Merge branch 'temporary-scan-captures' into 'master'

Temporary scan captures

See merge request openflexure/openflexure-microscope-server!10

openflexure_microscope/api/v1/blueprints/camera/capture.py

@@ -101,7 +101,7 @@ class ListAPI(MicroscopeView):
         payload = JsonPayload(request)
 
         filename = payload.param('filename')
-        temporary = payload.param('temporary', default=True, convert=bool)
+        temporary = payload.param('temporary', default=False, convert=bool)
         use_video_port = payload.param('use_video_port', default=False, convert=bool)
         bayer = payload.param('bayer', default=True, convert=bool)
         metadata = payload.param('metadata', default={}, convert=dict)

openflexure_microscope/camera/base.py

@@ -14,7 +14,7 @@ except ImportError:
     except ImportError:
         from _thread import get_ident
 
-from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH
+from .capture import CaptureObject, capture_from_dict, BASE_CAPTURE_PATH, TEMP_CAPTURE_PATH
 from openflexure_microscope.config import USER_CONFIG_DIR
 from openflexure_microscope.utilities import entry_by_id
 from openflexure_microscope.lock import StrictLock
@@ -111,6 +111,8 @@ class BaseCamera(object):
         self.paths = {
             'image': BASE_CAPTURE_PATH,
             'video': BASE_CAPTURE_PATH,
+            'image_tmp': TEMP_CAPTURE_PATH,
+            'video_tpm': TEMP_CAPTURE_PATH
         }  #: dict: Dictionary of capture paths
 
         # Capture data
@@ -292,7 +294,7 @@ class BaseCamera(object):
             write_to_file: bool = False,
             temporary: bool = True,
             filename: str = None,
-            folder: str = None,
+            folder: str = "",
             fmt: str = 'jpeg'):
 
         """
@@ -311,10 +313,8 @@ class BaseCamera(object):
             logging.debug(filename)
 
         # Generate folder
-        if folder:
+        base_folder = self.paths['image_tmp'] if temporary else self.paths['image']
-            folder = os.path.join(self.paths['image'], folder)
+        folder = os.path.join(base_folder, folder)
-        else:
-            folder = self.paths['image']
 
         # Create capture object
         output = CaptureObject(
@@ -357,10 +357,8 @@ class BaseCamera(object):
             logging.debug(filename)
 
         # Generate folder
-        if folder:
+        base_folder = self.paths['video_tmp'] if temporary else self.paths['video']
-            folder = os.path.join(self.paths['video'], folder)
+        folder = os.path.join(base_folder, folder)
-        else:
-            folder = self.paths['video']
 
         # Create capture object
         output = CaptureObject(

openflexure_microscope/camera/capture.py

@@ -1,6 +1,7 @@
 import uuid
 import io
 import os
+import shutil
 import glob
 import datetime
 import yaml
@@ -25,10 +26,7 @@ def clear_tmp():
     global TEMP_CAPTURE_PATH
 
     logging.info("Clearing {}...".format(TEMP_CAPTURE_PATH))
-    files = glob.glob('{}/*'.format(TEMP_CAPTURE_PATH))
+    shutil.rmtree(TEMP_CAPTURE_PATH)
-    for f in files:
-        os.remove(f)
-        logging.debug("Removed {}".format(f))
     logging.debug("Cleared {}.".format(TEMP_CAPTURE_PATH))
 
 
@@ -81,8 +79,8 @@ def capture_from_dict(capture_dict):
 
     # Get inherent capture information from database
     capture.file = capture_dict['path']
-    capture.split_file_path(capture.file)
     capture.temporary = capture_dict['temporary']
+    capture.split_file_path(capture.file)
 
     if capture.format.upper() in EXIF_FORMATS:
         md_exif = pull_usercomment_dict(capture.file)
@@ -137,9 +135,7 @@ class CaptureObject(object):
             filename = self.id
         self.filename = "{}.{}".format(filename, fmt)
 
-        # Create folder path. Default to BASE_CAPTURE_PATH
+        # Create folder path
-        if not folder:
-            folder = BASE_CAPTURE_PATH
         self.folder = folder
 
