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gui.py
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gui.py
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"""
https://github.com/thladnik/Generic3DAnnotator/gui.py - Main file for starting program/GUI.
Copyright (C) 2020 Tim Hladnik
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
import numpy as np
from matplotlib import cm
from PyQt5 import QtCore, QtWidgets
from PyQt5.QtWidgets import QLabel
import pyqtgraph as pg
import time
import trackpy as tp
import os
from queue import Queue
import pandas as pd
import sys
import gv
import file_handling
import median_subtraction
import util
################################
### Main window
class MainWindow(QtWidgets.QMainWindow):
def __init__(self):
QtWidgets.QMainWindow.__init__(self)
gv.w = self
# Setup
self.resize(1600, 1000)
self.set_title()
self.cw = QtWidgets.QWidget()
self.setCentralWidget(self.cw)
self.cw.setLayout(QtWidgets.QGridLayout())
################
# Create menu
self.mb = QtWidgets.QMenuBar()
self.setMenuBar(self.mb)
self.mb_file = self.mb.addMenu('File')
self.mb_file_open = self.mb_file.addAction('Open file...')
self.mb_file_open.setShortcut('Ctrl+O')
self.mb_file_open.triggered.connect(file_handling.open_file)
self.mb_file_import = self.mb_file.addAction('Import image sequence...')
self.mb_file_import.setShortcut('Ctrl+I')
self.mb_file_import.triggered.connect(file_handling.import_file)
self.mb_file_export = self.mb_file.addAction('Export scaled position data')
self.mb_file_export.setShortcut('Ctrl+E')
#self.mb_file_export.triggered.connect(lambda: self.exportPositionData(scaled=True))
self.mb_file_close = self.mb_file.addAction('Close file')
self.mb_file_close.triggered.connect(file_handling.close_file)
################
# Create ImageView
self.viewer = HDF5ImageView(self, show_second=True, update_fun=self.update_image)
self.cw.layout().addWidget(self.viewer, 0, 0)
self.particle_markers = pg.ScatterPlotItem(size=10,
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 0, 0, 255))
#self.particle_markers.sigClicked.connect(self.clicked_on_particle)
self.viewer.processed_view.addItem(self.particle_markers)
################
# Create right panel
self.rpanel = QtWidgets.QWidget()
self.rpanel.setFixedWidth(350)
self.rpanel.setLayout(QtWidgets.QVBoxLayout())
self.cw.layout().addWidget(self.rpanel, 0, 1)
########
# Phase selection
self.wdgt_phases = QtWidgets.QWidget()
self.wdgt_phases.setLayout(QtWidgets.QHBoxLayout())
label_phases = QLabel('Select phases')
label_phases.setStyleSheet('font-weight:bold;')
self.rpanel.layout().addWidget(label_phases)
self.wdgt_phases.btn_first = QtWidgets.QPushButton('<<')
self.wdgt_phases.btn_first.setFixedWidth(30)
self.wdgt_phases.btn_first.clicked.connect(lambda: self.change_current_phase(-10**10))
self.wdgt_phases.layout().addWidget(self.wdgt_phases.btn_first)
self.wdgt_phases.btn_previous = QtWidgets.QPushButton('<')
self.wdgt_phases.btn_previous.setFixedWidth(30)
self.wdgt_phases.btn_previous.clicked.connect(lambda: self.change_current_phase(-1))
self.wdgt_phases.layout().addWidget(self.wdgt_phases.btn_previous)
self.wdgt_phases.cb_phases = QtWidgets.QComboBox()
self.wdgt_phases.cb_phases.currentTextChanged.connect(self.set_group)
self.wdgt_phases.layout().addWidget(self.wdgt_phases.cb_phases)
self.wdgt_phases.btn_next = QtWidgets.QPushButton('>')
self.wdgt_phases.btn_next.setFixedWidth(30)
self.wdgt_phases.btn_next.clicked.connect(lambda: self.change_current_phase(1))
self.wdgt_phases.layout().addWidget(self.wdgt_phases.btn_next)
self.wdgt_phases.btn_last = QtWidgets.QPushButton('>>')
self.wdgt_phases.btn_last.setFixedWidth(30)
self.wdgt_phases.btn_last.clicked.connect(lambda: self.change_current_phase(10**10))
self.wdgt_phases.layout().addWidget(self.wdgt_phases.btn_last)
self.rpanel.layout().addWidget(self.wdgt_phases)
# Pipeline header
self.pipe_label = QtWidgets.QLabel('Processing pipeline')
self.pipe_label.setStyleSheet('font-weight:bold;')
self.rpanel.layout().addWidget(self.pipe_label)
self.wdgt_pipe_header = QtWidgets.QWidget()
self.wdgt_pipe_header.setLayout(QtWidgets.QHBoxLayout())
self.rpanel.layout().addWidget(self.wdgt_pipe_header)
# This phase
self.wdgt_pipe_header.btn_run_this_phase = QtWidgets.QPushButton('Run THIS')
self.wdgt_pipe_header.layout().addWidget(self.wdgt_pipe_header.btn_run_this_phase)
self.wdgt_pipe_header.btn_run_this_phase.clicked.connect(self.run_current_phase)
# All phases
self.wdgt_pipe_header.btn_run_all_phases = QtWidgets.QPushButton('Run ALL')
self.wdgt_pipe_header.layout().addWidget(self.wdgt_pipe_header.btn_run_all_phases)
self.wdgt_pipe_header.btn_run_all_phases.clicked.connect(self.run_all_phases)
# All phases w/o filtering
self.wdgt_pipe_header.btn_run_all_wo_filter = QtWidgets.QPushButton('Run ALL (w/o filter)')
self.wdgt_pipe_header.layout().addWidget(self.wdgt_pipe_header.btn_run_all_wo_filter)
self.wdgt_pipe_header.btn_run_all_wo_filter.clicked.connect(self.run_all_phases_wo_filter)
hspacer = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Minimum)
self.wdgt_pipe_header.layout().addItem(hspacer)
########
# Import image sequence
self.gb_import = QtWidgets.QGroupBox('1. Import image sequence')
self.gb_import.setLayout(QtWidgets.QVBoxLayout())
self.rpanel.layout().addWidget(self.gb_import)
self.gb_import.btn_import = QtWidgets.QPushButton('Import...')
self.gb_import.btn_import.clicked.connect(file_handling.import_file)
self.gb_import.layout().addWidget(self.gb_import.btn_import)
########
# Set ROI
self.gb_roi = QtWidgets.QGroupBox('2. Set ROI')
self.gb_roi.setLayout(QtWidgets.QGridLayout())
self.rpanel.layout().addWidget(self.gb_roi)
self.gb_roi.le_roi_data = QtWidgets.QLineEdit('')
self.gb_roi.le_roi_data.setEnabled(False)
self.gb_roi.layout().addWidget(self.gb_roi.le_roi_data, 0, 0, 1, 2)
# X length
self.gb_roi.layout().addWidget(QLabel('X-length'), 1, 0)
self.gb_roi.dsp_xlen = QtWidgets.QDoubleSpinBox()
self.gb_roi.dsp_xlen.setMinimum(1.)
self.gb_roi.dsp_xlen.setMaximum(10**10)
self.gb_roi.dsp_xlen.setSingleStep(0.1)
self.gb_roi.dsp_xlen.valueChanged.connect(lambda: self.update_roi_len_params('x'))
self.gb_roi.layout().addWidget(self.gb_roi.dsp_xlen, 1, 1)
# Y length
self.gb_roi.layout().addWidget(QLabel('Y-length'), 2, 0)
self.gb_roi.dsp_ylen = QtWidgets.QDoubleSpinBox()
self.gb_roi.dsp_ylen.setMinimum(1.)
self.gb_roi.dsp_ylen.setMaximum(10**10)
self.gb_roi.dsp_ylen.setSingleStep(0.1)
self.gb_roi.dsp_ylen.valueChanged.connect(lambda: self.update_roi_len_params('y'))
self.gb_roi.layout().addWidget(self.gb_roi.dsp_ylen, 2, 1)
########
# Filter ROI contents
self.gb_filter = QtWidgets.QGroupBox('3. Filter ROI contents')
self.gb_filter.setLayout(QtWidgets.QGridLayout())
self.rpanel.layout().addWidget(self.gb_filter)
# Segment length
self.gb_filter.seg_len = QtWidgets.QSpinBox()
self.gb_filter.seg_len.setMinimum(10)
self.gb_filter.seg_len.setMaximum(9999)
self.gb_filter.seg_len.setValue(200)
self.gb_filter.layout().addWidget(QLabel('Seg. len. [lower = less RAM]'), 0, 0)
self.gb_filter.layout().addWidget(self.gb_filter.seg_len, 0, 1)
# Median range
self.gb_filter.med_range = QtWidgets.QSpinBox()
self.gb_filter.med_range.setMinimum(1)
self.gb_filter.med_range.setMaximum(9999)
self.gb_filter.med_range.setValue(50)
self.gb_filter.layout().addWidget(QLabel('Range [lower = faster]'), 1, 0)
self.gb_filter.layout().addWidget(self.gb_filter.med_range, 1, 1)
# Run
self.gb_filter.btn_run = QtWidgets.QPushButton('Run filter')
self.gb_filter.btn_run.clicked.connect(self.run_roi_filter)
self.gb_filter.layout().addWidget(self.gb_filter.btn_run, 2, 0, 1, 2)
########
# Particle detection
self.gb_detection = QtWidgets.QGroupBox('4. Particle detection')
self.gb_detection.setLayout(QtWidgets.QGridLayout())
# Invert
self.gb_detection.layout().addWidget(QtWidgets.QLabel('Black-on-white'), 0, 0)
self.gb_detection.check_invert = QtWidgets.QCheckBox()
self.gb_detection.layout().addWidget(self.gb_detection.check_invert, 0, 1)
# Diameter
self.gb_detection.layout().addWidget(QtWidgets.QLabel('Diameter'), 1, 0)
