def concatenateImagePlus(files, outfile):
"""Concatenate images contained in files and save in outfile"""
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
options.setOpenAllSeries(1)
options.setQuiet(1)
images = BF.openImagePlus(options)
imageG = images[0]
nrPositions = len(images)
options.setOpenAllSeries(0)
nslices = imageG.getNSlices()
nframes = len(files)
nchannels = imageG.getNChannels()
luts = imageG.getLuts()
for i in range(0, nrPositions):
concatImgPlus = IJ.createHyperStack(
"ConcatFile", imageG.getWidth(), imageG.getHeight(),
imageG.getNChannels(), imageG.getNSlices(),
len(files), imageG.getBitDepth())
concatStack = ImageStack(imageG.getWidth(), imageG.getHeight())
IJ.showStatus("Concatenating files")
for file_ in files:
try:
print '...', basename(file_)
options.setSeriesOn(i, 1)
options.setId(file_)
image = BF.openImagePlus(options)[0]
imageStack = image.getImageStack()
sliceNr = imageStack.getSize()
for j in range(1, sliceNr+1):
concatStack.addSlice(imageStack.getProcessor(j))
image.close()
options.setSeriesOn(i, 0)
except Exception, e:
IJ.log("ERROR")
IJ.log(file_ + str(e))
raise
IJ.showProgress(files.index(file_), len(files))
concatImgPlus.setStack(concatStack, nchannels, nslices, nframes)
concatImgPlus.setCalibration(image.getCalibration())
concatImgPlus.setOpenAsHyperStack(True)
concatImgPlus.setLuts(luts)
concatImgPlus.close()
IJ.saveAs(concatImgPlus, "Tiff", outfile)
def readCZIattachment(imagefile,
stitchtiles=False,
setflatres=False,
readpylevel=0,
setconcat=False,
openallseries=False,
showomexml=False,
attach=False,
autoscale=True):
# define the reader options
reader_options, czireader = ImportTools.setReaderOptions(imagefile, stitchtiles=stitchtiles,
setflatres=setflatres,
setconcat=setconcat,
openallseries=openallseries,
showomexml=showomexml,
attach=attach,
autoscale=autoscale)
# open the ImgPlus
imps_attach = BF.openImagePlus(reader_options)
# read image data using the specified pyramid level
imp_attach, slices, width, height, pylevel = ImageTools.getImageSeries(imps_attach, series=readpylevel)
czireader.close()
return imp_attach
def openjpg(imagefile, metainfo, method='IJ',
series=0):
if method == 'IJ':
# using IJ static method
imp = IJ.openImage(imagefile)
if method == 'Opener':
# Using Opener class
imp = Opener().openImage(imagefile)
if method == 'BF':
# using BioFormats library
imps = BF.openImagePlus(imagefile)
# read image data using the specified pyramid level
imp, slices, width, height, pylevel = ImageTools.getImageSeries(imps, series=series)
metainfo['Output Slices'] = slices
metainfo['Output SizeX'] = width
metainfo['Output SizeY'] = height
return imp, metainfo
def findclearcell(inDir, currentDir, fileName):
print "Opening", fileName
file_path= os.path.join(currentDir, fileName)
options = ImporterOptions()
options.setId(file_path)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
if not imps:
return
IJ.selectWindow(fileName + " - C=2")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=1")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=0")
IJ.run("Close")
IJ.selectWindow(fileName + " - C=3")
IJ.run("8-bit")
IJ.run("Options...", "iterations=1 count=1 black edm=8-bit")
IJ.setThreshold(62, 255)
IJ.run("Convert to Mask", "method=Default backgorund=Dark black")
Macro.setOptions("Stack position")
for n in range(4,15):
n+=1
IJ.setSlice(n)
IJ.run(imp, "Analyze Particles...", "size=7.2-9 circularity=0.7-0.95 display")
def open_from_lif_series(fpath, i): options = ImporterOptions() options.setId(fpath) options.clearSeries() options.setSeriesOn(i, True) imps = BF.openImagePlus(options) return imps[0]
def showimage(self):
roim = RoiManager.getInstance()
if roim is None:
roim = RoiManager()
IJ.run("Close All")
IJ.run("Clear Results")
try:
roim.reset()
except AttributeError:
roim.runCommand("reset")
obj = self.fcsimages[self.idximg][0]
imgName = self.fcsimages[self.idximg][1]
img = BF.openImagePlus(imgName)[0]
img.setZ(obj[1][2]+1)
img.setC(3)
IJ.run(img, "Grays", "");
img.setC(1)
img.show()
#draw rois
for i in range(1, len(obj)+1):
PR = PointRoi(obj[i][0],obj[i][1])
try:
PR.setSize(3)
PR.setPointType(0)
roim.addRoi(PR)
except:
roim.addRoi(PR)
roim.runCommand('Show All with Labels')
def main(argv):
"""Segment mitochondria."""
datadir = '/Users/michielk/M3S1GNUds7'
filename = 'M3S1GNUds7_tiff.tif'
filepath = os.path.join(datadir, filename)
imp = BF.openImagePlus(filepath)
def readSingleChannelImg(imgFile): options = ImporterOptions() options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE) options.setId(imgFile) imps = BF.openImagePlus(options) ip = imps[0] return(ip)
def createOutputData( jobs ):
""" Reads out the meta data.
"""
failedImages = []
nJobs = len( jobs )
for n, j in enumerate( jobs ):
print( "Job " + str(n+1) + "/" + str( nJobs ) )
# load every image
metadata = []
nImages = len( j.sourceImages )
nChannels = -1
for m, img in enumerate( j.sourceImages ):
print( "\tReading image " + str(m+1) + "/" + str( nImages ) )
imgPath = os.path.join( j.sourcePath, img )
options = ImporterOptions()
options.setId( imgPath )
options.setSplitChannels( False )
options.setWindowless( True )
options.setVirtual( True )
imps = BF.openImagePlus( options )
if len(imps) == 0:
failedImages.append( imgPath )
print("t\tCould not load image: " + imgPath)
continue
# get the meta data
data = imps[0]
if nChannels == -1:
nChannels = data.getNChannels()
imgInfo = Info();
info = imgInfo.getImageInfo( data, data.getChannelProcessor() )
metadata.append( imgPath )
metadata.append( info )
j.outputData = '\n\n>>> next source file >>>\n\n'.join( metadata )
j.numChannels = nChannels
def concatenateImagePlus(files, outfile):
"""concatenate images contained in files and save in outfile"""
'''
if len(files) == 1:
IJ.log(files[0] + " has only one time point! Nothing to concatenate!")
return
'''
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
options.setOpenAllSeries(1)
options.setQuiet(1)
images = BF.openImagePlus(options)
imageG = images[0]
nrPositions = len(images)
options.setOpenAllSeries(0)
for i in range(0, nrPositions):
concatImgPlus = IJ.createHyperStack("ConcatFile", imageG.getWidth(), imageG.getHeight(), imageG.getNChannels(), imageG.getNSlices(), len(files), imageG.getBitDepth())
concatStack = ImageStack(imageG.getWidth(), imageG.getHeight())
IJ.showStatus("Concatenating files")
for file in files:
try:
IJ.log(" Add file " + file)
options.setSeriesOn(i,1)
options.setId(file)
image = BF.openImagePlus(options)[0]
imageStack = image.getImageStack()
sliceNr = imageStack.getSize()
for j in range(1, sliceNr+1):
concatStack.addSlice(imageStack.getProcessor(j))
image.close()
options.setSeriesOn(i,0)
except:
traceback.print_exc()
IJ.log(file + " failed to concatenate!")
IJ.showProgress(files.index(file), len(files))
concatImgPlus.setStack(concatStack)
concatImgPlus.setCalibration(image.getCalibration())
if len(images) > 1:
outfileP = addPositionName(i+1,outfile)
IJ.saveAs(concatImgPlus, "Tiff", outfileP)
else:
IJ.saveAs(concatImgPlus, "Tiff", outfile)
concatImgPlus.close()
def getImps(fpath): opt = IO() opt.setId(fpath) opt.setOpenAllSeries(True) impA = BF.openImagePlus(opt) print "Series number: " + str(len(impA)) #impA = BF.openImagePlus() return impA
def set_options(image, series = None):
"""
creates ImporterOptions object and sets options
returns the imps object
"""
if series is not None:
options = ImporterOptions()
options.setId(image)
options.setSeriesOn(s,True)
imps = BF.openImagePlus(options)
return imps
else:
print("no series found")
options = ImporterOptions()
options.setId(image)
imps = BF.openImagePlus(options)
return imps
def get_reader(file, inputMeta): options = ImporterOptions() options.setId(file) imps = BF.openImagePlus(options) reader = ImageReader() reader.setMetadataStore(inputMeta) reader.setId(file) return reader
def run_headless(filename, channel, target_folder = None, frames = None):
importOpt = ImporterOptions()
importOpt.setId(filename)
importOpt.setVirtual(1)
try:
imp = BF.openImagePlus(importOpt)[0]
except IOError, err:
IJ.showMessage("Not able to open " + filename + " " +str(err))
def get_image(input_file):
imp = BF.openImagePlus(input_file)[0]
# Reorder stack to swap Z and T if needed
nframes = imp.getDimensions()[4]
nslices = imp.getDimensions()[3]
if nframes == 1:
IJ.run("Re-order Hyperstack ...", "channels=[Channels (c)] slices=[Frames (t)] frames=[Slices (z)]");
return imp
def open_image(imgfile):
options = ImporterOptions()
options.setId(imgfile)
options.setSplitChannels(False)
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
imps = BF.openImagePlus(options)
splitimps = [ImagePlus("%s-C-%i" % (imps[0].getTitle(), i),imps[0].getStack().getProcessor(i)) for i in range(1,imps[0].getNChannels()+1)]
for si in splitimps:
si.setCalibration(imps[0].getCalibration().copy())
return imps[0], splitimps
def extractChannel(oirFile, ch): options = ImporterOptions() options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE) options.setId(oirFile) options.setCBegin(0, ch) options.setCEnd(0, ch) #options.setSeriesOn(1,True) imps = BF.openImagePlus(options) ip = imps[0] return(ip)
def openCroppedImageUsingBF(filepath,x,y,xw,yw,zs,ze, crop):
# read in and display ImagePlus(es) with arguments
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
if crop:
options.setCrop(True)
options.setCropRegion(0, Region(x,y,xw,yw))
options.setTBegin(0, zs)
options.setTEnd(0, ze)
options.setId(filepath)
imps = BF.openImagePlus(options)
return imps[0]
def open_msr(input_file):
options = ImporterOptions()
options.setId(input_file)
#options.clearSeries()
for s in [3,4,5]:
options.setSeriesOn(s, True)
imps = BF.openImagePlus(options)
imp1 = imps[1]
imp2 = imps[0]
imp3 = imps[2]
return imp1, imp2, imp3
def run(imagefile, useBF=True,
series=0,
filtertype='MEDIAN',
filterradius='5'):
#log.log(LogLevel.INFO, 'Image Filename : ' + imagefile)
log.info('Image Filename : ' + imagefile)
# get basic image metainfo
metainfo = get_metadata(imagefile, imageID=series)
for k, v in metainfo.items():
#log.log(LogLevel.INFO, str(k) + ' : ' + str(v))
log.info(str(k) + ' : ' + str(v))
if not useBF:
# using IJ static method
imp = IJ.openImage(imagefile)
if useBF:
# initialize the importer options for BioFormats
options = ImporterOptions()
options.setOpenAllSeries(True)
options.setShowOMEXML(False)
options.setConcatenate(True)
options.setAutoscale(True)
options.setId(imagefile)
options.setStitchTiles(True)
# open the ImgPlus
imps = BF.openImagePlus(options)
imp = imps[series]
# apply the filter
if filtertype != 'NONE':
# apply filter
#log.log(LogLevel.INFO, 'Apply Filter : ' + filtertype)
#log.log(LogLevel.INFO, 'Filter Radius : ' + str(filterradius))
log.info('Apply Filter : ' + filtertype)
log.info('Filter Radius : ' + str(filterradius))
# apply the filter based on the chosen type
imp = apply_filter(imp,
radius=filterradius,
filtertype=filtertype)
if filtertype == 'NONE':
#log.log(LogLevel.INFO, 'No filter selected. Do nothing.')
