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lumaviewpro.py
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lumaviewpro.py
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#!/usr/bin/python3
'''
MIT License
Copyright (c) 2024 Etaluma, Inc.
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
```
```
This open source software was developed for use with Etaluma microscopes.
AUTHORS:
Kevin Peter Hickerson, The Earthineering Company
Anna Iwaniec Hickerson, Keck Graduate Institute
Bryan Tiedemann, The Earthineering Company
Gerard Decker, The Earthineering Company
'''
# General
import copy
import logging
import datetime
from datetime import datetime as date_time
import math
import os
import pathlib
import matplotlib.pyplot as plt
from matplotlib.dates import ConciseDateFormatter
import numpy as np
import pandas as pd
import time
import json
import subprocess
import sys
import typing
import shutil
import userpaths
disable_homing = False
############################################################################
#---------------------Directory Initialization-----------------------------#
############################################################################
abspath = os.path.abspath(__file__)
basename = os.path.basename(__file__)
script_path = abspath[:-len(basename)]
print(f"Script Location: {script_path}")
os.chdir(script_path)
# The version.txt file is in the same directory as the actual script, so making sure it can find the version file.
global version
global windows_machine
windows_machine = False
if os.name == "nt":
windows_machine = True
version = ""
try:
with open("version.txt") as f:
version = f.readlines()[0].strip()
except:
pass
PROTOCOL_DATA_DIR_NAME = "ProtocolData"
try:
with open("marker.lvpinstalled") as f:
lvp_installed = True
except:
lvp_installed = False
if windows_machine and (lvp_installed == True):
print("Machine-Type - WINDOWS")
documents_folder = userpaths.get_my_documents()
os.chdir(documents_folder)
lvp_appdata = os.path.join(documents_folder, f"LumaViewPro {version}")
if os.path.exists(lvp_appdata):
pass
else:
os.mkdir(lvp_appdata)
source_path = lvp_appdata
print(f"Data Location: {source_path}")
os.chdir(source_path)
if os.path.exists(os.path.join(lvp_appdata, "data")):
pass
else:
shutil.copytree(os.path.join(script_path, "data"), os.path.join(lvp_appdata, "data"))
if os.path.exists(os.path.join(lvp_appdata, "logs")):
pass
else:
shutil.copytree(os.path.join(script_path, "logs"), os.path.join(lvp_appdata, "logs"))
elif windows_machine and (lvp_installed == False):
print("Machine-Type - WINDOWS (not installed)")
source_path = script_path
else:
print("Machine-Type - NON-WINDOWS")
source_path = script_path
############################################################################
#--------------------------------------------------------------------------#
############################################################################
from lvp_logger import logger
import tkinter
from tkinter import filedialog, Tk
from plyer import filechooser
import imagej.doctor
import imagej
imagej.doctor.checkup()
import scyjava
import modules.profiling_utils as profiling_utils
global profiling_helper
profiling_helper = None
if getattr(sys, 'frozen', False):
import pyi_splash # type: ignore
pyi_splash.update_text("")
# Deactivate kivy logging
#os.environ["KIVY_NO_CONSOLELOG"] = "1"
# Kivy configurations
# Configurations must be set befor Kivy is imported
from kivy.config import Config
Config.set('input', 'mouse', 'mouse, disable_multitouch')
Config.set('graphics', 'resizable', True) # this seemed to have no effect so may be unnessesary
Config.set('kivy', 'exit_on_escape', '0')
# if fixed size at launch
#Config.set('graphics', 'width', '1920')
#Config.set('graphics', 'height', '1080')
# if maximized at launch
Config.set('graphics', 'window_state', 'maximized')
import kivy
kivy.require("2.1.0")
from kivy.app import App
from kivy.factory import Factory
from kivy.graphics import RenderContext
from kivy.input.motionevent import MotionEvent
