From 090e4e0d1d8108dfd8f680e8c0d045236d014c5a Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 00:20:29 +0100
Subject: [PATCH 01/76] Add production plugin

---
 camacqplugins/production/__init__.py | 38 ++++++++++++++++++++++++++++
 requirements.txt                     |  2 +-
 setup.cfg                            |  2 +-
 setup.py                             |  1 +
 4 files changed, 41 insertions(+), 2 deletions(-)
 create mode 100644 camacqplugins/production/__init__.py

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
new file mode 100644
index 0000000..7770ded
--- /dev/null
+++ b/camacqplugins/production/__init__.py
@@ -0,0 +1,38 @@
+"""Provide a plugin for production standard flow."""
+import asyncio
+import logging
+
+import voluptuous as vol
+
+from camacq.plugins.sample import ACTION_TO_METHOD
+from camacq.util import read_csv
+
+_LOGGER = logging.getLogger(__name__)
+
+SAMPLE_STATE_FILE = "state_file"
+
+
+async def setup_module(center, config):
+    """Set up Leica api package."""
+    print("Production plugin setup!")
+
+    conf = config["production"]
+    state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
+    if state_file is None:
+        return
+    state_data = await center.add_executor_job(read_csv, state_file)
+    tasks = []
+    for data in state_data:
+        for action_id, options in ACTION_TO_METHOD.items():
+            schema = options["schema"]
+            try:
+                schema(data)
+            except vol.Invalid as exc:
+                _LOGGER.debug("Skipping action %s: %s", action_id, exc)
+                continue
+            tasks.append(
+                center.create_task(center.actions.call("sample", action_id, **data))
+            )
+
+    if tasks:
+        await asyncio.wait(tasks)
diff --git a/requirements.txt b/requirements.txt
index 552706a..438a380 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1 +1 @@
-camacq==0.4.0
\ No newline at end of file
+camacq==0.4.0
diff --git a/setup.cfg b/setup.cfg
index eca367a..9d95385 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -2,4 +2,4 @@
 max-line-length = 88
 
 [pydocstyle]
-add-ignore = D202
\ No newline at end of file
+add-ignore = D202
diff --git a/setup.py b/setup.py
index 0ffa448..8aada30 100644
--- a/setup.py
+++ b/setup.py
@@ -23,6 +23,7 @@
     packages=setuptools.find_packages(),
     python_requires=">=3.6",
     install_requires=REQUIRES,
+    entry_points={"camacq.plugins": ["production = camacqplugins.production",],},
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Programming Language :: Python",

From 2ea476d69ffa3947c222defb5fc5ca3ff19b0b42 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 04:10:24 +0100
Subject: [PATCH 02/76] Add pylintrc

---
 pylintrc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pylintrc b/pylintrc
index 5f3bd50..199fca4 100644
--- a/pylintrc
+++ b/pylintrc
@@ -7,4 +7,4 @@ disable=
   bad-continuation,
   duplicate-code,
   locally-disabled,
-  unused-argument,
\ No newline at end of file
+  unused-argument,

From 1cecc00478dcd57d45895eb889407df7524b0635 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 04:11:38 +0100
Subject: [PATCH 03/76] Add more event handlers

---
 camacqplugins/production/__init__.py | 68 ++++++++++++++++++++++------
 1 file changed, 55 insertions(+), 13 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 7770ded..ab2abbe 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -4,7 +4,7 @@
 
 import voluptuous as vol
 
-from camacq.plugins.sample import ACTION_TO_METHOD
+from camacq.helper.template import TemplateFunctions
 from camacq.util import read_csv
 
 _LOGGER = logging.getLogger(__name__)
@@ -18,21 +18,63 @@ async def setup_module(center, config):
 
     conf = config["production"]
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
-    if state_file is None:
-        return
+    if state_file is not None:
+        await load_sample(center, state_file)
+    else:
+        start_exp(center)
+
+    add_next_well(center)
+
+
+async def load_sample(center, state_file):
+    """Load sample state from file."""
     state_data = await center.add_executor_job(read_csv, state_file)
     tasks = []
     for data in state_data:
-        for action_id, options in ACTION_TO_METHOD.items():
-            schema = options["schema"]
-            try:
-                schema(data)
-            except vol.Invalid as exc:
-                _LOGGER.debug("Skipping action %s: %s", action_id, exc)
-                continue
-            tasks.append(
-                center.create_task(center.actions.call("sample", action_id, **data))
-            )
+        for action in center.actions.sample.values():
+            tasks.append(center.create_task(action(silent=True, **data)))
 
     if tasks:
         await asyncio.wait(tasks)
+
+
+def start_exp(center):
+    """Trigger on start experiment."""
+
+    async def start(center, event):
+        """Run on start event."""
+        print("Camacq started!!!")
+
+        await center.actions.sample.set_well(plate_name="00", well_x=0, well_y=0)
+
+    center.bus.register("camacq_start_event", start)
+
+
+def add_next_well(center):
+    """Add next well."""
+
+    async def well_event(center, event):
+        """Run on well event."""
+        print("Well event!!!")
+        if not match_event(event, field_x=1, field_y=2, well_img_ok=True):
+            return
+
+        plate_name = "00"
+        sample_helper = TemplateFunctions(center)
+        well_x, well_y = sample_helper.next_well_xy(plate_name, x_wells=12, y_wells=8)
+
+        await center.actions.sample.set_well(
+            plate_name=plate_name, well_x=well_x, well_y=well_y
+        )
+
+    center.bus.register("well_event", well_event)
+
+
+def match_event(event, **event_data):
+    """Return True if event matches."""
+    if not event_data or all(
+        val == getattr(event, key, None) for key, val in event_data.items()
+    ):
+        return True
+
+    return False

From 2d8caed3ae6f417b6c4e124554e829a8de31f9ab Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 14:23:45 +0100
Subject: [PATCH 04/76] Import event matcher

---
 camacqplugins/production/__init__.py | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index ab2abbe..5acd578 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -4,6 +4,7 @@
 
 import voluptuous as vol
 
+from camacq.event import match_event
 from camacq.helper.template import TemplateFunctions
 from camacq.util import read_csv
 
@@ -68,13 +69,3 @@ async def well_event(center, event):
         )
 
     center.bus.register("well_event", well_event)
-
-
-def match_event(event, **event_data):
-    """Return True if event matches."""
-    if not event_data or all(
-        val == getattr(event, key, None) for key, val in event_data.items()
-    ):
-        return True
-
-    return False

From 9994fac85748e07524480f6bfd9768b4d0a5d447 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 14:44:52 +0100
Subject: [PATCH 05/76] Use sample helper

---
 camacqplugins/production/__init__.py | 8 +++-----
 1 file changed, 3 insertions(+), 5 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 5acd578..3a3929c 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -6,6 +6,7 @@
 
 from camacq.event import match_event
 from camacq.helper.template import TemplateFunctions
+from camacq.plugins.sample.helper import next_well_xy
 from camacq.util import read_csv
 
 _LOGGER = logging.getLogger(__name__)
@@ -44,8 +45,6 @@ def start_exp(center):
 
     async def start(center, event):
         """Run on start event."""
-        print("Camacq started!!!")
-
         await center.actions.sample.set_well(plate_name="00", well_x=0, well_y=0)
 
     center.bus.register("camacq_start_event", start)
@@ -56,13 +55,12 @@ def add_next_well(center):
 
     async def well_event(center, event):
         """Run on well event."""
-        print("Well event!!!")
         if not match_event(event, field_x=1, field_y=2, well_img_ok=True):
             return
 
+        # TODO: Make plate and well coordinates configurable.
         plate_name = "00"
-        sample_helper = TemplateFunctions(center)
-        well_x, well_y = sample_helper.next_well_xy(plate_name, x_wells=12, y_wells=8)
+        well_x, well_y = next_well_xy(center.sample, plate_name, x_wells=12, y_wells=8)
 
         await center.actions.sample.set_well(
             plate_name=plate_name, well_x=well_x, well_y=well_y

From dee5216bfb5ce53042f3be268cf4c91f3f2db8c4 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 14:51:53 +0100
Subject: [PATCH 06/76] Clean up

---
 camacqplugins/production/__init__.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 3a3929c..8fb1a91 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -2,10 +2,7 @@
 import asyncio
 import logging
 
-import voluptuous as vol
-
 from camacq.event import match_event
-from camacq.helper.template import TemplateFunctions
 from camacq.plugins.sample.helper import next_well_xy
 from camacq.util import read_csv
 

From 724b0b32d9dda4ccb039f0a27638ac9597b9f89f Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 10 Nov 2019 14:53:40 +0100
Subject: [PATCH 07/76] Fix stale docstring

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 8fb1a91..19ca564 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -12,7 +12,7 @@
 
 
 async def setup_module(center, config):
-    """Set up Leica api package."""
+    """Set up production plugin."""
     print("Production plugin setup!")
 
     conf = config["production"]

From ee502c3e1c6aa7ecf6ff429f964d905d0b59d804 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 14:57:59 +0100
Subject: [PATCH 08/76] Add stop trigger

---
 camacqplugins/production/__init__.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 19ca564..3ed5ed5 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -23,6 +23,7 @@ async def setup_module(center, config):
         start_exp(center)
 
     add_next_well(center)
+    stop_exp(center)
 
 
 async def load_sample(center, state_file):
@@ -64,3 +65,22 @@ async def well_event(center, event):
         )
 
     center.bus.register("well_event", well_event)
+
+
+def stop_exp(center):
+    """Trigger to stop experiment."""
+
+    async def stop(center, event):
+        """Run to stop the experiment."""
+        next_well_x, _ = next_well_xy("00", 2, 2)
+
+        if (
+            not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            or next_well_x is not None
+        ):
+            return
+
+        await center.actions.automations.delay(seconds=2.0)
+        await center.actions.api.stop_imaging()
+
+    center.bus.register("well_event", stop)

From e8acede89f9bd1b739e9ddad1263246c25d3baca Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 20:57:17 +0100
Subject: [PATCH 09/76] Add image next well

---
 camacqplugins/production/__init__.py | 41 +++++++++++++++++++++++-----
 1 file changed, 34 insertions(+), 7 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 3ed5ed5..81d401f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -3,6 +3,7 @@
 import logging
 
 from camacq.event import match_event
+from camacq.plugins.leica.command import cam_com, del_com
 from camacq.plugins.sample.helper import next_well_xy
 from camacq.util import read_csv
 
@@ -23,6 +24,7 @@ async def setup_module(center, config):
         start_exp(center)
 
     add_next_well(center)
+    image_next_well(center)
     stop_exp(center)
 
 
@@ -41,17 +43,17 @@ async def load_sample(center, state_file):
 def start_exp(center):
     """Trigger on start experiment."""
 
-    async def start(center, event):
+    async def set_start_well(center, event):
         """Run on start event."""
         await center.actions.sample.set_well(plate_name="00", well_x=0, well_y=0)
 
-    center.bus.register("camacq_start_event", start)
+    center.bus.register("camacq_start_event", set_start_well)
 
 
 def add_next_well(center):
     """Add next well."""
 
-    async def well_event(center, event):
+    async def set_next_well(center, event):
         """Run on well event."""
         if not match_event(event, field_x=1, field_y=2, well_img_ok=True):
             return
@@ -64,13 +66,37 @@ async def well_event(center, event):
             plate_name=plate_name, well_x=well_x, well_y=well_y
         )
 
-    center.bus.register("well_event", well_event)
+    center.bus.register("well_event", set_next_well)
+
+
+def image_next_well(center):
+    """Image next well."""
+
+    async def send_cam_job(center, event):
+        """Run on well event."""
+        if event.well.images:
+            return
+
+        await center.actions.command.send(command=del_com())
+        # TODO: Make exp job configurable.
+        command = cam_com("p10xgain", event.well.x, event.well.y, 0, 1, 0, 0)
+        await center.actions.command.send(command=command)
+        command = cam_com("p10xgain", event.well.x, event.well.y, 1, 1, 0, 0)
+        await center.actions.command.send(command=command)
+
+        # TODO: Unregister rename image and set img ok.
+
+        await center.actions.command.start_imaging()
+        await asyncio.sleep(2.0)
+        await center.actions.command.send(command="/cmd:startcamscan")
+
+    center.bus.register("well_event", send_cam_job)
 
 
 def stop_exp(center):
     """Trigger to stop experiment."""
 
-    async def stop(center, event):
+    async def stop_imaging(center, event):
         """Run to stop the experiment."""
         next_well_x, _ = next_well_xy("00", 2, 2)
 
@@ -80,7 +106,8 @@ async def stop(center, event):
         ):
             return
 
-        await center.actions.automations.delay(seconds=2.0)
+        # Sleep to let images be completely scanned before stopping.
+        await asyncio.sleep(2.0)
         await center.actions.api.stop_imaging()
 
-    center.bus.register("well_event", stop)
+    center.bus.register("well_event", stop_imaging)

From d8342591ddefd50917217082138c9b86ce2ca568 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 21:13:59 +0100
Subject: [PATCH 10/76] Add todo comments

---
 camacqplugins/production/__init__.py | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 81d401f..b0925f1 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -55,10 +55,11 @@ def add_next_well(center):
 
     async def set_next_well(center, event):
         """Run on well event."""
+        # TODO: Make stop field coordinates configurable.
         if not match_event(event, field_x=1, field_y=2, well_img_ok=True):
             return
 
-        # TODO: Make plate and well coordinates configurable.
+        # TODO: Make well coordinates configurable.
         plate_name = "00"
         well_x, well_y = next_well_xy(center.sample, plate_name, x_wells=12, y_wells=8)
 
@@ -78,7 +79,7 @@ async def send_cam_job(center, event):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make exp job configurable.
+        # TODO: Make exp job and field coordinates configurable.
         command = cam_com("p10xgain", event.well.x, event.well.y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
         command = cam_com("p10xgain", event.well.x, event.well.y, 1, 1, 0, 0)
@@ -98,7 +99,8 @@ def stop_exp(center):
 
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
-        next_well_x, _ = next_well_xy("00", 2, 2)
+        # TODO: Make well layout and stop field coordinates configurable.
+        next_well_x, _ = next_well_xy("00", 12, 8)
 
         if (
             not match_event(event, field_x=1, field_y=2, well_img_ok=True)

From 0f05cea020a3a02d6e74070b11f48a6a3812b4d5 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 21:23:24 +0100
Subject: [PATCH 11/76] Finish add next well

---
 camacqplugins/production/__init__.py | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index b0925f1..47aefbb 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -55,13 +55,25 @@ def add_next_well(center):
 
     async def set_next_well(center, event):
         """Run on well event."""
-        # TODO: Make stop field coordinates configurable.
-        if not match_event(event, field_x=1, field_y=2, well_img_ok=True):
+        # TODO: Make well layout and stop field coordinates configurable.
+        plate_name = "00"
+        x_wells = 12
+        y_wells = 8
+        next_well_x, _ = next_well_xy(plate_name, x_wells, y_wells)
+
+        if (
+            not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            or next_well_x is None
+        ):
             return
 
-        # TODO: Make well coordinates configurable.
-        plate_name = "00"
-        well_x, well_y = next_well_xy(center.sample, plate_name, x_wells=12, y_wells=8)
+        await asyncio.sleep(2.0)
+        await center.actions.command.stop_imaging()
+        await asyncio.sleep(4.0)
+
+        well_x, well_y = next_well_xy(
+            center.sample, plate_name, x_wells=x_wells, y_wells=y_wells
+        )
 
         await center.actions.sample.set_well(
             plate_name=plate_name, well_x=well_x, well_y=well_y

From 65ae1481feddf91e4b6ee1153e22f04a2733c883 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 21:25:43 +0100
Subject: [PATCH 12/76] Extract delay time to constant

---
 camacqplugins/production/__init__.py | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 47aefbb..84627d5 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -10,6 +10,7 @@
 _LOGGER = logging.getLogger(__name__)
 
 SAMPLE_STATE_FILE = "state_file"
+START_STOP_DELAY = 2.0
 
 
 async def setup_module(center, config):
@@ -67,9 +68,9 @@ async def set_next_well(center, event):
         ):
             return
 
-        await asyncio.sleep(2.0)
+        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.stop_imaging()
-        await asyncio.sleep(4.0)
+        await asyncio.sleep(2 * START_STOP_DELAY)
 
         well_x, well_y = next_well_xy(
             center.sample, plate_name, x_wells=x_wells, y_wells=y_wells
@@ -100,7 +101,7 @@ async def send_cam_job(center, event):
         # TODO: Unregister rename image and set img ok.
 
         await center.actions.command.start_imaging()
-        await asyncio.sleep(2.0)
+        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.send(command="/cmd:startcamscan")
 
     center.bus.register("well_event", send_cam_job)
@@ -121,7 +122,7 @@ async def stop_imaging(center, event):
             return
 
         # Sleep to let images be completely scanned before stopping.
-        await asyncio.sleep(2.0)
+        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.api.stop_imaging()
 
     center.bus.register("well_event", stop_imaging)

From 8062bf951d135136d3d71a506dfb50c8107fcbec Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 21:50:59 +0100
Subject: [PATCH 13/76] Add calc gain

---
 camacqplugins/production/__init__.py | 44 ++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 84627d5..4e7ebd7 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -1,6 +1,8 @@
 """Provide a plugin for production standard flow."""
 import asyncio
 import logging
+import tempfile
+from pathlib import Path
 
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com
@@ -26,6 +28,7 @@ async def setup_module(center, config):
 
     add_next_well(center)
     image_next_well(center)
+    analyze_gain(center)
     stop_exp(center)
 
 
@@ -107,6 +110,47 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
+def analyze_gain(center):
+    """Analyze gain."""
+
+    async def calc_gain(center, event):
+        """Calculate correct gain."""
+        # TODO: Make event field coordinates, job id and save_path configurable.
+        field_x = 1
+        field_y = 1
+        job_id = 3
+        channel_id = 31
+        if not match_event(
+            event,
+            field_x=field_x,
+            field_y=field_y,
+            job_id=job_id,
+            channel_id=channel_id,
+        ):
+            return
+
+        await asyncio.sleep(START_STOP_DELAY)
+        await center.actions.command.stop_imaging()
+        await asyncio.sleep(START_STOP_DELAY)
+
+        # This should be a path to a base file name, not to an actual dir or file.
+        save_path = (
+            Path(tempfile.gettempdir())
+            / event.plate_name
+            / f"{event.well_x}--{event.well_y}"
+        )
+
+        await center.actions.plugins.gain.calc_gain(
+            plate_name=event.plate_name,
+            well_x=event.well_x,
+            well_y=event.well_y,
+            make_plots=True,
+            save_path=save_path,
+        )
+
+    center.bus.register("image_event", calc_gain)
+
+
 def stop_exp(center):
     """Trigger to stop experiment."""
 

From 9ed3a18ca0a51b04fb5bebfc4230dff52bef2da7 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 21:58:09 +0100
Subject: [PATCH 14/76] Add fixme comment

---
 camacqplugins/production/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 4e7ebd7..5e52a04 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -140,6 +140,7 @@ async def calc_gain(center, event):
             / f"{event.well_x}--{event.well_y}"
         )
 
+        # FIXME: Adjust the action type for plugins.gain to avoid period in the name.
         await center.actions.plugins.gain.calc_gain(
             plate_name=event.plate_name,
             well_x=event.well_x,

From 43b51d8320814965fd1b0eec6184835b5784766c Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Tue, 12 Nov 2019 22:25:58 +0100
Subject: [PATCH 15/76] Add set_exp_gain

---
 camacqplugins/production/__init__.py | 47 +++++++++++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 5e52a04..2b13be4 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -5,7 +5,7 @@
 from pathlib import Path
 
 from camacq.event import match_event
-from camacq.plugins.leica.command import cam_com, del_com
+from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
 from camacq.util import read_csv
 
@@ -29,6 +29,7 @@ async def setup_module(center, config):
     add_next_well(center)
     image_next_well(center)
     analyze_gain(center)
+    set_exp_gain(center)
     stop_exp(center)
 
 
@@ -152,6 +153,50 @@ async def calc_gain(center, event):
     center.bus.register("image_event", calc_gain)
 
 
+def set_exp_gain(center):
+    """Set experiment gain."""
+
+    async def set_gain(center, event):
+        """Set pmt gain."""
+        # TODO:  Make exp job names configurable.
+        exp_job_1 = "exp_job_1"
+        exp_job_2 = "exp_job_2"
+        exp_job_3 = "exp_job_3"
+
+        if event.channel_name == "green":
+            exp = exp_job_1
+            num = 1
+            gain = min(event.gain or 800, 800)
+        elif event.channel_name == "blue":
+            exp = exp_job_2
+            num = 1
+            gain = min(event.gain or 505, 610)
+        elif event.channel_name == "yellow":
+            exp = exp_job_2
+            num = 2
+            gain = min(event.gain or 655, 760)
+        elif event.channel_name == "red":
+            exp = exp_job_3
+            num = 2
+            gain = event.gain or 630
+            gain = min(gain + 25, 735)
+
+        command = gain_com(exp=exp, num=num, value=gain)
+
+        # Set the gain at the microscope.
+        await center.actions.command.send(command=command)
+        # Set the gain in the sample state.
+        await center.actions.sample.set_channel(
+            plate_name=event.plate_name,
+            well_x=event.well_x,
+            well_y=event.well_y,
+            channel_name=event.channel_name,
+            gain=gain,
+        )
+
+    center.bus.register("gain_calc_event", set_gain)
+
+
 def stop_exp(center):
     """Trigger to stop experiment."""
 

From f07f801a0519a20a6a27f6ab4fa6f1879f2131d3 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Wed, 13 Nov 2019 12:56:46 +0100
Subject: [PATCH 16/76] Add exp job

---
 camacqplugins/production/__init__.py | 30 ++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 2b13be4..794c081 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -30,6 +30,7 @@ async def setup_module(center, config):
     image_next_well(center)
     analyze_gain(center)
     set_exp_gain(center)
+    add_exp_job(center)
     stop_exp(center)
 
 
@@ -197,6 +198,35 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
+def add_exp_job(center):
+    """Add experiment job."""
+
+    async def add_cam_job(center, event):
+        """Add an experiment job to the cam list."""
+        # TODO: Make channels layout configurable.
+        if not match_event(event, channel_name="red") or len(event.well.channels) != 4:
+            return
+
+        # TODO: Make well layout configurable.
+        commands = []
+        for field_x in range(2):
+            for field_y in range(3):
+                cmd = cam_com(
+                    "p10xexp", event.well_x, event.well_y, field_x, field_y, 0, 0
+                )
+                commands.append(cmd)
+
+        await center.actions.command.send(command=del_com())
+        await center.actions.command.send_many(commands=commands)
+
+        # TODO: Turn on rename image and set_img_ok during experiment job phase.
+
+        await center.actions.command.start_imaging()
+        await center.actions.command.send(command="/cmd:startcamscan")
+
+    center.bus.register("channel_event", add_cam_job)
+
+
 def stop_exp(center):
     """Trigger to stop experiment."""
 

