def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_notepad()
self.ui.setupUi(self)
QtCore.QObject.connect(self.ui.button_change_cellid_parameters, QtCore.SIGNAL("clicked()"), self.change_cell_id_dialog)
QtCore.QObject.connect(self.ui.button_load_default_cellid_parameters, QtCore.SIGNAL("clicked()"), self.load_cell_id_dialog)
QtCore.QObject.connect(self.ui.working_directory, QtCore.SIGNAL("clicked()"), self.working_directory_dialog)
QtCore.QObject.connect(self.ui.cell_id_executable, QtCore.SIGNAL("clicked()"), self.cell_id_executable_dialog)
QtCore.QObject.connect(self.ui.fiji_executable, QtCore.SIGNAL("clicked()"), self.fiji_executable_dialog)
QtCore.QObject.connect(self.ui.spottyR_file, QtCore.SIGNAL("clicked()"), self.spottyR_file_dialog)
QtCore.QObject.connect(self.ui.pb_save_preferences, QtCore.SIGNAL("clicked()"), self.save_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_load_preferences, QtCore.SIGNAL("clicked()"), self.load_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_images_directory, QtCore.SIGNAL("clicked()"), self.images_directory_dialog)
QtCore.QObject.connect(self.ui.pb_save_session, QtCore.SIGNAL("clicked()"), self.save_session_dialog)
QtCore.QObject.connect(self.ui.pb_apply_session, QtCore.SIGNAL("clicked()"), self.apply_session_dialog)
QtCore.QObject.connect(self.ui.pb_load_session, QtCore.SIGNAL("clicked()"), self.load_session_dialog)
QtCore.QObject.connect(self.ui.prepare_structure, QtCore.SIGNAL("clicked()"), self.prepare_files_and_folder_structure)
QtCore.QObject.connect(self.ui.pb_run_fiji, QtCore.SIGNAL("clicked()"), self.run_fiji)
QtCore.QObject.connect(self.ui.pb_run_cell_id, QtCore.SIGNAL("clicked()"), self.run_cell_id)
QtCore.QObject.connect(self.ui.pb_run_spotty, QtCore.SIGNAL("clicked()"), self.run_spotty)
QtCore.QObject.connect(self.ui.pb_aggregate_and_plot, QtCore.SIGNAL("clicked()"), self.aggregate_and_plot)
QtCore.QObject.connect(self.ui.pb_run_all_steps, QtCore.SIGNAL("clicked()"), self.run_all_steps)
QtCore.QObject.connect(self.ui.pb_mark_detected_spots, QtCore.SIGNAL("clicked()"), self.mark_detected_spots)
QtCore.QObject.connect(self.ui.pushButton_2, QtCore.SIGNAL("clicked()"), self.end_session)
# load last preferences and last session into GUI if possible
lout = os.listdir(os.curdir)
lastprefs = "last_preferences.pref"
lastsession = "last_session.ssn"
if lastprefs in lout:
preferences_file = open(lastprefs, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
if lastsession in lout:
session_file = open(lastsession, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
self.ui.log_window.setText("Welcome to Spotalyser 0.9!")
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_notepad()
self.ui.setupUi(self)
QtCore.QObject.connect(self.ui.button_change_cellid_parameters,
QtCore.SIGNAL("clicked()"),
self.change_cell_id_dialog)
QtCore.QObject.connect(self.ui.button_load_default_cellid_parameters,
QtCore.SIGNAL("clicked()"),
self.load_cell_id_dialog)
QtCore.QObject.connect(self.ui.working_directory,
QtCore.SIGNAL("clicked()"),
self.working_directory_dialog)
QtCore.QObject.connect(self.ui.cell_id_executable,
QtCore.SIGNAL("clicked()"),
self.cell_id_executable_dialog)
QtCore.QObject.connect(self.ui.fiji_executable,
QtCore.SIGNAL("clicked()"),
self.fiji_executable_dialog)
QtCore.QObject.connect(self.ui.spottyR_file,
QtCore.SIGNAL("clicked()"),
self.spottyR_file_dialog)
QtCore.QObject.connect(self.ui.pb_save_preferences,
QtCore.SIGNAL("clicked()"),
self.save_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_load_preferences,
QtCore.SIGNAL("clicked()"),
self.load_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_images_directory,
QtCore.SIGNAL("clicked()"),
self.images_directory_dialog)
QtCore.QObject.connect(self.ui.pb_save_session,
QtCore.SIGNAL("clicked()"),
self.save_session_dialog)
QtCore.QObject.connect(self.ui.pb_apply_session,
QtCore.SIGNAL("clicked()"),
self.apply_session_dialog)
QtCore.QObject.connect(self.ui.pb_load_session,
QtCore.SIGNAL("clicked()"),
self.load_session_dialog)
QtCore.QObject.connect(self.ui.prepare_structure,
QtCore.SIGNAL("clicked()"),
self.prepare_files_and_folder_structure)
QtCore.QObject.connect(self.ui.pb_run_fiji, QtCore.SIGNAL("clicked()"),
self.run_fiji)
QtCore.QObject.connect(self.ui.pb_run_cell_id,
QtCore.SIGNAL("clicked()"), self.run_cell_id)
QtCore.QObject.connect(self.ui.pb_run_spotty,
QtCore.SIGNAL("clicked()"), self.run_spotty)
QtCore.QObject.connect(self.ui.pb_aggregate_and_plot,
QtCore.SIGNAL("clicked()"),
self.aggregate_and_plot)
QtCore.QObject.connect(self.ui.pb_run_all_steps,
QtCore.SIGNAL("clicked()"), self.run_all_steps)
QtCore.QObject.connect(self.ui.pb_mark_detected_spots,
QtCore.SIGNAL("clicked()"),
self.mark_detected_spots)
QtCore.QObject.connect(self.ui.pushButton_2,
QtCore.SIGNAL("clicked()"), self.end_session)
# load last preferences and last session into GUI if possible
lout = os.listdir(os.curdir)
lastprefs = "last_preferences.pref"
lastsession = "last_session.ssn"
if lastprefs in lout:
preferences_file = open(lastprefs, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
if lastsession in lout:
session_file = open(lastsession, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
self.ui.log_window.setText("Welcome to Spotalyser 0.9!")
