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request bin width for tiff and csv files
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@SofiaKapsiani
SofiaKapsiani committed Oct 11, 2024
1 parent 2fbe46e commit 134b3ad
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Showing 3 changed files with 107 additions and 20 deletions.
2 changes: 1 addition & 1 deletion main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
app.setWindowIcon(icon)

window = MainWindow(app)
window.setWindowTitle("FLIMPA (v1.0)")
window.setWindowTitle("FLIMPA (v1.1)")
window.setWindowIcon(icon) # Set the window icon here
window.showMaximized()

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30 changes: 19 additions & 11 deletions utils/lifetime_cal.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ def __init__(self, main_window, app):


# --- Image loading and lifetime calculation --- #
def load_raw_data(self, file_name):
def load_raw_data(self, file_name, bin_width):
"""Function for loading raw data files."""
try:
if file_name.endswith('.sdt'):
Expand All @@ -62,11 +62,7 @@ def load_raw_data(self, file_name):
items, 0, False)
self.shared_info.ptu_channel = items.index(item)
if not ok:
raise DataProcessingError("Channel selection cancelled by user.")




raise DataProcessingError("Channel selection cancelled by user.")

data = ptu[:, ..., self.shared_info.ptu_channel, :].sum(0)
# re-arrange channels to time-channels (change of intensity with time) and x-coordinate, y-coordinate (matches FLIMFit img)
Expand All @@ -77,9 +73,13 @@ def load_raw_data(self, file_name):
elif file_name.endswith('.tiff') or file_name.endswith('.tif'):
data = imread(file_name)
data = data.squeeze()
t_series = []
#t_resolution = 1 / (self.frequency * data.shape[0])
#t_series = np.asarray([i * t_resolution for i in range(data.shape[0])], dtype =np.float32)
if bin_width != None:
if bin_width == "estimate":
t_series = []
else:
t_series = np.asarray([i*10**(-9) * bin_width for i in range(data.shape[0])], dtype =np.float32)
else:
raise UnsupportedFileFormatError()

else:
raise UnsupportedFileFormatError()
Expand All @@ -103,7 +103,7 @@ def load_raw_data(self, file_name):
show_error_message(self.main_window, "Loading Error", f"An unexpected error occurred while loading the file: {e}")
raise FileLoadingError(f"Error loading file '{file_name}': {e}")

def load_irf(self, file_name):
def load_irf(self, file_name, bin_width):
try:
if file_name.endswith('.sdt'):
sdt_file = sdt.SdtFile(file_name)
Expand Down Expand Up @@ -147,7 +147,13 @@ def load_irf(self, file_name):
data = data.reshape((data.shape[0], 1, 1)).astype(np.float32)

# Calculate time series
t_series = []
if bin_width != None:
if bin_width == "estimate":
t_series = []
else:
t_series = np.asarray([i*10**(-9) * bin_width for i in range(data.shape[0])], dtype =np.float32)
else:
raise UnsupportedFileFormatError()

else:
raise UnsupportedFileFormatError("Only .sdt and .csv file formats are supported for IRF data.")
Expand Down Expand Up @@ -265,6 +271,7 @@ def ref_correction(self):
t_resolution = 1 / ( freq* ref_data.shape[0])
t_series = np.asarray([i * t_resolution for i in range(ref_data.shape[0])], dtype =np.float32)
self.shared_info.ref_files_dict[self.ref_filename]['t_series'] = t_series
print("bind width estimated as:", t_resolution*10**9, "ns")

# calculate reference g and s coordinates
ref_g, ref_s, _, _ = self.calc_Coordinates( data=ref_data, t_series=t_series, bins =bins_ref, min_photons=0, max_photons_t = False, mode_same = False)
Expand Down Expand Up @@ -324,6 +331,7 @@ def lifetime_parameters(self, filename, M_ref, phi_ref):
t_resolution = 1 / ( freq* raw_data.shape[0])
t_series = np.asarray([i * t_resolution for i in range(raw_data.shape[0])], dtype =np.float32)
self.shared_info.raw_data_dict[filename]['t_series'] = t_series
print("bind width estimated as:", t_resolution*10**9, "ns")

