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revert reorder
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@soham1202
soham1202 committed Dec 19, 2024
1 parent 33e1d53 commit 5d49b28
Showing 1 changed file with 189 additions and 189 deletions.
378 changes: 189 additions & 189 deletions software/control/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3359,195 +3359,6 @@ def set_autolevel(self,enabled):
print('set autolevel to ' + str(enabled))


class ImageArrayDisplayWindow(QMainWindow):

def __init__(self, window_title=''):
super().__init__()
self.setWindowTitle(window_title)
self.setWindowFlags(self.windowFlags() | Qt.CustomizeWindowHint)
self.setWindowFlags(self.windowFlags() & ~Qt.WindowCloseButtonHint)
self.widget = QWidget()

# interpret image data as row-major instead of col-major
pg.setConfigOptions(imageAxisOrder='row-major')

self.graphics_widget_1 = pg.GraphicsLayoutWidget()
self.graphics_widget_1.view = self.graphics_widget_1.addViewBox()
self.graphics_widget_1.view.setAspectLocked(True)
self.graphics_widget_1.img = pg.ImageItem(border='w')
self.graphics_widget_1.view.addItem(self.graphics_widget_1.img)
self.graphics_widget_1.view.invertY()

self.graphics_widget_2 = pg.GraphicsLayoutWidget()
self.graphics_widget_2.view = self.graphics_widget_2.addViewBox()
self.graphics_widget_2.view.setAspectLocked(True)
self.graphics_widget_2.img = pg.ImageItem(border='w')
self.graphics_widget_2.view.addItem(self.graphics_widget_2.img)
self.graphics_widget_2.view.invertY()

self.graphics_widget_3 = pg.GraphicsLayoutWidget()
self.graphics_widget_3.view = self.graphics_widget_3.addViewBox()
self.graphics_widget_3.view.setAspectLocked(True)
self.graphics_widget_3.img = pg.ImageItem(border='w')
self.graphics_widget_3.view.addItem(self.graphics_widget_3.img)
self.graphics_widget_3.view.invertY()

self.graphics_widget_4 = pg.GraphicsLayoutWidget()
self.graphics_widget_4.view = self.graphics_widget_4.addViewBox()
self.graphics_widget_4.view.setAspectLocked(True)
self.graphics_widget_4.img = pg.ImageItem(border='w')
self.graphics_widget_4.view.addItem(self.graphics_widget_4.img)
self.graphics_widget_4.view.invertY()
## Layout
layout = QGridLayout()
layout.addWidget(self.graphics_widget_1, 0, 0)
layout.addWidget(self.graphics_widget_2, 0, 1)
layout.addWidget(self.graphics_widget_3, 1, 0)
layout.addWidget(self.graphics_widget_4, 1, 1)
self.widget.setLayout(layout)
self.setCentralWidget(self.widget)

# set window size
desktopWidget = QDesktopWidget();
width = min(desktopWidget.height()*0.9,1000) #@@@TO MOVE@@@#
height = width
self.setFixedSize(int(width),int(height))

def display_image(self,image,illumination_source):
if illumination_source < 11:
self.graphics_widget_1.img.setImage(image,autoLevels=False)
elif illumination_source == 11:
self.graphics_widget_2.img.setImage(image,autoLevels=False)
elif illumination_source == 12:
self.graphics_widget_3.img.setImage(image,autoLevels=False)
elif illumination_source == 13:
self.graphics_widget_4.img.setImage(image,autoLevels=False)


class ConfigurationManager(QObject):
def __init__(self,filename="channel_configurations.xml"):
QObject.__init__(self)
self.config_filename = filename
self.configurations = []
self.read_configurations()

def save_configurations(self):
self.write_configuration(self.config_filename)

def write_configuration(self,filename):
self.config_xml_tree.write(filename, encoding="utf-8", xml_declaration=True, pretty_print=True)

def read_configurations(self):
if(os.path.isfile(self.config_filename)==False):
utils_config.generate_default_configuration(self.config_filename)
print('genenrate default config files')
self.config_xml_tree = etree.parse(self.config_filename)
self.config_xml_tree_root = self.config_xml_tree.getroot()
self.num_configurations = 0
for mode in self.config_xml_tree_root.iter('mode'):
self.num_configurations += 1
self.configurations.append(
Configuration(
mode_id = mode.get('ID'),
name = mode.get('Name'),
color = self.get_channel_color(mode.get('Name')),
exposure_time = float(mode.get('ExposureTime')),
analog_gain = float(mode.get('AnalogGain')),
illumination_source = int(mode.get('IlluminationSource')),
illumination_intensity = float(mode.get('IlluminationIntensity')),
camera_sn = mode.get('CameraSN'),
z_offset = float(mode.get('ZOffset')),
pixel_format = mode.get('PixelFormat'),
_pixel_format_options = mode.get('_PixelFormat_options'),
emission_filter_position = int(mode.get('EmissionFilterPosition', 1))
)
)

def update_configuration(self,configuration_id,attribute_name,new_value):
conf_list = self.config_xml_tree_root.xpath("//mode[contains(@ID," + "'" + str(configuration_id) + "')]")
mode_to_update = conf_list[0]
mode_to_update.set(attribute_name,str(new_value))
self.save_configurations()

def update_configuration_without_writing(self, configuration_id, attribute_name, new_value):
conf_list = self.config_xml_tree_root.xpath("//mode[contains(@ID," + "'" + str(configuration_id) + "')]")
mode_to_update = conf_list[0]
mode_to_update.set(attribute_name,str(new_value))

def write_configuration_selected(self,selected_configurations,filename): # to be only used with a throwaway instance
for conf in self.configurations:
self.update_configuration_without_writing(conf.id, "Selected", 0)
for conf in selected_configurations:
self.update_configuration_without_writing(conf.id, "Selected", 1)
self.write_configuration(filename)
for conf in selected_configurations:
self.update_configuration_without_writing(conf.id, "Selected", 0)

def get_channel_color(self, channel):
channel_info = CHANNEL_COLORS_MAP.get(self.extract_wavelength(channel), {'hex': 0xFFFFFF, 'name': 'gray'})
return channel_info['hex']

def extract_wavelength(self, name):
# Split the string and find the wavelength number immediately after "Fluorescence"
parts = name.split()
if 'Fluorescence' in parts:
index = parts.index('Fluorescence') + 1
if index < len(parts):
return parts[index].split()[0] # Assuming 'Fluorescence 488 nm Ex' and taking '488'
for color in ['R', 'G', 'B']:
if color in parts or "full_" + color in parts:
return color
return None


class ContrastManager:
def __init__(self):
self.contrast_limits = {}
self.acquisition_dtype = None

def update_limits(self, channel, min_val, max_val):
self.contrast_limits[channel] = (min_val, max_val)

def get_limits(self, channel, dtype=None):
if dtype is not None:
if self.acquisition_dtype is None:
self.acquisition_dtype = dtype
elif self.acquisition_dtype != dtype:
self.scale_contrast_limits(dtype)
return self.contrast_limits.get(channel, self.get_default_limits())

def get_default_limits(self):
if self.acquisition_dtype is None:
return (0, 1)
elif np.issubdtype(self.acquisition_dtype, np.integer):
info = np.iinfo(self.acquisition_dtype)
return (info.min, info.max)
elif np.issubdtype(self.acquisition_dtype, np.floating):
return (0.0, 1.0)
else:
return (0, 1)

def get_scaled_limits(self, channel, target_dtype):
min_val, max_val = self.get_limits(channel)
if self.acquisition_dtype == target_dtype:
return min_val, max_val

source_info = np.iinfo(self.acquisition_dtype)
target_info = np.iinfo(target_dtype)

scaled_min = (min_val - source_info.min) / (source_info.max - source_info.min) * (target_info.max - target_info.min) + target_info.min
scaled_max = (max_val - source_info.min) / (source_info.max - source_info.min) * (target_info.max - target_info.min) + target_info.min

return scaled_min, scaled_max

def scale_contrast_limits(self, target_dtype):
print(f"{self.acquisition_dtype} -> {target_dtype}")
for channel in self.contrast_limits.keys():
self.contrast_limits[channel] = self.get_scaled_limits(channel, target_dtype)

self.acquisition_dtype = target_dtype


class NavigationViewer(QFrame):

signal_coordinates_clicked = Signal(float, float) # Will emit x_mm, y_mm when clicked
Expand Down Expand Up @@ -3785,6 +3596,195 @@ def handle_mouse_click(self, evt):
return


class ImageArrayDisplayWindow(QMainWindow):

def __init__(self, window_title=''):
super().__init__()
self.setWindowTitle(window_title)
self.setWindowFlags(self.windowFlags() | Qt.CustomizeWindowHint)
self.setWindowFlags(self.windowFlags() & ~Qt.WindowCloseButtonHint)
self.widget = QWidget()