self.gb_detection.spn_diameter = QtWidgets.QSpinBox()
self.gb_detection.spn_diameter.valueChanged.connect(self.detection_diameter_validator)
self.gb_detection.spn_diameter.setMinimum(1)
self.gb_detection.spn_diameter.setMaximum(9999)
self.gb_detection.spn_diameter.setValue(11)
self.gb_detection.layout().addWidget(self.gb_detection.spn_diameter, 1, 1)
# Minmass
self.gb_detection.layout().addWidget(QtWidgets.QLabel('Min. brightness'), 2, 0)
self.gb_detection.spn_minmass = QtWidgets.QSpinBox()
self.gb_detection.spn_minmass.setMinimum(1)
self.gb_detection.spn_minmass.setMaximum(9999)
self.gb_detection.spn_minmass.setValue(100)
self.gb_detection.layout().addWidget(self.gb_detection.spn_minmass, 2, 1)
# Run
self.gb_detection.btn_run = QtWidgets.QPushButton('Run')
self.gb_detection.btn_run.clicked.connect(self.run_particle_detection)
self.gb_detection.layout().addWidget(self.gb_detection.btn_run, 3, 0, 1, 2)
self.rpanel.layout().addWidget(self.gb_detection)
########
# Particle tracking
self.gb_tracking = QtWidgets.QGroupBox('5. Trace particles')
self.gb_tracking.setLayout(QtWidgets.QGridLayout())
# Search range
self.gb_tracking.layout().addWidget(QtWidgets.QLabel('Search range'), 0, 0)
self.gb_tracking.spn_srange = QtWidgets.QSpinBox()
self.gb_tracking.spn_srange.setMinimum(1)
self.gb_tracking.spn_srange.setMaximum(9999)
self.gb_tracking.spn_srange.setValue(10)
self.gb_tracking.layout().addWidget(self.gb_tracking.spn_srange, 0, 1)
# Memory
self.gb_tracking.layout().addWidget(QtWidgets.QLabel('Search memory'), 1, 0)
self.gb_tracking.spn_smemory = QtWidgets.QSpinBox()
self.gb_tracking.spn_smemory.setMinimum(1)
self.gb_tracking.spn_smemory.setMaximum(9999)
self.gb_tracking.spn_smemory.setValue(10)
self.gb_tracking.layout().addWidget(self.gb_tracking.spn_smemory, 1, 1)
# Run
self.gb_tracking.btn_run = QtWidgets.QPushButton('Run')
self.gb_tracking.btn_run.clicked.connect(self.run_particle_tracking)
self.gb_tracking.layout().addWidget(self.gb_tracking.btn_run, 3, 0, 1, 2)
self.rpanel.layout().addWidget(self.gb_tracking)
# ########
# # Trace sorting
# self.gb_sorting = QtWidgets.QGroupBox('6. Particle tracking')
# self.gb_sorting.setLayout(QtWidgets.QGridLayout())
# # Toggle sorting
# self.gb_sorting.layout().addWidget(QtWidgets.QLabel('Toggle sorting'), 0, 0)
# self.gb_sorting.toggle_sorting = QtWidgets.QCheckBox()
# self.gb_sorting.toggle_sorting.setChecked(False)
# self.gb_sorting.toggle_sorting.clicked.connect(self.start_particle_id_sorting)
# self.gb_sorting.layout().addWidget(self.gb_sorting.toggle_sorting, 0, 1)
# self.rpanel.layout().addWidget(self.gb_sorting)
# # Save
# self.gb_sorting.btn_save = QtWidgets.QPushButton('Save')
# self.gb_sorting.btn_save.clicked.connect(self.save_particle_id_sorting)
# self.gb_sorting.btn_save.setEnabled(False)
# self.gb_sorting.layout().addWidget(self.gb_sorting.btn_save, 3, 0, 1, 2)
# Attrs
self.particle_id_map: dict = None
self.particle_labels = dict()
# Spacer
vSpacer = QtWidgets.QSpacerItem(1, 1, QtWidgets.QSizePolicy.Minimum, QtWidgets.QSizePolicy.Expanding)
self.rpanel.layout().addItem(vSpacer)
# Add statusbar
gv.statusbar = Statusbar()
self.setStatusBar(gv.statusbar)
self.show()
################
# UI
def update_roi_len_params(self, dim):
if 'x' in dim:
_xlen = gv.w.gb_roi.dsp_xlen.value()
gv.h5f.attrs[gv.KEY_ATTR_ROI_XLEN] = _xlen
if 'y' in dim:
_ylen = gv.w.gb_roi.dsp_ylen.value()
gv.h5f.attrs[gv.KEY_ATTR_ROI_YLEN] = _ylen
def detection_diameter_validator(self, value):
value = value + 1 if value % 2 == 0 else value
self.gb_detection.spn_diameter.setValue(value)
def update_ui(self):
if gv.KEY_ATTR_ROI_XLEN in gv.h5f.attrs:
self.gb_roi.dsp_xlen.setValue(gv.h5f.attrs[gv.KEY_ATTR_ROI_XLEN])
if gv.KEY_ATTR_ROI_YLEN in gv.h5f.attrs:
self.gb_roi.dsp_ylen.setValue(gv.h5f.attrs[gv.KEY_ATTR_ROI_YLEN])
if gv.KEY_ATTR_FILT_SEGLEN in gv.h5f.attrs:
self.gb_filter.seg_len.setValue(gv.h5f.attrs[gv.KEY_ATTR_FILT_SEGLEN])
if gv.KEY_ATTR_FILT_MEDRANGE in gv.h5f.attrs:
self.gb_filter.med_range.setValue(gv.h5f.attrs[gv.KEY_ATTR_FILT_MEDRANGE])
if gv.KEY_ATTR_DETECT_INV in gv.h5f.attrs:
self.gb_detection.check_invert.setCheckState(bool(gv.h5f.attrs[gv.KEY_ATTR_DETECT_INV]))
if gv.KEY_ATTR_DETECT_DIA in gv.h5f.attrs:
self.gb_detection.spn_diameter.setValue(gv.h5f.attrs[gv.KEY_ATTR_DETECT_DIA])
if gv.KEY_ATTR_DETECT_MINMASS in gv.h5f.attrs:
self.gb_detection.spn_minmass.setValue(gv.h5f.attrs[gv.KEY_ATTR_DETECT_MINMASS])
if gv.KEY_ATTR_TRACK_SRANGE in gv.h5f.attrs:
self.gb_tracking.spn_srange.setValue(gv.h5f.attrs[gv.KEY_ATTR_TRACK_SRANGE])
if gv.KEY_ATTR_TRACK_SMEM in gv.h5f.attrs:
self.gb_tracking.spn_smemory.setValue(gv.h5f.attrs[gv.KEY_ATTR_TRACK_SMEM])
# Update phases
self.wdgt_phases.cb_phases.clear()
phase_list = list(gv.h5f.file.keys())
phase_list.sort(key=util.natural_keys)
self.wdgt_phases.cb_phases.addItems(phase_list)
def change_current_phase(self, i):
old_idx = self.wdgt_phases.cb_phases.currentIndex()
max_idx = self.wdgt_phases.cb_phases.count() - 1
new_idx = old_idx + i
# Check limits
if new_idx < 0:
new_idx = 0
elif new_idx > max_idx:
new_idx = max_idx
# Change selection
self.wdgt_phases.cb_phases.setCurrentIndex(new_idx)
def set_title(self, sub=None):
sub = ' - {}'.format(sub) if not(sub is None) else ''
self.setWindowTitle('3D Annotator' + sub)
def set_group(self, group_name):
print(f'Set group to {group_name}')
if not(bool(group_name)):
return
gv.h5f = gv.h5f.file[group_name]
file_handling.open_trackpy()
self.viewer.group_updated()
self.viewer.update_roi_display()
@staticmethod
def get_particle_color(particle_id, order):
colors = gv.CMAP_COLORS
alpha = 250 // order if order > 0 else 255
if particle_id >= 0:
c = (*[int(255 * c) for c in colors[int(particle_id) % len(colors)]], alpha)
else:
c = (255, 0, 0, alpha)
return c
def get_particle_id(self, p) -> int:
# No particles set yet: -1
if 'particle' not in p:
return -1
# Return particle id, if mapping is unavailable
particle_id = p.particle
if gv.particle_map is None:
return int(particle_id)
# Return particle mapping, if available
frame_idx = p.frame
particle_id = gv.particle_map.loc[
(gv.particle_map['frame'] == frame_idx)
& (gv.particle_map['particle'] == particle_id), 'new_particle'] \
.values[0]
return int(particle_id)
def run_pipeline(self, group_names: list, _filter=True, _detection=True, _tracking=True):
filter_params = dict()
filter_params['roi_xlen'] = gv.h5f.attrs[gv.KEY_ATTR_ROI_XLEN]
filter_params['roi_ylen'] = gv.h5f.attrs[gv.KEY_ATTR_ROI_YLEN]
filter_params['roi_pos'] = gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_POS]
filter_params['roi_size'] = gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_SIZE]
filter_params['seg_len'] = self.gb_filter.seg_len.value()
filter_params['med_range'] = self.gb_filter.med_range.value()
filter_params['detect_invert'] = self.gb_detection.check_invert.isChecked()
filter_params['detect_diameter'] = self.gb_detection.spn_diameter.value()
filter_params['detect_minmass'] = self.gb_detection.spn_minmass.value()
filter_params['track_srange'] = self.gb_tracking.spn_srange.value()
filter_params['track_smemory'] = self.gb_tracking.spn_smemory.value()
print('Run pipeline')
for name in group_names:
print(f'For group {name}')
self.wdgt_phases.cb_phases.setCurrentText(name)
gv.app.processEvents()
if _filter:
# Set ROI
self.gb_roi.dsp_xlen.setValue(filter_params['roi_xlen'])
self.gb_roi.dsp_ylen.setValue(filter_params['roi_ylen'])
self.viewer.rect_roi.setPos(filter_params['roi_pos'])
self.viewer.rect_roi.setSize(filter_params['roi_size'])
self.gb_filter.seg_len.setValue(filter_params['seg_len'])
self.gb_filter.med_range.setValue(filter_params['med_range'])
# Run
self.run_roi_filter()
if _detection:
# Set detection
self.gb_detection.check_invert.setCheckState(filter_params['detect_invert'])
self.gb_detection.spn_diameter.setValue(filter_params['detect_diameter'])
self.gb_detection.spn_minmass.setValue(filter_params['detect_minmass'])
# Run
self.run_particle_detection(overwrite=True)
if _tracking:
# Set tracking
self.gb_tracking.spn_srange.setValue(filter_params['track_srange'])
self.gb_tracking.spn_smemory.setValue(filter_params['track_smemory'])
# Run
self.run_particle_tracking()
def run_current_phase(self):
phases = [self.wdgt_phases.cb_phases.currentText()]
self.run_pipeline(phases)
def run_all_phases(self, **kwargs):
phases = [self.wdgt_phases.cb_phases.itemText(i) for i in range(self.wdgt_phases.cb_phases.count())]
self.run_pipeline(phases, **kwargs)
def run_all_phases_wo_filter(self):
self.run_all_phases(_filter=None)
################
# UPDATE PLOT
def update_image(self):
"""Update HDF5Viewer"""
# Set current image frame
self.viewer.update_image()
# Remove all previous markers
self.particle_markers.clear()
# Clear particle_id labels
for id, label in self.particle_labels.items():
label.setText('')
# Plot particles
if gv.tpf is None:
return
# Set current frame index
frame_idx = self.viewer.slider.value()
# Display past particles
particle_trace_max = 5
spots = list()
for i in range(1, particle_trace_max):
idx = frame_idx-i
try:
rows = gv.tpf.get(idx).iterrows()
except Exception as exc:
rows = None
if rows is None:
continue
for _, p in rows:
particle_id = self.get_particle_id(p)
spots.append({'pos': [p.y, p.x],
'data': (particle_id, i),
'size': particle_trace_max-i,
'pen': self.get_particle_color(particle_id, i),
'brush': None})
# Plot current particle
try:
rows = gv.tpf.get(frame_idx).iterrows()
except Exception as exc:
rows = None
if rows is None:
return
# Display current points
for _, p in rows:
particle_id = self.get_particle_id(p)
pos = [p.y, p.x]
color = self.get_particle_color(particle_id, 0)
spots.append({'pos': pos,
'data': (particle_id, 0),
'size': 10,
'pen': color,
'brush': None})
# Add particle_id label
if particle_id not in self.particle_labels:
self.particle_labels[particle_id] = pg.TextItem(str(particle_id))
self.viewer.processed_view.addItem(self.particle_labels[particle_id])
# Set particle_id and position
self.particle_labels[particle_id].setText(str(particle_id))
self.particle_labels[particle_id].setPos(*pos)
# Add spots to scatter plot item
self.particle_markers.addPoints(spots)
################
# ROI & FILTER
def run_roi_filter(self):
# Fetch ROI coordinates
data = gv.h5f[gv.KEY_ORIGINAL][self.viewer.slider.value(),:,:]
img = self.viewer.original_item
im, coords = self.viewer.rect_roi.getArrayRegion(data, img, returnMappedCoords=True)
coords = coords.astype(int)
# Fetch filter parameters
seg_length = self.gb_filter.seg_len.value()
med_range = self.gb_filter.med_range.value()
gv.h5f.attrs[gv.KEY_ATTR_FILT_SEGLEN] = seg_length
gv.h5f.attrs[gv.KEY_ATTR_FILT_MEDRANGE] = med_range
# Run
median_subtraction.run(seg_length, med_range, coords)
# Set roi size and pos for comparison (later)
roi = self.viewer.rect_roi
gv.h5f[gv.KEY_PROCESSED].attrs[gv.KEY_ATTR_FILT_ROI_POS] = [roi.pos().x(), roi.pos().y()]
gv.h5f[gv.KEY_PROCESSED].attrs[gv.KEY_ATTR_FILT_ROI_SIZE] = [roi.size().x(), roi.size().y()]
################
# DETECTION
def run_particle_detection(self, overwrite=False):
print('Run particle detection')
invert = self.gb_detection.check_invert.isChecked()
diameter = self.gb_detection.spn_diameter.value()
minmass = self.gb_detection.spn_minmass.value()
gv.h5f.attrs[gv.KEY_ATTR_DETECT_INV] = invert
gv.h5f.attrs[gv.KEY_ATTR_DETECT_DIA] = diameter
gv.h5f.attrs[gv.KEY_ATTR_DETECT_MINMASS] = minmass
print(f'Invert {invert}')
print(f'Diameter {diameter}')
print(f'Minmass {minmass}')
trackpy_filepath = file_handling.get_trackpy_path()
mode = 'a'
# If detection file exists, ask if should be removed
if os.path.exists(trackpy_filepath):
if not(overwrite):
confirm_dialog = QtWidgets.QMessageBox.question(
gv.w, 'Overwrite?',
'Previous particle detection exists. Overwrite?',
QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No | QtWidgets.QMessageBox.Cancel,
QtWidgets.QMessageBox.No)
if confirm_dialog \
in [QtWidgets.QMessageBox.No, QtWidgets.QMessageBox.Cancel]:
return
print('Remove previous detection file')