# analyse manually masked data if availabe
if mask_data is not None:
Expand Down
95 changes: 87 additions & 8 deletions utils/toolbar.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from PySide6.QtWidgets import (QStatusBar, QMenuBar, QFileDialog, QInputDialog, QFileDialog, QLineEdit,
from PySide6.QtWidgets import (QStatusBar, QMenuBar, QFileDialog, QInputDialog, QFileDialog, QLineEdit, QLabel,QPushButton,
QProgressDialog, QApplication, QMessageBox, QComboBox, QVBoxLayout, QDialogButtonBox, QDialog)
from PySide6.QtGui import QDoubleValidator

from PySide6.QtCore import Qt, QTimer
import numpy as np
Expand Down Expand Up @@ -98,15 +99,63 @@ def enter_files_by_cond(self):
if condition:
self.data_condition = condition
fnames = self.file_manager()

def get_float_input(self):
dialog = QDialog(self.main_window)
dialog.setWindowTitle("Input Required")

layout = QVBoxLayout(dialog)

label = QLabel("Enter the bin width (in ns):", dialog)
layout.addWidget(label)

# Create a QLineEdit and set a QDoubleValidator for non-negative values and many decimal places
line_edit = QLineEdit(dialog)
validator = QDoubleValidator(0.0, 2.0, 50) # Non-negative range, 10 decimal places
validator.setNotation(QDoubleValidator.StandardNotation)
line_edit.setValidator(validator)
layout.addWidget(line_edit)

# Create an "Estimate" button
estimate_button = QPushButton("Estimate", dialog)
layout.addWidget(estimate_button)

# Create dialog buttons (OK and Cancel)
buttons = QDialogButtonBox(QDialogButtonBox.Ok | QDialogButtonBox.Cancel, dialog)
layout.addWidget(buttons)

# Connect signals
buttons.accepted.connect(dialog.accept)
buttons.rejected.connect(dialog.reject)

def estimate_bin_width():
# Set the bin width to "estimate"
line_edit.setText("estimate")
# Show a warning message
QMessageBox.warning(dialog, "Warning",
"You have selected 'estimate' for the bin width. This will be calculated as:\n"
"bin width = 1 / (laser repetition rate × bin number).\n\n"
"Please note that this estimation may lead to inaccurate results depending on your data acquisition settings. "
"Please ensure that your laser settings and detection conditions are suitable for this calculation.")

estimate_button.clicked.connect(estimate_bin_width)

if dialog.exec() == QDialog.Accepted:
# Check if user selected "estimate"
if line_edit.text() == "estimate":
return "estimate", True
else:
return float(line_edit.text()), True
else:
return None, False


def file_manager(self):
# Use getOpenFileNames for selecting multiple files
fnames, _ = QFileDialog.getOpenFileNames(self.main_window, "Select one or more files to open") # Adjust the title as needed
if not fnames:
return # Cancel if no files are selected

# channel used when loading .ptu files
self.shared_info.ptu_channel = None

Expand All @@ -119,6 +168,8 @@ def file_manager(self):
progress_dialog.setCancelButton(None)
#progress_dialog.setWindowFlag(Qt.WindowCloseButtonHint, False)

bin_width = None # Initialize bin_width variable to store the user input

try:
for i, fname in enumerate(fnames): # Iterate through the selected files
if fname:
Expand All @@ -127,8 +178,15 @@ def file_manager(self):
progress_dialog.setLabelText(f"Loading file {i+1} of {len(fnames)}")
QApplication.processEvents() # Process events to keep the UI responsive

