Merge branch 'master' of gitlab.esrf.fr:tomotools/tomoscan

tomoscan/esrf/hdf5scan.py

@@ -161,6 +161,8 @@ class HDF5TomoScan(TomoScanBase):
         # image dimensions
         self._x_pixel_size = None
         self._y_pixel_size = None
+        self._x_magnified_pixel_size = None
+        self._y_magnified_pixel_size = None
         # pixel dimensions (tuple)
         self._frames = None
         self._image_keys = None
@@ -235,7 +237,7 @@ class HDF5TomoScan(TomoScanBase):
         if not os.path.isfile(file_path):
             raise ValueError('given file path should be a file')
 
-        with h5py.File(file_path, 'r') as h5f:
+        with h5py.File(file_path, 'r', swmr=True) as h5f:
             for root_node in h5f.keys():
                 node = h5f[root_node]
                 if HDF5TomoScan.node_is_nxtomo(node) is True:
@@ -403,7 +405,7 @@ class HDF5TomoScan(TomoScanBase):
     def rotation_angle(self) -> typing.Union[None, list]:
         if self._rotation_angles is None:
             self._check_hdf5scan_validity()
-            with h5py.File(self.master_file, 'r') as h5_file:
+            with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
                 _rotation_angles = h5_file[self._entry][self._ROTATION_ANGLE_PATH][()]
                 # cast in float
                 self._rotation_angles = tuple([float(angle) for angle in _rotation_angles])
@@ -413,7 +415,7 @@ class HDF5TomoScan(TomoScanBase):
     def image_key(self) -> typing.Union[list, None]:
         if self._entry and self._image_keys is None:
             self._check_hdf5scan_validity()
-            with h5py.File(self.master_file, 'r') as h5_file:
+            with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
                 self._image_keys = h5_file[self._entry][self._IMG_KEY_PATH][()]
         return self._image_keys
 
@@ -421,7 +423,7 @@ class HDF5TomoScan(TomoScanBase):
     def image_key_control(self) -> typing.Union[list, None]:
         if self._entry and self._image_keys_control is None:
             self._check_hdf5scan_validity()
-            with h5py.File(self.master_file, 'r') as h5_file:
+            with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
                 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:
@@ -492,7 +494,7 @@ class HDF5TomoScan(TomoScanBase):
 
     def _get_x_y_pixel_values(self):
         """read x and y pixel values"""
-        with h5py.File(self.master_file, 'r') as h5_file:
+        with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
             x_pixel_dataset = h5_file[self._entry][self._X_PIXEL_SIZE_PATH]
             _x_pixel_size = self._get_value(x_pixel_dataset, default_unit='micrometer')
             y_pixel_dataset = h5_file[self._entry][self._Y_PIXEL_SIZE_PATH]
@@ -500,7 +502,7 @@ class HDF5TomoScan(TomoScanBase):
         return _x_pixel_size, _y_pixel_size
 
     def _get_x_y_magnified_pixel_values(self):
-        with h5py.File(self.master_file, 'r') as h5_file:
+        with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
             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='micrometer')
             y_m_pixel_dataset = h5_file[self._entry][self._Y_PIXEL_MAG_SIZE_PATH]
@@ -539,7 +541,7 @@ class HDF5TomoScan(TomoScanBase):
         if (self._distance is None and self.master_file and
                 os.path.exists(self.master_file)):
             self._check_hdf5scan_validity()
-            with h5py.File(self.master_file, 'r') as h5_file:
+            with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
                 distance_dataset = h5_file[self._entry][self._DISTANCE_PATH]
                 self._distance = self._get_value(distance_dataset, default_unit='m')
         return self._distance
@@ -549,7 +551,7 @@ class HDF5TomoScan(TomoScanBase):
         if (self._energy is None and self.master_file and
                 os.path.exists(self.master_file)):
             self._check_hdf5scan_validity()
-            with h5py.File(self.master_file, 'r') as h5_file:
+            with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
                 energy_dataset = h5_file[self._entry][self._ENERGY_PATH]
                 self._energy = self._get_value(energy_dataset, default_unit='keV')
         return self._energy
@@ -659,7 +661,7 @@ class HDF5TomoScan(TomoScanBase):
             raise ValueError('No master file provided')
         if self.entry is None:
             raise ValueError('No entry provided')
-        with h5py.File(self.master_file, 'r') as h5_file:
+        with h5py.File(self.master_file, 'r', swmr=True) as h5_file:
             if self._entry not in h5_file:
                 raise ValueError('Given entry %s is not in the master '
                                  'file %s' % (self._entry, self.master_file))

tomoscan/esrf/mock.py

@@ -246,7 +246,7 @@ class MockHDF5(_ScanMock):
     def _append_frame(self, data_, rotation_angle, image_key,
                       image_key_control):
 
-        with h5py.File(self.scan_master_file, 'r+') as h5_file:
+        with h5py.File(self.scan_master_file, 'r+', swmr=True) as h5_file:
             entry_one = h5_file.require_group(self.scan_entry)
             instrument_grp = entry_one.require_group('instrument')
             detector_grp = instrument_grp.require_group('detector')
@@ -297,7 +297,7 @@ class MockHDF5(_ScanMock):
             else:
                 new_count_time = [self._PROJ_COUNT, ]
 
-        with h5py.File(self.scan_master_file, 'a') as h5_file:
+        with h5py.File(self.scan_master_file, 'a', swmr=True) as h5_file:
             entry_one = h5_file.require_group(self.scan_entry)
             instrument_grp = entry_one.require_group('instrument')
             if 'NX_class' not in instrument_grp.attrs:
@@ -317,7 +317,7 @@ class MockHDF5(_ScanMock):
             sample_grp['rotation_angle'] = new_rot_angle
 
     def write_metadata(self, n_radio, scan_range, ref_n, dark_n):
-        with h5py.File(self.scan_master_file, 'a') as h5_file:
+        with h5py.File(self.scan_master_file, 'a', swmr=True) as h5_file:
             entry_one = h5_file.require_group(self.scan_entry)
             instrument_grp = entry_one.require_group('instrument')
             detector_grp = instrument_grp.require_group('detector')

tomoscan/version.py

@@ -68,7 +68,7 @@ RELEASE_LEVEL_VALUE = {"dev": 0,
 
 MAJOR = 0
 MINOR = 2
-MICRO = 2
+MICRO = 3
 RELEV = "dev"  # <16
 SERIAL = 0  # <16