         # Dictionary for storing custom metadata
@@ -185,7 +181,7 @@ class CaptureObject(object):
         file on disk.
 
         """
-        self.build_file_path(self.filename, self.folder)
+        self.build_file_path()
 
         # Byte bytestream properties
         self.bytestream = io.BytesIO()  # Byte bytestream that data will be written to
@@ -201,43 +197,30 @@ class CaptureObject(object):
         # Save initial metadata file
         self.save_metadata()
 
-    def build_file_path(
+    def build_file_path(self):
-            self,
-            filename: str,
-            folder: str):
         """
         Construct a full file path, based on filename, folder, and file format.
         Defaults to UUID.
-
-        Args:
-            filename (str): Filename of capture
-            folder (str): Directory on disk to store capture file
         """
         global TEMP_CAPTURE_PATH
+        # TODO: Combine this and split_file_path, and tidy. Let the device (camera) handle folders. This should be more basic.
+        # TODO: Even let the base camera manage moving captures to temp folder
+        # This module will clear out the temp folder, but won't MOVE anything there.
+        # In Base cameras new_image method, the full folder is constructed. Temp folder should be inserted there.
 
-        self.file = os.path.join(folder, filename)  # Full file name by joining given folder to given name
+        self.file = os.path.join(self.folder, self.filename)  # Full file name by joining given folder to given name
 
         self.split_file_path(self.file)  # Split file path into folder, filename, and basename
 
         # Check directory is a subdirectory of BASE_CAPTURE_PATH
+        # TODO: Do we need this?
         if not os.path.commonprefix([self.file, BASE_CAPTURE_PATH]) == BASE_CAPTURE_PATH:
             raise Exception("Captures cannot be stored in a lower-level directory than {}.".format(BASE_CAPTURE_PATH))
 
-        # Move to tmp directory if not being kept
-        if self.temporary:
-            self.file_notmp = self.file  # Store originally defined folder
-            self.filefolder = TEMP_CAPTURE_PATH
-            self.file = os.path.join(self.filefolder, self.filename)
-
         # Create folder and file
         if not os.path.exists(self.filefolder):
             os.makedirs(self.filefolder)
 
-        logging.debug(self.file)
-        logging.debug(self.filename)
-        logging.debug(self.basename)
-        logging.debug(self.filefolder)
-
     def split_file_path(self, filepath):
         """
         Take a full file path, and split it into separated class properties.
@@ -453,13 +436,6 @@ class CaptureObject(object):
 
     def save_file(self) -> bool:
         """Write the StreamObjects bytestream to a file."""
-        if self.temporary:  # If capture is currently temporary
-            self.load_file()  # Load data from tmp file into bytestream, if tmp file exists
-            self.temporary = False  # Flag as kept on disk
-            self.file = self.file_notmp  # Reset file path to non-temporary path
-            self.split_file_path(self.file)  # Set split properties based on new path
-            logging.info("Moved temporary file out to {}".format(self.file))
-
         if self.stream_exists:  # If there's a bytestream to save
             with open(self.file, 'ab') as f:  # Load file as bytes
                 logging.debug("Writing bytestream to file {}".format(self.file))
@@ -509,6 +485,7 @@ class CaptureObject(object):
         """Both clear the bytestream, and delete any associated on-disk data."""
         logging.info("Closing {}".format(self.id))
         self.delete_stream()
+        # Delete the file from disk if temporary
         if self.temporary:
             self.delete()
 

openflexure_microscope/plugins/default/scan/api.py

@@ -10,6 +10,7 @@ class TileScanAPI(MicroscopeViewPlugin):
 
         # Get params
         filename = payload.param('filename')
+        temporary = payload.param('temporary', default=False, convert=bool)
 
         step_size = payload.param('step_size', default=[2000, 1500, 100], convert=list)
         step_size = [int(i) for i in step_size]
@@ -37,6 +38,7 @@ class TileScanAPI(MicroscopeViewPlugin):
         task = self.microscope.task.start(
             self.plugin.tile,
             basename=filename,
+            temporary=temporary,
             step_size=step_size,
             grid=grid,
             style=style,
@@ -51,43 +53,3 @@ class TileScanAPI(MicroscopeViewPlugin):
 
