Added support for a fully mocked device
This commit is contained in:
jtc42
parent
eaa37f70e0
commit
4733b250ed
12 changed files with 283 additions and 41 deletions
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@ -12,14 +12,17 @@ from openflexure_microscope.api.exceptions import JSONExceptionHandler
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from openflexure_microscope.api.utilities import list_routes
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from openflexure_microscope import Microscope
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from openflexure_microscope.camera.pi import StreamingCamera
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try:
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from openflexure_microscope.camera.pi import StreamingCamera
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except ImportError:
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from openflexure_microscope.camera.mock import StreamingCamera
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from openflexure_microscope.stage.sanga import SangaStage
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from openflexure_microscope.stage.mock import MockStage
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from openflexure_microscope.camera.capture import build_captures_from_exif
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from openflexure_microscope.config import USER_CONFIG_DIR
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from openflexure_microscope.api.v1 import blueprints
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import time
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@ -101,7 +104,7 @@ def attach_microscope():
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# TODO: Tidy this up. api_stage may be referenced before assignment. Use some form of Maybe monad?
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try:
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api_stage = SangaStage()
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except (SerialException, OSError) as e:
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except Exception as e:
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logging.error(e)
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logging.warning("No valid stage hardware found. Falling back to mock stage!")
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api_stage = MockStage()
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@ -1,3 +0,0 @@
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__all__ = ['pi', 'base']
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from . import pi, base
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@ -167,15 +167,6 @@ class BaseCamera(metaclass=ABCMeta):
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self.stop_worker()
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logging.info("Closed {}".format(self))
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def wait_for_camera(self, timeout=5):
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"""Wait for camera object, with 5 second timeout."""
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timeout_time = time.time() + timeout
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while not self.camera:
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if time.time() > timeout_time:
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raise TimeoutError("Timeout waiting for camera")
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else:
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pass
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# START AND STOP WORKER THREAD
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def start_worker(self, timeout: int = 5) -> bool:
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217
openflexure_microscope/camera/mock.py
Normal file
217
openflexure_microscope/camera/mock.py
Normal file
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@ -0,0 +1,217 @@
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# -*- coding: utf-8 -*-
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"""
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"""
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from __future__ import division
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import io
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import time
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import numpy as np
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from PIL import Image
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import logging
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# Type hinting
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from typing import Tuple
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from .base import BaseCamera, CaptureObject
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# MAIN CLASS
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class StreamingCamera(BaseCamera):
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def __init__(self):
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# Run BaseCamera init
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BaseCamera.__init__(self)
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# Store state of StreamingCamera
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self.state.update({
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'stream_active': False,
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'record_active': False
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})
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# Update config properties
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self.image_resolution = (1312, 976)
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self.stream_resolution = (832, 624)
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self.numpy_resolution = (1312, 976)
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self.jpeg_quality = 75
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self.framerate = 10
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# Create an empty stream
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self.stream = io.BytesIO()
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# Start streaming
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self.start_worker()
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def initialisation(self):
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"""Run any initialisation code when the frame iterator starts."""
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pass
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def close(self):
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"""Close the Raspberry Pi StreamingCamera."""
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# Run BaseCamera close method
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BaseCamera.close(self)
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# HANDLE SETTINGS
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def read_config(self) -> dict:
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"""
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Return config dictionary of the StreamingCamera.
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"""
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conf_dict = {
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'stream_resolution': self.stream_resolution,
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'image_resolution': self.image_resolution,
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'numpy_resolution': self.numpy_resolution,
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'jpeg_quality': self.jpeg_quality
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}
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return conf_dict
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def apply_config(self, config: dict):
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"""
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Write a config dictionary to the StreamingCamera config.
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The passed dictionary may contain other parameters not relevant to
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camera config. Eg. Passing a general config file will work fine.
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Args:
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config (dict): Dictionary of config parameters.
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"""
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# TODO: Include timing and batching logic when applying PiCamera settings
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paused_stream = False
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logging.debug("StreamingCamera: Applying config:")
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logging.debug(config)
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with self.lock:
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# Apply valid config params to Picamera object
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if not self.state['record_active']: # If not recording a video
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# StreamingCamera parameters
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for key, value in config.items(): # For each provided setting
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if hasattr(self, key):
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setattr(self, key, value)
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# If stream was paused to update config, unpause
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if paused_stream:
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logging.info("Resuming stream.")
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self.start_stream_recording()
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else:
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raise Exception(
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"Cannot update camera config while recording is active.")
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def set_zoom(self, zoom_value: float = 1.) -> None:
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"""
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Change the camera zoom, handling re-centering and scaling.