From 11a892668fac6ddd6aa3a29cb78a96b6be1a0f10 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Wed, 13 Nov 2019 13:19:12 +0100
Subject: [PATCH 17/76] Add set img ok

---
 camacqplugins/production/__init__.py | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 794c081..b90e9e8 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -31,6 +31,7 @@ async def setup_module(center, config):
     analyze_gain(center)
     set_exp_gain(center)
     add_exp_job(center)
+    set_img_ok(center)
     stop_exp(center)
 
 
@@ -227,6 +228,26 @@ async def add_cam_job(center, event):
     center.bus.register("channel_event", add_cam_job)
 
 
+def set_img_ok(center):
+    """Set field as imaged ok."""
+
+    async def set_sample_img_ok(center, event):
+        """Set sample field img ok."""
+        if not match_event(event, job_id=5):
+            return
+
+        await center.actions.sample.set_field(
+            plate_name=event.plate_name,
+            well_x=event.well_x,
+            well_y=event.well_y,
+            field_x=event.field_x,
+            field_y=event.field_y,
+            img_ok=True,
+        )
+
+    return center.bus.register("image_event", set_sample_img_ok)
+
+
 def stop_exp(center):
     """Trigger to stop experiment."""
 

From 8598262bb3528f550a70be664f91133dfec4b871 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Wed, 13 Nov 2019 15:09:14 +0100
Subject: [PATCH 18/76] Add rename image

---
 camacqplugins/production/__init__.py | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index b90e9e8..1c9ffcf 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -32,6 +32,7 @@ async def setup_module(center, config):
     set_exp_gain(center)
     add_exp_job(center)
     set_img_ok(center)
+    rename_exp_image(center)
     stop_exp(center)
 
 
@@ -248,6 +249,33 @@ async def set_sample_img_ok(center, event):
     return center.bus.register("image_event", set_sample_img_ok)
 
 
+def rename_exp_image(center):
+    """Rename an experiment image."""
+
+    async def rename_image(center, event):
+        """Rename an image."""
+        if event.job_id not in (3, 4, 6):
+            return
+
+        if event.job_id == 3:
+            channel_id = event.channel_id
+        elif event.job_id == 4 and event.channel_id == 0:
+            channel_id = 1
+        elif event.job_id == 4 and event.channel_id == 1:
+            channel_id = 2
+        elif event.job_id == 6:
+            channel_id = 3
+
+        new_name = (
+            f"U{event.well_x:03}--V{event.well_y}--E{event.job_id}--X{event.field_x}"
+            f"--Y{event.field_y}--Z{event.z_slice}--C{channel_id}.ome.tif"
+        )
+
+        center.actions.rename(old_path=event.path, new_name=new_name)
+
+    center.bus.register("image_event", rename_image)
+
+
 def stop_exp(center):
     """Trigger to stop experiment."""
 

From 23c20ec538e290cae780823fe745657f5c816a99 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Thu, 14 Nov 2019 11:05:51 +0100
Subject: [PATCH 19/76] Add flake8 ignore

---
 setup.cfg | 1 +
 1 file changed, 1 insertion(+)

diff --git a/setup.cfg b/setup.cfg
index 9d95385..b3d11de 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -1,4 +1,5 @@
 [flake8]
+ignore = E231, W503
 max-line-length = 88
 
 [pydocstyle]

From 3002399ce7d24f987518bf7cca675273d1523665 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 15:00:06 +0100
Subject: [PATCH 20/76] Fix next well xy

---
 camacqplugins/production/__init__.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 1c9ffcf..8f1b3af 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -26,6 +26,8 @@ async def setup_module(center, config):
     else:
         start_exp(center)
 
+    # TODO: Only add wells if not loading sample state from file.
+
     add_next_well(center)
     image_next_well(center)
     analyze_gain(center)
@@ -67,7 +69,7 @@ async def set_next_well(center, event):
         plate_name = "00"
         x_wells = 12
         y_wells = 8
-        next_well_x, _ = next_well_xy(plate_name, x_wells, y_wells)
+        next_well_x, _ = next_well_xy(center.sample, plate_name, x_wells, y_wells)
 
         if (
             not match_event(event, field_x=1, field_y=2, well_img_ok=True)
@@ -79,9 +81,7 @@ async def set_next_well(center, event):
         await center.actions.command.stop_imaging()
         await asyncio.sleep(2 * START_STOP_DELAY)
 
-        well_x, well_y = next_well_xy(
-            center.sample, plate_name, x_wells=x_wells, y_wells=y_wells
-        )
+        well_x, well_y = next_well_xy(center.sample, plate_name, x_wells, y_wells)
 
         await center.actions.sample.set_well(
             plate_name=plate_name, well_x=well_x, well_y=well_y
@@ -282,7 +282,7 @@ def stop_exp(center):
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
         # TODO: Make well layout and stop field coordinates configurable.
-        next_well_x, _ = next_well_xy("00", 12, 8)
+        next_well_x, _ = next_well_xy(center.sample, "00", 12, 8)
 
         if (
             not match_event(event, field_x=1, field_y=2, well_img_ok=True)

From fa6f347c5c8d43a5046e6ce575df9b6d5251b6ba Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 15:50:40 +0100
Subject: [PATCH 21/76] Image next well based on sample

---
 camacqplugins/production/__init__.py | 52 ++++++++++++++++++++++------
 1 file changed, 41 insertions(+), 11 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 8f1b3af..1ab8697 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -23,13 +23,12 @@ async def setup_module(center, config):
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
     if state_file is not None:
         await load_sample(center, state_file)
+        image_next_well_on_sample(center)
     else:
         start_exp(center)
+        add_next_well(center)
+        image_next_well_on_event(center)
 
-    # TODO: Only add wells if not loading sample state from file.
-
-    add_next_well(center)
-    image_next_well(center)
     analyze_gain(center)
     set_exp_gain(center)
     add_exp_job(center)
@@ -41,13 +40,11 @@ async def setup_module(center, config):
 async def load_sample(center, state_file):
     """Load sample state from file."""
     state_data = await center.add_executor_job(read_csv, state_file)
-    tasks = []
     for data in state_data:
-        for action in center.actions.sample.values():
-            tasks.append(center.create_task(action(silent=True, **data)))
-
-    if tasks:
-        await asyncio.wait(tasks)
+        await center.actions.sample.set_plate(silent=True, **data)
+        await center.actions.sample.set_well(silent=True, **data)
+        await center.actions.sample.set_channel(silent=True, **data)
+        await center.actions.sample.set_field(silent=True, **data)
 
 
 def start_exp(center):
@@ -90,7 +87,40 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well(center):
+def image_next_well_on_sample(center):
+    """Image next well in existing sample."""
+
+    async def send_cam_job(center, event):
+        """Run on well event."""
+        # TODO: Make stop field coordinates configurable.
+        plate_name = "00"
+        next_well_x, next_well_y = next_well_xy(center.sample, plate_name)
+
+        if (
+            not match_event(event, event_type="camacq_start_event")
+            and not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            or next_well_x is None
+        ):
+            return
+
+        await center.actions.command.send(command=del_com())
+        # TODO: Make exp job and field coordinates configurable.
+        command = cam_com("p10xgain", next_well_x, next_well_y, 0, 1, 0, 0)
+        await center.actions.command.send(command=command)
+        command = cam_com("p10xgain", next_well_x, next_well_y, 1, 1, 0, 0)
+        await center.actions.command.send(command=command)
+
+        # TODO: Unregister rename image and set img ok.
+
+        await center.actions.command.start_imaging()
+        await asyncio.sleep(START_STOP_DELAY)
+        await center.actions.command.send(command="/cmd:startcamscan")
+
+    center.bus.register("camacq_start_event", send_cam_job)
+    center.bus.register("well_event", send_cam_job)
+
+
+def image_next_well_on_event(center):
     """Image next well."""
 
     async def send_cam_job(center, event):

From 4e1b61b49f3bfc171e547b30ea536e45da1f21be Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 16:01:37 +0100
Subject: [PATCH 22/76] Make job names configurable

---
 camacqplugins/production/__init__.py | 51 ++++++++++++++--------------
 1 file changed, 25 insertions(+), 26 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 1ab8697..a84de24 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -17,21 +17,25 @@
 
 async def setup_module(center, config):
     """Set up production plugin."""
-    print("Production plugin setup!")
-
     conf = config["production"]
+    gain_job = conf["gain_job_name"]
+    green_job = conf["green_job_name"]
+    blue_yellow_job = conf["blue_yellow_job_name"]
+    red_job = conf["red_job_name"]
+    exp_pattern = conf["exp_pattern_name"]
+
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
     if state_file is not None:
         await load_sample(center, state_file)
-        image_next_well_on_sample(center)
+        image_next_well_on_sample(center, gain_job)
     else:
         start_exp(center)
         add_next_well(center)
-        image_next_well_on_event(center)
+        image_next_well_on_event(center, gain_job)
 
     analyze_gain(center)
-    set_exp_gain(center)
-    add_exp_job(center)
+    set_exp_gain(center, green_job, blue_yellow_job, red_job)
+    add_exp_job(center, exp_pattern)
     set_img_ok(center)
     rename_exp_image(center)
     stop_exp(center)
@@ -87,7 +91,7 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well_on_sample(center):
+def image_next_well_on_sample(center, gain_job):
     """Image next well in existing sample."""
 
     async def send_cam_job(center, event):
@@ -104,10 +108,10 @@ async def send_cam_job(center, event):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make exp job and field coordinates configurable.
-        command = cam_com("p10xgain", next_well_x, next_well_y, 0, 1, 0, 0)
+        # TODO: Make field coordinates configurable.
+        command = cam_com(gain_job, next_well_x, next_well_y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
-        command = cam_com("p10xgain", next_well_x, next_well_y, 1, 1, 0, 0)
+        command = cam_com(gain_job, next_well_x, next_well_y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
         # TODO: Unregister rename image and set img ok.
@@ -120,7 +124,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def image_next_well_on_event(center):
+def image_next_well_on_event(center, gain_job):
     """Image next well."""
 
     async def send_cam_job(center, event):
@@ -129,10 +133,10 @@ async def send_cam_job(center, event):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make exp job and field coordinates configurable.
-        command = cam_com("p10xgain", event.well.x, event.well.y, 0, 1, 0, 0)
+        # TODO: Make field coordinates configurable.
+        command = cam_com(gain_job, event.well.x, event.well.y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
-        command = cam_com("p10xgain", event.well.x, event.well.y, 1, 1, 0, 0)
+        command = cam_com(gain_job, event.well.x, event.well.y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
         # TODO: Unregister rename image and set img ok.
@@ -186,30 +190,25 @@ async def calc_gain(center, event):
     center.bus.register("image_event", calc_gain)
 
 
-def set_exp_gain(center):
+def set_exp_gain(center, green_job, blue_yellow_job, red_job):
     """Set experiment gain."""
 
     async def set_gain(center, event):
         """Set pmt gain."""
-        # TODO:  Make exp job names configurable.
-        exp_job_1 = "exp_job_1"
-        exp_job_2 = "exp_job_2"
-        exp_job_3 = "exp_job_3"
-
         if event.channel_name == "green":
-            exp = exp_job_1
+            exp = green_job
             num = 1
             gain = min(event.gain or 800, 800)
         elif event.channel_name == "blue":
-            exp = exp_job_2
+            exp = blue_yellow_job
             num = 1
             gain = min(event.gain or 505, 610)
         elif event.channel_name == "yellow":
-            exp = exp_job_2
+            exp = blue_yellow_job
             num = 2
             gain = min(event.gain or 655, 760)
         elif event.channel_name == "red":
-            exp = exp_job_3
+            exp = red_job
             num = 2
             gain = event.gain or 630
             gain = min(gain + 25, 735)
@@ -230,7 +229,7 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center):
+def add_exp_job(center, exp_pattern):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
@@ -244,7 +243,7 @@ async def add_cam_job(center, event):
         for field_x in range(2):
             for field_y in range(3):
                 cmd = cam_com(
-                    "p10xexp", event.well_x, event.well_y, field_x, field_y, 0, 0
+                    exp_pattern, event.well_x, event.well_y, field_x, field_y, 0, 0
                 )
                 commands.append(cmd)
 

From 9090d0257ed77d45e1fbc8e73cb08c86790095e0 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 16:24:23 +0100
Subject: [PATCH 23/76] Register and unregister img ok and rename img

---
 camacqplugins/production/__init__.py | 40 +++++++++++++++++++---------
 1 file changed, 27 insertions(+), 13 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index a84de24..880d8ab 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -7,7 +7,7 @@
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
-from camacq.util import read_csv
+from camacq.util import dotdict, read_csv
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -23,21 +23,22 @@ async def setup_module(center, config):
     blue_yellow_job = conf["blue_yellow_job_name"]
     red_job = conf["red_job_name"]
     exp_pattern = conf["exp_pattern_name"]
+    subscriptions = dotdict()
 
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
     if state_file is not None:
         await load_sample(center, state_file)
-        image_next_well_on_sample(center, gain_job)
+        image_next_well_on_sample(center, gain_job, subscriptions)
     else:
         start_exp(center)
         add_next_well(center)
-        image_next_well_on_event(center, gain_job)
+        image_next_well_on_event(center, gain_job, subscriptions)
 
     analyze_gain(center)
     set_exp_gain(center, green_job, blue_yellow_job, red_job)
-    add_exp_job(center, exp_pattern)
-    set_img_ok(center)
-    rename_exp_image(center)
+    add_exp_job(center, exp_pattern, subscriptions)
+    subscriptions.set_img_ok = set_img_ok(center)
+    subscriptions.rename_exp_image = rename_exp_image(center)
     stop_exp(center)
 
 
@@ -91,7 +92,7 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well_on_sample(center, gain_job):
+def image_next_well_on_sample(center, gain_job, subscriptions):
     """Image next well in existing sample."""
 
     async def send_cam_job(center, event):
@@ -114,7 +115,12 @@ async def send_cam_job(center, event):
         command = cam_com(gain_job, next_well_x, next_well_y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
-        # TODO: Unregister rename image and set img ok.
+        if subscriptions.set_img_ok is not None:
+            subscriptions.set_img_ok()
+            subscriptions.set_img_ok = None
+        if subscriptions.rename_exp_image is not None:
+            subscriptions.rename_exp_image()
+            subscriptions.rename_exp_image = None
 
         await center.actions.command.start_imaging()
         await asyncio.sleep(START_STOP_DELAY)
@@ -124,7 +130,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def image_next_well_on_event(center, gain_job):
+def image_next_well_on_event(center, gain_job, subscriptions):
     """Image next well."""
 
     async def send_cam_job(center, event):
@@ -139,7 +145,12 @@ async def send_cam_job(center, event):
         command = cam_com(gain_job, event.well.x, event.well.y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
-        # TODO: Unregister rename image and set img ok.
+        if subscriptions.set_img_ok is not None:
+            subscriptions.set_img_ok()
+            subscriptions.set_img_ok = None
+        if subscriptions.rename_exp_image is not None:
+            subscriptions.rename_exp_image()
+            subscriptions.rename_exp_image = None
 
         await center.actions.command.start_imaging()
         await asyncio.sleep(START_STOP_DELAY)
@@ -229,7 +240,7 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center, exp_pattern):
+def add_exp_job(center, exp_pattern, subscriptions):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
@@ -250,7 +261,10 @@ async def add_cam_job(center, event):
         await center.actions.command.send(command=del_com())
         await center.actions.command.send_many(commands=commands)
 
-        # TODO: Turn on rename image and set_img_ok during experiment job phase.
+        if subscriptions.set_img_ok is not None:
+            subscriptions.set_img_ok = set_img_ok(center)
+        if subscriptions.rename_exp_image is None:
+            subscriptions.rename_exp_image = rename_exp_image(center)
 
         await center.actions.command.start_imaging()
         await center.actions.command.send(command="/cmd:startcamscan")
@@ -302,7 +316,7 @@ async def rename_image(center, event):
 
         center.actions.rename(old_path=event.path, new_name=new_name)
 
-    center.bus.register("image_event", rename_image)
+    return center.bus.register("image_event", rename_image)
 
 
 def stop_exp(center):

From 66a2c5165251622cd5047c81acf9b00798416dd4 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 16:51:52 +0100
Subject: [PATCH 24/76] Fix action calls after renaming action types

---
 camacqplugins/production/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 880d8ab..8b2b424 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -189,8 +189,7 @@ async def calc_gain(center, event):
             / f"{event.well_x}--{event.well_y}"
         )
 
-        # FIXME: Adjust the action type for plugins.gain to avoid period in the name.
-        await center.actions.plugins.gain.calc_gain(
+        await center.actions.gain.calc_gain(
             plate_name=event.plate_name,
             well_x=event.well_x,
             well_y=event.well_y,
@@ -314,7 +313,7 @@ async def rename_image(center, event):
             f"--Y{event.field_y}--Z{event.z_slice}--C{channel_id}.ome.tif"
         )
 
-        center.actions.rename(old_path=event.path, new_name=new_name)
+        center.actions.rename_image.rename_image(old_path=event.path, new_name=new_name)
 
     return center.bus.register("image_event", rename_image)
 

From 223f1dda4daa52230727b0785b95bb17b99581c5 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 18:53:53 +0100
Subject: [PATCH 25/76] Fix plot save path

---
 camacqplugins/production/__init__.py | 44 ++++++++++++++++++----------
 1 file changed, 28 insertions(+), 16 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 8b2b424..73f636f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -4,6 +4,8 @@
 import tempfile
 from pathlib import Path
 
+import voluptuous as vol
+
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
@@ -14,27 +16,33 @@
 SAMPLE_STATE_FILE = "state_file"
 START_STOP_DELAY = 2.0
 
+CONFIG_SCHEMA = vol.Schema({"plot_save_path": vol.IsDir()}, extra=vol.ALLOW_EXTRA)
+
 
 async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
-    gain_job = conf["gain_job_name"]
+
+    conf = CONFIG_SCHEMA(conf)
+
+    gain_pattern = conf["gain_pattern_name"]
     green_job = conf["green_job_name"]
     blue_yellow_job = conf["blue_yellow_job_name"]
     red_job = conf["red_job_name"]
     exp_pattern = conf["exp_pattern_name"]
+    plot_save_path = conf.get("plot_save_path")
     subscriptions = dotdict()
 
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
     if state_file is not None:
         await load_sample(center, state_file)
-        image_next_well_on_sample(center, gain_job, subscriptions)
+        image_next_well_on_sample(center, gain_pattern, subscriptions)
     else:
         start_exp(center)
         add_next_well(center)
-        image_next_well_on_event(center, gain_job, subscriptions)
+        image_next_well_on_event(center, gain_pattern, subscriptions)
 
-    analyze_gain(center)
+    analyze_gain(center, plot_save_path)
     set_exp_gain(center, green_job, blue_yellow_job, red_job)
     add_exp_job(center, exp_pattern, subscriptions)
     subscriptions.set_img_ok = set_img_ok(center)
@@ -92,7 +100,7 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well_on_sample(center, gain_job, subscriptions):
+def image_next_well_on_sample(center, gain_pattern, subscriptions):
     """Image next well in existing sample."""
 
     async def send_cam_job(center, event):
@@ -110,9 +118,9 @@ async def send_cam_job(center, event):
 
         await center.actions.command.send(command=del_com())
         # TODO: Make field coordinates configurable.
-        command = cam_com(gain_job, next_well_x, next_well_y, 0, 1, 0, 0)
+        command = cam_com(gain_pattern, next_well_x, next_well_y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
-        command = cam_com(gain_job, next_well_x, next_well_y, 1, 1, 0, 0)
+        command = cam_com(gain_pattern, next_well_x, next_well_y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
         if subscriptions.set_img_ok is not None:
@@ -130,7 +138,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def image_next_well_on_event(center, gain_job, subscriptions):
+def image_next_well_on_event(center, gain_pattern, subscriptions):
     """Image next well."""
 
     async def send_cam_job(center, event):
@@ -140,9 +148,9 @@ async def send_cam_job(center, event):
 
         await center.actions.command.send(command=del_com())
         # TODO: Make field coordinates configurable.
-        command = cam_com(gain_job, event.well.x, event.well.y, 0, 1, 0, 0)
+        command = cam_com(gain_pattern, event.well.x, event.well.y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
-        command = cam_com(gain_job, event.well.x, event.well.y, 1, 1, 0, 0)
+        command = cam_com(gain_pattern, event.well.x, event.well.y, 1, 1, 0, 0)
         await center.actions.command.send(command=command)
 
         if subscriptions.set_img_ok is not None:
@@ -159,7 +167,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def analyze_gain(center):
+def analyze_gain(center, save_path):
     """Analyze gain."""
 
     async def calc_gain(center, event):
@@ -182,12 +190,16 @@ async def calc_gain(center, event):
         await center.actions.command.stop_imaging()
         await asyncio.sleep(START_STOP_DELAY)
 
+        nonlocal save_path
+        if save_path is None:
+            save_path = Path(tempfile.gettempdir()) / event.plate_name
+        else:
+            save_path = Path(save_path)
+        if not save_path.exists():
+            await center.add_executor_job(save_path.mkdir)
+
         # This should be a path to a base file name, not to an actual dir or file.
-        save_path = (
-            Path(tempfile.gettempdir())
-            / event.plate_name
-            / f"{event.well_x}--{event.well_y}"
-        )
+        save_path = save_path / f"{event.well_x}--{event.well_y}"
 
         await center.actions.gain.calc_gain(
             plate_name=event.plate_name,

From 6397483fe4ed5ae2b03b590e3bfc5708afa8f3e2 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 20:31:42 +0100
Subject: [PATCH 26/76] Make stop work on state file

---
 camacqplugins/production/__init__.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 73f636f..715b4c1 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -16,6 +16,7 @@
 SAMPLE_STATE_FILE = "state_file"
 START_STOP_DELAY = 2.0
 
+# pylint: disable=no-value-for-parameter
 CONFIG_SCHEMA = vol.Schema({"plot_save_path": vol.IsDir()}, extra=vol.ALLOW_EXTRA)
 
 
@@ -35,11 +36,15 @@ async def setup_module(center, config):
 
     state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
     if state_file is not None:
+        x_wells = None
+        y_wells = None
         await load_sample(center, state_file)
         image_next_well_on_sample(center, gain_pattern, subscriptions)
     else:
+        x_wells = 12
+        y_wells = 8
         start_exp(center)
-        add_next_well(center)
+        add_next_well(center, x_wells, y_wells)
         image_next_well_on_event(center, gain_pattern, subscriptions)
 
     analyze_gain(center, plot_save_path)
@@ -47,7 +52,7 @@ async def setup_module(center, config):
     add_exp_job(center, exp_pattern, subscriptions)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
-    stop_exp(center)
+    stop_exp(center, x_wells, y_wells)
 
 
 async def load_sample(center, state_file):
@@ -70,15 +75,13 @@ async def set_start_well(center, event):
     center.bus.register("camacq_start_event", set_start_well)
 
 
-def add_next_well(center):
+def add_next_well(center, x_wells, y_wells):
     """Add next well."""
 
     async def set_next_well(center, event):
         """Run on well event."""
         # TODO: Make well layout and stop field coordinates configurable.
         plate_name = "00"
-        x_wells = 12
-        y_wells = 8
         next_well_x, _ = next_well_xy(center.sample, plate_name, x_wells, y_wells)
 
         if (
@@ -325,18 +328,20 @@ async def rename_image(center, event):
             f"--Y{event.field_y}--Z{event.z_slice}--C{channel_id}.ome.tif"
         )
 
-        center.actions.rename_image.rename_image(old_path=event.path, new_name=new_name)
+        await center.actions.rename_image.rename_image(
+            old_path=event.path, new_name=new_name
+        )
 
     return center.bus.register("image_event", rename_image)
 
 
-def stop_exp(center):
+def stop_exp(center, x_wells, y_wells):
     """Trigger to stop experiment."""
 
