From 4d82b4df8a02ee478ce1a58e88ffe6a64da121fb Mon Sep 17 00:00:00 2001
From: Joel Collins <joel@jtcollins.net>
Date: Wed, 6 Mar 2019 17:04:32 +0000
Subject: [PATCH] Initial tile/stack plugin

---
 .../plugins/default/stack/__init__.py         |   1 +
 .../plugins/default/stack/plugin.py           | 147 ++++++++++++++++++
 2 files changed, 148 insertions(+)
 create mode 100644 openflexure_microscope/plugins/default/stack/__init__.py
 create mode 100644 openflexure_microscope/plugins/default/stack/plugin.py

diff --git a/openflexure_microscope/plugins/default/stack/__init__.py b/openflexure_microscope/plugins/default/stack/__init__.py
new file mode 100644
index 00000000..a80a0e5a
--- /dev/null
+++ b/openflexure_microscope/plugins/default/stack/__init__.py
@@ -0,0 +1 @@
+from .plugin import StackPlugin
diff --git a/openflexure_microscope/plugins/default/stack/plugin.py b/openflexure_microscope/plugins/default/stack/plugin.py
new file mode 100644
index 00000000..2763c55c
--- /dev/null
+++ b/openflexure_microscope/plugins/default/stack/plugin.py
@@ -0,0 +1,147 @@
+import time
+import numpy as np
+from typing import Tuple
+import uuid
+
+from openflexure_microscope.camera.base import generate_basename
+from openflexure_microscope.plugins import MicroscopePlugin
+from openflexure_microscope.utilities import set_properties
+
+
+class StackPlugin(MicroscopePlugin):
+    """
+    Stack and tile plugin
+    """
+
+    api_views = {}
+
+    def do_capture(self,
+                   basename,
+                   scan_id,
+                   use_video_port: bool = False,
+                   resize: Tuple[int, int] = None,
+                   bayer: bool = False):
+
+        # Construct a tile filename
+        filename = "{}_{}_{}_{}".format(basename, *self.microscope.stage.position)
+        foldername = "SCAN_{}".format(basename)
+
+        # Create output object
+        output = self.microscope.camera.new_image(
+            write_to_file=True,
+            temporary=False,
+            filename=filename,
+            folder=foldername)
+
+        # Capture
+        self.microscope.camera.capture(
+            output,
+            use_video_port=use_video_port,
+            resize=resize,
+            bayer=bayer)
+
+        # Affix metadata
+        metadata = {}
+        tags = ['stack']
+
+        metadata.update({
+            'Position': self.microscope.state['stage']['position'],
+            'Stack ID': scan_id
+        })
+
+        output.put_metadata(metadata)
+        output.put_tags(tags)
+
+    def tile(
+            self,
+            basename: str = None,
+            step_size: int = [2000, 1500],
+            grid: list = [3, 3],
+            autofocus_dz: int = 20,
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = False):
+
+        # Generate a basename if none given
+        if not basename:
+            basename = generate_basename()
+
+        # Generate a stack ID
+        scan_id = uuid.uuid4().hex
+
+        # Store initial position
+        initial_position = self.microscope.stage.position
+
+        # Check if autofocus is enabled
+        if autofocus_dz and hasattr(self.microscope.plugin, 'default_autofocus'):
+            autofocus_enabled = True
+        else:
+            autofocus_enabled = False
+
+        xdirection = 1
+
+        with self.microscope.lock:
+
+            for i in range(grid[0]):
+                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.do_capture(
+                        basename,
+                        scan_id,
+                        use_video_port=use_video_port,
+                        resize=resize,
+                        bayer=bayer
+                    )
+
+                    if j != grid[0] - 1:
+                        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_abs(initial_position)
+
+    def stack(
+            self,
+            basename: str = None,
+            step_size: int = 100,
+            steps: list = 5,
+            center: bool = True,
+            use_video_port: bool = False,
+            resize: Tuple[int, int] = None,
+            bayer: bool = False):
+
+        # Generate a basename if none given
+        if not basename:
+            basename = generate_basename()
+
+        # Generate a stack ID
+        scan_id = uuid.uuid4().hex
+
+        # Store initial position
+        initial_position = self.microscope.stage.position
+
+        # Move to center scan
+        if center:
+            self.microscope.stage.move_rel([0, 0, int((-step_size * steps)/2)])
+
+        with self.microscope.lock:
+
+            for i in range(steps):
+
+                self.do_capture(
+                    basename,
+                    scan_id,
+                    use_video_port=use_video_port,
+                    resize=resize,
+                    bayer=bayer
+                )
+
+                if i != steps - 1:
+                    self.microscope.stage.move_rel([0, 0, step_size])
+
+            self.microscope.stage.move_abs(initial_position)