log.info('No filter selected. Do nothing.')
return imp
def open_czi(filepath,series):
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
from loci.common import Region
options = ImporterOptions()
options.setId( filepath )
options.setSeriesOn(series-1,True)
imp = BF.openImagePlus(options)[0]
cal=imp.getCalibration()
cal.pixelWidth = cal.pixelWidth*2 **(series)
cal.pixelHeight = cal.pixelHeight*2**(series)
return imp
def imageloader(path, debug=False):
'''
Wrapper to deal with opening bioformat images properly in macros
Returns an ImagePlus if successful and exception if not.
Read ij.ImagePlus and loci.plugins.BF.openImagePlus for details.
'''
from ij import ImagePlus
from loci.plugins import BF
ext = os.path.splitext(path)[1]
if ext in BIOFORMATS:
return BF.openImagePlus(path)[0]
else:
return ImagePlus(path)
def main():
files = []
for filt in img_extensions.split(";"):
if len(filt.strip()) > 0:
files += glob.glob(os.path.join(str(input_dir), filt.strip()))
else:
files += glob.glob(os.path.join(str(input_dir), "*.*"))
break
if len(files) == 0:
IJ.showMessage("No files found in '{}'\nfor extensions '{}'".format(
str(input_dir), img_extensions))
else:
for fn in files:
try:
imp = BF.openImagePlus(fn)[0]
except:
IJ.showMessage(
"Could not open file '{}' (skipping).\nUse extension filter to filter non-image files..."
.format(str(fn)))
continue
img = IJF.wrap(imp)
cali = imp.getCalibration().copy()
if pixel_width > 0:
cali.pixelWidth = pixel_width
cali.pixelHeight = pixel_width
cali.setUnit("micron")
if frame_interval > 0:
cali.frameInterval = frame_interval
cali.setTimeUnit("sec.")
imp_out = smooth_temporal_gradient(ops, img, sigma_xy, sigma_t,
frame_start, frame_end,
normalize_output)
imp_out.setCalibration(cali)
channels = ChannelSplitter.split(imp_out)
fn_basename = os.path.splitext(fn)[0]
IJ.save(channels[0], "{}_shrinkage.tiff".format(fn_basename))
IJ.save(channels[1], "{}_growth.tiff".format(fn_basename))
print("{} processed".format(fn_basename))
IJ.showMessage(
"Growth/shrinkage extraction of {} inputs finsihed.".format(
len(files)))
def openImage(self, imageFile):
try:
images = BF.openImagePlus(imageFile)
self.imp = images[0]
except UnknownFormatException:
return None
if self.imp.getNChannels() < 2:
IJ.error("Bad image format", "Image must contain at lease 2 channels!")
return None
if not self.pairs or \
not self.methods:
self.getOptionsDialog(self.imp)
title = self.imp.title
self.imp.title = title[:title.rfind('.')]
return self.imp
def main(argv):
"""Convert .dm3 files to tifs."""
inputdir = 'INPUTDIR'
outputdir = 'OUTPUTDIR'
output_postfix = 'OUTPUT_POSTFIX'
infiles = glob.glob(os.path.join(inputdir, '*.dm3'))
for infile in infiles:
imp = BF.openImagePlus(infile)
tail = os.path.split(infile)[1]
filename = os.path.splitext(tail)[0][-4:] + output_postfix + '.tif'
outpath = os.path.join(outputdir, filename)
IJ.save(imp[0], outpath)
def open_msr(input_file):
IJ.log("Reading images from {}".format(input_file))
options = ImporterOptions()
options.setId(input_file)
#options.clearSeries()
for s in [2,3,4,5]:
options.setSeriesOn(s, True)
imps = BF.openImagePlus(options)
if len(imps) == 4:
imp1 = imps[2]
imp2 = imps[1]
imp3 = imps[3]
elif len(imps) == 2:
IJ.log(" -- Only two channels found. Replicating first as third.")