class StartQT4(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_notepad()
self.ui.setupUi(self)
QtCore.QObject.connect(self.ui.button_change_cellid_parameters, QtCore.SIGNAL("clicked()"), self.change_cell_id_dialog)
QtCore.QObject.connect(self.ui.button_load_default_cellid_parameters, QtCore.SIGNAL("clicked()"), self.load_cell_id_dialog)
QtCore.QObject.connect(self.ui.working_directory, QtCore.SIGNAL("clicked()"), self.working_directory_dialog)
QtCore.QObject.connect(self.ui.cell_id_executable, QtCore.SIGNAL("clicked()"), self.cell_id_executable_dialog)
QtCore.QObject.connect(self.ui.fiji_executable, QtCore.SIGNAL("clicked()"), self.fiji_executable_dialog)
QtCore.QObject.connect(self.ui.spottyR_file, QtCore.SIGNAL("clicked()"), self.spottyR_file_dialog)
QtCore.QObject.connect(self.ui.pb_save_preferences, QtCore.SIGNAL("clicked()"), self.save_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_load_preferences, QtCore.SIGNAL("clicked()"), self.load_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_images_directory, QtCore.SIGNAL("clicked()"), self.images_directory_dialog)
QtCore.QObject.connect(self.ui.pb_save_session, QtCore.SIGNAL("clicked()"), self.save_session_dialog)
QtCore.QObject.connect(self.ui.pb_apply_session, QtCore.SIGNAL("clicked()"), self.apply_session_dialog)
QtCore.QObject.connect(self.ui.pb_load_session, QtCore.SIGNAL("clicked()"), self.load_session_dialog)
QtCore.QObject.connect(self.ui.prepare_structure, QtCore.SIGNAL("clicked()"), self.prepare_files_and_folder_structure)
QtCore.QObject.connect(self.ui.pb_run_fiji, QtCore.SIGNAL("clicked()"), self.run_fiji)
QtCore.QObject.connect(self.ui.pb_run_cell_id, QtCore.SIGNAL("clicked()"), self.run_cell_id)
QtCore.QObject.connect(self.ui.pb_run_spotty, QtCore.SIGNAL("clicked()"), self.run_spotty)
QtCore.QObject.connect(self.ui.pb_aggregate_and_plot, QtCore.SIGNAL("clicked()"), self.aggregate_and_plot)
QtCore.QObject.connect(self.ui.pb_run_all_steps, QtCore.SIGNAL("clicked()"), self.run_all_steps)
QtCore.QObject.connect(self.ui.pb_mark_detected_spots, QtCore.SIGNAL("clicked()"), self.mark_detected_spots)
QtCore.QObject.connect(self.ui.pushButton_2, QtCore.SIGNAL("clicked()"), self.end_session)
# load last preferences and last session into GUI if possible
lout = os.listdir(os.curdir)
lastprefs = "last_preferences.pref"
lastsession = "last_session.ssn"
if lastprefs in lout:
preferences_file = open(lastprefs, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
if lastsession in lout:
session_file = open(lastsession, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
self.ui.log_window.setText("Welcome to Spotalyser 0.9!")
