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
#Define results output folder
folder = input_folder+"timepoints/"
if not os.path.exists(folder):
os.mkdir(folder)
# collect list of files to be processed
#file_list = [filename for filename in os.listdir(input_folder) if ".tif" in filename]
# Recursive option
file_list = [os.path.join(dp, f) for dp, dn, fn in os.walk(input_folder) for f in fn if '.tif' in f]
for file_path in file_list:
# read in and display ImagePlus(es) with arguments
options = ImporterOptions()
options.setId(file_path)
options.setSplitTimepoints(True)
imps = BF.openImagePlus(options)
for imp in imps:
imp.show()
name = imp.getTitle()
details = name.split("_")[0]
print file_path
pos = details.split('Pos')[1]
time = name.split("=")[1]
image_type = re.split(r'.lif |- |_|\\', file_path)[-3]
mutant = re.split(r'.lif |- |_|\\', file_path)[-6]
cotrans = re.split(r'.lif |- |_|\\', file_path)[-5]
new_name = mutant+"_"+cotrans+"_pos_"+pos+"_t_"+time+"_"+image_type
print new_name
IJ.saveAs(imp, "Tiff", os.path.join(folder, new_name))
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")