Blackened files

openflexure_microscope/api/v1/blueprints/base.py

@@ -39,10 +39,8 @@ class SnapshotAPI(MicroscopeView):
         # Restart stream worker thread
         self.microscope.camera.start_worker()
 
-        return Response(
-            self.microscope.camera.get_frame(),
-            mimetype="image/jpeg",
-        )
+        return Response(self.microscope.camera.get_frame(), mimetype="image/jpeg")
+
 
 class StateAPI(MicroscopeView):
     def get(self):
@@ -240,7 +238,8 @@ def construct_blueprint(microscope_obj):
     )
 
     blueprint.add_url_rule(
-        "/snapshot", view_func=SnapshotAPI.as_view("snapshot", microscope=microscope_obj)
+        "/snapshot",
+        view_func=SnapshotAPI.as_view("snapshot", microscope=microscope_obj),
     )
 
     blueprint.add_url_rule(

openflexure_microscope/api/v1/blueprints/task.py

@@ -134,12 +134,8 @@ def construct_blueprint(microscope_obj):
 
     blueprint = Blueprint("task_blueprint", __name__)
 
-    blueprint.add_url_rule(
-        "/", view_func=TaskListAPI.as_view("task_list")
-    )
+    blueprint.add_url_rule("/", view_func=TaskListAPI.as_view("task_list"))
 
-    blueprint.add_url_rule(
-        "/<task_id>/", view_func=TaskAPI.as_view("task")
-    )
+    blueprint.add_url_rule("/<task_id>/", view_func=TaskAPI.as_view("task"))
 
     return blueprint

openflexure_microscope/camera/base.py

@@ -120,15 +120,10 @@ class BaseCamera(metaclass=ABCMeta):
         self.stream_timeout = 20
         self.stream_timeout_enabled = False
 
-        self.state = {
-            "board": None
-        }
+        self.state = {"board": None}
 
         # TODO: Load/save these to config
-        self.paths = {
-            "default": BASE_CAPTURE_PATH,
-            "temp": TEMP_CAPTURE_PATH
-        }
+        self.paths = {"default": BASE_CAPTURE_PATH, "temp": TEMP_CAPTURE_PATH}
 
         # Capture data
         self.images = []
@@ -296,7 +291,7 @@ class BaseCamera(metaclass=ABCMeta):
         output = CaptureObject(filepath=filepath)
         # Insert a temporary tag if temporary
         if temporary:
-            output.put_tags(['temporary'])
+            output.put_tags(["temporary"])
 
         # Update capture list
         self.images.append(output)
@@ -339,7 +334,7 @@ class BaseCamera(metaclass=ABCMeta):
         output = CaptureObject(filepath=filepath)
         # Insert a temporary tag if temporary
         if temporary:
-            output.put_tags(['temporary'])
+            output.put_tags(["temporary"])
 
         # Update capture list
         self.videos.append(output)

openflexure_microscope/camera/capture.py

@@ -27,7 +27,7 @@ def pull_usercomment_dict(filepath):
     try:
         exif_dict = piexif.load(filepath)
     except InvalidImageDataError:
-        logging.error("Invalid data at {}. Skipping.".format(filepath))
+        logging.warning("Invalid data at {}. Skipping.".format(filepath))
         return None
     if "Exif" in exif_dict and 37510 in exif_dict["Exif"]:
         return yaml.load(exif_dict["Exif"][37510].decode())
@@ -316,4 +316,4 @@ class CaptureObject(object):
             return False
 
     def close(self):
-        pass
+        pass

openflexure_microscope/camera/mock.py

@@ -16,7 +16,7 @@ import logging
 # Type hinting
 from typing import Tuple
 
-from .base import BaseCamera, CaptureObject
+from openflexure_microscope.camera.base import BaseCamera
 