def change_cell_id_dialog(self):
cellID1 = self.ui.lineEdit_max_dist_over_waist.text()
cellID2 = self.ui.lineEdit_max_split_over_minor_axis.text()
cellID3 = self.ui.lineEdit_min_pixels_per_cell.text()
cellID4 = self.ui.lineEdit_max_pixels_per_cell.text()
cellID5 = self.ui.lineEdit_background_reject_factor.text()
cellID6 = self.ui.lineEdit_tracking_comparison.text()
# If the user does not enter values, the default values specified in global_vars are assumed:
param_dict = PARAM_DICT
if cellID1 != "":
param_dict["max_dist_over_waist"] = float(cellID1)
if cellID2 != "":
param_dict["max_split_over_minor_axis"] = float(cellID2)
if cellID3 != "":
param_dict["min_pixels_per_cell"] = float(cellID3)
if cellID4 != "":
param_dict["max_pixels_per_cell"] = float(cellID4)
if cellID5 != "":
param_dict["background_reject_factor"] = float(cellID5)
if cellID6 != "":
param_dict["tracking_comparison"] = float(cellID6)
param_file=join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS)
set_parameters(param_dict, param_file)
log_text = "Loading default cell ID parameters for unspecified values.\n"
log_text += "Setting cell ID parameters to: "+str(param_dict)
print log_text
self.ui.log_window.setText(log_text)
def load_cell_id_dialog(self):
global SIC_ROOT
global SIC_SCRIPTS
global SIC_CELLID_PARAMS
print "param_dict =", load_parameters(param_file=join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS))
param_dict = load_parameters(param_file=join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS))
self.ui.lineEdit_max_dist_over_waist.setText(str(param_dict["max_dist_over_waist"]))
self.ui.lineEdit_max_split_over_minor_axis.setText(str(param_dict["max_split_over_minor_axis"]))
self.ui.lineEdit_min_pixels_per_cell.setText(str(param_dict["min_pixels_per_cell"]))
self.ui.lineEdit_max_pixels_per_cell.setText(str(param_dict["max_pixels_per_cell"]))
self.ui.lineEdit_background_reject_factor.setText(str(param_dict["background_reject_factor"]))
self.ui.lineEdit_tracking_comparison.setText(str(param_dict["tracking_comparison"]))
def working_directory_dialog(self):
workingdir = QtGui.QFileDialog.getExistingDirectory(self, "Select", ".", options = QtGui.QFileDialog.DontResolveSymlinks)
if workingdir:
self.ui.lineEditworking_directory.setText(workingdir)
global SIC_ROOT
SIC_ROOT = str(workingdir)
def cell_id_executable_dialog(self):
cellidexe = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if cellidexe:
self.ui.lineEditcell_id_executable.setText(cellidexe)
global SIC_CELLID
SIC_CELLID = str(cellidexe)
def fiji_executable_dialog(self):
fijiexe = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if fijiexe:
self.ui.lineEditfiji_executable.setText(fijiexe)
global SIC_FIJI
SIC_FIJI = str(fijiexe)
def spottyR_file_dialog(self):
spottyfile = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if spottyfile:
self.ui.lineEditspottyR_file.setText(spottyfile)
global SIC_SPOTTY
SIC_SPOTTY = str(spottyfile)
def save_preferences_dialog(self):
global SIC_ROOT
global SIC_CELLID
global SIC_FIJI
global SIC_SPOTTY
preferences_dict = {}
preferences_dict["workingdir"] = SIC_ROOT
preferences_dict["cellidexe"] = SIC_CELLID
preferences_dict["fijiexe"] = SIC_FIJI
preferences_dict["spottyfile"] = SIC_SPOTTY
defaultFileName = "Preferences_"+str(date.today())+".pref"
filename = str(QtGui.QFileDialog.getSaveFileName(None, QtCore.QString("Save preferences..."), defaultFileName))
if filename:
preferences_file = open(filename, 'w')
pickle.dump(preferences_dict, preferences_file)
def load_preferences_dialog(self):
filename = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if filename:
preferences_file = open(filename, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
def images_directory_dialog(self):
imagesdir = QtGui.QFileDialog.getExistingDirectory(self, "Select", ".", options = QtGui.QFileDialog.DontResolveSymlinks)
if imagesdir:
self.ui.le_images_directory.setText(imagesdir)
global SIC_ORIG
SIC_ORIG_PATH = str(imagesdir)
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
def save_session_dialog(self):
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
session_dict = {}
session_dict["imagesdir"] = SIC_ORIG
session_dict["niba_id"] = NIBA_ID
session_dict["dic_id"] = DIC_ID
defaultFileName = "Session_"+str(date.today())+".ssn"
filename = str(QtGui.QFileDialog.getSaveFileName(None, QtCore.QString("Save session..."), defaultFileName));
if filename:
session_file = open(filename, 'w')
