Merge pull request #62 from kif/ID02

Id02

plugins/id02/metadata.py

@@ -7,7 +7,7 @@
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "26/08/2021"
+__date__ = "18/03/2022"
 __status__ = "development"
 __version__ = "0.9.2"
 
@@ -16,9 +16,12 @@
 import json
 import numpy
 from dahu.plugin import Plugin
-from dahu import version as dahu_version
 from dahu.utils import get_isotime, fully_qualified_name
-import PyTango
+try:
+    import PyTango
+except ImportError:
+    PyTango = None
+
 import logging
 logger = logging.getLogger("id02.metadata")
 from .common import StringTypes, Nexus, ensure_str
@@ -237,7 +240,10 @@ def read_c216(self):
         """
         Manage the metadata coming from C216 Time Frame Generator
         """
+        if PyTango is None:
+            self.log_error("PyTango is needed to connect to C216", do_raise=True)
         c216ds = PyTango.DeviceProxy(str(self.c216))
+        c216ds.set_timeout_millis(5000)
         if c216ds.CompStatus("Tango::RUNNING") == "Tango::ON":
             msg = "C216 is running while reading counters ... possible issue"
             self._logging.append(msg)
@@ -280,7 +286,10 @@ def read_c216(self):
                 self.tfg_grp[key].attrs["interpretation"] = "scalar"
 
         # raw scalers:
-        raw_scalers = c216ds.ReadScalersForNLiveFrames([0, frames - 1])
+        blocksize = 512
+        raw_scalers = numpy.concatenate([c216ds.ReadScalersForNLiveFrames([start, min(start + blocksize, frames) - 1])
+                                         for start in range(0, frames, blocksize)])
+
         raw_scalers.shape = frames, -1
         counters = raw_scalers.shape[1]
         self.mcs_grp["HS32C"] = raw_scalers

plugins/id02/nexus.py

@@ -1,10 +1,10 @@
 """Module for writing HDF5 in the Nexus style"""
 
-__author__ = "Jerome Kieffer"
+__author__ = "Jérôme Kieffer"
 __contact__ = "[email protected]"
 __license__ = "MIT"
 __copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
-__date__ = "20/02/2020"
+__date__ = "29/01/2024"
 __status__ = "production"
 __docformat__ = 'restructuredtext'
 
@@ -85,13 +85,14 @@ class Nexus(object):
     TODO: make it thread-safe !!!
     """
 
-    def __init__(self, filename, mode=None, creator=None):
+    def __init__(self, filename, mode=None, creator=None, start_time=None):
         """
         Constructor
 
         :param filename: name of the hdf5 file containing the nexus
         :param mode: can be 'r', 'a', 'w', '+' ....
         :param creator: set as attr of the NXroot
+        :param start_time: set as attr of the NXroot
         """
         self.filename = os.path.abspath(filename)
         self.mode = mode
@@ -105,12 +106,18 @@ def __init__(self, filename, mode=None, creator=None):
                 self.mode = "r"
             else:
                 self.mode = "a"
-        self.h5 = h5py.File(self.filename, mode=self.mode)
+
+        if self.mode == "r" and h5py.version.version_tuple >= (2, 9):
+            self.file_handle = open(self.filename, mode=self.mode + "b")
+            self.h5 = h5py.File(self.file_handle, mode=self.mode)
+        else:
+            self.file_handle = None
+            self.h5 = h5py.File(self.filename, mode=self.mode)
         self.to_close = []
 
-        if not pre_existing:
+        if not pre_existing or "w" in mode:
             self.h5.attrs["NX_class"] = "NXroot"
-            self.h5.attrs["file_time"] = get_isotime()
+            self.h5.attrs["file_time"] = get_isotime(start_time)
             self.h5.attrs["file_name"] = self.filename
             self.h5.attrs["HDF5_Version"] = h5py.version.hdf5_version
             self.h5.attrs["creator"] = creator or self.__class__.__name__
@@ -125,6 +132,8 @@ def close(self, end_time=None):
                 entry["end_time"] = end_time
             self.h5.attrs["file_update_time"] = get_isotime()
         self.h5.close()
+        if self.file_handle:
+            self.file_handle.close()
 
     # Context manager for "with" statement compatibility
     def __enter__(self, *arg, **kwarg):
@@ -133,6 +142,10 @@ def __enter__(self, *arg, **kwarg):
     def __exit__(self, *arg, **kwarg):
         self.close()
 
+    def flush(self):
+        if self.h5:
+            self.h5.flush()
+
     def get_entry(self, name):
         """
         Retrieves an entry from its name