def register(self):
if self.ui.radioButton_01.isChecked():
print(
'the lama can only operate registrations with multiple localization files'
)
else:
files = define_file_type(self)
pxl = int(self.ui.lineEdit_15.text())
if self.ui.checkBox_02.isChecked():
fixed_ind = 1
else:
fixed_ind = 0
fix_val = int(self.ui.lineEdit_17.text())
roi = define_roi(self)
disp = int(self.ui.lineEdit_32.text())
if self.ui.radioButton_05.isChecked():
reg_ind = 1
else:
reg_ind = 0
if (len(files) % 3) != 0:
print(
'Wrong number of files! The lama always needs 3 files to calculate a registration: A bead file from the first chanel (MCA format), a bead file from the second channel (MCA format), and a localization file from the second channel (MALK format).'
)
else:
lc.calc_registration(files, disp, reg_ind)
lc.statement()
def analyze_hc_cluster(self):
append = '_statMIA'
files = define_file_type(self)
roi = define_roi(self)
eps = float(self.ui.lineEdit_36.text())
pmin = int(self.ui.lineEdit_37.text())
pxl = int(self.ui.lineEdit_15.text())
cond = 0
if self.ui.checkBox_04.isChecked():
cond = 1
for i in range(0, len(files)):
print('condense locs')
hcaType = '/hca_analysis.txt'
lc.hierarchical_cluster_Analysis(files[i], roi, pxl, eps, pmin,
cond, append, hcaType)
'''
if self.ui.checkBox_04.isChecked():
for i in range (0, len(files)):
print ('condense locs')
hcaType = '/hca_condensed_roi.txt'
lc.hierarchical_cluster_Analysis_condensed(files[i], roi, pxl, eps, pmin, append, hcaType)
else:
for i in range (0,len(files)):
hcaType = '/hca_roi.txt'
lc.hierarchical_cluster_Analysis(files[i], roi, pxl, eps, pmin, append, hcaType)
'''
lc.statement()
def cbc_procedure(self):
append = '_statMIA'
files = define_file_type(self)
r_max = int(self.ui.lineEdit_33.text())
inc_num = int(self.ui.lineEdit_34.text())
wf = float(self.ui.lineEdit_35.text())
roi = define_roi(self)
if self.ui.radioButton_01.isChecked(
) and self.ui.radioButton_07.isChecked():
print(
'the lama can only operate cbc analysis with multiple localization files'
)
elif self.ui.radioButton_01.isChecked():
lc.cbc_cluster(files[0], roi, r_max, inc_num, wf, append)
else:
if self.ui.radioButton_07.isChecked():
for i in range(0, len(files), 2):
print('the lama calculates colocalization maps via CBC')
lc.cbc_coloc(files[i], files[i + 1], roi, r_max, inc_num,
wf, append)
else:
for i in range(0, len(files)):
print('the lama calculates cluster maps via CBC')
lc.cbc_cluster(files[i], roi, r_max, inc_num, wf, append)
lc.statement()
def visualize(self):
pxl = int(self.ui.lineEdit_15.text())
acc = int(self.ui.lineEdit_16.text())
if self.ui.checkBox_01.isChecked():
conv_ind = 1
else:
conv_ind = 0
if self.ui.checkBox_02.isChecked():
fixed_ind = 1
else:
fixed_ind = 0
fix_val = int(self.ui.lineEdit_17.text())
if self.ui.checkBox_03.isChecked():
mca_ind = 1
else:
mca_ind = 0
if self.ui.radioButton_03.isChecked():
cbc_ind = 0
roi = define_roi(self)
else:
cbc_ind = 1
roi = define_cbc_roi(self)
thr = float(self.ui.lineEdit_18.text())
min_r = float(self.ui.lineEdit_19.text())
max_r = float(self.ui.lineEdit_20.text())
files = define_file_type(self)
append = '_statMIA'
for i in range(0, len(files)):
lc.analyze_roi_int(roi, pxl, files[i], conv_ind, acc, fixed_ind,
fix_val, cbc_ind, mca_ind, thr, min_r, max_r,