pickle.dump(session_dict, session_file)
def apply_session_dialog(self):
global SIC_ORIG
SIC_ORIG_PATH = str(self.ui.le_images_directory.text())
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
def load_session_dialog(self):
filename = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if filename:
session_file = open(filename, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
def prepare_files_and_folder_structure(self):
global SIC_ROOT
global SIC_FIJI
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
SIC_FIJI = str(self.ui.lineEditfiji_executable.text())
fiji = SIC_FIJI
mskpath = SIC_ROOT
skip = [SIC_ORIG, SIC_SCRIPTS, "orig", "orig1", "orig2", "orig3", "orig4", "orig5", "orig6"]
create_dirs = [SIC_PROCESSED, SIC_RESULTS]
#check_for = [join(SIC_ROOT, SIC_SCRIPTS, FIJI_STANDARD_SCRIPT), join(SIC_ROOT, SIC_ORIG)]
check_for = [FIJI_STANDARD_SCRIPT, FIJI_SLICE_SCRIPT, join(SIC_ROOT, SIC_ORIG)] # Should check fiji scripts in eclipse workspace
prepare_structure(mskpath, skip, create_dirs, check_for, fiji)
copy_NIBA_files_to_processed(join(SIC_ROOT, SIC_ORIG), join(SIC_ROOT, SIC_PROCESSED), NIBA_ID)
link_DIC_files_to_processed(join(SIC_ROOT, SIC_ORIG), join(SIC_ROOT, SIC_PROCESSED), DIC_ID)
#copy_DIC_files_to_processed(join(SIC_ROOT, SIC_ORIG), join(SIC_ROOT, SIC_PROCESSED), DIC_ID)
def run_fiji(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_FIJI
fiji = SIC_FIJI
mskpath = join(SIC_ROOT, SIC_PROCESSED)
#script_filename = join(SIC_ROOT, SIC_SCRIPTS, FIJI_STANDARD_SCRIPT)
#slice_filename = join(SIC_ROOT, SIC_SCRIPTS, FIJI_SLICE_SCRIPT)
script_filename = join(os.getcwd(), FIJI_STANDARD_SCRIPT)
slice_filename = join(os.getcwd(), FIJI_SLICE_SCRIPT)
niba = NIBA_ID
dic = DIC_ID
#run_fiji_standard_mode(mskpath, script_filename, niba, fiji)
run_fiji_standard_mode_select_quarter_slices(mskpath, script_filename, slice_filename, niba, dic, fiji)
def run_cell_id(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_LINKS
global SIC_FILE_CORRESPONDANCE
global NIBA_ID
global DIC_ID
global SIC_CELLID
global SIC_CELLID_PARAMS
filename = join(SIC_ROOT, SIC_PROCESSED, SIC_FILE_CORRESPONDANCE)
mskpath = join(SIC_ROOT, SIC_PROCESSED)
niba = NIBA_ID
dic = DIC_ID
options_fn = join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS)
output_prefix = join(SIC_ROOT, SIC_PROCESSED)
niba2dic, dic2niba, o2n = create_map_image_data(filename, mskpath, niba, dic)
sourcepath = join(SIC_ROOT, SIC_PROCESSED)
targetpath = join(SIC_ROOT, SIC_PROCESSED)
create_symlinks(o2n, sourcepath, targetpath)
prepare_b_and_f_single_files(niba2dic, o2n, mskpath)
run_cellid(mskpath, SIC_CELLID, join(SIC_ROOT, SIC_PROCESSED, SIC_BF_LISTFILE),
join(SIC_ROOT, SIC_PROCESSED, SIC_F_LISTFILE),
options_fn,
output_prefix)
global d
d = {
"niba2dic" : niba2dic,
"dic2niba" : dic2niba,
"o2n" : o2n,
}
def run_spotty(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_LINKS
global SIC_SPOTTY
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
mskpath = join(SIC_ROOT, SIC_PROCESSED)
#cellid_results_path = join(SIC_ROOT, SIC_PROCESSED)
headers, data = load_fiji_results_and_create_mappings(mskpath)
filename2pixel_list = create_mappings_filename2pixel_list((headers, data), mskpath)
global d
o2n = d["o2n"]
filename2cells, filename2hist, filename2cell_number = load_cellid_files_and_create_mappings_from_bounds(filename2pixel_list, o2n, mskpath)
spotty=SIC_SPOTTY
cluster_with_spotty(mskpath, spotty, GMAX) # TODO: GMAX from GUI
d["filename2pixel_list"] = filename2pixel_list
d["headers"] = headers
d["data"] = data
d["filename2cells"] = filename2cells
d["filename2hist"] = filename2hist
d["filename2cell_number"] = filename2cell_number
def aggregate_and_plot(self):
global SIC_ORIG
global SIC_ROOT
global SIC_PROCESSED
global SIC_RESULTS
global SIC_DATA_PICKLE
mskpath = join(SIC_ROOT, SIC_PROCESSED)
global d
try:
d
except NameError:
d = pickle.load(file(join(SIC_ROOT, SIC_PROCESSED, SIC_DATA_PICKLE)))
o2n = d["o2n"]
spots = aggregate_spots(o2n, mskpath)
d["spots"] = spots
pickle.dump(d, file(join(SIC_ROOT, SIC_RESULTS, SIC_DATA_PICKLE), "w"))
histogram_intensities(spots, mskpath)
scatterplot_intensities(spots, mskpath)
spots_per_cell_distribution(spots, mskpath)
pl.show()
def run_all_steps(self):
global SIC_ROOT
global SIC_PROCESSED
self.prepare_files_and_folder_structure()
self.run_fiji()
self.run_cell_id()
self.run_spotty()
self.aggregate_and_plot()
#FIXME: why does this not work under Windows?