# interpret image data as row-major instead of col-major
pg.setConfigOptions(imageAxisOrder='row-major')

self.graphics_widget_1 = pg.GraphicsLayoutWidget()
self.graphics_widget_1.view = self.graphics_widget_1.addViewBox()
self.graphics_widget_1.view.setAspectLocked(True)
self.graphics_widget_1.img = pg.ImageItem(border='w')
self.graphics_widget_1.view.addItem(self.graphics_widget_1.img)
self.graphics_widget_1.view.invertY()

self.graphics_widget_2 = pg.GraphicsLayoutWidget()
self.graphics_widget_2.view = self.graphics_widget_2.addViewBox()
self.graphics_widget_2.view.setAspectLocked(True)
self.graphics_widget_2.img = pg.ImageItem(border='w')
self.graphics_widget_2.view.addItem(self.graphics_widget_2.img)
self.graphics_widget_2.view.invertY()

self.graphics_widget_3 = pg.GraphicsLayoutWidget()
self.graphics_widget_3.view = self.graphics_widget_3.addViewBox()
self.graphics_widget_3.view.setAspectLocked(True)
self.graphics_widget_3.img = pg.ImageItem(border='w')
self.graphics_widget_3.view.addItem(self.graphics_widget_3.img)
self.graphics_widget_3.view.invertY()

self.graphics_widget_4 = pg.GraphicsLayoutWidget()
self.graphics_widget_4.view = self.graphics_widget_4.addViewBox()
self.graphics_widget_4.view.setAspectLocked(True)
self.graphics_widget_4.img = pg.ImageItem(border='w')
self.graphics_widget_4.view.addItem(self.graphics_widget_4.img)
self.graphics_widget_4.view.invertY()
## Layout
layout = QGridLayout()
layout.addWidget(self.graphics_widget_1, 0, 0)
layout.addWidget(self.graphics_widget_2, 0, 1)
layout.addWidget(self.graphics_widget_3, 1, 0)
layout.addWidget(self.graphics_widget_4, 1, 1)
self.widget.setLayout(layout)
self.setCentralWidget(self.widget)

# set window size
desktopWidget = QDesktopWidget();
width = min(desktopWidget.height()*0.9,1000) #@@@TO MOVE@@@#
height = width
self.setFixedSize(int(width),int(height))

def display_image(self,image,illumination_source):
if illumination_source < 11:
self.graphics_widget_1.img.setImage(image,autoLevels=False)
elif illumination_source == 11:
self.graphics_widget_2.img.setImage(image,autoLevels=False)
elif illumination_source == 12:
self.graphics_widget_3.img.setImage(image,autoLevels=False)
elif illumination_source == 13:
self.graphics_widget_4.img.setImage(image,autoLevels=False)


class ConfigurationManager(QObject):
def __init__(self,filename="channel_configurations.xml"):
QObject.__init__(self)
self.config_filename = filename
self.configurations = []
self.read_configurations()

def save_configurations(self):
self.write_configuration(self.config_filename)

def write_configuration(self,filename):
self.config_xml_tree.write(filename, encoding="utf-8", xml_declaration=True, pretty_print=True)