         # return a handle on the autofocus task
         return jsonify(task.state), 202
-
-
-class ZStackAPI(MicroscopeViewPlugin):
-    def post(self):
-        payload = JsonPayload(request)
-
-        # Get params
-        name = payload.param('name')
-        step_size = payload.param('step_size', default=100, convert=int)
-        steps = payload.param('steps', default=5, convert=int)
-        center = payload.param('center', default=True, convert=bool)
-
-        use_video_port = payload.param('use_video_port', default=False, convert=bool)
-        resize = payload.param('size', default=None)
-        if resize:
-            if ('width' in resize) and ('height' in resize):
-                resize = (int(resize['width']), int(resize['height']))  # Convert dict to tuple
-            else:
-                abort(404)
-
-        bayer = payload.param('bayer', default=True, convert=bool)
-        metadata = payload.param('metadata', default={}, convert=dict)
-        tags = payload.param('tags', default=[], convert=list)
-
-        print("Running tile scan...")
-        task = self.microscope.task.start(
-            self.plugin.stack,
-            basename=name,
-            step_size=step_size,
-            steps=steps,
-            center=center,
-            use_video_port=use_video_port,
-            resize=resize,
-            bayer=bayer,
-            metadata=metadata,
-            tags=tags
-        )
-
-        # return a handle on the autofocus task
-        return jsonify(task.state), 202

openflexure_microscope/plugins/default/scan/plugin.py

@@ -7,7 +7,7 @@ import logging
 from openflexure_microscope.camera.base import generate_basename
 from openflexure_microscope.plugins import MicroscopePlugin
 
-from .api import TileScanAPI, ZStackAPI
+from .api import TileScanAPI
 
 def construct_grid(initial, step_sizes, n_steps, style='raster'):
     """
@@ -48,12 +48,12 @@ class ScanPlugin(MicroscopePlugin):
 
     api_views = {
         '/tile': TileScanAPI,
-        '/stack': ZStackAPI,
     }
 
     def capture(self,
                 basename,
                 scan_id,
+                temporary: bool = False,
                 use_video_port: bool = False,
                 resize: Tuple[int, int] = None,
                 bayer: bool = False,
@@ -62,14 +62,14 @@ class ScanPlugin(MicroscopePlugin):
 
         # Construct a tile filename
         filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position)
-        foldername = "SCAN_{}".format(basename)
+        folder = "SCAN_{}".format(basename)
 
         # Create output object
         output = self.microscope.camera.new_image(
             write_to_file=True,
-            temporary=False,
+            temporary=temporary,
             filename=filename,
-            folder=foldername)
+            folder=folder)
 
         # Capture
         self.microscope.camera.capture(
@@ -94,6 +94,7 @@ class ScanPlugin(MicroscopePlugin):
     def tile(
             self,
             basename: str = None,
+            temporary: bool = False,
             step_size: int = [2000, 1500, 100],
             grid: list = [3, 3, 5],
             style='raster',
@@ -178,6 +179,7 @@ class ScanPlugin(MicroscopePlugin):
                     self.capture(
                         basename,
                         scan_id,
+                        temporary=temporary,
                         use_video_port=use_video_port,
                         resize=resize,
                         bayer=bayer,
@@ -188,6 +190,7 @@ class ScanPlugin(MicroscopePlugin):
                     logging.debug("Entering z-stack")
                     self.stack(
                         basename=basename,
+                        temporary=temporary,
                         scan_id=scan_id,
                         step_size=step_size[2],
                         steps=grid[2],
@@ -212,6 +215,7 @@ class ScanPlugin(MicroscopePlugin):
     def stack(
             self,
             basename: str = None,
+            temporary: bool = False,
             scan_id: str = None,
             step_size: int = 100,
             steps: int = 5,
@@ -251,6 +255,7 @@ class ScanPlugin(MicroscopePlugin):
                 self.capture(
                     basename,
                     scan_id,
+                    temporary=temporary,
                     use_video_port=use_video_port,
                     resize=resize,
                     bayer=bayer,