Merge pull request #774 from henrypinkard/main

Working Python acquisiton engine/backend + tests + RAM Storage for Python and Java

.github/workflows/Java_dependency_update.yml

@@ -1,4 +1,4 @@
-# When NDTiff, AcqEngJ, or NDViewer update, a automatic push
+# When NDStorage, AcqEngJ, or NDViewer update, a automatic push
 # to the dependency-update branch of pycro-manager will be generated
 # that updates the version in their POM.xml files
 # This script should then:

build_automation/update_PycroManagerJava.py

@@ -6,12 +6,12 @@
 def read_versions(root):
     versions = {}
     versions['PycroManagerJava'] = Version(root.find("version").text)
-    # iterate through the dependencies and get NDTiff, NDViewer, and AcqEngJ
+    # iterate through the dependencies and get NDStorage, NDViewer, and AcqEngJ
     dependencies = root.findall(".//dependency")
     for dependency in dependencies:
         artifactId = dependency.find("artifactId").text
         version = dependency.find("version").text
-        if artifactId in ["NDTiffStorage", "NDViewer", "AcqEngJ"]:
+        if artifactId in ["NDStorage", "NDViewer", "AcqEngJ"]:
             versions[artifactId] = Version(version)
     return versions
 

build_automation/update_dependency.py

@@ -1,6 +1,6 @@
 """
-Script for updating NDTiff/AcqEngJ/NDViewer to latest version
-It runs on the *-update branch and is called by an action in NDTiff/AcqEngJ/NDViewer repo
+Script for updating NDStorage/AcqEngJ/NDViewer to latest version
+It runs on the *-update branch and is called by an action in NDStorage/AcqEngJ/NDViewer repo
 """
 
 import xml.etree.ElementTree as ET

build_automation/update_mm_ivy.py

@@ -15,7 +15,7 @@
 def read_versions(root):
     versions = {}
     versions['PycroManagerJava'] = Version(root.find("version").text)
-    # iterate through the dependencies and get NDTiff, NDViewer, and AcqEngJ
+    # iterate through the dependencies and get NDStorage, NDViewer, and AcqEngJ
     dependencies = root.findall(".//dependency")
     for dependency in dependencies:
         artifactId = dependency.find("artifactId").text

java/pom.xml

@@ -2,7 +2,7 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>org.micro-manager.pycro-manager</groupId>
     <artifactId>PycroManagerJava</artifactId>
-     <version>0.46.8</version>
+     <version>0.46.9</version>
     <packaging>jar</packaging>
     <name>Pycro-Manager Java</name>
     <description>The Java components of Pycro-Manager</description>
@@ -65,7 +65,7 @@
       <dependency>
          <groupId>org.micro-manager.ndtiffstorage</groupId>
          <artifactId>NDTiffStorage</artifactId>
-     <version>2.17.0</version>
+     <version>2.18.0</version>
       </dependency>
   </dependencies>
 
@@ -154,4 +154,4 @@
       </repository>
    </distributionManagement>
 
-</project>
+</project>

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

@@ -64,7 +64,6 @@ public void start() {
                ex.printStackTrace();
                throw new RuntimeException(ex);
             }
-
             pushSocket_.push(e);
             if (e.isAcquisitionEventsFinishedNotification()) {
                eventsFinished = true;

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

@@ -234,7 +234,11 @@ public String getDiskLocation() {
 
    public void close() {
       try {
-         storage_.closeAndWait();
+         if (!(storage_ instanceof NDRAMStorage)) {
+            // If its RAM storage, the python side may want to hang onto it
+            storage_.closeAndWait();
+            storage_ = null;
+         }
       } catch (InterruptedException e) {
          throw new RuntimeException(e);
       }

pycromanager/__init__.py

@@ -8,5 +8,5 @@
 from pycromanager.core import Core
 from pyjavaz import JavaObject, JavaClass, PullSocket, PushSocket
 from pycromanager.acquisition.acq_eng_py.main.acq_notification import AcqNotification
-from ndtiff import Dataset
+from ndstorage import Dataset
 from ._version import __version__, version_info

pycromanager/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 33, 0)
+version_info = (0, 34, 0)
 __version__ = ".".join(map(str, version_info))

pycromanager/acquisition/RAMStorage_java.py

@@ -0,0 +1,75 @@
+from pyjavaz.wrappers import JavaObject
+from ndstorage.ndstorage_base import NDStorageBase
+
+class NDRAMDatasetJava(NDStorageBase):
+    """
+    A python class that wraps a Java-backend RAM data storage.
+
+    This class maintains an index of which images have been saved, but otherwise routes all calls to the Java
+    implementation of the RAM data storage.
+    """
+
+    def __init__(self, java_RAM_data_storage):
+        super().__init__()
+        self._java_RAM_data_storage = java_RAM_data_storage
+        self._index_keys = set()
+
+    def __del__(self):
+        self.close()
+
+    def close(self):
+        self._java_RAM_data_storage = None # allow the Java side to be garbage collected
+
+    def add_available_axes(self, image_coordinates):
+        """
+        The Java RAM storage has received a new image with the given axes. Add these axes to the index.
+        """
+        self._index_keys.add(frozenset(image_coordinates.items()))
+        # update information about the available images
+        self._update_axes(image_coordinates)
+        self._new_image_event.set()
+        if self.dtype is None:
+            image = self.read_image(**image_coordinates)
+            self._infer_image_properties(image)
+
+    def get_image_coordinates_list(self):
+        """
+        Return a list of every combination of axes that has an image in this dataset
+        """
+        frozen_set_list = list(self._index_keys)
+        # convert to dict
+        return [{axis_name: position for axis_name, position in key} for key in frozen_set_list]
+
+    def is_finished(self) -> bool:
+        return self._java_RAM_data_storage.is_finished()
+
+    def has_image(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        return key in self._index_keys
+
+    def read_image(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        if key not in self._index_keys:
+            return None
+        java_hashmap = JavaObject('java.util.HashMap')
+        for k, v in axes.items():
+            java_hashmap.put(k, v)
+        tagged_image = self._java_RAM_data_storage.get_image(java_hashmap)
+        pixels = tagged_image.pix
+        metadata = tagged_image.tags
+        return pixels.reshape(metadata['Height'], metadata['Width'])
+
+    def read_metadata(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        if key not in self._index_keys:
+            return None
+        java_hashmap = JavaObject('java.util.HashMap')
+        for k, v in axes.items():
+            java_hashmap.put(k, v)
+        tagged_image = self._java_RAM_data_storage.get_image(java_hashmap)
+        return tagged_image.tags
+
+

pycromanager/acquisition/acq_constructor.py

@@ -31,7 +31,7 @@ def __new__(cls,
 
         if _PYMMCORES:
             # Python backend detected, so create a python backend acquisition
-            specific_arg_names = [k for k in signature(JavaBackendAcquisition.__init__).parameters.keys() if k != 'self']
+            specific_arg_names = [k for k in signature(PythonBackendAcquisition.__init__).parameters.keys() if k != 'self']
             for name in specific_arg_names:
                 if name in kwargs:
                     named_args[name] = kwargs[name]