imp1 = imps[1]
imp2 = imps[0]
imp3 = imps[0]
else:
raise RuntimeError("unknown channels")
widths = set([imp1.width, imp2.width, imp3.width])
heights = set([imp1.height, imp2.height, imp3.height])
if len(widths) > 1 or len(heights) > 1:
new_width = max(widths)
new_height = max(heights)
IJ.log(" -- Resolution of images does not match. Resampling to highest resolution: {} x {}".format(new_width, new_height))
cal = imp1.getCalibration()
imp1 = imp1.resize(new_width, new_height, "bilinear")
imp2 = imp2.resize(new_width, new_height, "bilinear")
imp3 = imp3.resize(new_width, new_height, "bilinear")
imp1.setCalibration(cal)
imp2.setCalibration(cal)
imp3.setCalibration(cal)
return imp1, imp2, imp3
def setUp(self):
self.t = set_up_params(output_path_dir, test=False)
self.cp = cab.cp
self.change_ini()
self.d, self.s = self.t.startScript()
#self.cp.update("ChannelOptions", {"c1opt_boollist": "[False, False, False, True]"})
#self.cp.readIni()
from ij import IJ
from loci.plugins import BF
for i, f in enumerate(self.d.filenames):
imp = BF.openImagePlus(f)[0]
# imp.show()
cab.headless = True
self.imp = cab.Image(f, self.d, self.s, False)
self.db = cab.db_interface(inipath, self.imp)
def load_ome_img(file_name):
"""
:param file_name:
:return:
"""
imps = BF.openImagePlus(file_name)
imag = imps[0]
# parse metadata
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(file_name)
print(omeMeta)
reader.close()
return (imag, omeMeta)
def open_czi_series(file_name, series_number, rect=False):
# see https://downloads.openmicroscopy.org/bio-formats/5.5.1/api/loci/plugins/in/ImporterOptions.html
options = ImporterOptions()
options.setId(file_name)
options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
# select image to open
options.setOpenAllSeries(False)
options.setAutoscale(False)
options.setSeriesOn(series_number, True)
# default is not to crop
options.setCrop(False)
if rect: # crop if asked for
options.setCrop(True)
options.setCropRegion(series_number, Region(rect[0], rect[1], rect[2], rect[3]))
imps = BF.openImagePlus(options)
return imps[0]
def openImageFile(folder, imageFile):
folder = folder.decode('utf8')
imageFile = imageFile.decode('utf8')
imagePath = str(folder)+"/"+str(imageFile)
reader, options = readImageFile(imagePath)
seriesCount = reader.getSeriesCount() #Nombre de séries
zDepthByChannel = reader.getSizeZ() #Profondeur Z
#imageStackImps = BF.openImagePlus(options)
seriesOfImageFile = []
for numberSerie in range(seriesCount):
options.setSeriesOn(numberSerie,True); #Pour LIF - compter les séries - https://gist.github.com/ctrueden/6282856
imageStackImps = BF.openImagePlus(options);
#print imageStackImps
mainImageStackImp = imageStackImps[-1] #0
mainImageStackImp.setTitle(str(imageFile)+"_"+str(numberSerie))
seriesOfImageFile.append(mainImageStackImp)
#return mainImageStackImp
return seriesOfImageFile
def get_image(info, default_path, used_files):
"""handle getting image from file"""
check_for_file_overlap_OK = False;
while not check_for_file_overlap_OK:
info.set_input_file_path(file_location_chooser(default_path));
if info.get_input_file_path() in used_files:
dlg = GenericDialog("Image already used...");
dlg.addMessage("This image has already been used in this analysis run. \n " +
"Continue with this image, or choose a new one?");
dlg.setOKLabel("Continue");
dlg.setCancelLabel("Choose again...");
dlg.showDialog();
check_for_file_overlap_OK = False if dlg.wasCanceled() else True;
else:
check_for_file_overlap_OK = True;
import_opts, info = choose_series(info.get_input_file_path(), info)
imps = bf.openImagePlus(import_opts);
imp = imps[0];
try:
memory_usage = IJ.currentMemory()/IJ.maxMemory();
print("memory usage = " +str(memory_usage));
# arbitrary limit...
if memory_usage > 0.95:
IJ.run(imp, "8-bit", "");
print("WARNING - IMAGE CONVERTED TO 8 BIT TO CONSERVE MEMORY!");
info.set_metadata_file_path(os.path.splitext(info.get_input_file_path())[0] + ".txt");
metadata = import_iq3_metadata(info.get_metadata_file_path());
IJ.run(imp, "Properties...", "channels=" + str(int(metadata['n_channels'])) +
" slices=" + str(int(metadata['z_pixels'])) +
" frames=1 unit=" + str(metadata['x_unit']) +
" pixel_width=" + str(metadata['x_physical_size']) +
" pixel_height=" + str(metadata['y_physical_size']) +
" voxel_depth=" + str(metadata['z_extent']/metadata['z_pixels']));
info.set_xy_pixel_size_um(metadata['x_physical_size']);
info.set_z_plane_spacing_um(metadata['z_extent']/metadata['z_pixels']);
info = parse_info_from_filename(info);
except e as Exception:
print(e.message);
finally:
if imp is not None:
imp.close();
return imp, info;
def split_image(file_):
print "Processing: %s" %(basename(file_))
#load with loci (allows also to load *.czi)
images = BF.openImagePlus(file_)
image = images[0]
#split channels
chSp = ChannelSplitter()
title = splitext(image.title)[0]
imageC = chSp.split(image)
print "Number of channels: ", len(imageC)
for iCh in range(0, len(imageC)):
imageStack = imageC[iCh].getImageStack()
for iSlice in range(0,imageC[0].getNSlices()):
#print iSlice
impOut = ImagePlus("outImg", imageStack.getProcessor(iSlice+1))
ntitle = to_wellbased_nameing_scheme(title, iCh+1, iSlice+1)
IJ.log("Image: %s -> %s " %(title, ntitle))
IJ.saveAs(impOut, "Tiff", join(outdir, ntitle) )
def main(input_dir, file_contains, params):
file_list = glob.glob(os.path.join(str(input_dir), "*.{}".format(file_ext)))
file_contains = file_contains.strip()
if len(file_contains) > 0:
file_list = filter(lambda x: file_contains in os.path.basename(x), file_list)
if len(file_list) == 0:
IJ.showMessage("No files found to process.")
return
for input_file in file_list:
imp = BF.openImagePlus(input_file)[0]
path = os.path.dirname(input_file)
file_name = os.path.basename(input_file)
run_trackmate(imp, path, file_name, params, batch_mode=True)
IJ.showMessage("Processing of {} input files done.".format(len(file_list)))
def process(srcDir, dstDir, nameContains, currentDir, fileName, keepDirectories, anneBoleyn, overOut):
print "Opening", fileName
saveDir = currentDir.replace(srcDir, dstDir) if keepDirectories else dstDir
head, tail = os.path.splitext(fileName)
imps = BF.openImagePlus(os.path.join(currentDir, fileName))
for imp in imps:
if not anneBoleyn:
print "Now showing image..."
