From 265eed7bfac79ea03140cca1c540e9f3a9738d84 Mon Sep 17 00:00:00 2001
From: Joel Collins <jc2450@bath.ac.uk>
Date: Wed, 29 Jan 2020 16:16:09 +0000
Subject: [PATCH] Fixed picamera setup

---
 .../picamera_autocalibrate/extension.py       |  4 ++--
 .../api/v2/views/actions/stage.py             |  2 +-
 openflexure_microscope/camera/pi.py           | 10 ++++----
 openflexure_microscope/microscope.py          | 23 ++++++++-----------
 4 files changed, 18 insertions(+), 21 deletions(-)

diff --git a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
index 37cbe8cb..343a2c02 100644
--- a/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
+++ b/openflexure_microscope/api/default_extensions/picamera_autocalibrate/extension.py
@@ -21,8 +21,8 @@ def recalibrate(microscope):
     """
     scamera = microscope.camera
     with scamera.lock:
-        assert not scamera.status["record_active"], "Can't recalibrate while recording!"
-        streaming = scamera.status["stream_active"]
+        assert not scamera.record_active, "Can't recalibrate while recording!"
+        streaming = scamera.stream_active
         if streaming:
             logging.info("Stopping stream before recalibration")
             scamera.stop_stream_recording(resolution=(640, 480))
diff --git a/openflexure_microscope/api/v2/views/actions/stage.py b/openflexure_microscope/api/v2/views/actions/stage.py
index 8b1020eb..6aa969bb 100644
--- a/openflexure_microscope/api/v2/views/actions/stage.py
+++ b/openflexure_microscope/api/v2/views/actions/stage.py
@@ -53,7 +53,7 @@ class MoveStageAPI(View):
             logging.warning("Unable to move. No stage found.")
 
         # TODO: Make schema for microscope status
-        return jsonify(microscope.status["stage"]["position"])
+        return jsonify(microscope.state["stage"]["position"])
 
 
 @ThingAction
diff --git a/openflexure_microscope/camera/pi.py b/openflexure_microscope/camera/pi.py
index 8f2a4d94..d1b71141 100644
--- a/openflexure_microscope/camera/pi.py
+++ b/openflexure_microscope/camera/pi.py
@@ -333,13 +333,13 @@ class PiCameraStreamer(BaseCamera):
         Change the camera zoom, handling re-centering and scaling.
         """
         with self.lock:
-            self.status["zoom_value"] = float(zoom_value)
-            if self.status["zoom_value"] < 1:
-                self.status["zoom_value"] = 1
+            self.zoom_value = float(zoom_value)
+            if self.zoom_value < 1:
+                self.zoom_value = 1
             # Richard's code for zooming !
             fov = self.camera.zoom
             centre = np.array([fov[0] + fov[2] / 2.0, fov[1] + fov[3] / 2.0])
-            size = 1.0 / self.status["zoom_value"]
+            size = 1.0 / self.zoom_value
             # If the new zoom value would be invalid, move the centre to
             # keep it within the camera's sensor (this is only relevant
             # when zooming out, if the FoV is not centred on (0.5, 0.5)
@@ -552,7 +552,7 @@ class PiCameraStreamer(BaseCamera):
         if isinstance(output, CaptureObject):
             target = output.file
         else:
-            target = target
+            target = output
 
         with self.lock:
             logging.info("Capturing to {}".format(output))
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index b061bf32..f1023e13 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -76,7 +76,7 @@ class Microscope:
         ### Detector
         if configuration.get("camera"):
             camera_type = configuration["camera"].get("type")
-            if camera_type == "PiCamera" or camera_type == "PiCameraStreamer":
+            if camera_type in ("PiCamera", "PiCameraStreamer"):
                 try:
                     self.camera = PiCameraStreamer()
                 except Exception as e:
@@ -87,12 +87,8 @@ class Microscope:
         if configuration.get("stage"):
             stage_type = configuration["stage"].get("type")
             stage_port = configuration["stage"].get("port")
-            if stage_type == "SangaBoard" or camera_type == "SangaStage":
-                try:
-                    self.stage = SangaStage(port=stage_port)
-                except Exception as e:
-                    logging.error(e)
-                    logging.warning("No compatible stage hardware found.")
+            if stage_type in ("SangaBoard", "SangaStage"):
+                self.stage = SangaStage(port=stage_port)
 
         ### Fallbacks
         if not self.camera:
@@ -180,13 +176,14 @@ class Microscope:
                 # Read LST. Returns None if no LST is active
                 lst_arr = self.camera.read_lens_shading_table()
 
-                b64_string, dtype, shape = serialise_array_b64(lst_arr)
+                if lst_arr:
+                    b64_string, dtype, shape = serialise_array_b64(lst_arr)
 
-                settings_current["camera"]["lens_shading_table"] = {
-                    "b64_string": b64_string,
-                    "dtype": dtype,
-                    "shape": shape,
-                }
+                    settings_current["camera"]["lens_shading_table"] = {
+                        "b64_string": b64_string,
+                        "dtype": dtype,
+                        "shape": shape,
+                    }
 
         # If attached to a stage
         if self.stage: