Merge pull request #848 from TheDeanLab/842-configurationyaml-configurator-gui

842 configurationyaml configurator gui

Author: AdvancedImagingUTSW

src/navigate/config/config.py

@@ -44,7 +44,7 @@
 import yaml
 
 # Local Imports
-
+from navigate.tools.common_functions import build_ref_name
 
 def get_navigate_path():
     """Establish a program home directory in AppData/Local/.navigate for Windows
@@ -764,10 +764,8 @@ def verify_waveform_constants(manager, configuration):
                         waveform_dict[microscope_name][zoom],
                         laser,
                         {
-                            "amplitude": config_dict["remote_focus_device"][
-                                "amplitude"
-                            ],
-                            "offset": config_dict["remote_focus_device"]["offset"],
+                            "amplitude": 0,
+                            "offset": 0,
                             # "percent_smoothing": "0",
                             # "delay": config_dict["remote_focus_device"][
                             #     "delay"
@@ -864,9 +862,9 @@ def verify_waveform_constants(manager, configuration):
                         waveform_dict[microscope_name],
                         zoom,
                         {
-                            "amplitude": "0.11",
-                            "offset": config_dict["galvo"][i]["offset"],
-                            "frequency": config_dict["galvo"][i]["frequency"],
+                            "amplitude": "0",
+                            "offset": 0,
+                            "frequency": 10,
                         },
                     )
                 else:
@@ -896,12 +894,8 @@ def verify_waveform_constants(manager, configuration):
     other_constants_dict = {
         "remote_focus_settle_duration": "0",
         "percent_smoothing": "0",
-        "remote_focus_delay": config_dict["remote_focus_device"][
-            "delay"
-        ],
-        "remote_focus_ramp_falling": config_dict["remote_focus_device"][
-            "ramp_falling"
-        ]
+        "remote_focus_delay": "0",
+        "remote_focus_ramp_falling": "5"
     }
     if (
         "other_constants" not in waveform_dict.keys()
@@ -924,7 +918,16 @@ def verify_configuration(manager, configuration):
     
     Supports old version of configurations.
     """
+    channel_count = 5
+    # generate hardware header section
     device_config = configuration["configuration"]["microscopes"]
+    hardware_dict = {}
+    ref_list = {
+        "camera": [],
+        "stage": [],
+        "zoom": None,
+        "mirror": None,
+    }
     for microscope_name in device_config.keys():
         # camera
         # delay_percent -> delay
@@ -938,3 +941,54 @@ def verify_configuration(manager, configuration):
             remote_focus_config["ramp_falling"] = remote_focus_config.get("ramp_falling_percent", 5)
         if "delay" not in remote_focus_config.keys():
             remote_focus_config["delay"] = remote_focus_config.get("delay_percent", 0)
+        
+        # daq
+        daq_type = device_config[microscope_name]["daq"]["hardware"]["type"]
+        if not daq_type.lower().startswith("synthetic"):
+            hardware_dict["daq"] = {"type": daq_type}
+
+        # camera
+        if "camera" not in hardware_dict:  
+            hardware_dict["camera"] = []
+        camera_idx = build_ref_name("-", camera_config["hardware"]["type"], camera_config["hardware"]["serial_number"])
+        if camera_idx not in ref_list["camera"]:
+            ref_list["camera"].append(camera_idx)
+            hardware_dict["camera"].append(camera_config["hardware"])
+
+        try:
+            channel_count = max(channel_count, camera_config.get("count", 5))
+        except TypeError:
+            channel_count = 5
+
+        # zoom (one zoom)
+        if "zoom" not in hardware_dict:
+            zoom_config = device_config[microscope_name]["zoom"]["hardware"]
+            # zoom_idx = build_ref_name("-", zoom_config["type"], zoom_config["servo_id"])
+            hardware_dict["zoom"] = zoom_config
+
+        # filter wheel
+        if "filter_wheel" not in hardware_dict:
+            filter_wheel_config = device_config[microscope_name]["filter_wheel"]["hardware"]
+            hardware_dict["filter_wheel"] = filter_wheel_config
+        # stage
+        if "stage" not in hardware_dict:
+            hardware_dict["stage"] = []
+        stages = device_config[microscope_name]["stage"]["hardware"]
+        if type(stages) != ListProxy:
+            stages = [stages]
+        for i, stage in enumerate(stages):
+            stage_idx = build_ref_name("-", stage["type"], stage["serial_number"])
+            if stage_idx not in ref_list["stage"]:
+                hardware_dict["stage"].append(stage)
+
+        # mirror
+        if "mirror" in device_config[microscope_name].keys() and "mirror" not in hardware_dict:
+            hardware_dict["mirror"] = device_config[microscope_name]["mirror"]["hardware"]
+
+    if "daq" not in hardware_dict:
+        hardware_dict["daq"] = {
+            "type": "synthetic"
+        }
+    update_config_dict(manager, configuration["configuration"], "hardware", hardware_dict)
+
+    update_config_dict(manager, configuration["configuration"], "gui", {"channels": {"count": channel_count}})

