Added support for a fully mocked device

openflexure_microscope/api/app.py

@@ -12,14 +12,17 @@ from openflexure_microscope.api.exceptions import JSONExceptionHandler
 from openflexure_microscope.api.utilities import list_routes
 
 from openflexure_microscope import Microscope
-from openflexure_microscope.camera.pi import StreamingCamera
+
+try:
+    from openflexure_microscope.camera.pi import StreamingCamera
+except ImportError:
+    from openflexure_microscope.camera.mock import StreamingCamera
+
 from openflexure_microscope.stage.sanga import SangaStage
 from openflexure_microscope.stage.mock import MockStage
 
 from openflexure_microscope.camera.capture import build_captures_from_exif
-
 from openflexure_microscope.config import USER_CONFIG_DIR
-
 from openflexure_microscope.api.v1 import blueprints
 
 import time
@@ -101,7 +104,7 @@ def attach_microscope():
     # TODO: Tidy this up. api_stage may be referenced before assignment. Use some form of Maybe monad?
     try:
         api_stage = SangaStage()
-    except (SerialException, OSError) as e:
+    except Exception as e:
         logging.error(e)
         logging.warning("No valid stage hardware found. Falling back to mock stage!")
         api_stage = MockStage()

openflexure_microscope/camera/__init__.py

@@ -1,3 +0,0 @@
-__all__ = ['pi', 'base']
-
-from . import pi, base

openflexure_microscope/camera/base.py

@@ -167,15 +167,6 @@ class BaseCamera(metaclass=ABCMeta):
         self.stop_worker()
         logging.info("Closed {}".format(self))
 
-    def wait_for_camera(self, timeout=5):
-        """Wait for camera object, with 5 second timeout."""
-        timeout_time = time.time() + timeout
-        while not self.camera:
-            if time.time() > timeout_time:
-                raise TimeoutError("Timeout waiting for camera")
-            else:
-                pass
-
     # START AND STOP WORKER THREAD
 
     def start_worker(self, timeout: int = 5) -> bool:

openflexure_microscope/camera/mock.py

@@ -0,0 +1,217 @@
+# -*- coding: utf-8 -*-
+
+"""
+"""
+
+from __future__ import division
+
+import io
+import time
+import numpy as np
+from PIL import Image
+
+import logging
+
+# Type hinting
+from typing import Tuple
+
+from .base import BaseCamera, CaptureObject
+
+
+# MAIN CLASS
+class StreamingCamera(BaseCamera):
+
+    def __init__(self):
+        # Run BaseCamera init
+        BaseCamera.__init__(self)
+
+        # Store state of StreamingCamera
+        self.state.update({
+            'stream_active': False,
+            'record_active': False
+        })
+
+        # Update config properties
+        self.image_resolution = (1312, 976)
+        self.stream_resolution = (832, 624)
+        self.numpy_resolution = (1312, 976)
+        self.jpeg_quality = 75
+        self.framerate = 10
+
+        # Create an empty stream
+        self.stream = io.BytesIO()
+
+        # Start streaming
+        self.start_worker()
+
+    def initialisation(self):
+        """Run any initialisation code when the frame iterator starts."""
+        pass
+
+    def close(self):
+        """Close the Raspberry Pi StreamingCamera."""
+        # Run BaseCamera close method
+        BaseCamera.close(self)
+
+    # HANDLE SETTINGS
+    def read_config(self) -> dict:
+        """
+        Return config dictionary of the StreamingCamera.
+        """
+
+        conf_dict = {
+            'stream_resolution': self.stream_resolution,
+            'image_resolution': self.image_resolution,
+            'numpy_resolution': self.numpy_resolution,
+            'jpeg_quality': self.jpeg_quality
+        }
+
+        return conf_dict
+
+    def apply_config(self, config: dict):
+        """
+        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.
+        """
+        # TODO: Include timing and batching logic when applying PiCamera settings
+
+        paused_stream = False
+        logging.debug("StreamingCamera: Applying config:")
+        logging.debug(config)
+
+        with self.lock:
+
+            # Apply valid config params to Picamera object
+            if not self.state['record_active']:  # If not recording a video
+
+                # StreamingCamera parameters
+                for key, value in config.items():  # For each provided setting
+                    if hasattr(self, key):
+                        setattr(self, key, value)
+
+                # If stream was paused to update config, unpause
+                if paused_stream:
+                    logging.info("Resuming stream.")
+                    self.start_stream_recording()
+
+            else:
+                raise Exception(
+                    "Cannot update camera config while recording is active.")
+
+    def set_zoom(self, zoom_value: float = 1.) -> None:
+        """
+        Change the camera zoom, handling re-centering and scaling.
+        """
+        logging.warning("Zoom not implemented in mock camera")
+
+    # LAUNCH ACTIONS
+
+    def start_preview(self, fullscreen=True, window=None):
+        """Start the on board GPU camera preview."""
+        logging.warning("GPU preview not implemented in mock camera")
+
+    def stop_preview(self):
+        """Stop the on board GPU camera preview."""
+        logging.warning("GPU preview not implemented in mock camera")
+
+
+    def start_recording(
+            self,
+            output,
+            fmt: str = 'h264',
+            quality: int = 15):
+        """Start recording.
+
+        Start a new video recording, writing to a output object.
+
+        Args:
+            output (CaptureObject/str): Output object to write data bytes to.
+            fmt (str): Format of the capture.
+            quality (int): Video recording quality.
+
+        Returns:
+            output_object (str/BytesIO): Target object.
+
+        """
+        with self.lock:
+            # Start recording method only if a current recording is not running
+            logging.warning("Recording not implemented in mock camera")
+
+
+    def stop_recording(self):
+        """Stop the last started video recording on splitter port 2."""
+        with self.lock:
+            logging.warning("Recording not implemented in mock camera")
+
+    def capture(
+            self,
+            output,
+            fmt: str = 'jpeg',
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = True):
+        """
+        Capture a still image to a StreamObject.
+
+        Defaults to JPEG format.
+        Target object can be overridden for development purposes.
+
+        Args:
+            output (CaptureObject/str): Output object to write data bytes to.
+            use_video_port (bool): Capture from the video port used for streaming. Lower resolution, faster.
+            fmt (str): Format of the capture.
+            resize ((int, int)): Resize the captured image.
+            bayer (bool): Store raw bayer data in capture
+        """
+
+        with self.lock:
+            logging.warning("Capture not implemented in mock camera")
+
+
+    def gen_img(self):
+        imarray = np.random.rand(self.stream_resolution[1], self.stream_resolution[0], 3) * 255
+        im = Image.fromarray(imarray.astype('uint8')).convert('L')
+        im.save(self.stream, format="JPEG")
+
+    # HANDLE STREAM FRAMES
+
+    def frames(self):
+        """
+        Create generator that returns frames from the camera.
+
+        Records video from port 1 to a byte stream,
+        and iterates sequential frames.
+        """
+        # Run this initialisation method
+        self.initialisation()
+
+        # Update state
+        logging.debug("STREAM ACTIVE")
+
+        # While the iterator is not closed
+        try:
+            while True:
+                # reset stream for next frame
+                self.stream.seek(0)
+                self.stream.truncate()
+                # to stream, read the new frame
+                time.sleep(1 / self.framerate * 0.1)
+
+                # yield the result to be read
+                self.gen_img()
+                frame = self.stream.getvalue()
+
+                # ensure the size of package is right
+                if len(frame) == 0:
+                    pass
+                else:
+                    yield frame
+
+        # When GeneratorExit or StopIteration raised, run cleanup code
+        finally:
+            logging.debug("FRAME ITERATOR END")

openflexure_microscope/camera/pi.py

@@ -529,6 +529,15 @@ class StreamingCamera(BaseCamera):
 
     # HANDLE STREAM FRAMES
 
+    def wait_for_camera(self, timeout=5):
+        """Wait for camera object, with 5 second timeout."""
+        timeout_time = time.time() + timeout
+        while not self.camera:
+            if time.time() > timeout_time:
+                raise TimeoutError("Timeout waiting for camera")
+            else:
+                pass
+
     def frames(self):
         """
         Create generator that returns frames from the camera.

