From 35e0d1913e67f46471c3f31f33855260c6988b6b Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nstuurman@altoslabs.com>
Date: Tue, 5 Sep 2023 10:06:05 -0700
Subject: [PATCH 1/4] StackResampler: clear queue when initializing
 projections. Otherwise, strange ghost images appear when re-utilizing an
 instance of this class.

---
 .../main/java/org/micromanager/lightsheet/StackResampler.java   | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/java/src/main/java/org/micromanager/lightsheet/StackResampler.java b/java/src/main/java/org/micromanager/lightsheet/StackResampler.java
index 40a1e6cc..18298974 100644
--- a/java/src/main/java/org/micromanager/lightsheet/StackResampler.java
+++ b/java/src/main/java/org/micromanager/lightsheet/StackResampler.java
@@ -345,6 +345,8 @@ private void precomputeReconWeightings() {
     * projection and recon arrays.
     */
    public void initializeProjections() {
+      // Not quite sure why, but this is needed to be able to re-utilize this Resampler.
+      imageQueue_.clear();
       int reconImageZShape = this.reconImageShape_[0];
       int reconImageYShape = this.reconImageShape_[1];
       int reconImageXShape = this.reconImageShape_[2];

From 82f55c6079c1a9a645f3d64ab05262820956fd96 Mon Sep 17 00:00:00 2001
From: Nico Stuurman <nstuurman@altoslabs.com>
Date: Tue, 5 Sep 2023 10:46:14 -0700
Subject: [PATCH 2/4] Bump java version to 0.43.1

---
 java/pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/pom.xml b/java/pom.xml
index 0ed8ce65..13030f7e 100644
--- a/java/pom.xml
+++ b/java/pom.xml
@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.43.0</version>
+     <version>0.43.1</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>

From f7e9f4d05aa596227f2ec3dc1fd0f005d6eeec0f Mon Sep 17 00:00:00 2001
From: LabelFree <ivan.ivanov@czbiohub.org>
Date: Tue, 5 Sep 2023 17:26:01 -0700
Subject: [PATCH 3/4] add equal exposures to channel sequencing test

---
 pycromanager/test/test_acquisition.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/pycromanager/test/test_acquisition.py b/pycromanager/test/test_acquisition.py
index 6f79bcc3..075c3224 100644
--- a/pycromanager/test/test_acquisition.py
+++ b/pycromanager/test/test_acquisition.py
@@ -152,11 +152,16 @@ def test_channel_seq_acq(launch_mm_headless, setup_data_folder):
     Test that channels can be sequenced
 
     """
+    channels = ['DAPI', 'FITC', 'Rhodamine', 'Cy5']
+    channel_exposures_ms = [10] * len(channels)  # exposure times may be provided, but must be all equal
+
     mmc = Core()
+    mmc.set_exposure(2)
     mmc.set_property('LED', 'Sequence', 'On')
 
     events = multi_d_acquisition_events(channel_group='Channel-Multiband',
-                                        channels=['DAPI', 'FITC', 'Rhodamine', 'Cy5'])
+                                        channels=channels,
+                                        channel_exposures_ms=channel_exposures_ms)
 
     def hook_fn(_events):
         assert check_acq_sequenced(_events, len(events)), 'Sequenced acquisition is not built correctly'

From 07cc3583319adb5aa6e7f5f1bbb283052a599d0b Mon Sep 17 00:00:00 2001
From: talonchandler <ivan.ivanov@czbiohub.org>
Date: Wed, 6 Sep 2023 14:18:40 -0700
Subject: [PATCH 4/4] update channel seq tests

---
 pycromanager/test/test_acquisition.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)

diff --git a/pycromanager/test/test_acquisition.py b/pycromanager/test/test_acquisition.py
index 075c3224..bad90cb1 100644
--- a/pycromanager/test/test_acquisition.py
+++ b/pycromanager/test/test_acquisition.py
@@ -151,6 +151,29 @@ def test_channel_seq_acq(launch_mm_headless, setup_data_folder):
     """
     Test that channels can be sequenced
 
+    """
+    channels = ['DAPI', 'FITC', 'Rhodamine', 'Cy5']
+
+    mmc = Core()
+    mmc.set_property('LED', 'Sequence', 'On')
+
+    events = multi_d_acquisition_events(channel_group='Channel-Multiband',
+                                        channels=channels)
+
+    def hook_fn(_events):
+        assert check_acq_sequenced(_events, len(events)), 'Sequenced acquisition is not built correctly'
+        return None  # no need to actually acquire the data
+
+    with Acquisition(setup_data_folder, 'acq', show_display=False,
+                     pre_hardware_hook_fn=hook_fn) as acq:
+        acq.acquire(events)
+
+
+def test_channel_exp_seq_acq(launch_mm_headless, setup_data_folder):
+    """
+    Test that channels can be sequenced when equal exposure times for each
+    channel are provided
+
     """
     channels = ['DAPI', 'FITC', 'Rhodamine', 'Cy5']
     channel_exposures_ms = [10] * len(channels)  # exposure times may be provided, but must be all equal