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Fixed bugs in histogram plot
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Houman.M_Dastjerdi committed Jul 11, 2024
1 parent ea09e56 commit c60307e
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Showing 3 changed files with 143 additions and 23 deletions.
51 changes: 50 additions & 1 deletion piscat/GUI/Projects/tab_localization.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -136,12 +136,14 @@ def createThirdExclusiveGroup(self):

def createFourthExclusiveGroup(self):
self.checkbox_filter_double_PSF = QtWidgets.QCheckBox("Filter dense PSFs", self)
self.checkbox_filter_border = QtWidgets.QCheckBox("Filter border PSFs", self)
self.checkbox_filter_side_lobes_PSF = QtWidgets.QCheckBox("Filter side lobes PSFs", self)
self.checkbox_filter_asymmetry_PSF = QtWidgets.QCheckBox("Filter asymmetry PSFs", self)
self.checkbox_2DFitting = QtWidgets.QCheckBox("2D Gaussian Fitting", self)
self.checkbox_crappy_frames = QtWidgets.QCheckBox("Filter outlier frames", self)

self.checkbox_filter_asymmetry_PSF.toggled.connect(lambda: self.add_line_asymmetry_PSF())
self.checkbox_filter_border.toggled.connect(lambda: self.add_line_border_margin_PSF())
self.checkbox_2DFitting.toggled.connect(lambda: self.add_line_2DFitting())
self.checkbox_crappy_frames.toggled.connect(lambda: self.add_line_crappy_frames())

Expand All @@ -155,7 +157,8 @@ def createFourthExclusiveGroup(self):
self.grid_filters.addWidget(self.checkbox_filter_side_lobes_PSF, 2, 0)
self.grid_filters.addWidget(self.checkbox_filter_asymmetry_PSF, 3, 0)
self.grid_filters.addWidget(self.checkbox_2DFitting, 4, 0)
self.grid_filters.addWidget(self.btn_filtering, 5, 0)
self.grid_filters.addWidget(self.checkbox_filter_border, 5, 0)
self.grid_filters.addWidget(self.btn_filtering, 6, 0)

self.groupBox_filters.setLayout(self.grid_filters)

Expand All @@ -177,6 +180,21 @@ def add_line_crappy_frames(self):
layout.widget().deleteLater()
self.grid_filters.removeItem(layout)

def add_line_border_margin_PSF(self):
if self.checkbox_filter_border.isChecked():
self.line_border_margin = QtWidgets.QLineEdit(self)
self.line_border_margin.setPlaceholderText("border margin")
self.line_border_margin_label = QtWidgets.QLabel("border margin (px):")

self.grid_filters.addWidget(self.line_border_margin_label, 5, 1)
self.grid_filters.addWidget(self.line_border_margin, 5, 2)

if not self.checkbox_filter_border.isChecked():
for i_ in range(1, 5, 1):
layout = self.grid_filters.itemAtPosition(5, i_)
if layout is not None:
layout.widget().deleteLater()
self.grid_filters.removeItem(layout)
def add_line_asymmetry_PSF(self):
if self.checkbox_filter_asymmetry_PSF.isChecked():
self.line_asymmetry_PSF = QtWidgets.QLineEdit(self)
Expand Down Expand Up @@ -524,6 +542,19 @@ def get_values_crappy_frames(self):

self.empty_value_box_flag = False

def get_values_border_filtering(self):
try:
self.border_margin = int(self.line_border_margin.text())
self.empty_value_box_flag = True

except:
self.msg_box3 = QtWidgets.QMessageBox()
self.msg_box3.setWindowTitle("Warning!")
self.msg_box3.setText("Please filled all parameters!")
self.msg_box3.exec_()

self.empty_value_box_flag = False

def get_values_asymmetry_filtering(self):
try:
self.scale = int(self.line_asymmetry_PSF.text())
Expand Down Expand Up @@ -802,6 +833,22 @@ def do_Filtering(self):
):
pass