# Check if the file is a .tif or .tiff and if bin_width is already set
if fname.lower().endswith(('.tif', '.tiff')) and bin_width is None:
# Prompt the user for bin_width only once
bin_width, ok = self.get_float_input()
if not ok or bin_width is None:
break # If the user cancels or no valid input, exit

# Assuming you have a mechanism to process and display each file
data, t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname)
data, t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname, bin_width)

filename = fname.split('/')[-1].split('\\')[-1].split(".")[0]
# check if entry is duplicate and if so rename it
Expand All @@ -154,6 +212,7 @@ def file_manager(self):
self.data_condition = "None"
return fnames


def load_masks(self):
# Select one or more files to open
fnames, _ = QFileDialog.getOpenFileNames(self.main_window, "Select one or more files to open")
Expand All @@ -175,6 +234,7 @@ def load_masks(self):
# Disable the close button and remove the cancel button
progress_dialog.setCancelButton(None)
#progress_dialog.setWindowFlag(Qt.WindowCloseButtonHint, False)
bin_width = None # Initialize bin_width variable to store the user input

try:
for i, fname in enumerate(fnames): # Iterate through the selected files
Expand All @@ -184,8 +244,15 @@ def load_masks(self):
progress_dialog.setLabelText(f"Loading file {i+1} of {len(fnames)}")
QApplication.processEvents() # Process events to keep the UI responsive

# Check if the file is a .tif or .tiff and if bin_width is already set
if fname.lower().endswith(('.tif', '.tiff')) and bin_width is None:
# Prompt the user for bin_width only once
bin_width, ok = self.get_float_input()
if not ok or bin_width is None:
break # If the user cancels or no valid input, exit

# Assuming you have a mechanism to process and display each file
data, t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname)
data, t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname, bin_width)

filename_original = fname.split('/')[-1].split('\\')[-1].split(".")[0]
masked_data, mask_arr = LifetimeData(self.main_window, self.app).mask_data(masks_dir, filename_original, data)
Expand Down Expand Up @@ -225,8 +292,6 @@ def load_masks_cond(self):
self.data_condition = condition
fnames = self.load_masks()



def handle_duplicates(self, filename):
"""Function to rename duplicate entries"""
base_filename = filename
Expand All @@ -238,8 +303,15 @@ def handle_duplicates(self, filename):

def load_ref_file(self):
fname, _ = QFileDialog.getOpenFileName(self.main_window," Selet a reference file to open")

bin_width = None
if fname.lower().endswith(('.tif', '.tiff')) and bin_width is None:
# Prompt the user for bin_width only once
bin_width, ok = self.get_float_input()
if not ok or bin_width is None:
return # If the user cancels or no val

ref_data,t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname)
ref_data,t_series = LifetimeData(self.main_window, self.app).load_raw_data(fname, bin_width)
filename = fname.split('/')[-1].split('\\')[-1].split(".")[0]
# updated reference bins based on time channels of reference file
self.shared_info.ref_files_dict[filename] = {"ref_data":ref_data, "t_series":t_series, "bins_ref": ref_data.shape[0] } # Assuming you want to store the full path
Expand All @@ -248,8 +320,15 @@ def load_ref_file(self):

def load_irf_file(self):
fname, _ = QFileDialog.getOpenFileName(self.main_window," Selet a reference file to open")

bin_width = None
if fname.lower().endswith('.csv') and bin_width is None:
# Prompt the user for bin_width only once
bin_width, ok = self.get_float_input()
if not ok or bin_width is None:
return # If the user cancels or no val

ref_data,t_series = LifetimeData(self.main_window, self.app).load_irf(fname)
ref_data,t_series = LifetimeData(self.main_window, self.app).load_irf(fname, bin_width)
filename = fname.split('/')[-1].split('\\')[-1].split(".")[0]

self.shared_info.ref_files_dict[filename] = {"ref_data":ref_data, "t_series":t_series, "bins_ref" : 1} # Assuming you want to store the full path
Expand Down

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