def preprocess(filePath, fileName, fileID):
global radius
global circularity
global size
global lowerThreshold
global upperThreshold
global bytesInMB
curr = IJ.openImage(filePath + '/' + fileName)
c1, c2, c3 = ChannelSplitter.split(curr) # type:
c1.show()
c2.show()
IJ.log("before blur: " + str(IJ.currentMemory()/bytesInMB) + " MB")
IJ.run(c1,"Gaussian Blur...","sigma=%i" %radius)
IJ.log("after blur: " + str(IJ.currentMemory()/bytesInMB) + " MB" + "\n")
IJ.setThreshold(c1, lowerThreshold, upperThreshold)
#IJ.run("Set Measurements...", "mean center redirect=C2-GT_%s-Stitch.tif decimal=1" %fileID)
#IJ.run("Set Measurements...", "mean center redirect=C2-GT_A4-Stitch.tif decimal=1")
IJ.run("Set Measurements...", "mean center redirect=C2-GT_%s-Stitch.tif decimal=1" %fileID) # there is a space after "redirect ="
# produces 1980 cells but totally wrong measurements, record them next time when continued manually
IJ.run(c1, "Analyze Particles...", "size=50.00-Infinity circularity=0.70-1.00 show=Nothing display exclude include")
# I suspect that IJ.run(c1, "Analyze Particles...", "size=%s-Infinity circularity=%s-1.00 show=Nothing display exclude include" %(size, circularity)) works
c1.changes = False
c1.close()
c2.close()
return c3
def main():
global bytesInMB
x = 3
for file in os.listdir(tiff_path): # goes through each tiff file
fileID = file[3:5] # ex: A3
channel = preprocess(tiff_path, file, fileID)
IJ.log("after preprocess: " + str(IJ.currentMemory()/bytesInMB) + " MB")
IJ.run("Collect Garbage")
IJ.log("after garbage collect/before csvPreprocess: " + str(IJ.currentMemory()/bytesInMB) + " MB" + "\n")
data = csvPreprocess(fileID)
IJ.log("after csvPreprocess: " + str(IJ.currentMemory()/bytesInMB) + " MB")
IJ.run("Collect Garbage")
IJ.log("after garbage collect: " + str(IJ.currentMemory()/bytesInMB) + " MB")
sys.exit(0)
"""
def get_free_memory():
"""gets the free memory thats available to ImageJ
Returns
-------
free_memory : integer
the free memory in bytes
"""
max_memory = int(IJ.maxMemory())
used_memory = int(IJ.currentMemory())
free_memory = max_memory - used_memory
return free_memory
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;
