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;