src/navigate/config/configuration_database.py

@@ -0,0 +1,243 @@
+camera_device_types = {
+    "Hamamatsu ORCA Lightning": "HamamatsuOrcaLightning",
+    "Hamamatsu ORCA Fire": "HamamatsuOrcaFire",
+    "Hamamatsu Flash 4.0": "HamamatsuOrca",
+    "Photometrics Iris 15B": "Photometrics",
+    "Virtual Device": "synthetic"
+}
+
+camera_hardware_widgets = {
+    "hardware/type": ["Device Type", "Combobox", "string", camera_device_types, None],
+    "hardware/serial_number": ["Serial Number", "Input", "string", None, 'Example: "302352"'],
+    "hardware/camera_connection": ["Camera Connection", "Input", "string", None, "*Photometrics Iris 15B only"],
+    "defect_correct_mode": ["Defect Correct Mode", "Combobox", "string", {"On": 2.0, "Off": 1.0}, None],
+    "delay": ["Delay (ms)", "Spinbox", "float", None, None],
+    "flip_x": ["Flip X", "Checkbutton", "bool", None, None],
+    "flip_y": ["Flip Y", "Checkbutton", "bool", None, None],
+    "count": ["Microscope Channel Count", "Spinbox", "int", {"from": 5, "to": 10, "step": 1}, None]
+}
+
+filter_wheel_device_types = {
+    "Sutter Instruments": "SutterFilterWheel",
+    "Applied Scientific Instrumentation": "ASI",
+    "Virtual Device": "synthetic",
+}
+
+filter_wheel_widgets = {
+    "filter_name": ["Filter Name", "Input", "string", None, "Example: Empty-Alignment"],
+    "filter_value": ["Filter Value", "Input", "string", None, "Example: 0"],
+    "button_1": ["Delete", "Button", {"delete": True}],
+    "frame_config": {"ref": "available_filters", "format": "item(filter_name,filter_value),", "direction": "horizon"}
+}
+
+filter_wheel_hardware_widgets = {
+    "hardware/type": ["Device Type", "Combobox", "string", filter_wheel_device_types, None],
+    "hardware/wheel_number": ["Number of Wheels", "Spinbox", "int", None, "Example: 1"],
+    "hardware/port": ["Serial Port", "Input", "string", None, "Example: COM1"],
+    "hardware/baudrate": ["Baudrate", "Input", "int", None, "Example: 9200"],
+    "filter_wheel_delay": ["Filter Wheel Delay (s)", "Input", "float", None, "Example: 0.03"],
+    "button_1": ["Add Available Filters", "Button", {"widgets":filter_wheel_widgets, "ref": "available_filters", "direction": "horizon"}]
+}
+
+daq_device_types = {
+    "National Instruments": "NI",
+}
+
+daq_hardware_widgets = {
+    "hardware/type": ["Device Type", "Combobox", "string", daq_device_types, None],
+    "sample_rate": ["Sample Rate", "Input", "int", None, "Example: 9600"],
+    "master_trigger_out_line": ["Master Trigger Out", "Input", "string", None, "Example: PXI6259/port0/line1"],
+    "camera_trigger_out_line": ["Camera Trigger Out", "Input", "string", None, "Example: /PXI6259/ctr0"],
+    "trigger_source": ["Trigger Source", "Input", "string", None, "Example: /PXI6259/PFI0"],
+    "laser_port_switcher": ["Laser Switcher Port", "Input", "string", None, "Example: PXI6733/port0/line0"],
+    "laser_switch_state": ["Laser Switch On State", "Combobox", "bool", [True, False], None],
+}
+
+shutter_device_types = {
+    "Analog/Digital Device": "NI",
+    "Virtual Device": "synthetic",
+}
+
+shutter_hardware_widgets = {
