Moved hardware config to a runtime config YAML file in home

openflexure_microscope/__init__.py

@@ -1,4 +1,5 @@
-__all__ = ['Microscope']
+__all__ = ['Microscope', 'config']
 __version__ = "0.1.0"
 
 from .microscope import Microscope
+from . import config

openflexure_microscope/api/v1.py

@@ -261,7 +261,7 @@ class PositionAPI(MicroscopeView):
         return jsonify(self.microscope.state['position'])
 
 app.add_url_rule(
-    uri('/position/'), 
+    uri('/position/'),
     view_func=PositionAPI.as_view('position', microscope=api_microscope))
 
 

openflexure_microscope/camera/config.py

@@ -1,39 +0,0 @@
-import yaml
-
-TYPES = {
-    'stream_resolution': tuple,
-    'video_resolution': tuple,
-    'image_resolution': tuple,
-    'numpy_resolution': tuple,
-    'jpeg_quality': int,
-    'framerate': int,
-    'awb_mode': str,
-    'red_gain': float,
-    'blue_gain': float,
-    'shutter_speed': int,
-    'saturation': int,
-    'analog_gain': float,
-    'digital_gain': float,
-}
-
-
-def convert_config(config: dict) -> dict:
-    """Convert datatype of config based on type dictionary."""
-    global TYPES
-
-    for key in config:
-        if key in TYPES:
-            config[key] = TYPES[key](config[key])
-
-    return config
-
-
-def load_config(yaml_path: str) -> dict:
-    """Load YAML file, pass through dictionary conversion, and return."""
-    with open(yaml_path) as config_file:
-        return yaml.load(config_file)
-
-
-def save_config(config: dict, yaml_path: str):
-    with open('yaml_path', 'w') as outfile:
-        yaml.dump(config, outfile)

openflexure_microscope/camera/config_picamera.yaml

@@ -1,35 +0,0 @@
-# Exposure mode
-exposure_mode: 'off'
-
-# The analog gain offers higher sensitivity and less noise than using digital gain only
-analog_gain: 1.
-digital_gain: 1.
-
-# When queried, the shutter_speed property returns the shutter speed of the camera in microseconds, 
-# or 0 which indicates that the speed will be automatically determined.
-# If high value does not work, need to decrease the fps for streaming
-shutter_speed: 30000
-
-# Auto white balance: The red and blue values are returned Fraction instances. 
-# The values will be between 0.0 and 8.0.
-awb_mode: 'off'
-
-# If not using auto, then you can change the awb_gains
-red_gain: 1.3
-blue_gain: 1.2
-
-# Color saturation of the camera as an integer between -100 and 100. 
-saturation: 0
-
-# ISO Valid values are between 0 (auto) and 800 (1600 is not available?). 
-# ISO value is not used anyway as we are fixing the gains
-iso: 500
-
-# Resolutions for streaming and capture
-video_resolution: [832, 624]
-image_resolution: [2592, 1944]
-numpy_resolution: [1312, 976]
-
-# Capture quality
-jpeg_quality: 75
-framerate: 24

openflexure_microscope/camera/pi.py

@@ -47,21 +47,27 @@ import threading
 from .base import BaseCamera, StreamObject
 # Richard's fix gain
 from .set_picamera_gain import set_analog_gain, set_digital_gain
-# Manage config
-from .config import load_config, save_config, convert_config
-
-HERE = os.path.abspath(os.path.dirname(__file__))
-DEFAULT_CONFIG_PATH = os.path.join(HERE, 'config_picamera.yaml')
 
 
 class StreamingCamera(BaseCamera):
-    """Raspberry Pi camera implementation of StreamingCamera."""
+    """Raspberry Pi camera implementation of StreamingCamera.
-    def __init__(self):
+
+    Args:
+        config (dict): Dictionary of config parameters to apply on init. If None, will default to basic config.
+    """
+    def __init__(self, config: dict=None):
         # Run BaseCamera init
         BaseCamera.__init__(self)
         # Attach to Pi camera
         self.camera = picamera.PiCamera()  #: :py:class:`picamera.PiCamera`: Picamera object
 