openflexure_microscope/plugins/default/camera_calibration/recalibrate_utils.py

@@ -1,8 +1,8 @@
 import numpy as np
-from picamera import PiCamera
-from picamera.array import PiRGBArray, PiBayerArray
 import time
 
+from picamera import PiCamera
+from picamera.array import PiRGBArray, PiBayerArray
 
 def rgb_image(camera, resize=None, **kwargs):
     """Capture an image and return an RGB numpy array"""

openflexure_microscope/plugins/loader.py

@@ -78,8 +78,13 @@ def load_plugin_module(plugin_path):
 
     # If the loader was found (i.e. plugin probably exists)
     if check_module(plugin_path):
-        plugin_module = importlib.import_module(plugin_path)
+        try:
-        plugin_name = name_from_module(plugin_path)
+            plugin_module = importlib.import_module(plugin_path)
+            plugin_name = name_from_module(plugin_path)
+        except Exception as e:
+            logging.error("Error loading plugin.")
+            logging.error(e)
+            return None, None
 
     # If no loader was found, try finding a file from path
     else:
@@ -156,24 +161,28 @@ class PluginMount(object):
         """
         plugin_class, plugin_name = class_from_map(plugin_map)
 
-        pythonsafe_plugin_name = plugin_name.replace("/", "_")
+        if plugin_class is not None:
 
-        if plugin_class and plugin_name:
+            pythonsafe_plugin_name = plugin_name.replace("/", "_")
-            plugin_object = plugin_class()
 
-            if hasattr(self, plugin_name):  # If a plugin with the same name is already attached.
+            if plugin_class and plugin_name:
-                logging.warning(ConColors.WARNING + "A plugin named {} has already been loaded. Skipping {}.".format(plugin_name, plugin_map) + ConColors.ENDC)
+                plugin_object = plugin_class()
 
-            elif isinstance(plugin_object, MicroscopePlugin):  # If plugin_object is an instance of MicroscopePlugin
+                if hasattr(self, plugin_name):  # If a plugin with the same name is already attached.
-                # Attach plugin_object to the plugin mount
+                    logging.warning(ConColors.WARNING + "A plugin named {} has already been loaded. Skipping {}.".format(plugin_name, plugin_map) + ConColors.ENDC)
-                setattr(self, pythonsafe_plugin_name, plugin_object)
-                self.plugins.append((plugin_name, plugin_object))
 
-                # Grant plugin access to the hardware
+                elif isinstance(plugin_object, MicroscopePlugin):  # If plugin_object is an instance of MicroscopePlugin
-                plugin_object.microscope = self.parent
+                    # Attach plugin_object to the plugin mount
+                    setattr(self, pythonsafe_plugin_name, plugin_object)
+                    self.plugins.append((plugin_name, plugin_object))
 
-                logging.info(ConColors.OKGREEN + "Plugin {} loaded as {}.".format(plugin_map, plugin_name) + ConColors.ENDC)
+                    # Grant plugin access to the hardware
+                    plugin_object.microscope = self.parent
 
+                    logging.info(ConColors.OKGREEN + "Plugin {} loaded as {}.".format(plugin_map, plugin_name) + ConColors.ENDC)
+
+        else:
+            logging.error("Error loading plugin. Moving on.")
 