append)
lc.statement()
def detectBeads(self):
files = define_file_type(self)
roi = define_roi(self)
r_min = int(self.ui.lineEdit_28.text())
r_max = int(self.ui.lineEdit_29.text())
on_min = int(self.ui.lineEdit_30.text())
on_max = int(self.ui.lineEdit_31.text())
lc.callBeadDetection(files, roi, r_min, r_max, on_min, on_max)
lc.statement()
def NeNA_acc(self):
append = '_statMIA'
files = define_file_type(self)
roi = define_roi(self)
if self.ui.radioButton_01.isChecked():
lc.calc_NeNA(files[0], roi, append)
else:
for i in range(0, len(files)):
lc.calc_NeNA(files[i], roi, append)
lc.statement()
def Thompson_acc(self):
append = '_statMIA'
files = define_file_type(self)
con_fac = float(self.ui.lineEdit_12.text())
pxl_size = float(self.ui.lineEdit_21.text())
noise = float(self.ui.lineEdit_23.text())
sigma = float(self.ui.lineEdit_13.text())
roi = define_roi(self)
if self.ui.radioButton_01.isChecked():
lc.calc_Thompson(files[0], roi, con_fac, pxl_size, noise, sigma,
append)
else:
for i in range(0, len(files)):
lc.calc_Thompson(files[i], roi, con_fac, pxl_size, noise,
sigma, append)
lc.statement()
def DBSCAN_procedure(self):
append = '_statMIA'
files = define_file_type(self)
roi = define_roi(self)
eps = float(self.ui.lineEdit_36.text())
pmin = int(self.ui.lineEdit_37.text())
pxl = int(self.ui.lineEdit_15.text())
if self.ui.radioButton_10.isChecked():
noise_ind = float(self.ui.lineEdit_38.text())
for i in range(0, len(files)):
lc.OPTICS_based_clustering(files[i], roi, eps, noise_ind, pmin,
pxl, append)
else:
for i in range(0, len(files)):
lc.DBSCAN_based_clustering(files[i], roi, eps, pmin, pxl,
append)
lc.statement()
def smEmiter_procedure(self):
append = '_statMIA'
files = define_file_type(self)
roi = define_roi(self)
rMin = int(self.ui.lineEdit_41.text())
rMax = int(self.ui.lineEdit_42.text())
iMin = int(self.ui.lineEdit_43.text())
iMax = int(self.ui.lineEdit_44.text())
if self.ui.checkBox_05.isChecked():
pType = 1
else:
pType = 0
p = float(self.ui.lineEdit_45.text())
eps = float(self.ui.lineEdit_36.text())
pmin = int(self.ui.lineEdit_37.text())
lc.count_emitters(self.filename, files, roi, rMin, rMax, iMin, iMax,
pType, p, eps, pmin, append)
lc.statement()
def ripley(self):
append = '_statMIA'
files = define_file_type(self)
pxl = int(self.ui.lineEdit_15.text())
if self.ui.checkBox_02.isChecked():
fixed_ind = 1
else:
fixed_ind = 0
fix_val = int(self.ui.lineEdit_17.text())
edge = float(self.ui.lineEdit_24.text()) * 1000
radius = float(self.ui.lineEdit_25.text()) * 1000
inc_num = int(self.ui.lineEdit_26.text())
if self.file_type == 0:
rois = roi = np.zeros([1, 2])
rois[0, 0] = float(self.ui.lineEdit_02.text()) * 1000
rois[0, 1] = float(self.ui.lineEdit_04.text()) * 1000
lc.calc_ripley(files[0], rois, edge, radius, inc_num, pxl,
fixed_ind, fix_val, append)
else:
for i in range(0, len(files), 2):
rois = lc.calc_ripley_rois(files[i + 1])
lc.calc_ripley(files[i], rois, edge, radius, inc_num, pxl,
fixed_ind, fix_val, append)
lc.statement()
def save_settings(self):
dir_name = self.save_filename
settings = np.zeros([53, 1])
# Main / Input
if self.ui.radioButton_01.isChecked():
settings[0] = 1
# Main / ROI
settings[1] = float(self.ui.lineEdit_02.text())
settings[2] = float(self.ui.lineEdit_03.text())
settings[3] = float(self.ui.lineEdit_04.text())