if not self.ui.cb_decimal_separator.isChecked(): # then we want to replace . by ,
mskpath=join(SIC_ROOT, SIC_PROCESSED)
#print "replacing decimal separators on mskpath =", mskpath
replace_decimal_separators(mskpath)
pl.show()
def file_save(self):
fd = QtGui.QFileDialog(self)
self.filename = fd.getOpenFileName()
from os.path import isfile
if isfile(self.filename):
file = open(self.filename, 'w')
file.write(self.ui.editor_window.toPlainText())
file.close()
def mark_detected_spots(self):
global SIC_ROOT
global SIC_ORIG
global SIC_PROCESSED
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
mskpath = join(SIC_ROOT, SIC_PROCESSED)
draw_spots_for_session(mskpath=join(SIC_ROOT, SIC_PROCESSED), infofile="all_spots.xls") # FIXME: load
rename_dirs(SIC_ORIG, mskpath)
def end_session(self):
# auto-save machine to preferences file
# auto-save session to session file
global SIC_ROOT
global SIC_ORIG
global SIC_SCRIPTS
global SIC_CELLID
global SIC_FIJI
global SIC_SPOTTY
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
try:
# save current preferences to last_preferences.pref
preferences_dict = {}
preferences_dict["workingdir"] = str(self.ui.lineEditworking_directory.text())
preferences_dict["cellidexe"] = str(self.ui.lineEditcell_id_executable.text())
preferences_dict["fijiexe"] = str(self.ui.lineEditfiji_executable.text())
preferences_dict["spottyfile"] = str(self.ui.lineEditspottyR_file.text())
preferences_file = open(join(os.curdir, "last_preferences.pref"), "w")
pickle.dump(preferences_dict, preferences_file)
# save current session to last_session.ssn
session_dict = {}
session_dict["imagesdir"] = str(self.ui.le_images_directory.text())
session_dict["niba_id"] = str(self.ui.le_niba_id.text())
session_dict["dic_id"] = str(self.ui.le_dic_id.text())
session_file = open(join(os.curdir, "last_session.ssn"), 'w')
pickle.dump(session_dict, session_file)
# This is so that the window closes no matter which variables are set
except:
pass
self.close()
class StartQT4(QtGui.QMainWindow):
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_notepad()
self.ui.setupUi(self)
QtCore.QObject.connect(self.ui.button_change_cellid_parameters,
QtCore.SIGNAL("clicked()"),
self.change_cell_id_dialog)
QtCore.QObject.connect(self.ui.button_load_default_cellid_parameters,
QtCore.SIGNAL("clicked()"),
self.load_cell_id_dialog)
QtCore.QObject.connect(self.ui.working_directory,
QtCore.SIGNAL("clicked()"),
self.working_directory_dialog)
QtCore.QObject.connect(self.ui.cell_id_executable,
QtCore.SIGNAL("clicked()"),
self.cell_id_executable_dialog)
QtCore.QObject.connect(self.ui.fiji_executable,
QtCore.SIGNAL("clicked()"),
self.fiji_executable_dialog)
QtCore.QObject.connect(self.ui.spottyR_file,
QtCore.SIGNAL("clicked()"),
self.spottyR_file_dialog)
QtCore.QObject.connect(self.ui.pb_save_preferences,
QtCore.SIGNAL("clicked()"),
self.save_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_load_preferences,
QtCore.SIGNAL("clicked()"),
self.load_preferences_dialog)
QtCore.QObject.connect(self.ui.pb_images_directory,
QtCore.SIGNAL("clicked()"),
self.images_directory_dialog)
QtCore.QObject.connect(self.ui.pb_save_session,
QtCore.SIGNAL("clicked()"),
self.save_session_dialog)
QtCore.QObject.connect(self.ui.pb_apply_session,
QtCore.SIGNAL("clicked()"),
self.apply_session_dialog)
QtCore.QObject.connect(self.ui.pb_load_session,
QtCore.SIGNAL("clicked()"),
self.load_session_dialog)
QtCore.QObject.connect(self.ui.prepare_structure,
QtCore.SIGNAL("clicked()"),
self.prepare_files_and_folder_structure)
QtCore.QObject.connect(self.ui.pb_run_fiji, QtCore.SIGNAL("clicked()"),
self.run_fiji)
QtCore.QObject.connect(self.ui.pb_run_cell_id,
QtCore.SIGNAL("clicked()"), self.run_cell_id)
QtCore.QObject.connect(self.ui.pb_run_spotty,
QtCore.SIGNAL("clicked()"), self.run_spotty)
QtCore.QObject.connect(self.ui.pb_aggregate_and_plot,
QtCore.SIGNAL("clicked()"),
self.aggregate_and_plot)
QtCore.QObject.connect(self.ui.pb_run_all_steps,
QtCore.SIGNAL("clicked()"), self.run_all_steps)
QtCore.QObject.connect(self.ui.pb_mark_detected_spots,
QtCore.SIGNAL("clicked()"),
self.mark_detected_spots)
QtCore.QObject.connect(self.ui.pushButton_2,
QtCore.SIGNAL("clicked()"), self.end_session)
# load last preferences and last session into GUI if possible
lout = os.listdir(os.curdir)
lastprefs = "last_preferences.pref"
lastsession = "last_session.ssn"
if lastprefs in lout:
preferences_file = open(lastprefs, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
if lastsession in lout:
session_file = open(lastsession, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
self.ui.log_window.setText("Welcome to Spotalyser 0.9!")
