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

README.md

@@ -8,10 +8,9 @@ This includes basic installation instructions suitable for most users.
 Full developer documentation can be found on [**ReadTheDocs**](https://openflexure-microscope-software.readthedocs.io/). 
 This includes installing the server in a mode better suited for active development.
 
-## Installation
+## Developer installation
 
 * `git clone https://gitlab.com/openflexure/openflexure-microscope-server.git`
-* (If running on a microscope Pi) `ofm activate`
 * `poetry install`
 * `poetry run build_static`
 

openflexure_microscope/api/default_extensions/autofocus.py

@@ -217,6 +217,13 @@ def move_and_find_focus(microscope, dz):
         return m.sharpest_z_on_move(0)
 
 
+def move_and_measure(microscope, dz):
+    """Make a relative Z move and return the sharpness data"""
+    with monitor_sharpness(microscope) as m:
+        m.focus_rel(dz)
+        return m.data_dict()
+
+
 def fast_autofocus(microscope, dz=2000, backlash=None):
     """Perform a down-up-down-up autofocus"""
     with monitor_sharpness(
@@ -333,14 +340,37 @@ class MeasureSharpnessAPI(View):
         return {"sharpness": measure_sharpness(microscope)}
 
 
+class MoveAndMeasureAPI(ActionView):
+    """
+    Move the stage and measure dynamic sharpness
+    """
+
+    args = {"dz": fields.List(fields.Int(), required=True)}
+
+    def post(self, args):
+        microscope = find_component("org.openflexure.microscope")
+
+        if not microscope:
+            abort(503, "No microscope connected. Unable to autofocus.")
+
+        if microscope.has_real_stage():
+            # Acquire microscope lock with 1s timeout
+            with microscope.lock(timeout=1):
+                # Run fast_up_down_up_autofocus
+                return move_and_measure(microscope, dz=args.get("dz"))
+
+        else:
+            abort(503, "No stage connected. Unable to autofocus.")
+
+
 class AutofocusAPI(ActionView):
     """
     Run a standard autofocus
     """
+
     args = {"dz": fields.List(fields.Int())}
 
     def post(self, args):
-        payload = JsonResponse(request)
         microscope = find_component("org.openflexure.microscope")
 
         if not microscope:
@@ -363,9 +393,10 @@ class FastAutofocusAPI(ActionView):
     """
     Run a fast autofocus
     """
+
     args = {
         "dz": fields.Int(missing=2000),
-        "backlash": fields.Int(missing=25, minimum=0)
+        "backlash": fields.Int(missing=25, minimum=0),
     }
 
     def post(self, args):
@@ -403,7 +434,17 @@ autofocus_extension_v2.add_method(
     fast_up_down_up_autofocus, "fast_up_down_up_autofocus"
 )
 autofocus_extension_v2.add_method(autofocus, "autofocus")
+autofocus_extension_v2.add_method(move_and_measure, "move_and_measure")
 
-autofocus_extension_v2.add_view(MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness")
+autofocus_extension_v2.add_view(
+    MeasureSharpnessAPI, "/measure_sharpness", endpoint="measure_sharpness"
+)
 autofocus_extension_v2.add_view(AutofocusAPI, "/autofocus", endpoint="autofocus")
-autofocus_extension_v2.add_view(FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus")
+autofocus_extension_v2.add_view(
+    FastAutofocusAPI, "/fast_autofocus", endpoint="fast_autofocus"
+)
+
+autofocus_extension_v2.add_view(
+    MoveAndMeasureAPI, "/move_and_measure", endpoint="move_and_measure"
+)
+

poetry.lock

@@ -926,6 +926,11 @@ markupsafe = [
     {file = "MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl", hash = "sha256:ba59edeaa2fc6114428f1637ffff42da1e311e29382d81b339c1817d37ec93c6"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win32.whl", hash = "sha256:b00c1de48212e4cc9603895652c5c410df699856a2853135b3967591e4beebc2"},
     {file = "MarkupSafe-1.1.1-cp37-cp37m-win_amd64.whl", hash = "sha256:9bf40443012702a1d2070043cb6291650a0841ece432556f784f004937f0f32c"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:6788b695d50a51edb699cb55e35487e430fa21f1ed838122d722e0ff0ac5ba15"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_i686.whl", hash = "sha256:cdb132fc825c38e1aeec2c8aa9338310d29d337bebbd7baa06889d09a60a1fa2"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:13d3144e1e340870b25e7b10b98d779608c02016d5184cfb9927a9f10c689f42"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-win32.whl", hash = "sha256:596510de112c685489095da617b5bcbbac7dd6384aeebeda4df6025d0256a81b"},
+    {file = "MarkupSafe-1.1.1-cp38-cp38-win_amd64.whl", hash = "sha256:e8313f01ba26fbbe36c7be1966a7b7424942f670f38e666995b88d012765b9be"},
     {file = "MarkupSafe-1.1.1.tar.gz", hash = "sha256:29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b"},
 ]
 marshmallow = [

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.masonry.api"
 
 [tool.poetry]
 name = "openflexure-microscope-server"
-version = "2.5.0"
+version = "2.6.0-alpha.1"
 description = "Python module, and Flask-based web API, to run the OpenFlexure Microscope."
 
 authors = [