setInt(basic, t)
basic.exec(
imp, None, None,
"Estimate shading profiles", "Estimate both flat-field and dark-field",
lambda_estimate, lambda_flat, lambda_dark,
"Ignore", "Compute shading only"
)
ff_channel = WindowManager.getImage('Flat-field:' + title)
ff_channel.copy()
ff_imp.setSlice(channel + 1)
ff_imp.paste()
ff_channel.close()
df_channel = WindowManager.getImage('Dark-field:' + title)
df_channel.copy()
df_imp.setSlice(channel + 1)
df_imp.paste()
df_channel.close()
imp.close()
# Setting the active slice back to 1 seems to fix an issue where
# the last slice was empty in the saved TIFFs. Not sure why.
ff_imp.setSlice(1)
df_imp.setSlice(1)
ff_filename = '%s/%s-ffp-basic.tif' % (output_dir, experiment_name)
IJ.saveAsTiff(ff_imp, ff_filename)
ff_imp.show()
ff_imp.close()
df_filename = '%s/%s-dfp-basic.tif' % (output_dir, experiment_name)
IJ.saveAsTiff(df_imp, df_filename)
df_imp.show()
df_imp.close()
print "Done!"
# Performs scaling
if (gd.wasOKed()):
anchorTiles = range(startTile,finishTile+1,stepSize)
print anchorTiles
for i in anchorTiles:
if (i+stepSize-1 > finishTile):
lastAnchorTile = finishTile
else:
lastAnchorTile = i+stepSize-1
iterTiles = range(i,lastAnchorTile+1)
params = "open=[" + theFilePath + "] color_mode=Default view=Hyperstack stack_order=XYCZT series_list=" + str(i) + "-" + str(lastAnchorTile)
print params
IJ.run("Bio-Formats Importer", params)
imageIDList = WindowManager.getIDList()
if (len(imageIDList) == len(iterTiles)):
count = 0
for j in imageIDList:
theImage = WindowManager.getImage(j)
print theImage.getTitle()
params2 = "x=" + str(ratio) + " y=" + str(ratio) + " z=1.0 interpolation=Bilinear average create title=doggie"
IJ.run(theImage,"Scale...",params2)
theImage.close()
saveImage = WindowManager.getImage("doggie")
IJ.saveAsTiff(saveImage,theDirectory+baseName+"_resized/tile_"+str(iterTiles[count])+".tif")
saveImage.close()
count = count + 1
else:
print "Open image count does not match tile count!"
"std_dev_distance_to_surface median_distance_to_surface centre_of_mass " +
"bounding_box dots_size=5 font_size=10 " +
"redirect_to=none")
IJ.run("3D OC Options", params)
params = ("threshold=" + str(intThreshold) +
" slice=1 min.=" + str(sizeThreshold) + " max.=24903680 objects surfaces statistics")
IJ.redirectErrorMessages(True)
IJ.run(dataImage, "3D Objects Counter", params)
dataImage.changes = False
dataImage.close()
## Saves the results table, surfaces image output, and run configuration
surfacesImage = WindowManager.getImage("Surface map of " + dataImage.getTitle())
IJ.run(surfacesImage,"8-bit","")
surfacesImage = make_image_binary(surfacesImage)
IJ.saveAsTiff(surfacesImage,parentLSMFilePath + "_tiles/surfaces/C" + str(analysisChannel) + "-tile_" + str(tile) + ".tif")
surfacesImage.close()
objectsImage = WindowManager.getImage("Objects map of " + dataImage.getTitle())
IJ.run(objectsImage,"8-bit","")
objectsImage = make_image_binary(objectsImage)
IJ.saveAsTiff(objectsImage,parentLSMFilePath + "_tiles/maps/C" + str(analysisChannel) + "-tile_" + str(tile) + ".tif")
objectsImage.close()
IJ.selectWindow("Results")
IJ.saveAs("Results",parentLSMFilePath + "_tiles/objects/C" + str(analysisChannel) + "-tile_" + str(tile) + ".csv")
configData = ("Parent LSM file: " + parentLSMFilePath + "\n" +
"Analysis channel: " + str(analysisChannel) + "\n" +
"Bleeding channel: " + str(bleedingChannel) + "\n" +
"Refractive correction reference channel: " + str(refChannel) + "\n" +
"Intensity threshold (0-255): " + str(intThreshold) + "\n" +
"Size threshold (voxels): " + str(sizeThreshold) + "\n" +
for channel in range(1, (number_of_channels_in_mouse + 1)):
channel_files = getChannelFiles(MouseIDFiles, channel)
# get the full path
chf_fpaths = [path.join(In_dir, x) for x in channel_files]
# get the minimum and maximum pixel value
min_pixval, max_pixval = get_enhance_bounds(
chf_fpaths, low_theshold, high_threshold)
IJ.log("Found pixel bounds " + str(min_pixval) + " and " +
str(max_pixval) + " for channel " + str(channel))
counter = 1
for chfile in chf_fpaths:
# open file
ch_img = Opener().openImage(chfile)
ch_tit = ch_img.getTitle()
# adjust contrast
ch_img.getProcessor().setMinAndMax(min_pixval, max_pixval)
# convert to 8-bit (which also applies the contrast)
ImageConverter(ch_img).convertToGray8()
# save
IJ.saveAsTiff(ch_img, path.join(Out_dir, ch_tit))
# close and flush
ch_img.close()
ch_img.flush()
print("Image " + str(counter) + " of " + str(len(chf_fpaths)) +
" processed")
counter += 1
IJ.log('Mouse ' + MouseID + ' processed')
print("DONE, find your results in " + Out_dir)