def change_cell_id_dialog(self):
cellID1 = self.ui.lineEdit_max_dist_over_waist.text()
cellID2 = self.ui.lineEdit_max_split_over_minor_axis.text()
cellID3 = self.ui.lineEdit_min_pixels_per_cell.text()
cellID4 = self.ui.lineEdit_max_pixels_per_cell.text()
cellID5 = self.ui.lineEdit_background_reject_factor.text()
cellID6 = self.ui.lineEdit_tracking_comparison.text()
# If the user does not enter values, the default values specified in global_vars are assumed:
param_dict = PARAM_DICT
if cellID1 != "":
param_dict["max_dist_over_waist"] = float(cellID1)
if cellID2 != "":
param_dict["max_split_over_minor_axis"] = float(cellID2)
if cellID3 != "":
param_dict["min_pixels_per_cell"] = float(cellID3)
if cellID4 != "":
param_dict["max_pixels_per_cell"] = float(cellID4)
if cellID5 != "":
param_dict["background_reject_factor"] = float(cellID5)
if cellID6 != "":
param_dict["tracking_comparison"] = float(cellID6)
param_file = join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS)
set_parameters(param_dict, param_file)
log_text = "Loading default cell ID parameters for unspecified values.\n"
log_text += "Setting cell ID parameters to: " + str(param_dict)
print log_text
self.ui.log_window.setText(log_text)
def load_cell_id_dialog(self):
global SIC_ROOT
global SIC_SCRIPTS
global SIC_CELLID_PARAMS
print "param_dict =", load_parameters(
param_file=join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS))
param_dict = load_parameters(
param_file=join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS))
self.ui.lineEdit_max_dist_over_waist.setText(
str(param_dict["max_dist_over_waist"]))
self.ui.lineEdit_max_split_over_minor_axis.setText(
str(param_dict["max_split_over_minor_axis"]))
self.ui.lineEdit_min_pixels_per_cell.setText(
str(param_dict["min_pixels_per_cell"]))
self.ui.lineEdit_max_pixels_per_cell.setText(
str(param_dict["max_pixels_per_cell"]))
self.ui.lineEdit_background_reject_factor.setText(
str(param_dict["background_reject_factor"]))
self.ui.lineEdit_tracking_comparison.setText(
str(param_dict["tracking_comparison"]))
def working_directory_dialog(self):
workingdir = QtGui.QFileDialog.getExistingDirectory(
self, "Select", ".", options=QtGui.QFileDialog.DontResolveSymlinks)
if workingdir:
self.ui.lineEditworking_directory.setText(workingdir)
global SIC_ROOT
SIC_ROOT = str(workingdir)
def cell_id_executable_dialog(self):
cellidexe = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if cellidexe:
self.ui.lineEditcell_id_executable.setText(cellidexe)
global SIC_CELLID
SIC_CELLID = str(cellidexe)
def fiji_executable_dialog(self):
fijiexe = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if fijiexe:
self.ui.lineEditfiji_executable.setText(fijiexe)
global SIC_FIJI
SIC_FIJI = str(fijiexe)
def spottyR_file_dialog(self):
spottyfile = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if spottyfile:
self.ui.lineEditspottyR_file.setText(spottyfile)
global SIC_SPOTTY
SIC_SPOTTY = str(spottyfile)
def save_preferences_dialog(self):
global SIC_ROOT
global SIC_CELLID
global SIC_FIJI
global SIC_SPOTTY
preferences_dict = {}
preferences_dict["workingdir"] = SIC_ROOT
preferences_dict["cellidexe"] = SIC_CELLID
preferences_dict["fijiexe"] = SIC_FIJI
preferences_dict["spottyfile"] = SIC_SPOTTY
defaultFileName = "Preferences_" + str(date.today()) + ".pref"
filename = str(
QtGui.QFileDialog.getSaveFileName(
None, QtCore.QString("Save preferences..."), defaultFileName))
if filename:
preferences_file = open(filename, 'w')
pickle.dump(preferences_dict, preferences_file)
def load_preferences_dialog(self):
filename = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if filename:
preferences_file = open(filename, 'r')
preferences_dict = pickle.load(preferences_file)
global SIC_ROOT
SIC_ROOT = preferences_dict["workingdir"]
global SIC_CELLID
SIC_CELLID = preferences_dict["cellidexe"]
global SIC_FIJI
SIC_FIJI = preferences_dict["fijiexe"]
global SIC_SPOTTY
SIC_SPOTTY = preferences_dict["spottyfile"]
self.ui.lineEditworking_directory.setText(SIC_ROOT)
self.ui.lineEditcell_id_executable.setText(SIC_CELLID)
self.ui.lineEditfiji_executable.setText(SIC_FIJI)
self.ui.lineEditspottyR_file.setText(SIC_SPOTTY)
def images_directory_dialog(self):
imagesdir = QtGui.QFileDialog.getExistingDirectory(
self, "Select", ".", options=QtGui.QFileDialog.DontResolveSymlinks)
if imagesdir:
self.ui.le_images_directory.setText(imagesdir)
global SIC_ORIG
SIC_ORIG_PATH = str(imagesdir)
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
def save_session_dialog(self):
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
session_dict = {}
session_dict["imagesdir"] = SIC_ORIG
session_dict["niba_id"] = NIBA_ID
session_dict["dic_id"] = DIC_ID
defaultFileName = "Session_" + str(date.today()) + ".ssn"
filename = str(
QtGui.QFileDialog.getSaveFileName(
None, QtCore.QString("Save session..."), defaultFileName))
if filename:
session_file = open(filename, 'w')
pickle.dump(session_dict, session_file)
def apply_session_dialog(self):
global SIC_ORIG
SIC_ORIG_PATH = str(self.ui.le_images_directory.text())
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
def load_session_dialog(self):
filename = QtGui.QFileDialog.getOpenFileName(self, "Select", ".")
