PR#100 merge bug fix

software/control/core/core.py

@@ -24,6 +24,7 @@
     from control.multipoint_built_in_functionalities import malaria_rtp
 
 import control.utils as utils
+import control.utils_channel as utils_channel
 import control.utils_config as utils_config
 import control.tracking as tracking
 import control.serial_peripherals as serial_peripherals
@@ -499,7 +500,7 @@ def __init__(
     def turn_on_illumination(self):
         if self.illuminationController is not None and not "LED matrix" in self.currentConfiguration.name:
             self.illuminationController.turn_on_illumination(
-                int(utils.extract_wavelength_from_config_name(self.currentConfiguration.name))
+                int(utils_channel.extract_wavelength_from_config_name(self.currentConfiguration.name))
             )
         elif SUPPORT_SCIMICROSCOPY_LED_ARRAY and "LED matrix" in self.currentConfiguration.name:
             self.led_array.turn_on_illumination()
@@ -510,7 +511,7 @@ def turn_on_illumination(self):
     def turn_off_illumination(self):
         if self.illuminationController is not None and not "LED matrix" in self.currentConfiguration.name:
             self.illuminationController.turn_off_illumination(
-                int(utils.extract_wavelength_from_config_name(self.currentConfiguration.name))
+                int(utils_channel.extract_wavelength_from_config_name(self.currentConfiguration.name))
             )
         elif SUPPORT_SCIMICROSCOPY_LED_ARRAY and "LED matrix" in self.currentConfiguration.name:
             self.led_array.turn_off_illumination()
@@ -563,7 +564,7 @@ def set_illumination(self, illumination_source, intensity, update_channel_settin
             # update illumination
             if self.illuminationController is not None:
                 self.illuminationController.set_intensity(
-                    int(utils.extract_wavelength_from_config_name(self.currentConfiguration.name)), intensity
+                    int(utils_channel.extract_wavelength_from_config_name(self.currentConfiguration.name)), intensity
                 )
             elif ENABLE_NL5 and NL5_USE_DOUT and "Fluorescence" in self.currentConfiguration.name:
                 wavelength = int(self.currentConfiguration.name[13:16])

software/control/utils.py

@@ -11,7 +11,6 @@
 from scipy.ndimage import label
 from scipy import signal
 import os
-from control._def import CHANNEL_COLORS_MAP
 from typing import Optional, Tuple
 from enum import Enum, auto
 import squid.logging
@@ -175,22 +174,6 @@ def ensure_directory_exists(raw_string_path: str):
     path.mkdir(parents=True, exist_ok=True)
 
 
-def extract_wavelength_from_config_name(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
-
-
-def get_channel_color(channel):
-    channel_info = CHANNEL_COLORS_MAP.get(extract_wavelength_from_config_name(channel), {"hex": 0xFFFFFF, "name": "gray"})
-    return channel_info["hex"]
 class SpotDetectionMode(Enum):
     """Specifies which spot to detect when multiple spots are present.
 

software/control/utils_channel.py

@@ -0,0 +1,18 @@
+from control._def import CHANNEL_COLORS_MAP
+
+def extract_wavelength_from_config_name(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
+
+
+def get_channel_color(channel):
+    channel_info = CHANNEL_COLORS_MAP.get(extract_wavelength_from_config_name(channel), {"hex": 0xFFFFFF, "name": "gray"})
+    return channel_info["hex"]

software/control/utils_config.py

@@ -2,8 +2,7 @@
 from pydantic_xml import BaseXmlModel, element, attr
 from typing import List, Optional
 from pathlib import Path
-import control.utils as utils
-
+import control.utils_channel as utils_channel
 
 class LaserAFConfig(BaseModel):
     """Pydantic model for laser autofocus configuration"""
@@ -34,7 +33,7 @@ class ChannelMode(BaseXmlModel, tag='mode'):
 
     def __init__(self, **data):
         super().__init__(**data)
-        self.color = utils.get_channel_color(self.name)
+        self.color = utils_channel.get_channel_color(self.name)
 
 class ChannelConfig(BaseXmlModel, tag='modes'):
     """Root configuration file model"""

software/main_hcs.py

@@ -58,8 +58,7 @@ def show_acq_config(cfm):
         log.error("Couldn't setup logging to file!")
         sys.exit(1)
 
-    log.info(f"Squid Repository State: {
-.get_squid_repo_state_description()}")
+    log.info(f"Squid Repository State: {control.utils.get_squid_repo_state_description()}")
 
     legacy_config = False
     cf_editor_parser = ConfigParser()

software/setup_22.04.sh

@@ -56,7 +56,7 @@ mkdir -p "$SQUID_SOFTWARE_ROOT/cache"
 # install libraries 
 pip3 install qtpy pyserial pandas imageio crc==1.3.0 lxml numpy tifffile scipy napari pyreadline3
 pip3 install opencv-python-headless opencv-contrib-python-headless
-pip3 install napari[all] scikit-image dask_image ome_zarr aicsimageio basicpy pytest pytest-qt gitpython matplotlib
+pip3 install napari[all] scikit-image dask_image ome_zarr aicsimageio basicpy pytest pytest-qt gitpython matplotlib pydantic_xml
 
 # install camera drivers
 cd "$DAHENG_CAMERA_DRIVER_ROOT"