A simple program to auto generate a Micro-manager startup script from a Micro manager configuration file

config_to_beanshell.py

#!/usr/bin/python
import sys
import csv
from string import Template

###############################################################################
# CMD Line Usage
###############################################################################

def print_usage():
    sys.stdout.write("Usage:\n")
    sys.stdout.write("python config_to_beanshell.py input_cfg output_bsh\n\n")
    sys.stdout.write("Example:\n")
    sys.stdout.write("python config_to_beanshell.py "
                     "'C:\Program Files\Micro-Manager-1.4\MMConfig_demo.cfg' "
                     "demo_startup.bsh")

###############################################################################
# Template Stubs
###############################################################################

def bsh_newline():
    return "\n"


def bsh_comment(comment):
    TEMPLATE = Template("""
/** ********** $comment ********** **/
""")
    return TEMPLATE.substitute(comment=comment)


def bsh_autogen_header():
    TEMPLATE = """
/**
*******************************************************************************
**************************** autogenerated ************************************
*******************************************************************************
**/
"""
    return TEMPLATE


def bsh_autogen_footer():
    return bsh_autogen_header()


def bsh_init_false():
    TEMPLATE = """
/*** Reset **/
mmc.reset();
mmc.setProperty("Core", "Initialize", "0");
"""
    return TEMPLATE


def bsh_new_load_device_map():
    TEMPLATE = """
Hashtable deviceLoadMap = new Hashtable();
"""
    return TEMPLATE


def bsh_load_device_map(device_label, init_state):
    TEMPLATE = Template("""deviceLoadMap.put("$device_label", $state);\n""")
    return TEMPLATE.substitute(
            device_label=device_label,
            state='true' if init_state else 'false')


def bsh_load_device(device_label, library, adapter):
    TEMPLATE = Template("""
try {
    // Loading device $device_label  
    mmc.loadDevice("$device_label", "$library", "$adapter");
    deviceLoadMap.put("$device_label", true);
} catch (java.lang.Exception ex) {
    deviceLoadMap.put("$device_label", false);
    gui.logMessage("Exception loading '$device_label':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
};
""")
    return TEMPLATE.substitute(
            device_label=device_label,
            library=library,
            adapter=adapter)


def bsh_set_property(device_label, property_label, value):
    TEMPLATE = Template("""
try {
    // Setting property $property_label
    if (deviceLoadMap.containsKey("$device_label") &&
        deviceLoadMap.get("$device_label")) {
        mmc.setProperty("$device_label", "$property_label", "$value");
    } else {
        gui.logMessage("Skipping setting property '$property_label' on device '$device_label'");
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting property: '$device_label' '$property_label':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
};
""")
    return TEMPLATE.substitute(
            device_label=device_label,
            property_label=property_label,
            value=value)


def bsh_set_parent(device_label, parent_label):
    TEMPLATE = Template("""
try {
    // Setting parent for $device_label
    if (deviceLoadMap.containsKey("$device_label") &&
        deviceLoadMap.get("$device_label")) {
        mmc.setParentLabel("$device_label", "$parent_label");
    } else {
        gui.logMessage("Skipping setting parent '$parent_label' of device '$device_label'");
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting parent '$parent_label' of device '$device_label':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
};
""")
    return TEMPLATE.substitute(
            device_label=device_label,
            parent_label=parent_label)


def bsh_new_init_device_map():
    TEMPLATE = """
Hashtable deviceInitMap = new Hashtable();
"""
    return TEMPLATE


def bsh_init_device_map(device_label, init_state):
    TEMPLATE = Template("""deviceInitMap.put("$device_label", $state);\n""")
    return TEMPLATE.substitute(
            device_label=device_label,
            state='true' if init_state else 'false')


def bsh_init_device(device_label):
    TEMPLATE = Template("""
try {
    // Initializing device $device_label
    if (deviceLoadMap.containsKey("$device_label") &&
        deviceLoadMap.get("$device_label")) {
        mmc.initializeDevice("$device_label");
        deviceInitMap.put("$device_label", true);
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception initializing device '$device_label'");
    gui.logMessage(ex.getMessage());
    gui.logMessage("Unloading device...");

