Merge branch 'master' of https://gitlab.com/openflexure/openflexure-microscope-server

openflexure_microscope/api/app.py

@@ -1,5 +1,11 @@
 #!/usr/bin/env python
 
+import time
+import atexit
+import logging
+import sys
+import os
+
 from flask import (
     Flask, jsonify, send_file)
 
@@ -13,23 +19,22 @@ from openflexure_microscope.api.utilities import list_routes
 
 from openflexure_microscope import Microscope
 
-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
+# Import device modules
-import atexit
+# NB this will eventually be handled by the RC file, so you can choose what device
-import logging
+# class should be attached.
-import sys
+try:
-import os
+    from openflexure_microscope.camera.pi import PiCameraStreamer
+except ImportError:
+    logging.warning("Unable to import PiCameraStreamer")
+from openflexure_microscope.camera.mock import MockStreamer
+
+from openflexure_microscope.stage.sanga import SangaStage
+from openflexure_microscope.stage.mock import MockStage
+
 
 # Handle logging
 is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
@@ -96,30 +101,37 @@ def attach_microscope():
     global api_microscope, stored_image_list
     logging.debug("First request made. Populating microscope with hardware...")
 
+    # Initialise camera
     logging.debug("Creating camera object...")
-    # TODO: Try except finally, like with stage
+    try:
-    api_camera = StreamingCamera()
+        api_camera = PiCameraStreamer()
+    except Exception as e:
+        logging.error(e)
+        logging.warning("No valid camera hardware found. Falling back to mock camera!")
+        api_camera = MockStreamer()
 
+    # Initialise stage
     logging.debug("Creating stage object...")
-    # TODO: Tidy this up. api_stage may be referenced before assignment. Use some form of Maybe monad?
     try:
         api_stage = SangaStage()
     except Exception as e:
         logging.error(e)
         logging.warning("No valid stage hardware found. Falling back to mock stage!")
         api_stage = MockStage()
-    finally:
-        logging.debug("Attaching devices to microscope...")
-        api_microscope.attach(
-            api_camera,
-            api_stage
-        )
 
-        logging.debug("Restoring captures...")
+    # Attach devices to microscope
-        if stored_image_list:
+    logging.debug("Attaching devices to microscope...")
-            api_microscope.camera.images = stored_image_list
+    api_microscope.attach(
+        api_camera,
+        api_stage
+    )
 
-        logging.debug("Microscope successfully attached!")
+    # Restore loaded capture array to camera object
+    logging.debug("Restoring captures...")
+    if stored_image_list:
+        api_microscope.camera.images = stored_image_list
+
+    logging.debug("Microscope successfully attached!")
 
 
 # WEBAPP ROUTES

openflexure_microscope/camera/mock.py

@@ -19,13 +19,13 @@ from .base import BaseCamera, CaptureObject
 
 
 # MAIN CLASS
-class StreamingCamera(BaseCamera):
+class MockStreamer(BaseCamera):
 
     def __init__(self):
         # Run BaseCamera init
         BaseCamera.__init__(self)
 
-        # Store state of StreamingCamera
+        # Store state of PiCameraStreamer
         self.state.update({
             'stream_active': False,
             'record_active': False
@@ -49,14 +49,14 @@ class StreamingCamera(BaseCamera):
         pass
 
     def close(self):
-        """Close the Raspberry Pi StreamingCamera."""
+        """Close the Raspberry Pi PiCameraStreamer."""
         # Run BaseCamera close method
         BaseCamera.close(self)
 
     # HANDLE SETTINGS
     def read_config(self) -> dict:
         """
-        Return config dictionary of the StreamingCamera.
+        Return config dictionary of the PiCameraStreamer.
         """
 
         conf_dict = {
@@ -70,7 +70,7 @@ class StreamingCamera(BaseCamera):
 
     def apply_config(self, config: dict):
         """
-        Write a config dictionary to the StreamingCamera config.
+        Write a config dictionary to the PiCameraStreamer config.
 
         The passed dictionary may contain other parameters not relevant to
         camera config. Eg. Passing a general config file will work fine.
@@ -81,7 +81,7 @@ class StreamingCamera(BaseCamera):
         # TODO: Include timing and batching logic when applying PiCamera settings
 
         paused_stream = False
-        logging.debug("StreamingCamera: Applying config:")
+        logging.debug("PiCameraStreamer: Applying config:")
         logging.debug(config)
 
         with self.lock:
@@ -89,7 +89,7 @@ class StreamingCamera(BaseCamera):
             # Apply valid config params to Picamera object
             if not self.state['record_active']:  # If not recording a video
 
-                # StreamingCamera parameters
+                # PiCameraStreamer parameters
                 for key, value in config.items():  # For each provided setting
                     if hasattr(self, key):
                         setattr(self, key, value)

openflexure_microscope/camera/pi.py

@@ -1,7 +1,7 @@
 # -*- coding: utf-8 -*-
 
 """
-Raspberry Pi camera implementation of the StreamingCamera class.
+Raspberry Pi camera implementation of the PiCameraStreamer class.
 
 NOTES:
 Still port used for image capture
@@ -12,7 +12,7 @@ Video port:
     Splitter port 2: Video capture
     Splitter port 3: [Currently unused]
 
-StreamingCamera streams at video_resolution
+PiCameraStreamer streams at video_resolution
 Camera capture resolution set to stream_resolution in frames()
 Video port uses that resolution for everything. If a different resolution
 is specified for video capture, this is handled by the resizer.
@@ -41,8 +41,8 @@ from .set_picamera_gain import set_analog_gain, set_digital_gain
 
 
 # MAIN CLASS
-class StreamingCamera(BaseCamera):
+class PiCameraStreamer(BaseCamera):
-    """Raspberry Pi camera implementation of StreamingCamera."""
+    """Raspberry Pi camera implementation of PiCameraStreamer."""
     picamera_settings_keys = [
         'exposure_mode',
         'analog_gain',
@@ -61,7 +61,7 @@ class StreamingCamera(BaseCamera):
         # Attach to Pi camera
         self.camera = picamera.PiCamera()  #: :py:class:`picamera.PiCamera`: Picamera object
 
-        # Store state of StreamingCamera
+        # Store state of PiCameraStreamer
         self.state.update({
             'stream_active': False,
             'record_active': False,
@@ -87,7 +87,7 @@ class StreamingCamera(BaseCamera):
         pass
 
     def close(self):
-        """Close the Raspberry Pi StreamingCamera."""
+        """Close the Raspberry Pi PiCameraStreamer."""
         # Run BaseCamera close method
         BaseCamera.close(self)
         # Detach Pi camera
@@ -97,7 +97,7 @@ class StreamingCamera(BaseCamera):
     # HANDLE SETTINGS
     def read_config(self) -> dict:
         """
-        Return config dictionary of the StreamingCamera.
+        Return config dictionary of the PiCameraStreamer.
         """
 
         conf_dict = {
@@ -109,7 +109,7 @@ class StreamingCamera(BaseCamera):
         }
 
         # PiCamera parameters
-        for key in StreamingCamera.picamera_settings_keys:
+        for key in PiCameraStreamer.picamera_settings_keys:
             try:
                 value = getattr(self.camera, key)
                 logging.debug("Reading PiCamera().{}: {}".format(key, value))
@@ -121,7 +121,7 @@ class StreamingCamera(BaseCamera):
 
     def apply_config(self, config: dict):
         """
-        Write a config dictionary to the StreamingCamera config.
+        Write a config dictionary to the PiCameraStreamer config.
 
         The passed dictionary may contain other parameters not relevant to
         camera config. Eg. Passing a general config file will work fine.
@@ -132,7 +132,7 @@ class StreamingCamera(BaseCamera):
         # TODO: Include timing and batching logic when applying PiCamera settings
 
         paused_stream = False
-        logging.debug("StreamingCamera: Applying config:")
+        logging.debug("PiCameraStreamer: Applying config:")
         logging.debug(config)
 
         with self.lock:
@@ -150,7 +150,7 @@ class StreamingCamera(BaseCamera):
                 if 'picamera_settings' in config:  # If new settings are given
                     self.apply_picamera_settings(config['picamera_settings'], pause_for_effect=True)
 
-                # StreamingCamera parameters
+                # PiCameraStreamer parameters
                 for key, value in config.items():  # For each provided setting
                     if (key != 'picamera_settings') and hasattr(self, key):
                         setattr(self, key, value)

openflexure_microscope/stage/sanga.py

@@ -194,13 +194,6 @@ class SangaStage(BaseStage):
         """De-energise the stepper motor coils"""
         self.board.release_motors()
 
-    def __del__(self):
-        """Close the port when the object is deleted
-        
-        NB if the object is created in a with statement, this will cause
-        the port to be closed at the end of the with block."""
-        self.close()
-
     def __enter__(self):
         """When we use this in a with statement, remember where we started."""
         self._position_on_enter = self.position

openflexure_microscope/stage/sangaboard/extensible_serial_instrument.py

@@ -26,8 +26,8 @@ from serial import PARITY_NONE, PARITY_EVEN, PARITY_ODD, PARITY_MARK, PARITY_SPA
 from serial import STOPBITS_ONE, STOPBITS_ONE_POINT_FIVE, STOPBITS_TWO
 import io
 import time
-import warnings
 import logging
+import warnings
 
 class ExtensibleSerialInstrument(object):
     """
@@ -54,7 +54,7 @@ class ExtensibleSerialInstrument(object):
     ignore_echo = False
     port_settings = {}
 
-    def __init__(self, port, **kwargs):
+    def __init__(self, port=None, **kwargs):
         """
         Set up the serial port and so on.
         """
@@ -64,7 +64,7 @@ class ExtensibleSerialInstrument(object):
         self.open(port, False) # Eventually this shouldn't rely on init...
         logging.info("Opened ESI connection to port {}".format(port))
 
-    def open(self, port, quiet=True):
+    def open(self, port=None, quiet=True):
         """Open communications with the serial port.
         
         If no port is specified, it will attempt to autodetect.  If quiet=True
@@ -74,6 +74,8 @@ class ExtensibleSerialInstrument(object):
             if hasattr(self,'_ser') and self._ser.isOpen():
                 if not quiet: logging.warning("Attempted to open an already-open port!")
                 return
+            if port is None: 
+                port=self.find_port()
             assert port is not None, "We don't have a serial port to open, meaning you didn't specify a valid port.  Are you sure the instrument is connected?"
             self._ser = serial.Serial(port,**self.port_settings)
             #the block above wraps the serial IO layer with a text IO layer
@@ -82,28 +84,33 @@ class ExtensibleSerialInstrument(object):
             assert self.test_communications(), "The instrument doesn't seem to be responding.  Did you specify the right port?"
 
     def close(self):
-        """Release the serial port"""
+        """Cleanly close the device. Includes proper logging statements."""
         logging.debug("Closing serial connection")
         with self.communications_lock:
             try:
                 self._ser.close()
             except Exception as e:
-                logging.warning("The serial port didn't close cleanly:", e)
+                logging.warning("The serial port didn't close cleanly: {}".format(e))
-        logging.debug("Connection closed")
+            logging.debug("Connection closed")
 
     def __del__(self):
-        """Close the port when the object is deleted
+        """Emergency close the device. Try to avoid having to use this."""
-        
+        if hasattr(self, '_ser') and self._ser.isOpen():
-        NB if the object is created in a with statement, this will cause
+            with self.communications_lock:
-        the port to be closed at the end of the with block."""
+                print(
-        self.close()
+                    "Closing an open serial communication has been triggered by garbage collection!\n"\
+                    "Please close this device more sensibly in future.")
+                try:
+                    self._ser.close()
+                except Exception as e:
+                    print("The serial port didn't close cleanly: {}".format(e))
 
     def __enter__(self):
         return self
 
     def __exit__(self, type, value, traceback):
-        """Close down the instrument.  This happens in __del__ though."""
+        """Cleanly close down the instrument at end of a with block."""
-        pass
+        self.close()
         
     def write(self,query_string):
         """Write a string to the serial port"""
@@ -232,7 +239,7 @@ class ExtensibleSerialInstrument(object):
                 reply = self.readline().strip()
                 res=re.search(response_regex, reply, flags=re_flags)
                 if res is not None:
-                    warnings.warn("Query suceeded after initially receieving unmatched response ('%s') to '%s'. Match pattern /%s/ (generated regex /%s/)"%(original_reply, query_string, response_string, response_regex),RuntimeWarning)
+                    warnings.warn("Query suceeded after initially receieving unmatched response ('%s') to '%s'. Match pattern /%s/ (generated regex /%s/)"%(original_reply, query_string, response_string, response_regex), RuntimeWarning)
             else:
                 raise ValueError("Stage response to '%s' ('%s') wasn't matched by /%s/ (generated regex /%s/)" % (query_string, original_reply, response_string, response_regex))
         try:
@@ -242,9 +249,8 @@ class ExtensibleSerialInstrument(object):
             else:
                 return parsed_result
         except ValueError:
-            logging.error("Parsing Error")
+            logging.info("Matched Groups: {}".format(res.groups()))
-            logging.info("Matched Groups:", res.groups())
+            logging.info("Parsing Functions {}:".format(parse_function))
-            logging.info("Parsing Functions:", parse_function)
             raise ValueError("Stage response to %s ('%s') couldn't be parsed by the supplied function" % (query_string, reply))
     def int_query(self, query_string, **kwargs):
         """Perform a query and return the result(s) as integer(s) (see parsedQuery)"""
@@ -261,7 +267,32 @@ class ExtensibleSerialInstrument(object):
         Usually this function sends a command and checks for a known reply."""
         with self.communications_lock:
             return True
-    
+
+    def find_port(self):
+        """Iterate through the available serial ports and query them to see
+        if our instrument is there."""
+        with self.communications_lock:
+            success = False
+            for port_name, _, _ in serial.tools.list_ports.comports(): #loop through serial ports, apparently 256 is the limit?!
+                try:
+                    logging.info("Trying port {}".format(port_name))
+                    self.open(port_name)
+                    success = True
+                    logging.info("Success!")
+                except:
+                    pass
+                finally:
+                    try:
+                        self.close()
+                    except:
+                        pass #we don't care if there's an error closing the port...
+                if success:
+                    break #again, make sure this happens *after* closing the port
+            if success:
+                return port_name
+            else:
+                return None
+
 class OptionalModule(object):
     """This allows a `ExtensibleSerialInstrument` to have optional features.
 

openflexure_microscope/stage/sangaboard/sangaboard.py

@@ -81,13 +81,8 @@ class Sangaboard(ExtensibleSerialInstrument):
         it doesn't need to be named.
         """
 
-        # If no port is specified
-        if not port:
-            # Scan all available ports, and check for valid firmware
-            scanned_port = self.scan_ports()
-
         # Initialise basic serial instrument with specified
-        ExtensibleSerialInstrument.__init__(self, scanned_port, **kwargs)
+        ExtensibleSerialInstrument.__init__(self, port, **kwargs)
 
         try:
             # Make absolutely sure that whatever port we're on is valid
@@ -119,37 +114,11 @@ class Sangaboard(ExtensibleSerialInstrument):
             logging.error("You may need to update the firmware running on the Sangaboard.")
             raise e
 
-    def scan_ports(self):
+    def test_communications(self):
-        """Iterate through the available serial ports and query them to see
+        """
-        if our instrument is there."""
+        Overrides superclass, used in self.open(), and port scanning
-        logging.debug("Running Sangaboard port scanner")
+        """
-        with self.communications_lock:
+        return self.check_valid_firmware()
-            success = False
-            for port_name, _, _ in serial.tools.list_ports.comports(): #loop through serial ports, apparently 256 is the limit?!
-                try:
-                    logging.info("Trying port {}".format(port_name))
-                    self.open(port_name)
-                    success = True
-
-                    logging.info("Checking firmware")
-                    fw = self.check_valid_firmware()
-                    if not fw:
-                        success = False
-                except Exception as e:
-                    logging.warning("Error on port {}".format(port_name))
-                    logging.warning(e)
-                    pass
-                finally:
-                    try:
-                        self.close()
-                    except:
-                        pass #we don't care if there's an error closing the port...
-                if success:
-                    break #again, make sure this happens *after* closing the port
-            if success:
-                return port_name
-            else:
-                return None
 
     def check_valid_firmware(self):
         logging.debug("Running firmware checks")

poetry.lock

@@ -180,6 +180,7 @@ version = "1.13.1b0"
 reference = "b39c2b6e42f5f7f57bb46eafcb5c9e2bbdb5d0cb"
 type = "git"
 url = "https://github.com/rwb27/picamera.git"
+
 [[package]]
 category = "main"
 description = "Python Imaging Library (Fork)"
@@ -242,6 +243,14 @@ chardet = ">=3.0.2,<3.1.0"
 idna = ">=2.5,<2.9"
 urllib3 = ">=1.21.1,<1.25.0 || >1.25.0,<1.25.1 || >1.25.1,<1.26"
 
+[[package]]
+category = "dev"
+description = "a python refactoring library..."
+name = "rope"
+optional = false
+python-versions = "*"
+version = "0.14.0"
+
 [[package]]
 category = "main"
 description = "A module to control Raspberry Pi GPIO channels"
@@ -381,7 +390,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 version = "0.15.4"
 
 [metadata]
-content-hash = "33585d30bda3df47511879542dd7c778bb1922947b650a5554c231a0be7c8b4a"
+content-hash = "c2fee81479442877ae94095d15f05018dc5290eee42edeb7d79d067fdf0ffab6"
 python-versions = "^3.5"
 