imp.show()
IJ.run(imp, "Blue", "")
fs = FileSaver(imp)
if not os.path.exists(saveDir):
os.makedirs(saveDir)
if not overOut:
if os.path.exists(saveDir + "\\" + head + ".jpg"):
print "This JPG exists already and will not be overwritten. Moving on..."
else:
print "Saving to", os.path.join(saveDir, head + ".jpg")
fs.saveAsJpeg(os.path.join(saveDir, head + ".jpg"))
imp.close()
def loadResultsFile(resfile):
my_file = open(resfile, 'r')
my_file.seek(0)
for line in my_file:
tabLine = line.split('\t')
if tabLine[0].isdigit():
#first pt
if re.search( 'R\d_P(\d)_K\d_Ch\d-Ch\d.zen', tabLine[1]).group(1) == '1':
filename = re.split('_R\d_P(\d)_K\d_Ch\d-Ch\d.zen', os.path.basename(tabLine[2]))[0] + '.xml'
dirName = os.path.dirname(tabLine[2])
dirName = dirName.replace("Z:", "X:")
filename = os.path.join(dirName,filename)
obj, imgName = getPosition(filename)
img = BF.openImagePlus(imgName)[0]
img.show()
#while (line = my_file.readline()):
# print "aline"
print "finished"
my_file.close()
def import_image(filename,
color_mode='color',
split_c=False, split_z=False, split_t=False):
"""Open an image file using the Bio-Formats importer.
Parameters
----------
filename : str
The full path to the file to be imported through Bio-Formats.
color_mode : str, optional
The color mode to be used for the resulting ImagePlus, one of 'color',
'composite', 'gray' and 'default'.
split_c : bool, optional
Whether to split the channels into separate ImagePlus objects.
split_z : bool, optional
Whether to split the z-slices into separate ImagePlus objects.
split_t : bool, optional
Whether to split the time points into separate ImagePlus objects.
Returns
-------
ij.ImagePlus[]
A list of ImagePlus objects resulting from the import.
"""
options = ImporterOptions()
mode = {
'color' : ImporterOptions.COLOR_MODE_COLORIZED,
'composite' : ImporterOptions.COLOR_MODE_COMPOSITE,
'gray' : ImporterOptions.COLOR_MODE_GRAYSCALE,
'default' : ImporterOptions.COLOR_MODE_DEFAULT,
}
options.setColorMode(mode[color_mode])
options.setSplitChannels(split_c)
options.setSplitFocalPlanes(split_z)
options.setSplitTimepoints(split_t)
options.setId(filename)
log.info("Reading [%s]", filename)
orig_imps = BF.openImagePlus(options)
log.debug("Opened [%s] %s", filename, type(orig_imps))
return orig_imps
def readbf(imagefile, metainfo,
setflatres=False,
readpylevel=0,
setconcat=False,
openallseries=True,
showomexml=False,
autoscale=True,
stitchtiles=True):
# initialize the importer options
options = ImporterOptions()
options.setOpenAllSeries(openallseries)
options.setShowOMEXML(showomexml)
options.setConcatenate(setconcat)
options.setAutoscale(autoscale)
options.setId(imagefile)
options.setStitchTiles(stitchtiles)
# in case of concat=True all series set number of series = 1
# and set pyramidlevel = 0 (1st level) since there will be only one
# unless setflatres = True --> read pyramid levels
series = metainfo['SeriesCount_BF']
if setconcat and setflatres:
series = 1
readpylevel = 0
metainfo['Pyramid Level Output'] = readpylevel
# open the ImgPlus
imps = BF.openImagePlus(options)
# read image data using the specified pyramid level
imp, slices, width, height, pylevel = ImageTools.getImageSeries(imps, series=readpylevel)
metainfo['Output Slices'] = slices
metainfo['Output SizeX'] = width
metainfo['Output SizeY'] = height
return imp, metainfo
def main():
root = myDir.getPath() # get the root out the java file object
print(root)
import os, glob
# set up bioformats
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
options.setGroupFiles(True) # if the files are named logically if will group them into a stack
# this will do the maximum intensity projection
from ij.plugin import ZProjector
Zproj = ZProjector()
for path, subdirs, files in os.walk(root):
print(path)
# just get the one of the files that matches your image pattern
flist = glob.glob(os.path.join(path,"*.tif"))
print(len(flist))
if( flist ):
file = flist[0]
print("Processing {}".format(file))
options.setId(file)
imp = BF.openImagePlus(options)[0]
# show the image if you want to see it
IJ.run(imp, "Grays", "")
imp.show()
imp_max = Zproj.run(imp,'max')
IJ.run(imp_max, "Grays", "")
imp_max.show()
# save the Z projection
IJ.save(imp_max,file.rsplit('_',1)[0]+'_processed.tif')
def run(imagefile, useBF=True, series=0):
log.info('Image Filename : ' + imagefile)
if not useBF:
# using IJ static method
imp = IJ.openImage(imagefile)
if useBF:
# initialize the importer options
options = ImporterOptions()
options.setOpenAllSeries(True)
options.setShowOMEXML(False)
options.setConcatenate(True)
options.setAutoscale(True)
options.setId(imagefile)
# open the ImgPlus
imps = BF.openImagePlus(options)
imp = imps[series]
# apply the filter
if FILTERTYPE != 'NONE':
# apply filter
log.info('Apply Filter : ' + FILTERTYPE)
log.info('Filter Radius : ' + str(FILTER_RADIUS))
# apply the filter based on the choosen type
imp = apply_filter(imp,
radius=FILTER_RADIUS,
filtertype=FILTERTYPE)
if FILTERTYPE == 'NONE':
log.info('No filter selected. Do nothing.')