+    "type": ["Device Type", "Combobox", "string", shutter_device_types, None],
+    "channel": ["NI Channel", "Input", "string", None, "Example: PXI6259/port0/line0"],
+    "min": ["Minimum Voltage", "Spinbox", "float", None, "Example: 0"],
+    "max": ["Maximum Voltage", "Spinbox", "float", None, "Example: 5"],
+    "frame_config": {"ref": "hardware"}
+}
+
+stage_device_types = {
+    "Applied Scientific Instrumentation": "ASI",
+    "Analog/Digital Device": "GalvoNIStage",
+    "Mad City Labs": "MCL",
+    "Physik Instrumente": "PI",
+    "Sutter Instruments": "MP285",
+    "ThorLabs KCube Inertial Device": "Thorlabs",
+    "Virtual Device": "synthetic",
+}
+
+stage_hardware_widgets = {
+    "type": ["Device Type", "Combobox", "string", stage_device_types, None],
+    "serial_number": ["Serial Number", "Input", "string", None, None],
+    "axes": ["Axes", "Input", "string", None, "Example: [x, y, z]"],
+    "axes_mapping": ["Axes Mapping", "Input", "string", None, "Example: [X, M, Y]"],
+    "volts_per_micron": ["Volts Per Micron", "Spinbox", "float", {"from": 0, "to": 100, "step":0.1}, "*Analog/Digital Device only"],
+    "min": ["Minimum Volts", "Spinbox", "float", {"from": 0, "to": 5, "step": 0.1}, "*Analog/Digital Device only",],
+    "max": ["Maximum Volts", "Spinbox", "float", {"from": 1, "to": 100, "step": 0.1}, "*Analog/Digital Device only",],
+    "controllername": ["Controller Name", "Input", "string", None, "*Physik Instrumente only. Example: 'C-884'"],
+    "stages": ["PI Stages", "Input", "string", None, "*Physik Instrumente only. Example: L-509.20DG10 L-509.40DG10"],
+    "refmode": ["REF Modes", "Input", "string", None, "*Physik Instrumente only. Example: FRF FRF"],
+    "port": ["Serial Port", "Input", "string", None, "Example: COM1"],
+    "baudrate": ["Baudrate", "Input", "int", None, "Example: 9200"],
+    "button_2": ["Delete", "Button", {"delete": True}],
+    "frame_config": {"collapsible": True, "title": "Stage", "ref": "hardware", "format": "list-dict"}
+}
+
+stage_top_widgets = {
+    "button_1": ["Add New Stage Device", "Button", {"widgets": stage_hardware_widgets, "ref": "hardware", "parent": "hardware"}],
+}
+
+stage_constants_widgets = {
+    "joystick_axes": ["Joystick Axes", "Input", "string", None, "Example: [x, y, z]"],
+    "x_min": ["Min X", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, None],
+    "x_max": ["Max X", "Spinbox", "float", {"from": 0, "to": 10000, "step": 1000}, None],
+    "y_min": ["Min Y", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, None],
+    "y_max": ["Max Y", "Spinbox", "float", {"from": 0, "to": 10000, "step": 1000}, None],
+    "z_min": ["Min Z", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, None],
+    "z_max": ["Max Z", "Spinbox", "float", {"from": 0, "to": 10000, "step": 1000}, None],
+    "theta_min": ["Min Theta", "Spinbox", "float", {"from": 0, "to": 360, "step": 1000}, None],
+    "theta_max": ["Max Theta", "Spinbox", "float", {"from": 0, "to": 360, "step": 1000}, None],
+    "f_min": ["Min Focus", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, None],
