Made it work for excalibur

malcolm/imalcolm.py

@@ -255,7 +255,8 @@ def main():
     sys.path.insert(0,
                     "/dls_sw/work/tools/RHEL6-x86_64/odin/venv/lib/python2.7/"
                     "site-packages")
-    require("tornado", "numpy", "cothread", "ruamel.yaml",
+    sys.path.append("/dls_sw/work/common/python/cothread")
+    require("tornado", "numpy", "ruamel.yaml",
             "scanpointgenerator", "plop", "pygelf", "h5py")
     #sys.path.append(os.path.join(os.path.dirname(__file__), "..", "..", "scanpointgenerator"))
     sys.path.append(

malcolm/modules/ADCore/parts/detectordriverpart.py

@@ -79,7 +79,7 @@ def run(self, context, update_completed_steps):
         # update_completed_steps come in
         try:
             child.when_value_matches(
-                "arrayCounter", self.done_when_reaches, timeout=0.1)
+                "arrayCounter", self.done_when_reaches, timeout=5.0)
         except TimeoutError:
             raise ValueError("Detector %r didn't produce %s frames in time" % (
                 self.params.mri, self.done_when_reaches))

malcolm/modules/BL14I/BL14I-ML-MALC-01.yaml

@@ -1,35 +1,36 @@
 #!/home/qvr31998/malcolm/pymalcolm/malcolm/imalcolm.py
 
-- parameters.string:
+- builtin.defines.string:
     name: configDir
-    description: Where to store saved configs
-    default: /dls_sw/i14/epics/malcolm
+    value: /dls_sw/i14/epics/malcolm
 
-- blocks.xspress3.Xspress3DetectorManager:
+- xspress3.blocks.xspress3_detector_manager_block:
     pvPrefix: BL14I-EA-XSP3-01
     mriPrefix: BL14I-ML-XSP3-01
     configDir: $(configDir)
 
-#- blocks.excalibur.ExcaliburDetectorManager:
-#    pvPrefix: BL14I-EA-EXCBR-01
-#    mriPrefix: BL14I-ML-EXCBR-01
-#    configDir: $(configDir)
+- excalibur.blocks.excalibur_detector_runnable_block:
+    pvPrefix: BL14I-EA-EXCBR-01
+    mriPrefix: BL14I-ML-EXCBR-01
+    configDir: $(configDir)
 
-- blocks.demo.I14PMACManager:
+- BL14I.blocks.pmac_runnable_block:
     mriPrefix: BL14I-ML-BRICK-14
     configDir: $(configDir)
 
-- blocks.pandabox.PandABoxManager:
+- ADPandABlocks.blocks.pandablocks_runnable_block:
     pvPrefix: BL14I-MO-PANDA-01
     mriPrefix: BL14I-ML-PANDA-01
     hostname: bl14i-mo-pandabox-01
     configDir: $(configDir)
 
-- blocks.demo.I14Manager:
+- BL14I.blocks.xspress3_scan_block:
     mri: BL14I-ML-SCAN-01
     det: BL14I-ML-XSP3-01
     brick: BL14I-ML-BRICK-14
     pandabox: BL14I-ML-PANDA-01
     configDir: $(configDir)
 
-- comms.pva.PvaServerComms:
+- pva.blocks.pva_server_block:
+    mri: $(yamlname):PVA-SERVER
+

malcolm/modules/BL14I/blocks/__init__.py

@@ -0,0 +1,7 @@
+from malcolm.yamlutil import make_block_creator, check_yaml_names
+
+pmac_runnable_block = make_block_creator(__file__, "pmac_runnable_block.yaml")
+xspress3_scan_block = make_block_creator(__file__, "xspress3_scan_block.yaml")
+
+__all__ = check_yaml_names(globals())
+

malcolm/blocks/demo/I14PMACManager.yaml → malcolm/modules/BL14I/blocks/pmac_runnable_block.yaml

@@ -1,38 +1,28 @@
-- parameters.string:
+- builtin.parameters.string:
     name: mriPrefix
     description: MRI for created block
 
-- parameters.string:
+- builtin.parameters.string:
     name: configDir
     description: Where to store saved configs
 
-- controllers.RunnableController:
+- scanning.controllers.RunnableController:
     mri: $(mriPrefix)
     configDir: $(configDir)
 
-#- includes.pmac.compoundmotor_collection:
-#    mri: I18-T1-X
-#    prefix: BL18I-MO-TABLE-01:CSX
-#    scannable: t1x
-
-#- includes.pmac.compoundmotor_collection:
-#    mri: I18-T1-Y
-#    prefix: BL18I-MO-TABLE-01:HEIGHT
-#    scannable: sc_MicroFocusSampleY
-
-- includes.pmac.rawmotor_collection:
+- pmac.includes.rawmotor_collection:
     mri: BL14I-ML-STAGE-01:XC
     prefix: BL14I-MO-STEP-14:M1
     motorPrefix: BL14I-MO-STAGE-01:XC
     scannable: stage1_x
 
