Merge branch 'main' into lightSheetFixes

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.41.2</version>
+     <version>0.41.6</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>
@@ -54,7 +54,7 @@
       <dependency>
          <groupId>org.micro-manager.acqengj</groupId>
          <artifactId>AcqEngJ</artifactId>
-     <version>0.29.1</version>
+     <version>0.30.0</version>
       </dependency>
       <dependency>
          <groupId>org.micro-manager.ndviewer</groupId>
@@ -64,7 +64,7 @@
       <dependency>
          <groupId>org.micro-manager.ndtiffstorage</groupId>
          <artifactId>NDTiffStorage</artifactId>
-     <version>2.13.1</version>
+     <version>2.14.0</version>
       </dependency>
   </dependencies>
 

java/src/main/java/org/micromanager/explore/ExploreAcqUIAndStorage.java

@@ -412,8 +412,15 @@ public void finish() {
          storage_.setDisplaySettings(displaySettings);
          storage_.finishedWriting();
       }
-      display_.setWindowTitle(getUniqueAcqName() + " (Finished)");
-      displayCommunicationExecutor_.shutdown();
+
+      try {
+         storage_.checkForWritingException();
+         display_.setWindowTitle(name_ + " (Finished)");
+      } catch (Exception e) {
+         display_.setWindowTitle(name_ + " (Finished with saving error)");
+      } finally {
+         displayCommunicationExecutor_.shutdown();
+      }
       displayCommunicationExecutor_ = null;
    }
 

java/src/main/java/org/micromanager/remote/RemoteEventSource.java

@@ -54,7 +54,6 @@ public RemoteEventSource() {
             System.out.println("pull socket started");
             while (true) {
                List<AcquisitionEvent> eList = pullSocket_.next();
-               System.out.println("got something from pull socket");
                boolean finished = eList.get(eList.size() - 1).isAcquisitionFinishedEvent();
                Future result = acq_.submitEventIterator(eList.iterator());
                result.get(); //propogate any exceptions
@@ -65,14 +64,12 @@ public RemoteEventSource() {
             }
          } catch (InterruptedException e) {
             // it was aborted
-            System.out.println("pull socket interrupted");
          } catch (Exception e) {
             e.printStackTrace();
             if (!executor_.isShutdown()) {
                acq_.abort(e);
             }
          } finally {
-            System.out.println("pull socket closed");
             pullSocket_.close();
          }
 

java/src/main/java/org/micromanager/remote/RemoteViewerStorageAdapter.java

@@ -234,8 +234,14 @@ public void finish() {
       }
 
       if (showViewer_) {
-         viewer_.setWindowTitle(name_ + " (Finished)");
-         displayCommunicationExecutor_.shutdown();
+         try {
+            storage_.checkForWritingException();
+            viewer_.setWindowTitle(name_ + " (Finished)");
+         } catch (Exception e) {
+            viewer_.setWindowTitle(name_ + " (Finished with saving error)");
+         } finally {
+            displayCommunicationExecutor_.shutdown();
+         }
       }
       finished_ = true;
    }

pycromanager/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 27, 5)
+version_info = (0, 28, 1)
 __version__ = ".".join(map(str, version_info))

pycromanager/acq_util.py

@@ -7,7 +7,7 @@
 import copy
 import types
 import numpy as np
-from typing import Union, List
+from typing import Union, List, Iterable
 
 SUBPROCESSES = []
 
