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 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 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 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 saveMip(img, file_path):
if mipPrefTIFF:
FileSaver(img).saveAsTiff(file_path + ".tiff")
if mipPrefJPG:
FileSaver(img).saveAsJpeg(file_path + ".jpg")
for root, dirs, files in os.walk(inDir):
for file in files:
if file.endswith(fileExt):
logging.info('Starting image #%i (%s)', imageCount, str(file))
options = ImporterOptions()
options.setAutoscale(True)
options.setId(os.path.join(root, file))
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
imageCount += 1
for imp in imps:
reader = ImageReader()
omeMeta = MetadataTools.createOMEXMLMetadata()
reader.setMetadataStore(omeMeta)
reader.setId(os.path.join(root, file))
filename = str(imp)
channel_id = int(re.findall("C=(\d)", filename)[0])
channel_name = omeMeta.getChannelName(0, channel_id)
out_name = filename.split('"')[1]
out_name = out_name.split(fileExt)[0] + "_" + str(channel_name)
out_name = out_name.replace(" ", "")
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!"
def imageprojector(channels, timelist_unsorted, dirs):
""" Projects .lif timepoints and saves in a common directory,
as well as channel separated directories. """
# Defines in path
path = str(Experiment)
# BF Importer
options = ImporterOptions()
try:
options.setId(path)
except Exception(e):
print str(e)
options.setOpenAllSeries(True)
options.setSplitTimepoints(True)
options.setSplitChannels(True)
imps = BF.openImagePlus(options)
timelist = [x for item in timelist_unsorted for x in repeat(item, channels)]
timelist, imps = zip(*sorted(zip(timelist, imps)))
counter_C0 = -1
counter_C1 = -1
counter_C2 = -1
# Opens all images, splits channels, z-projects and saves to disk
for imp in (imps):
# Projection, Sum Intensity
project = ZProjector()
project.setMethod(ZProjector.SUM_METHOD)
project.setImage(imp)
project.doProjection()
impout = project.getProjection()
projection = impout.getTitle()
try:
# Saves channels to disk,
# add more channels here if desired,
# remember to define new counters.
if "C=0" in projection:
counter_C0 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C0).zfill(3) + "C0"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C0"],
"Scan" + str(counter_C0).zfill(3) + "C0"))
elif "C=1" in projection:
counter_C1 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C1).zfill(3) + "C1"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C1"],
"Scan" + str(counter_C1).zfill(3) + "C1"))
elif "C=2" in projection:
counter_C2 += 1
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections"],
"Scan" + str(counter_C2).zfill(3) + "C2"))
IJ.saveAs(impout, "TIFF", os.path.join(dirs["Projections_C2"],
"Scan" + str(counter_C2).zfill(3) + "C2"))
except IOException:
print "Directory does not exist"
raise
IJ.log("Images projected and saved to disk")