if gv.tpf is not None:
gv.tpf.close()
gv.tpf = None
mode = 'w'
# Disable window
gv.statusbar.showMessage('Run particle detection')
gv.w.setEnabled(False)
gv.app.processEvents()
# Run detection
with tp.PandasHDFStoreBig(trackpy_filepath, mode=mode) as s:
tp.batch(gv.h5f[gv.KEY_PROCESSED], diameter, invert=invert, minmass=minmass, output=s, processes='auto')
# Enable window
gv.w.setEnabled(True)
gv.statusbar.set_ready()
# Open detection file
gv.tpf = tp.PandasHDFStoreBig(trackpy_filepath)
################
# TRACKING
def run_particle_tracking(self):
srange = self.gb_tracking.spn_srange.value()
smemory = self.gb_tracking.spn_smemory.value()
gv.h5f.attrs[gv.KEY_ATTR_TRACK_SRANGE] = srange
gv.h5f.attrs[gv.KEY_ATTR_TRACK_SMEM] = smemory
filepath = file_handling.get_trackpy_path()
with tp.PandasHDFStoreBig(filepath) as s:
pred = tp.predict.NearestVelocityPredict(span=5)
for linked in pred.link_df_iter(s, srange, memory=smemory):
s.put(linked)
################
# SORTING
# def start_particle_id_sorting(self):
# # Load id mapping file
# filepath = f'{gv.filepath}.{gv.EXT_TRACKPY}.{gv.EXT_ID_MAP}'
#
# # Create if it doesn't exist yet (on first sorting)
# if not (os.path.exists(filepath)):
# print(f'Create {gv.EXT_ID_MAP} file')
# dfs = list()
# for frame_idx in gv.tpf.frames:
# df = gv.tpf.get(frame_idx)
# df = df.reset_index() # Important for sorting, else duplicate indices
# print(f'Fetch particle ids for frame {frame_idx}. Shape {df.shape}')
# dfs.append(df[['frame', 'particle']])
#
# new_df = pd.concat(dfs)
# new_df.insert(len(new_df.keys()), 'new_particle', new_df['particle'])
# new_df.to_hdf(filepath, 'df')
#
# gv.particle_map = pd.read_hdf(filepath, 'df')
#
# self.gb_sorting.btn_save.setEnabled(True)
#
# def save_particle_id_sorting(self):
# print(self.particle_id_map)
#
# self.particle_id_map = None
# # TODO: iterate over frames, map ids and save to file
# self.gb_sorting.toggle_sorting.setChecked(False)
#
# def clicked_on_particle(self, obj, points):
# # Only if sorting is toggled
# if not (self.gb_sorting.toggle_sorting.isChecked()):
# return
#
# # Click on 1st particle: copy id
# if not (hasattr(self, 'current_particle_id')) \
# or self.current_particle_id is None:
# self.current_particle_id = points[0].data()[0]
# print(f'Set particle {self.current_particle_id}')
# return
#
# # Click on 2nd particle: overwrite with last id
# id = points[0].data()[0]
# confirm_dialog = QtWidgets.QMessageBox.question(
# gv.w, 'Overwrite?',
# f'Set particle {id} to {self.current_particle_id}?',
# QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No,
# QtWidgets.QMessageBox.No)
#
# if confirm_dialog == QtWidgets.QMessageBox.No:
# self.current_particle_id = None
# return
#
# print(f'Set particle {id} to {self.current_particle_id}')
# gv.particle_map.loc[(gv.particle_map['particle'] == self.current_particle_id), 'new_particle'] = id
# # self.particle_id_map[id] = self.current_particle_id
# self.current_particle_id = None
################################
# Statusbar widget
class Statusbar(QtWidgets.QStatusBar):
def __init__(self):
QtWidgets.QStatusBar.__init__(self)
self.set_ready()
self.progressbar = QtWidgets.QProgressBar()
self.progressbar.setMaximumWidth(300)
self.addPermanentWidget(self.progressbar)
self.progressbar.hide()
def start_blocking(self, msg):
self.setEnabled(False)
self.showMessage(msg)
gv.app.processEvents()
def set_ready(self):
self.setEnabled(True)
self.showMessage('Ready')
gv.app.processEvents()
def start_progress(self, descr, max_value):
self.progressbar.show()
self.showMessage(descr)
self.progressbar.setMaximum(max_value)
gv.w.setEnabled(False)
gv.app.processEvents()
def set_progress(self, value):
self.progressbar.setValue(value)
gv.app.processEvents()
def end_progress(self):
self.progressbar.hide()
self.showMessage('Ready')
gv.w.setEnabled(True)
gv.app.processEvents()
################################
# HDF5ImageView
"""
HDF5ImageView is an image view for displaying memory-mapped image sequences from HDF5 formatted files in pyqtgraph.
