set `HDF5_USE_FILE_LOCKING` when read a file

tomoscan/esrf/hdf5scan.py

@@ -232,6 +232,7 @@ class HDF5TomoScan(TomoScanBase):
             raise ValueError('given file path should be a file')
 
         with h5py.File(file_path, 'r', swmr=True) as h5f:
+            os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
             for root_node in h5f.keys():
                 node = h5f[root_node]
                 if HDF5TomoScan.node_is_nxtomo(node) is True:
@@ -406,6 +407,7 @@ class HDF5TomoScan(TomoScanBase):
         if self._rotation_angles is None:
             self._check_hdf5scan_validity()
             with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+                os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
                 _rotation_angles = h5_file[self._entry][self._ROTATION_ANGLE_PATH][()]
                 # cast in float
                 self._rotation_angles = tuple([float(angle) for angle in _rotation_angles])
@@ -416,6 +418,7 @@ class HDF5TomoScan(TomoScanBase):
         if self._entry and self._image_keys is None:
             self._check_hdf5scan_validity()
             with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+                os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
                 self._image_keys = h5_file[self._entry][self._IMG_KEY_PATH][()]
         return self._image_keys
 
@@ -424,6 +427,7 @@ class HDF5TomoScan(TomoScanBase):
         if self._entry and self._image_keys_control is None:
             self._check_hdf5scan_validity()
             with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+                os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
                 if self._IMG_KEY_CONTROL_PATH in h5_file[self._entry]:
                     self._image_keys_control = h5_file[self._entry][self._IMG_KEY_CONTROL_PATH][()]
                 else:
@@ -497,6 +501,7 @@ class HDF5TomoScan(TomoScanBase):
     def _get_x_y_pixel_values(self):
         """read x and y pixel values"""
         with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+            os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
             x_pixel_dataset = h5_file[self._entry][self._X_PIXEL_SIZE_PATH]
             _x_pixel_size = self._get_value(x_pixel_dataset, default_unit='meter')
             y_pixel_dataset = h5_file[self._entry][self._Y_PIXEL_SIZE_PATH]
@@ -505,6 +510,7 @@ class HDF5TomoScan(TomoScanBase):
 
     def _get_x_y_magnified_pixel_values(self):
         with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+            os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
             x_m_pixel_dataset = h5_file[self._entry][self._X_PIXEL_MAG_SIZE_PATH]
             _x_m_pixel_size = self._get_value(x_m_pixel_dataset, default_unit='meter')
             y_m_pixel_dataset = h5_file[self._entry][self._Y_PIXEL_MAG_SIZE_PATH]
@@ -513,6 +519,7 @@ class HDF5TomoScan(TomoScanBase):
 
     def _get_fov(self):
         with h5py.File(self.master_file, 'r', swmr=True, libver='latest') as h5_file:
+            os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
             if self._FOV_PATH in h5_file[self._entry]:
                 fov = h5_file[self._entry][self._FOV_PATH][()]
                 return _FOV.from_value(fov)
@@ -556,6 +563,7 @@ class HDF5TomoScan(TomoScanBase):
                 os.path.exists(self.master_file)):
             self._check_hdf5scan_validity()
             with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+                os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
                 distance_dataset = h5_file[self._entry][self._DISTANCE_PATH]
                 self._distance = self._get_value(distance_dataset, default_unit='m')
         return self._distance
@@ -577,6 +585,7 @@ class HDF5TomoScan(TomoScanBase):
                 os.path.exists(self.master_file)):
             self._check_hdf5scan_validity()
             with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+                os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
                 energy_dataset = h5_file[self._entry][self._ENERGY_PATH]
                 self._energy = self._get_value(energy_dataset, default_unit='keV')
         return self._energy
@@ -685,6 +694,7 @@ class HDF5TomoScan(TomoScanBase):
         if self.entry is None:
             raise ValueError('No entry provided')
         with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
+            os.environ["HDF5_USE_FILE_LOCKING"] = "FALSE"
             if self._entry not in h5_file:
                 raise ValueError('Given entry %s is not in the master '
                                  'file %s' % (self._entry, self.master_file))