def __init__(self, parent=None, o_norm=None):
display(
HTML(
'<span style="font-size: 20px; color:blue">Check UI that poped up \
(maybe hidden behind this browser!)</span>'))
if o_norm:
self.o_norm = o_norm
#self.list_files = self.o_norm.data['sample']['file_name']
#self.list_data = self.o_norm.data['sample']['data']
QMainWindow.__init__(self, parent=parent)
self.ui = UiMainWindow()
self.ui.setupUi(self)
self.init_statusbar()
self.setWindowTitle("Background ROI Selection Tool")
self.ui.image_view = pg.ImageView()
self.ui.image_view.ui.roiBtn.hide()
self.ui.image_view.ui.menuBtn.hide()
top_layout = QtGui.QVBoxLayout()
top_layout.addWidget(self.ui.image_view)
self.ui.widget.setLayout(top_layout)
self.init_widgets()
self.integrate_images()
self.display_image()
class Interface(QMainWindow):
roi_width = 0.01
roi_selected = {} #nice formatting of list_roi for outside access
live_data = []
o_norm = None
roi_column_width = 70
integrated_image = None
integrated_image_size = {'width': -1, 'height': -1}
list_roi = {} # 'row": {'x0':None, 'y0': None, 'x1': None, 'y1': None}
default_roi = {'x0': 0, 'y0': 0, 'x1': 50, 'y1': 50, 'id': None}
def __init__(self, parent=None, o_norm=None):
display(
HTML(
'<span style="font-size: 20px; color:blue">Check UI that poped up \
(maybe hidden behind this browser!)</span>'))
if o_norm:
self.o_norm = o_norm
#self.list_files = self.o_norm.data['sample']['file_name']
#self.list_data = self.o_norm.data['sample']['data']
QMainWindow.__init__(self, parent=parent)
self.ui = UiMainWindow()
self.ui.setupUi(self)
self.init_statusbar()
self.setWindowTitle("Background ROI Selection Tool")
self.ui.image_view = pg.ImageView()
self.ui.image_view.ui.roiBtn.hide()
self.ui.image_view.ui.menuBtn.hide()
top_layout = QtGui.QVBoxLayout()
top_layout.addWidget(self.ui.image_view)
self.ui.widget.setLayout(top_layout)
self.init_widgets()
self.integrate_images()
self.display_image()
def init_widgets(self):
nbr_columns = self.ui.table_roi.columnCount()
for _col in range(nbr_columns):
self.ui.table_roi.setColumnWidth(_col, self.roi_column_width)
def init_statusbar(self):
self.eventProgress = QtGui.QProgressBar(self.ui.statusbar)
self.eventProgress.setMinimumSize(20, 14)
self.eventProgress.setMaximumSize(540, 100)
self.eventProgress.setVisible(False)
self.ui.statusbar.addPermanentWidget(self.eventProgress)
# self.parent.eventProgress = QtGui.QProgressBar(self.ui.statusbar)
# self.parent.eventProgress.setMinimumSize(20, 14)
# self.parent.eventProgress.setMaximumSize(540, 100)
# self.parent.eventProgress.setVisible(False)
# self.ui.statusbar.addPermanentWidget(self.parent.eventProgress)
def __get_recap(self, data_array):
if data_array:
[height, width] = np.shape(data_array[0])
nbr_sample = len(data_array)
else:
nbr_sample = '0'
[height, width] = ['N/A', 'N/A']
return [nbr_sample, height, width]
def __built_html_table_row_3_columns(self, name, nbr, height, width):
_html = '<tr><td>' + str(name) + '</td><td>' + str(nbr) + '</td><td>' + str(height) + \
'*' + str(width) + '</td></tr>'
return _html
def recap(self):
"""Display nbr of files loaded and size. This can be used to figure why a normalization failed"""
[nbr_sample, height_sample,
width_sample] = self.__get_recap(self.o_norm.data['sample']['data'])
[nbr_ob, height_ob,
width_ob] = self.__get_recap(self.o_norm.data['ob']['data'])
[nbr_df, height_df,
width_df] = self.__get_recap(self.o_norm.data['df']['data'])
html = '<table><tr><td width="30%"><strong>Type</strong></td><td><strong>Number</strong></td><td>' + \
'<strong>Size (height*width)</strong></td></tr>'
html += self.__built_html_table_row_3_columns('sample', nbr_sample,
height_sample,
width_sample)
html += self.__built_html_table_row_3_columns('ob', nbr_ob, height_ob,
width_ob)
html += self.__built_html_table_row_3_columns('df', nbr_df, height_df,
width_df)
html += '</table>'
display(HTML(html))
def integrate_images(self):
self.integrated_image = np.mean(self.o_norm.data['sample']['data'],
axis=0)