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
         # TODO: Make well layout and stop field coordinates configurable.
-        next_well_x, _ = next_well_xy(center.sample, "00", 12, 8)
+        next_well_x, _ = next_well_xy(center.sample, "00", x_wells, y_wells)
 
         if (
             not match_event(event, field_x=1, field_y=2, well_img_ok=True)

From 93e1a926c34842a37fc7cddad9d79f61ba30f042 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 15 Nov 2019 20:45:09 +0100
Subject: [PATCH 27/76] Add fixme comment

---
 camacqplugins/production/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 715b4c1..629624e 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -52,6 +52,7 @@ async def setup_module(center, config):
     add_exp_job(center, exp_pattern, subscriptions)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
+    # FIXME: Make stop exp work for state file.
     stop_exp(center, x_wells, y_wells)
 
 

From d78115e5bc33136be1d310e2a5e5993d80094bfe Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 16 Nov 2019 15:03:13 +0100
Subject: [PATCH 28/76] Fix set img ok

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 629624e..a45cafa 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -292,7 +292,7 @@ def set_img_ok(center):
 
     async def set_sample_img_ok(center, event):
         """Set sample field img ok."""
-        if not match_event(event, job_id=5):
+        if not match_event(event, job_id=6):
             return
 
         await center.actions.sample.set_field(

From d21b13ff2dcec8a5d603c260f5d13775133eec92 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 16 Nov 2019 15:45:29 +0100
Subject: [PATCH 29/76] Remove start and stop delay

---
 camacqplugins/production/__init__.py | 9 ---------
 1 file changed, 9 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index a45cafa..9a0112d 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -1,5 +1,4 @@
 """Provide a plugin for production standard flow."""
-import asyncio
 import logging
 import tempfile
 from pathlib import Path
@@ -14,7 +13,6 @@
 _LOGGER = logging.getLogger(__name__)
 
 SAMPLE_STATE_FILE = "state_file"
-START_STOP_DELAY = 2.0
 
 # pylint: disable=no-value-for-parameter
 CONFIG_SCHEMA = vol.Schema({"plot_save_path": vol.IsDir()}, extra=vol.ALLOW_EXTRA)
@@ -91,9 +89,7 @@ async def set_next_well(center, event):
         ):
             return
 
-        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.stop_imaging()
-        await asyncio.sleep(2 * START_STOP_DELAY)
 
         well_x, well_y = next_well_xy(center.sample, plate_name, x_wells, y_wells)
 
@@ -135,7 +131,6 @@ async def send_cam_job(center, event):
             subscriptions.rename_exp_image = None
 
         await center.actions.command.start_imaging()
-        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.send(command="/cmd:startcamscan")
 
     center.bus.register("camacq_start_event", send_cam_job)
@@ -165,7 +160,6 @@ async def send_cam_job(center, event):
             subscriptions.rename_exp_image = None
 
         await center.actions.command.start_imaging()
-        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.send(command="/cmd:startcamscan")
 
     center.bus.register("well_event", send_cam_job)
@@ -190,9 +184,7 @@ async def calc_gain(center, event):
         ):
             return
 
-        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.command.stop_imaging()
-        await asyncio.sleep(START_STOP_DELAY)
 
         nonlocal save_path
         if save_path is None:
@@ -351,7 +343,6 @@ async def stop_imaging(center, event):
             return
 
         # Sleep to let images be completely scanned before stopping.
-        await asyncio.sleep(START_STOP_DELAY)
         await center.actions.api.stop_imaging()
 
     center.bus.register("well_event", stop_imaging)

From cbd3d333c1071558339a91689649a2e029249855 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 16 Nov 2019 16:33:26 +0100
Subject: [PATCH 30/76] Extend config schema

---
 camacqplugins/production/__init__.py | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 9a0112d..0ae2ac9 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -15,15 +15,22 @@
 SAMPLE_STATE_FILE = "state_file"
 
 # pylint: disable=no-value-for-parameter
-CONFIG_SCHEMA = vol.Schema({"plot_save_path": vol.IsDir()}, extra=vol.ALLOW_EXTRA)
+CONFIG_SCHEMA = vol.Schema(
+    {
+        vol.Required("gain_pattern_name"): vol.Coerce(str),
+        vol.Required("green_job_name"): vol.Coerce(str),
+        vol.Required("blue_yellow_job_name"): vol.Coerce(str),
+        vol.Required("red_job_name"): vol.Coerce(str),
+        vol.Required("exp_pattern_name"): vol.Coerce(str),
+        "plot_save_path": vol.IsDir(),
+    },
+    extra=vol.ALLOW_EXTRA,
+)
 
 
 async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
-
-    conf = CONFIG_SCHEMA(conf)
-
     gain_pattern = conf["gain_pattern_name"]
     green_job = conf["green_job_name"]
     blue_yellow_job = conf["blue_yellow_job_name"]

From b50643d70af5a7436bf6fdc48e26e5eb5e3e81fe Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 17 Nov 2019 14:44:39 +0100
Subject: [PATCH 31/76] Update readme

---
 README.md | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/README.md b/README.md
index 1309904..2970a9f 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,36 @@ Plugins for camacq
 
 ## Usage
 
+To allow the user to set up the sample state before starting an
+experiment, camacq can load the sample state from a file. In the production
+configuration section there is an option to specify a path to a csv
+file.
+
+```yaml
+production:
+  state_file: '/sample_state.csv'
+```
+
+Each row in the csv file should represent a state of a sample container,
+ie plate, well, field or channel. The csv file should also have a
+header. See below.
+
+```
+plate_name,well_x,well_y,channel_name,gain
+00,1,1,blue,600
+```
+
+This example will set create a plate '00', a well (1, 1), a blue channel
+and set the gain of the blue channel to 600.
+
+```
+plate_name,well_x,well_y,field_x,field_y
+00,1,1,1,1
+```
+
+This example will create a plate '00' a well (1, 1) and a field (1, 1)
+in the sample state.
+
 ## Installation
 
 ### Requirements

From 64f32833caec045a56a87546a8be0db3b14bb18f Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 17 Nov 2019 15:16:19 +0100
Subject: [PATCH 32/76] Add channels config

---
 camacqplugins/production/__init__.py | 57 +++++++++++++---------------
 1 file changed, 26 insertions(+), 31 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 0ae2ac9..5e7d9fd 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -18,13 +18,19 @@
 CONFIG_SCHEMA = vol.Schema(
     {
         vol.Required("gain_pattern_name"): vol.Coerce(str),
-        vol.Required("green_job_name"): vol.Coerce(str),
-        vol.Required("blue_yellow_job_name"): vol.Coerce(str),
-        vol.Required("red_job_name"): vol.Coerce(str),
         vol.Required("exp_pattern_name"): vol.Coerce(str),
+        vol.Required("channels"): [
+            {
+                vol.Required("channel"): vol.Coerce(str),
+                vol.Required("job_name"): vol.Coerce(str),
+                vol.Required("detector_num"): vol.Coerce(int),
+                vol.Required("default_gain"): vol.Coerce(int),
+                vol.Required("max_gain"): vol.Coerce(int),
+            }
+        ],
         "plot_save_path": vol.IsDir(),
+        SAMPLE_STATE_FILE: vol.IsFile(),
     },
-    extra=vol.ALLOW_EXTRA,
 )
 
 
@@ -32,14 +38,12 @@ async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
     gain_pattern = conf["gain_pattern_name"]
-    green_job = conf["green_job_name"]
-    blue_yellow_job = conf["blue_yellow_job_name"]
-    red_job = conf["red_job_name"]
     exp_pattern = conf["exp_pattern_name"]
+    channels = conf["channels"]
     plot_save_path = conf.get("plot_save_path")
     subscriptions = dotdict()
 
-    state_file = conf.get(SAMPLE_STATE_FILE) if conf else None
+    state_file = conf.get(SAMPLE_STATE_FILE)
     if state_file is not None:
         x_wells = None
         y_wells = None
@@ -53,8 +57,8 @@ async def setup_module(center, config):
         image_next_well_on_event(center, gain_pattern, subscriptions)
 
     analyze_gain(center, plot_save_path)
-    set_exp_gain(center, green_job, blue_yellow_job, red_job)
-    add_exp_job(center, exp_pattern, subscriptions)
+    set_exp_gain(center, channels)
+    add_exp_job(center, channels, exp_pattern, subscriptions)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
     # FIXME: Make stop exp work for state file.
@@ -215,28 +219,17 @@ async def calc_gain(center, event):
     center.bus.register("image_event", calc_gain)
 
 
-def set_exp_gain(center, green_job, blue_yellow_job, red_job):
+def set_exp_gain(center, channels):
     """Set experiment gain."""
 
     async def set_gain(center, event):
         """Set pmt gain."""
-        if event.channel_name == "green":
-            exp = green_job
-            num = 1
-            gain = min(event.gain or 800, 800)
-        elif event.channel_name == "blue":
-            exp = blue_yellow_job
-            num = 1
-            gain = min(event.gain or 505, 610)
-        elif event.channel_name == "yellow":
-            exp = blue_yellow_job
-            num = 2
-            gain = min(event.gain or 655, 760)
-        elif event.channel_name == "red":
-            exp = red_job
-            num = 2
-            gain = event.gain or 630
-            gain = min(gain + 25, 735)
+        for channel in channels:
+            if event.channel_name != channel["channel"]:
+                continue
+            exp = channel["job_name"]
+            num = channel["detector_num"]
+            gain = min(event.gain or channel["default_gain"], channel["max_gain"])
 
         command = gain_com(exp=exp, num=num, value=gain)
 
@@ -254,13 +247,15 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center, exp_pattern, subscriptions):
+def add_exp_job(center, channels, exp_pattern, subscriptions):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
         """Add an experiment job to the cam list."""
-        # TODO: Make channels layout configurable.
-        if not match_event(event, channel_name="red") or len(event.well.channels) != 4:
+        last_channel = channels[-1]
+        if not match_event(event, channel_name=last_channel["channel"]) or len(
+            event.well.channels
+        ) != len(channels):
             return
 
         # TODO: Make well layout configurable.

From 542895c584c58f367e98c237d43ae03eb30da2ec Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 17 Nov 2019 15:19:13 +0100
Subject: [PATCH 33/76] Add todo comment

---
 camacqplugins/production/__init__.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 5e7d9fd..7ba6791 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -303,6 +303,7 @@ async def set_sample_img_ok(center, event):
 
 def rename_exp_image(center):
     """Rename an experiment image."""
+    # TODO: Make experiment pattern job_ids configurable.
 
     async def rename_image(center, event):
         """Rename an image."""

From ee927b34754a68e5c6125df60a20a8e0e5854e9e Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 17 Nov 2019 15:48:45 +0100
Subject: [PATCH 34/76] Add well layout option

---
 camacqplugins/production/__init__.py | 57 ++++++++++++++++++----------
 1 file changed, 37 insertions(+), 20 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 7ba6791..ffe441f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -28,6 +28,10 @@
                 vol.Required("max_gain"): vol.Coerce(int),
             }
         ],
+        vol.Required("well_layout"): {
+            vol.Required("x_fields"): vol.Coerce(int),
+            vol.Required("y_fields"): vol.Coerce(int),
+        },
         "plot_save_path": vol.IsDir(),
         SAMPLE_STATE_FILE: vol.IsFile(),
     },
@@ -40,6 +44,7 @@ async def setup_module(center, config):
     gain_pattern = conf["gain_pattern_name"]
     exp_pattern = conf["exp_pattern_name"]
     channels = conf["channels"]
+    well_layout = conf["well_layout"]
     plot_save_path = conf.get("plot_save_path")
     subscriptions = dotdict()
 
@@ -48,21 +53,21 @@ async def setup_module(center, config):
         x_wells = None
         y_wells = None
         await load_sample(center, state_file)
-        image_next_well_on_sample(center, gain_pattern, subscriptions)
+        image_next_well_on_sample(center, gain_pattern, subscriptions, well_layout)
     else:
         x_wells = 12
         y_wells = 8
         start_exp(center)
-        add_next_well(center, x_wells, y_wells)
+        add_next_well(center, x_wells, y_wells, well_layout)
         image_next_well_on_event(center, gain_pattern, subscriptions)
 
     analyze_gain(center, plot_save_path)
     set_exp_gain(center, channels)
-    add_exp_job(center, channels, exp_pattern, subscriptions)
+    add_exp_job(center, channels, exp_pattern, subscriptions, well_layout)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
     # FIXME: Make stop exp work for state file.
-    stop_exp(center, x_wells, y_wells)
+    stop_exp(center, x_wells, y_wells, well_layout)
 
 
 async def load_sample(center, state_file):
@@ -85,17 +90,21 @@ async def set_start_well(center, event):
     center.bus.register("camacq_start_event", set_start_well)
 
 
-def add_next_well(center, x_wells, y_wells):
+def add_next_well(center, x_wells, y_wells, well_layout):
     """Add next well."""
 
     async def set_next_well(center, event):
         """Run on well event."""
-        # TODO: Make well layout and stop field coordinates configurable.
         plate_name = "00"
         next_well_x, _ = next_well_xy(center.sample, plate_name, x_wells, y_wells)
 
         if (
-            not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            not match_event(
+                event,
+                field_x=well_layout["x_fields"] - 1,
+                field_y=well_layout["y_fields"] - 1,
+                well_img_ok=True,
+            )
             or next_well_x is None
         ):
             return
@@ -111,24 +120,28 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well_on_sample(center, gain_pattern, subscriptions):
+def image_next_well_on_sample(center, gain_pattern, subscriptions, well_layout):
     """Image next well in existing sample."""
 
     async def send_cam_job(center, event):
         """Run on well event."""
-        # TODO: Make stop field coordinates configurable.
         plate_name = "00"
         next_well_x, next_well_y = next_well_xy(center.sample, plate_name)
 
         if (
             not match_event(event, event_type="camacq_start_event")
-            and not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            and not match_event(
+                event,
+                field_x=well_layout["x_fields"] - 1,
+                field_y=well_layout["y_fields"] - 1,
+                well_img_ok=True,
+            )
             or next_well_x is None
         ):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make field coordinates configurable.
+        # TODO: Make field coordinates for gain job configurable.
         command = cam_com(gain_pattern, next_well_x, next_well_y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
         command = cam_com(gain_pattern, next_well_x, next_well_y, 1, 1, 0, 0)
@@ -157,7 +170,7 @@ async def send_cam_job(center, event):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make field coordinates configurable.
+        # TODO: Make field coordinates for gain job configurable.
         command = cam_com(gain_pattern, event.well.x, event.well.y, 0, 1, 0, 0)
         await center.actions.command.send(command=command)
         command = cam_com(gain_pattern, event.well.x, event.well.y, 1, 1, 0, 0)
@@ -181,7 +194,8 @@ def analyze_gain(center, save_path):
 
     async def calc_gain(center, event):
         """Calculate correct gain."""
-        # TODO: Make event field coordinates, job id and save_path configurable.
+        # TODO: Make last gain image field coordinates, job id
+        # and save_path configurable.
         field_x = 1
         field_y = 1
         job_id = 3
@@ -247,7 +261,7 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center, channels, exp_pattern, subscriptions):
+def add_exp_job(center, channels, exp_pattern, subscriptions, well_layout):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
@@ -258,10 +272,9 @@ async def add_cam_job(center, event):
         ) != len(channels):
             return
 
-        # TODO: Make well layout configurable.
         commands = []
-        for field_x in range(2):
-            for field_y in range(3):
+        for field_x in range(well_layout["x_fields"]):
+            for field_y in range(well_layout["y_fields"]):
                 cmd = cam_com(
                     exp_pattern, event.well_x, event.well_y, field_x, field_y, 0, 0
                 )
@@ -331,16 +344,20 @@ async def rename_image(center, event):
     return center.bus.register("image_event", rename_image)
 
 
-def stop_exp(center, x_wells, y_wells):
+def stop_exp(center, x_wells, y_wells, well_layout):
     """Trigger to stop experiment."""
 
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
-        # TODO: Make well layout and stop field coordinates configurable.
         next_well_x, _ = next_well_xy(center.sample, "00", x_wells, y_wells)
 
         if (
-            not match_event(event, field_x=1, field_y=2, well_img_ok=True)
+            not match_event(
+                event,
+                field_x=well_layout["x_fields"] - 1,
+                field_y=well_layout["y_fields"] - 1,
+                well_img_ok=True,
+            )
             or next_well_x is not None
         ):
             return

From 57b8ea5cedf56234fe50deb1d6d8f99798bcfa99 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 17 Nov 2019 15:49:36 +0100
Subject: [PATCH 35/76] Clean up

---
 camacqplugins/production/__init__.py | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index ffe441f..acc15d7 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -14,7 +14,6 @@
 
 SAMPLE_STATE_FILE = "state_file"
 
-# pylint: disable=no-value-for-parameter
 CONFIG_SCHEMA = vol.Schema(
     {
         vol.Required("gain_pattern_name"): vol.Coerce(str),
@@ -32,6 +31,7 @@
             vol.Required("x_fields"): vol.Coerce(int),
             vol.Required("y_fields"): vol.Coerce(int),
         },
+        # pylint: disable=no-value-for-parameter
         "plot_save_path": vol.IsDir(),
         SAMPLE_STATE_FILE: vol.IsFile(),
     },
@@ -362,7 +362,6 @@ async def stop_imaging(center, event):
         ):
             return
 
-        # Sleep to let images be completely scanned before stopping.
         await center.actions.api.stop_imaging()
 
     center.bus.register("well_event", stop_imaging)

From 460744ac412f9df652f5129d43334b76d11ffef5 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 29 Nov 2019 17:44:48 +0100
Subject: [PATCH 36/76] Guard against duplicate image events

---
 camacqplugins/production/__init__.py | 56 +++++++++++++++++-----------
 1 file changed, 34 insertions(+), 22 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index acc15d7..b585a9f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -1,4 +1,5 @@
 """Provide a plugin for production standard flow."""
+import asyncio
 import logging
 import tempfile
 from pathlib import Path
@@ -61,7 +62,7 @@ async def setup_module(center, config):
         add_next_well(center, x_wells, y_wells, well_layout)
         image_next_well_on_event(center, gain_pattern, subscriptions)
 
-    analyze_gain(center, plot_save_path)
+    analyze_gain(center, plot_save_path, asyncio.Lock())
     set_exp_gain(center, channels)
     add_exp_job(center, channels, exp_pattern, subscriptions, well_layout)
     subscriptions.set_img_ok = set_img_ok(center)
@@ -189,7 +190,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def analyze_gain(center, save_path):
+def analyze_gain(center, save_path, gain_lock):
     """Analyze gain."""
 
     async def calc_gain(center, event):
@@ -209,26 +210,37 @@ async def calc_gain(center, event):
         ):
             return
 
-        await center.actions.command.stop_imaging()
-
-        nonlocal save_path
-        if save_path is None:
-            save_path = Path(tempfile.gettempdir()) / event.plate_name
-        else:
-            save_path = Path(save_path)
-        if not save_path.exists():
-            await center.add_executor_job(save_path.mkdir)
-
-        # This should be a path to a base file name, not to an actual dir or file.
-        save_path = save_path / f"{event.well_x}--{event.well_y}"
-
-        await center.actions.gain.calc_gain(
-            plate_name=event.plate_name,
-            well_x=event.well_x,
-            well_y=event.well_y,
-            make_plots=True,
-            save_path=save_path,
-        )
+        # Guard against duplicate image events.
+        async with gain_lock:
+            well = center.sample.get_well(
+                plate_name=event.plate_name, well_x=event.well_x, well_y=event.well_y
+            )
+            gain_set = any(
+                channel.gain is not None for channel in well.channels.values()
+            )
+            if gain_set:
+                return
+
+            await center.actions.command.stop_imaging()
+
+            nonlocal save_path
+            if save_path is None:
+                save_path = Path(tempfile.gettempdir()) / event.plate_name
+            else:
+                save_path = Path(save_path)
+            if not save_path.exists():
+                await center.add_executor_job(save_path.mkdir)
+
+            # This should be a path to a base file name, not to an actual dir or file.
+            save_path = save_path / f"{event.well_x}--{event.well_y}"
+
+            await center.actions.gain.calc_gain(
+                plate_name=event.plate_name,
+                well_x=event.well_x,
+                well_y=event.well_y,
+                make_plots=True,
+                save_path=save_path,
+            )
 
     center.bus.register("image_event", calc_gain)
 

From 44db2d36f0b2acc723f0be79a3c66dc39637f317 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 29 Nov 2019 19:21:29 +0100
Subject: [PATCH 37/76] Add debug script

---
 scripts/debug.py | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 scripts/debug.py

diff --git a/scripts/debug.py b/scripts/debug.py
new file mode 100644
index 0000000..3a4ff8c
--- /dev/null
+++ b/scripts/debug.py
@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+"""Start camacq to debug in vscode."""
+from camacq.__main__ import main
+
+
+if __name__ == "__main__":
+    main(args=["--log-level", "debug"])

From 4d213d6cb118873898e84586c07dc7ec56b6a384 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 29 Nov 2019 19:23:57 +0100
Subject: [PATCH 38/76] Fix stop experiment

---
 camacqplugins/production/__init__.py | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index b585a9f..7fb5294 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -67,7 +67,6 @@ async def setup_module(center, config):
     add_exp_job(center, channels, exp_pattern, subscriptions, well_layout)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
-    # FIXME: Make stop exp work for state file.
     stop_exp(center, x_wells, y_wells, well_layout)
 
 
@@ -295,7 +294,7 @@ async def add_cam_job(center, event):
         await center.actions.command.send(command=del_com())
         await center.actions.command.send_many(commands=commands)
 
-        if subscriptions.set_img_ok is not None:
+        if subscriptions.set_img_ok is None:
             subscriptions.set_img_ok = set_img_ok(center)
         if subscriptions.rename_exp_image is None:
             subscriptions.rename_exp_image = rename_exp_image(center)
@@ -362,18 +361,16 @@ def stop_exp(center, x_wells, y_wells, well_layout):
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
         next_well_x, _ = next_well_xy(center.sample, "00", x_wells, y_wells)
+        match = match_event(
+            event,
+            field_x=well_layout["x_fields"] - 1,
+            field_y=well_layout["y_fields"] - 1,
+            well_img_ok=True,
+        )
 