if self.checkbox_filter_border.isChecked():
self.get_values_border_filtering()
if self.empty_value_box_flag:
self.df_PSFs_s_filter = self.df_PSFs_s_filter[(self.df_PSFs_s_filter['x'] > self.border_margin) &
(self.df_PSFs_s_filter['x'] < (self.input_video.shape[
2] - self.border_margin)) &
(self.df_PSFs_s_filter['y'] > self.border_margin) &
(self.df_PSFs_s_filter['y'] < (self.input_video.shape[
1] - self.border_margin))]

self.setting_localization["Flag_border_PSFs_filter"] = True
self.setting_localization["border_margin"] = self.border_margin

self.PSFs_Particels_num["#PSFs_after_border_PSFs_filter"] = self.df_PSFs_s_filter.shape[0]
self.empty_value_box_flag = False

if self.checkbox_2DFitting.isChecked():
self.get_values_2DFitting()
if self.empty_value_box_flag:
Expand Down Expand Up @@ -840,6 +887,8 @@ def do_Filtering(self):
] = self.df_PSFs_s_filter.shape[0]
self.empty_value_box_flag = False



self.update_localization.emit(self.df_PSFs_s_filter)
self.output_setting_Tab_Localization.emit(self.setting_localization)
self.output_number_PSFs_tracking.emit(self.PSFs_Particels_num)
Expand Down
75 changes: 69 additions & 6 deletions piscat/GUI/Projects/tab_plot_histogram.py
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,8 @@
from PySide6 import QtCore, QtWidgets

from piscat.Analysis.plot_protein_histogram import PlotProteinHistogram
import os
import time


class Histogram_GUI(QtWidgets.QWidget):
Expand Down Expand Up @@ -29,6 +31,10 @@ def __init__(self, parent=None):
self.plot_hist.clicked.connect(self.do_hist)
self.plot_hist.setFixedWidth(150)

self.save_hist = QtWidgets.QPushButton("save_histogram")
self.save_hist.clicked.connect(self.save_histogram)
self.save_hist.setFixedWidth(150)

self.le_lower_contrast_trim = QtWidgets.QLineEdit()
self.le_lower_contrast_trim.setPlaceholderText("lower_limitation")
self.le_lower_contrast_trim_label = QtWidgets.QLabel("lower limitation (Contrast):")
Expand Down Expand Up @@ -69,6 +75,7 @@ def __init__(self, parent=None):
self.grid.addWidget(self.createFirstExclusiveGroup(), 0, 0)
self.grid.addWidget(self.createSecondExclusiveGroup(), 1, 0)
self.grid.addWidget(self.plot_hist, 2, 0)
self.grid.addWidget(self.save_hist, 3, 0)

self.setLayout(self.grid)

Expand Down Expand Up @@ -114,8 +121,8 @@ def do_hist(self):
self.get_values_histogram_plot()
if self.empty_value_box_flag:
if self.groupBox_gmm.isChecked():
his_ = PlotProteinHistogram(intersection_display_flag=False)
his_(
self.his_ = PlotProteinHistogram(intersection_display_flag=False)
self.his_(
folder_name="",
particles=self.input_data,
batch_size=self.batch_size,
Expand All @@ -124,7 +131,7 @@ def do_hist(self):
MinPeakProminence=0,
)

his_.plot_histogram(
self.his_.plot_histogram(
bins=self.n_bins,
upper_limitation=self.upper_limit,
lower_limitation=self.lower_limit,
Expand All @@ -134,17 +141,28 @@ def do_hist(self):
Flag_GMM_fit=True,
max_n_components=self.max_n_components,
)

#
# self.his_. plot_fit_histogram(bins=self.n_bins,
# upper_limitation=self.upper_limit,
# lower_limitation=self.lower_limit,
# step_range=self.step_limit,
# face="g",
# edge="y",
# Flag_GMM_fit=True,
# max_n_components=self.max_n_components,
# )
else:
his_ = PlotProteinHistogram(intersection_display_flag=False)
his_(
self.his_ = PlotProteinHistogram(intersection_display_flag=False)
self.his_(
folder_name="",
particles=self.input_data,
batch_size=self.batch_size,
video_frame_num=self.number_frames,
MinPeakWidth=self.minPeak_width,
MinPeakProminence=0,
)
his_.plot_histogram(
self.his_.plot_histogram(
bins=self.n_bins,
upper_limitation=self.upper_limit,
lower_limitation=self.lower_limit,
Expand All @@ -154,8 +172,53 @@ def do_hist(self):
Flag_GMM_fit=False,
max_n_components=self.max_n_components,
)