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"""
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logging.warning("Zoom not implemented in mock camera")
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# LAUNCH ACTIONS
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def start_preview(self, fullscreen=True, window=None):
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"""Start the on board GPU camera preview."""
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logging.warning("GPU preview not implemented in mock camera")
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def stop_preview(self):
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"""Stop the on board GPU camera preview."""
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logging.warning("GPU preview not implemented in mock camera")
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def start_recording(
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self,
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output,
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fmt: str = 'h264',
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quality: int = 15):
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"""Start recording.
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Start a new video recording, writing to a output object.
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Args:
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output (CaptureObject/str): Output object to write data bytes to.
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fmt (str): Format of the capture.
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quality (int): Video recording quality.
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Returns:
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output_object (str/BytesIO): Target object.
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"""
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with self.lock:
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# Start recording method only if a current recording is not running
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logging.warning("Recording not implemented in mock camera")
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def stop_recording(self):
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"""Stop the last started video recording on splitter port 2."""
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with self.lock:
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logging.warning("Recording not implemented in mock camera")
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def capture(
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self,
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output,
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fmt: str = 'jpeg',
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use_video_port: bool = False,
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resize: Tuple[int, int] = None,
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bayer: bool = True):
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"""
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Capture a still image to a StreamObject.
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Defaults to JPEG format.
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Target object can be overridden for development purposes.
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Args:
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output (CaptureObject/str): Output object to write data bytes to.
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use_video_port (bool): Capture from the video port used for streaming. Lower resolution, faster.
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fmt (str): Format of the capture.
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resize ((int, int)): Resize the captured image.
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bayer (bool): Store raw bayer data in capture
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"""
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with self.lock:
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logging.warning("Capture not implemented in mock camera")
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def gen_img(self):
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imarray = np.random.rand(self.stream_resolution[1], self.stream_resolution[0], 3) * 255
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im = Image.fromarray(imarray.astype('uint8')).convert('L')
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im.save(self.stream, format="JPEG")
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# HANDLE STREAM FRAMES
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def frames(self):
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"""
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Create generator that returns frames from the camera.
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Records video from port 1 to a byte stream,
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and iterates sequential frames.
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"""
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# Run this initialisation method
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self.initialisation()
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# Update state
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logging.debug("STREAM ACTIVE")
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# While the iterator is not closed
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try:
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while True:
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# reset stream for next frame
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self.stream.seek(0)
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self.stream.truncate()
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# to stream, read the new frame
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time.sleep(1 / self.framerate * 0.1)
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# yield the result to be read
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self.gen_img()
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frame = self.stream.getvalue()
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# ensure the size of package is right
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if len(frame) == 0:
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pass
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else:
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yield frame
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# When GeneratorExit or StopIteration raised, run cleanup code
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finally:
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logging.debug("FRAME ITERATOR END")
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@ -529,6 +529,15 @@ class StreamingCamera(BaseCamera):
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# HANDLE STREAM FRAMES
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def wait_for_camera(self, timeout=5):
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"""Wait for camera object, with 5 second timeout."""
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timeout_time = time.time() + timeout
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while not self.camera:
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if time.time() > timeout_time:
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raise TimeoutError("Timeout waiting for camera")
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else:
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pass
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def frames(self):
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"""
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Create generator that returns frames from the camera.
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@ -1,8 +1,8 @@
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import numpy as np
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from picamera import PiCamera
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from picamera.array import PiRGBArray, PiBayerArray
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import time
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from picamera import PiCamera
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from picamera.array import PiRGBArray, PiBayerArray
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def rgb_image(camera, resize=None, **kwargs):
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"""Capture an image and return an RGB numpy array"""
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@ -78,8 +78,13 @@ def load_plugin_module(plugin_path):
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# If the loader was found (i.e. plugin probably exists)
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if check_module(plugin_path):
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plugin_module = importlib.import_module(plugin_path)
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plugin_name = name_from_module(plugin_path)
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try:
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plugin_module = importlib.import_module(plugin_path)
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plugin_name = name_from_module(plugin_path)
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except Exception as e:
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logging.error("Error loading plugin.")
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logging.error(e)
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return None, None
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# If no loader was found, try finding a file from path
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else:
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@ -156,24 +161,28 @@ class PluginMount(object):
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"""
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plugin_class, plugin_name = class_from_map(plugin_map)
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pythonsafe_plugin_name = plugin_name.replace("/", "_")
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if plugin_class is not None:
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if plugin_class and plugin_name:
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plugin_object = plugin_class()
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pythonsafe_plugin_name = plugin_name.replace("/", "_")
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if hasattr(self, plugin_name): # If a plugin with the same name is already attached.
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logging.warning(ConColors.WARNING + "A plugin named {} has already been loaded. Skipping {}.".format(plugin_name, plugin_map) + ConColors.ENDC)
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if plugin_class and plugin_name:
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plugin_object = plugin_class()
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elif isinstance(plugin_object, MicroscopePlugin): # If plugin_object is an instance of MicroscopePlugin
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# Attach plugin_object to the plugin mount
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setattr(self, pythonsafe_plugin_name, plugin_object)
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self.plugins.append((plugin_name, plugin_object))
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if hasattr(self, plugin_name): # If a plugin with the same name is already attached.
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logging.warning(ConColors.WARNING + "A plugin named {} has already been loaded. Skipping {}.".format(plugin_name, plugin_map) + ConColors.ENDC)
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# Grant plugin access to the hardware
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plugin_object.microscope = self.parent
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elif isinstance(plugin_object, MicroscopePlugin): # If plugin_object is an instance of MicroscopePlugin
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# Attach plugin_object to the plugin mount
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setattr(self, pythonsafe_plugin_name, plugin_object)
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self.plugins.append((plugin_name, plugin_object))
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logging.info(ConColors.OKGREEN + "Plugin {} loaded as {}.".format(plugin_map, plugin_name) + ConColors.ENDC)
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# Grant plugin access to the hardware
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plugin_object.microscope = self.parent
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logging.info(ConColors.OKGREEN + "Plugin {} loaded as {}.".format(plugin_map, plugin_name) + ConColors.ENDC)
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else:
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logging.error("Error loading plugin. Moving on.")
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class MicroscopePlugin:
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"""
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@ -28,6 +28,7 @@ from serial import STOPBITS_ONE, STOPBITS_ONE_POINT_FIVE, STOPBITS_TWO
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import io
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import time
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import warnings
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import logging
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class ExtensibleSerialInstrument(object):
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"""
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@ -58,8 +59,11 @@ class ExtensibleSerialInstrument(object):
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"""
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Set up the serial port and so on.
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"""
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logging.info("Updating BSI port settings")
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self.port_settings.update(kwargs)
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logging.info("Opening BSI connection to port {}".format(port))
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self.open(port, False) # Eventually this shouldn't rely on init...
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logging.info("Opened BSI connection to port {}".format(port))
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def open(self, port=None, quiet=True):
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"""Open communications with the serial port.
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@ -81,11 +85,13 @@ class ExtensibleSerialInstrument(object):
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def close(self):
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"""Release the serial port"""
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logging.debug("Closing serial connection")
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with self.communications_lock:
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try:
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self._ser.close()
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except Exception as e:
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print("The serial port didn't close cleanly:", e)
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logging.debug("Connection closed")
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def __del__(self):
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"""Close the port when the object is deleted
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@ -12,6 +12,7 @@ import time
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from .extensible_serial_instrument import ExtensibleSerialInstrument, OptionalModule, QueriedProperty, EIGHTBITS, PARITY_NONE, STOPBITS_ONE
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import re
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import warnings
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import logging
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class Sangaboard(ExtensibleSerialInstrument):
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"""Class managing serial communications with a Sangaboard
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@ -68,6 +69,7 @@ class Sangaboard(ExtensibleSerialInstrument):
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"""
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super(Sangaboard, self).__init__(port, **kwargs)
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try:
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logging.debug("Running firmware checks")
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# Request firmware version from the board
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self.firmware = self.query("version",timeout=2).rstrip()
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# The slightly complicated regexp below will match the version string,
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16
poetry.lock
generated
16
poetry.lock
generated
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@ -255,11 +255,11 @@ category = "main"
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description = "SciPy: Scientific Library for Python"
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name = "scipy"
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optional = false
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python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
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version = "1.2.1"
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python-versions = ">=3.5"
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version = "1.3.0"
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[package.dependencies]
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numpy = ">=1.8.2"
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numpy = ">=1.13.3"
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[[package]]
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category = "main"
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@ -271,11 +271,11 @@ version = "1.12.0"
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[[package]]
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category = "dev"
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description = "This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms."
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description = "This package provides 23 stemmers for 22 languages generated from Snowball algorithms."
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name = "snowballstemmer"
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optional = false
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python-versions = "*"
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version = "1.2.1"
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version = "1.9.0"
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[[package]]
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category = "dev"
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@ -381,7 +381,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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version = "0.15.4"
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[metadata]
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content-hash = "14a52bee3012c7880e4c87e940639606eb88ad7320e262d5228566b6df1ef601"
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content-hash = "ec0d5aa30422b8f44fb92e8e818120d4f0e1b084773594ce2531e31db5af26f4"
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python-versions = "^3.5"
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[metadata.hashes]
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@ -412,9 +412,9 @@ pytz = ["303879e36b721603cc54604edcac9d20401bdbe31e1e4fdee5b9f98d5d31dfda", "d74
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pyyaml = ["3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf", "40c71b8e076d0550b2e6380bada1f1cd1017b882f7e16f09a65be98e017f211a", "558dd60b890ba8fd982e05941927a3911dc409a63dcb8b634feaa0cda69330d3", "a7c28b45d9f99102fa092bb213aa12e0aaf9a6a1f5e395d36166639c1f96c3a1", "aa7dd4a6a427aed7df6fb7f08a580d68d9b118d90310374716ae90b710280af1", "bc558586e6045763782014934bfaf39d48b8ae85a2713117d16c39864085c613", "d46d7982b62e0729ad0175a9bc7e10a566fc07b224d2c79fafb5e032727eaa04", "d5eef459e30b09f5a098b9cea68bebfeb268697f78d647bd255a085371ac7f3f", "e01d3203230e1786cd91ccfdc8f8454c8069c91bee3962ad93b87a4b2860f537", "e170a9e6fcfd19021dd29845af83bb79236068bf5fd4df3327c1be18182b2531"]
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requests = ["11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4", "9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31"]
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"rpi.gpio" = ["a4210ad63bfe844e43995286de0d3950dfacfa0f3799bb9392770ac54a7d2e47"]
|
||||
scipy = ["014cb900c003b5ac81a53f2403294e8ecf37aedc315b59a6b9370dce0aa7627a", "281a34da34a5e0de42d26aed692ab710141cad9d5d218b20643a9cb538ace976", "588f9cc4bfab04c45fbd19c1354b5ade377a8124d6151d511c83730a9b6b2338", "5a10661accd36b6e2e8855addcf3d675d6222006a15795420a39c040362def66", "628f60be272512ca1123524969649a8cb5ae8b31cca349f7c6f8903daf9034d7", "6dcc43a88e25b815c2dea1c6fac7339779fc988f5df8396e1de01610604a7c38", "70e37cec0ac0fe95c85b74ca4e0620169590fd5d3f44765f3c3a532cedb0e5fd", "7274735fb6fb5d67d3789ddec2cd53ed6362539b41aa6cc0d33a06c003aaa390", "78e12972e144da47326958ac40c2bd1c1cca908edc8b01c26a36f9ffd3dce466", "790cbd3c8d09f3a6d9c47c4558841e25bac34eb7a0864a9def8f26be0b8706af", "79792c8fe8e9d06ebc50fe23266522c8c89f20aa94ac8e80472917ecdce1e5ba", "865afedf35aaef6df6344bee0de391ee5e99d6e802950a237f9fb9b13e441f91", "870fd401ec7b64a895cff8e206ee16569158db00254b2f7157b4c9a5db72c722", "963815c226b29b0176d5e3d37fc9de46e2778ce4636a5a7af11a48122ef2577c", "9726791484f08e394af0b59eb80489ad94d0a53bbb58ab1837dcad4d58489863", "9de84a71bb7979aa8c089c4fb0ea0e2ed3917df3fb2a287a41aaea54bbad7f5d", "b2c324ddc5d6dbd3f13680ad16a29425841876a84a1de23a984236d1afff4fa6", "b86ae13c597fca087cb8c193870507c8916cefb21e52e1897da320b5a35075e5", "ba0488d4dbba2af5