@@ -107,8 +107,9 @@ def multi_d_acquisition_events(
     channel_group: str=None,
     channels: list=None,
     channel_exposures_ms: list=None,
-    xy_positions=None,
-    xyz_positions=None,
+    xy_positions: Iterable=None,
+    xyz_positions: Iterable=None,
+    position_labels: List[str]=None,
     order: str="tpcz",
     keep_shutter_open_between_channels: bool=False,
     keep_shutter_open_between_z_steps: bool=False,
@@ -142,17 +143,13 @@ def multi_d_acquisition_events(
     channel_exposures_ms : list of floats or ints
         list of camera exposure times corresponding to each channel. The length of this list
         should be the same as the the length of the list of channels (Default value = None)
-    xy_positions : arraylike
-        N by 2 array where N is the number of XY stage positions, and the 2 are the X and Y
-        coordinates (Default value = None)
-    xyz_positions : arraylike
-        N by 3 array where N is the number of XY stage positions, and the 3 are the X, Y and Z coordinates.
+    xy_positions : iterable
+        An array of shape (N, 2) containing N (X, Y) stage coordinates. (Default value = None)
+    xyz_positions : iterable
+        An array of shape (N, 3) containing N (X, Y, Z) stage coordinates. (Default value = None).
         If passed then z_start, z_end, and z_step will be relative to the z_position in xyz_positions. (Default value = None)
-    z_positions : arraylike
-        The z_positions for each xy point. Either 1D (shape: (N,) ) to specify the center z position for each xy point,
-        or 2D (shape: (N, n_z) ) to fully specify the xyz points.
-        If z_positions is 1D and z_start, z_end and z_step are not None then relative
-        z_positions will be created using np.arange(z_position + z_start, z_position + z_end, z_step)
+    position_labels : iterable
+        An array of length N containing position labels for each of the XY stage positions. (Default value = None)
     order : str
         string that specifies the order of different dimensions. Must have some ordering of the letters
         c, t, p, and z. For example, 'tcz' would run a timelapse where z stacks would be acquired at each channel in
@@ -174,14 +171,29 @@ def multi_d_acquisition_events(
     order = order.lower()
     if "p" in order and "z" in order and order.index("p") > order.index("z"):
         raise ValueError(
-            "This function requres that the xy position come earlier in the order than z"
+            "This function requires that the xy position come earlier in the order than z"
         )
     if isinstance(time_interval_s, list):
         if len(time_interval_s) != num_time_points:
             raise ValueError(
                 "Length of time interval list should be equal to num_time_points"
             )
-    has_zsteps = z_start is not None and z_step is not None and z_end is not None
+    if position_labels is not None:
+        if xy_positions is not None and len(xy_positions) != len(position_labels):
+            raise ValueError("xy_positions and position_labels must be of equal length")
+        if xyz_positions is not None and len(xyz_positions) != len(position_labels):
+            raise ValueError("xyz_positions and position_labels must be of equal length")
+
+    # If any of z_start, z_step, z_end are provided, then they should all be provided
+    # Here we can't use `all` as some of the values of z_start, z_step, z_end
+    # may be zero and all((0,)) = False
+    has_zsteps = False
+    if any([z_start, z_step, z_end]):
+        if not None in [z_start, z_step, z_end]:
+            has_zsteps = True
+        else:
+            raise ValueError('All of z_start, z_step, and z_end must be provided')
+
     z_positions = None
     if xy_positions is not None:
         xy_positions = np.asarray(xy_positions)
@@ -205,6 +217,9 @@ def multi_d_acquisition_events(
                 pos.append(z + z_rel)
             z_positions = np.asarray(pos)
 
+    if position_labels is None and xy_positions is not None:
+        position_labels = list(range(len(xy_positions)))
+
     def generate_events(event, order):
         if len(order) == 0:
             yield event
@@ -224,7 +239,8 @@ def generate_events(event, order):
                 yield generate_events(new_event, order[1:])
         elif order[0] == "z" and z_positions is not None:
             if "axes" in event and "position" in event["axes"]:
-                zs = z_positions[event["axes"]["position"]]
+                pos_idx = position_labels.index(event["axes"]["position"])
+                zs = z_positions[pos_idx]
             else:
                 zs = z_positions
 
@@ -236,9 +252,9 @@ def generate_events(event, order):
                     new_event["keep_shutter_open"] = True
                 yield generate_events(new_event, order[1:])
         elif order[0] == "p" and xy_positions is not None:
-            for p_index, xy in enumerate(xy_positions):
+            for p_label, xy in zip(position_labels, xy_positions):
                 new_event = copy.deepcopy(event)
-                new_event["axes"]["position"] = p_index
+                new_event["axes"]["position"] = p_label
                 new_event["x"] = xy[0]
                 new_event["y"] = xy[1]
                 yield generate_events(new_event, order[1:])

pycromanager/acquisitions.py

@@ -26,7 +26,6 @@ def __init__(self, message):
 # prevent problems with pickling when running them in differnet process
 
 def _run_acq_event_source(acquisition, event_port, event_queue, debug=False):
-    print('running event source')
     event_socket = PushSocket(event_port, debug=debug)
     try:
         while True:

pycromanager/test/conftest.py

@@ -78,72 +78,72 @@ def download_mm_nightly():
 