 [metadata.hashes]
@@ -411,6 +420,7 @@ pyserial = ["6e2d401fdee0eab996cf734e67773a0143b932772ca8b42451440cfed942c627",
 pytz = ["303879e36b721603cc54604edcac9d20401bdbe31e1e4fdee5b9f98d5d31dfda", "d747dd3d23d77ef44c6a3526e274af6efeb0a6f1afd5a69ba4d5be4098c8e141"]
 pyyaml = ["3d7da3009c0f3e783b2c873687652d83b1bbfd5c88e9813fb7e5b03c0dd3108b", "3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf", "40c71b8e076d0550b2e6380bada1f1cd1017b882f7e16f09a65be98e017f211a", "558dd60b890ba8fd982e05941927a3911dc409a63dcb8b634feaa0cda69330d3", "a7c28b45d9f99102fa092bb213aa12e0aaf9a6a1f5e395d36166639c1f96c3a1", "aa7dd4a6a427aed7df6fb7f08a580d68d9b118d90310374716ae90b710280af1", "bc558586e6045763782014934bfaf39d48b8ae85a2713117d16c39864085c613", "d46d7982b62e0729ad0175a9bc7e10a566fc07b224d2c79fafb5e032727eaa04", "d5eef459e30b09f5a098b9cea68bebfeb268697f78d647bd255a085371ac7f3f", "e01d3203230e1786cd91ccfdc8f8454c8069c91bee3962ad93b87a4b2860f537", "e170a9e6fcfd19021dd29845af83bb79236068bf5fd4df3327c1be18182b2531"]
 requests = ["11e007a8a2aa0323f5a921e9e6a2d7e4e67d9877e85773fba9ba6419025cbeb4", "9cf5292fcd0f598c671cfc1e0d7d1a7f13bb8085e9a590f48c010551dc6c4b31"]
+rope = ["6b728fdc3e98a83446c27a91fc5d56808a004f8beab7a31ab1d7224cecc7d969", "c5c5a6a87f7b1a2095fb311135e2a3d1f194f5ecb96900fdd0a9100881f48aaf", "f0dcf719b63200d492b85535ebe5ea9b29e0d0b8aebeb87fe03fc1a65924fdaf"]
 "rpi.gpio" = ["a4210ad63bfe844e43995286de0d3950dfacfa0f3799bb9392770ac54a7d2e47"]
 scipy = ["03b1e0775edbe6a4c64effb05fff2ce1429b76d29d754aa5ee2d848b60033351", "09d008237baabf52a5d4f5a6fcf9b3c03408f3f61a69c404472a16861a73917e", "10325f0ffac2400b1ec09537b7e403419dcd25d9fee602a44e8a32119af9079e", "1db9f964ed9c52dc5bd6127f0dd90ac89791daa690a5665cc01eae185912e1ba", "409846be9d6bdcbd78b9e5afe2f64b2da5a923dd7c1cd0615ce589489533fdbb", "4907040f62b91c2e170359c3d36c000af783f0fa1516a83d6c1517cde0af5340", "6c0543f2fdd38dee631fb023c0f31c284a532d205590b393d72009c14847f5b1", "826b9f5fbb7f908a13aa1efd4b7321e36992f5868d5d8311c7b40cf9b11ca0e7", "a7695a378c2ce402405ea37b12c7a338a8755e081869bd6b95858893ceb617ae", "a84c31e8409b420c3ca57fd30c7589378d6fdc8d155d866a7f8e6e80dec6fd06", "adadeeae5500de0da2b9e8dd478520d0a9945b577b2198f2462555e68f58e7ef", "b283a76a83fe463c9587a2c88003f800e08c3929dfbeba833b78260f9c209785", "c19a7389ab3cd712058a8c3c9ffd8d27a57f3d84b9c91a931f542682bb3d269d", "c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a", "c5ea60ece0c0c1c849025bfc541b60a6751b491b6f11dd9ef37ab5b8c9041921", "db61a640ca20f237317d27bc658c1fc54c7581ff7f6502d112922dc285bdabee"]
 six = ["3350809f0555b11f552448330d0b52d5f24c91a322ea4a15ef22629740f3761c", "d16a0141ec1a18405cd4ce8b4613101da75da0e9a7aec5bdd4fa804d0e0eba73"]

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "openflexure_microscope"
-version = "1.1.0"
+version = "1.1.1"
 description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
 
 authors = [
@@ -37,3 +37,4 @@ picamera = { git = "https://github.com/rwb27/picamera.git", branch = "lens-shadi
 
 [tool.poetry.dev-dependencies]
 sphinxcontrib-httpdomain = "^1.7"
+rope = "^0.14.0"

tests/test_camera.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-from openflexure_microscope.camera.pi import StreamingCamera, CaptureObject
+from openflexure_microscope.camera.pi import PiCameraStreamer, CaptureObject
 
 import os
 import io
@@ -279,7 +279,7 @@ class TestThreadStarting(unittest.TestCase):
 
 
 if __name__ == '__main__':
-    with StreamingCamera() as camera:
+    with PiCameraStreamer() as camera:
 
         suites = [
             unittest.TestLoader().loadTestsFromTestCase(TestCaptureMethods),

tests/test_plugins.py

@@ -1,5 +1,5 @@
 #!/usr/bin/env python
-from openflexure_microscope.camera.pi import StreamingCamera
+from openflexure_microscope.camera.pi import PiCameraStreamer
 from openflexure_stage import OpenFlexureStage
 from openflexure_microscope import Microscope, config
 
@@ -31,7 +31,9 @@ class TestPluginMethods(unittest.TestCase):
 
 if __name__ == '__main__':
 
-        with Microscope(StreamingCamera(), OpenFlexureStage("/dev/ttyUSB0")) as microscope:
+        with Microscope() as microscope:
+
+            microscope.attach(PiCameraStreamer(), OpenFlexureStage())
 
             microscope.plugin.attach("openflexure_microscope.plugins.testing:Plugin")