def start_masking_menu():
wlist = WindowManager.getImageTitles()
gd = GenericDialog('Masking - Setup')
gd.setCancelLabel('Exit')
gd.addChoice('Create mask from', wlist, wlist[0])
gd.addNumericField("Gaussian blur:", 0, 1)
gd.addNumericField("Fixed threshold:", 0, 0)
gd.addCheckbox('Use automatic thresholding', False)
gd.addChoice('Method', ['Default', 'Huang', 'Otsu', 'Yen'], 'Default')
gd.showDialog()
if gd.wasCanceled():
return False
pdic = {}
pdic['sel_win'] = gd.getNextChoice()
pdic['sigma'] = gd.getNextNumber()
pdic['threshold'] = gd.getNextNumber()
pdic['use_auto'] = gd.getNextBoolean()
pdic['thresh_method'] = gd.getNextChoice()
return pdic
def perform_manual_qc(imp, rois, important_channel=1):
"""given cell rois generated by automatic methods, allow user to delete/add/redraw as appropriate"""
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
sat_frac = 0.99 if (ch + 1) == important_channel else 0.01
IJ.run(imp, "Enhance Contrast", "saturated={}".format(sat_frac))
imp.setC(important_channel)
IJ.setTool("freehand")
proceed = False
roim = RoiManager()
roim.runCommand("Show all with labels")
for roi in rois:
roim.addRoi(roi)
auto_rois_only = rois
while not proceed:
dialog = NonBlockingGenericDialog("Perform manual segmentation")
dialog.setOKLabel("Proceed to next image...")
dialog.addMessage("Perform manual correction of segmentation: ")
dialog.addMessage(
"Draw around cells and add to the region of interest manager (Ctrl+T). "
)
dialog.addMessage("Delete and redraw cells as appropriate. ")
dialog.addMessage(
"Then press \"proceed to next image\" when all cells have been added. "
)
dialog.showDialog()
if dialog.wasCanceled():
print("Manual segmentation canceled")
return auto_rois_only
elif dialog.wasOKed():
if roim.getCount() == 0:
rois = []
confirm_dialog = GenericDialog("Continue?")
confirm_dialog.addMessage(
"No rois selected in this FOV. Are you sure you want to proceed?"
)
confirm_dialog.setOKLabel("Yes, proceed")
confirm_dialog.setCancelLabel("No, not yet")
confirm_dialog.showDialog()
if confirm_dialog.wasOKed():
proceed = True
else:
rois = roim.getRoisAsArray()
proceed = True
roim.reset()
roim.close()
for ch in range(imp.getNChannels()):
imp.setC(ch + 1)
IJ.run(imp, "Enhance Contrast", "saturated={}".format(0.35))
imp.setC(important_channel)
return rois
def warning_dialog(message):
"""show a warning dialog with a user-defined message"""
dialog = GenericDialog("Warning!");
dialog.setCancelLabel("Cancel analysis");
if type(message) is list:
for line in message:
dialog.addMessage(line);
else:
dialog.addMessage(message);
dialog.showDialog();
if dialog.wasCanceled():
raise KeyboardInterrupt("Run canceled");
return;
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;
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK')
gd.addMessage(
'CMTK Registration suite is open source software released under GPLv3', )
gd.addMessage('Currently installed CMTK version: ' +
cmtkgui.installed_version())
gd.addMessage('CMTK binary directory: ' + cmtkgui.bin_dir())
gd.setCancelLabel("CMTK Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher",
"http://www.nitrc.org/projects/cmtk/")
from ij.gui import GenericDialog
import sys
from java.lang.System import getProperty
sys.path.append(getProperty("fiji.dir") + "/plugins/CMTK_Registration")
gd = GenericDialog('About CMTK')
gd.addMessage('CMTK Registration suite is open source software released under GPLv3',)
gd.addMessage('Currently installed CMTK version: '+cmtkgui.installed_version())
gd.addMessage('CMTK binary directory: '+cmtkgui.bin_dir())
gd.setCancelLabel("CMTK Web Page")
gd.showDialog()
if gd.wasCanceled():
from ij import IJ
IJ.runPlugIn("ij.plugin.BrowserLauncher", "http://www.nitrc.org/projects/cmtk/")