 @pytest.fixture(scope="session")
 def install_mm(download_mm_nightly):
-    # make sure MM is not already running (used for local testing)
+    mm_installed = False
+    mm_running = False
+    mm_install_dir = os.path.join(os.path.expanduser('~'), "Micro-Manager-nightly")
+
+    # check if there is currently a Micro-manager instance running (used for local testing)
     if is_port_in_use(4827):
+        mm_running = True
+        print('Using Micro-manager running on port 4827 for testing')
         yield
     else:
-        mm_app_found = False
-        mm_install_dir = os.path.join(os.path.expanduser('~'), "Micro-Manager-nightly")
-
-        # check if there is currently a Micro-manager instance running (used for local testing)
-        if is_port_in_use(4827):
-            yield
+        if os.path.isdir(mm_install_dir):
+            # Check if Micro-manager installation is present in mm_install_dir.
+            # If so, the latest Micro-manager nightly build will not be installed.
+            print(f'Existing Micro-manager installation found at {mm_install_dir}')
         else:
-            if os.path.isdir(mm_install_dir):
-                # Check if Micro-manager installation is present in mm_install_dir.
-                # If so, the latest Micro-manager nightly build will not be installed.
-                mm_app_found = True
-                print(f'Existing Micro-manager installation found at {mm_install_dir}')
+            # Install Micro-manager nightly build. Currently only supported on Windows platforms
+            # To run tests on other platform, please place a working Micro-manager installation in "~/Micro-Manager-nightly"
+            mm_installed = True
+
+            if sys.platform.startswith('win'):
+                mm_installer = download_mm_nightly
+                mm_install_log_path = os.path.join(os.path.dirname(mm_installer), "mm_install.log")
+            else:
+                raise RuntimeError(
+                    '''Micro-manager nightly build installation is currently only supported on Windows platforms. 
+                To run tests on other platform, please place a working Micro-manager installation in 
+                "~/Micro-Manager-nightly"'''
+                )
+
+            os.mkdir(mm_install_dir)
+
+            print(f'Installing Micro-manager nightly build at: {mm_install_dir}')
+            cmd = f"{mm_installer} /SP /VERYSILENT /SUPRESSMSGBOXES /CURRENTUSER /DIR={mm_install_dir} /LOG={mm_install_log_path}"
+            subprocess.run(cmd, shell=True)
+
+            # find pycro-manager/java path
+            if os.path.isdir('java'):
+                java_path = os.path.abspath('java')
+            # in case cwd is '/pycromanager/test'
+            elif os.path.isdir('../../java'):
+                java_path = os.path.abspath('../../java')
             else:
-                # Install Micro-manager nightly build. Currently only supported on Windows platforms
-                # To run tests on other platform, please place a working Micro-manager installation in "~/Micro-Manager-nightly"
-                if sys.platform.startswith('win'):
-                    mm_installer = download_mm_nightly
-                    mm_install_log_path = os.path.join(os.path.dirname(mm_installer), "mm_install.log")
-                else:
-                    raise RuntimeError(
-                        '''Micro-manager nightly build installation is currently only supported on Windows platforms. 
-                    To run tests on other platform, please place a working Micro-manager installation in 
-                    "~/Micro-Manager-nightly"'''
-                    )
-
-                os.mkdir(mm_install_dir)
-
-                print(f'Installing Micro-manager nightly build at: {mm_install_dir}')
-                cmd = f"{mm_installer} /SP /VERYSILENT /SUPRESSMSGBOXES /CURRENTUSER /DIR={mm_install_dir} /LOG={mm_install_log_path}"
-                subprocess.run(cmd, shell=True)
-
-                # find pycro-manager/java path
-                if os.path.isdir('java'):
-                    java_path = os.path.abspath('java')
-                # in case cwd is '/pycromanager/test'
-                elif os.path.isdir('../../java'):
-                    java_path = os.path.abspath('../../java')
-                else:
-                    raise RuntimeError('Could not find pycro-manager/java path')
-
-                # Update pycromanager jar files packaged with the Micro-manager nightly build
-                # Files are updated only if they are larger version
-                if os.path.isdir(os.path.join(java_path, 'target')):
-                    replace_jars(os.path.join(java_path, 'target'), os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'),
-                         ['PycroManagerJava'])
-                # Copy dependency jar files if present in target/dependency
-                if os.path.isdir(os.path.join(java_path, 'target/dependency')):
-                    replace_jars(os.path.join(java_path, 'target/dependency'), os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'),
-                         ['AcqEngJ', 'NDTiffStorage', 'NDViewer'])
-                # Copy dependency jar files if present in ../../REPO_NAME/target
-                for repo_name in ['AcqEngJ', 'NDTiffStorage', 'NDViewer']:
-                    if os.path.isdir(os.path.join(java_path, f'../../{repo_name}/target')):
-                        replace_jars(os.path.join(java_path, f'../../{repo_name}/target'),
-                                     os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'), [repo_name])
-
-            yield mm_install_dir
-
-        # cleanup only if Micro-manager was installed in this session
-        if not mm_app_found:
-            os.remove(mm_install_log_path)
-            # fails, because MM is still running, I think
-            # shutil.rmtree(mm_install_dir)
+                raise RuntimeError('Could not find pycro-manager/java path')
+
+            # Update pycromanager jar files packaged with the Micro-manager nightly build
+            # Files are updated only if they are larger version
+            if os.path.isdir(os.path.join(java_path, 'target')):
+                replace_jars(os.path.join(java_path, 'target'), os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'),
+                        ['PycroManagerJava'])
+            # Copy dependency jar files if present in target/dependency
+            if os.path.isdir(os.path.join(java_path, 'target/dependency')):
+                replace_jars(os.path.join(java_path, 'target/dependency'), os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'),
+                        ['AcqEngJ', 'NDTiffStorage', 'NDViewer'])
+            # Copy dependency jar files if present in ../../REPO_NAME/target
+            for repo_name in ['AcqEngJ', 'NDTiffStorage', 'NDViewer']:
+                if os.path.isdir(os.path.join(java_path, f'../../{repo_name}/target')):
+                    replace_jars(os.path.join(java_path, f'../../{repo_name}/target'),
+                                    os.path.join(mm_install_dir, 'plugins', 'Micro-Manager'), [repo_name])
+
+        yield mm_install_dir
+
+    # cleanup only if Micro-manager was installed in this session
+    if not mm_running and mm_installed:
+        os.remove(mm_install_log_path)
+        # fails, because MM is still running, I think
+        # shutil.rmtree(mm_install_dir)
 
 
 @pytest.fixture(scope="session")