# self.his_.plot_fit_histogram(bins=self.n_bins,
# upper_limitation=self.upper_limit,
# lower_limitation=self.lower_limit,
# step_range=self.step_limit,
# face="g",
# edge="y",
# Flag_GMM_fit=False,
# max_n_components=self.max_n_components,
# )

self.empty_value_box_flag = False

def save_histogram(self):

self.file_path = False
self.file_path = QtWidgets.QFileDialog.getExistingDirectory(
self, "Select Folder", os.path.expanduser("~"), QtWidgets.QFileDialog.ShowDirsOnly
)
timestr = time.strftime("%Y%m%d-%H%M%S")
name_mkdir = timestr
try:
dr_mk = os.path.join(self.file_path, name_mkdir)
os.mkdir(dr_mk)
print("Directory ", name_mkdir, " Created ")
except FileExistsError:
dr_mk = os.path.join(self.file_path, name_mkdir)
print("Directory ", name_mkdir, " already exists")

self.file_path = dr_mk

if self.file_path:
if self.groupBox_gmm.isChecked():
self.his_.save_hist_data(self.file_path,
name='plot_hist_',
upper_limitation=self.upper_limit,
lower_limitation=self.lower_limit,
Flag_GMM_fit=True,
max_n_components=self.max_n_components)
else:
self.his_.save_hist_data(self.file_path,
name='plot_hist.h5',
upper_limitation=self.upper_limit,
lower_limitation=self.lower_limit,
Flag_GMM_fit=False,
max_n_components=self.max_n_components)

def get_values_histogram_plot(self):
try:
self.minPeak_width = float(self.min_peak_width.text())
Expand Down
40 changes: 24 additions & 16 deletions piscat/Trajectory/temporal_filtering.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -184,28 +184,36 @@ def v_profile(self, df_PSFs, window_size=2000):

start_frame = np.max([0, first_frame - window_size])
end_frame = np.min([self.video.shape[0], last_frame + window_size])

particle_center_intensity_follow_backward = self.video[
int(start_frame) : int(first_frame), y_first_frame, x_first_frame
]
particle_center_intensity_follow_forward = self.video[
int(last_frame) : int(end_frame), y_last_frame, x_last_frame
]

particle_center_intensity_follow = np.concatenate(
(
particle_center_intensity_follow_backward,
particle_center_intensity,
particle_center_intensity_follow_forward,
),
axis=0,
)
particle_center_intensity = []
for f_, x_, y_ in zip(particle_frame, particle_X, particle_Y):
particle_center_intensity.append(self.video[int(f_), int(y_), int(x_)])

particle_center_intensity_follow = self.video[start_frame:end_frame, y_first_frame, x_first_frame]
particle_frame_follow = list(range(int(start_frame), int(end_frame)))


# particle_center_intensity_follow_backward = self.video[
# int(start_frame) : int(first_frame), y_first_frame, x_first_frame
# ]
# particle_center_intensity_follow_forward = self.video[
# int(last_frame) : int(end_frame), y_last_frame, x_last_frame
# ]

# particle_center_intensity_follow = np.concatenate(
# (
# particle_center_intensity_follow_backward,
# particle_center_intensity,
# particle_center_intensity_follow_forward,
# ),
# axis=0,
# )
trajectories = []
trajectories.append(intensity_horizontal)
trajectories.append(intensity_vertical)
trajectories.append(particle_center_intensity)
trajectories.append(particle_center_intensity_follow)
trajectories.append(particle_frame)
trajectories.append(particle_frame_follow)
trajectories.append(particle_sigma)
trajectories.append(particle_X)
trajectories.append(particle_Y)
Expand Down

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