[_height, _width] = np.shape(self.integrated_image)
self.integrated_image_size['height'] = _height
self.integrated_image_size['width'] = _width
def _clean_image(self, image):
_result_inf = np.where(np.isinf(image))
image[_result_inf] = np.NaN
return image
def display_image(self):
_image = np.transpose(self.integrated_image)
_image = self._clean_image(_image)
self.ui.image_view.setImage(_image)
def remove_row_entry(self, row):
_roi_id = self.list_roi[row]['id']
self.ui.image_view.removeItem(_roi_id)
del self.list_roi[row]
#rename row
new_list_roi = {}
new_row_index = 0
for _previous_row_index in self.list_roi.keys():
new_list_roi[new_row_index] = self.list_roi[_previous_row_index]
new_row_index += 1
self.list_roi = new_list_roi
def remove_roi_button_clicked(self):
self.ui.table_roi.blockSignals(True)
_selection = self.ui.table_roi.selectedRanges()
row = _selection[0].topRow()
old_nbr_row = self.ui.table_roi.rowCount()
# remove entry from list of roi
self.remove_row_entry(row)
# update table of rois
self.update_table_roi_ui()
self.ui.table_roi.blockSignals(False)
self.check_add_remove_button_widgets_status()
# update selection
new_nbr_row = self.ui.table_roi.rowCount()
if new_nbr_row == 0:
return
if row == (old_nbr_row - 1):
row = new_nbr_row - 1
_new_selection = QtGui.QTableWidgetSelectionRange(row, 0, row, 3)
self.ui.table_roi.setRangeSelected(_new_selection, True)
def clear_table(self):
nbr_row = self.ui.table_roi.rowCount()
for _row in np.arange(nbr_row):
self.ui.table_roi.removeRow(0)
def update_table_roi_ui(self):
"""Using list_roi as reference, repopulate the table_roi_ui"""
self.ui.table_roi.blockSignals(True)
list_roi = self.list_roi
self.clear_table()
_index_row = 0
for _roi_key in list_roi.keys():
_roi = list_roi[_roi_key]
self.ui.table_roi.insertRow(_index_row)
self._set_item_value(_index_row, 0, _roi['x0'])
# _item = QtGui.QTableWidgetItem(str(_roi['x0']))
# self.ui.table_roi.setItem(_index_row, 0, _item)
self._set_item_value(_index_row, 1, _roi['y0'])
# _item = QtGui.QTableWidgetItem(str(_roi['y0']))
# self.ui.table_roi.setItem(_index_row, 1, _item)
self._set_item_value(_index_row, 2, _roi['x1'])
# _item = QtGui.QTableWidgetItem(str(_roi['x1']))
# self.ui.table_roi.setItem(_index_row, 2, _item)
self._set_item_value(_index_row, 3, _roi['y1'])
# _item = QtGui.QTableWidgetItem(str(_roi['y1']))
# self.ui.table_roi.setItem(_index_row, 3, _item)
_index_row += 1
self.ui.table_roi.blockSignals(False)
#self.ui.table_roi.itemChanged['QTableWidgetItem*'].connect(self.update_table_roi)
def _set_item_value(self, row=0, column=0, value=-1):
_item = QtGui.QTableWidgetItem(str(value))
self.ui.table_roi.setItem(row, column, _item)
def check_roi_validity(self, value, x_axis=True):
"""Make sure the ROI selected or defined stays within the image size"""
min_value = 0
value = np.int(value)
if x_axis:
max_value = self.integrated_image_size['width']
else:
max_value = self.integrated_image_size['height']
if value < 0:
return min_value
if value > max_value:
return max_value
return value
def update_table_roi(self, item):
"""Using the table_roi_ui as reference, will update the list_roi dictionary"""
self.ui.table_roi.blockSignals(True)
nbr_row = self.ui.table_roi.rowCount()
new_list_roi = OrderedDict()
old_list_roi = self.list_roi
for _row in np.arange(nbr_row):
_roi = {}
# checking that x0, y0, x1 and y1 stay within the range of the image
_x0 = self.check_roi_validity(self._get_item_value(_row, 0))
_y0 = self.check_roi_validity(self._get_item_value(_row, 1),
x_axis=False)
_x1 = self.check_roi_validity(self._get_item_value(_row, 2))
_y1 = self.check_roi_validity(self._get_item_value(_row, 3),
x_axis=False)
# updating table content (in case some of the roi were out of scope
self._set_item_value(_row, 0, _x0)
self._set_item_value(_row, 1, _y0)
self._set_item_value(_row, 2, _x1)
self._set_item_value(_row, 3, _y1)
_roi['x0'] = _x0
_roi['y0'] = _y0
_roi['x1'] = _x1
_roi['y1'] = _y1
_roi['id'] = old_list_roi[_row]['id']
new_list_roi[_row] = _roi