if filename:
session_file = open(filename, 'r')
session_dict = pickle.load(session_file)
global SIC_ORIG
SIC_ORIG_PATH = session_dict["imagesdir"]
SIC_ORIG = SIC_ORIG_PATH.split(r"/")[-1]
global NIBA_ID
NIBA_ID = session_dict["niba_id"]
global DIC_ID
DIC_ID = session_dict["dic_id"]
self.ui.le_images_directory.setText(SIC_ORIG_PATH)
self.ui.le_niba_id.setText(NIBA_ID)
self.ui.le_dic_id.setText(DIC_ID)
def prepare_files_and_folder_structure(self):
global SIC_ROOT
global SIC_FIJI
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
SIC_FIJI = str(self.ui.lineEditfiji_executable.text())
fiji = SIC_FIJI
mskpath = SIC_ROOT
skip = [
SIC_ORIG, SIC_SCRIPTS, "orig", "orig1", "orig2", "orig3", "orig4",
"orig5", "orig6"
]
create_dirs = [SIC_PROCESSED, SIC_RESULTS]
#check_for = [join(SIC_ROOT, SIC_SCRIPTS, FIJI_STANDARD_SCRIPT), join(SIC_ROOT, SIC_ORIG)]
check_for = [
FIJI_STANDARD_SCRIPT, FIJI_SLICE_SCRIPT,
join(SIC_ROOT, SIC_ORIG)
] # Should check fiji scripts in eclipse workspace
prepare_structure(mskpath, skip, create_dirs, check_for, fiji)
copy_NIBA_files_to_processed(join(SIC_ROOT, SIC_ORIG),
join(SIC_ROOT, SIC_PROCESSED), NIBA_ID)
link_DIC_files_to_processed(join(SIC_ROOT, SIC_ORIG),
join(SIC_ROOT, SIC_PROCESSED), DIC_ID)
#copy_DIC_files_to_processed(join(SIC_ROOT, SIC_ORIG), join(SIC_ROOT, SIC_PROCESSED), DIC_ID)
def run_fiji(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_FIJI
fiji = SIC_FIJI
mskpath = join(SIC_ROOT, SIC_PROCESSED)
#script_filename = join(SIC_ROOT, SIC_SCRIPTS, FIJI_STANDARD_SCRIPT)
#slice_filename = join(SIC_ROOT, SIC_SCRIPTS, FIJI_SLICE_SCRIPT)
script_filename = join(os.getcwd(), FIJI_STANDARD_SCRIPT)
slice_filename = join(os.getcwd(), FIJI_SLICE_SCRIPT)
niba = NIBA_ID
dic = DIC_ID
#run_fiji_standard_mode(mskpath, script_filename, niba, fiji)
run_fiji_standard_mode_select_quarter_slices(mskpath, script_filename,
slice_filename, niba, dic,
fiji)
def run_cell_id(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_LINKS
global SIC_FILE_CORRESPONDANCE
global NIBA_ID
global DIC_ID
global SIC_CELLID
global SIC_CELLID_PARAMS
filename = join(SIC_ROOT, SIC_PROCESSED, SIC_FILE_CORRESPONDANCE)
mskpath = join(SIC_ROOT, SIC_PROCESSED)
niba = NIBA_ID
dic = DIC_ID
options_fn = join(SIC_ROOT, SIC_SCRIPTS, SIC_CELLID_PARAMS)
output_prefix = join(SIC_ROOT, SIC_PROCESSED)
niba2dic, dic2niba, o2n = create_map_image_data(
filename, mskpath, niba, dic)
sourcepath = join(SIC_ROOT, SIC_PROCESSED)
targetpath = join(SIC_ROOT, SIC_PROCESSED)
create_symlinks(o2n, sourcepath, targetpath)
prepare_b_and_f_single_files(niba2dic, o2n, mskpath)
run_cellid(mskpath, SIC_CELLID,
join(SIC_ROOT, SIC_PROCESSED, SIC_BF_LISTFILE),
join(SIC_ROOT, SIC_PROCESSED, SIC_F_LISTFILE), options_fn,
output_prefix)
global d
d = {
"niba2dic": niba2dic,
"dic2niba": dic2niba,
"o2n": o2n,
}
def run_spotty(self):
global SIC_ROOT
global SIC_PROCESSED
global SIC_LINKS
global SIC_SPOTTY
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
mskpath = join(SIC_ROOT, SIC_PROCESSED)
#cellid_results_path = join(SIC_ROOT, SIC_PROCESSED)
headers, data = load_fiji_results_and_create_mappings(mskpath)
filename2pixel_list = create_mappings_filename2pixel_list(
(headers, data), mskpath)
global d
o2n = d["o2n"]
filename2cells, filename2hist, filename2cell_number = load_cellid_files_and_create_mappings_from_bounds(
filename2pixel_list, o2n, mskpath)
spotty = SIC_SPOTTY
cluster_with_spotty(mskpath, spotty, GMAX) # TODO: GMAX from GUI
d["filename2pixel_list"] = filename2pixel_list
d["headers"] = headers
d["data"] = data
d["filename2cells"] = filename2cells
d["filename2hist"] = filename2hist
d["filename2cell_number"] = filename2cell_number
def aggregate_and_plot(self):
global SIC_ORIG
global SIC_ROOT
global SIC_PROCESSED
global SIC_RESULTS
global SIC_DATA_PICKLE
mskpath = join(SIC_ROOT, SIC_PROCESSED)
global d
try:
d
except NameError:
d = pickle.load(
file(join(SIC_ROOT, SIC_PROCESSED, SIC_DATA_PICKLE)))
o2n = d["o2n"]
spots = aggregate_spots(o2n, mskpath)
d["spots"] = spots
pickle.dump(d, file(join(SIC_ROOT, SIC_RESULTS, SIC_DATA_PICKLE), "w"))
histogram_intensities(spots, mskpath)
scatterplot_intensities(spots, mskpath)
spots_per_cell_distribution(spots, mskpath)
pl.show()
def run_all_steps(self):
global SIC_ROOT
global SIC_PROCESSED
self.prepare_files_and_folder_structure()
self.run_fiji()
self.run_cell_id()
self.run_spotty()
self.aggregate_and_plot()
#FIXME: why does this not work under Windows?
if not self.ui.cb_decimal_separator.isChecked(
): # then we want to replace . by ,
mskpath = join(SIC_ROOT, SIC_PROCESSED)
#print "replacing decimal separators on mskpath =", mskpath
replace_decimal_separators(mskpath)
pl.show()
def file_save(self):
fd = QtGui.QFileDialog(self)
self.filename = fd.getOpenFileName()
from os.path import isfile
if isfile(self.filename):
file = open(self.filename, 'w')
file.write(self.ui.editor_window.toPlainText())
file.close()
def mark_detected_spots(self):
global SIC_ROOT
global SIC_ORIG
global SIC_PROCESSED
SIC_ROOT = str(self.ui.lineEditworking_directory.text())
mskpath = join(SIC_ROOT, SIC_PROCESSED)
draw_spots_for_session(mskpath=join(SIC_ROOT, SIC_PROCESSED),
infofile="all_spots.xls") # FIXME: load
rename_dirs(SIC_ORIG, mskpath)
def end_session(self):
# auto-save machine to preferences file
# auto-save session to session file
global SIC_ROOT
global SIC_ORIG
global SIC_SCRIPTS
global SIC_CELLID
global SIC_FIJI
global SIC_SPOTTY
global NIBA_ID
NIBA_ID = str(self.ui.le_niba_id.text())
global DIC_ID
DIC_ID = str(self.ui.le_dic_id.text())
try:
# save current preferences to last_preferences.pref
preferences_dict = {}
preferences_dict["workingdir"] = str(
self.ui.lineEditworking_directory.text())
preferences_dict["cellidexe"] = str(
self.ui.lineEditcell_id_executable.text())
preferences_dict["fijiexe"] = str(
self.ui.lineEditfiji_executable.text())
preferences_dict["spottyfile"] = str(
self.ui.lineEditspottyR_file.text())
preferences_file = open(join(os.curdir, "last_preferences.pref"),
"w")
pickle.dump(preferences_dict, preferences_file)
# save current session to last_session.ssn
session_dict = {}
session_dict["imagesdir"] = str(self.ui.le_images_directory.text())
session_dict["niba_id"] = str(self.ui.le_niba_id.text())
session_dict["dic_id"] = str(self.ui.le_dic_id.text())
session_file = open(join(os.curdir, "last_session.ssn"), 'w')
pickle.dump(session_dict, session_file)
# This is so that the window closes no matter which variables are set
except:
pass
self.close()