-- includes.pmac.rawmotor_collection:
+- pmac.includes.rawmotor_collection:
     mri: BL14I-ML-STAGE-01:YC
     prefix: BL14I-MO-STEP-14:M2
     motorPrefix: BL14I-MO-STAGE-01:YC
     scannable: stage1_y
 
-- includes.pmac.trajectory_collection:
+- pmac.includes.trajectory_collection:
     mri: $(mriPrefix):TRAJ
     prefix: BL14I-MO-STEP-14
     statPrefix: BL14I-MO-STEP-14

malcolm/blocks/demo/I14Manager.yaml → malcolm/modules/BL14I/blocks/xspress3_scan_block.yaml

@@ -1,39 +1,39 @@
-- parameters.string:
+- builtin.parameters.string:
     name: mri
     description: MRI for created block
 
-- parameters.string:
+- builtin.parameters.string:
     name: det
     description: MRI for detector DetectorManager object
 
-- parameters.string:
+- builtin.parameters.string:
     name: brick
     description: MRI for brick PMACManager object
 
-- parameters.string:
+- builtin.parameters.string:
     name: pandabox
     description: MRI for PandABoxManager object
 
-- parameters.string:
+- builtin.parameters.string:
     name: configDir
     description: Where to store saved configs
 
-- controllers.RunnableController:
+- scanning.controllers.RunnableController:
     mri: $(mri)
     axesToMove: [stage1_x, stage1_y]
     configDir: $(configDir)
 
-- parts.ADCore.DatasetTablePart:
+- ADCore.parts.DatasetTablePart:
     name: DSET
 
-- parts.pmac.PmacRunnableChildPart:
+- pmac.parts.PmacRunnableChildPart:
     name: BRICK
     mri: $(brick)
 
-- parts.ADCore.DatasetRunnableChildPart:
+- ADCore.parts.DatasetRunnableChildPart:
     name: DET
     mri: $(det)
 
-- parts.ADCore.DatasetRunnableChildPart:
+- ADCore.parts.DatasetRunnableChildPart:
     name: PANDABOX
     mri: $(pandabox)

malcolm/modules/builtin/parts/childpart.py

@@ -1,5 +1,7 @@
 import re
 
+import numpy as np
+
 from malcolm.compat import OrderedDict
 from malcolm.core import Part, REQUIRED, method_takes, serialize_object, \
     Attribute, Subscribe, Unsubscribe, Put
@@ -152,7 +154,9 @@ def report_modified(self, context):
             attr = getattr(child, name)
             if isinstance(attr, Attribute) and "config" in attr.meta.tags:
                 current_value = serialize_object(attr.value)
-                if original_value != current_value:
+                try:
+                    np.testing.assert_equal(original_value, current_value)
+                except AssertionError:
                     we_modified = name in self.we_modified
                     ret.append(ModifiedInfo(
                         name, original_value, current_value, we_modified))

malcolm/modules/excalibur/parts/femdriverpart.py

@@ -1,11 +1,13 @@
 from malcolm.modules.builtin.parts import StatefulChildPart
 from malcolm.modules.scanning.controllers import RunnableController
-from malcolm.modules.ADCore.infos import NDArrayDatasetInfo
+from malcolm.modules.ADCore.infos import NDArrayDatasetInfo, UniqueIdInfo
 
 
 class FemDriverPart(StatefulChildPart):
     # Only need to report that we will make a dataset, top level will do all
     # control
     @RunnableController.ReportStatus
-    def report_configuration(self, _):
-        return [NDArrayDatasetInfo(rank=2)]
+    def report_configuration(self, context):
+        child = context.block_view(self.params.mri)
+        return [
+            NDArrayDatasetInfo(rank=2), UniqueIdInfo(child.arrayCounter.value)]

malcolm/modules/excalibur/parts/vdswrapperpart.py

@@ -69,14 +69,17 @@ def __init__(self, params):
 
     @RunnableController.Abort
     @RunnableController.Reset
+    @RunnableController.PostRunIdle
     def abort(self, context):
         self.close_files()
 
     def close_files(self):
         for file_ in self.raw_datasets + [self.vds]:
             if file_ is not None and file_.id.valid:
-                self._logger.info("Closing file %s", file_)
+                self.log.info("Closing file %s", file_)
                 file_.close()
+        self.raw_datasets = []
+        self.vds = None
 
     def _create_dataset_infos(self, generator, filename):
         uniqueid_path = "/entry/NDAttributes/NDArrayUniqueId"
@@ -118,10 +121,9 @@ def configure(self, context, completed_steps, steps_to_do, part_info,
                   params):
         self.done_when_reaches = completed_steps + steps_to_do
 