 
 # MAIN CLASS
@@ -26,11 +26,9 @@ class MockStreamer(BaseCamera):
         BaseCamera.__init__(self)
 
         # Store state of PiCameraStreamer
-        self.state.update({
-            "stream_active": False, 
-            "record_active": False,
-            "board": None
-        })
+        self.state.update(
+            {"stream_active": False, "record_active": False, "board": None}
+        )
 
         # Update config properties
         self.image_resolution = (1312, 976)
@@ -57,7 +55,12 @@ class MockStreamer(BaseCamera):
         )
 
         draw = ImageDraw.Draw(image)
-        draw.text((20, 70), "Camera disconnected: {}".format(datetime.now().strftime("%d/%m/%Y, %H:%M:%S")))
+        draw.text(
+            (20, 70),
+            "Camera disconnected: {}".format(
+                datetime.now().strftime("%d/%m/%Y, %H:%M:%S")
+            ),
+        )
 
         image.save(self.stream, format="JPEG")
 
@@ -80,12 +83,14 @@ class MockStreamer(BaseCamera):
         conf_dict = BaseCamera.read_config(self)
 
         # Include device-specific config items
-        conf_dict.update({
-            "stream_resolution": self.stream_resolution,
-            "image_resolution": self.image_resolution,
-            "numpy_resolution": self.numpy_resolution,
-            "jpeg_quality": self.jpeg_quality,
-        })
+        conf_dict.update(
+            {
+                "stream_resolution": self.stream_resolution,
+                "image_resolution": self.image_resolution,
+                "numpy_resolution": self.numpy_resolution,
+                "jpeg_quality": self.jpeg_quality,
+            }
+        )
 
         return conf_dict
 
@@ -179,7 +184,7 @@ class MockStreamer(BaseCamera):
 
         with self.lock:
             if isinstance(output, str):
-                output = open(output, 'wb')
+                output = open(output, "wb")
 
             output.write(self.stream.getvalue())
 

openflexure_microscope/camera/pi.py

@@ -66,12 +66,14 @@ class PiCameraStreamer(BaseCamera):
         )  #: :py:class:`picamera.PiCamera`: Picamera object
 
         # Store state of PiCameraStreamer
-        self.state.update({
-            "stream_active": False, 
-            "record_active": False, 
-            "preview_active": False,
-            "board": f"picamera_{self.camera.revision}",
-        })
+        self.state.update(
+            {
+                "stream_active": False,
+                "record_active": False,
+                "preview_active": False,
+                "board": f"picamera_{self.camera.revision}",
+            }
+        )
 
         # Reset variable states
         self.set_zoom(1.0)
@@ -113,13 +115,15 @@ class PiCameraStreamer(BaseCamera):
         conf_dict = BaseCamera.read_config(self)
 
         # Include device-specific config items
-        conf_dict.update({
-            "stream_resolution": self.stream_resolution,
-            "image_resolution": self.image_resolution,
-            "numpy_resolution": self.numpy_resolution,
-            "jpeg_quality": self.jpeg_quality,
-            "picamera_settings": {},
-        })
+        conf_dict.update(
+            {
+                "stream_resolution": self.stream_resolution,
+                "image_resolution": self.image_resolution,
+                "numpy_resolution": self.numpy_resolution,
+                "jpeg_quality": self.jpeg_quality,
+                "picamera_settings": {},
+            }
+        )
 
         # Include a subset of picamera properties
         # TODO: Expand this subset so we have more metadata?
@@ -333,7 +337,7 @@ class PiCameraStreamer(BaseCamera):
                 return output
 
             else:
-                logging.error(
+                logging.warning(
                     "Cannot start a new recording\
                     until the current recording has stopped."
                 )

openflexure_microscope/common/tasks/__init__.py

@@ -10,5 +10,14 @@ __all__ = [
     "ThreadTerminationError",
 ]
 