 class MicroscopePlugin:
     """

openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py

@@ -28,6 +28,7 @@ from serial import STOPBITS_ONE, STOPBITS_ONE_POINT_FIVE, STOPBITS_TWO
 import io
 import time
 import warnings
+import logging
 
 class ExtensibleSerialInstrument(object):
     """
@@ -58,8 +59,11 @@ class ExtensibleSerialInstrument(object):
         """
         Set up the serial port and so on.
         """
+        logging.info("Updating BSI port settings")
         self.port_settings.update(kwargs)
+        logging.info("Opening BSI connection to port {}".format(port))
         self.open(port, False) # Eventually this shouldn't rely on init...
+        logging.info("Opened BSI connection to port {}".format(port))
 
     def open(self, port=None, quiet=True):
         """Open communications with the serial port.
@@ -81,11 +85,13 @@ class ExtensibleSerialInstrument(object):
 
     def close(self):
         """Release the serial port"""
+        logging.debug("Closing serial connection")
         with self.communications_lock:
             try:
                 self._ser.close()
             except Exception as e:
                 print("The serial port didn't close cleanly:", e)
+        logging.debug("Connection closed")
 
     def __del__(self):
         """Close the port when the object is deleted

openflexure_microscope/stage/sangaboard/sangaboard.py

@@ -12,6 +12,7 @@ import time
 from .extensible_serial_instrument import ExtensibleSerialInstrument, OptionalModule, QueriedProperty, EIGHTBITS, PARITY_NONE, STOPBITS_ONE
 import re
 import warnings
+import logging
 
 class Sangaboard(ExtensibleSerialInstrument):
     """Class managing serial communications with a Sangaboard
@@ -68,6 +69,7 @@ class Sangaboard(ExtensibleSerialInstrument):
         """
         super(Sangaboard, self).__init__(port, **kwargs)
         try:
+            logging.debug("Running firmware checks")
             # Request firmware version from the board
             self.firmware = self.query("version",timeout=2).rstrip()
             # The slightly complicated regexp below will match the version string,

poetry.lock

@@ -255,11 +255,11 @@ category = "main"
 description = "SciPy: Scientific Library for Python"
 name = "scipy"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
+python-versions = ">=3.5"
-version = "1.2.1"
+version = "1.3.0"
 
 [package.dependencies]
-numpy = ">=1.8.2"
+numpy = ">=1.13.3"
 
 [[package]]
 category = "main"
@@ -271,11 +271,11 @@ version = "1.12.0"
 
 [[package]]
 category = "dev"
-description = "This package provides 16 stemmer algorithms (15 + Poerter English stemmer) generated from Snowball algorithms."
+description = "This package provides 23 stemmers for 22 languages generated from Snowball algorithms."
 name = "snowballstemmer"
 optional = false
 python-versions = "*"
-version = "1.2.1"
+version = "1.9.0"
 
 [[package]]
 category = "dev"
@@ -381,7 +381,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "0.15.4"
 
 [metadata]
-content-hash = "14a52bee3012c7880e4c87e940639606eb88ad7320e262d5228566b6df1ef601"
+content-hash = "ec0d5aa30422b8f44fb92e8e818120d4f0e1b084773594ce2531e31db5af26f4"
 python-versions = "^3.5"
 
 [metadata.hashes]
@@ -412,9 +412,9 @@ pytz = ["303879e36b721603cc54604edcac9d20401bdbe31e1e4fdee5b9f98d5d31dfda", "d74
 pyyaml = ["3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf", "40c71b8e076d0550b2e6380bada1f1cd1017b882f7e16f09a65be98e017f211a", "558dd60b890ba8fd982e05941927a3911dc409a63dcb8b634feaa0cda69330d3", "a7c28b45d9f99102fa092bb213aa12e0aaf9a6a1f5e395d36166639c1f96c3a1", "aa7dd4a6a427aed7df6fb7f08a580d68d9b118d90310374716ae90b710280af1", "bc558586e6045763782014934bfaf39d48b8ae85a2713117d16c39864085c613", "d46d7982b62e0729ad0175a9bc7e10a566fc07b224d2c79fafb5e032727eaa04", "d5eef459e30b09f5a098b9cea68bebfeb268697f78d647bd255a085371ac7f3f", "e01d3203230e1786cd91ccfdc8f8454c8069c91bee3962ad93b87a4b2860f537", "e170a9e6fcfd19021dd29845af83bb79236068bf5fd4df3327c1be18182b2531"]
 requests = ["11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4", "9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31"]
 "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"]

pyproject.toml

@@ -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"

test1.py

@@ -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()