+    "f_max": ["Max Focus", "Spinbox", "float", {"from": 0, "to": 10000, "step": 1000}, None],
+    "x_offset": ["Offset of X", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, "Example: 0"],
+    "y_offset": ["Offset of Y", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, "Example: 0"],
+    "z_offset": ["Offset of Z", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, "Example: 0"],
+    "theta_offset": ["Offset of Theta", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, "Example: 0"],
+    "f_offset": ["Offset of Focus", "Spinbox", "float", {"from": -100000, "to": 10000, "step": 1000}, "Example: 0"],
+    "frame_config": {"collapsible": True, "title": "Stage Constants"}
+}
+
+remote_focus_device_types = {
+    "Equipment Solutions": "EquipmentSolutions",
+    "Analog Device": "NI",
+    "Virtual Device": "synthetic"
+}
+
+remote_focus_hardware_widgets = {
+    "type": ["Device Type", "Combobox", "string", remote_focus_device_types, None],
+    "channel": ["DAQ Channel", "Input", "string", None, "Example: PXI6259/ao3"],
+    "min": ["Minimum Voltage", "Spinbox", "float", {"from": -10, "to": 10, "step": 1}, None],
+    "max": ["Maximum Voltage", "Spinbox", "float", {"from": 0, "to": 10, "step": 1}, None],
+    "comport": ["Serial Port", "Input", "string", None, "*Equipment Solutions only"],
+    "baudrate": ["Baudrate", "Input", "int", None, "*Equipment Solutions only. Example: 9200"],
+    "frame_config": {"ref": "hardware"}
+}
+
+galvo_device_types = {
+    "Analog Device": "NI",
+    "Virtual Device": "synthetic"
+}
+
+waveform_types = {
+    "Sine": "sine",
+    "Sawtooth": "sawtooth",
+    "Square": "square",
+}
+
+galvo_hardware_widgets = {
+    "hardware/type": ["Device Type", "Combobox", "string", galvo_device_types, None],
+    "hardware/channel": ["DAQ Channel", "Input", "string", None, "Example: PXI6259/ao1"],
+    "hardware/min": ["Minimum Voltage", "Spinbox", "float", {"from": -10, "to": 10, "step": 0.1}, None],
+    "hardware/max": ["Maximum Voltage", "Spinbox", "float", {"from": 0, "to": 10, "step": 0.1}, None],
+    "waveform": ["Waveform", "Combobox", "string", waveform_types, None],
+    "phase": ["Phase", "Input", "string", None, "Example: 1.57"],
+    "button_1": ["Delete", "Button", {"delete": True}],
+    "frame_config": {"collapsible": True, "title": "Galvo Device", "ref": "None", "format": "list-dict"}
+}
+
+galvo_top_widgets = {
+    "button_1": ["Add New Device", "Button", {"widgets": galvo_hardware_widgets, "parent": "hardware"}],
+}
+
+zoom_device_types = {
+    "Dynamixel": "DynamixelZoom",
+    "Virtual Device": "synthetic"
+}
+
+zoom_position_widgets = {
+    "zoom_value": ["Zoom Value", "Input", "string", None, "Example: 16x"],
+    "position": ["Position", "Input", "float", None, "Example: 1000"],
+    "pixel_size": ["Pixel Size (um)", "Input", "float", None, "Example: 0.5"],
+    "button_1": ["Delete", "Button", {"delete": True}],
+    "frame_config": {"ref": "position;pixel_size", "format": "item(zoom_value, position);item(zoom_value, pixel_size)", "direction": "horizon"}
+}
+
+zoom_hardware_widgets = {
