labscript-suite · chrisjbillington · Jun 25, 2020 · Jun 25, 2020
diff --git a/labscript_devices/AlazarTechBoard.py b/labscript_devices/AlazarTechBoard.py
@@ -316,7 +316,7 @@ def init(self):
     def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
         self.h5file = h5file  # We'll need this in transition_to_manual
         self.device_name = device_name
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             print("\nUsing "+h5file)
             self.atsparam = atsparam = labscript_utils.properties.get(
                 hdf5_file, device_name, 'device_properties')
@@ -379,7 +379,7 @@ def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
 
         # Store the actual acquisition rate back as an attribute.
         # Again, this should be done as an ACQUISITIONS table entry, but not today
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r+') as hdf5_file:
             hdf5_file['devices'][device_name].attrs.create(
                 'acquisition_rate', actual_acquisition_rate, dtype='int32')
 
@@ -585,7 +585,7 @@ def transition_to_manual(self):
         # Waits on the acquisition thread, and manages the lock
         self.wait_acquisition_complete()
         # Write data to HDF5 file
-        with h5py.File(self.h5file) as hdf5_file:
+        with h5py.File(self.h5file, 'r+') as hdf5_file:
             grp = hdf5_file.create_group('/data/traces/'+self.device_name)
             if self.channels & ats.CHANNEL_A:
                 dsetA = grp.create_dataset(

diff --git a/labscript_devices/FunctionRunner/labscript_devices.py b/labscript_devices/FunctionRunner/labscript_devices.py
@@ -50,7 +50,7 @@ def func(shot_context, t, ...):
         recommended place to do it is within the group 'data/<device_name>', for
         example:
 
-            with h5py.File(self.h5_file) as f:
+            with h5py.File(self.h5_file, 'r+') as f:
                 data_group = f['data'].create_group(self.device_name)
                 # save datasets/attributes within this group
 

diff --git a/labscript_devices/IMAQdxCamera/blacs_workers.py b/labscript_devices/IMAQdxCamera/blacs_workers.py
@@ -429,7 +429,7 @@ def transition_to_manual(self):
 
         print(f"Saving {len(self.images)}/{len(self.exposures)} images.")
 
-        with h5py.File(self.h5_filepath) as f:
+        with h5py.File(self.h5_filepath, 'r+') as f:
             # Use orientation for image path, device_name if orientation unspecified
             if self.orientation is not None:
                 image_path = 'images/' + self.orientation

diff --git a/labscript_devices/LightCrafterDMD.py b/labscript_devices/LightCrafterDMD.py
@@ -317,7 +317,7 @@ def program_manual(self, values):
         return {}
 
     def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             if 'IMAGE_TABLE' in group:
                 table_data = group['IMAGE_TABLE'][:]

diff --git a/labscript_devices/NovaTechDDS9M.py b/labscript_devices/NovaTechDDS9M.py
@@ -457,7 +457,7 @@ def transition_to_buffered(self,device_name,h5file,initial_values,fresh):
         self.final_values = {}
         static_data = None
         table_data = None
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             # If there are values to set the unbuffered outputs to, set them now:
             if 'STATIC_DATA' in group:

diff --git a/labscript_devices/PhaseMatrixQuickSyn.py b/labscript_devices/PhaseMatrixQuickSyn.py
@@ -333,7 +333,7 @@ def transition_to_buffered(self,device_name,h5file,initial_values,fresh):
         self.initial_values = initial_values
         # Store the final values to for use during transition_to_static:
         self.final_values = {}
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/'+device_name]
             # If there are values to set the unbuffered outputs to, set them now:
             if 'STATIC_DATA' in group:

diff --git a/labscript_devices/TekScope/blacs_workers.py b/labscript_devices/TekScope/blacs_workers.py
@@ -17,7 +17,7 @@ def init(self):
     def transition_to_buffered(self, device_name, h5file, front_panel_values, refresh):
         self.h5file = h5file  # We'll need this in transition_to_manual
         self.device_name = device_name
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             print('\n' + h5file)
             self.scope_params = scope_params = labscript_utils.properties.get(
                 hdf5_file, device_name, 'device_properties')
@@ -53,7 +53,7 @@ def transition_to_manual(self):
             data[ch] = vals[ch]
 
         # Open the file after download so as not to hog the file lock
-        with h5py.File(self.h5file) as hdf_file:
+        with h5py.File(self.h5file, 'r+') as hdf_file:
             grp = hdf_file.create_group('/data/traces')
             print('Saving traces...')
             dset = grp.create_dataset(self.device_name, data=data)

diff --git a/labscript_devices/ZaberStageController/blacs_workers.py b/labscript_devices/ZaberStageController/blacs_workers.py
@@ -90,7 +90,7 @@ def program_manual(self, values):
         return self.check_remote_values()
 
     def transition_to_buffered(self, device_name, h5file, initial_values, fresh):
-        with h5py.File(h5file) as hdf5_file:
+        with h5py.File(h5file, 'r') as hdf5_file:
             group = hdf5_file['/devices/' + device_name]
             if 'static_values' in group:
                 data = group['static_values']

diff --git a/labscript_devices/imaqdx_server.py b/labscript_devices/imaqdx_server.py
@@ -363,7 +363,7 @@ def transition_to_static(self, h5_filepath):
             #     # Just save the first however many we were expecting:
             #     self.imgs = self.imgs[:n_images]
 
-            with h5py.File(h5_filepath) as h5_file:
+            with h5py.File(h5_filepath, 'r+') as h5_file:
                 # Use orientation for image path, camera_name if orientation unspecified
                 if self.device_properties['orientation']:
                     image_path = self.image_path + _ensure_str(self.device_properties['orientation'])