from kivy.properties import StringProperty, ObjectProperty, BooleanProperty, ListProperty
#from kivy.properties import BoundedNumericProperty, ColorProperty, OptionProperty, NumericProperty
from kivy.clock import Clock
from kivy.metrics import dp
#from kivy.animation import Animation
from kivy.graphics import Line, Color, Rectangle, Ellipse
from kivy_garden.matplotlib.backend_kivyagg import FigureCanvasKivyAgg
# User Interface
from kivy.uix.accordion import AccordionItem
from kivy.uix.boxlayout import BoxLayout
from kivy.uix.floatlayout import FloatLayout
from kivy.uix.scatter import Scatter
from kivy.uix.widget import Widget
from kivy.uix.slider import Slider
from kivy.uix.image import Image
from kivy.uix.button import Button
from kivy.uix.scrollview import ScrollView
from kivy.uix.popup import Popup
from kivy.uix.label import Label
# Video Related
from kivy.graphics.texture import Texture
# User Interface Custom Widgets
from custom_widgets.range_slider import RangeSlider
from custom_widgets.progress_popup import show_popup
#post processing
from image_stitcher import image_stitcher
from modules.video_builder import VideoBuilder
from modules.tiling_config import TilingConfig
import modules.common_utils as common_utils
import labware
from modules.autofocus_executor import AutofocusExecutor
from modules.stitcher import Stitcher
import modules.binning as binning
from modules.composite_generation import CompositeGeneration
from modules.contrast_stretcher import ContrastStretcher
import modules.coord_transformations as coord_transformations
import modules.labware_loader as labware_loader
import modules.objectives_loader as objectives_loader
from modules.protocol import Protocol
from modules.sequenced_capture_executor import SequencedCaptureExecutor
from modules.sequenced_capture_run_modes import SequencedCaptureRunMode
from modules.stack_builder import StackBuilder
from modules.zstack_config import ZStackConfig
from modules.json_helper import CustomJSONizer
from modules.timedelta_formatter import strfdelta
import modules.imagej_helper as imagej_helper
import modules.zprojector as zprojector
from modules.video_writer import VideoWriter
import cv2
import skimage
# Hardware
import lumascope_api
import post_processing
import image_utils
import image_utils_kivy
global lumaview
global settings
global cell_count_content
global graphing_controls
global wellplate_loader
wellplate_loader = None
global objective_helper
objective_helper = None
global coordinate_transformer
coordinate_transformer = None
global ij_helper
ij_helper = None
global sequenced_capture_executor
sequenced_capture_executor = None
# global autofocus_executor
# autofocus_executor = None
global live_histo_setting
live_histo_setting = False
global last_save_folder
last_save_folder = None
global stage
stage = None
global ENGINEERING_MODE
ENGINEERING_MODE = False
global debug_counter
debug_counter = 0
start_str = time.strftime("%Y %m %d %H_%M_%S")
start_str = str(int(round(time.time() * 1000)))
global focus_round
focus_round = 0
def set_last_save_folder(dir: pathlib.Path | None):
if dir is None:
return
global last_save_folder
last_save_folder=dir
def focus_log(positions, values):
global focus_round
if False:
os.chdir(source_path)
try:
file = open('./logs/focus_log.txt', 'a')
except:
if not os.path.isdir('./logs'):
raise FileNotFoundError("Couldn't find 'logs' directory.")
else:
raise
for i, p in enumerate(positions):
mssg = str(focus_round) + '\t' + str(p) + '\t' + str(values[i]) + '\n'
file.write(mssg)
file.close()
focus_round += 1
def _handle_ui_for_leds_off():
global lumaview
for layer in common_utils.get_layers():
lumaview.ids['imagesettings_id'].ids[layer].ids['enable_led_btn'].state = 'normal'
def _handle_ui_for_led(layer: str, enabled: bool, **kwargs):
global lumaview
if enabled:
state = "down"
else:
state = "normal"
lumaview.ids['imagesettings_id'].ids[layer].ids['enable_led_btn'].state = state
def scope_leds_off():
global lumaview
if not lumaview.scope.led:
logger.warning('[LVP Main ] LED controller not available.')