-from .pool import tasks, states, current_task, update_task_progress, cleanup_tasks, remove_task, update_task_data, taskify
+from .pool import (
+    tasks,
+    states,
+    current_task,
+    update_task_progress,
+    cleanup_tasks,
+    remove_task,
+    update_task_data,
+    taskify,
+)
 from .thread import ThreadTerminationError

openflexure_microscope/common/tasks/pool.py

@@ -43,6 +43,7 @@ class TaskMaster:
 
 # Task management
 
+
 def tasks():
     """
     Dictionary of tasks in default taskmaster
@@ -62,6 +63,7 @@ def states():
     global _default_task_master
     return _default_task_master.states
 
+
 def cleanup_tasks():
     global _default_task_master
     return _default_task_master.cleanup()
@@ -74,6 +76,7 @@ def remove_task(task_id: str):
 
 # Operations on the current task
 
+
 def current_task():
     current_task_thread = threading.current_thread()
     if not isinstance(current_task_thread, TaskThread):
@@ -97,6 +100,7 @@ def update_task_data(data: dict):
 
 # Main "taskify" functions
 
+
 def taskify(f):
     """
     A decorator that wraps the passed in function

openflexure_microscope/common/tasks/thread.py

@@ -41,7 +41,7 @@ class TaskThread(threading.Thread):
         self._return_value = None  # Return value
         self._start_time = None  # Task start time
         self._end_time = None  # Task end time
-        
+
         # Public state properties
         self.progress: int = None  # Percent progress of the task
         self.data = {}  # Dictionary of custom data added during the task

openflexure_microscope/devel/__init__.py

@@ -11,7 +11,12 @@ from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
 from openflexure_microscope.api.utilities import JsonResponse
 
 # Task management
-from openflexure_microscope.common.tasks import current_task, update_task_progress, update_task_data, taskify
+from openflexure_microscope.common.tasks import (
+    current_task,
+    update_task_progress,
+    update_task_data,
+    taskify,
+)
 
 # Exceptions
 from openflexure_microscope.exceptions import TaskDeniedException

openflexure_microscope/microscope.py

@@ -7,8 +7,9 @@ import pkg_resources
 import uuid
 
 from openflexure_microscope.stage.base import BaseStage
-
+from openflexure_microscope.stage.mock import MockStage
 from openflexure_microscope.camera.base import BaseCamera
+from openflexure_microscope.camera.mock import MockStreamer
 
 from openflexure_microscope.plugins import PluginMount
 from openflexure_microscope.task import TaskOrchestrator
@@ -141,6 +142,22 @@ class Microscope:
         logging.info("Repopulating PluginMount...")
         self.attach_plugins(self.plugin_maps)
 
+    def has_real_stage(self):
+        if hasattr(self, "stage") and not isinstance(
+                self.stage, MockStage
+        ):
+            return True
+        else:
+            return False
+
+    def has_real_camera(self):
+        if hasattr(self, "camera") and not isinstance(
+                self.camera, MockStreamer
+        ):
+            return True
+        else:
+            return False
+
     # Create unified state
     @property
     def state(self):

openflexure_microscope/plugins/default/autofocus/api.py

@@ -6,7 +6,7 @@ from openflexure_microscope.devel import (
     JsonResponse,
     request,
     jsonify,
-    taskify
+    taskify,
 )
 
 

openflexure_microscope/plugins/default/camera_calibration/plugin.py

@@ -4,7 +4,7 @@ from openflexure_microscope.devel import (
     JsonResponse,
     request,
     jsonify,
-    taskify
+    taskify,
 )
 
 import logging

openflexure_microscope/plugins/default/scan/api.py

@@ -4,7 +4,7 @@ from openflexure_microscope.devel import (
     request,
     jsonify,
     abort,
-    taskify
+    taskify,
 )
 
 import logging

openflexure_microscope/plugins/default/scan/plugin.py

@@ -1,13 +1,13 @@
 import time
-import numpy as np
 from typing import Tuple
+from functools import reduce
 import uuid
 import itertools
 import logging
 
 from openflexure_microscope.camera.base import generate_basename
 
-from openflexure_microscope.devel import MicroscopePlugin
+from openflexure_microscope.devel import MicroscopePlugin, update_task_progress, update_task_data
 