+        # Store state of StreamingCamera
+        self.state.update({
+            'stream_active': False,
+            'record_active': False,
+            'preview_active': False,
+        })
+
         # Default camera config
         self.config.update({
             'video_resolution': (832, 624),
@@ -70,13 +76,11 @@ class StreamingCamera(BaseCamera):
             'jpeg_quality': 75,
         })
 
-        # Store state of StreamingCamera
+        # Load config dictionary if passed
-        self.state.update({
+        if config:
-            'stream_active': False,
+            self.update_settings(config)
-            'record_active': False,
-            'preview_active': False,
-        })
 
+        # Start streaming
         self.start_worker()
 
     def initialisation(self):
@@ -91,74 +95,82 @@ class StreamingCamera(BaseCamera):
         if self.camera:
             self.camera.close()
 
+
     # HANDLE SETTINGS
-    def load_config(self, config_path: str=None):
+    @property
+    def supports_lens_shading(self):
+        """Determine whether the picamera module supports lens shading.
+
+        As of March 2018, picamera did not wrap the necessary MMAL commands to
+        set the lens shading table, or to write the value of analog or digital
+        gain.  I have a forked version of the library that does support these.
+        For ease of use by people who don't want those features, this library
+        does not have a hard dependency on lens shading.  However, we need to
+        check in some places whether it's available.
         """
-        Open config_picamera.yaml file and write to camera.
+        return hasattr(self.camera, "lens_shading_table")
 
-        Args:
+    def update_lens_shading(self, shading_array: np.ndarray):
-            config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
+        if not self.supports_lens_shading:
-        """
+            logging.error("the currently-installed picamera library does not support all "
-        global DEFAULT_CONFIG_PATH
+            "the features of the openflexure microscope software.  These features "
-        if not config_path:
+            "include lens shading control and setting the analog/digital gain.\n"
-            config_data = load_config(DEFAULT_CONFIG_PATH)
+            "\n"
-        else:
+            "See the installation instructions for how to fix this:\n"
-            config_data = load_config(config_path)
+            "https://github.com/rwb27/openflexure_microscope_software")
-
-        self.update_settings(config_data)
-
-    def save_config(self, config_path: str=None):
-        """
-        Save current config dictionary to a YAML file.
-
-        Args:
-            config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
-        """
-        global DEFAULT_CONFIG_PATH
-        if not config_path:
-            config_path = DEFAULT_CONFIG_PATH
-
-        save_config(self.config, config_path)
 
     def update_settings(self, config: dict) -> None:
         """
         Write a config dictionary to the StreamingCamera config.
 
+        The passed dictionary may contain other parameters not relevant to
+        camera config. Eg. Passing a general config file will work fine.
+
         Args:
             config (dict): Dictionary of config parameters.
         """
-
-        self.config = convert_config(config)  # Convert loaded dictionary to valid config dictionary
-        logging.debug(self.config)
-
         paused_stream = False
 
         # Apply valid config params to Picamera object
         if not self.state['record_active']:  # If not recording a video
 
+            logging.debug("Applying config:")
+            logging.debug(config)
+
+            # Pause stream while changing settings
             if self.state['stream_active']:  # If stream is active
                 logging.info("Pausing stream to update config.")
                 self.pause_stream_for_capture()  # Pause stream
                 paused_stream = True  # Remember to unpause stream when done
 
-            # Camera AWB
+            # PiCamera parameters (applied directly to PiCamera object)
-            if 'awb_mode' in config:
+            picamera_keys = [
-                self.camera.awb_mode = config['awb_mode']
+                'exposure_mode',
-            if 'red_gain' in config and 'blue_gain' in config:
+                'awb_mode',
-                self.camera.awb_gains = (
+                'awb_gains',
-                    config['red_gain'],
+                'framerate',
-                    config['blue_gain'])
+                'shutter_speed',
+                'saturation',
+                'led'
+            ]
+            if 'picamera_params' in config:
+                for key in picamera_keys:
+                    if key in config['picamera_params']:
+                        logging.debug("Setting parameter {}: {}".format(key, config['picamera_params'][key]))
+                        setattr(self.camera, key, config['picamera_params'][key])
+
+            # StreamingCamera parameters (applied via StreamingCamera config)
+            config_keys = [
+                'video_resolution',
+                'image_resolution',
+                'numpy_resolution',
+                'jpeg_quality', ]
+
+            for key in config_keys:
+                if key in config:
+                    logging.debug("Setting parameter {}: {}".format(key, config[key]))
+                    self.config[key] = config[key]
 
