Merge branch 'temporary-scan-captures' into 'master'
Temporary scan captures See merge request openflexure/openflexure-microscope-server!10
This commit is contained in:
Joel Collins
commit
941aadebfe
5 changed files with 34 additions and 92 deletions
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@ -101,7 +101,7 @@ class ListAPI(MicroscopeView):
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payload = JsonPayload(request)
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filename = payload.param('filename')
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temporary = payload.param('temporary', default=True, convert=bool)
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temporary = payload.param('temporary', default=False, convert=bool)
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use_video_port = payload.param('use_video_port', default=False, convert=bool)
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bayer = payload.param('bayer', default=True, convert=bool)
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metadata = payload.param('metadata', default={}, convert=dict)
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@ -14,7 +14,7 @@ except ImportError:
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except ImportError:
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from _thread import get_ident
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from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH
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from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH, TEMP_CAPTURE_PATH
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from openflexure_microscope.config import USER_CONFIG_DIR
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from openflexure_microscope.utilities import entry_by_id
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from openflexure_microscope.lock import StrictLock
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@ -111,6 +111,8 @@ class BaseCamera(object):
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self.paths = {
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'image': BASE_CAPTURE_PATH,
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'video': BASE_CAPTURE_PATH,
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'image_tmp': TEMP_CAPTURE_PATH,
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'video_tpm': TEMP_CAPTURE_PATH
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} #: dict: Dictionary of capture paths
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# Capture data
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@ -292,7 +294,7 @@ class BaseCamera(object):
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write_to_file: bool = False,
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temporary: bool = True,
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filename: str = None,
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folder: str = None,
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folder: str = "",
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fmt: str = 'jpeg'):
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"""
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@ -311,10 +313,8 @@ class BaseCamera(object):
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logging.debug(filename)
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# Generate folder
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if folder:
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folder = os.path.join(self.paths['image'], folder)
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else:
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folder = self.paths['image']
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base_folder = self.paths['image_tmp'] if temporary else self.paths['image']
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folder = os.path.join(base_folder, folder)
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# Create capture object
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output = CaptureObject(
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@ -357,10 +357,8 @@ class BaseCamera(object):
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logging.debug(filename)
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# Generate folder
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if folder:
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folder = os.path.join(self.paths['video'], folder)
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else:
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folder = self.paths['video']
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base_folder = self.paths['video_tmp'] if temporary else self.paths['video']
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folder = os.path.join(base_folder, folder)
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# Create capture object
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output = CaptureObject(
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@ -1,6 +1,7 @@
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import uuid
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import io
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import os
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import shutil
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import glob
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import datetime
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import yaml
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@ -25,10 +26,7 @@ def clear_tmp():
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global TEMP_CAPTURE_PATH
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logging.info("Clearing {}...".format(TEMP_CAPTURE_PATH))
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files = glob.glob('{}/*'.format(TEMP_CAPTURE_PATH))
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for f in files:
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os.remove(f)
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logging.debug("Removed {}".format(f))
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shutil.rmtree(TEMP_CAPTURE_PATH)
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logging.debug("Cleared {}.".format(TEMP_CAPTURE_PATH))
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@ -81,8 +79,8 @@ def capture_from_dict(capture_dict):
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# Get inherent capture information from database
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capture.file = capture_dict['path']
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capture.split_file_path(capture.file)
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capture.temporary = capture_dict['temporary']
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capture.split_file_path(capture.file)
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if capture.format.upper() in EXIF_FORMATS:
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md_exif = pull_usercomment_dict(capture.file)
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@ -137,9 +135,7 @@ class CaptureObject(object):
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filename = self.id
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self.filename = "{}.{}".format(filename, fmt)
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# Create folder path. Default to BASE_CAPTURE_PATH
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if not folder:
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folder = BASE_CAPTURE_PATH
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# Create folder path
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self.folder = folder
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# Dictionary for storing custom metadata
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@ -185,7 +181,7 @@ class CaptureObject(object):
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file on disk.
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"""
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self.build_file_path(self.filename, self.folder)
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self.build_file_path()
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# Byte bytestream properties
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self.bytestream = io.BytesIO() # Byte bytestream that data will be written to
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@ -201,43 +197,30 @@ class CaptureObject(object):
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# Save initial metadata file
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self.save_metadata()
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def build_file_path(
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self,
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filename: str,
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folder: str):
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def build_file_path(self):
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"""
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Construct a full file path, based on filename, folder, and file format.
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Defaults to UUID.
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Args:
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filename (str): Filename of capture
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folder (str): Directory on disk to store capture file
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"""
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global TEMP_CAPTURE_PATH
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# TODO: Combine this and split_file_path, and tidy. Let the device (camera) handle folders. This should be more basic.
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# TODO: Even let the base camera manage moving captures to temp folder
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# This module will clear out the temp folder, but won't MOVE anything there.
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# In Base cameras new_image method, the full folder is constructed. Temp folder should be inserted there.
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self.file = os.path.join(folder, filename) # Full file name by joining given folder to given name
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self.file = os.path.join(self.folder, self.filename) # Full file name by joining given folder to given name
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self.split_file_path(self.file) # Split file path into folder, filename, and basename
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# Check directory is a subdirectory of BASE_CAPTURE_PATH
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# TODO: Do we need this?