 from .api import TileScanAPI
 
@@ -53,16 +53,26 @@ class ScanPlugin(MicroscopePlugin):
 
     api_views = {"/tile": TileScanAPI}
 
+    def __init__(self):
+        self.images_to_be_captured: int = 1
+        update_task_data({"images_to_be_captured": self.images_to_be_captured})
+
+    @property
+    def progress(self):
+        progress = (self.images_captured_so_far / self.images_to_be_captured) * 100
+        logging.info(progress)
+        return progress
+
     def capture(
-        self,
-        basename,
-        scan_id,
-        temporary: bool = False,
-        use_video_port: bool = False,
-        resize: Tuple[int, int] = None,
-        bayer: bool = False,
-        metadata: dict = {},
-        tags: list = [],
+            self,
+            basename,
+            scan_id,
+            temporary: bool = False,
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = False,
+            metadata: dict = {},
+            tags: list = [],
     ):
 
         # Construct a tile filename
@@ -97,21 +107,26 @@ class ScanPlugin(MicroscopePlugin):
         output.put_tags(tags)
 
     def tile(
-        self,
-        basename: str = None,
-        temporary: bool = False,
-        step_size: int = [2000, 1500, 100],
-        grid: list = [3, 3, 5],
-        style="raster",
-        autofocus_dz: int = 50,
-        use_video_port: bool = False,
-        resize: Tuple[int, int] = None,
-        bayer: bool = False,
-        fast_autofocus=False,
-        metadata: dict = {},
-        tags: list = [],
+            self,
+            basename: str = None,
+            temporary: bool = False,
+            step_size: int = [2000, 1500, 100],
+            grid: list = [3, 3, 5],
+            style="raster",
+            autofocus_dz: int = 50,
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = False,
+            fast_autofocus=False,
+            metadata: dict = {},
+            tags: list = [],
     ):
 
+        # Keep task progress
+        # TODO: Make this line not nasty
+        self.images_to_be_captured = reduce((lambda x, y: x * y), grid)
+        self.images_captured_so_far = 0
+
         # Generate a basename if none given
         if not basename:
             basename = generate_basename()
@@ -123,19 +138,24 @@ class ScanPlugin(MicroscopePlugin):
         initial_position = self.microscope.stage.position
 
         # Add scan metadata
-        if not "time" in metadata:
+        if "time" not in metadata:
             metadata["time"] = generate_basename()
 
         # Check if autofocus is enabled
-        if autofocus_dz and hasattr(self.microscope.plugin, "default_autofocus"):
+        if (
+                autofocus_dz
+                and hasattr(self.microscope.plugin, "default_autofocus")
+                and self.microscope.has_real_stage()
+                and self.microscope.has_real_camera()
+        ):
             autofocus_enabled = True
         else:
             autofocus_enabled = False
 
         if fast_autofocus and not hasattr(
-            self.microscope.plugin.default_autofocus, "monitor_sharpness"
+                self.microscope.plugin.default_autofocus, "monitor_sharpness"
         ):
-            logging.error(
+            logging.warning(
                 "Can't use fast autofocus in the scan - the default plugin doesn't support monitor_sharpness; maybe it is too old?"
             )
             fast_autofocus = False
@@ -198,6 +218,9 @@ class ScanPlugin(MicroscopePlugin):
                         metadata=metadata,
                         tags=tags,
                     )
+                    # Update task progress
+                    self.images_captured_so_far += 1
+                    update_task_progress(self.progress)
                 else:
                     logging.debug("Entering z-stack")
                     self.stack(
@@ -218,7 +241,7 @@ class ScanPlugin(MicroscopePlugin):
                 next_z = self.microscope.stage.position[2]
                 if fast_autofocus:
                     next_z += (
-                        autofocus_dz / 2
+                            autofocus_dz / 2
                     )  # Fast autofocus requires us to start at the top of the range
                     if grid[2] > 1:
                         next_z -= int(
@@ -229,19 +252,19 @@ class ScanPlugin(MicroscopePlugin):
         self.microscope.stage.move_abs(initial_position)
 
     def stack(
-        self,
-        basename: str = None,
-        temporary: bool = False,
-        scan_id: str = None,
-        step_size: int = 100,
-        steps: int = 5,
-        center: bool = True,
-        return_to_start: bool = True,
-        use_video_port: bool = False,
-        resize: Tuple[int, int] = None,
-        bayer: bool = False,
-        metadata: dict = {},
-        tags: list = [],
+            self,
+            basename: str = None,
+            temporary: bool = False,
+            scan_id: str = None,
+            step_size: int = 100,
+            steps: int = 5,
+            center: bool = True,
+            return_to_start: bool = True,
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = False,
+            metadata: dict = {},
+            tags: list = [],
     ):
 
         # Generate a basename if none given
@@ -278,6 +301,9 @@ class ScanPlugin(MicroscopePlugin):
                     metadata=metadata,
                     tags=tags,
                 )
+                # Update task progress
+                self.images_captured_so_far += 1
+                update_task_progress(self.progress)
 
                 if i != steps - 1:
                     logging.debug("Moving z by {}".format(step_size))

openflexure_microscope/plugins/loader.py

@@ -87,7 +87,7 @@ def load_plugin_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.warning("Error loading plugin.")
             logging.error(e)
             return None, None
 
@@ -216,7 +216,7 @@ class PluginMount(object):
                     )
 
         else:
-            logging.error(f"Error loading plugin {plugin_map}. Moving on.")
+            logging.warning(f"Error loading plugin {plugin_map}. Moving on.")
 
 
 class MicroscopePlugin:

openflexure_microscope/plugins/testing/form_example/api.py

@@ -3,7 +3,7 @@ from openflexure_microscope.devel import (
     JsonResponse,
     request,
     jsonify,
-    taskify
+    taskify,
 )
 
 import logging

openflexure_microscope/plugins/testing/form_example/plugin.py

@@ -72,7 +72,7 @@ class ExamplePlugin(MicroscopePlugin):
             time.sleep(1)
 
             # Update task progress (if running as a task)
-            percent_complete = int(((t + 1)/run_time)*100)
+            percent_complete = int(((t + 1) / run_time) * 100)
             update_task_progress(percent_complete)
 
         return vals

openflexure_microscope/stage/base.py

@@ -1,3 +1,4 @@
+import numpy as np
 from abc import ABCMeta, abstractmethod
 from openflexure_microscope.common.lock import StrictLock
 
@@ -110,4 +111,4 @@ class BaseStage(metaclass=ABCMeta):
         array of 3D positions with x=y=0.  This, along with all the
         keyword arguments, is then passed to ``scan_linear``.
         """
-        return self.scan_linear([[0, 0, z] for z in dz], **kwargs)
+        return self.scan_linear([[0, 0, z] for z in dz], **kwargs)

openflexure_microscope/stage/mock.py

@@ -5,6 +5,7 @@ from collections.abc import Iterable
 import numpy as np
 import time
 
+
 class MockStage(BaseStage):
     def __init__(self, port=None, **kwargs):
         BaseStage.__init__(self)
@@ -68,7 +69,9 @@ class MockStage(BaseStage):
         else:
             self._backlash = np.array([int(blsh)] * self.n_axes, dtype=np.int)
 
-    def move_rel(self, displacement: list, axis=None, backlash=True, simulate_time: bool=True):
+    def move_rel(
+        self, displacement: list, axis=None, backlash=True, simulate_time: bool = True
+    ):
         if simulate_time:
             time.sleep(1)
         if axis is not None:
@@ -81,7 +84,7 @@ class MockStage(BaseStage):
 
             self._position = list(np.array(self._position) + np.array(move))
 