return
lumaview.scope.leds_off()
logger.info('[LVP Main ] lumaview.scope.leds_off()')
_handle_ui_for_leds_off()
def is_image_saving_enabled() -> bool:
if ENGINEERING_MODE == True:
if lumaview.ids['motionsettings_id'].ids['protocol_settings_id'].ids['protocol_disable_image_saving_id'].active:
return False
return True
def _update_step_number_callback(step_num: int):
protocol_settings = lumaview.ids['motionsettings_id'].ids['protocol_settings_id']
protocol_settings.curr_step = step_num-1
protocol_settings.update_step_ui()
def go_to_step(
protocol: Protocol,
step_idx: int,
ignore_auto_gain: bool = False,
include_move: bool = True
):
num_steps = protocol.num_steps()
protocol_settings = lumaview.ids['motionsettings_id'].ids['protocol_settings_id']
if num_steps <= 0:
protocol_settings.curr_step = -1
protocol_settings.update_step_ui()
return
if (step_idx < 0) or (step_idx >= num_steps):
protocol_settings.curr_step = -1
protocol_settings.update_step_ui()
return
step = protocol.step(idx=step_idx)
protocol_settings.ids['step_name_input'].text = step["Name"]
if step['Name'] == '':
step_name = common_utils.generate_default_step_name(
well_label=step["Well"],
color=step['Color'],
z_height_idx=step['Z-Slice'],
tile_label=step['Tile']
)
protocol_settings.ids['step_name_input'].hint_text = step_name
# Convert plate coordinates to stage coordinates
if include_move:
_, labware = get_selected_labware()
sx, sy = coordinate_transformer.plate_to_stage(
labware=labware,
stage_offset=settings['stage_offset'],
px=step["X"],
py=step["Y"]
)
# Move into position
if lumaview.scope.motion.driver:
move_absolute_position('X', sx)
move_absolute_position('Y', sy)
move_absolute_position('Z', step["Z"])
else:
logger.warning('[LVP Main ] Motion controller not available.')
color = step['Color']
layer = lumaview.ids['imagesettings_id'].ids[color]
# open ImageSettings
lumaview.ids['imagesettings_id'].ids['toggle_imagesettings'].state = 'down'
lumaview.ids['imagesettings_id'].toggle_settings()
# set accordion item to corresponding channel
id = f"{color}_accordion"
lumaview.ids['imagesettings_id'].ids[id].collapse = False
# set autofocus checkbox
logger.info(f'[LVP Main ] autofocus: {step["Auto_Focus"]}')
settings[color]['autofocus'] = step['Auto_Focus']
layer.ids['autofocus'].active = step['Auto_Focus']
# set false_color checkbox
logger.info(f'[LVP Main ] false_color: {step["False_Color"]}')
settings[color]['false_color'] = step['False_Color']
layer.ids['false_color'].active = step['False_Color']
# set illumination settings, text, and slider
logger.info(f'[LVP Main ] ill: {step["Illumination"]}')
settings[color]['ill'] = step["Illumination"]
layer.ids['ill_text'].text = str(step["Illumination"])
layer.ids['ill_slider'].value = float(step["Illumination"])
# set gain settings, text, and slider
logger.info(f'[LVP Main ] gain: {step["Gain"]}')
settings[color]['gain'] = step["Gain"]
layer.ids['gain_text'].text = str(step["Gain"])
layer.ids['gain_slider'].value = float(step["Gain"])
# set auto_gain checkbox
logger.info(f'[LVP Main ] auto_gain: {step["Auto_Gain"]}')
settings[color]['auto_gain'] = step["Auto_Gain"]
layer.ids['auto_gain'].active = step["Auto_Gain"]
# set exposure settings, text, and slider
logger.info(f'[LVP Main ] exp: {step["Exposure"]}')
settings[color]['exp'] = step["Exposure"]
layer.ids['exp_text'].text = str(step["Exposure"])
layer.ids['exp_slider'].value = float(step["Exposure"])
# acquire type
for acquire_sel in ('acquire_video', 'acquire_image', 'acquire_none'):
layer.ids[acquire_sel].active = False
if step['Acquire'] == 'video':
layer.ids['acquire_video'].active = True
elif step['Acquire'] == 'image':
layer.ids['acquire_image'].active = True
else:
layer.ids['acquire_none'].active = True
layer.apply_settings(ignore_auto_gain=ignore_auto_gain)
def get_binning_from_ui() -> int:
try:
return int(lumaview.ids['motionsettings_id'].ids['microscope_settings_id'].ids['binning_spinner'].text)
except:
return 1
def get_zstack_params() -> dict:
zstack_settings = lumaview.ids['motionsettings_id'].ids['verticalcontrol_id'].ids['zstack_id']
range = float(zstack_settings.ids['zstack_range_id'].text)
step_size = float(zstack_settings.ids['zstack_stepsize_id'].text)
z_reference = common_utils.convert_zstack_reference_position_setting_to_config(
text_label=zstack_settings.ids['zstack_spinner'].text
)
return {
'range': range,
'step_size': step_size,
'z_reference': z_reference,
}
def get_zstack_positions() -> tuple[bool, dict]:
config = get_zstack_params()
current_pos = lumaview.scope.get_current_position('Z')
zstack_config = ZStackConfig(
range=config['range'],
step_size=config['step_size'],
current_z_reference=config['z_reference'],
current_z_value=current_pos
)
if zstack_config.number_of_steps() <= 0:
return False, {None: None}
return True, zstack_config.step_positions()
def get_layer_configs(
specific_layers: list | None = None,
) -> dict[dict]:
layer_configs = {}
for layer in common_utils.get_layers():
if (specific_layers is not None) and (layer not in specific_layers):
continue
layer_configs[layer] = {}
layer_settings = settings[layer]
acquire = layer_settings['acquire']
video_config = layer_settings['video_config']
autofocus = layer_settings['autofocus']
false_color = layer_settings['false_color']
illumination = round(layer_settings['ill'], common_utils.max_decimal_precision('illumination'))
gain = round(layer_settings['gain'], common_utils.max_decimal_precision('gain'))
auto_gain = common_utils.to_bool(layer_settings['auto_gain'])
exposure = round(layer_settings['exp'], common_utils.max_decimal_precision('exposure'))
focus = layer_settings['focus']
layer_configs[layer] = {
'acquire': acquire,
'video_config': video_config,
'autofocus': autofocus,
'false_color': false_color,
'illumination': illumination,
'gain': gain,
'auto_gain': auto_gain,
'exposure': exposure,
'focus': focus
}
return layer_configs
def get_active_layer_config() -> tuple[str, dict]:
c_layer = None
for layer in common_utils.get_layers():
accordion = layer + '_accordion'
if lumaview.ids['imagesettings_id'].ids[accordion].collapse == False:
c_layer = layer
break
if c_layer is None:
raise Exception("No layer currently selected")
layer_configs = get_layer_configs(
specific_layers=[c_layer]
)
return c_layer, layer_configs[c_layer]
def get_current_plate_position():
if not lumaview.scope.motion.driver:
logger.error(f"Cannot retrieve current plate position")
return {
'x': 0,
'y': 0,
'z': 0
}
pos = lumaview.scope.get_current_position(axis=None)
_, labware = get_selected_labware()
px, py = coordinate_transformer.stage_to_plate(
labware=labware,
stage_offset=settings['stage_offset'],
sx=pos['X'],
sy=pos['Y'],
)
return {
'x': round(px, common_utils.max_decimal_precision('x')),
'y': round(py, common_utils.max_decimal_precision('y')),
'z': round(pos['Z'], common_utils.max_decimal_precision('z'))
}
def get_current_frame_dimensions() -> dict:
microscope_settings = lumaview.ids['motionsettings_id'].ids['microscope_settings_id']
try:
frame_width = int(microscope_settings.ids['frame_width_id'].text)
frame_height = int(microscope_settings.ids['frame_height_id'].text)
except:
raise ValueError(f"Invalid value for frame width/height")
frame = {
'width': frame_width,
'height': frame_height
}
return frame
def get_protocol_time_params() -> dict:
protocol_settings = lumaview.ids['motionsettings_id'].ids['protocol_settings_id']
try:
period = float(protocol_settings.ids['capture_period'].text)
except:
period = 1
period = datetime.timedelta(minutes=period)
try:
duration = float(protocol_settings.ids['capture_dur'].text)
except:
duration = 1
duration = datetime.timedelta(hours=duration)
return {
'period': period,
'duration': duration
}
