def readSingleChannelImg(imgFile): options = ImporterOptions() options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE) options.setId(imgFile) imps = BF.openImagePlus(options) ip = imps[0] return(ip)
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 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 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_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 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 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 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')
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()
for l in open(filetab):
f = l.strip().split()
out = f[0]
ch1 = '%s/%s' %(path,f[1])
ch2 = '%s/%s' %(path,f[2])
print('%s: opening %s and %s' %(out,ch1,ch2))
ch1 = ij.IJ.openImage(ch1)
conv = ImageConverter(ch1)
conv.convertToGray16()
# ch1.show()
ch2 = ij.IJ.openImage(ch2)
conv = ImageConverter(ch2)
conv.convertToGray16()
# ch2.show()
# ch1.close()
# ch2.close()
mrg = RGBStackMerge.mergeChannels([ch1, ch2], False)
# mrg.show()
mrgf = '%s/%s.merged.tiff' %(path,out)
ij.IJ.saveAs(mrg,"Tiff",mrgf)
mrg.close()
opts = ImporterOptions()
opts.setId(mrgf)
opts.setColorMode(ImporterOptions.COLOR_MODE_COMPOSITE)
bio = BF.openImagePlus(opts)[0]
# bio.show()
ij.IJ.saveAs(bio.flatten(), "Tiff", '%s/%s.flat.tiff' %(path,out))
# bio.close()
# while(True): continue
# read in and display ImagePlus object(s)
from loci.plugins import BF
file = "/Users/curtis/data/tubhiswt4D.ome.tif"
imps = BF.openImagePlus(file)
for imp in imps:
imp.show()
# read in and display ImagePlus(es) with arguments
from loci.common import Region
from loci.plugins.in import ImporterOptions
options = ImporterOptions()
options.setColorMode(ImporterOptions.COLOR_MODE_GRAYSCALE)
options.setCrop(True)
options.setCropRegion(0, Region(15, 25, 50, 70))
options.setId(file)
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
# parse metadata
from loci.formats import ImageReader
from loci.formats import MetadataTools
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!)
from ij import IJ