return imp
import os, sys
from ij import IJ
from ij.io import FileSaver
from loci.plugins import BF
from subprocess import call
from ij.plugin import ZProjector
try:
filepath = getArgument()
except Exception, e:
sys.exit(" no file " + e)
try:
imp = BF.openImagePlus(filepath)
image = imp[0]
zProj = ZProjector(image)
zProj.setMethod(zProj.MAX_METHOD)
zProj.doProjection()
imgMax = zProj.getProjection()
#imgMax.show()
FileSaver(imgMax).saveAsTiff(os.path.splitext(filepath)[0] + "_MAX.tif")
except Exception, e:
sys.exit(e)
except Exception, e:
sys.exit(e)
arg = re.split('\s+-c', arg)
if len(arg)>1:
xmlfile = arg[0]
ch = int(arg[1])
else:
xmlfile = arg[0]
ch = 1
#open xml file and parse it
tree = ET.parse(xmlfile)
root = tree.getroot()
obj, imgName = getPosition(root)
print imgName
#open image
img = BF.openImagePlus(imgName)[0]
img.setZ(obj[1][2]+1)
img.setC(int(ch))
img.show()
#draw rois
for i in range(1, len(obj)+1):
PR = PointRoi(obj[i][0],obj[i][1])
try:
PR.setSize(3)
PR.setPointType(0)
roim.addRoi(PR)
except:
roim.addRoi(PR)
from ij import IJ as ij
from ij.plugin.frame import RoiManager
from ij.gui import Roi, PolygonRoi
from loci.plugins import BF
from loci.common import Region
from loci.plugins.in import ImporterOptions
from loci.formats import ImageReader, ImageWriter
from loci.formats import MetadataTools
from ome.xml.meta import OMEXMLMetadata
file = "%s"
options = ImporterOptions()
options.setId(file)
imps = BF.openImagePlus(options)
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(file)
roiCount = omeMeta.getROICount()
if roiCount > 1:
sys.exit(0)
omeMetaStr = omeMeta.dumpXML()
shape = omeMeta.getShapeType(0,0)
if 'Polygon' not in shape:
for ch in range(1, channels + 1):
projector = ZProjector(ImagePlus("C%i" % ch, splitter.getChannel(image, ch)))
projector.setMethod(ZProjector.MAX_METHOD)
projector.doProjection()
proj = projector.getProjection()
enhancer.equalize(proj)
chimps.append(proj)
return RGBStackMerge.mergeChannels(chimps, False)
manders = MandersColocalization()
results = ResultsTable()
for imageFile in os.listdir(inputDir):
print "Opening " + imageFile
try:
images = BF.openImagePlus(inputDir + imageFile)
image = images[0]
except UnknownFormatException:
continue
preview = getPreview(image)
preview.show()
rm = RoiManager()
dialog = WaitForUserDialog("Action required", "Please select regions of interest in this image. Click OK when done.")
dialog.show()
rm.close()
splitter = ChannelSplitter()
imp1 = ImagePlus("CH1", splitter.getChannel(image, imageA))
imp2 = ImagePlus("CH2", splitter.getChannel(image, imageB))
title = image.getTitle()
title = title[:title.rfind('.')]
image.close()
else:
pixels = False
if flat and pixels:
print("Both --flat and --pixels cannot be specified simultaneously.")
sys.exit(1)
print referenceFile
print objectListFile
print outputFile
# Open source image
try:
image = IJ.openImage(referenceFile)
except Exception:
images = BF.openImagePlus(referenceFile)
image = images[0]
calibration = image.getCalibration()
zscale = calibration.getZ(1) / calibration.getX(1)
channels = image.getNChannels()
# Read objects
objects = csv.reader(open(objectListFile))
fmin = []
fmax = []
thrF = 50.000
sx = image.getWidth()
sy = image.getHeight()
sz = image.getNSlices()
options['edgeXY'] = True if args.exclude_edge_z: if str(args.exclude_edge_z).upper() == "TRUE": options['edgeZ'] = False else: options['edgeZ'] = True else: options['inputFile'] = "sample.tif" options['outputDir'] = "./" if options['paramsOut'] == None: results = [] try: image = IJ.openImage(options['inputFile']) except Exception: images = BF.openImagePlus(options['inputFile']) image = images[0] if options['oneShot']: results.append(runSimulation(options, image)) else: parameters = makeParameters(options) for index in range(0, len(parameters)): options.update(parameters[index]) results.append(runSimulation(options, image)) resultsTable = ResultsTable() resultsTable.showRowNumbers(False) for i in range(0, len(results)): if options['oneShot']:
def processMovie(root, files, outfile):
"""Concatenate images and write ome.tiff file.