def get_selected_labware() -> tuple[str, labware.WellPlate]:
protocol_settings = lumaview.ids['motionsettings_id'].ids['protocol_settings_id']
labware_id = protocol_settings.ids['labware_spinner'].text
if len(labware_id) < 1:
labware_id = settings['protocol']['labware']
try:
labware = wellplate_loader.get_plate(plate_key=labware_id)
return labware_id, labware
except Exception as e:
logger.error("LVP Main: Settings file issue. Replace file with a known working version")
logger.error(e)
def get_image_capture_config_from_ui() -> dict:
microscope_settings = lumaview.ids['motionsettings_id'].ids['microscope_settings_id']
output_format = {
'live': microscope_settings.ids['live_image_output_format_spinner'].text,
'sequenced': microscope_settings.ids['sequenced_image_output_format_spinner'].text,
}
use_full_pixel_depth = lumaview.ids['viewer_id'].ids['scope_display_id'].use_full_pixel_depth
return {
'output_format': output_format,
'use_full_pixel_depth': use_full_pixel_depth,
}
def get_sequenced_capture_config_from_ui() -> dict:
objective_id, _ = get_current_objective_info()
time_params = get_protocol_time_params()
labware_id, _ = get_selected_labware()
protocol_settings = lumaview.ids['motionsettings_id'].ids['protocol_settings_id']
tiling = protocol_settings.ids['tiling_size_spinner'].text
use_zstacking = protocol_settings.ids['acquire_zstack_id'].active
frame_dimensions = get_current_frame_dimensions()
zstack_params = get_zstack_params()
layer_configs = get_layer_configs()
config = {
'labware_id': labware_id,
'objective_id': objective_id,
'zstack_params': zstack_params,
'use_zstacking': use_zstacking,
'tiling': tiling,
'layer_configs': layer_configs,
'period': time_params['period'],
'duration': time_params['duration'],
'frame_dimensions': frame_dimensions,
'binning_size': get_binning_from_ui(),
}
return config
def get_auto_gain_settings() -> dict:
autogain_settings = settings['protocol']['autogain'].copy()
autogain_settings['max_duration'] = datetime.timedelta(seconds=autogain_settings['max_duration_seconds'])
del autogain_settings['max_duration_seconds']
return autogain_settings
def create_hyperstacks_if_needed():
image_capture_config = get_image_capture_config_from_ui()
if image_capture_config['output_format']['sequenced'] == 'ImageJ Hyperstack':
_, objective = get_current_objective_info()
stack_builder = StackBuilder()
stack_builder.load_folder(
path=sequenced_capture_executor.run_dir(),
tiling_configs_file_loc=pathlib.Path(source_path) / "data" / "tiling.json",
binning_size=get_binning_from_ui(),
focal_length=objective['focal_length'],
)
def get_current_objective_info() -> tuple[str, dict]:
objective_id = settings['objective_id']
objective = objective_helper.get_objective_info(objective_id=objective_id)
return objective_id, objective
def _handle_ui_update_for_axis(axis: str):
axis = axis.upper()
if axis == 'Z':
lumaview.ids['motionsettings_id'].ids['verticalcontrol_id'].update_gui()
elif axis in ('X', 'Y', 'XY'):
lumaview.ids['motionsettings_id'].update_xy_stage_control_gui()
# Wrapper function when moving to update UI position
def move_absolute_position(
axis: str,
pos: float,
wait_until_complete: bool = False,
overshoot_enabled: bool = True
):
lumaview.scope.move_absolute_position(
axis=axis,
pos=pos,
wait_until_complete=wait_until_complete,
overshoot_enabled=overshoot_enabled
)
_handle_ui_update_for_axis(axis=axis)
# Wrapper function when moving to update UI position
def move_relative_position(
axis: str,
um: float,
wait_until_complete: bool = False,
overshoot_enabled: bool = True
):
lumaview.scope.move_relative_position(
axis=axis,
um=um,
wait_until_complete=wait_until_complete,
overshoot_enabled=overshoot_enabled
)
_handle_ui_update_for_axis(axis=axis)
def move_home(axis: str):
global version
axis = axis.upper()
Window.set_title(f"Lumaview Pro {version} | Homing, please wait...")