Adapted in part from pyqtgraph's ImageView:
> ImageView.py - Widget for basic image dispay and analysis
> Copyright 2010 Luke Campagnola
> Distributed under MIT/X11 license. See license.txt for more information.
2020 Tim Hladnik
"""
class HDF5ImageView(QtWidgets.QWidget):
def __init__(self, *args, show_second=False, update_fun=None, original_name=None,**kwargs):
QtWidgets.QWidget.__init__(self, *args, **kwargs)
self.original_name = original_name
self.setLayout(QtWidgets.QVBoxLayout())
self.vwdgt = QtWidgets.QWidget(self)
self.vwdgt.setLayout(QtWidgets.QGridLayout())
self.layout().addWidget(self.vwdgt)
self.slider = QtWidgets.QSlider(QtCore.Qt.Horizontal)
self.slider.setTickPosition(QtWidgets.QSlider.TicksBelow)
self.layout().addWidget(self.slider)
if update_fun is None:
self.slider.valueChanged.connect(self.update_image)
else:
self.slider.valueChanged.connect(update_fun)
# Viewbox
self.original_view = pg.ViewBox()
self.original_view.setAspectLocked(True)
# Original graphics view
self.original_graphics_view = pg.GraphicsView(self.vwdgt)
self.vwdgt.layout().addWidget(self.original_graphics_view, 0, 0)
self.original_graphics_view.setCentralItem(self.original_view)
# Scene
self.original_scene = self.original_graphics_view.scene()
# Image item
self.original_item = pg.ImageItem()
self.original_view.addItem(self.original_item)
self.processed_item = None
if show_second:
# Viewbox
self.processed_view = pg.ViewBox()
self.processed_view.setAspectLocked(True)
# Original graphics view
self.processed_graphics_view = pg.GraphicsView(self.vwdgt)
self.vwdgt.layout().addWidget(self.processed_graphics_view, 0, 1)
self.processed_graphics_view.setCentralItem(self.processed_view)
# Scene
self.processed_scene = self.processed_graphics_view.scene()
# Image item
self.processed_item = pg.ImageItem()
self.processed_view.addItem(self.processed_item)
self.playTimer = QtCore.QTimer()
self.playTimer.timeout.connect(self.timeout)
self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown, QtCore.Qt.Key_A, QtCore.Qt.Key_D]
self.keysPressed = dict()
self._filters = dict()
self.playRate = 0
self._rotation = 0
self._flip_ud = False
self._flip_lr = False
def group_updated(self):
if gv.KEY_ORIGINAL not in gv.h5f:
self.slider.setEnabled(False)
return
self.slider.setEnabled(True)
z_len = gv.h5f[gv.KEY_ORIGINAL].shape[0]-1
self.slider.setMinimum(0)
self.slider.setValue(0)
self.slider.setMaximum(z_len)
self.slider.setTickInterval(1//(100/z_len))
self.update_image()
def set_rotation(self, dir):
self._rotation = dir
def set_flip_ud(self, flip):
self._flip_ud = flip
def set_flip_lr(self, flip):
self._flip_lr = flip
def _rotate(self, im):
return np.rot90(im, self._rotation)
def _flip(self, im):
if self._flip_ud:
im = np.flip(im, -1)
if self._flip_lr:
im = np.flip(im, -2)
return im
def update_image(self):
original_name = gv.KEY_ORIGINAL if self.original_name is None else self.original_name
# Original
if gv.h5f is None or original_name not in gv.h5f:
im = np.array([[[0]]])
else:
im = gv.h5f[original_name][self.slider.value(),:,:]
self.original_item.setImage(self._rotate(self._flip(im)))
if self.processed_item is None:
return
if gv.h5f is None or gv.KEY_PROCESSED not in gv.h5f:
im = np.array([[[0]]])
else:
im = gv.h5f[gv.KEY_PROCESSED][self.slider.value(), :, :]
self.processed_item.setImage(self._rotate(self._flip(im)))