+    "type": ["Device Type", "Combobox", "string", zoom_device_types, None],
+    "servo_id": ["Servo ID", "Input", "string", None, "Example: 1"],
+    "port": ["Serial Port", "Input", "string", None, "Example: COM1"],
+    "baudrate": ["Baudrate", "Input", "int", None, "Example: 9600"],
+    "button_1": ["Add Zoom Value", "Button", {"widgets":zoom_position_widgets, "ref": "position;pixel_size", "direction": "horizon"}],
+    "frame_config": {"ref": "hardware"}
+}
+
+mirror_device_types = {
+    "Imagine Optics": "ImagineOpticsMirror",
+    "Virtual Device": "SyntheticMirror"
+}
+
+mirror_hardware_widgets = {
+    "type": ["Device Type", "Combobox", "string", mirror_device_types, None],
+    "frame_config": {"ref": "hardware"}
+}
+
+laser_device_types = {
+    "Analog Device": "NI",
+    "Virtual Device": "synthetic"
+}
+
+laser_hardware_widgets = {
+    "wavelength": ["Wavelength", "Input", "int", None, None, "Example: 488"],
+    "onoff": ["On/Off Setting", "Label", None, None, None],
+    "onoff/hardware/type": ["Type", "Combobox", "string", laser_device_types, None],
+    "onoff/hardware/channel": ["DAQ Channel", "Input", "string", None, "Example: PXI6733/port0/line2"],
+    "onoff/hardware/min": ["Minimum Voltage", "Spinbox", "float", {"from": 0, "to": 100, "step": 1}, None],
+    "onoff/hardware/max": ["Maximum Voltage", "Spinbox", "float", {"from": 0, "to": 100, "step": 1}, None],
+    "power": ["Power Setting", "Label", None, None, None],
+    "power/hardware/type": ["Type", "Combobox", "string", laser_device_types, None],
+    "power/hardware/channel": ["DAQ Channel", "Input", "string", None, "Example: PXI6733/ao0"],
+    "power/hardware/min": ["Minimum Voltage", "Spinbox", "float", {"from": 0, "to": 100, "step": 1}, None],
+    "power/hardware/max": ["Maximum Voltage", "Spinbox", "float", {"from": 0, "to": 100, "step": 1}, None],
+    "button_1": ["Delete", "Button", {"delete": True}],
+    "frame_config": {"collapsible": True, "title": "Wavelength", "format": "list-dict", "ref": "None"}
+}
+
+laser_top_widgets = {
+    "button_1": ["Add Wavelength", "Button", {"widgets": laser_hardware_widgets, "parent": "hardware"}],
+}
+
+hardwares_dict = {
+    "Camera": camera_hardware_widgets,
+    "Data Acquisition Card": daq_hardware_widgets,
+    "Filter Wheel": (None, filter_wheel_hardware_widgets, filter_wheel_widgets),
+    "Galvo": (galvo_top_widgets, galvo_hardware_widgets, None),
+    "Lasers": (laser_top_widgets, laser_hardware_widgets, None),
+    "Remote Focus Devices": remote_focus_hardware_widgets,
+    "Adaptive Optics": mirror_hardware_widgets,
+    "Shutters": shutter_hardware_widgets,
+    "Stages": (stage_top_widgets, stage_hardware_widgets, stage_constants_widgets),
+    "Zoom Device": (None, zoom_hardware_widgets, zoom_position_widgets)
+}
+
+hardwares_config_name_dict = {
+    "Camera": "camera",
+    "Data Acquisition Card": "daq",
+    "Filter Wheel": "filter_wheel",
+    "Galvo": "galvo",
+    "Lasers": "lasers",
+    "Remote Focus Devices": "remote_focus_device",
+    "Adaptive Optics": "mirror",
+    "Shutters": "shutter",
+    "Stages": "stage",
+    "Zoom Device": "zoom",
+}