if axis == 'Z':
lumaview.scope.zhome()
elif axis == 'XY':
lumaview.scope.xyhome()
_handle_ui_update_for_axis(axis=axis)
Clock.schedule_once(lambda dt: Window.set_title(f"Lumaview Pro {version}"), 1)
def live_histo_off():
if live_histo_setting == True and lumaview.ids['viewer_id'].ids['scope_display_id'].use_live_image_histogram_equalization == True:
lumaview.ids['viewer_id'].ids['scope_display_id'].use_live_image_histogram_equalization = False
logger.info('[LVP Main ] Live Histogram Equalization] False')
def live_histo_reverse():
if live_histo_setting == True and lumaview.ids['viewer_id'].ids['scope_display_id'].use_live_image_histogram_equalization == False:
lumaview.ids['viewer_id'].ids['scope_display_id'].use_live_image_histogram_equalization = True
logger.info('[LVP Main ] Live Histogram Equalization] True')
# -------------------------------------------------------------------------
# SCOPE DISPLAY Image representing the microscope camera
# -------------------------------------------------------------------------
class ScopeDisplay(Image):
record = BooleanProperty(None)
record = False
play = BooleanProperty(None)
play = True
def __init__(self, **kwargs):
super(ScopeDisplay,self).__init__(**kwargs)
logger.info('[LVP Main ] ScopeDisplay.__init__()')
self.use_bullseye = False
self.use_crosshairs = False
self.use_live_image_histogram_equalization = False
self._contrast_stretcher = ContrastStretcher(
window_len=3,
bottom_pct=0.3,
top_pct=0.3,
)
self.use_full_pixel_depth = False
self.start()
def start(self, fps = 10):
logger.info('[LVP Main ] ScopeDisplay.start()')
self.fps = fps
logger.info('[LVP Main ] Clock.schedule_interval(self.update, 1.0 / self.fps)')
Clock.schedule_interval(self.update_scopedisplay, 1.0 / self.fps)
def stop(self):
logger.info('[LVP Main ] ScopeDisplay.stop()')
logger.info('[LVP Main ] Clock.unschedule(self.update)')
Clock.unschedule(self.update_scopedisplay)
def touch(self, target: Widget, event: MotionEvent):
if event.is_touch and (event.device == 'mouse') and (event.button == 'right'):
norm_texture_width, norm_texture_height = self.norm_image_size
norm_texture_x_min = self.center_x - norm_texture_width/2
norm_texture_x_max = self.center_x + norm_texture_width/2
norm_texture_y_min = self.center_y - norm_texture_height/2
norm_texture_y_max = self.center_y + norm_texture_height/2
click_pos_x = event.pos[0]
click_pos_y = event.pos[1]
# Check if click occurred within texture
if (click_pos_x >= norm_texture_x_min) and (click_pos_x <= norm_texture_x_max) and \
(click_pos_y >= norm_texture_y_min) and (click_pos_y <= norm_texture_y_max):
norm_texture_click_pos_x = click_pos_x - norm_texture_x_min
norm_texture_click_pos_y = click_pos_y - norm_texture_y_min
texture_width, texture_height = self.texture_size
# Scale to image pixels
texture_click_pos_x = norm_texture_click_pos_x * texture_width / norm_texture_width
texture_click_pos_y = norm_texture_click_pos_y * texture_height / norm_texture_height
# Distance from center
x_dist_pixel = texture_click_pos_x - texture_width/2 # Positive means to the right of center
y_dist_pixel = texture_click_pos_y - texture_height/2 # Positive means above center
_, objective = get_current_objective_info()
pixel_size_um = common_utils.get_pixel_size(
focal_length=objective['focal_length'],
binning_size=get_binning_from_ui(),
)
x_dist_um = x_dist_pixel * pixel_size_um
y_dist_um = y_dist_pixel * pixel_size_um
move_relative_position(axis='X', um=x_dist_um)
move_relative_position(axis='Y', um=y_dist_um)
@staticmethod
def add_crosshairs(image):
height, width = image.shape[0], image.shape[1]
if image.ndim == 3:
is_color = True
else:
is_color = False
center_x = round(width/2)
center_y = round(height/2)
# Crosshairs - 2 pixels wide
if is_color:
image[:,center_x-1:center_x+1,:] = 255
image[center_y-1:center_y+1,:,:] = 255
else:
image[:,center_x-1:center_x+1] = 255
image[center_y-1:center_y+1,:] = 255
# Radiating circles
num_circles = 4
minimum_dimension = min(height, width)
circle_spacing = round(minimum_dimension/ 2 / num_circles)
for i in range(num_circles):
radius = (i+1) * circle_spacing
rr, cc = skimage.draw.circle_perimeter(center_y, center_x, radius=radius, shape=image.shape)
image[rr, cc] = 255
# To make circles 2 pixel wide...
rr, cc = skimage.draw.circle_perimeter(center_y, center_x, radius=radius+1, shape=image.shape)
image[rr, cc] = 255
return image
@staticmethod
def transform_to_bullseye(image):
image_bullseye = np.zeros((*image.shape, 3), dtype=np.uint8)
# The range is defined by (start_value, end_value]
# key: [start_value, end_value, RGB Value]
color_map = {
0: [ -1, 5, 0, 0, 0],
1: [ 5, 15, 0, 255, 0],
2: [ 15, 25, 0, 0, 0],
3: [ 25, 35, 0, 255, 0],
4: [ 35, 45, 0, 0, 0],
5: [ 45, 55, 0, 255, 0],
6: [ 55, 65, 0, 0, 0],
7: [ 65, 75, 0, 255, 0],
8: [ 75, 85, 0, 0, 0],
9: [ 85, 95, 0, 255, 0],
10: [ 95, 105, 0, 0, 0],
11: [105, 115, 0, 255, 0],
12: [115, 125, 0, 0, 0],
13: [125, 135, 0, 0, 255],
14: [135, 145, 0, 0, 0],
15: [145, 155, 0, 255, 0],
16: [155, 165, 0, 0, 0],
17: [165, 175, 0, 255, 0],
18: [175, 185, 0, 0, 0],
19: [185, 195, 0, 255, 0],
20: [195, 205, 0, 0, 0],
21: [205, 215, 0, 255, 0],
22: [215, 225, 0, 0, 0],
23: [225, 235, 0, 255, 0],
24: [235, 245, 0, 0, 0],
25: [245, 255, 255, 0, 0]
}
for key in color_map.keys():
start, end, *_rgb = color_map[key]
boolean_array = np.logical_and(image > start, image <= end)
image_bullseye[boolean_array] = _rgb
return image_bullseye
def update_scopedisplay(self, dt=0):
global lumaview
global debug_counter
if lumaview.scope.camera.active == False:
self.source = "./data/icons/camera to USB.png"
return
image = lumaview.scope.get_image(force_to_8bit=True)
if (image is False) or (image.size == 0):
return
if ENGINEERING_MODE == True:
debug_counter += 1
if debug_counter == 30:
debug_counter = 0
if debug_counter % 10 == 0:
mean = round(np.mean(a=image), 2)
stddev = round(np.std(a=image), 2)
af_score = lumaview.scope.focus_function(
image=image,
include_logging=False
)
open_layer = None
for layer in common_utils.get_layers():
accordion = layer + '_accordion'
if lumaview.ids['imagesettings_id'].ids[accordion].collapse == False:
open_layer = layer
break
if open_layer is not None:
lumaview.ids['imagesettings_id'].ids[open_layer].ids['image_stats_mean_id'].text = f"Mean: {mean}"
lumaview.ids['imagesettings_id'].ids[open_layer].ids['image_stats_stddev_id'].text = f"StdDev: {stddev}"
lumaview.ids['imagesettings_id'].ids[open_layer].ids['image_af_score_id'].text = f"AF Score: {af_score}"
if debug_counter % 3 == 0:
if self.use_bullseye:
image_bullseye = self.transform_to_bullseye(image=image)
if self.use_crosshairs:
image_bullseye = self.add_crosshairs(image=image_bullseye)
texture = Texture.create(size=(image_bullseye.shape[1],image_bullseye.shape[0]), colorfmt='rgb')
texture.blit_buffer(image_bullseye.tobytes(), colorfmt='rgb', bufferfmt='ubyte')
self.texture = texture
if not self.use_bullseye:
if self.use_live_image_histogram_equalization:
image = self._contrast_stretcher.update(image)
# image=cv2.normalize(src=image, dst=None, alpha=0, beta=255, norm_type=cv2.NORM_MINMAX, dtype=cv2.CV_8U)
if self.use_crosshairs:
image = self.add_crosshairs(image=image)
# Convert to texture for display (using OpenGL)
texture = Texture.create(size=(image.shape[1],image.shape[0]), colorfmt='luminance')
texture.blit_buffer(image.flatten(), colorfmt='luminance', bufferfmt='ubyte')
self.texture = texture
if self.record == True:
lumaview.live_capture()
# -------------------------------------------------------------------------
# COMPOSITE CAPTURE FloatLayout with shared capture capabilities
# -------------------------------------------------------------------------
class CompositeCapture(FloatLayout):
def __init__(self, **kwargs):
super(CompositeCapture,self).__init__(**kwargs)
# Gets the current well label (ex. A1, C2, ...)
def get_well_label(self):
_, labware = get_selected_labware()
# Get target position
try:
x_target = lumaview.scope.get_target_position('X')
y_target = lumaview.scope.get_target_position('Y')
except:
logger.exception('[LVP Main ] Error talking to Motor board.')
raise
x_target, y_target = coordinate_transformer.stage_to_plate(