def read_configurations(self):
if(os.path.isfile(self.config_filename)==False):
utils_config.generate_default_configuration(self.config_filename)
print('genenrate default config files')
self.config_xml_tree = etree.parse(self.config_filename)
self.config_xml_tree_root = self.config_xml_tree.getroot()
self.num_configurations = 0
for mode in self.config_xml_tree_root.iter('mode'):
self.num_configurations += 1
self.configurations.append(
Configuration(
mode_id = mode.get('ID'),
name = mode.get('Name'),
color = self.get_channel_color(mode.get('Name')),
exposure_time = float(mode.get('ExposureTime')),
analog_gain = float(mode.get('AnalogGain')),
illumination_source = int(mode.get('IlluminationSource')),
illumination_intensity = float(mode.get('IlluminationIntensity')),
camera_sn = mode.get('CameraSN'),
z_offset = float(mode.get('ZOffset')),
pixel_format = mode.get('PixelFormat'),
_pixel_format_options = mode.get('_PixelFormat_options'),
emission_filter_position = int(mode.get('EmissionFilterPosition', 1))
)
)

def update_configuration(self,configuration_id,attribute_name,new_value):
conf_list = self.config_xml_tree_root.xpath("//mode[contains(@ID," + "'" + str(configuration_id) + "')]")
mode_to_update = conf_list[0]
mode_to_update.set(attribute_name,str(new_value))
self.save_configurations()

def update_configuration_without_writing(self, configuration_id, attribute_name, new_value):
conf_list = self.config_xml_tree_root.xpath("//mode[contains(@ID," + "'" + str(configuration_id) + "')]")
mode_to_update = conf_list[0]
mode_to_update.set(attribute_name,str(new_value))

def write_configuration_selected(self,selected_configurations,filename): # to be only used with a throwaway instance
for conf in self.configurations:
self.update_configuration_without_writing(conf.id, "Selected", 0)
for conf in selected_configurations:
self.update_configuration_without_writing(conf.id, "Selected", 1)
self.write_configuration(filename)
for conf in selected_configurations:
self.update_configuration_without_writing(conf.id, "Selected", 0)

def get_channel_color(self, channel):
channel_info = CHANNEL_COLORS_MAP.get(self.extract_wavelength(channel), {'hex': 0xFFFFFF, 'name': 'gray'})
return channel_info['hex']

def extract_wavelength(self, name):
# Split the string and find the wavelength number immediately after "Fluorescence"
parts = name.split()
if 'Fluorescence' in parts:
index = parts.index('Fluorescence') + 1
if index < len(parts):
return parts[index].split()[0] # Assuming 'Fluorescence 488 nm Ex' and taking '488'
for color in ['R', 'G', 'B']:
if color in parts or "full_" + color in parts:
return color
return None


class ContrastManager:
def __init__(self):
self.contrast_limits = {}
self.acquisition_dtype = None

def update_limits(self, channel, min_val, max_val):
self.contrast_limits[channel] = (min_val, max_val)

def get_limits(self, channel, dtype=None):
if dtype is not None:
if self.acquisition_dtype is None:
self.acquisition_dtype = dtype
elif self.acquisition_dtype != dtype:
self.scale_contrast_limits(dtype)
return self.contrast_limits.get(channel, self.get_default_limits())

def get_default_limits(self):
if self.acquisition_dtype is None:
return (0, 1)
elif np.issubdtype(self.acquisition_dtype, np.integer):
info = np.iinfo(self.acquisition_dtype)
return (info.min, info.max)
elif np.issubdtype(self.acquisition_dtype, np.floating):
return (0.0, 1.0)
else:
return (0, 1)

def get_scaled_limits(self, channel, target_dtype):
min_val, max_val = self.get_limits(channel)
if self.acquisition_dtype == target_dtype:
return min_val, max_val

source_info = np.iinfo(self.acquisition_dtype)
target_info = np.iinfo(target_dtype)

scaled_min = (min_val - source_info.min) / (source_info.max - source_info.min) * (target_info.max - target_info.min) + target_info.min
scaled_max = (max_val - source_info.min) / (source_info.max - source_info.min) * (target_info.max - target_info.min) + target_info.min

return scaled_min, scaled_max

def scale_contrast_limits(self, target_dtype):
print(f"{self.acquisition_dtype} -> {target_dtype}")
for channel in self.contrast_limits.keys():
self.contrast_limits[channel] = self.get_scaled_limits(channel, target_dtype)

self.acquisition_dtype = target_dtype


class PlateReaderNavigationController(QObject): # Not implemented for Prior stage

signal_homing_complete = Signal()
Expand Down

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