If image contains already multiple time points just copy the image"""
files.sort()
options = ImporterOptions()
options.setId(files[0])
options.setVirtual(1)
image = BF.openImagePlus(options)
image = image[0]
if image.getNFrames() > 1:
msg = ("%s Contains multiple time points. Can only concatenate"
" single time points!" %files[0])
raise RuntimeError(msg)
image.close()
reader = ImageReader()
reader.setMetadataStore(MetadataTools.createOMEXMLMetadata())
reader.setId(files[0])
timeInfo = []
omeOut = reader.getMetadataStore()
omeOut = setUpXml(omeOut, image, files)
reader.close()
image.close()
itime = 0
for fileName in files:
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(fileName)
timeInfo.append(getTimePoint(reader, omeMeta))
nrImages = reader.getImageCount()
for i in range(0, reader.getImageCount()):
try:
dT = round(timeInfo[files.index(fileName)]-timeInfo[0],2)
except:
dT = (timeInfo[files.index(fileName)]-timeInfo[0]).seconds
omeOut.setPlaneDeltaT(dT, 0, i + itime*nrImages)
omeOut.setPlanePositionX(omeOut.getPlanePositionX(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionY(omeOut.getPlanePositionY(0,i), 0, i + itime*nrImages)
omeOut.setPlanePositionZ(omeOut.getPlanePositionZ(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheC(omeOut.getPlaneTheC(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheT(omeOut.getPlaneTheT(0,i), 0, i + itime*nrImages)
omeOut.setPlaneTheZ(omeOut.getPlaneTheZ(0,i), 0, i + itime*nrImages)
itime = itime + 1
reader.close()
IJ.showProgress(files.index(fileName), len(files))
try:
omeOut.setPixelsTimeIncrement(float(dT/(len(files)-1)), 0)
except:
omeOut.setPixelsTimeIncrement(0, 0)
if len(files) <= 1:
raise RuntimeError('Found only one file. Nothing to concatenate')
outfile = concatenateImagePlus(files, outfile)
filein = RandomAccessInputStream(outfile)
fileout = RandomAccessOutputStream(outfile)
saver = TiffSaver(fileout, outfile)
saver.overwriteComment(filein, omeOut.dumpXML())
fileout.close()
filein.close()
@String(label="Base Directory", style="") str_dir
@String(label="Image Title", style="") str_img_nam
@String(label="Image Extension", style="", value=".tif") str_img_ext
file = str_dir + "/" + str_img_nam + str_img_ext
# read in and display ImagePlus object(s)
from loci.plugins import BF
from loci.formats import ImageReader
from loci.formats import MetadataTools
from ij import IJ
from ome.units import UNITS
imps = BF.openImagePlus(file)
for imp in imps:
imp.show()
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(file)
seriesCount = reader.getSeriesCount()
reader.close()
# print out series count from two different places (they should always match!)
imageCount = omeMeta.getImageCount()
IJ.log("Total # of image series (from BF reader): " + str(seriesCount))
IJ.log("Total # of image series (from OME metadata): " + str(imageCount))
physSizeX = omeMeta.getPixelsPhysicalSizeX(0)
physSizeY = omeMeta.getPixelsPhysicalSizeY(0)
physSizeZ = omeMeta.getPixelsPhysicalSizeZ(0)
IJ.log("Physical calibration:")
if (physSizeX is not None):
IJ.log("\tX = " + str(physSizeX.value()) + " " + physSizeX.unit().getSymbol()
+ " = " + str(physSizeX.value(UNITS.MICROM)) + " microns")
# USER PARAMETERS TO CHANGE
#############################
#Diameter in microns
cellDiameter=3.0
# The minimum intensity for a peak to be considered
minPeak=0
#Use point(1), icosphere(2), or icosphere but limited to the first 3495 points in X (3)
plotType=USE_POINT
# diameter Cell visualization
cellIcosophere=3.0
#Open the image and duplicate it to get an 8 Bits version use to plot
od = OpenDialog("Open image file", None)
srcFile = od.getPath()
srcDir = od.getDirectory()
imp = BF.openImagePlus(srcFile)[0]
imp8Bits = imp.duplicate()
ImageConverter(imp8Bits).convertToGray8()
print "Image " + srcFile + " open successfully!"
#Create the coordinate.txt file to ouput the point coordinate
coordinateFile = open(srcDir + "coordinate.txt", "w")
print "Created " +srcDir + "coordinate.txt"
# If minPeak is set to 0, set it to automatically.
if minPeak == 0:
minPeak = AutoThresholder().getThreshold("Percentile", imp.getStatistics().histogram);
#Get the pixel calibration
cal=imp.getCalibration()
#Set Gaussian Sigma parameters for the Difference of Gaussian
sigmaLarge=[cellDiameter/cal.pixelWidth,cellDiameter/cal.pixelHeight,cellDiameter/cal.pixelDepth]
sigmaSmall=[a/2 for a in sigmaLarge]
def regBf(fn=None, imp=None, refId=None):
"""
Register a time series stack to a specified reference slice,
from a file (imported by BioFormat) or a stack ImagePlus.
Returns a registered ImagePlus.
The stack must have only 1 z layer.
refId is in the format of [int channel, int slice, int frame]
If no refId is supplied, will use the first slice [1,1,1]
Note: since TurboReg is used for registeration, there will be
temporary opened image windows.
"""
## Prepare the right ImagePlus
if imp is None:
if fn is None:
od = OpenDialog("Choose a file", None)
filename = od.getFileName()
if filename is None:
print "User canceled the dialog!"
return
else:
directory = od.getDirectory()
filepath = directory + filename
print "Selected file path:", filepath
else:
if os.path.exists(fn) and os.path.isfile(fn):
filepath = fn
else:
print "File does not exist!"
return
imps = BF.openImagePlus(filepath)
imp = imps[0]
if imp is None:
print "Cannot load file!"
return
else:
if fn is not None:
print "File or ImagePlus? Cannot load both."
return
width = imp.getWidth()
height = imp.getHeight()
# C
nChannels = imp.getNChannels()
# Z
nSlices = imp.getNSlices()
# T
nFrames = imp.getNFrames()
# pixel size
calibration = imp.getCalibration()
# Only supoort one z layer
if nSlices != 1:
print "Only support 1 slice at Z dimension."
return
# set registration reference slice
if refId is None:
refC = 1
refZ = 1
refT = 1
else:
refC = refId[0]
refZ = refId[1]
refT = refId[2]
if (refC not in range(1, nChannels+1) or
refZ not in range(1, nSlices+1) or
refT not in range(1, nFrames+1) ):
print "Invalid reference image!"