-    def move_abs(self, final, simulate_time: bool=True, **kwargs):
+    def move_abs(self, final, simulate_time: bool = True, **kwargs):
         if simulate_time:
             time.sleep(1)
 

openflexure_microscope/stage/sangaboard/sangaboard.py

@@ -136,7 +136,7 @@ class Sangaboard(ExtensibleSerialInstrument):
             # make sure we close the serial port cleanly (otherwise it hangs open).
             self.close()
             logging.error(e)
-            logging.error(
+            logging.warning(
                 "You may need to update the firmware running on the Sangaboard."
             )
             raise e
@@ -164,12 +164,12 @@ class Sangaboard(ExtensibleSerialInstrument):
                     r"OpenFlexure Motor Board v(([\d]+)(?:\.([\d]+))+)", self.firmware
                 )
             if not match:
-                logging.error(
+                logging.warning(
                     'Version string "{}" not recognised.'.format(self.firmware)
                 )
                 return False
         else:
-            logging.error("No firmware version string was returned.")
+            logging.warning("No firmware version string was returned.")
             return False
 
         # Check for matching/valid version number
@@ -179,7 +179,7 @@ class Sangaboard(ExtensibleSerialInstrument):
         self.firmware_version = match.group(1)
 
         if version_tuple not in Sangaboard.valid_firmwares:
-            logging.error(
+            logging.warning(
                 "This version of the Python module requires firmware v0.5 (with legacy support for v0.4)"
             )
             return False

openflexure_microscope/task.py

@@ -1,5 +1,11 @@
 import logging
-from openflexure_microscope.common.tasks import tasks, states, taskify, cleanup_tasks, remove_task
+from openflexure_microscope.common.tasks import (
+    tasks,
+    states,
+    taskify,
+    cleanup_tasks,
+    remove_task,
+)
 
 
 class TaskOrchestrator:
@@ -14,7 +20,9 @@ class TaskOrchestrator:
 
     @property
     def tasks(self):
-        logging.warning("TaskOrchestrator class is deprecated. Please use common.tasks.tasks().values() instead.")
+        logging.warning(
+            "TaskOrchestrator class is deprecated. Please use common.tasks.tasks().values() instead."
+        )
         return tasks().values()
 
     @property
@@ -22,7 +30,9 @@ class TaskOrchestrator:
         """
         Returns a list of dictionary representations of all tasks in the session.
         """
-        logging.warning("TaskOrchestrator class is deprecated. Please use common.tasks.tasks() instead.")
+        logging.warning(
+            "TaskOrchestrator class is deprecated. Please use common.tasks.tasks() instead."
+        )
         return states()
 
     def task_from_id(self, task_id: str):
@@ -41,7 +51,9 @@ class TaskOrchestrator:
             function (function): The target function to run in the background
             args, kwargs: Arguments that will be passed to `function` at runtime.
         """
-        logging.warning("TaskOrchestrator class is deprecated. Please use common.tasks.taskify() instead.")
+        logging.warning(
+            "TaskOrchestrator class is deprecated. Please use common.tasks.taskify() instead."
+        )
         return taskify(function)(*args, **kwargs)
 
     def clean(self):
@@ -49,12 +61,16 @@ class TaskOrchestrator:
         Remove all inactive tasks from the task array.
         This will remove tasks that either finished or never started.
         """
-        logging.warning("TaskOrchestrator class is deprecated. Please use common.tasks.cleanup_tasks() instead.")
+        logging.warning(
+            "TaskOrchestrator class is deprecated. Please use common.tasks.cleanup_tasks() instead."
+        )
         cleanup_tasks()
 
     def delete(self, task_id: str):
         """
         Delete a given task by ID, only if task is not currently running.
         """
-        logging.warning("TaskOrchestrator class is deprecated. Please use common.tasks.remove_task() instead.")
+        logging.warning(
+            "TaskOrchestrator class is deprecated. Please use common.tasks.remove_task() instead."
+        )
         remove_task(task_id)