    try {
        mmc.unloadDevice("$device_label");
        deviceInitMap.put("$device_label", false);
    } catch (java.lang.Exception ex2) {
        gui.logMessage("Exception unloading device '$device_label'");
        gui.logMessage(ex2.getMessage());
        gui.logMessage("ignoring...");
    }
}
""")
    return TEMPLATE.substitute(
            device_label=device_label)


def bsh_set_label(device_label, state, label):
    TEMPLATE = Template("""
try {
    // Setting state label for $device_label
    if (deviceInitMap.containsKey("$device_label") &&
        deviceInitMap.get("$device_label")) {
        mmc.defineStateLabel("$device_label", $state, "$state_label");
    } else {
        gui.logMessage("Skipping setting state label '$state_label' of device '$device_label'");
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting state label '$state_label' of device '$device_label':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
};
""")
    return TEMPLATE.substitute(
        device_label=device_label,
        state=int(state),
        state_label=label)


def bsh_set_config_group(group_label, config_label, device_label, property_label, value):
    TEMPLATE = Template("""
try {
    // Setting config group $group_label : $config_label : $property_label
    if (deviceInitMap.containsKey("$device_label") &&
        deviceInitMap.get("$device_label")) {
        mmc.defineConfig("$group_label", "$config_label", 
                         "$device_label", "$property_label", "$value");
    } else {
        gui.logMessage("Skipping setting config group '$group_label':'$config_label' property '$property_label'");
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting config group '$group_label' property '$property_label':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
};
""")
    return TEMPLATE.substitute(
            group_label=group_label,
            config_label=config_label,
            device_label=device_label,
            property_label=property_label,
            value=value)


def bsh_set_pixel_size_config(res_id, device_label, property_label, value):
    TEMPLATE = Template("""
try {
    // Setting pixel config for $res_id
    if (deviceInitMap.containsKey("$device_label") &&
        deviceInitMap.get("$device_label")) {
        mmc.definePixelSizeConfig("$res_id", "$device_label", "$property_label", "$value");
    } else {
        gui.logMessage("Skipping setting pixel size config '$res_id' for device '$device_label'");
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting pixel config '$res_id':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
}
""")
    return TEMPLATE.substitute(
            res_id=res_id,
            device_label=device_label,
            property_label=property_label,
            value=value)


def bsh_set_pixel_size(res_id, pixel_size):
    TEMPLATE = Template("""
try {
    // set pixel size for pixel config $res_id
    if (deviceInitMap.containsKey("$device_label") &&
        deviceInitMap.get("$device_label")) {
        mmc.setPixelSizeUm("$res_id", $pixel_size);
    } else {
        gui.logMessage("Skipping setting pixel size for config '$res_id');
    }
} catch (java.lang.Exception ex) {
    gui.logMessage("Exception setting pixel size for config '$res_id':");
    gui.logMessage(ex.getMessage());
    gui.logMessage("ignoring...");
}
""")
    return TEMPLATE.substitute(
            res_id=res_id,
            pixel_size=pixel_size)


def bsh_wait_for_system():
    TEMPLATE = """
/** ********** wait for system ********** **/

// try to set startup config
if (mmc.isConfigDefined("System", "Startup")) {
    mmc.setConfig("System", "Startup");
}
mmc.waitForSystem();
mmc.updateCoreProperties();
mmc.updateSystemStateCache();
"""
    return TEMPLATE


def bsh_update_gui():
    TEMPLATE = """
/** ********** update gui ********** **/
    
gui.refreshGUIFromCache();

"""
    return TEMPLATE

###############################################################################
# MAIN
###############################################################################
if __name__ == '__main__':
    if len(sys.argv) != 3:
        print_usage()
        sys.exit(1)
    try:
        input_fh = open(sys.argv[1], 'r')
        output_fh = open(sys.argv[2], 'wb')
    except IOError as exp:
        print >> sys.stderr, exp 
        sys.exit(1)
     
    mm_devices = []
    mm_properties = []
    mm_parents = []
    mm_labels = []
    mm_config_groups = []
    mm_config_pixel = []
    mm_pixel_size = []

    with input_fh, output_fh:
        reader = csv.reader(input_fh)
        try:
            #---------------------------------
            #--- parse micromanger config ----
            #---------------------------------
            for line, row in enumerate(reader):
                if len(row) == 0:
                    # skip newlines 
                    continue
                if row[0].startswith("#"):
                    # skip comments
                    continue
                if row[0] == "Device":
                    if len(row) != 4:
                        err = "Invalid Device -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_devices.append(tuple(row[1:])) 
                    continue
                if row[0] == "Property":
                    if len(row) != 4:
                        err = "Invalid Property -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    if row[1] == 'Core' and row[2] == 'Initialize':
                        # we will explicitly call this  
                        continue
                    mm_properties.append(tuple(row[1:]))
                    continue
                if row[0] == "Parent":
                    if len(row) != 3:
                        err = "Invalid Parent -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_parents.append(tuple(row[1:])) 
                    continue
                if row[0] == "Label":
                    if len(row) != 4:
                        err = "Invalid Label -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_labels.append(tuple(row[1:]))
                    continue
                if row[0] == "ConfigGroup":
                    if len(row) != 6:
                        err = "Invalid ConfigGroup -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_config_groups.append(tuple(row[1:]))
                    continue
                if row[0] == "ConfigPixelSize":
                    if len(row) != 5:
                        err = "Invalid ConfigPixelSize -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_config_pixel.append(tuple(row[1:]))
                    continue
                if row[0] == "PixelSize_um":
                    if len(row) != 3:
                        err = "Invalid PixelSize_um -> line: {}".format(line + 1)
                        print >> sys.stderr, err
                        sys.exit(1)
                    mm_pixel_size.append(tuple(row[1:]))
                    continue
           
            #----------------------------------
            #--- generate beanshell script ---
            #----------------------------------

            # autogen header
            output_fh.write(bsh_autogen_header())

            # set initialized to false
            output_fh.write(bsh_init_false());
 
            # write out device load map
            output_fh.write(bsh_comment("Device load map"))
            output_fh.write(bsh_new_load_device_map());
            for dev_params in mm_devices:
                device_label = dev_params[0]
                output_fh.write(bsh_load_device_map(device_label, False))

            # load devices
            output_fh.write(bsh_comment("Devices"))
            for dev_params in mm_devices:
                output_fh.write(bsh_load_device(*dev_params))
            
            # set properties
            output_fh.write(bsh_comment("Pre-init settings for devices"))
            for prop_params in mm_properties:
                output_fh.write(bsh_set_property(*prop_params))
            
            # set parent references
            output_fh.write(bsh_comment("Hub (parent) references"))
            for parent_params in mm_parents:
                output_fh.write(bsh_set_parent(*parent_params))
            
            # write out device initialized map
            output_fh.write(bsh_comment("Device init map"))
            output_fh.write(bsh_new_init_device_map());
            for dev_params in mm_devices:
                device_label = dev_params[0]
                output_fh.write(bsh_init_device_map(device_label, False))

            # initialize devices
            output_fh.write(bsh_comment("Initialize Devices"))
            for dev_params in mm_devices:
                device_label = dev_params[0]
                output_fh.write(bsh_init_device(device_label))
            
            # set labels
            output_fh.write(bsh_comment("Labels"))
            for label_params in mm_labels:
                output_fh.write(bsh_set_label(*label_params))
            
            # set config groups
            output_fh.write(bsh_comment("Configuration presets"))
            for config_params in mm_config_groups:
                output_fh.write(bsh_set_config_group(*config_params))

            # set pixel size config
            output_fh.write(bsh_comment("Pixel Size Config"))
            for config_params in mm_config_pixel:
                output_fh.write(bsh_set_pixel_size_config(*config_params))

            # set pixel size
            output_fh.write(bsh_comment("Pixel Size UM"))
            for pixel_params in mm_pixel_size:
                output_fh.write(bsh_set_pixel_size(*pixel_params))

            # update system system cache and refresh gui from cache
            output_fh.write(bsh_wait_for_system())
            output_fh.write(bsh_update_gui());
            
            # write autogen footer
            output_fh.write(bsh_autogen_footer());
        
        except csv.Error as exp:
            err = "Parse Error, file: {}, line: {}, err: {}".format(sys.argv[1], line + 1, exp)
            print >> sys.stderr, err
            sys.exit(1)
        except IOError as exp:
            err = "Write Error, file: {}, err: {}".format(sys.argv[1], exp)
            print >> sys.stderr, err
            sys.exit(1)
            
    sys.stdout.write("Success!\n")
    sys.exit(0)