-        if (
-            not match_event(
-                event,
-                field_x=well_layout["x_fields"] - 1,
-                field_y=well_layout["y_fields"] - 1,
-                well_img_ok=True,
-            )
-            or next_well_x is not None
-        ):
+        if not match or next_well_x is not None:
             return
 
-        await center.actions.api.stop_imaging()
+        await center.actions.command.stop_imaging()
 
     center.bus.register("well_event", stop_imaging)

From d5d3f522b9414202e5f7d27168216b0b8d84183f Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 29 Nov 2019 20:31:24 +0100
Subject: [PATCH 39/76] Add production config template

---
 config_templates/production.yml | 56 +++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 config_templates/production.yml

diff --git a/config_templates/production.yml b/config_templates/production.yml
new file mode 100644
index 0000000..8d55429
--- /dev/null
+++ b/config_templates/production.yml
@@ -0,0 +1,56 @@
+production:
+  #state_file: "/path/to/sample_state.csv"
+  gain_pattern_name: p10xgain
+  exp_pattern_name: p10xexp
+  channels:
+  - channel: green
+    job_name: green10x
+    detector_num: 1
+    default_gain: 800
+    max_gain: 800
+  - channel: blue
+    job_name: blue10x
+    detector_num: 1
+    default_gain: 505
+    max_gain: 610
+  - channel: yellow
+    job_name: blue10x
+    detector_num: 2
+    default_gain: 655
+    max_gain: 760
+  - channel: red
+    job_name: red10x
+    detector_num: 2
+    default_gain: 630
+    max_gain: 735
+  well_layout:
+    x_fields: 2
+    y_fields: 3
+  #plot_save_path: "/path/to/gains/dir/00/"
+
+  gain:
+    channels:
+    - channel: green
+      init_gain: [450, 495, 540, 585, 630, 675, 720, 765, 810, 855, 900]
+    - channel: blue
+      # 63x
+      #init_gain: [750, 730, 765, 800, 835, 870, 905]
+      # 10x
+      init_gain: [700, 735, 770, 805, 840, 875, 910]
+    - channel: yellow
+      # 63x
+      #init_gain: [550, 585, 620, 655, 690, 725, 760]
+      # 10x
+      init_gain: [700, 735, 770, 805, 840, 875, 910]
+    - channel: red
+      # 63x
+      #init_gain: [525, 560, 595, 630, 665, 700, 735]
+      # 10x
+      init_gain: [600, 635, 670, 705, 740, 775, 810]
+    #save_dir: "/path/to/gains/dir"
+
+rename_image:
+
+leica:
+  host: localhost
+  #imaging_dir: '/path/to/imaging_dir'

From 51f1bb5be6e9ba4668de258518c9d9be661b1503 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 13:56:00 +0100
Subject: [PATCH 40/76] Set gain fields from well layout

---
 camacqplugins/production/__init__.py | 72 +++++++++++++++-------------
 1 file changed, 38 insertions(+), 34 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 7fb5294..b965704 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -2,6 +2,7 @@
 import asyncio
 import logging
 import tempfile
+from math import ceil
 from pathlib import Path
 
 import voluptuous as vol
@@ -46,6 +47,8 @@ async def setup_module(center, config):
     exp_pattern = conf["exp_pattern_name"]
     channels = conf["channels"]
     well_layout = conf["well_layout"]
+    x_fields = well_layout["x_fields"]
+    y_fields = well_layout["y_fields"]
     plot_save_path = conf.get("plot_save_path")
     subscriptions = dotdict()
 
@@ -54,20 +57,24 @@ async def setup_module(center, config):
         x_wells = None
         y_wells = None
         await load_sample(center, state_file)
-        image_next_well_on_sample(center, gain_pattern, subscriptions, well_layout)
+        image_next_well_on_sample(
+            center, gain_pattern, subscriptions, x_fields, y_fields
+        )
     else:
         x_wells = 12
         y_wells = 8
         start_exp(center)
-        add_next_well(center, x_wells, y_wells, well_layout)
-        image_next_well_on_event(center, gain_pattern, subscriptions)
+        add_next_well(center, x_wells, y_wells, x_fields, y_fields)
+        image_next_well_on_event(
+            center, gain_pattern, subscriptions, x_fields, y_fields
+        )
 
     analyze_gain(center, plot_save_path, asyncio.Lock())
     set_exp_gain(center, channels)
-    add_exp_job(center, channels, exp_pattern, subscriptions, well_layout)
+    add_exp_job(center, channels, exp_pattern, subscriptions, x_fields, y_fields)
     subscriptions.set_img_ok = set_img_ok(center)
     subscriptions.rename_exp_image = rename_exp_image(center)
-    stop_exp(center, x_wells, y_wells, well_layout)
+    stop_exp(center, x_wells, y_wells, x_fields, y_fields)
 
 
 async def load_sample(center, state_file):
@@ -90,7 +97,7 @@ async def set_start_well(center, event):
     center.bus.register("camacq_start_event", set_start_well)
 
 
-def add_next_well(center, x_wells, y_wells, well_layout):
+def add_next_well(center, x_wells, y_wells, x_fields, y_fields):
     """Add next well."""
 
     async def set_next_well(center, event):
@@ -100,10 +107,7 @@ async def set_next_well(center, event):
 
         if (
             not match_event(
-                event,
-                field_x=well_layout["x_fields"] - 1,
-                field_y=well_layout["y_fields"] - 1,
-                well_img_ok=True,
+                event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
             )
             or next_well_x is None
         ):
@@ -120,7 +124,7 @@ async def set_next_well(center, event):
     center.bus.register("well_event", set_next_well)
 
 
-def image_next_well_on_sample(center, gain_pattern, subscriptions, well_layout):
+def image_next_well_on_sample(center, gain_pattern, subscriptions, x_fields, y_fields):
     """Image next well in existing sample."""
 
     async def send_cam_job(center, event):
@@ -131,21 +135,21 @@ async def send_cam_job(center, event):
         if (
             not match_event(event, event_type="camacq_start_event")
             and not match_event(
-                event,
-                field_x=well_layout["x_fields"] - 1,
-                field_y=well_layout["y_fields"] - 1,
-                well_img_ok=True,
+                event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
             )
             or next_well_x is None
         ):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make field coordinates for gain job configurable.
-        command = cam_com(gain_pattern, next_well_x, next_well_y, 0, 1, 0, 0)
-        await center.actions.command.send(command=command)
-        command = cam_com(gain_pattern, next_well_x, next_well_y, 1, 1, 0, 0)
-        await center.actions.command.send(command=command)
+
+        gain_x_field = ceil(x_fields / 2) - 1
+        field_y = ceil(y_fields / 2) - 1
+        for field_x in range(gain_x_field, gain_x_field + 2):
+            command = cam_com(
+                gain_pattern, next_well_x, next_well_y, field_x, field_y, 0, 0
+            )
+            await center.actions.command.send(command=command)
 
         if subscriptions.set_img_ok is not None:
             subscriptions.set_img_ok()
@@ -161,7 +165,7 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def image_next_well_on_event(center, gain_pattern, subscriptions):
+def image_next_well_on_event(center, gain_pattern, subscriptions, x_fields, y_fields):
     """Image next well."""
 
     async def send_cam_job(center, event):
@@ -170,11 +174,14 @@ async def send_cam_job(center, event):
             return
 
         await center.actions.command.send(command=del_com())
-        # TODO: Make field coordinates for gain job configurable.
-        command = cam_com(gain_pattern, event.well.x, event.well.y, 0, 1, 0, 0)
-        await center.actions.command.send(command=command)
-        command = cam_com(gain_pattern, event.well.x, event.well.y, 1, 1, 0, 0)
-        await center.actions.command.send(command=command)
+
+        gain_x_field = ceil(x_fields / 2) - 1
+        field_y = ceil(y_fields / 2) - 1
+        for field_x in range(gain_x_field, gain_x_field + 2):
+            command = cam_com(
+                gain_pattern, event.well.x, event.well.y, field_x, field_y, 0, 0
+            )
+            await center.actions.command.send(command=command)
 
         if subscriptions.set_img_ok is not None:
             subscriptions.set_img_ok()
@@ -272,7 +279,7 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center, channels, exp_pattern, subscriptions, well_layout):
+def add_exp_job(center, channels, exp_pattern, subscriptions, x_fields, y_fields):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
@@ -284,8 +291,8 @@ async def add_cam_job(center, event):
             return
 
         commands = []
-        for field_x in range(well_layout["x_fields"]):
-            for field_y in range(well_layout["y_fields"]):
+        for field_x in range(x_fields):
+            for field_y in range(y_fields):
                 cmd = cam_com(
                     exp_pattern, event.well_x, event.well_y, field_x, field_y, 0, 0
                 )
@@ -355,17 +362,14 @@ async def rename_image(center, event):
     return center.bus.register("image_event", rename_image)
 
 
-def stop_exp(center, x_wells, y_wells, well_layout):
+def stop_exp(center, x_wells, y_wells, x_fields, y_fields):
     """Trigger to stop experiment."""
 
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
         next_well_x, _ = next_well_xy(center.sample, "00", x_wells, y_wells)
         match = match_event(
-            event,
-            field_x=well_layout["x_fields"] - 1,
-            field_y=well_layout["y_fields"] - 1,
-            well_img_ok=True,
+            event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
         )
 
         if not match or next_well_x is not None:

From 8e28e82ba4b02b585eebbe31f5c60a811c10c8cb Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 14:50:06 +0100
Subject: [PATCH 41/76] Set last gain coordinate from well layout

---
 camacqplugins/production/__init__.py | 100 +++++++++++++++------------
 1 file changed, 56 insertions(+), 44 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index b965704..0f7fd4d 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -69,7 +69,7 @@ async def setup_module(center, config):
             center, gain_pattern, subscriptions, x_fields, y_fields
         )
 
-    analyze_gain(center, plot_save_path, asyncio.Lock())
+    analyze_gain(center, plot_save_path, asyncio.Lock(), x_fields, y_fields)
     set_exp_gain(center, channels)
     add_exp_job(center, channels, exp_pattern, subscriptions, x_fields, y_fields)
     subscriptions.set_img_ok = set_img_ok(center)
@@ -141,25 +141,15 @@ async def send_cam_job(center, event):
         ):
             return
 
-        await center.actions.command.send(command=del_com())
-
-        gain_x_field = ceil(x_fields / 2) - 1
-        field_y = ceil(y_fields / 2) - 1
-        for field_x in range(gain_x_field, gain_x_field + 2):
-            command = cam_com(
-                gain_pattern, next_well_x, next_well_y, field_x, field_y, 0, 0
-            )
-            await center.actions.command.send(command=command)
-
-        if subscriptions.set_img_ok is not None:
-            subscriptions.set_img_ok()
-            subscriptions.set_img_ok = None
-        if subscriptions.rename_exp_image is not None:
-            subscriptions.rename_exp_image()
-            subscriptions.rename_exp_image = None
-
-        await center.actions.command.start_imaging()
-        await center.actions.command.send(command="/cmd:startcamscan")
+        await send_gain_jobs(
+            center,
+            gain_pattern,
+            next_well_x,
+            next_well_y,
+            x_fields,
+            y_fields,
+            subscriptions,
+        )
 
     center.bus.register("camacq_start_event", send_cam_job)
     center.bus.register("well_event", send_cam_job)
@@ -173,38 +163,26 @@ async def send_cam_job(center, event):
         if event.well.images:
             return
 
-        await center.actions.command.send(command=del_com())
-
-        gain_x_field = ceil(x_fields / 2) - 1
-        field_y = ceil(y_fields / 2) - 1
-        for field_x in range(gain_x_field, gain_x_field + 2):
-            command = cam_com(
-                gain_pattern, event.well.x, event.well.y, field_x, field_y, 0, 0
-            )
-            await center.actions.command.send(command=command)
-
-        if subscriptions.set_img_ok is not None:
-            subscriptions.set_img_ok()
-            subscriptions.set_img_ok = None
-        if subscriptions.rename_exp_image is not None:
-            subscriptions.rename_exp_image()
-            subscriptions.rename_exp_image = None
-
-        await center.actions.command.start_imaging()
-        await center.actions.command.send(command="/cmd:startcamscan")
+        await send_gain_jobs(
+            center,
+            gain_pattern,
+            event.well.x,
+            event.well.y,
+            x_fields,
+            y_fields,
+            subscriptions,
+        )
 
     center.bus.register("well_event", send_cam_job)
 
 
-def analyze_gain(center, save_path, gain_lock):
+def analyze_gain(center, save_path, gain_lock, x_fields, y_fields):
     """Analyze gain."""
 
     async def calc_gain(center, event):
         """Calculate correct gain."""
-        # TODO: Make last gain image field coordinates, job id
-        # and save_path configurable.
-        field_x = 1
-        field_y = 1
+        # TODO: Make job id and channel id configurable.
+        field_x, field_y = get_last_gain_coords(x_fields, y_fields)
         job_id = 3
         channel_id = 31
         if not match_event(
@@ -378,3 +356,37 @@ async def stop_imaging(center, event):
         await center.actions.command.stop_imaging()
 
     center.bus.register("well_event", stop_imaging)
+
+
+def get_last_gain_coords(x_fields, y_fields):
+    """Return a tuple with last gain coordinates x and y.
+
+    The gain coordinates will be the two most centered fields.
+    """
+    last_x_field = ceil(x_fields / 2)
+    last_y_field = ceil(y_fields / 2) - 1
+    return last_x_field, last_y_field
+
+
+async def send_gain_jobs(
+    center, gain_job, well_x, well_y, x_fields, y_fields, subscriptions
+):
+    """Send gain cam jobs for the center fields of a well."""
+    field_x, field_y = get_last_gain_coords(x_fields, y_fields)
+    field_x = field_x - 1  # set the start x field coord
+
+    await center.actions.command.send(command=del_com())
+
+    for field_x in range(field_x, field_x + 2):
+        command = cam_com(gain_job, well_x, well_y, field_x, field_y, 0, 0)
+        await center.actions.command.send(command=command)
+
+    if subscriptions.set_img_ok is not None:
+        subscriptions.set_img_ok()
+        subscriptions.set_img_ok = None
+    if subscriptions.rename_exp_image is not None:
+        subscriptions.rename_exp_image()
+        subscriptions.rename_exp_image = None
+
+    await center.actions.command.start_imaging()
+    await center.actions.command.send(command="/cmd:startcamscan")

From d4070e86c68b2adedf5a70eb9f19b0b7e799b5f9 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 15:17:03 +0100
Subject: [PATCH 42/76] Make job ids configurable

---
 camacqplugins/production/__init__.py | 55 +++++++++++++++++++---------
 config_templates/production.yml      |  6 +++
 2 files changed, 43 insertions(+), 18 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 0f7fd4d..6386782 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -19,7 +19,12 @@
 CONFIG_SCHEMA = vol.Schema(
     {
         vol.Required("gain_pattern_name"): vol.Coerce(str),
+        vol.Required("gain_job_id"): vol.Coerce(int),
+        vol.Required("gain_job_channels"): vol.Coerce(int),
         vol.Required("exp_pattern_name"): vol.Coerce(str),
+        vol.Required("exp_job_ids"): vol.All(
+            [vol.Coerce(int)], vol.Length(min=3, max=3)
+        ),
         vol.Required("channels"): [
             {
                 vol.Required("channel"): vol.Coerce(str),
@@ -44,7 +49,10 @@ async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
     gain_pattern = conf["gain_pattern_name"]
+    gain_job_id = conf["gain_job_id"]
+    gain_job_channels = conf["gain_job_channels"]
     exp_pattern = conf["exp_pattern_name"]
+    exp_job_ids = conf["exp_job_ids"]
     channels = conf["channels"]
     well_layout = conf["well_layout"]
     x_fields = well_layout["x_fields"]
@@ -69,11 +77,21 @@ async def setup_module(center, config):
             center, gain_pattern, subscriptions, x_fields, y_fields
         )
 
-    analyze_gain(center, plot_save_path, asyncio.Lock(), x_fields, y_fields)
+    analyze_gain(
+        center,
+        plot_save_path,
+        asyncio.Lock(),
+        x_fields,
+        y_fields,
+        gain_job_id,
+        gain_job_channels,
+    )
     set_exp_gain(center, channels)
-    add_exp_job(center, channels, exp_pattern, subscriptions, x_fields, y_fields)
+    add_exp_job(
+        center, channels, exp_pattern, subscriptions, x_fields, y_fields, exp_job_ids
+    )
     subscriptions.set_img_ok = set_img_ok(center)
-    subscriptions.rename_exp_image = rename_exp_image(center)
+    subscriptions.rename_exp_image = rename_exp_image(center, exp_job_ids)
     stop_exp(center, x_wells, y_wells, x_fields, y_fields)
 
 
@@ -176,20 +194,20 @@ async def send_cam_job(center, event):
     center.bus.register("well_event", send_cam_job)
 
 
-def analyze_gain(center, save_path, gain_lock, x_fields, y_fields):
+def analyze_gain(
+    center, save_path, gain_lock, x_fields, y_fields, gain_job_id, gain_job_channels
+):
     """Analyze gain."""
 
     async def calc_gain(center, event):
         """Calculate correct gain."""
-        # TODO: Make job id and channel id configurable.
         field_x, field_y = get_last_gain_coords(x_fields, y_fields)
-        job_id = 3
-        channel_id = 31
+        channel_id = gain_job_channels - 1
         if not match_event(
             event,
             field_x=field_x,
             field_y=field_y,
-            job_id=job_id,
+            job_id=gain_job_id,
             channel_id=channel_id,
         ):
             return
@@ -257,7 +275,9 @@ async def set_gain(center, event):
     center.bus.register("gain_calc_event", set_gain)
 
 
-def add_exp_job(center, channels, exp_pattern, subscriptions, x_fields, y_fields):
+def add_exp_job(
+    center, channels, exp_pattern, subscriptions, x_fields, y_fields, exp_job_ids
+):
     """Add experiment job."""
 
     async def add_cam_job(center, event):
@@ -282,7 +302,7 @@ async def add_cam_job(center, event):
         if subscriptions.set_img_ok is None:
             subscriptions.set_img_ok = set_img_ok(center)
         if subscriptions.rename_exp_image is None:
-            subscriptions.rename_exp_image = rename_exp_image(center)
+            subscriptions.rename_exp_image = rename_exp_image(center, exp_job_ids)
 
         await center.actions.command.start_imaging()
         await center.actions.command.send(command="/cmd:startcamscan")
@@ -310,22 +330,21 @@ async def set_sample_img_ok(center, event):
     return center.bus.register("image_event", set_sample_img_ok)
 
 
-def rename_exp_image(center):
+def rename_exp_image(center, exp_job_ids):
     """Rename an experiment image."""
-    # TODO: Make experiment pattern job_ids configurable.
 
     async def rename_image(center, event):
         """Rename an image."""
-        if event.job_id not in (3, 4, 6):
+        if event.job_id not in exp_job_ids:
             return
 
-        if event.job_id == 3:
-            channel_id = event.channel_id
-        elif event.job_id == 4 and event.channel_id == 0:
+        if event.job_id == exp_job_ids[0]:
+            channel_id = 0
+        elif event.job_id == exp_job_ids[1] and event.channel_id == 0:
             channel_id = 1
-        elif event.job_id == 4 and event.channel_id == 1:
+        elif event.job_id == exp_job_ids[1] and event.channel_id == 1:
             channel_id = 2
-        elif event.job_id == 6:
+        elif event.job_id == exp_job_ids[2]:
             channel_id = 3
 
         new_name = (
diff --git a/config_templates/production.yml b/config_templates/production.yml
index 8d55429..01dcf70 100644
--- a/config_templates/production.yml
+++ b/config_templates/production.yml
@@ -1,7 +1,13 @@
 production:
   #state_file: "/path/to/sample_state.csv"
   gain_pattern_name: p10xgain
+  gain_job_id: 3
+  gain_job_channels: 32
   exp_pattern_name: p10xexp
+  exp_job_ids:
+   - 3
+   - 4
+   - 6
   channels:
   - channel: green
     job_name: green10x

From dc9803c8131e38846474a3a104189784dbbe150e Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 15:27:30 +0100
Subject: [PATCH 43/76] Make rename image more robust

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 6386782..cacb23d 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -335,7 +335,7 @@ def rename_exp_image(center, exp_job_ids):
 
     async def rename_image(center, event):
         """Rename an image."""
-        if event.job_id not in exp_job_ids:
+        if event.job_id not in exp_job_ids or event.channel_id not in (0, 1):
             return
 
         if event.job_id == exp_job_ids[0]:

From 55335303f76cf39ce3632436de0aea8a0f429eb3 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 15:46:16 +0100
Subject: [PATCH 44/76] Update pylintrc

---
 pylintrc | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/pylintrc b/pylintrc
index 199fca4..29a954e 100644
--- a/pylintrc
+++ b/pylintrc
@@ -1,6 +1,9 @@
 [MASTER]
 reports=no
 
+max-args=7
+max-locals=20
+
 # Black needs to disable wrong-hanging-indent.
 
 disable=

From 30d2c35352dbbd92a76ee806bded80bcb515a55f Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 16:30:36 +0100
Subject: [PATCH 45/76] Make plate name constant

---
 camacqplugins/production/__init__.py | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index cacb23d..84efbde 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -14,6 +14,7 @@
 
 _LOGGER = logging.getLogger(__name__)
 
+PLATE_NAME = "00"
 SAMPLE_STATE_FILE = "state_file"
 
 CONFIG_SCHEMA = vol.Schema(
@@ -110,7 +111,7 @@ def start_exp(center):
 
     async def set_start_well(center, event):
         """Run on start event."""
-        await center.actions.sample.set_well(plate_name="00", well_x=0, well_y=0)
+        await center.actions.sample.set_well(plate_name=PLATE_NAME, well_x=0, well_y=0)
 
     center.bus.register("camacq_start_event", set_start_well)
 
@@ -120,8 +121,7 @@ def add_next_well(center, x_wells, y_wells, x_fields, y_fields):
 
     async def set_next_well(center, event):
         """Run on well event."""
-        plate_name = "00"
-        next_well_x, _ = next_well_xy(center.sample, plate_name, x_wells, y_wells)
+        next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
 
         if (
             not match_event(
@@ -133,10 +133,10 @@ async def set_next_well(center, event):
 
         await center.actions.command.stop_imaging()
 
-        well_x, well_y = next_well_xy(center.sample, plate_name, x_wells, y_wells)
+        well_x, well_y = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
 
         await center.actions.sample.set_well(
-            plate_name=plate_name, well_x=well_x, well_y=well_y
+            plate_name=PLATE_NAME, well_x=well_x, well_y=well_y
         )
 
     center.bus.register("well_event", set_next_well)
@@ -147,8 +147,7 @@ def image_next_well_on_sample(center, gain_pattern, subscriptions, x_fields, y_f
 
     async def send_cam_job(center, event):
         """Run on well event."""
-        plate_name = "00"
-        next_well_x, next_well_y = next_well_xy(center.sample, plate_name)
+        next_well_x, next_well_y = next_well_xy(center.sample, PLATE_NAME)
 
         if (
             not match_event(event, event_type="camacq_start_event")

From 75c04e412175aa2bfcb07777d7b0747c819004b6 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 16:36:41 +0100
Subject: [PATCH 46/76] Fix rename name

---
 camacqplugins/production/__init__.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 84efbde..cf4e282 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -347,8 +347,9 @@ async def rename_image(center, event):
             channel_id = 3
 
         new_name = (
-            f"U{event.well_x:03}--V{event.well_y}--E{event.job_id}--X{event.field_x}"
-            f"--Y{event.field_y}--Z{event.z_slice}--C{channel_id}.ome.tif"
+            f"U{event.well_x:02}--V{event.well_y:02}--E{event.job_id:02}--"
+            f"X{event.field_x:02}--Y{event.field_y:02}--"
+            f"Z{event.z_slice:02}--C{channel_id:02}.ome.tif"
         )
 
         await center.actions.rename_image.rename_image(

From 869c2e98447fe4c9586f41fa5d1e323244a91694 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 16:37:10 +0100
Subject: [PATCH 47/76] Clean up

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index cf4e282..01ff85b 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -364,7 +364,7 @@ def stop_exp(center, x_wells, y_wells, x_fields, y_fields):
 
     async def stop_imaging(center, event):
         """Run to stop the experiment."""
-        next_well_x, _ = next_well_xy(center.sample, "00", x_wells, y_wells)
+        next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
         match = match_event(
             event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
         )

From b72d12ae699c6984f1a2a9405d9391a39d9e7439 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 30 Nov 2019 23:58:59 +0100
Subject: [PATCH 48/76] Refactor to use flow instance

---
 camacqplugins/production/__init__.py | 616 +++++++++++++--------------
 pylintrc                             |   3 -
 2 files changed, 307 insertions(+), 312 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 01ff85b..23319a0 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -10,7 +10,7 @@
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
-from camacq.util import dotdict, read_csv
+from camacq.util import read_csv
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -49,332 +49,354 @@
 async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
-    gain_pattern = conf["gain_pattern_name"]
-    gain_job_id = conf["gain_job_id"]
-    gain_job_channels = conf["gain_job_channels"]
-    exp_pattern = conf["exp_pattern_name"]
-    exp_job_ids = conf["exp_job_ids"]
-    channels = conf["channels"]
-    well_layout = conf["well_layout"]
-    x_fields = well_layout["x_fields"]
-    y_fields = well_layout["y_fields"]
-    plot_save_path = conf.get("plot_save_path")
-    subscriptions = dotdict()
-
+    flow = WorkFlow(center, conf)
     state_file = conf.get(SAMPLE_STATE_FILE)
-    if state_file is not None:
-        x_wells = None
-        y_wells = None
-        await load_sample(center, state_file)
-        image_next_well_on_sample(
-            center, gain_pattern, subscriptions, x_fields, y_fields
-        )
-    else:
-        x_wells = 12
-        y_wells = 8
-        start_exp(center)
-        add_next_well(center, x_wells, y_wells, x_fields, y_fields)
-        image_next_well_on_event(
-            center, gain_pattern, subscriptions, x_fields, y_fields
-        )
-
-    analyze_gain(
-        center,
-        plot_save_path,
-        asyncio.Lock(),
-        x_fields,
-        y_fields,
-        gain_job_id,
-        gain_job_channels,
-    )
-    set_exp_gain(center, channels)
-    add_exp_job(
-        center, channels, exp_pattern, subscriptions, x_fields, y_fields, exp_job_ids
-    )
-    subscriptions.set_img_ok = set_img_ok(center)
-    subscriptions.rename_exp_image = rename_exp_image(center, exp_job_ids)
-    stop_exp(center, x_wells, y_wells, x_fields, y_fields)
-
-
-async def load_sample(center, state_file):
-    """Load sample state from file."""
-    state_data = await center.add_executor_job(read_csv, state_file)
-    for data in state_data:
-        await center.actions.sample.set_plate(silent=True, **data)
-        await center.actions.sample.set_well(silent=True, **data)
-        await center.actions.sample.set_channel(silent=True, **data)
-        await center.actions.sample.set_field(silent=True, **data)
-
-
-def start_exp(center):
-    """Trigger on start experiment."""
-
-    async def set_start_well(center, event):
-        """Run on start event."""
-        await center.actions.sample.set_well(plate_name=PLATE_NAME, well_x=0, well_y=0)
-
-    center.bus.register("camacq_start_event", set_start_well)
-
-
-def add_next_well(center, x_wells, y_wells, x_fields, y_fields):
-    """Add next well."""
-
-    async def set_next_well(center, event):
-        """Run on well event."""
-        next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
-
-        if (
-            not match_event(
-                event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
+    await flow.setup(state_file)
+
+
+class WorkFlow:
+    """Represent the production workflow."""
+
+    # pylint: disable=too-many-instance-attributes
+
+    def __init__(self, center, conf):
+        """Set up instance."""
+        self._center = center
+        self.gain_pattern = conf["gain_pattern_name"]
+        self.gain_job_id = conf["gain_job_id"]
+        self.gain_job_channels = conf["gain_job_channels"]
+        self.exp_pattern = conf["exp_pattern_name"]
+        self.exp_job_ids = conf["exp_job_ids"]
+        self.channels = conf["channels"]
+        well_layout = conf["well_layout"]
+        self.x_fields = well_layout["x_fields"]
+        self.y_fields = well_layout["y_fields"]
+        self.plot_save_path = conf.get("plot_save_path")
+        self._remove_set_img_ok = None
+        self._remove_rename_image = None
+
+    async def setup(self, state_file):
+        """Set up the flow."""
+        if state_file is not None:
+            x_wells = None
+            y_wells = None
+            await self.load_sample(state_file)
+            self.image_next_well_on_sample()
+        else:
+            x_wells = 12
+            y_wells = 8
+            self.start_exp()
+            self.add_next_well(x_wells, y_wells)
+            self.image_next_well_on_event()
+
+        self.analyze_gain(asyncio.Lock())
+        self.set_exp_gain()
+        self.add_exp_job()
+        self._remove_set_img_ok = self.set_img_ok()
+        self._remove_rename_image = self.rename_exp_image()
+        self.stop_exp(x_wells, y_wells)
+
+    async def load_sample(self, state_file):
+        """Load sample state from file."""
+        state_data = await self._center.add_executor_job(read_csv, state_file)
+        for data in state_data:
+            await self._center.actions.sample.set_plate(silent=True, **data)
+            await self._center.actions.sample.set_well(silent=True, **data)
+            await self._center.actions.sample.set_channel(silent=True, **data)
+            await self._center.actions.sample.set_field(silent=True, **data)
+
+    def start_exp(self):
+        """Trigger on start experiment."""
+
+        async def set_start_well(center, event):
+            """Run on start event."""
+            await center.actions.sample.set_well(
+                plate_name=PLATE_NAME, well_x=0, well_y=0
             )
-            or next_well_x is None
-        ):
-            return
-
-        await center.actions.command.stop_imaging()
 
-        well_x, well_y = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
+        return self._center.bus.register("camacq_start_event", set_start_well)
 
-        await center.actions.sample.set_well(
-            plate_name=PLATE_NAME, well_x=well_x, well_y=well_y
-        )
+    def add_next_well(self, x_wells, y_wells):
+        """Add next well."""
 
-    center.bus.register("well_event", set_next_well)
+        async def set_next_well(center, event):
+            """Run on well event."""
+            next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
 
+            if (
+                not match_event(
+                    event,
+                    field_x=self.x_fields - 1,
+                    field_y=self.y_fields - 1,
+                    well_img_ok=True,
+                )
+                or next_well_x is None
+            ):
+                return
 
-def image_next_well_on_sample(center, gain_pattern, subscriptions, x_fields, y_fields):
-    """Image next well in existing sample."""
+            await center.actions.command.stop_imaging()
 
-    async def send_cam_job(center, event):
-        """Run on well event."""
-        next_well_x, next_well_y = next_well_xy(center.sample, PLATE_NAME)
+            well_x, well_y = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
 
-        if (
-            not match_event(event, event_type="camacq_start_event")
-            and not match_event(
-                event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
+            await center.actions.sample.set_well(
+                plate_name=PLATE_NAME, well_x=well_x, well_y=well_y
             )
-            or next_well_x is None
-        ):
-            return
-
-        await send_gain_jobs(
-            center,
-            gain_pattern,
-            next_well_x,
-            next_well_y,
-            x_fields,
-            y_fields,
-            subscriptions,
-        )
-
-    center.bus.register("camacq_start_event", send_cam_job)
-    center.bus.register("well_event", send_cam_job)
-
-
-def image_next_well_on_event(center, gain_pattern, subscriptions, x_fields, y_fields):
-    """Image next well."""
-
-    async def send_cam_job(center, event):
-        """Run on well event."""
-        if event.well.images:
-            return
-
-        await send_gain_jobs(
-            center,
-            gain_pattern,
-            event.well.x,
-            event.well.y,
-            x_fields,
-            y_fields,
-            subscriptions,
-        )
-
-    center.bus.register("well_event", send_cam_job)
-
-
-def analyze_gain(
-    center, save_path, gain_lock, x_fields, y_fields, gain_job_id, gain_job_channels
-):
-    """Analyze gain."""
-
-    async def calc_gain(center, event):
-        """Calculate correct gain."""
-        field_x, field_y = get_last_gain_coords(x_fields, y_fields)
-        channel_id = gain_job_channels - 1
-        if not match_event(
-            event,
-            field_x=field_x,
-            field_y=field_y,
-            job_id=gain_job_id,
-            channel_id=channel_id,
-        ):
-            return
-
-        # Guard against duplicate image events.
-        async with gain_lock:
-            well = center.sample.get_well(
-                plate_name=event.plate_name, well_x=event.well_x, well_y=event.well_y
+
+        return self._center.bus.register("well_event", set_next_well)
+
+    def image_next_well_on_sample(self):
+        """Image next well in existing sample."""
+
+        async def send_cam_job(center, event):
+            """Run on well event."""
+            next_well_x, next_well_y = next_well_xy(center.sample, PLATE_NAME)
+
+            if (
+                not match_event(event, event_type="camacq_start_event")
+                and not match_event(
+                    event,
+                    field_x=self.x_fields - 1,
+                    field_y=self.y_fields - 1,
+                    well_img_ok=True,
+                )
+                or next_well_x is None
+            ):
+                return
+
+            await self.send_gain_jobs(
+                next_well_x, next_well_y,
             )
-            gain_set = any(
-                channel.gain is not None for channel in well.channels.values()
+
+        removes = []
+        removes.append(self._center.bus.register("camacq_start_event", send_cam_job))
+        removes.append(self._center.bus.register("well_event", send_cam_job))
+
+        def remove_callback():
+            """Remove all registered listeners of this method."""
+            for remove in removes:
+                remove()
+            removes.clear()
+
+        return remove_callback
+
+    def image_next_well_on_event(self):
+        """Image next well."""
+
+        async def send_cam_job(center, event):
+            """Run on well event."""
+            if event.well.images:
+                return
+
+            await self.send_gain_jobs(
+                event.well.x, event.well.y,
             )
-            if gain_set:
+
+        return self._center.bus.register("well_event", send_cam_job)
+
+    def analyze_gain(self, gain_lock):
+        """Analyze gain."""
+
+        async def calc_gain(center, event):
+            """Calculate correct gain."""
+            field_x, field_y = get_last_gain_coords(self.x_fields, self.y_fields)
+            channel_id = self.gain_job_channels - 1
+            if not match_event(
+                event,
+                field_x=field_x,
+                field_y=field_y,
+                job_id=self.gain_job_id,
+                channel_id=channel_id,
+            ):
                 return
 
-            await center.actions.command.stop_imaging()
+            # Guard against duplicate image events.
+            async with gain_lock:
+                well = center.sample.get_well(
+                    plate_name=event.plate_name,
+                    well_x=event.well_x,
+                    well_y=event.well_y,
+                )
+                gain_set = any(
+                    channel.gain is not None for channel in well.channels.values()
+                )
+                if gain_set:
+                    return
+
+                await center.actions.command.stop_imaging()
+
+                if self.plot_save_path is None:
+                    save_path = Path(tempfile.gettempdir()) / event.plate_name
+                else:
+                    save_path = Path(self.plot_save_path)
+                if not save_path.exists():
+                    await center.add_executor_job(save_path.mkdir)
+
+                # This should be a path to a base file name, not to a dir or file.
+                save_path = save_path / f"{event.well_x}--{event.well_y}"
+
+                await center.actions.gain.calc_gain(
+                    plate_name=event.plate_name,
+                    well_x=event.well_x,
+                    well_y=event.well_y,
+                    make_plots=True,
+                    save_path=save_path,
+                )
 
-            nonlocal save_path
-            if save_path is None:
-                save_path = Path(tempfile.gettempdir()) / event.plate_name
-            else:
-                save_path = Path(save_path)
-            if not save_path.exists():
-                await center.add_executor_job(save_path.mkdir)
+        return self._center.bus.register("image_event", calc_gain)
 
-            # This should be a path to a base file name, not to an actual dir or file.
-            save_path = save_path / f"{event.well_x}--{event.well_y}"
+    def set_exp_gain(self):
+        """Set experiment gain."""
 
-            await center.actions.gain.calc_gain(
+        async def set_gain(center, event):
+            """Set pmt gain."""
+            for channel in self.channels:
+                if event.channel_name != channel["channel"]:
+                    continue
+                exp = channel["job_name"]
+                num = channel["detector_num"]
+                gain = min(event.gain or channel["default_gain"], channel["max_gain"])
+
+            command = gain_com(exp=exp, num=num, value=gain)
+
+            # Set the gain at the microscope.
+            await center.actions.command.send(command=command)
+            # Set the gain in the sample state.
+            await center.actions.sample.set_channel(
                 plate_name=event.plate_name,
                 well_x=event.well_x,
                 well_y=event.well_y,
-                make_plots=True,
-                save_path=save_path,
+                channel_name=event.channel_name,
+                gain=gain,
             )
 
-    center.bus.register("image_event", calc_gain)
-
-
-def set_exp_gain(center, channels):
-    """Set experiment gain."""
-
-    async def set_gain(center, event):
-        """Set pmt gain."""
-        for channel in channels:
-            if event.channel_name != channel["channel"]:
-                continue
-            exp = channel["job_name"]
-            num = channel["detector_num"]
-            gain = min(event.gain or channel["default_gain"], channel["max_gain"])
-
-        command = gain_com(exp=exp, num=num, value=gain)
-
-        # Set the gain at the microscope.
-        await center.actions.command.send(command=command)
-        # Set the gain in the sample state.
-        await center.actions.sample.set_channel(
-            plate_name=event.plate_name,
-            well_x=event.well_x,
-            well_y=event.well_y,
-            channel_name=event.channel_name,
-            gain=gain,
-        )
-
-    center.bus.register("gain_calc_event", set_gain)
-
-
-def add_exp_job(
-    center, channels, exp_pattern, subscriptions, x_fields, y_fields, exp_job_ids
-):
-    """Add experiment job."""
-
-    async def add_cam_job(center, event):
-        """Add an experiment job to the cam list."""
-        last_channel = channels[-1]
-        if not match_event(event, channel_name=last_channel["channel"]) or len(
-            event.well.channels
-        ) != len(channels):
-            return
-
-        commands = []
-        for field_x in range(x_fields):
-            for field_y in range(y_fields):
-                cmd = cam_com(
-                    exp_pattern, event.well_x, event.well_y, field_x, field_y, 0, 0
-                )
-                commands.append(cmd)
-
-        await center.actions.command.send(command=del_com())
-        await center.actions.command.send_many(commands=commands)
-
-        if subscriptions.set_img_ok is None:
-            subscriptions.set_img_ok = set_img_ok(center)
-        if subscriptions.rename_exp_image is None:
-            subscriptions.rename_exp_image = rename_exp_image(center, exp_job_ids)
+        return self._center.bus.register("gain_calc_event", set_gain)
 
-        await center.actions.command.start_imaging()
-        await center.actions.command.send(command="/cmd:startcamscan")
+    def add_exp_job(self):
+        """Add experiment job."""
 
-    center.bus.register("channel_event", add_cam_job)
+        async def add_cam_job(center, event):
+            """Add an experiment job to the cam list."""
+            last_channel = self.channels[-1]
+            if not match_event(event, channel_name=last_channel["channel"]) or len(
+                event.well.channels
+            ) != len(self.channels):
+                return
 
+            commands = []
+            for field_x in range(self.x_fields):
+                for field_y in range(self.y_fields):
+                    cmd = cam_com(
+                        self.exp_pattern,
+                        event.well_x,
+                        event.well_y,
+                        field_x,
+                        field_y,
+                        0,
+                        0,
+                    )
+                    commands.append(cmd)
+
+            await center.actions.command.send(command=del_com())
+            await center.actions.command.send_many(commands=commands)
+
+            if self._remove_set_img_ok is None:
+                self._remove_set_img_ok = self.set_img_ok()
+            if self._remove_rename_image is None:
+                self._remove_rename_image = self.rename_exp_image()
+
+            await center.actions.command.start_imaging()
+            await center.actions.command.send(command="/cmd:startcamscan")
+
+        return self._center.bus.register("channel_event", add_cam_job)
+
+    def set_img_ok(self):
+        """Set field as imaged ok."""
+
+        async def set_sample_img_ok(center, event):
+            """Set sample field img ok."""
+            if not match_event(event, job_id=6):
+                return
 
-def set_img_ok(center):
-    """Set field as imaged ok."""
+            await center.actions.sample.set_field(
+                plate_name=event.plate_name,
+                well_x=event.well_x,
+                well_y=event.well_y,
+                field_x=event.field_x,
+                field_y=event.field_y,
+                img_ok=True,
+            )
 
-    async def set_sample_img_ok(center, event):
-        """Set sample field img ok."""
-        if not match_event(event, job_id=6):
-            return
+        return self._center.bus.register("image_event", set_sample_img_ok)
 
-        await center.actions.sample.set_field(
-            plate_name=event.plate_name,
-            well_x=event.well_x,
-            well_y=event.well_y,
-            field_x=event.field_x,
-            field_y=event.field_y,
-            img_ok=True,
-        )
+    def rename_exp_image(self):
+        """Rename an experiment image."""
 
-    return center.bus.register("image_event", set_sample_img_ok)
+        async def rename_image(center, event):
+            """Rename an image."""
+            if event.job_id not in self.exp_job_ids or event.channel_id not in (0, 1):
+                return
 
+            if event.job_id == self.exp_job_ids[0]:
+                channel_id = 0
+            elif event.job_id == self.exp_job_ids[1] and event.channel_id == 0:
+                channel_id = 1
+            elif event.job_id == self.exp_job_ids[1] and event.channel_id == 1:
+                channel_id = 2
+            elif event.job_id == self.exp_job_ids[2]:
+                channel_id = 3
+
+            new_name = (
+                f"U{event.well_x:02}--V{event.well_y:02}--E{event.job_id:02}--"
+                f"X{event.field_x:02}--Y{event.field_y:02}--"
+                f"Z{event.z_slice:02}--C{channel_id:02}.ome.tif"
+            )
 
-def rename_exp_image(center, exp_job_ids):
-    """Rename an experiment image."""
+            await center.actions.rename_image.rename_image(
+                old_path=event.path, new_name=new_name
+            )
 
-    async def rename_image(center, event):
-        """Rename an image."""
-        if event.job_id not in exp_job_ids or event.channel_id not in (0, 1):
-            return
+        return self._center.bus.register("image_event", rename_image)
 
-        if event.job_id == exp_job_ids[0]:
-            channel_id = 0
-        elif event.job_id == exp_job_ids[1] and event.channel_id == 0:
-            channel_id = 1
-        elif event.job_id == exp_job_ids[1] and event.channel_id == 1:
-            channel_id = 2
-        elif event.job_id == exp_job_ids[2]:
-            channel_id = 3
+    def stop_exp(self, x_wells, y_wells):
+        """Trigger to stop experiment."""
 
-        new_name = (
-            f"U{event.well_x:02}--V{event.well_y:02}--E{event.job_id:02}--"
-            f"X{event.field_x:02}--Y{event.field_y:02}--"
-            f"Z{event.z_slice:02}--C{channel_id:02}.ome.tif"
-        )
+        async def stop_imaging(center, event):
+            """Run to stop the experiment."""
+            next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
+            match = match_event(
+                event,
+                field_x=self.x_fields - 1,
+                field_y=self.y_fields - 1,
+                well_img_ok=True,
+            )
 
-        await center.actions.rename_image.rename_image(
-            old_path=event.path, new_name=new_name
-        )
+            if not match or next_well_x is not None:
+                return
 
-    return center.bus.register("image_event", rename_image)
+            await center.actions.command.stop_imaging()
 
+        return self._center.bus.register("well_event", stop_imaging)
 
-def stop_exp(center, x_wells, y_wells, x_fields, y_fields):
-    """Trigger to stop experiment."""
+    async def send_gain_jobs(self, well_x, well_y):
+        """Send gain cam jobs for the center fields of a well."""
+        field_x, field_y = get_last_gain_coords(self.x_fields, self.y_fields)
+        field_x = field_x - 1  # set the start x field coord
 
-    async def stop_imaging(center, event):
-        """Run to stop the experiment."""
-        next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
-        match = match_event(
-            event, field_x=x_fields - 1, field_y=y_fields - 1, well_img_ok=True,
-        )
+        await self._center.actions.command.send(command=del_com())
 
-        if not match or next_well_x is not None:
-            return
+        for field_x in range(field_x, field_x + 2):
+            command = cam_com(self.gain_pattern, well_x, well_y, field_x, field_y, 0, 0)
+            await self._center.actions.command.send(command=command)
 
-        await center.actions.command.stop_imaging()
+        if self._remove_set_img_ok is not None:
+            self._remove_set_img_ok()
+            self._remove_set_img_ok = None
+        if self._remove_rename_image is not None:
+            self._remove_rename_image()
+            self._remove_rename_image = None
 
-    center.bus.register("well_event", stop_imaging)
+        await self._center.actions.command.start_imaging()
+        await self._center.actions.command.send(command="/cmd:startcamscan")
 
 
 def get_last_gain_coords(x_fields, y_fields):
@@ -385,27 +407,3 @@ def get_last_gain_coords(x_fields, y_fields):
     last_x_field = ceil(x_fields / 2)
     last_y_field = ceil(y_fields / 2) - 1
     return last_x_field, last_y_field
-
-
-async def send_gain_jobs(
-    center, gain_job, well_x, well_y, x_fields, y_fields, subscriptions
-):
-    """Send gain cam jobs for the center fields of a well."""
-    field_x, field_y = get_last_gain_coords(x_fields, y_fields)
-    field_x = field_x - 1  # set the start x field coord
-
-    await center.actions.command.send(command=del_com())
-
-    for field_x in range(field_x, field_x + 2):
-        command = cam_com(gain_job, well_x, well_y, field_x, field_y, 0, 0)
-        await center.actions.command.send(command=command)
-
-    if subscriptions.set_img_ok is not None:
-        subscriptions.set_img_ok()
-        subscriptions.set_img_ok = None
-    if subscriptions.rename_exp_image is not None:
-        subscriptions.rename_exp_image()
-        subscriptions.rename_exp_image = None
-
-    await center.actions.command.start_imaging()
-    await center.actions.command.send(command="/cmd:startcamscan")
diff --git a/pylintrc b/pylintrc
index 29a954e..199fca4 100644
--- a/pylintrc
+++ b/pylintrc
@@ -1,9 +1,6 @@
 [MASTER]
 reports=no
 
-max-args=7
-max-locals=20
-
 # Black needs to disable wrong-hanging-indent.
 
 disable=

From 4450b523ebaa3e24a69d2b7f6c7438dcd5d35bd7 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 1 Dec 2019 02:11:02 +0100
Subject: [PATCH 49/76] Use config for last job id

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 23319a0..01b6be9 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -314,7 +314,7 @@ def set_img_ok(self):
 
         async def set_sample_img_ok(center, event):
             """Set sample field img ok."""
-            if not match_event(event, job_id=6):
+            if not match_event(event, job_id=self.exp_job_ids[-1]):
                 return
 
             await center.actions.sample.set_field(

From 780b519fd5a78cba207a8b02a5ca5666ace09cf1 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 1 Dec 2019 22:26:13 +0100
Subject: [PATCH 50/76] Add first production test

---
 requirements_test.txt               |   6 ++
 tests/conftest.py                   |  12 ++++
 tests/production/test_production.py | 108 ++++++++++++++++++++++++++++
 tox.ini                             |   9 ++-
 4 files changed, 132 insertions(+), 3 deletions(-)
 create mode 100644 requirements_test.txt
 create mode 100644 tests/conftest.py
 create mode 100644 tests/production/test_production.py

diff --git a/requirements_test.txt b/requirements_test.txt
new file mode 100644
index 0000000..3bc9366
--- /dev/null
+++ b/requirements_test.txt
@@ -0,0 +1,6 @@
+asynctest==0.13.0
+pytest==5.3.1
+pytest-asyncio==0.10.0
+pytest-cov==2.8.1
+pytest-mock==1.12.1
+pytest-timeout==1.3.3
diff --git a/tests/conftest.py b/tests/conftest.py
new file mode 100644
index 0000000..3ae48e2
--- /dev/null
+++ b/tests/conftest.py
@@ -0,0 +1,12 @@
+"""Provide package level pytest fixtures."""
+import pytest
+
+from camacq.control import Center
+
+
+@pytest.fixture
+def center(event_loop):
+    """Give access to center via fixture."""
+    _center = Center(loop=event_loop)
+    _center._track_tasks = True  # pylint: disable=protected-access
+    yield _center
diff --git a/tests/production/test_production.py b/tests/production/test_production.py
new file mode 100644
index 0000000..6c9294e
--- /dev/null
+++ b/tests/production/test_production.py
@@ -0,0 +1,108 @@
+"""Test the production plugin."""
+from asynctest import patch
+import pytest
+from ruamel.yaml import YAML
+
+from camacq import plugins
+from camacq.plugins.api import ImageEvent
+
+# All test coroutines will be treated as marked.
+pytestmark = pytest.mark.asyncio  # pylint: disable=invalid-name
+
+CONFIG = """
+production:
+  gain_pattern_name: p10xgain
+  gain_job_id: 3
+  gain_job_channels: 32
+  exp_pattern_name: p10xexp
+  exp_job_ids:
+   - 3
+   - 4
+   - 6
+  channels:
+  - channel: green
+    job_name: green10x
+    detector_num: 1
+    default_gain: 800
+    max_gain: 800
+  - channel: blue
+    job_name: blue10x
+    detector_num: 1
+    default_gain: 800
+    max_gain: 800
+  - channel: yellow
+    job_name: blue10x
+    detector_num: 2
+    default_gain: 695
+    max_gain: 800
+  - channel: red
+    job_name: red10x
+    detector_num: 2
+    default_gain: 700
+    max_gain: 800
+  well_layout:
+    x_fields: 2
+    y_fields: 3
+gain:
+  channels:
+  - channel: green
+    init_gain: [450, 495, 540, 585, 630, 675, 720, 765, 810, 855, 900]
+  - channel: blue
+    # 63x
+    #init_gain: [750, 730, 765, 800, 835, 870, 905]
+    # 10x
+    init_gain: [700, 735, 770, 805, 840, 875, 910]
+  - channel: yellow
+    # 63x
+    #init_gain: [550, 585, 620, 655, 690, 725, 760]
+    # 10x
+    init_gain: [700, 735, 770, 805, 840, 875, 910]
+  - channel: red
+    # 63x
+    #init_gain: [525, 560, 595, 630, 665, 700, 735]
+    # 10x
+    init_gain: [600, 635, 670, 705, 740, 775, 810]
+"""
+
+
+@pytest.fixture(name="calc_gain")
+def calc_gain_fixture():
+    """Mock calc_gain plugin function."""
+    with patch("camacq.plugins.gain.calc_gain") as mock_gain, patch(
+        "camacq.plugins.gain.make_proj"
+    ):
+        yield mock_gain
+
+
+class WorkflowImageEvent(ImageEvent):
+    """Represent a test image event."""
+
+    event_type = "workflow_image_event"
+
+    @property
+    def job_id(self):
+        """:int: Return job id of the image."""
+        return self.data.get("job_id")
+
+
+async def test_duplicate_image_events(center, calc_gain):
+    """Test duplicate image events."""
+    config = YAML(typ="safe").load(CONFIG)
+    await plugins.setup_module(center, config)
+
+    event = WorkflowImageEvent(
+        {
+            "path": "test_path",
+            "plate_name": "00",
+            "well_x": 0,
+            "well_y": 0,
+            "field_x": 1,
+            "field_y": 1,
+            "job_id": 3,
+            "channel_id": 31,
+        }
+    )
+    await center.bus.notify(event)
+    await center.wait_for()
+
+    assert calc_gain.call_count == 1
diff --git a/tox.ini b/tox.ini
index 0212152..052b4a5 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,6 +1,9 @@
 [tox]
-envlist=py36, py37
+envlist = py36, py37
 
 [testenv]
-commands=pytest
-deps=pytest
+commands =
+  pytest --timeout=30 --cov=camacqplugins --cov-report= {posargs}
+deps =
+  -rrequirements.txt
+  -rrequirements_test.txt

From 0009f5e02af544c08597f9818731597aeb321822 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 1 Dec 2019 22:47:43 +0100
Subject: [PATCH 51/76] Extend test

---
 tests/production/test_production.py | 45 ++++++++++++++++++++++-------
 1 file changed, 34 insertions(+), 11 deletions(-)

diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index 6c9294e..dd1b678 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -1,4 +1,8 @@
 """Test the production plugin."""
+import tempfile
+from pathlib import Path
+from unittest.mock import call
+
 from asynctest import patch
 import pytest
 from ruamel.yaml import YAML
@@ -68,12 +72,17 @@
 @pytest.fixture(name="calc_gain")
 def calc_gain_fixture():
     """Mock calc_gain plugin function."""
-    with patch("camacq.plugins.gain.calc_gain") as mock_gain, patch(
-        "camacq.plugins.gain.make_proj"
-    ):
+    with patch("camacq.plugins.gain.calc_gain") as mock_gain:
         yield mock_gain
 
 
+@pytest.fixture(name="make_proj")
+def make_proj_fixture():
+    """Mock make_proj image function."""
+    with patch("camacq.plugins.gain.make_proj") as mock_proj:
+        yield mock_proj
+
+
 class WorkflowImageEvent(ImageEvent):
     """Represent a test image event."""
 
@@ -85,24 +94,38 @@ def job_id(self):
         return self.data.get("job_id")
 
 
-async def test_duplicate_image_events(center, calc_gain):
+async def test_duplicate_image_events(center, calc_gain, make_proj):
     """Test duplicate image events."""
     config = YAML(typ="safe").load(CONFIG)
     await plugins.setup_module(center, config)
+    plate_name = "00"
+    well_x = 0
+    well_y = 0
+    field_x = 1
+    field_y = 1
+    job_id = 3
+    channel_id = 31
+    save_path = Path(tempfile.gettempdir()) / plate_name
+    save_path = save_path / f"{well_x}--{well_y}"
+    test_projs = ["test"]
+    make_proj.return_value = test_projs
 
     event = WorkflowImageEvent(
         {
             "path": "test_path",
-            "plate_name": "00",
-            "well_x": 0,
-            "well_y": 0,
-            "field_x": 1,
-            "field_y": 1,
-            "job_id": 3,
-            "channel_id": 31,
+            "plate_name": plate_name,
+            "well_x": well_x,
+            "well_y": well_y,
+            "field_x": field_x,
+            "field_y": field_y,
+            "job_id": job_id,
+            "channel_id": channel_id,
         }
     )
     await center.bus.notify(event)
     await center.wait_for()
 
     assert calc_gain.call_count == 1
+    assert calc_gain.call_args == call(
+        center, config, plate_name, well_x, well_y, test_projs, True, str(save_path),
+    )

From ec6b4e74e19a733f9eb5f89ff8701d64bbaefe50 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 1 Dec 2019 23:43:53 +0100
Subject: [PATCH 52/76] Test duplicate image events

---
 tests/production/test_production.py | 81 +++++++++++++++--------------
 1 file changed, 42 insertions(+), 39 deletions(-)

diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index dd1b678..47d3794 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -3,12 +3,14 @@
 from pathlib import Path
 from unittest.mock import call
 
-from asynctest import patch
 import pytest
+import voluptuous as vol
+from asynctest import CoroutineMock
 from ruamel.yaml import YAML
 
 from camacq import plugins
 from camacq.plugins.api import ImageEvent
+from camacq.plugins.gain import GainCalcEvent
 
 # All test coroutines will be treated as marked.
 pytestmark = pytest.mark.asyncio  # pylint: disable=invalid-name
@@ -47,42 +49,9 @@
   well_layout:
     x_fields: 2
     y_fields: 3
-gain:
-  channels:
-  - channel: green
-    init_gain: [450, 495, 540, 585, 630, 675, 720, 765, 810, 855, 900]
-  - channel: blue
-    # 63x
-    #init_gain: [750, 730, 765, 800, 835, 870, 905]
-    # 10x
-    init_gain: [700, 735, 770, 805, 840, 875, 910]
-  - channel: yellow
-    # 63x
-    #init_gain: [550, 585, 620, 655, 690, 725, 760]
-    # 10x
-    init_gain: [700, 735, 770, 805, 840, 875, 910]
-  - channel: red
-    # 63x
-    #init_gain: [525, 560, 595, 630, 665, 700, 735]
-    # 10x
-    init_gain: [600, 635, 670, 705, 740, 775, 810]
 """
 
 
-@pytest.fixture(name="calc_gain")
-def calc_gain_fixture():
-    """Mock calc_gain plugin function."""
-    with patch("camacq.plugins.gain.calc_gain") as mock_gain:
-        yield mock_gain
-
-
-@pytest.fixture(name="make_proj")
-def make_proj_fixture():
-    """Mock make_proj image function."""
-    with patch("camacq.plugins.gain.make_proj") as mock_proj:
-        yield mock_proj
-
-
 class WorkflowImageEvent(ImageEvent):
     """Represent a test image event."""
 
@@ -94,7 +63,7 @@ def job_id(self):
         return self.data.get("job_id")
 
 
-async def test_duplicate_image_events(center, calc_gain, make_proj):
+async def test_duplicate_image_events(center):
     """Test duplicate image events."""
     config = YAML(typ="safe").load(CONFIG)
     await plugins.setup_module(center, config)
@@ -107,8 +76,36 @@ async def test_duplicate_image_events(center, calc_gain, make_proj):
     channel_id = 31
     save_path = Path(tempfile.gettempdir()) / plate_name
     save_path = save_path / f"{well_x}--{well_y}"
-    test_projs = ["test"]
-    make_proj.return_value = test_projs
+    calc_gain = CoroutineMock()
+
+    async def fire_gain_event(**kwargs):
+        """Fire gain event."""
+        well_x = kwargs.get("well_x")
+        well_y = kwargs.get("well_y")
+        plate_name = kwargs.get("plate_name")
+        gains = {
+            "green": 800,
+            "blue": 700,
+            "yellow": 600,
+            "red": 500,
+        }
+        for channel_name, gain in gains.items():
+            event = GainCalcEvent(
+                {
+                    "plate_name": plate_name,
+                    "well_x": well_x,
+                    "well_y": well_y,
+                    "channel_name": channel_name,
+                    "gain": gain,
+                }
+            )
+            await center.bus.notify(event)
+
+    calc_gain.side_effect = fire_gain_event
+
+    center.actions.register(
+        "gain", "calc_gain", calc_gain, vol.Schema({}, extra=vol.ALLOW_EXTRA)
+    )
 
     event = WorkflowImageEvent(
         {
@@ -122,10 +119,16 @@ async def test_duplicate_image_events(center, calc_gain, make_proj):
             "channel_id": channel_id,
         }
     )
-    await center.bus.notify(event)
+    center.create_task(center.bus.notify(event))
+    center.create_task(center.bus.notify(event))
     await center.wait_for()
 
     assert calc_gain.call_count == 1
     assert calc_gain.call_args == call(
-        center, config, plate_name, well_x, well_y, test_projs, True, str(save_path),
+        action_id="calc_gain",
+        plate_name=plate_name,
+        well_x=well_x,
+        well_y=well_y,
+        make_plots=True,
+        save_path=save_path,
     )

From 0207cae47e8d25adeddc49d297b666e4af70a8ca Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 1 Dec 2019 23:55:33 +0100
Subject: [PATCH 53/76] Use next and generator expression

---
 camacqplugins/production/__init__.py | 16 ++++++++++------
 1 file changed, 10 insertions(+), 6 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 01b6be9..839805b 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -249,12 +249,16 @@ def set_exp_gain(self):
 
         async def set_gain(center, event):
             """Set pmt gain."""
-            for channel in self.channels:
-                if event.channel_name != channel["channel"]:
-                    continue
-                exp = channel["job_name"]
-                num = channel["detector_num"]
-                gain = min(event.gain or channel["default_gain"], channel["max_gain"])
+            channel = next(
+                (
+                    channel
+                    for channel in self.channels
+                    if event.channel_name == channel["channel"]
+                )
+            )
+            exp = channel["job_name"]
+            num = channel["detector_num"]
+            gain = min(event.gain or channel["default_gain"], channel["max_gain"])
 
             command = gain_com(exp=exp, num=num, value=gain)
 

From 907d4d091733da77d02e9af4dc1477d70f18bba8 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Mon, 2 Dec 2019 00:11:26 +0100
Subject: [PATCH 54/76] Clean up test

---
 tests/production/test_production.py | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index 47d3794..f59dd13 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -70,25 +70,22 @@ async def test_duplicate_image_events(center):
     plate_name = "00"
     well_x = 0
     well_y = 0
-    field_x = 1
-    field_y = 1
-    job_id = 3
-    channel_id = 31
     save_path = Path(tempfile.gettempdir()) / plate_name
     save_path = save_path / f"{well_x}--{well_y}"
     calc_gain = CoroutineMock()
+    gains = {
+        "green": 800,
+        "blue": 700,
+        "yellow": 600,
+        "red": 500,
+    }
 
     async def fire_gain_event(**kwargs):
         """Fire gain event."""
         well_x = kwargs.get("well_x")
         well_y = kwargs.get("well_y")
         plate_name = kwargs.get("plate_name")
-        gains = {
-            "green": 800,
-            "blue": 700,
-            "yellow": 600,
-            "red": 500,
-        }
+
         for channel_name, gain in gains.items():
             event = GainCalcEvent(
                 {
@@ -113,10 +110,10 @@ async def fire_gain_event(**kwargs):
             "plate_name": plate_name,
             "well_x": well_x,
             "well_y": well_y,
-            "field_x": field_x,
-            "field_y": field_y,
-            "job_id": job_id,
-            "channel_id": channel_id,
+            "field_x": 1,
+            "field_y": 1,
+            "job_id": 3,
+            "channel_id": 31,
         }
     )
     center.create_task(center.bus.notify(event))
@@ -132,3 +129,6 @@ async def fire_gain_event(**kwargs):
         make_plots=True,
         save_path=save_path,
     )
+    for channel_name, gain in gains.items():
+        channel = center.sample.get_channel(plate_name, well_x, well_y, channel_name)
+        assert channel.gain == gain

From 5d7546cd3f84d285c8f8049644966f2b97000232 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Mon, 2 Dec 2019 01:13:17 +0100
Subject: [PATCH 55/76] Add load sample test

---
 camacqplugins/production/__init__.py |  8 ++++++--
 tests/production/test_production.py  | 22 ++++++++++++++++++++++
 2 files changed, 28 insertions(+), 2 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 839805b..16b3b61 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -100,8 +100,12 @@ async def load_sample(self, state_file):
         """Load sample state from file."""
         state_data = await self._center.add_executor_job(read_csv, state_file)
         for data in state_data:
-            await self._center.actions.sample.set_plate(silent=True, **data)
-            await self._center.actions.sample.set_well(silent=True, **data)
+            if data["plate_name"] not in self._center.sample.plates:
+                await self._center.actions.sample.set_plate(silent=True, **data)
+            if (data["well_x"], data["well_y"]) not in self._center.sample.plates[
+                data["plate_name"]
+            ].wells:
+                await self._center.actions.sample.set_well(silent=True, **data)
             await self._center.actions.sample.set_channel(silent=True, **data)
             await self._center.actions.sample.set_field(silent=True, **data)
 
diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index f59dd13..9764897 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -51,6 +51,14 @@
     y_fields: 3
 """
 
+SAMPLE_STATE = """
+plate_name,well_x,well_y,channel_name,gain
+00,0,0
+00,0,1
+00,1,0
+00,1,1
+""".strip()
+
 
 class WorkflowImageEvent(ImageEvent):
     """Represent a test image event."""
@@ -132,3 +140,17 @@ async def fire_gain_event(**kwargs):
     for channel_name, gain in gains.items():
         channel = center.sample.get_channel(plate_name, well_x, well_y, channel_name)
         assert channel.gain == gain
+
+
+async def test_load_sample(center, tmp_path):
+    """Test loading sample state from file."""
+    state_file = tmp_path / "state_file.csv"
+    state_file.write_text(SAMPLE_STATE)
+    config = YAML(typ="safe").load(CONFIG)
+    config["production"]["state_file"] = str(state_file)
+    plate_name = "00"
+    await plugins.setup_module(center, config)
+    await center.wait_for()
+
+    plate = center.sample.get_plate(plate_name)
+    assert len(plate.wells) == 4

From 2ec2dd87535feaebaa4b45f816e1ec0087847cd7 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Mon, 2 Dec 2019 01:26:54 +0100
Subject: [PATCH 56/76] Clean up test

---
 tests/production/test_production.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index 9764897..6c47d3b 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -1,6 +1,4 @@
 """Test the production plugin."""
-import tempfile
-from pathlib import Path
 from unittest.mock import call
 
 import pytest
@@ -71,14 +69,16 @@ def job_id(self):
         return self.data.get("job_id")
 
 
-async def test_duplicate_image_events(center):
+async def test_duplicate_image_events(center, tmp_path):
     """Test duplicate image events."""
     config = YAML(typ="safe").load(CONFIG)
-    await plugins.setup_module(center, config)
     plate_name = "00"
     well_x = 0
     well_y = 0
-    save_path = Path(tempfile.gettempdir()) / plate_name
+    save_path = tmp_path / plate_name
+    await center.add_executor_job(save_path.mkdir)
+    config["production"]["plot_save_path"] = save_path
+    await plugins.setup_module(center, config)
     save_path = save_path / f"{well_x}--{well_y}"
     calc_gain = CoroutineMock()
     gains = {

From 587190ddf7868cfa424c40e0647e2c0eda0e0b02 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Mon, 2 Dec 2019 01:41:22 +0100
Subject: [PATCH 57/76] Fix well check

---
 camacqplugins/production/__init__.py | 3 ++-
 tests/production/test_production.py  | 7 +++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 16b3b61..312eecd 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -102,7 +102,8 @@ async def load_sample(self, state_file):
         for data in state_data:
             if data["plate_name"] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
-            if (data["well_x"], data["well_y"]) not in self._center.sample.plates[
+            well_coord = int(data["well_x"]), int(data["well_y"])
+            if well_coord not in self._center.sample.plates[
                 data["plate_name"]
             ].wells:
                 await self._center.actions.sample.set_well(silent=True, **data)
diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index 6c47d3b..5e148b9 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -50,8 +50,9 @@
 """
 
 SAMPLE_STATE = """
-plate_name,well_x,well_y,channel_name,gain
-00,0,0
+plate_name,well_x,well_y,channel_name,gain,field_x,field_y
+00,0,0,,,0,0
+00,0,0,,,0,1
 00,0,1
 00,1,0
 00,1,1
@@ -154,3 +155,5 @@ async def test_load_sample(center, tmp_path):
 
     plate = center.sample.get_plate(plate_name)
     assert len(plate.wells) == 4
+    well = center.sample.get_well(plate_name, 0, 0)
+    assert len(well.fields) == 2

From e56075bb09c6a7984658665e102cbdf7427cccad Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 17:42:10 +0100
Subject: [PATCH 58/76] Add missing stop command on next sample well

---
 camacqplugins/production/__init__.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 312eecd..8e49ef5 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -103,9 +103,7 @@ async def load_sample(self, state_file):
             if data["plate_name"] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
             well_coord = int(data["well_x"]), int(data["well_y"])
-            if well_coord not in self._center.sample.plates[
-                data["plate_name"]
-            ].wells:
+            if well_coord not in self._center.sample.plates[data["plate_name"]].wells:
                 await self._center.actions.sample.set_well(silent=True, **data)
             await self._center.actions.sample.set_channel(silent=True, **data)
             await self._center.actions.sample.set_field(silent=True, **data)
@@ -168,6 +166,7 @@ async def send_cam_job(center, event):
             ):
                 return
 
+            await center.actions.command.stop_imaging()
             await self.send_gain_jobs(
                 next_well_x, next_well_y,
             )

From 47187b7617d6c3b9b22430a300afff844974989a Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 18:19:54 +0100
Subject: [PATCH 59/76] Do not stop imaging on first well

---
 camacqplugins/production/__init__.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 8e49ef5..8d86eec 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -166,7 +166,8 @@ async def send_cam_job(center, event):
             ):
                 return
 
-            await center.actions.command.stop_imaging()
+            if center.sample.images:
+                await center.actions.command.stop_imaging()
             await self.send_gain_jobs(
                 next_well_x, next_well_y,
             )

From 2dc5fdfea64dfc9befa38728e37185a50966445d Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 18:21:33 +0100
Subject: [PATCH 60/76] Add log message on experiment stop

---
 camacqplugins/production/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 8d86eec..790b2df 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -384,6 +384,8 @@ async def stop_imaging(center, event):
 
             await center.actions.command.stop_imaging()
 
+            _LOGGER.info("Congratulations, experiment is finished!")
+
         return self._center.bus.register("well_event", stop_imaging)
 
     async def send_gain_jobs(self, well_x, well_y):

From 5b384864b0107371b790b7d5d02f91c970512d48 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 18:24:00 +0100
Subject: [PATCH 61/76] Remove not needed lock

---
 camacqplugins/production/__init__.py | 52 ++++++++++------------------
 1 file changed, 19 insertions(+), 33 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 790b2df..ed6011d 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -1,5 +1,4 @@
 """Provide a plugin for production standard flow."""
-import asyncio
 import logging
 import tempfile
 from math import ceil
@@ -89,7 +88,7 @@ async def setup(self, state_file):
             self.add_next_well(x_wells, y_wells)
             self.image_next_well_on_event()
 
-        self.analyze_gain(asyncio.Lock())
+        self.analyze_gain()
         self.set_exp_gain()
         self.add_exp_job()
         self._remove_set_img_ok = self.set_img_ok()
@@ -198,7 +197,7 @@ async def send_cam_job(center, event):
 
         return self._center.bus.register("well_event", send_cam_job)
 
-    def analyze_gain(self, gain_lock):
+    def analyze_gain(self):
         """Analyze gain."""
 
         async def calc_gain(center, event):
@@ -214,38 +213,25 @@ async def calc_gain(center, event):
             ):
                 return
 
-            # Guard against duplicate image events.
-            async with gain_lock:
-                well = center.sample.get_well(
-                    plate_name=event.plate_name,
-                    well_x=event.well_x,
-                    well_y=event.well_y,
-                )
-                gain_set = any(
-                    channel.gain is not None for channel in well.channels.values()
-                )
-                if gain_set:
-                    return
+            await center.actions.command.stop_imaging()
 
-                await center.actions.command.stop_imaging()
+            if self.plot_save_path is None:
+                save_path = Path(tempfile.gettempdir()) / event.plate_name
+            else:
+                save_path = Path(self.plot_save_path)
+            if not save_path.exists():
+                await center.add_executor_job(save_path.mkdir)
 
-                if self.plot_save_path is None:
-                    save_path = Path(tempfile.gettempdir()) / event.plate_name
-                else:
-                    save_path = Path(self.plot_save_path)
-                if not save_path.exists():
-                    await center.add_executor_job(save_path.mkdir)
-
-                # This should be a path to a base file name, not to a dir or file.
-                save_path = save_path / f"{event.well_x}--{event.well_y}"
-
-                await center.actions.gain.calc_gain(
-                    plate_name=event.plate_name,
-                    well_x=event.well_x,
-                    well_y=event.well_y,
-                    make_plots=True,
-                    save_path=save_path,
-                )
+            # This should be a path to a base file name, not to a dir or file.
+            save_path = save_path / f"{event.well_x}--{event.well_y}"
+
+            await center.actions.gain.calc_gain(
+                plate_name=event.plate_name,
+                well_x=event.well_x,
+                well_y=event.well_y,
+                make_plots=True,
+                save_path=save_path,
+            )
 
         return self._center.bus.register("image_event", calc_gain)
 

From 5df05a3cb1b01c9354899df6a5b080fd5fcb69b0 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 19:21:55 +0100
Subject: [PATCH 62/76] Fix rename of last field before next well

---
 camacqplugins/production/__init__.py | 111 +++++++++++++--------------
 1 file changed, 52 insertions(+), 59 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index ed6011d..fb6e84f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -71,8 +71,7 @@ def __init__(self, center, conf):
         self.x_fields = well_layout["x_fields"]
         self.y_fields = well_layout["y_fields"]
         self.plot_save_path = conf.get("plot_save_path")
-        self._remove_set_img_ok = None
-        self._remove_rename_image = None
+        self._remove_handle_exp_image = None
 
     async def setup(self, state_file):
         """Set up the flow."""
@@ -91,8 +90,7 @@ async def setup(self, state_file):
         self.analyze_gain()
         self.set_exp_gain()
         self.add_exp_job()
-        self._remove_set_img_ok = self.set_img_ok()
-        self._remove_rename_image = self.rename_exp_image()
+        self._remove_handle_exp_image = self.handle_exp_image()
         self.stop_exp(x_wells, y_wells)
 
     async def load_sample(self, state_file):
@@ -294,63 +292,23 @@ async def add_cam_job(center, event):
             await center.actions.command.send(command=del_com())
             await center.actions.command.send_many(commands=commands)
 
-            if self._remove_set_img_ok is None:
-                self._remove_set_img_ok = self.set_img_ok()
-            if self._remove_rename_image is None:
-                self._remove_rename_image = self.rename_exp_image()
+            if self._remove_handle_exp_image is None:
+                self._remove_handle_exp_image = self.handle_exp_image()
 
             await center.actions.command.start_imaging()
             await center.actions.command.send(command="/cmd:startcamscan")
 
         return self._center.bus.register("channel_event", add_cam_job)
 
-    def set_img_ok(self):
-        """Set field as imaged ok."""
+    def handle_exp_image(self):
+        """Handle experiment image."""
 
-        async def set_sample_img_ok(center, event):
-            """Set sample field img ok."""
-            if not match_event(event, job_id=self.exp_job_ids[-1]):
-                return
-
-            await center.actions.sample.set_field(
-                plate_name=event.plate_name,
-                well_x=event.well_x,
-                well_y=event.well_y,
-                field_x=event.field_x,
-                field_y=event.field_y,
-                img_ok=True,
-            )
+        async def on_exp_image(center, event):
+            """Run on experiment image event."""
+            await self.rename_image(center, event)
+            await self.set_sample_img_ok(center, event)
 
-        return self._center.bus.register("image_event", set_sample_img_ok)
-
-    def rename_exp_image(self):
-        """Rename an experiment image."""
-
-        async def rename_image(center, event):
-            """Rename an image."""
-            if event.job_id not in self.exp_job_ids or event.channel_id not in (0, 1):
-                return
-
-            if event.job_id == self.exp_job_ids[0]:
-                channel_id = 0
-            elif event.job_id == self.exp_job_ids[1] and event.channel_id == 0:
-                channel_id = 1
-            elif event.job_id == self.exp_job_ids[1] and event.channel_id == 1:
-                channel_id = 2
-            elif event.job_id == self.exp_job_ids[2]:
-                channel_id = 3
-
-            new_name = (
-                f"U{event.well_x:02}--V{event.well_y:02}--E{event.job_id:02}--"
-                f"X{event.field_x:02}--Y{event.field_y:02}--"
-                f"Z{event.z_slice:02}--C{channel_id:02}.ome.tif"
-            )
-
-            await center.actions.rename_image.rename_image(
-                old_path=event.path, new_name=new_name
-            )
-
-        return self._center.bus.register("image_event", rename_image)
+        return self._center.bus.register("image_event", on_exp_image)
 
     def stop_exp(self, x_wells, y_wells):
         """Trigger to stop experiment."""
@@ -385,16 +343,51 @@ async def send_gain_jobs(self, well_x, well_y):
             command = cam_com(self.gain_pattern, well_x, well_y, field_x, field_y, 0, 0)
             await self._center.actions.command.send(command=command)
 
-        if self._remove_set_img_ok is not None:
-            self._remove_set_img_ok()
-            self._remove_set_img_ok = None
-        if self._remove_rename_image is not None:
-            self._remove_rename_image()
-            self._remove_rename_image = None
+        if self._remove_handle_exp_image is not None:
+            self._remove_handle_exp_image()
+            self._remove_handle_exp_image = None
 
         await self._center.actions.command.start_imaging()
         await self._center.actions.command.send(command="/cmd:startcamscan")
 
+    async def rename_image(self, center, event):
+        """Rename an image."""
+        if event.job_id not in self.exp_job_ids or event.channel_id not in (0, 1):
+            return
+
+        if event.job_id == self.exp_job_ids[0]:
+            channel_id = 0
+        elif event.job_id == self.exp_job_ids[1] and event.channel_id == 0:
+            channel_id = 1
+        elif event.job_id == self.exp_job_ids[1] and event.channel_id == 1:
+            channel_id = 2
+        elif event.job_id == self.exp_job_ids[2]:
+            channel_id = 3
+
+        new_name = (
+            f"U{event.well_x:02}--V{event.well_y:02}--E{event.job_id:02}--"
+            f"X{event.field_x:02}--Y{event.field_y:02}--"
+            f"Z{event.z_slice:02}--C{channel_id:02}.ome.tif"
+        )
+
+        await center.actions.rename_image.rename_image(
+            old_path=event.path, new_name=new_name
+        )
+
+    async def set_sample_img_ok(self, center, event):
+        """Set sample field img ok."""
+        if not match_event(event, job_id=self.exp_job_ids[-1]):
+            return
+
+        await center.actions.sample.set_field(
+            plate_name=event.plate_name,
+            well_x=event.well_x,
+            well_y=event.well_y,
+            field_x=event.field_x,
+            field_y=event.field_y,
+            img_ok=True,
+        )
+
 
 def get_last_gain_coords(x_fields, y_fields):
     """Return a tuple with last gain coordinates x and y.

From 666f5102ba3a3494d6e8ed12f822f8f72abd083c Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Fri, 6 Dec 2019 20:54:26 +0100
Subject: [PATCH 63/76] Fix production config template indent

---
 config_templates/production.yml | 40 ++++++++++++++++-----------------
 1 file changed, 20 insertions(+), 20 deletions(-)

diff --git a/config_templates/production.yml b/config_templates/production.yml
index 01dcf70..4ecdd38 100644
--- a/config_templates/production.yml
+++ b/config_templates/production.yml
@@ -34,26 +34,26 @@ production:
     y_fields: 3
   #plot_save_path: "/path/to/gains/dir/00/"
 
-  gain:
-    channels:
-    - channel: green
-      init_gain: [450, 495, 540, 585, 630, 675, 720, 765, 810, 855, 900]
-    - channel: blue
-      # 63x
-      #init_gain: [750, 730, 765, 800, 835, 870, 905]
-      # 10x
-      init_gain: [700, 735, 770, 805, 840, 875, 910]
-    - channel: yellow
-      # 63x
-      #init_gain: [550, 585, 620, 655, 690, 725, 760]
-      # 10x
-      init_gain: [700, 735, 770, 805, 840, 875, 910]
-    - channel: red
-      # 63x
-      #init_gain: [525, 560, 595, 630, 665, 700, 735]
-      # 10x
-      init_gain: [600, 635, 670, 705, 740, 775, 810]
-    #save_dir: "/path/to/gains/dir"
+gain:
+  channels:
+  - channel: green
+    init_gain: [450, 495, 540, 585, 630, 675, 720, 765, 810, 855, 900]
+  - channel: blue
+    # 63x
+    #init_gain: [750, 730, 765, 800, 835, 870, 905]
+    # 10x
+    init_gain: [700, 735, 770, 805, 840, 875, 910]
+  - channel: yellow
+    # 63x
+    #init_gain: [550, 585, 620, 655, 690, 725, 760]
+    # 10x
+    init_gain: [700, 735, 770, 805, 840, 875, 910]
+  - channel: red
+    # 63x
+    #init_gain: [525, 560, 595, 630, 665, 700, 735]
+    # 10x
+    init_gain: [600, 635, 670, 705, 740, 775, 810]
+  #save_dir: "/path/to/gains/dir"
 
 rename_image:
 

From 52988fc97c89ac1932e1551b0edad06f65e5d61b Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 13:35:49 +0100
Subject: [PATCH 64/76] Fix stop on wells left

---
 camacqplugins/production/__init__.py | 27 ++++++++++++++++++---------
 1 file changed, 18 insertions(+), 9 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index fb6e84f..dddc160 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -72,6 +72,7 @@ def __init__(self, center, conf):
         self.y_fields = well_layout["y_fields"]
         self.plot_save_path = conf.get("plot_save_path")
         self._remove_handle_exp_image = None
+        self.wells_left = set()
 
     async def setup(self, state_file):
         """Set up the flow."""
@@ -83,6 +84,11 @@ async def setup(self, state_file):
         else:
             x_wells = 12
             y_wells = 8
+            self.wells_left = {
+                (well_x, well_y)
+                for well_x in range(x_wells)
+                for well_y in range(y_wells)
+            }
             self.start_exp()
             self.add_next_well(x_wells, y_wells)
             self.image_next_well_on_event()
@@ -91,11 +97,12 @@ async def setup(self, state_file):
         self.set_exp_gain()
         self.add_exp_job()
         self._remove_handle_exp_image = self.handle_exp_image()
-        self.stop_exp(x_wells, y_wells)
+        self.stop_exp()
 
     async def load_sample(self, state_file):
         """Load sample state from file."""
         state_data = await self._center.add_executor_job(read_csv, state_file)
+        self.wells_left = {(data["well_x"], data["well_y"]) for data in state_data}
         for data in state_data:
             if data["plate_name"] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
@@ -121,7 +128,9 @@ def add_next_well(self, x_wells, y_wells):
 
         async def set_next_well(center, event):
             """Run on well event."""
-            next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
+            next_well_x, next_well_y = next_well_xy(
+                center.sample, PLATE_NAME, x_wells, y_wells
+            )
 
             if (
                 not match_event(
@@ -131,16 +140,15 @@ async def set_next_well(center, event):
                     well_img_ok=True,
                 )
                 or next_well_x is None
+                or (next_well_x, next_well_y) not in self.wells_left
             ):
                 return
 
             await center.actions.command.stop_imaging()
-
-            well_x, well_y = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
-
             await center.actions.sample.set_well(
-                plate_name=PLATE_NAME, well_x=well_x, well_y=well_y
+                plate_name=PLATE_NAME, well_x=next_well_x, well_y=next_well_y
             )
+            self.wells_left.pop((next_well_x, next_well_y))
 
         return self._center.bus.register("well_event", set_next_well)
 
@@ -160,6 +168,7 @@ async def send_cam_job(center, event):
                     well_img_ok=True,
                 )
                 or next_well_x is None
+                or (next_well_x, next_well_y) not in self.wells_left
             ):
                 return
 
@@ -168,6 +177,7 @@ async def send_cam_job(center, event):
             await self.send_gain_jobs(
                 next_well_x, next_well_y,
             )
+            self.wells_left.pop((next_well_x, next_well_y))
 
         removes = []
         removes.append(self._center.bus.register("camacq_start_event", send_cam_job))
@@ -310,12 +320,11 @@ async def on_exp_image(center, event):
 
         return self._center.bus.register("image_event", on_exp_image)
 
-    def stop_exp(self, x_wells, y_wells):
+    def stop_exp(self):
         """Trigger to stop experiment."""
 
         async def stop_imaging(center, event):
             """Run to stop the experiment."""
-            next_well_x, _ = next_well_xy(center.sample, PLATE_NAME, x_wells, y_wells)
             match = match_event(
                 event,
                 field_x=self.x_fields - 1,
@@ -323,7 +332,7 @@ async def stop_imaging(center, event):
                 well_img_ok=True,
             )
 
-            if not match or next_well_x is not None:
+            if not match or self.wells_left:
                 return
 
             await center.actions.command.stop_imaging()

From 5a15029222dfd03d91778a4b7915299a78eb1060 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 13:50:46 +0100
Subject: [PATCH 65/76] Refactor to simplify into one case

---
 camacqplugins/production/__init__.py | 80 ++++------------------------
 1 file changed, 11 insertions(+), 69 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index dddc160..bde1e17 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -6,6 +6,7 @@
 
 import voluptuous as vol
 
+from camacq.const import CAMACQ_START_EVENT
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
@@ -77,31 +78,26 @@ def __init__(self, center, conf):
     async def setup(self, state_file):
         """Set up the flow."""
         if state_file is not None:
-            x_wells = None
-            y_wells = None
-            await self.load_sample(state_file)
-            self.image_next_well_on_sample()
+            state_data = await self._center.add_executor_job(read_csv, state_file)
         else:
             x_wells = 12
             y_wells = 8
-            self.wells_left = {
-                (well_x, well_y)
+            state_data = [
+                {"plate_name": PLATE_NAME, "well_x": well_x, "well_y": well_y}
                 for well_x in range(x_wells)
                 for well_y in range(y_wells)
-            }
-            self.start_exp()
-            self.add_next_well(x_wells, y_wells)
-            self.image_next_well_on_event()
+            ]
 
+        await self.load_sample(state_data)
+        self.image_next_well_on_sample()
         self.analyze_gain()
         self.set_exp_gain()
         self.add_exp_job()
         self._remove_handle_exp_image = self.handle_exp_image()
         self.stop_exp()
 
-    async def load_sample(self, state_file):
-        """Load sample state from file."""
-        state_data = await self._center.add_executor_job(read_csv, state_file)
+    async def load_sample(self, state_data):
+        """Load sample state."""
         self.wells_left = {(data["well_x"], data["well_y"]) for data in state_data}
         for data in state_data:
             if data["plate_name"] not in self._center.sample.plates:
@@ -112,46 +108,6 @@ async def load_sample(self, state_file):
             await self._center.actions.sample.set_channel(silent=True, **data)
             await self._center.actions.sample.set_field(silent=True, **data)
 
-    def start_exp(self):
-        """Trigger on start experiment."""
-
-        async def set_start_well(center, event):
-            """Run on start event."""
-            await center.actions.sample.set_well(
-                plate_name=PLATE_NAME, well_x=0, well_y=0
-            )
-
-        return self._center.bus.register("camacq_start_event", set_start_well)
-
-    def add_next_well(self, x_wells, y_wells):
-        """Add next well."""
-
-        async def set_next_well(center, event):
-            """Run on well event."""
-            next_well_x, next_well_y = next_well_xy(
-                center.sample, PLATE_NAME, x_wells, y_wells
-            )
-
-            if (
-                not match_event(
-                    event,
-                    field_x=self.x_fields - 1,
-                    field_y=self.y_fields - 1,
-                    well_img_ok=True,
-                )
-                or next_well_x is None
-                or (next_well_x, next_well_y) not in self.wells_left
-            ):
-                return
-
-            await center.actions.command.stop_imaging()
-            await center.actions.sample.set_well(
-                plate_name=PLATE_NAME, well_x=next_well_x, well_y=next_well_y
-            )
-            self.wells_left.pop((next_well_x, next_well_y))
-
-        return self._center.bus.register("well_event", set_next_well)
-
     def image_next_well_on_sample(self):
         """Image next well in existing sample."""
 
@@ -160,7 +116,7 @@ async def send_cam_job(center, event):
             next_well_x, next_well_y = next_well_xy(center.sample, PLATE_NAME)
 
             if (
-                not match_event(event, event_type="camacq_start_event")
+                not match_event(event, event_type=CAMACQ_START_EVENT)
                 and not match_event(
                     event,
                     field_x=self.x_fields - 1,
@@ -180,7 +136,7 @@ async def send_cam_job(center, event):
             self.wells_left.pop((next_well_x, next_well_y))
 
         removes = []
-        removes.append(self._center.bus.register("camacq_start_event", send_cam_job))
+        removes.append(self._center.bus.register(CAMACQ_START_EVENT, send_cam_job))
         removes.append(self._center.bus.register("well_event", send_cam_job))
 
         def remove_callback():
@@ -191,20 +147,6 @@ def remove_callback():
 
         return remove_callback
 
-    def image_next_well_on_event(self):
-        """Image next well."""
-
-        async def send_cam_job(center, event):
-            """Run on well event."""
-            if event.well.images:
-                return
-
-            await self.send_gain_jobs(
-                event.well.x, event.well.y,
-            )
-
-        return self._center.bus.register("well_event", send_cam_job)
-
     def analyze_gain(self):
         """Analyze gain."""
 