bf9596b849873102d612e49a118c512d9d302ceafa36e01a", "d78702af4102a3a4e23bb7372cec283e78f32f5573d92091aa6aaba870370fe1", "def0e5d681dd3eb562b059d355ae8bebe27f5cc455ab7c2b6655586b63d3a8ea", "e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c", "e2cfcbab37c082a5087aba5ff00209999053260441caadd4f0e8f4c2d6b72088", "e742f1f5dcaf222e8471c37ee3d1fd561568a16bb52e031c25674ff1cf9702d5", "f06819b028b8ef9010281e74c59cb35483933583043091ed6b261bb1540f11cc", "f15f2d60a11c306de7700ee9f65df7e9e463848dbea9c8051e293b704038da60", "f31338ee269d201abe76083a990905473987371ff6f3fdb76a3f9073a361cf37", "f6b88c8d302c3dac8dff7766955e38d670c82e0d79edfc7eae47d6bb2c186594"]
|
||||
scipy = ["03b1e0775edbe6a4c64effb05fff2ce1429b76d29d754aa5ee2d848b60033351", "09d008237baabf52a5d4f5a6fcf9b3c03408f3f61a69c404472a16861a73917e", "10325f0ffac2400b1ec09537b7e403419dcd25d9fee602a44e8a32119af9079e", "1db9f964ed9c52dc5bd6127f0dd90ac89791daa690a5665cc01eae185912e1ba", "409846be9d6bdcbd78b9e5afe2f64b2da5a923dd7c1cd0615ce589489533fdbb", "4907040f62b91c2e170359c3d36c000af783f0fa1516a83d6c1517cde0af5340", "6c0543f2fdd38dee631fb023c0f31c284a532d205590b393d72009c14847f5b1", "826b9f5fbb7f908a13aa1efd4b7321e36992f5868d5d8311c7b40cf9b11ca0e7", "a7695a378c2ce402405ea37b12c7a338a8755e081869bd6b95858893ceb617ae", "a84c31e8409b420c3ca57fd30c7589378d6fdc8d155d866a7f8e6e80dec6fd06", "adadeeae5500de0da2b9e8dd478520d0a9945b577b2198f2462555e68f58e7ef", "b283a76a83fe463c9587a2c88003f800e08c3929dfbeba833b78260f9c209785", "c19a7389ab3cd712058a8c3c9ffd8d27a57f3d84b9c91a931f542682bb3d269d", "c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a", "c5ea60ece0c0c1c849025bfc541b60a6751b491b6f11dd9ef37ab5b8c9041921", "db61a640ca20f237317d27bc658c1fc54c7581ff7f6502d112922dc285bdabee"]
|
||||
six = ["3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c", "d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"]
|
||||
snowballstemmer = ["919f26a68b2c17a7634da993d91339e288964f93c274f1343e3bbbe2096e1128", "9f3bcd3c401c3e862ec0ebe6d2c069ebc012ce142cce209c098ccb5b09136e89"]
|
||||
snowballstemmer = ["9f3b9ffe0809d174f7047e121431acf99c89a7040f0ca84f94ba53a498e6d0c9"]
|
||||
sphinx = ["22538e1bbe62b407cf5a8aabe1bb15848aa66bb79559f42f5202bbce6b757a69", "f9a79e746b87921cabc3baa375199c6076d1270cee53915dbd24fdbeaaacc427"]
|
||||
sphinxcontrib-applehelp = ["edaa0ab2b2bc74403149cb0209d6775c96de797dfd5b5e2a71981309efab3897", "fb8dee85af95e5c30c91f10e7eb3c8967308518e0f7488a2828ef7bc191d0d5d"]
|
||||
sphinxcontrib-devhelp = ["6c64b077937330a9128a4da74586e8c2130262f014689b4b89e2d08ee7294a34", "9512ecb00a2b0821a146736b39f7aeb90759834b07e81e8cc23a9c70bacb9981"]
|
||||
|
|
|
|||
|
|
@ -28,12 +28,12 @@ Flask = "^1.0"
|
|||
pyyaml = "^3.13"
|
||||
numpy = "1.16.4" # Exact version until we can guarantee a wheel
|
||||
Pillow = "^5.4"
|
||||
"RPi.GPIO" = "^0.6.5"
|
||||
openflexure-stage = "^0.2.1"
|
||||
flask-cors = "^3.0"
|
||||
scipy = "1.3.0" # Exact version until we can guarantee a wheel
|
||||
|
||||
picamera = { git = "https://github.com/rwb27/picamera.git", branch = "lens-shading" } # Lens shading requires >1.14 or RWB fork, lens-shading branch.
|
||||
"RPi.GPIO" = { version = "^0.6.5", optional = true }
|
||||
|
||||
[tool.poetry.dev-dependencies]
|
||||
sphinxcontrib-httpdomain = "^1.7"
|
||||
|
|
|
|||
8
test1.py
Normal file
8
test1.py
Normal file
|
|
@ -0,0 +1,8 @@
|
|||
from openflexure_microscope.stage.sangaboard import Sangaboard
|
||||
|
||||
import logging
|
||||
import sys
|
||||
|
||||
logging.basicConfig(stream=sys.stdout, level=logging.DEBUG)
|
||||
|
||||
stage = Sangaboard()
|
||||
Loading…
Add table
Add a link
Reference in a new issue