settings[4] = float(self.ui.lineEdit_05.text())
settings[5] = float(self.ui.lineEdit_06.text())
settings[6] = float(self.ui.lineEdit_07.text())
settings[7] = float(self.ui.lineEdit_08.text())
settings[8] = float(self.ui.lineEdit_09.text())
settings[9] = float(self.ui.lineEdit_10.text())
settings[10] = float(self.ui.lineEdit_11.text())
# Main / Setup
settings[11] = float(self.ui.lineEdit_12.text())
settings[12] = float(self.ui.lineEdit_13.text())
settings[13] = float(self.ui.lineEdit_14.text())
# Visualize / Iamge
settings[14] = float(self.ui.lineEdit_15.text())
settings[15] = float(self.ui.lineEdit_16.text())
settings[16] = float(self.ui.lineEdit_17.text())
if self.ui.radioButton_03.isChecked():
settings[17] = 1
if self.ui.checkBox_01.isChecked():
settings[18] = 1
if self.ui.checkBox_02.isChecked():
settings[19] = 1
# Visualize / MCA
if self.ui.checkBox_03.isChecked():
settings[20] = 1
settings[21] = float(self.ui.lineEdit_18.text())
settings[22] = float(self.ui.lineEdit_19.text())
settings[23] = float(self.ui.lineEdit_20.text())
# Precision / Theoretical
settings[24] = float(self.ui.lineEdit_21.text())
settings[25] = float(self.ui.lineEdit_22.text())
settings[26] = float(self.ui.lineEdit_23.text())
# Ripley's K-function
settings[27] = float(self.ui.lineEdit_24.text())
settings[28] = float(self.ui.lineEdit_25.text())
settings[29] = float(self.ui.lineEdit_26.text())
# Register / Bead Detection
settings[30] = float(self.ui.lineEdit_28.text())
settings[31] = float(self.ui.lineEdit_29.text())
settings[32] = float(self.ui.lineEdit_30.text())
settings[33] = float(self.ui.lineEdit_31.text())
# Register / Registration
settings[34] = float(self.ui.lineEdit_32.text())
if self.ui.radioButton_05.isChecked():
settings[35] = 1
# CBC
settings[36] = float(self.ui.lineEdit_33.text())
settings[37] = float(self.ui.lineEdit_34.text())
settings[38] = float(self.ui.lineEdit_35.text())
if self.ui.radioButton_07.isChecked():
settings[39] = 1
# Hierarchical Clustering / sort
if self.ui.radioButton_10.isChecked():
settings[40] = 1
settings[41] = float(self.ui.lineEdit_36.text())
settings[42] = float(self.ui.lineEdit_37.text())
settings[43] = float(self.ui.lineEdit_38.text())
# Hierarchical Clustering / MCA
if self.ui.checkBox_04.isChecked():
settings[44] = 1
# Stoichiometry
settings[45] = float(self.ui.lineEdit_39.text())
settings[46] = float(self.ui.lineEdit_40.text())
settings[47] = float(self.ui.lineEdit_41.text())
settings[48] = float(self.ui.lineEdit_42.text())
settings[49] = float(self.ui.lineEdit_43.text())
settings[50] = float(self.ui.lineEdit_44.text())
if self.ui.checkBox_05.isChecked():
settings[51] = 1
if self.ui.checkBox_06.isChecked():
settings[52] = 1
la.write_settings(settings, dir_name)
lc.statement()
def import_settings(self):
settings = lc.load_settings(self.import_filename)
# Main / Input
if settings[0, 0] == 1.0:
self.ui.radioButton_01.setChecked(True)
else:
self.ui.radioButton_02.setChecked(True)
# Main / ROI
self.ui.lineEdit_02.setText(str(settings[1, 0]))
self.ui.lineEdit_03.setText(str(settings[2, 0]))
self.ui.lineEdit_04.setText(str(settings[3, 0]))
self.ui.lineEdit_05.setText(str(settings[4, 0]))
self.ui.lineEdit_06.setText(str(settings[5, 0]))
self.ui.lineEdit_07.setText(str(settings[6, 0]))