return
stack = imp.getImageStack()
registeredStack = ImageStack(width, height, nChannels*nFrames*nSlices)
# setup windows, these are needed by TurboReg
tmpip = FloatProcessor(width, height)
refWin = ImageWindow(ImagePlus("ref", tmpip))
bounds = refWin.getBounds()
# refWin.setVisible(False)
toRegWin = ImageWindow(ImagePlus("toReg", tmpip))
toRegWin.setLocation(bounds.width + bounds.x, bounds.y)
# toRegWin.setVisible(False)
toTransformWin = ImageWindow(ImagePlus("toTransform", tmpip))
toTransformWin.setLocation(2 * bounds.width + bounds.x, bounds.y)
# toTransformWin.setVisible(False)
# get reference image
refImp = ImagePlus("ref", stack.getProcessor(imp.getStackIndex(refC, refZ, refT)))
refWin.setImage(refImp)
tr = TurboReg_()
for t in xrange(1, nFrames+1):
IJ.showProgress(t-1, nFrames)
# print "t ", t
# do TurboReg on reference channel
toRegId = imp.getStackIndex(refC, refZ, t)
toRegImp = ImagePlus("toReg", stack.getProcessor(toRegId))
toRegWin.setImage(toRegImp)
regArg = "-align " +\
"-window " + toRegImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-window " + refImp.getTitle() + " " +\
"0 0 " + str(width - 1) + " " + str(height - 1) + " " +\
"-rigidBody " +\
str(width / 2) + " " + str(height / 2) + " " +\
str(width / 2) + " " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
"0 " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
str(width - 1) + " " + str(height / 2) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(regArg)
registeredImp = tr.getTransformedImage()
sourcePoints = tr.getSourcePoints()
targetPoints = tr.getTargetPoints()
registeredStack.setProcessor(registeredImp.getProcessor(), toRegId)
# toRegImp.flush()
# apply transformation on other channels
for c in xrange(1, nChannels+1):
# print "c ", c
if c == refC:
continue
toTransformId = imp.getStackIndex(c, 1, t)
toTransformImp = ImagePlus("toTransform", stack.getProcessor(toTransformId))
toTransformWin.setImage(toTransformImp)
transformArg = "-transform " +\
"-window " + toTransformImp.getTitle() + " " +\
str(width) + " " + str(height) + " " +\
"-rigidBody " +\
str(sourcePoints[0][0]) + " " +\
str(sourcePoints[0][1]) + " " +\
str(targetPoints[0][0]) + " " +\
str(targetPoints[0][1]) + " " +\
str(sourcePoints[1][0]) + " " +\
str(sourcePoints[1][1]) + " " +\
str(targetPoints[1][0]) + " " +\
str(targetPoints[1][1]) + " " +\
str(sourcePoints[2][0]) + " " +\
str(sourcePoints[2][1]) + " " +\
str(targetPoints[2][0]) + " " +\
str(targetPoints[2][1]) + " " +\
"-hideOutput"
tr = TurboReg_()
tr.run(transformArg)
registeredStack.setProcessor(tr.getTransformedImage().getProcessor(), toTransformId)
# toTransformImp.flush()
sourcePoints = None
targetPoints = None
IJ.showProgress(t, nFrames)
IJ.showStatus("Frames registered: " + str(t) + "/" + str(nFrames))
refWin.close()
toRegWin.close()
toTransformWin.close()
imp2 = ImagePlus("reg_"+imp.getTitle(), registeredStack)
imp2.setCalibration(imp.getCalibration().copy())
imp2.setDimensions(nChannels, nSlices, nFrames)
# print "type ", imp.getType()
# print "type ", imp2.getType()
# print nChannels, " ", nSlices, " ", nFrames
# print registeredStack.getSize()
for key in imp.getProperties().stringPropertyNames():
imp2.setProperty(key, imp.getProperty(key))
# comp = CompositeImage(imp2, CompositeImage.COLOR)
# comp.show()
# imp2 = imp.clone()
# imp2.setStack(registeredStack)
# imp2.setTitle("reg"+imp.getTitle())
# imp2.show()
# imp.show()
return imp2
from ij import IJ
from ij.io import DirectoryChooser
import os
from loci.plugins import BF
from loci.plugins.in import ImporterOptions
inputFolder = DirectoryChooser('Set input directory.').getDirectory()
outputFolder = DirectoryChooser('Set output directory.').getDirectory()
for filename in os.listdir(inputFolder):
if '.zvi' in filename:
id = inputFolder +'/'+ filename;
options = ImporterOptions();
options.setId(id);
options.setAutoscale(True);
options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE);
image = BF.openImagePlus(options)[0];
nameWithoutExt = os.path.splitext(filename)[0]
# Export the image
save_path = outputFolder +'/' + nameWithoutExt + '.ome.tif'
IJ.run(image, "Bio-Formats Exporter", "save=" + save_path + " compression=Uncompressed");
image.close()
overlayImage.setSlice(2)
IJ.run(overlayImage, "Delete Slice", "")
return overlayImage
#### Main Stuff #####
outputFilePath = inputDirectory + '/' + outputFile
if os.path.isfile(outputFilePath):
os.remove(outputFilePath)
outputFile = open(outputFilePath, 'a')
for fileName in os.listdir(inputDirectory):
print 'Processing Image ' , fileName
if '.tif' in fileName:
#print 'Opening image...'
imps = BF.openImagePlus(os.path.join(inputDirectory, fileName))
image = imps[0]
image.show()
# Select tumor
WaitForUserDialog("Select the tumor by hand.").show()
# Measure Area
currentROI = image.getROI()
image.setRoi(currentRoi)
stats = image.getStatistics(Measurements.AREA)
currentArea = stats.area
image.killRoi()
# Create an overlay
if currentROI is not None:
overlayImage = createOverlay(image, selectedROI)
else:
