From 89ea6a69de44b5ec4423145a2c603f03a2bd0c93 Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Thu, 7 Mar 2019 10:58:08 +0000
Subject: [PATCH] Fixed imports, and PEP8 styling

---
 .../plugins/default/scan/__init__.py          |  2 +-
 .../plugins/default/scan/api.py               | 47 +++++++++----------
 .../plugins/default/scan/plugin.py            | 14 +++---
 3 files changed, 30 insertions(+), 33 deletions(-)

diff --git a/openflexure_microscope/plugins/default/scan/__init__.py b/openflexure_microscope/plugins/default/scan/__init__.py
index a80a0e5a..d1e1d942 100644
--- a/openflexure_microscope/plugins/default/scan/__init__.py
+++ b/openflexure_microscope/plugins/default/scan/__init__.py
@@ -1 +1 @@
-from .plugin import StackPlugin
+from .plugin import ScanPlugin
diff --git a/openflexure_microscope/plugins/default/scan/api.py b/openflexure_microscope/plugins/default/scan/api.py
index 97d18c45..7cc7c9f0 100644
--- a/openflexure_microscope/plugins/default/scan/api.py
+++ b/openflexure_microscope/plugins/default/scan/api.py
@@ -1,5 +1,3 @@
-import numpy as np
-
 from openflexure_microscope.api.v1.views import MicroscopeViewPlugin
 from openflexure_microscope.api.utilities import JsonPayload
 
@@ -9,7 +7,7 @@ from flask import request, jsonify, abort
 class TileScanAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonPayload(request)
-        
+
         # Get params
         name = payload.param('name')
         step_size = payload.param('step_size', default=[2000, 1500], convert=list)
@@ -31,29 +29,28 @@ class TileScanAPI(MicroscopeViewPlugin):
         print("Running tile scan...")
         task = self.microscope.task.start(
             self.plugin.tile,
-            basename = name,
-            step_size = step_size,
-            grid = grid,
-            autofocus_dz = autofocus_dz,
-            use_video_port = use_video_port,
-            resize = resize,
-            bayer = bayer,
-            metadata = metadata,
-            tags = tags
+            basename=name,
+            step_size=step_size,
+            grid=grid,
+            autofocus_dz=autofocus_dz,
+            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)
 
 
-
 class ZStackAPI(MicroscopeViewPlugin):
     def post(self):
         payload = JsonPayload(request)
-        
+
         # Get params
         name = payload.param('name')
-        step_size = payload.param('step_size', default=[2000, 1500], convert=list)
+        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)
 
@@ -72,16 +69,16 @@ class ZStackAPI(MicroscopeViewPlugin):
         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
+            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)
\ No newline at end of file
+        return jsonify(task.state, 202)
diff --git a/openflexure_microscope/plugins/default/scan/plugin.py b/openflexure_microscope/plugins/default/scan/plugin.py
index 5fe1273a..3fc9e27e 100644
--- a/openflexure_microscope/plugins/default/scan/plugin.py
+++ b/openflexure_microscope/plugins/default/scan/plugin.py
@@ -5,10 +5,10 @@ import uuid
 
 from openflexure_microscope.camera.base import generate_basename
 from openflexure_microscope.plugins import MicroscopePlugin
-from openflexure_microscope.utilities import set_properties
 
 from .api import TileScanAPI, ZStackAPI
 
+
 class ScanPlugin(MicroscopePlugin):
     """
     Stack and tile plugin
@@ -19,7 +19,6 @@ class ScanPlugin(MicroscopePlugin):
         '/stack': ZStackAPI,
     }
 
-
     def capture(self,
                 basename,
                 scan_id,
@@ -95,7 +94,8 @@ class ScanPlugin(MicroscopePlugin):
                 for j in range(grid[1]):
 
                     if autofocus_enabled:
-                        self.microscope.plugin.default_autofocus.autofocus(range(-2*autofocus_dz, 3*autofocus_dz, autofocus_dz))
+                        self.microscope.plugin.default_autofocus.autofocus(
+                            range(-2 * autofocus_dz, 3 * autofocus_dz, autofocus_dz))
 
                     self.capture(
                         basename,
@@ -108,11 +108,11 @@ class ScanPlugin(MicroscopePlugin):
                     )
 
                     if j != grid[0] - 1:
-                        self.microscope.stage.move_rel([step_size[0]*xdirection, 0, 0])
+                        self.microscope.stage.move_rel([step_size[0] * xdirection, 0, 0])
 
                 xdirection *= -1
                 if i != grid[1] - 1:
-                    self.microscope.stage.move_rel([256*xdirection, step_size[1], 0])
+                    self.microscope.stage.move_rel([256 * xdirection, step_size[1], 0])
 
             self.microscope.stage.move_abs(initial_position)
 
@@ -120,7 +120,7 @@ class ScanPlugin(MicroscopePlugin):
             self,
             basename: str = None,
             step_size: int = 100,
-            steps: list = 5,
+            steps: int = 5,
             center: bool = True,
             use_video_port: bool = False,
             resize: Tuple[int, int] = None,
@@ -140,7 +140,7 @@ class ScanPlugin(MicroscopePlugin):
 
         # Move to center scan
         if center:
-            self.microscope.stage.move_rel([0, 0, int((-step_size * steps)/2)])
+            self.microscope.stage.move_rel([0, 0, int((-step_size * steps) / 2)])
 
         with self.microscope.lock: