From 9c47686db810f7a3cfecec65b8f8f1ef639fc402 Mon Sep 17 00:00:00 2001
From: snyder18 <snyder18@stanford.edu>
Date: Mon, 30 Jul 2018 11:13:38 -0700
Subject: [PATCH 1/2] Made modifications to the xy stage acq to acquire dark
 frames automatically for each position.  Minor addition to eo_acquisition for
 ease of dark frame acquisitions.

---
 harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py |  5 ++++-
 python/eo_acquisition.py                           | 10 ++++++++++
 python/xy_stage_acquisition.py                     |  2 ++
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py b/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
index 524b78f..677f83e 100644
--- a/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
+++ b/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
@@ -25,7 +25,7 @@ def run(self):
         self.bcount.
         """
         # Move to initial (xoffset, yoffset) position.
-        self._moveTo(self.xoffset, self.yoffset)
+        self._moveTo(self.xoffset, self.yoffset)     
 
         # Loop over image sequence.
         actuateXed = False
@@ -50,6 +50,9 @@ def run(self):
             for i in range(self.imcount):
                 self.take_image(seqno, exptime, openShutter, actuateXed,
                                 image_type, file_template=file_template)
+            # Take dark frame(s)
+            for i in range(self.dcount):
+                self.dark_image(seqno, exptime)
             # Take bias frame(s).
             for i in range(self.bcount):
                 self.bias_image(seqno)
diff --git a/python/eo_acquisition.py b/python/eo_acquisition.py
index 51c5059..c4ff243 100644
--- a/python/eo_acquisition.py
+++ b/python/eo_acquisition.py
@@ -359,6 +359,16 @@ def bias_image(self, seqno, max_tries=3):
         self.take_image(seqno, exptime, openShutter, actuateXed, "BIAS",
                         timeout=150, max_tries=max_tries)
 
+    def dark_image(self, seqno, exptime, max_tries=3):
+        """
+        Take dark image
+        """
+        openShutter = False
+        actuateXed = False
+        timeout = int(max(150, exptime + 20))
+        self.take_image(seqno, exptime, openShutter, actuateXed, "DARK",
+                        timeout=timeout, max_tries=max_tries)
+
     def measured_flux(self, wl, seqno=0, fluxcal_time=2.):
         """
         Compute the measured flux by taking an exposure at the
diff --git a/python/xy_stage_acquisition.py b/python/xy_stage_acquisition.py
index f18254f..2a02d9d 100644
--- a/python/xy_stage_acquisition.py
+++ b/python/xy_stage_acquisition.py
@@ -22,6 +22,8 @@ def __init__(self, seqfile, acq_config_file, acqname, metadata,
 
         self.bcount = int(self.eo_config.get('%s_BCOUNT' % acqname.upper(),
                                              default=1))
+        self.dcount = int(self.eo_config.get('%s_DCOUNT' % acqname.upper(),
+                                             default=0))
         self.imcount = int(self.eo_config.get('%s_IMCOUNT' % acqname.upper(),
                                               default=1))
         self.xoffset = float(self.eo_config.get('%s_XOFFSET' % acqname.upper(),

From c5fff4b78e9b1fdba9c2399aa16a2df8e7fc6e8b Mon Sep 17 00:00:00 2001
From: snyder18 <snyder18@stanford.edu>
Date: Wed, 1 Aug 2018 10:29:54 -0700
Subject: [PATCH 2/2] Made requested changes to whitespace.

---
 harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py b/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
index 677f83e..514a7ca 100644
--- a/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
+++ b/harnessed_jobs/xy_stage_acq/v0/ccs_xy_stage_acq.py
@@ -25,7 +25,7 @@ def run(self):
         self.bcount.
         """
         # Move to initial (xoffset, yoffset) position.
-        self._moveTo(self.xoffset, self.yoffset)     
+        self._moveTo(self.xoffset, self.yoffset)
 
         # Loop over image sequence.
         actuateXed = False