-            # Camera framerate
-            if 'framerate' in config:
-                self.camera.framerate = config['framerate']
-            # Camera exposure
-            if 'shutter_speed' in config:
-                self.camera.shutter_speed = config['shutter_speed']
-            if 'saturation' in config:
-                self.camera.saturation = config['saturation']
-            # Camera misc.
-            self.camera.led = False
             # Richard's library to set analog and digital gains
             if 'analog_gain' in config:
                 set_analog_gain(self.camera, config['analog_gain'])
@@ -464,8 +476,6 @@ class StreamingCamera(BaseCamera):
 
         self.wait_for_camera()
 
-        # Load config file
-        self.load_config()
         # Set stream resolution
         self.camera.resolution = self.config['video_resolution']
 
@@ -490,7 +500,7 @@ class StreamingCamera(BaseCamera):
                 self.stream.seek(0)
                 self.stream.truncate()
                 # to stream, read the new frame
-                time.sleep(1/self.config['framerate']*0.1)
+                time.sleep(1/self.camera.framerate*0.1)
                 # yield the result to be read
                 frame = self.stream.getvalue()
 

openflexure_microscope/config.py

@@ -0,0 +1,71 @@
+import yaml
+import os
+import logging
+import shutil
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+DEFAULT_CONFIG_PATH = os.path.join(HERE, 'openflexurerc.default.yaml')
+USER_CONFIG_PATH = os.path.join(os.path.expanduser("~"), "openflexurerc.yaml")
+
+TYPES = {
+    'stream_resolution': tuple,
+    'video_resolution': tuple,
+    'image_resolution': tuple,
+    'numpy_resolution': tuple,
+    'jpeg_quality': int,
+    'analog_gain': float,
+    'digital_gain': float,
+}
+
+
+def convert_config(config: dict) -> dict:
+    """Convert datatype of config based on type dictionary."""
+    global TYPES
+
+    for key in config:
+        if key in TYPES:
+            config[key] = TYPES[key](config[key])
+
+    return config
+
+
+def load_config(config_path: str=None) -> dict:
+    """
+    Open openflexurerc.yaml file and write to the microscope devices.
+
+    Args:
+        config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
+    """
+    global DEFAULT_CONFIG_PATH, USER_CONFIG_PATH
+
+    if not config_path:
+        if os.path.exists(USER_CONFIG_PATH):  # If user config file already exists
+            config_path = USER_CONFIG_PATH  # Load it
+        else:  # If user config file doesn't yet exist
+            logging.warning("No user config found. Loading system defaults...")
+            logging.info("Copying default config to user config...")
+            shutil.copyfile(DEFAULT_CONFIG_PATH, USER_CONFIG_PATH)
+            logging.info("Loading user config...")
+            config_path = USER_CONFIG_PATH  # Load defaults in
+
+    with open(config_path) as config_file:
+        config_data = yaml.load(config_file)
+
+    # Store config dictionary to self
+    return convert_config(config_data)
+
+
+def save_config(self, config_dict: dict, config_path: str=None):
+    """
+    Save current config dictionary to a YAML file.
+
+    Args:
+        config_dict (dict): Dictionary of config data to save.
+        config_path (str): Path to the config YAML file. If `None`, defaults to `DEFAULT_CONFIG_PATH`
+    """
+    global USER_CONFIG_PATH
+    if not config_path:
+        config_path = USER_CONFIG_PATH
+
+    with open(config_path, 'w') as outfile:
+        yaml.dump(config_dict, outfile)

openflexure_microscope/microscope.py

@@ -3,12 +3,14 @@
 Defines a microscope object, binding a camera and stage with basic functionality.
 """
 import logging
+import os
 import numpy as np
 
 from openflexure_stage import OpenFlexureStage
 from .camera.pi import StreamingCamera
 
-from .plugins import PluginMount, load_plugin, search_plugin_paths
+from .plugins import PluginMount, load_plugin, search_plugin_dirs
+from .config import load_config, save_config, convert_config
 
 
 class Microscope(object):
@@ -20,8 +22,11 @@ class Microscope(object):
     Args:
         camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
         microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
+        load_config (bool): Should a config file be automatically loaded on init?
+        config_path (str): Path to the config YAML file to be loaded. If None, defaults to USER_CONFIG_PATH.
     """
     def __init__(self, camera: StreamingCamera, stage: OpenFlexureStage):
+
         self.attach(camera, stage)
 
         # Create plugin mountpoint
@@ -40,7 +45,7 @@ class Microscope(object):
         self.camera.close()
         self.stage.close()
 
-    def attach(self, camera: StreamingCamera, stage: OpenFlexureStage):
+    def attach(self, camera: StreamingCamera, stage: OpenFlexureStage, apply_config: bool=True):
         """
         Retroactively attaches a camera and stage to the microscope object.
 
@@ -50,6 +55,7 @@ class Microscope(object):
         Args:
             camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
             microscope (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
+            apply_config (bool): Should the microscope config dictionary be applied to the attached hardware?
         """
 
         self.camera = camera  #: :py:class:`openflexure_microscope.camera.pi.StreamingCamera`: Picamera object
@@ -69,7 +75,8 @@ class Microscope(object):
             plugin_paths (list): List of strings of plugin directories.
             include_default (bool): Also load plugins from the module default directory (DEFAULT_PLUGIN_PATH)
         """
-        plugins_list = search_plugin_paths(plugin_paths, include_default=include_default)
+        # TODO: Get paths from rc file
+        plugins_list = search_plugin_dirs(plugin_paths, include_default=include_default)
 
         for i in plugins_list:
             module = load_plugin(i)

openflexure_microscope/openflexurerc.default.yaml

@@ -0,0 +1,20 @@
+# The analog gain offers higher sensitivity and less noise than using digital gain only
+analog_gain: 1.
+digital_gain: 1.
+
+# Resolutions for streaming and capture
+video_resolution: [832, 624]
+image_resolution: [2592, 1944]
+numpy_resolution: [1312, 976]
+
+# Capture quality
+jpeg_quality: 75
+
+picamera_params:
+  exposure_mode: 'off'
+  awb_mode: 'off'
+  awb_gains: [1.3, 1.2]
+  framerate: 24
+  shutter_speed: 30000
+  saturation: 0
+  led: false

requirements.txt

@@ -1,7 +1,7 @@
 -e git://github.com/rwb27/openflexure_nano_motor_controller.git#egg=openflexure_stage
+-e git://github.com/rwb27/picamera.git#egg=picamera
 
 flask >= 0.12.3
-picamera==1.13
 pyyaml==3.13
 numpy
 Pillow

tests/test_plugins.py

@@ -1,15 +1,16 @@
 #!/usr/bin/env python
 from openflexure_microscope.camera.pi import StreamingCamera
 from openflexure_stage import OpenFlexureStage
-from openflexure_microscope import Microscope
+from openflexure_microscope import Microscope, config
-from openflexure_microscope.plugins import PluginMount, load_plugin, search_plugin_paths
 
 import atexit
 import logging, sys
 logging.basicConfig(stream=sys.stderr, level=logging.DEBUG)
 
 if __name__ == '__main__':
-    microscope = Microscope(StreamingCamera(), OpenFlexureStage("/dev/ttyUSB0"))
+    openflexurerc = config.load_config()
+
+    microscope = Microscope(StreamingCamera(openflexurerc), OpenFlexureStage("/dev/ttyUSB0"))
 
     microscope.find_plugins()  # Automatically find microscope plugins
 
@@ -18,4 +19,4 @@ if __name__ == '__main__':
     microscope.plugin.test1.run()
     microscope.plugin.test2.run()
 
-    microscope.close()
+    microscope.close()