def update_roi_display(self):
if hasattr(self, 'rect_roi'):
self.original_view.removeItem(self.rect_roi)
del self.rect_roi
if gv.h5f is None:
return
image_size = gv.h5f[gv.KEY_ORIGINAL].shape[1:3]
self.rect_roi = pg.RectROI([0,0], [1,1],
pen=pg.mkPen((255, 0, 0)),
maxBounds=QtCore.QRectF(0, 0, *image_size))
self.rect_roi.sigRegionChangeFinished.connect(self.update_roi_params)
self.original_view.addItem(self.rect_roi)
if gv.KEY_ATTR_FILT_ROI_POS in gv.h5f.attrs and gv.KEY_ATTR_FILT_ROI_SIZE in gv.h5f.attrs:
pos_ = gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_POS]
size_ = gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_SIZE]
else:
pos_ = [0, 0]
size_ = image_size
self.rect_roi.setPos(pg.Point(pos_))
self.rect_roi.setSize(pg.Point(size_))
@staticmethod
def update_roi_params(roi: pg.RectROI):
if gv.h5f is None:
return
_pos = [roi.pos().x(), roi.pos().y()]
_size = [roi.size().x(), roi.size().y()]
gv.w.gb_roi.le_roi_data.setText('Pos {:.1f}/{:.1f} / Size {:.1f}/{:.1f}'.format(*_pos, *_size))
if gv.KEY_PROCESSED in gv.h5f:
processed = gv.h5f[gv.KEY_PROCESSED]
mark = False
if gv.KEY_ATTR_FILT_ROI_POS in processed.attrs and gv.KEY_ATTR_FILT_ROI_SIZE in processed.attrs:
_pos_prev = processed.attrs[gv.KEY_ATTR_FILT_ROI_POS]
_size_prev = processed.attrs[gv.KEY_ATTR_FILT_ROI_SIZE]
mark = not(np.all(np.isclose(_pos, _pos_prev)) and np.all(np.isclose(_size, _size_prev)))
if mark:
gv.w.gb_roi.le_roi_data.setStyleSheet('color:#FF0000')
else:
gv.w.gb_roi.le_roi_data.setStyleSheet('color:#000000')
gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_POS] = _pos
gv.h5f.attrs[gv.KEY_ATTR_FILT_ROI_SIZE] = _size
gv.w.update_roi_len_params('xy')
def play(self, rate=None):
"""Begin automatically stepping frames forward at the given rate (in fps).
This can also be accessed by pressing the spacebar."""
# print "play:", rate
if rate is None:
rate = 10
self.playRate = rate
if rate == 0:
self.playTimer.stop()
return
self.lastPlayTime = time.time()
if not self.playTimer.isActive():
self.playTimer.start(16)
def timeout(self):
now = time.time()
dt = now - self.lastPlayTime
if dt < 0:
return
n = int(self.playRate * dt)
if n != 0:
self.lastPlayTime += (float(n)/self.playRate)
if self.slider.value()+n > gv.h5f[gv.KEY_ORIGINAL].shape[0]:
self.play(0)
self.jumpFrames(n)
def jumpFrames(self, n):
"""Move video frame ahead n frames (may be negative)"""
self.slider.setValue(self.slider.value()+n)
def keyPressEvent(self, ev):
if ev.key() == QtCore.Qt.Key_Space:
if self.playRate == 0:
self.play()
else:
self.play(0)
ev.accept()
elif ev.key() == QtCore.Qt.Key_1:
self.play(5)
ev.accept()
elif ev.key() == QtCore.Qt.Key_2:
self.play(10)
ev.accept()
elif ev.key() == QtCore.Qt.Key_3:
self.play(20)
ev.accept()
elif ev.key() == QtCore.Qt.Key_Home:
self.slider.setValue(0)
self.play(0)
ev.accept()
elif ev.key() == QtCore.Qt.Key_End:
self.slider.setValue(self.dset.shape[0] - 1)
self.play(0)
ev.accept()
elif ev.key() in self.noRepeatKeys:
ev.accept()
if ev.isAutoRepeat():
return
self.keysPressed[ev.key()] = 1
self.evalKeyState()
else:
QtWidgets.QWidget.keyPressEvent(self, ev)
def keyReleaseEvent(self, ev):
if ev.key() in [QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End]:
ev.accept()
elif ev.key() in self.noRepeatKeys:
ev.accept()
if ev.isAutoRepeat():
return