From c62d7fff509c417360333b449703d58db4d67f0f Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 14:10:54 +0100
Subject: [PATCH 66/76] Clean up strings

---
 README.md                            |   2 +-
 camacqplugins/production/__init__.py | 116 +++++++++++++++++----------
 config_templates/production.yml      |   2 +-
 tests/production/test_production.py  |   2 +-
 4 files changed, 75 insertions(+), 47 deletions(-)

diff --git a/README.md b/README.md
index 2970a9f..746dca8 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@ file.
 
 ```yaml
 production:
-  state_file: '/sample_state.csv'
+  sample_state_file: '/sample_state.csv'
 ```
 
 Each row in the csv file should represent a state of a sample container,
diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index bde1e17..702368c 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -6,7 +6,7 @@
 
 import voluptuous as vol
 
-from camacq.const import CAMACQ_START_EVENT
+from camacq.const import CAMACQ_START_EVENT, CHANNEL_EVENT, IMAGE_EVENT, WELL_EVENT
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
 from camacq.plugins.sample.helper import next_well_xy
@@ -14,34 +14,53 @@
 
 _LOGGER = logging.getLogger(__name__)
 
+CONF_GAIN_PATTERN_NAME = "gain_pattern_name"
+CONF_GAIN_JOB_ID = "gain_job_id"
+CONF_GAIN_JOB_CHANNELS = "gain_job_channels"
+CONF_EXP_PATTERN_NAME = "exp_pattern_name"
+CONF_EXP_JOB_IDS = "exp_job_ids"
+CONF_CHANNELS = "channels"
+CONF_CHANNEL = "channel"
+CONF_JOB_NAME = "job_name"
+CONF_DETECTOR_NUM = "detector_num"
+CONF_DEFAULT_GAIN = "default_gain"
+CONF_MAX_GAIN = "max_gain"
+CONF_WELL_LAYOUT = "well_layout"
+CONF_X_FIELDS = "x_fields"
+CONF_Y_FIELDS = "y_fields"
+CONF_PLOT_SAVE_PATH = "plot_save_path"
+CONF_SAMPLE_STATE_FILE = "sample_state_file"
+
 PLATE_NAME = "00"
-SAMPLE_STATE_FILE = "state_file"
+SAMPLE_PLATE_NAME = "plate_name"
+SAMPLE_WELL_X = "well_x"
+SAMPLE_WELL_Y = "well_y"
 
 CONFIG_SCHEMA = vol.Schema(
     {
-        vol.Required("gain_pattern_name"): vol.Coerce(str),
-        vol.Required("gain_job_id"): vol.Coerce(int),
-        vol.Required("gain_job_channels"): vol.Coerce(int),
-        vol.Required("exp_pattern_name"): vol.Coerce(str),
-        vol.Required("exp_job_ids"): vol.All(
+        vol.Required(CONF_GAIN_PATTERN_NAME): vol.Coerce(str),
+        vol.Required(CONF_GAIN_JOB_ID): vol.Coerce(int),
+        vol.Required(CONF_GAIN_JOB_CHANNELS): vol.Coerce(int),
+        vol.Required(CONF_EXP_PATTERN_NAME): vol.Coerce(str),
+        vol.Required(CONF_EXP_JOB_IDS): vol.All(
             [vol.Coerce(int)], vol.Length(min=3, max=3)
         ),
-        vol.Required("channels"): [
+        vol.Required(CONF_CHANNELS): [
             {
-                vol.Required("channel"): vol.Coerce(str),
-                vol.Required("job_name"): vol.Coerce(str),
-                vol.Required("detector_num"): vol.Coerce(int),
-                vol.Required("default_gain"): vol.Coerce(int),
-                vol.Required("max_gain"): vol.Coerce(int),
+                vol.Required(CONF_CHANNEL): vol.Coerce(str),
+                vol.Required(CONF_JOB_NAME): vol.Coerce(str),
+                vol.Required(CONF_DETECTOR_NUM): vol.Coerce(int),
+                vol.Required(CONF_DEFAULT_GAIN): vol.Coerce(int),
+                vol.Required(CONF_MAX_GAIN): vol.Coerce(int),
             }
         ],
-        vol.Required("well_layout"): {
-            vol.Required("x_fields"): vol.Coerce(int),
-            vol.Required("y_fields"): vol.Coerce(int),
+        vol.Required(CONF_WELL_LAYOUT): {
+            vol.Required(CONF_X_FIELDS): vol.Coerce(int),
+            vol.Required(CONF_Y_FIELDS): vol.Coerce(int),
         },
         # pylint: disable=no-value-for-parameter
-        "plot_save_path": vol.IsDir(),
-        SAMPLE_STATE_FILE: vol.IsFile(),
+        CONF_PLOT_SAVE_PATH: vol.IsDir(),
+        CONF_SAMPLE_STATE_FILE: vol.IsFile(),
     },
 )
 
@@ -50,7 +69,7 @@ async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
     flow = WorkFlow(center, conf)
-    state_file = conf.get(SAMPLE_STATE_FILE)
+    state_file = conf.get(CONF_SAMPLE_STATE_FILE)
     await flow.setup(state_file)
 
 
@@ -62,16 +81,16 @@ class WorkFlow:
     def __init__(self, center, conf):
         """Set up instance."""
         self._center = center
-        self.gain_pattern = conf["gain_pattern_name"]
-        self.gain_job_id = conf["gain_job_id"]
-        self.gain_job_channels = conf["gain_job_channels"]
-        self.exp_pattern = conf["exp_pattern_name"]
-        self.exp_job_ids = conf["exp_job_ids"]
-        self.channels = conf["channels"]
-        well_layout = conf["well_layout"]
-        self.x_fields = well_layout["x_fields"]
-        self.y_fields = well_layout["y_fields"]
-        self.plot_save_path = conf.get("plot_save_path")
+        self.gain_pattern = conf[CONF_GAIN_PATTERN_NAME]
+        self.gain_job_id = conf[CONF_GAIN_JOB_ID]
+        self.gain_job_channels = conf[CONF_GAIN_JOB_CHANNELS]
+        self.exp_pattern = conf[CONF_EXP_PATTERN_NAME]
+        self.exp_job_ids = conf[CONF_EXP_JOB_IDS]
+        self.channels = conf[CONF_CHANNELS]
+        well_layout = conf[CONF_WELL_LAYOUT]
+        self.x_fields = well_layout[CONF_X_FIELDS]
+        self.y_fields = well_layout[CONF_Y_FIELDS]
+        self.plot_save_path = conf.get(CONF_PLOT_SAVE_PATH)
         self._remove_handle_exp_image = None
         self.wells_left = set()
 
@@ -83,7 +102,11 @@ async def setup(self, state_file):
             x_wells = 12
             y_wells = 8
             state_data = [
-                {"plate_name": PLATE_NAME, "well_x": well_x, "well_y": well_y}
+                {
+                    SAMPLE_PLATE_NAME: PLATE_NAME,
+                    SAMPLE_WELL_X: well_x,
+                    SAMPLE_WELL_Y: well_y,
+                }
                 for well_x in range(x_wells)
                 for well_y in range(y_wells)
             ]
@@ -98,12 +121,17 @@ async def setup(self, state_file):
 
     async def load_sample(self, state_data):
         """Load sample state."""
-        self.wells_left = {(data["well_x"], data["well_y"]) for data in state_data}
+        self.wells_left = {
+            (data[SAMPLE_WELL_X], data[SAMPLE_WELL_Y]) for data in state_data
+        }
         for data in state_data:
-            if data["plate_name"] not in self._center.sample.plates:
+            if data[SAMPLE_PLATE_NAME] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
-            well_coord = int(data["well_x"]), int(data["well_y"])
-            if well_coord not in self._center.sample.plates[data["plate_name"]].wells:
+            well_coord = int(data[SAMPLE_WELL_X]), int(data[SAMPLE_WELL_Y])
+            if (
+                well_coord
+                not in self._center.sample.plates[data[SAMPLE_PLATE_NAME]].wells
+            ):
                 await self._center.actions.sample.set_well(silent=True, **data)
             await self._center.actions.sample.set_channel(silent=True, **data)
             await self._center.actions.sample.set_field(silent=True, **data)
@@ -137,7 +165,7 @@ async def send_cam_job(center, event):
 
         removes = []
         removes.append(self._center.bus.register(CAMACQ_START_EVENT, send_cam_job))
-        removes.append(self._center.bus.register("well_event", send_cam_job))
+        removes.append(self._center.bus.register(WELL_EVENT, send_cam_job))
 
         def remove_callback():
             """Remove all registered listeners of this method."""
@@ -183,7 +211,7 @@ async def calc_gain(center, event):
                 save_path=save_path,
             )
 
-        return self._center.bus.register("image_event", calc_gain)
+        return self._center.bus.register(IMAGE_EVENT, calc_gain)
 
     def set_exp_gain(self):
         """Set experiment gain."""
@@ -194,12 +222,12 @@ async def set_gain(center, event):
                 (
                     channel
                     for channel in self.channels
-                    if event.channel_name == channel["channel"]
+                    if event.channel_name == channel[CONF_CHANNEL]
                 )
             )
-            exp = channel["job_name"]
-            num = channel["detector_num"]
-            gain = min(event.gain or channel["default_gain"], channel["max_gain"])
+            exp = channel[CONF_JOB_NAME]
+            num = channel[CONF_DETECTOR_NUM]
+            gain = min(event.gain or channel[CONF_DEFAULT_GAIN], channel[CONF_MAX_GAIN])
 
             command = gain_com(exp=exp, num=num, value=gain)
 
@@ -222,7 +250,7 @@ def add_exp_job(self):
         async def add_cam_job(center, event):
             """Add an experiment job to the cam list."""
             last_channel = self.channels[-1]
-            if not match_event(event, channel_name=last_channel["channel"]) or len(
+            if not match_event(event, channel_name=last_channel[CONF_CHANNEL]) or len(
                 event.well.channels
             ) != len(self.channels):
                 return
@@ -250,7 +278,7 @@ async def add_cam_job(center, event):
             await center.actions.command.start_imaging()
             await center.actions.command.send(command="/cmd:startcamscan")
 
-        return self._center.bus.register("channel_event", add_cam_job)
+        return self._center.bus.register(CHANNEL_EVENT, add_cam_job)
 
     def handle_exp_image(self):
         """Handle experiment image."""
@@ -260,7 +288,7 @@ async def on_exp_image(center, event):
             await self.rename_image(center, event)
             await self.set_sample_img_ok(center, event)
 
-        return self._center.bus.register("image_event", on_exp_image)
+        return self._center.bus.register(IMAGE_EVENT, on_exp_image)
 
     def stop_exp(self):
         """Trigger to stop experiment."""
@@ -281,7 +309,7 @@ async def stop_imaging(center, event):
 
             _LOGGER.info("Congratulations, experiment is finished!")
 
-        return self._center.bus.register("well_event", stop_imaging)
+        return self._center.bus.register(WELL_EVENT, stop_imaging)
 
     async def send_gain_jobs(self, well_x, well_y):
         """Send gain cam jobs for the center fields of a well."""
diff --git a/config_templates/production.yml b/config_templates/production.yml
index 4ecdd38..3a28568 100644
--- a/config_templates/production.yml
+++ b/config_templates/production.yml
@@ -1,5 +1,5 @@
 production:
-  #state_file: "/path/to/sample_state.csv"
+  #sample_state_file: "/path/to/sample_state.csv"
   gain_pattern_name: p10xgain
   gain_job_id: 3
   gain_job_channels: 32
diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index 5e148b9..cad6475 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -148,7 +148,7 @@ async def test_load_sample(center, tmp_path):
     state_file = tmp_path / "state_file.csv"
     state_file.write_text(SAMPLE_STATE)
     config = YAML(typ="safe").load(CONFIG)
-    config["production"]["state_file"] = str(state_file)
+    config["production"]["sample_state_file"] = str(state_file)
     plate_name = "00"
     await plugins.setup_module(center, config)
     await center.wait_for()

From 39cf3f5a9d9c39b67e5917048b6b8f9a01c34c69 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 14:16:41 +0100
Subject: [PATCH 67/76] Clean up

---
 camacqplugins/production/__init__.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 702368c..0ca701f 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -121,13 +121,11 @@ async def setup(self, state_file):
 
     async def load_sample(self, state_data):
         """Load sample state."""
-        self.wells_left = {
-            (data[SAMPLE_WELL_X], data[SAMPLE_WELL_Y]) for data in state_data
-        }
         for data in state_data:
             if data[SAMPLE_PLATE_NAME] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
             well_coord = int(data[SAMPLE_WELL_X]), int(data[SAMPLE_WELL_Y])
+            self.wells_left.add(well_coord)
             if (
                 well_coord
                 not in self._center.sample.plates[data[SAMPLE_PLATE_NAME]].wells

From 6a2c3be667353bb585cbb0cff31c44b4d6317c34 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 14:54:16 +0100
Subject: [PATCH 68/76] Load csv file during validation

---
 camacqplugins/production/__init__.py | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 0ca701f..d8c83ca 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -36,6 +36,13 @@
 SAMPLE_WELL_X = "well_x"
 SAMPLE_WELL_Y = "well_y"
 
+
+@vol.truth
+def is_csv(value):
+    """Return true if value ends with .csv."""
+    return value.endswith(".csv")
+
+
 CONFIG_SCHEMA = vol.Schema(
     {
         vol.Required(CONF_GAIN_PATTERN_NAME): vol.Coerce(str),
@@ -60,7 +67,7 @@
         },
         # pylint: disable=no-value-for-parameter
         CONF_PLOT_SAVE_PATH: vol.IsDir(),
-        CONF_SAMPLE_STATE_FILE: vol.IsFile(),
+        CONF_SAMPLE_STATE_FILE: vol.All(vol.IsFile(), is_csv, read_csv),
     },
 )
 
@@ -69,8 +76,8 @@ async def setup_module(center, config):
     """Set up production plugin."""
     conf = config["production"]
     flow = WorkFlow(center, conf)
-    state_file = conf.get(CONF_SAMPLE_STATE_FILE)
-    await flow.setup(state_file)
+    state_data = conf.get(CONF_SAMPLE_STATE_FILE)
+    await flow.setup(state_data)
 
 
 class WorkFlow:
@@ -94,11 +101,9 @@ def __init__(self, center, conf):
         self._remove_handle_exp_image = None
         self.wells_left = set()
 
-    async def setup(self, state_file):
+    async def setup(self, state_data):
         """Set up the flow."""
-        if state_file is not None:
-            state_data = await self._center.add_executor_job(read_csv, state_file)
-        else:
+        if state_data is None:
             x_wells = 12
             y_wells = 8
             state_data = [

From e489c387cbdc6b974e8f4d5b2217f63755bed77b Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 14:54:49 +0100
Subject: [PATCH 69/76] Fix set remove

---
 camacqplugins/production/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index d8c83ca..52f047d 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -164,7 +164,7 @@ async def send_cam_job(center, event):
             await self.send_gain_jobs(
                 next_well_x, next_well_y,
             )
-            self.wells_left.pop((next_well_x, next_well_y))
+            self.wells_left.remove((next_well_x, next_well_y))
 
         removes = []
         removes.append(self._center.bus.register(CAMACQ_START_EVENT, send_cam_job))

From 561ad98e612484d92298a4335c08bc2038800695 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 15:04:48 +0100
Subject: [PATCH 70/76] Clean up

---
 camacqplugins/production/__init__.py | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 52f047d..6abf0ca 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -77,6 +77,18 @@ async def setup_module(center, config):
     conf = config["production"]
     flow = WorkFlow(center, conf)
     state_data = conf.get(CONF_SAMPLE_STATE_FILE)
+    if state_data is None:
+        x_wells = 12
+        y_wells = 8
+        state_data = [
+            {
+                SAMPLE_PLATE_NAME: PLATE_NAME,
+                SAMPLE_WELL_X: well_x,
+                SAMPLE_WELL_Y: well_y,
+            }
+            for well_x in range(x_wells)
+            for well_y in range(y_wells)
+        ]
     await flow.setup(state_data)
 
 
@@ -103,19 +115,6 @@ def __init__(self, center, conf):
 
     async def setup(self, state_data):
         """Set up the flow."""
-        if state_data is None:
-            x_wells = 12
-            y_wells = 8
-            state_data = [
-                {
-                    SAMPLE_PLATE_NAME: PLATE_NAME,
-                    SAMPLE_WELL_X: well_x,
-                    SAMPLE_WELL_Y: well_y,
-                }
-                for well_x in range(x_wells)
-                for well_y in range(y_wells)
-            ]
-
         await self.load_sample(state_data)
         self.image_next_well_on_sample()
         self.analyze_gain()

From 3162c8616bd386ad0ae5624c95b75ca1b96ac3bb Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 16:02:12 +0100
Subject: [PATCH 71/76] Add sample state file validation

---
 camacqplugins/production/__init__.py | 38 ++++++++++++++++++++++++++--
 1 file changed, 36 insertions(+), 2 deletions(-)

diff --git a/camacqplugins/production/__init__.py b/camacqplugins/production/__init__.py
index 6abf0ca..d151b75 100644
--- a/camacqplugins/production/__init__.py
+++ b/camacqplugins/production/__init__.py
@@ -9,6 +9,7 @@
 from camacq.const import CAMACQ_START_EVENT, CHANNEL_EVENT, IMAGE_EVENT, WELL_EVENT
 from camacq.event import match_event
 from camacq.plugins.leica.command import cam_com, del_com, gain_com
+from camacq.plugins.sample import ACTION_TO_METHOD, ACTION_SET_PLATE
 from camacq.plugins.sample.helper import next_well_xy
 from camacq.util import read_csv
 
@@ -43,6 +44,37 @@ def is_csv(value):
     return value.endswith(".csv")
 
 
+def is_sample_state(value):
+    """Validate state data.
+
+    At least one sample action must validate per sample data item.
+    """
+    for idx, data in enumerate(value):
+        valid = False
+        error = None
+        for action, settings in ACTION_TO_METHOD.items():
+            if action == ACTION_SET_PLATE:
+                continue
+            schema = settings["schema"]
+            try:
+                data.update(schema(data))
+            except vol.Invalid as exc:
+                error = exc
+                continue
+            else:
+                valid = True
+
+        if not valid:
+            _LOGGER.error(
+                "The sample state file contains invalid data at row %s: %s",
+                idx + 2,
+                error,
+            )
+            raise error
+
+    return value
+
+
 CONFIG_SCHEMA = vol.Schema(
     {
         vol.Required(CONF_GAIN_PATTERN_NAME): vol.Coerce(str),
@@ -67,7 +99,9 @@ def is_csv(value):
         },
         # pylint: disable=no-value-for-parameter
         CONF_PLOT_SAVE_PATH: vol.IsDir(),
-        CONF_SAMPLE_STATE_FILE: vol.All(vol.IsFile(), is_csv, read_csv),
+        CONF_SAMPLE_STATE_FILE: vol.All(
+            vol.IsFile(), is_csv, read_csv, is_sample_state
+        ),
     },
 )
 
@@ -128,7 +162,7 @@ async def load_sample(self, state_data):
         for data in state_data:
             if data[SAMPLE_PLATE_NAME] not in self._center.sample.plates:
                 await self._center.actions.sample.set_plate(silent=True, **data)
-            well_coord = int(data[SAMPLE_WELL_X]), int(data[SAMPLE_WELL_Y])
+            well_coord = data[SAMPLE_WELL_X], data[SAMPLE_WELL_Y]
             self.wells_left.add(well_coord)
             if (
                 well_coord

From ed963259c6b18d5beef6d6ad80284acdc39a8898 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 16:04:43 +0100
Subject: [PATCH 72/76] Fix test

---
 tests/production/test_production.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/tests/production/test_production.py b/tests/production/test_production.py
index cad6475..99e670d 100644
--- a/tests/production/test_production.py
+++ b/tests/production/test_production.py
@@ -70,8 +70,8 @@ def job_id(self):
         return self.data.get("job_id")
 
 
-async def test_duplicate_image_events(center, tmp_path):
-    """Test duplicate image events."""
+async def test_image_events(center, tmp_path):
+    """Test image events."""
     config = YAML(typ="safe").load(CONFIG)
     plate_name = "00"
     well_x = 0
@@ -126,7 +126,6 @@ async def fire_gain_event(**kwargs):
         }
     )
     center.create_task(center.bus.notify(event))
-    center.create_task(center.bus.notify(event))
     await center.wait_for()
 
     assert calc_gain.call_count == 1

From 2a46109ac00105f2416828b55d8274fa550ab7e6 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 16:54:23 +0100
Subject: [PATCH 73/76] Update readmes

---
 README.md                          | 57 +++++++++++++++---------------
 camacqplugins/production/README.md | 55 ++++++++++++++++++++++++++++
 2 files changed, 83 insertions(+), 29 deletions(-)
 create mode 100644 camacqplugins/production/README.md

diff --git a/README.md b/README.md
index 746dca8..48124df 100644
--- a/README.md
+++ b/README.md
@@ -1,45 +1,44 @@
 # camacq-plugins
 
-Plugins for camacq
+Plugins for camacq:
 
-## Usage
+- [production](camacqplugins/production)
 
-To allow the user to set up the sample state before starting an
-experiment, camacq can load the sample state from a file. In the production
-configuration section there is an option to specify a path to a csv
-file.
+## Installation
 
-```yaml
-production:
-  sample_state_file: '/sample_state.csv'
-```
+- Clone and install the package.
 
-Each row in the csv file should represent a state of a sample container,
-ie plate, well, field or channel. The csv file should also have a
-header. See below.
+    ```sh
+    # Clone the repo.
+    git clone https://github.com/CellProfiling/camacq-plugins.git
+    # Enter directory.
+    cd camacq-plugins
+    # Install package.
+    pip install .
+    # Test that program is callable and show help.
+    camacq -h
+    ```
 
-```
-plate_name,well_x,well_y,channel_name,gain
-00,1,1,blue,600
-```
+### Requirements
 
-This example will set create a plate '00', a well (1, 1), a blue channel
-and set the gain of the blue channel to 600.
+- Python version 3.6+.
+- camacq >= 0.4.0
 
-```
-plate_name,well_x,well_y,field_x,field_y
-00,1,1,1,1
-```
-
-This example will create a plate '00' a well (1, 1) and a field (1, 1)
-in the sample state.
+## Usage
 
-## Installation
+Add configuration for the plugin you want to run.
+See the [config_templates](config_templates/) directory for example configuration.
 
-### Requirements
+Then start `camacq`.
 
-## Compatibility
+```sh
+camacq
+```
 
 ## Licence
 
+- Apache-2.0.
+
 ## Authors
+
+- Martin Hjelmare
diff --git a/camacqplugins/production/README.md b/camacqplugins/production/README.md
new file mode 100644
index 0000000..72d24e0
--- /dev/null
+++ b/camacqplugins/production/README.md
@@ -0,0 +1,55 @@
+# Production
+
+## Usage
+
+Add configuration for the `production`, `gain`, `leica` and `rename` plugin, in the `camacq` configuration file.
+See the [config_templates](config_templates/) directory for example configuration.
+
+```yaml
+production:
+  ...
+
+gain:
+  ...
+
+rename_image:
+
+leica:
+  ...
+```
+
+Then start `camacq`.
+
+```sh
+camacq
+```
+
+To allow the user to set up the sample state before starting an
+experiment, camacq can load the sample state from a file. In the production
+configuration section there is an option to specify a path to a csv
+file.
+
+```yaml
+production:
+  sample_state_file: '/sample_state.csv'
+```
+
+Each row in the csv file should represent at least one state of a sample container,
+ie well, field or channel. A plate name must also be included. The csv file should have a
+header. See below.
+
+```csv
+plate_name,well_x,well_y,channel_name,gain
+00,1,1,blue,600
+```
+
+This example will set a plate '00', a well (1, 1), a blue channel
+and set the gain of the blue channel to 600.
+
+```csv
+plate_name,well_x,well_y,field_x,field_y
+00,1,1,1,1
+```
+
+This example will create a plate '00' a well (1, 1) and a field (1, 1)
+in the sample state.

From 42ad2dda6c9ca463ff160fd301ad516209ebf4d4 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 17:00:05 +0100
Subject: [PATCH 74/76] Fix readme relative link

---
 README.md                          | 2 +-
 camacqplugins/production/README.md | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 48124df..de2c026 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 Plugins for camacq:
 
-- [production](camacqplugins/production)
+- [production](camacqplugins/production/)
 
 ## Installation
 
diff --git a/camacqplugins/production/README.md b/camacqplugins/production/README.md
index 72d24e0..3ce9c4c 100644
--- a/camacqplugins/production/README.md
+++ b/camacqplugins/production/README.md
@@ -3,7 +3,7 @@
 ## Usage
 
 Add configuration for the `production`, `gain`, `leica` and `rename` plugin, in the `camacq` configuration file.
-See the [config_templates](config_templates/) directory for example configuration.
+See the [config_templates](../config_templates/) directory for example configuration.
 
 ```yaml
 production:

From 7212ed0e5d5930f4ec055322185f80fd72a69d45 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sat, 7 Dec 2019 17:03:07 +0100
Subject: [PATCH 75/76] Add Python 3.8 tox env

---
 tox.ini | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tox.ini b/tox.ini
index 052b4a5..d3f181a 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,5 @@
 [tox]
-envlist = py36, py37
+envlist = py36, py37, py38
 
 [testenv]
 commands =

From 3af927b83cc6f2db0ebfd175f63ee77e0ab8a050 Mon Sep 17 00:00:00 2001
From: Martin Hjelmare <marhje52@kth.se>
Date: Sun, 8 Dec 2019 01:45:17 +0100
Subject: [PATCH 76/76] Skip missing tox interpreters

---
 tox.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tox.ini b/tox.ini
index d3f181a..bf47625 100644
--- a/tox.ini
+++ b/tox.ini
@@ -1,5 +1,6 @@
 [tox]
 envlist = py36, py37, py38
+skip_missing_interpreters = True
 
 [testenv]
 commands =