self.ui.lineEdit_08.setText(str(settings[7, 0]))
self.ui.lineEdit_09.setText(str(settings[8, 0]))
self.ui.lineEdit_10.setText(str(settings[9, 0]))
self.ui.lineEdit_11.setText(str(settings[10, 0]))
# Main / Setup
self.ui.lineEdit_12.setText(str(settings[11, 0]))
self.ui.lineEdit_13.setText(str(settings[12, 0]))
self.ui.lineEdit_14.setText(str(settings[13, 0]))
# Visualize / Iamge
self.ui.lineEdit_15.setText(str(int(settings[14, 0])))
self.ui.lineEdit_16.setText(str(int(settings[15, 0])))
self.ui.lineEdit_17.setText(str(int(settings[16, 0])))
if settings[17, 0] == 1.0:
self.ui.radioButton_03.setChecked(True)
else:
self.ui.radioButton_04.setChecked(True)
if settings[18, 0] == 1.0:
self.ui.checkBox_01.setChecked(True)
else:
self.ui.checkBox_01.setChecked(False)
if settings[19, 0] == 1.0:
self.ui.checkBox_02.setChecked(True)
else:
self.ui.checkBox_02.setChecked(False)
# Visualize / MCA
if settings[20, 0] == 1.0:
self.ui.checkBox_03.setChecked(True)
else:
self.ui.checkBox_03.setChecked(False)
self.ui.lineEdit_18.setText(str(int(settings[21, 0])))
self.ui.lineEdit_19.setText(str(int(settings[22, 0])))
self.ui.lineEdit_20.setText(str(int(settings[23, 0])))
# Precision / Theoretical
self.ui.lineEdit_21.setText(str(settings[24, 0]))
self.ui.lineEdit_22.setText(str(settings[25, 0]))
self.ui.lineEdit_23.setText(str(settings[26, 0]))
# Ripley's K-function
self.ui.lineEdit_24.setText(str(settings[27, 0]))
self.ui.lineEdit_25.setText(str(settings[28, 0]))
self.ui.lineEdit_26.setText(str(int(settings[29, 0])))
# Register / Bead Detection
self.ui.lineEdit_28.setText(str(int(settings[30, 0])))
self.ui.lineEdit_29.setText(str(int(settings[31, 0])))
self.ui.lineEdit_30.setText(str(int(settings[32, 0])))
self.ui.lineEdit_31.setText(str(int(settings[33, 0])))
# Register / Registration
self.ui.lineEdit_32.setText(str(int(settings[34, 0])))
if settings[35, 0] == 1.0:
self.ui.radioButton_05.setChecked(True)
else:
self.ui.radioButton_06.setChecked(True)
# CBC
self.ui.lineEdit_33.setText(str(int(settings[36, 0])))
self.ui.lineEdit_34.setText(str(int(settings[37, 0])))
self.ui.lineEdit_35.setText(str(settings[38, 0]))
if settings[39, 0] == 1.0:
self.ui.radioButton_07.setChecked(True)
else:
self.ui.radioButton_08.setChecked(True)
# Hierarchical Clustering / sort
if settings[40, 0] == 1.0:
self.ui.radioButton_10.setChecked(True)
else:
self.ui.radioButton_09.setChecked(True)
self.ui.lineEdit_36.setText(str(int(settings[41, 0])))
self.ui.lineEdit_37.setText(str(int(settings[42, 0])))
self.ui.lineEdit_38.setText(str(settings[43, 0]))
# Hierarchical Clustering / MCA
if settings[44, 0] == 1.0:
self.ui.chekBox_04.setChecked(True)
else:
self.ui.checkBox_04.setChecked(False)
# Stoichiometry
self.ui.lineEdit_39.setText(str(int(settings[45, 0])))
self.ui.lineEdit_40.setText(str(int(settings[46, 0])))
self.ui.lineEdit_41.setText(str(int(settings[47, 0])))
self.ui.lineEdit_42.setText(str(int(settings[48, 0])))
self.ui.lineEdit_43.setText(str(settings[49, 0]))
self.ui.lineEdit_44.setText(str(settings[50, 0]))
if settings[51, 0] == 1.0:
self.ui.chekBox_05.setChecked(True)
else:
self.ui.checkBox_05.setChecked(False)
if settings[52, 0] == 1.0:
self.ui.chekBox_06.setChecked(True)
else:
self.ui.checkBox_06.setChecked(False)
lc.statement()