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

Temporary scan captures

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

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,