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if not os.path.commonprefix([self.file, BASE_CAPTURE_PATH]) == BASE_CAPTURE_PATH:
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raise Exception("Captures cannot be stored in a lower-level directory than {}.".format(BASE_CAPTURE_PATH))
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# Move to tmp directory if not being kept
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if self.temporary:
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self.file_notmp = self.file # Store originally defined folder
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self.filefolder = TEMP_CAPTURE_PATH
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self.file = os.path.join(self.filefolder, self.filename)
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# Create folder and file
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if not os.path.exists(self.filefolder):
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os.makedirs(self.filefolder)
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logging.debug(self.file)
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logging.debug(self.filename)
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logging.debug(self.basename)
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logging.debug(self.filefolder)
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def split_file_path(self, filepath):
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"""
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Take a full file path, and split it into separated class properties.
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@ -453,13 +436,6 @@ class CaptureObject(object):
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def save_file(self) -> bool:
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"""Write the StreamObjects bytestream to a file."""
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if self.temporary: # If capture is currently temporary
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self.load_file() # Load data from tmp file into bytestream, if tmp file exists
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self.temporary = False # Flag as kept on disk
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self.file = self.file_notmp # Reset file path to non-temporary path
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self.split_file_path(self.file) # Set split properties based on new path
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logging.info("Moved temporary file out to {}".format(self.file))
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if self.stream_exists: # If there's a bytestream to save
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with open(self.file, 'ab') as f: # Load file as bytes
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logging.debug("Writing bytestream to file {}".format(self.file))
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@ -509,6 +485,7 @@ class CaptureObject(object):
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"""Both clear the bytestream, and delete any associated on-disk data."""
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logging.info("Closing {}".format(self.id))
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self.delete_stream()
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# Delete the file from disk if temporary
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if self.temporary:
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self.delete()
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@ -10,6 +10,7 @@ class TileScanAPI(MicroscopeViewPlugin):
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# Get params
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filename = payload.param('filename')
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temporary = payload.param('temporary', default=False, convert=bool)
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step_size = payload.param('step_size', default=[2000, 1500, 100], convert=list)
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step_size = [int(i) for i in step_size]
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@ -37,6 +38,7 @@ class TileScanAPI(MicroscopeViewPlugin):
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task = self.microscope.task.start(
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self.plugin.tile,
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basename=filename,
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temporary=temporary,
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step_size=step_size,
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grid=grid,
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style=style,
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@ -51,43 +53,3 @@ class TileScanAPI(MicroscopeViewPlugin):
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# return a handle on the autofocus task
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return jsonify(task.state), 202
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class ZStackAPI(MicroscopeViewPlugin):
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def post(self):
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payload = JsonPayload(request)
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# Get params
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name = payload.param('name')
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step_size = payload.param('step_size', default=100, convert=int)
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steps = payload.param('steps', default=5, convert=int)
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center = payload.param('center', default=True, convert=bool)
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use_video_port = payload.param('use_video_port', default=False, convert=bool)
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resize = payload.param('size', default=None)
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if resize:
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if ('width' in resize) and ('height' in resize):
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resize = (int(resize['width']), int(resize['height'])) # Convert dict to tuple
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else:
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abort(404)
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bayer = payload.param('bayer', default=True, convert=bool)
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metadata = payload.param('metadata', default={}, convert=dict)
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tags = payload.param('tags', default=[], convert=list)
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print("Running tile scan...")
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task = self.microscope.task.start(
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self.plugin.stack,
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basename=name,
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step_size=step_size,
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steps=steps,
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center=center,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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metadata=metadata,
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tags=tags
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)
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# return a handle on the autofocus task
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return jsonify(task.state), 202
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@ -7,7 +7,7 @@ import logging
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from openflexure_microscope.camera.base import generate_basename
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from openflexure_microscope.plugins import MicroscopePlugin
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from .api import TileScanAPI, ZStackAPI
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from .api import TileScanAPI
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def construct_grid(initial, step_sizes, n_steps, style='raster'):
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"""
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@ -48,12 +48,12 @@ class ScanPlugin(MicroscopePlugin):
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api_views = {
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'/tile': TileScanAPI,
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'/stack': ZStackAPI,
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}
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def capture(self,
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basename,
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scan_id,
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temporary: bool = False,
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use_video_port: bool = False,
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resize: Tuple[int, int] = None,
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bayer: bool = False,
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@ -62,14 +62,14 @@ class ScanPlugin(MicroscopePlugin):
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# Construct a tile filename
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filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position)
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foldername = "SCAN_{}".format(basename)
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folder = "SCAN_{}".format(basename)
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# Create output object
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output = self.microscope.camera.new_image(
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write_to_file=True,
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temporary=False,
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temporary=temporary,
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filename=filename,
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folder=foldername)
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folder=folder)
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# Capture
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self.microscope.camera.capture(
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@ -94,6 +94,7 @@ class ScanPlugin(MicroscopePlugin):
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def tile(
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self,
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basename: str = None,
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temporary: bool = False,
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step_size: int = [2000, 1500, 100],
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grid: list = [3, 3, 5],
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style='raster',
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@ -178,6 +179,7 @@ class ScanPlugin(MicroscopePlugin):
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self.capture(
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basename,
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scan_id,
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temporary=temporary,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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@ -188,6 +190,7 @@ class ScanPlugin(MicroscopePlugin):
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logging.debug("Entering z-stack")
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self.stack(
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basename=basename,
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temporary=temporary,
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scan_id=scan_id,
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step_size=step_size[2],
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steps=grid[2],
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@ -212,6 +215,7 @@ class ScanPlugin(MicroscopePlugin):
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def stack(
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self,
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basename: str = None,
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temporary: bool = False,
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scan_id: str = None,
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step_size: int = 100,
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steps: int = 5,
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@ -251,6 +255,7 @@ class ScanPlugin(MicroscopePlugin):
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self.capture(
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basename,
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scan_id,
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temporary=temporary,
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use_video_port=use_video_port,
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resize=resize,
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bayer=bayer,
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