-        self._logger.debug("Creating ExternalLinks from VDS to FEM1.h5")
+        self.log.debug("Creating ExternalLinks from VDS to FEM1.h5")
         self.vds_path = os.path.join(params.fileDir, self.OUTPUT_FILE)
-        raw_file_path = os.path.join(params.fileDir,
-                                     self.RAW_FILE_TEMPLATE.format(1))
+        raw_file_path = self.RAW_FILE_TEMPLATE.format(1)
         node_tree = list(self.default_node_tree)
         for axis in params.generator.axes:
             for base in self.set_bases:
@@ -143,7 +145,7 @@ def configure(self, context, completed_steps, steps_to_do, part_info,
             self.vds.create_dataset(self.SUM, initial_shape,
                                     maxshape=max_shape, dtype="float64")
 
-        self._logger.debug("Calling vds-gen to create dataset in VDS")
+        self.log.debug("Calling vds-gen to create dataset in VDS")
         files = [self.RAW_FILE_TEMPLATE.format(fem) for fem in self.fems]
         shape = [str(d) for d in params.generator.shape] + \
                 [str(self.stripe_height), str(self.stripe_width)]
@@ -162,14 +164,18 @@ def configure(self, context, completed_steps, steps_to_do, part_info,
                     self.TARGET_NODE, "/entry/detector/detector"]
         # Define output file path
         command += [self.OUTPUT, self.OUTPUT_FILE]
-        command += [self.LOG_LEVEL, "1"] # str(self._logger.level / 10)]
-        self.log_info("Command: %s", command)
+        command += [self.LOG_LEVEL, "1"] # str(self.log.level / 10)]
+        self.log.info("Command: %s", command)
         check_call(command)
 
         # Store required attributes
         self.raw_paths = [os.path.abspath(os.path.join(params.fileDir, file_))
                           for file_ in files]
 
+        # Open the VDS
+        self.vds = h5.File(self.vds_path, self.APPEND, libver="latest")
+
+
         # Return the dataset information
         dataset_infos = list(self._create_dataset_infos(
             params.generator, self.vds_path))
@@ -184,39 +190,35 @@ def seek(self, context, completed_steps, steps_to_do, part_info):
     @RunnableController.Run
     @RunnableController.Resume
     def run(self, context, update_completed_steps):
-        self.vds = h5.File(self.vds_path, self.APPEND, libver="latest")
-        try:
-            # Wait until raw files exist and have UniqueIDArray
+        if not self.raw_datasets:
             for path_ in self.raw_paths:
-                self.log_info("Waiting for file %s to be created", path_)
+                self.log.info("Waiting for file %s to be created", path_)
                 while not os.path.exists(path_):
                     context.sleep(1)
                 self.raw_datasets.append(
                     h5.File(path_, self.READ, libver="latest", swmr=True))
             for dataset in self.raw_datasets:
-                self.log_info("Waiting for id in file %s", dataset)
+                self.log.info("Waiting for id in file %s", dataset)
                 while self.ID not in dataset:
-                    context.sleep(1)
-
-            self.log_info("Monitoring raw files until ID reaches %s",
+                    context.sleep(0.1)
+        try:
+            self.log.info("Monitoring raw files until ID reaches %s",
                           self.done_when_reaches)
             while self.id < self.done_when_reaches:
                 context.sleep(0.1)  # Allow while loop to be aborted
                 ids = []
                 for dataset in self.raw_datasets:
                     ids.append(self.get_id(dataset))
                 if min(ids) > self.id:
-                    self.log_info("Raw ID changed: %s - "
+                    self.log.info("Raw ID changed: %s - "
                                   "Updating VDS ID and Sum", min(ids))
                     idx = ids.index(min(ids))
                     self.update_id(idx)
                     self.update_sum(idx)
 
-            self.log_info("ID reached: %s", self.id)
+            self.log.info("ID reached: %s", self.id)
         except Exception as error:
-            self.log_error("Error in run. Message:\n%s", error.message)
-            raise
-        finally:
+            self.log.exception("Error in run. Message:\n%s", error.message)
             self.close_files()
 
     @property
@@ -228,14 +230,14 @@ def get_id(self, file_):
             file_[self.ID].refresh()
             return max(file_[self.ID].value.flatten())
         else:
-            self.log_warning("File %s does not exist or does not have a "
+            self.log.warning("File %s does not exist or does not have a "
                              "UniqueIDArray, returning 0", file_)
             return 0
 
     def update_id(self, min_dataset):
         min_id = self.raw_datasets[min_dataset][self.ID]
 
-        self.log_debug("ID shape:\n%s", min_id.shape)
+        self.log.debug("ID shape:\n%s", min_id.shape)
         self.vds[self.ID].resize(min_id.shape)
         self.vds[self.ID][...] = min_id
 
@@ -254,6 +256,6 @@ def update_sum(self, min_dataset):
         mask = min_sum < 0
         sum_[mask] = -1
 
-        self.log_debug("Sum shape:\n%s", sum_.shape)
+        self.log.debug("Sum shape:\n%s", sum_.shape)
         self.vds[self.SUM].resize(sum_.shape)
         self.vds[self.SUM][...] = sum_