self.list_roi = new_list_roi
self.update_image_view_item()
self.ui.table_roi.blockSignals(False)
def update_image_view_item(self):
self.clear_roi_on_image_view()
list_roi = self.list_roi
for _row in list_roi.keys():
_roi = list_roi[_row]
_x0 = np.int(_roi['x0'])
_y0 = np.int(_roi['y0'])
_x1 = np.int(_roi['x1'])
_y1 = np.int(_roi['y1'])
_width = np.abs(_x1 - _x0)
_height = np.abs(_y1 - _y0)
_roi_id = self.init_roi(x0=_x0,
y0=_y0,
width=_width,
height=_height)
_roi['id'] = _roi_id
list_roi[_row] = _roi
self.list_roi = list_roi
def _get_item_value(self, row, column):
_item = self.ui.table_roi.item(row, column)
if _item:
return str(_item.text())
else:
return ''
def roi_manually_moved(self):
list_roi = self.list_roi
for _row in list_roi.keys():
_roi = list_roi[_row]
roi_id = _roi['id']
region = roi_id.getArraySlice(self.integrated_image,
self.ui.image_view.imageItem)
x0 = region[0][0].start
x1 = region[0][0].stop
y0 = region[0][1].start
y1 = region[0][1].stop
_roi['x0'] = x0
_roi['x1'] = x1
_roi['y0'] = y0
_roi['y1'] = y1
list_roi[_row] = _roi
self.list_roi = list_roi
self.update_table_roi_ui()
def clear_roi_on_image_view(self):
list_roi = self.list_roi
for _row in list_roi.keys():
_roi = list_roi[_row]
roi_id = _roi['id']
self.ui.image_view.removeItem(roi_id)
def add_roi_button_clicked(self):
self.clear_roi_on_image_view()
self.ui.table_roi.blockSignals(True)
_selection = self.ui.table_roi.selectedRanges()
if _selection:
row = _selection[0].topRow()
else:
row = 0
# init new row with default value
self.ui.table_roi.insertRow(row)
_default_roi = self.default_roi
_item = QtGui.QTableWidgetItem(str(_default_roi['x0']))
self.ui.table_roi.setItem(row, 0, _item)
_item = QtGui.QTableWidgetItem(str(_default_roi['y0']))
self.ui.table_roi.setItem(row, 1, _item)
_item = QtGui.QTableWidgetItem(str(_default_roi['x1']))
self.ui.table_roi.setItem(row, 2, _item)
_item = QtGui.QTableWidgetItem(str(_default_roi['y1']))
self.ui.table_roi.setItem(row, 3, _item)
# save new list_roi dictionary
nbr_row = self.ui.table_roi.rowCount()
list_roi = OrderedDict()
for _row in np.arange(nbr_row):
_roi = {}
_x0 = self._get_item_value(_row, 0)
_roi['x0'] = np.int(_x0)
_y0 = self._get_item_value(_row, 1)
_roi['y0'] = np.int(_y0)
_x1 = self._get_item_value(_row, 2)
_roi['x1'] = np.int(_x1)
_y1 = self._get_item_value(_row, 3)
_roi['y1'] = np.int(_y1)
x0_int = int(_x0)
y0_int = int(_y0)
width_int = np.abs(x0_int - int(_x1))
height_int = np.abs(y0_int - int(_y1))
_roi_id = self.init_roi(x0=x0_int,
y0=y0_int,
width=width_int,
height=height_int)
_roi['id'] = _roi_id
list_roi[_row] = _roi
self.list_roi = list_roi
self.ui.table_roi.blockSignals(False)
self.check_add_remove_button_widgets_status()
if not _selection:
_new_selection = QtGui.QTableWidgetSelectionRange(0, 0, 0, 3)
self.ui.table_roi.setRangeSelected(_new_selection, True)
def init_roi(self, x0=0, y0=0, width=0, height=0):
_color = QtGui.QColor(62, 13, 244)
_pen = QtGui.QPen()
_pen.setColor(_color)
_pen.setWidthF(self.roi_width)
_roi_id = pg.ROI([x0, y0], [width, height], pen=_pen, scaleSnap=True)
_roi_id.addScaleHandle([1, 1], [0, 0])
_roi_id.addScaleHandle([0, 0], [1, 1])
self.ui.image_view.addItem(_roi_id)
# add connection to roi
_roi_id.sigRegionChanged.connect(self.roi_manually_moved)
return _roi_id
def check_add_remove_button_widgets_status(self):
nbr_row = self.ui.table_roi.rowCount()
if nbr_row > 0:
self.ui.remove_roi_button.setEnabled(True)
else:
self.ui.remove_roi_button.setEnabled(False)
def format_roi(self):
roi_selected = {}
for _key in self.list_roi.keys():
_roi = self.list_roi[_key]
x0 = _roi['x0']
y0 = _roi['y0']
x1 = _roi['x1']
y1 = _roi['y1']
new_entry = {'x0': x0, 'y0': y0, 'x1': x1, 'y1': y1}
roi_selected[_key] = new_entry
self.roi_selected = roi_selected
def apply_clicked(self):
self.update_table_roi(None) #check ROI before leaving application
self.format_roi()
self.close()
def cancel_clicked(self):
self.close()
def closeEvent(self, eventhere=None):
print("Leaving Parameters Selection UI")